pmid title sentence year journal region virus mutation mutation_start mutation_end gene gene_start gene_end disease disease_start disease_end 11019512 [Incidence of amantadine-resistant influenza A (genotype Ser-31-Asn) in nursing homes in Niigata, Japan]. [Incidence of amantadine-resistant influenza A (genotype Ser-31-Asn) in nursing homes in Niigata, Japan]. 2000 Kansenshogaku zasshi Title IV S31N;S31N 57;57 67;67 11090164 Vaccinia virus F12L protein is required for actin tail formation, normal plaque size, and virulence. Vaccinia virus F12L protein is required for actin tail formation, normal plaque size, and virulence. 2000 Journal of virology Title IV F12L 15 19 12062395 Influenza virus carrying an R292K mutation in the neuraminidase gene is not transmitted in ferrets. Influenza virus carrying an R292K mutation in the neuraminidase gene is not transmitted in ferrets. 2002 Antiviral research Title IV R292K;R292K 28;28 33;33 50 63 12103431 The H274Y mutation in the influenza A/H1N1 neuraminidase active site following oseltamivir phosphate treatment leave virus severely compromised both in vitro and in vivo. The H274Y mutation in the influenza A/H1N1 neuraminidase active site following oseltamivir phosphate treatment leave virus severely compromised both in vitro and in vivo. 2002 Antiviral research Title IV H274Y;H274Y 4;4 9;9 43 56 16140782 Membrane structures of the hemifusion-inducing fusion peptide mutant G1S and the fusion-blocking mutant G1V of influenza virus hemagglutinin suggest a mechanism for pore opening in membrane fusion. Membrane structures of the hemifusion-inducing fusion peptide mutant G1S and the fusion-blocking mutant G1V of influenza virus hemagglutinin suggest a mechanism for pore opening in membrane fusion. 2005 Journal of virology Title IV G1S;G1V;G1S;G1V 69;104;69;104 72;107;72;107 HA 127 140 17917748 Homology modeling and examination of the effect of the D92E mutation on the H5N1 nonstructural protein NS1 effector domain. Homology modeling and examination of the effect of the D92E mutation on the H5N1 nonstructural protein NS1 effector domain. 2007 Journal of molecular modeling Title IV D92E 55 59 NS1 103 106 19015327 Activity of the oral neuraminidase inhibitor A-322278 against the oseltamivir-resistant H274Y (A/H1N1) influenza virus mutant in mice. Activity of the oral neuraminidase inhibitor A-322278 against the oseltamivir-resistant H274Y (A/H1N1) influenza virus mutant in mice. 2009 Antimicrobial agents and chemotherapy Title IV H274Y 88 93 21 34 19451021 Genetic microheterogeneity of emerging H275Y influenza virus A (H1N1) in Toronto, Ontario, Canada from the 2007-2008 respiratory season. Genetic microheterogeneity of emerging H275Y influenza virus A (H1N1) in Toronto, Ontario, Canada from the 2007-2008 respiratory season. 2009 Journal of clinical virology Title IV H275Y;H275Y 39;39 44;44 19857993 Evaluation of a rapid molecular algorithm for detection of pandemic influenza A (H1N1) 2009 virus and screening for a key oseltamivir resistance (H275Y) substitution in neuraminidase. Evaluation of a rapid molecular algorithm for detection of pandemic influenza A (H1N1) 2009 virus and screening for a key oseltamivir resistance (H275Y) substitution in neuraminidase. 2010 Journal of clinical virology Title IV H275Y 146 151 169 182 19889895 Rapid and specific detection of amantadine-resistant influenza A viruses with a Ser31Asn mutation by the cycling probe method. Rapid and specific detection of amantadine-resistant influenza A viruses with a Ser31Asn mutation by the cycling probe method. 2010 Journal of clinical microbiology Title IV S31N 80 88 19911968 Clinical effectiveness of oseltamivir and zanamivir for treatment of influenza A virus subtype H1N1 with the H274Y mutation: a Japanese, multicenter study of the 2007-2008 and 2008-2009 influenza seasons. Clinical effectiveness of oseltamivir and zanamivir for treatment of influenza A virus subtype H1N1 with the H274Y mutation: a Japanese, multicenter study of the 2007-2008 and 2008-2009 influenza seasons. 2009 Clinical infectious diseases Title IV H274Y 109 114 19934602 A Serine12Stop mutation in PB1-F2 of the 2009 pandemic (H1N1) influenza A: a possible reason for its enhanced transmission and pathogenicity to humans. A Serine12Stop mutation in PB1-F2 of the 2009 pandemic (H1N1) influenza A: a possible reason for its enhanced transmission and pathogenicity to humans. 2009 Journal of veterinary science Title IV E12X;E12X 6;6 14;14 PB1F2 27 33 19943705 Oseltamivir resistance and the H274Y neuraminidase mutation in seasonal, pandemic and highly pathogenic influenza viruses. Oseltamivir resistance and the H274Y neuraminidase mutation in seasonal, pandemic and highly pathogenic influenza viruses. 2009 Drugs Title IV H274Y 31 36 37 50 19962344 Emergence of H274Y oseltamivir-resistant A(H1N1) influenza viruses in Japan during the 2008-2009 season. Emergence of H274Y oseltamivir-resistant A(H1N1) influenza viruses in Japan during the 2008-2009 season. 2010 Journal of clinical virology Title IV H274Y;H274Y 13;13 18;18 20367331 Quasispecies of the D225G substitution in the hemagglutinin of pandemic influenza A(H1N1) 2009 virus from patients with severe disease in Hong Kong, China. Quasispecies of the D225G substitution in the hemagglutinin of pandemic influenza A(H1N1) 2009 virus from patients with severe disease in Hong Kong, China. 2010 The Journal of infectious diseases Title IV D225G;D225G 20;20 25;25 HA 46 59 20385168 Detection of the rapid emergence of the H275Y mutation associated with oseltamivir resistance in severe pandemic influenza virus A/H1N1 09 infections. Detection of the rapid emergence of the H275Y mutation associated with oseltamivir resistance in severe pandemic influenza virus A/H1N1 09 infections. 2010 Antiviral research Title IV H275Y 40 45 20668122 Highly sensitive and quantitative detection of the H274Y oseltamivir resistance mutation in seasonal A/H1N1 influenza virus. Highly sensitive and quantitative detection of the H274Y oseltamivir resistance mutation in seasonal A/H1N1 influenza virus. 2010 Journal of clinical microbiology Title IV H274Y;H274Y 51;51 56;56 20689744 The PB2-E627K mutation attenuates viruses containing the 2009 H1N1 influenza pandemic polymerase. The PB2-E627K mutation attenuates viruses containing the 2009 H1N1 influenza pandemic polymerase. 2010 mBio Title IV E627K 8 13 PB2 4 7 20826688 Altered receptor specificity and cell tropism of D222G hemagglutinin mutants isolated from fatal cases of pandemic A(H1N1) 2009 influenza virus. Altered receptor specificity and cell tropism of D222G hemagglutinin mutants isolated from fatal cases of pandemic A(H1N1) 2009 influenza virus. 2010 Journal of virology Title IV D222G;D222G 49;49 54;54 HA 55 68 20833142 Solution NMR structure of the V27A drug resistant mutant of influenza A M2 channel. Solution NMR structure of the V27A drug resistant mutant of influenza A M2 channel. 2010 Biochemical and biophysical research communications Title IV V27A 30 34 M2 72 74 20920297 Characterization of an H3N2 triple reassortant influenza virus with a mutation at the receptor binding domain (D190A) that occurred upon virus transmission from turkeys to pigs. Characterization of an H3N2 triple reassortant influenza virus with a mutation at the receptor binding domain (D190A) that occurred upon virus transmission from turkeys to pigs. 2010 Virology journal Title IV D190A;D190A 111;111 116;116 21084483 A single N66S mutation in the PB1-F2 protein of influenza A virus increases virulence by inhibiting the early interferon response in vivo. A single N66S mutation in the PB1-F2 protein of influenza A virus increases virulence by inhibiting the early interferon response in vivo. 2011 Journal of virology Title IV N66S 9 13 PB1F2 30 36 21106781 The I222V neuraminidase mutation has a compensatory role in replication of an oseltamivir-resistant influenza virus A/H3N2 E119V mutant. The I222V neuraminidase mutation has a compensatory role in replication of an oseltamivir-resistant influenza virus A/H3N2 E119V mutant. 2011 Journal of clinical microbiology Title IV I222V;E119V 4;123 9;128 10 23 21172786 Pandemic H1N1 2009 influenza virus with the H275Y oseltamivir resistance neuraminidase mutation shows a small compromise in enzyme activity and viral fitness. Pandemic H1N1 2009 influenza virus with the H275Y oseltamivir resistance neuraminidase mutation shows a small compromise in enzyme activity and viral fitness. 2011 The Journal of antimicrobial chemotherapy Title IV H275Y 44 49 73 86 21226922 Influenza A virus NS1 gene mutations F103L and M106I increase replication and virulence. Influenza A virus NS1 gene mutations F103L and M106I increase replication and virulence. 2011 Virology journal Title IV F103L;M106I 37;47 42;52 NS1 18 21 21367898 Effect of an asparagine-to-serine mutation at position 294 in neuraminidase on the pathogenicity of highly pathogenic H5N1 influenza A virus. Effect of an asparagine-to-serine mutation at position 294 in neuraminidase on the pathogenicity of highly pathogenic H5N1 influenza A virus. 2011 Journal of virology Title IV N294S 13 58 62 75 21422222 Combinatorial effect of two framework mutations (E119V and I222L) in the neuraminidase active site of H3N2 influenza virus on resistance to oseltamivir. Combinatorial effect of two framework mutations (E119V and I222L) in the neuraminidase active site of H3N2 influenza virus on resistance to oseltamivir. 2011 Antimicrobial agents and chemotherapy Title IV E119V;I222L 49;59 54;64 73 86 21628810 Simultaneous detection and subtyping of H274Y-positive influenza A (H1N1) using pyrosequencing. Simultaneous detection and subtyping of H274Y-positive influenza A (H1N1) using pyrosequencing. 2011 Journal of infection in developing countries Title IV H274Y 40 54 21816827 Biochemical impact of the host adaptation-associated PB2 E627K mutation on the temperature-dependent RNA synthesis kinetics of influenza A virus polymerase complex. Biochemical impact of the host adaptation-associated PB2 E627K mutation on the temperature-dependent RNA synthesis kinetics of influenza A virus polymerase complex. 2011 The Journal of biological chemistry Title IV E627K 57 62 PB2 53 56 21865430 High-resolution melting approach to efficient identification and quantification of H275Y mutant influenza H1N1/2009 virus in mixed-virus-population samples. High-resolution melting approach to efficient identification and quantification of H275Y mutant influenza H1N1/2009 virus in mixed-virus-population samples. 2011 Journal of clinical microbiology Title IV H275Y 83 88 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. 2011 PloS one Title IV D222G 10 15 HA 32 45 21980293 Multidrug resistant 2009 A/H1N1 influenza clinical isolate with a neuraminidase I223R mutation retains its virulence and transmissibility in ferrets. Multidrug resistant 2009 A/H1N1 influenza clinical isolate with a neuraminidase I223R mutation retains its virulence and transmissibility in ferrets. 2011 PLoS pathogens Title IV I223R;I223R 80;80 85;85 66 79 22243670 Neuraminidase H275Y and hemagglutinin D222G mutations in a fatal case of 2009 pandemic influenza A (H1N1) virus infection. Neuraminidase H275Y and hemagglutinin D222G mutations in a fatal case of 2009 pandemic influenza A (H1N1) virus infection. 2012 Influenza and other respiratory viruses Title IV H275Y;D222G 14;38 19;43 HA;NA 24;0 37;13 Influenza A virus H1N1 infection 87 121 22363521 Frequency of D222G and Q223R hemagglutinin mutants of pandemic (H1N1) 2009 influenza virus in Japan between 2009 and 2010. Frequency of D222G and Q223R hemagglutinin mutants of pandemic (H1N1) 2009 influenza virus in Japan between 2009 and 2010. 2012 PloS one Title IV D222G;Q223R 13;23 18;28 HA 29 42 22525464 A single point mutation (Y89F) within the non-structural protein 1 of influenza A viruses limits epithelial cell tropism and virulence in mice. A single point mutation (Y89F) within the non-structural protein 1 of influenza A viruses limits epithelial cell tropism and virulence in mice. 2012 The American journal of pathology Title IV Y89F 25 29 NS 42 66 22535992 Recovery of influenza B virus with the H273Y point mutation in the neuraminidase active site from a human patient. Recovery of influenza B virus with the H273Y point mutation in the neuraminidase active site from a human patient. 2012 Journal of clinical microbiology Title IV H273Y;H273Y 39;39 44;44 67 80 22574858 Long time scale GPU dynamics reveal the mechanism of drug resistance of the dual mutant I223R/H275Y neuraminidase from H1N1-2009 influenza virus. Long time scale GPU dynamics reveal the mechanism of drug resistance of the dual mutant I223R/H275Y neuraminidase from H1N1-2009 influenza virus. 2012 Biochemistry Title IV I223R;H275Y;I223R;H275Y 88;94;88;94 93;99;93;99 100 113 22581100 Molecular mechanism of the enhanced virulence of 2009 pandemic influenza A (H1N1) virus from D222G mutation in the hemagglutinin: a molecular modeling study. Molecular mechanism of the enhanced virulence of 2009 pandemic influenza A (H1N1) virus from D222G mutation in the hemagglutinin: a molecular modeling study. 2012 Journal of molecular modeling Title IV D222G 93 98 HA 115 128 22621130 The new temperature-sensitive mutation PA-F35S for developing recombinant avian live attenuated H5N1 influenza vaccine. The new temperature-sensitive mutation PA-F35S for developing recombinant avian live attenuated H5N1 influenza vaccine. 2012 Virology journal Title IV F35S 42 46 PA 39 41 22796550 Development and evaluation of a line probe assay for rapid typing of influenza viruses and detection of the H274Y mutation. Development and evaluation of a line probe assay for rapid typing of influenza viruses and detection of the H274Y mutation. 2012 Journal of virological methods Title IV H274Y 108 113 22808250 Mouse-adapted H9N2 influenza A virus PB2 protein M147L and E627K mutations are critical for high virulence. Mouse-adapted H9N2 influenza A virus PB2 protein M147L and E627K mutations are critical for high virulence. 2012 PloS one Title IV M147L;E627K;M147L;E627K 49;59;49;59 54;64;54;64 PB2 37 40 22837199 The H275Y neuraminidase mutation of the pandemic A/H1N1 influenza virus lengthens the eclipse phase and reduces viral output of infected cells, potentially compromising fitness in ferrets. The H275Y neuraminidase mutation of the pandemic A/H1N1 influenza virus lengthens the eclipse phase and reduces viral output of infected cells, potentially compromising fitness in ferrets. 2012 Journal of virology Title IV H275Y;H275Y 4;4 9;9 10 23 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. 2012 PLoS pathogens Title IV I223R 54 59 60 73 23053629 Molecular mechanisms underlying oseltamivir resistance mediated by an I117V substitution in the neuraminidase of subtype H5N1 avian influenza A viruses. Molecular mechanisms underlying oseltamivir resistance mediated by an I117V substitution in the neuraminidase of subtype H5N1 avian influenza A viruses. 2013 The Journal of infectious diseases Title IV I117V 70 75 96 109 23077315 The compensatory G88R change is essential in restoring the normal functions of influenza A/WSN/33 virus matrix protein 1 with a disrupted nuclear localization signal. The compensatory G88R change is essential in restoring the normal functions of influenza A/WSN/33 virus matrix protein 1 with a disrupted nuclear localization signal. 2013 Journal of virology Title IV G88R;G88R 17;17 21;21 M 104 110 23131559 A single E105K mutation far from the active site of influenza B virus neuraminidase contributes to reduced susceptibility to multiple neuraminidase-inhibitor drugs. A single E105K mutation far from the active site of influenza B virus neuraminidase contributes to reduced susceptibility to multiple neuraminidase-inhibitor drugs. 2012 Biochemical and biophysical research communications Title IV E105K;E105K 9;9 14;14 NA;NA 70;134 83;147 23152521 Systematic identification of H274Y compensatory mutations in influenza A virus neuraminidase by high-throughput screening. Systematic identification of H274Y compensatory mutations in influenza A virus neuraminidase by high-throughput screening. 2013 Journal of virology Title IV H274Y;H274Y 29;29 34;34 79 92 23192869 Pandemic 2009 H1N1 influenza A virus carrying a Q136K mutation in the neuraminidase gene is resistant to zanamivir but exhibits reduced fitness in the guinea pig transmission model. Pandemic 2009 H1N1 influenza A virus carrying a Q136K mutation in the neuraminidase gene is resistant to zanamivir but exhibits reduced fitness in the guinea pig transmission model. 2013 Journal of virology Title IV Q136K 48 53 70 83 23242536 A cluster of patients infected with I221V influenza b virus variants with reduced oseltamivir susceptibility--North Carolina and South Carolina, 2010-2011. A cluster of patients infected with I221V influenza b virus variants with reduced oseltamivir susceptibility--North Carolina and South Carolina, 2010-2011. 2013 The Journal of infectious diseases Title IV I221V 36 41 23302696 Structure and inhibition of the drug-resistant S31N mutant of the M2 ion channel of influenza A virus. Structure and inhibition of the drug-resistant S31N mutant of the M2 ion channel of influenza A virus. 2013 Proc Natl Acad Sci U S A Title IV S31N 47 51 M2 66 68 23307364 A serine-to-asparagine mutation at position 314 of H5N1 avian influenza virus NP is a temperature-sensitive mutation that interferes with nuclear localization of NP. A serine-to-asparagine mutation at position 314 of H5N1 avian influenza virus NP is a temperature-sensitive mutation that interferes with nuclear localization of NP. 2013 Archives of virology Title IV S314N;S314N 2;2 47;47 NP;NP 78;162 80;164 23436652 Structural and functional characterization of K339T substitution identified in the PB2 subunit cap-binding pocket of influenza A virus. Structural and functional characterization of K339T substitution identified in the PB2 subunit cap-binding pocket of influenza A virus. 2013 The Journal of biological chemistry Title IV K339T 46 51 PB2 83 86 23437766 Discovery of novel dual inhibitors of the wild-type and the most prevalent drug-resistant mutant, S31N, of the M2 proton channel from influenza A virus. Discovery of novel dual inhibitors of the wild-type and the most prevalent drug-resistant mutant, S31N, of the M2 proton channel from influenza A virus. 2013 Journal of medicinal chemistry Title IV S31N 98 102 M2 111 113 23514882 Molecular basis of the receptor binding specificity switch of the hemagglutinins from both the 1918 and 2009 pandemic influenza A viruses by a D225G substitution. Molecular basis of the receptor binding specificity switch of the hemagglutinins from both the 1918 and 2009 pandemic influenza A viruses by a D225G substitution. 2013 Journal of virology Title IV D225G 143 148 HA 66 80 23536663 Substitutions T200A and E227A in the hemagglutinin of pandemic 2009 influenza A virus increase lethality but decrease transmission. Substitutions T200A and E227A in the hemagglutinin of pandemic 2009 influenza A virus increase lethality but decrease transmission. 2013 Journal of virology Title IV T200A;E227A;T200A;E227A 14;24;14;24 19;29;19;29 HA 37 50 23794010 Insight into the oseltamivir resistance R292K mutation in H5N1 influenza virus: a molecular docking and molecular dynamics approach. Insight into the oseltamivir resistance R292K mutation in H5N1 influenza virus: a molecular docking and molecular dynamics approach. 2014 Cell biochemistry and biophysics Title IV R292K 40 45 23860768 Resistance to neuraminidase inhibitors conferred by an R292K mutation in a human influenza virus H7N9 isolate can be masked by a mixed R/K viral population. Resistance to neuraminidase inhibitors conferred by an R292K mutation in a human influenza virus H7N9 isolate can be masked by a mixed R/K viral population. 2013 mBio Title IV R292K 55 60 14 27 23886034 Influenza A/Hong Kong/156/1997(H5N1) virus NS1 gene mutations F103L and M106I both increase IFN antagonism, virulence and cytoplasmic localization but differ in binding to RIG-I and CPSF30. Influenza A/Hong Kong/156/1997(H5N1) virus NS1 gene mutations F103L and M106I both increase IFN antagonism, virulence and cytoplasmic localization but differ in binding to RIG-I and CPSF30. 2013 Virology journal Title IV F103L;M106I 62;72 67;77 NS1 43 46 23902660 Frequency of D222G haemagglutinin mutant of pandemic (H1N1) pdm09 influenza virus in Tunisia between 2009 and 2011. Frequency of D222G haemagglutinin mutant of pandemic (H1N1) pdm09 influenza virus in Tunisia between 2009 and 2011. 2013 Diagnostic pathology Title IV D222G 13 18 HA 19 33 23951116 Resistance mutation R292K is induced in influenza A(H6N2) virus by exposure of infected mallards to low levels of oseltamivir. Resistance mutation R292K is induced in influenza A(H6N2) virus by exposure of infected mallards to low levels of oseltamivir. 2013 PloS one Title IV R292K 20 25 23994833 Mutation tryptophan to leucine at position 222 of haemagglutinin could facilitate H3N2 influenza A virus infection in dogs. Mutation tryptophan to leucine at position 222 of haemagglutinin could facilitate H3N2 influenza A virus infection in dogs. 2013 The Journal of general virology Title IV W222L 9 46 HA 50 64 24012880 The hemagglutinin mutation E391K of pandemic 2009 influenza revisited. The hemagglutinin mutation E391K of pandemic 2009 influenza revisited. 2014 Molecular phylogenetics and evolution Title IV E391K 27 32 HA 4 17 24020758 Effects of the Q223R mutation in the hemagglutinin (HA) of egg-adapted pandemic 2009 (H1N1) influenza A virus on virus growth and binding of HA to human- and avian-type cell receptors. Effects of the Q223R mutation in the hemagglutinin (HA) of egg-adapted pandemic 2009 (H1N1) influenza A virus on virus growth and binding of HA to human- and avian-type cell receptors. 2013 Acta virologica Title IV Q223R 15 20 HA;HA;HA 52;141;37 54;143;50 24055835 Insights into susceptibility of antiviral drugs against the E119G mutant of 2009 influenza A (H1N1) neuraminidase by molecular dynamics simulations and free energy calculations. Insights into susceptibility of antiviral drugs against the E119G mutant of 2009 influenza A (H1N1) neuraminidase by molecular dynamics simulations and free energy calculations. 2013 Antiviral research Title IV E119G 60 65 100 113 24074585 Mutation from arginine to lysine at the position 189 of hemagglutinin contributes to the antigenic drift in H3N2 swine influenza viruses. Mutation from arginine to lysine at the position 189 of hemagglutinin contributes to the antigenic drift in H3N2 swine influenza viruses. 2013 Virology Title IV R189K 14 52 HA 56 69 24237039 3-Azatetracyclo[5.2.1.1(5,8).0(1,5)]undecane derivatives: from wild-type inhibitors of the M2 ion channel of influenza A virus to derivatives with potent activity against the V27A mutant. 3-Azatetracyclo[5.2.1.1(5,8).0(1,5)]undecane derivatives: from wild-type inhibitors of the M2 ion channel of influenza A virus to derivatives with potent activity against the V27A mutant. 2013 Journal of medicinal chemistry Title IV V27A 175 179 M2 91 93 24257603 Emergence of the virulence-associated PB2 E627K substitution in a fatal human case of highly pathogenic avian influenza virus A(H7N7) infection as determined by Illumina ultra-deep sequencing. Emergence of the virulence-associated PB2 E627K substitution in a fatal human case of highly pathogenic avian influenza virus A(H7N7) infection as determined by Illumina ultra-deep sequencing. 2014 Journal of virology Title IV E627K 42 47 PB2 38 41 Influenza A virus H7N7 infection 104 143 24366752 A conformational restriction in the influenza A virus neuraminidase binding site by R152 results in a combinational effect of I222T and H274Y on oseltamivir resistance. A conformational restriction in the influenza A virus neuraminidase binding site by R152 results in a combinational effect of I222T and H274Y on oseltamivir resistance. 2014 Antimicrobial agents and chemotherapy Title IV I222T;H274Y;I222T;H274Y 126;136;126;136 131;141;131;141 54 67 24394699 The PB2 E627K mutation contributes to the high polymerase activity and enhanced replication of H7N9 influenza virus. The PB2 E627K mutation contributes to the high polymerase activity and enhanced replication of H7N9 influenza virus. 2014 The Journal of general virology Title IV E627K;E627K 8;8 13;13 PB2 4 7 24566185 Fitness costs for Influenza B viruses carrying neuraminidase inhibitor-resistant substitutions: underscoring the importance of E119A and H274Y. Fitness costs for Influenza B viruses carrying neuraminidase inhibitor-resistant substitutions: underscoring the importance of E119A and H274Y. 2014 Antimicrobial agents and chemotherapy Title IV E119A;H274Y;E119A;H274Y 127;137;127;137 132;142;132;142 47 60 24795482 A novel I221L substitution in neuraminidase confers high-level resistance to oseltamivir in influenza B viruses. A novel I221L substitution in neuraminidase confers high-level resistance to oseltamivir in influenza B viruses. 2014 The Journal of infectious diseases Title IV I221L;I221L 8;8 13;13 30 43 24818619 Hemagglutinin mutation D222N of the 2009 pandemic H1N1 influenza virus alters receptor specificity without affecting virulence in mice. Hemagglutinin mutation D222N of the 2009 pandemic H1N1 influenza virus alters receptor specificity without affecting virulence in mice. 2014 Virus research Title IV D222N 23 28 HA 0 13 24824345 Effects of a hemagglutinin D222G substitution on the pathogenicity of 2009 influenza A (H1N1) virus in mice. Effects of a hemagglutinin D222G substitution on the pathogenicity of 2009 influenza A (H1N1) virus in mice. 2014 Archives of virology Title IV D222G 27 32 HA 13 26 24951824 The R292K mutation that confers resistance to neuraminidase inhibitors leads to competitive fitness loss of A/Shanghai/1/2013 (H7N9) influenza virus in ferrets. The R292K mutation that confers resistance to neuraminidase inhibitors leads to competitive fitness loss of A/Shanghai/1/2013 (H7N9) influenza virus in ferrets. 2014 The Journal of infectious diseases Title IV R292K 4 9 46 59 25033052 Y155H amino acid substitution in influenza A(H1N1)pdm09 viruses does not confer a phenotype of reduced susceptibility to neuraminidase inhibitors. Y155H amino acid substitution in influenza A(H1N1)pdm09 viruses does not confer a phenotype of reduced susceptibility to neuraminidase inhibitors. 2014 Euro surveillance Title IV Y155H;Y155H 0;0 5;5 121 134 25066276 Development and clinical testing of a simple, low-density gel element array for influenza identification, subtyping, and H275Y detection. Development and clinical testing of a simple, low-density gel element array for influenza identification, subtyping, and H275Y detection. 2014 Journal of virological methods Title IV H275Y 121 126 25194918 PB2-E627K and PA-T97I substitutions enhance polymerase activity and confer a virulent phenotype to an H6N1 avian influenza virus in mice. PB2-E627K and PA-T97I substitutions enhance polymerase activity and confer a virulent phenotype to an H6N1 avian influenza virus in mice. 2014 Virology Title IV E627K;T97I;E627K;T97I 4;17;4;17 9;21;9;21 PA;PB2 14;0 16;3 25409547 The K526R substitution in viral protein PB2 enhances the effects of E627K on influenza virus replication. The K526R substitution in viral protein PB2 enhances the effects of E627K on influenza virus replication. 2014 Nature communications Title IV K526R;E627K 4;68 9;73 PB2 40 43 25470189 Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel. Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel. 2014 Journal of the American Chemical Society Title IV S31N;S31N 136;136 140;140 M2 173 175 25505461 D701N mutation in the PB2 protein contributes to the pathogenicity of H5N1 avian influenza viruses but not transmissibility in guinea pigs. D701N mutation in the PB2 protein contributes to the pathogenicity of H5N1 avian influenza viruses but not transmissibility in guinea pigs. 2014 Frontiers in microbiology Title IV D701N 0 5 PB2 22 25 25588658 Detection of a transient R292K mutation in influenza A/H3N2 viruses shed for several weeks by an immunocompromised patient. Detection of a transient R292K mutation in influenza A/H3N2 viruses shed for several weeks by an immunocompromised patient. 2015 Journal of clinical microbiology Title IV R292K;R292K 25;25 30;30 25589893 Identification of novel compounds against an R294K substitution of influenza A (H7N9) virus using ensemble based drug virtual screening. Identification of novel compounds against an R294K substitution of influenza A (H7N9) virus using ensemble based drug virtual screening. 2015 International journal of medical sciences Title IV R294K 45 50 25616792 Oseltamivir-resistant influenza A (H1N1) virus strain with an H274Y mutation in neuraminidase persists without drug pressure in infected mallards. Oseltamivir-resistant influenza A (H1N1) virus strain with an H274Y mutation in neuraminidase persists without drug pressure in infected mallards. 2015 Applied and environmental microbiology Title IV H274Y;H274Y 62;62 67;67 80 93 25641917 Identification of potential virulence determinants associated H9N2 avian influenza virus PB2 E627K mutation by comparative proteomics. Identification of potential virulence determinants associated H9N2 avian influenza virus PB2 E627K mutation by comparative proteomics. 2015 Proteomics Title IV E627K;E627K 93;93 98;98 PB2 89 92 25782865 Rapid emergence of a PB2-E627K substitution confers a virulent phenotype to an H9N2 avian influenza virus during adoption in mice. Rapid emergence of a PB2-E627K substitution confers a virulent phenotype to an H9N2 avian influenza virus during adoption in mice. 2015 Archives of virology Title IV E627K;E627K 25;25 30;30 PB2 21 24 25817403 A single NS2 mutation of K86R promotes PR8 vaccine donor virus growth in Vero cells. A single NS2 mutation of K86R promotes PR8 vaccine donor virus growth in Vero cells. 2015 Virology Title IV K86R 25 29 NS2 9 12 25899336 New polycyclic dual inhibitors of the wild type and the V27A mutant M2 channel of the influenza A virus with unexpected binding mode. New polycyclic dual inhibitors of the wild type and the V27A mutant M2 channel of the influenza A virus with unexpected binding mode. 2015 European journal of medicinal chemistry Title IV V27A 56 60 M2 68 70 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. 2015 PloS one Title IV H275Y;I223V 14;24 19;29 47 60 25998916 H5N1 influenza A virus with K193E and G225E double mutations in haemagglutinin is attenuated and immunogenic in mice. H5N1 influenza A virus with K193E and G225E double mutations in haemagglutinin is attenuated and immunogenic in mice. 2015 The Journal of general virology Title IV K193E;G225E;K193E;G225E 28;38;28;38 33;43;33;43 HA 64 78 26000865 Synergistic Effect of S224P and N383D Substitutions in the PA of H5N1 Avian Influenza Virus Contributes to Mammalian Adaptation. Synergistic Effect of S224P and N383D Substitutions in the PA of H5N1 Avian Influenza Virus Contributes to Mammalian Adaptation. 2015 Scientific reports Title IV S224P;N383D;S224P;N383D 22;32;22;32 27;37;27;37 PA 59 61 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. 2014 Emerging microbes & infections Title IV R292K;R292K 92;92 97;97 26071346 Quantitative analysis of influenza A (H3N2) E119V and R292K variants in clinical specimens by real-time reverse transcription polymerase chain reaction. Quantitative analysis of influenza A (H3N2) E119V and R292K variants in clinical specimens by real-time reverse transcription polymerase chain reaction. 2015 Journal of clinical virology Title IV E119V;R292K;E119V;R292K 44;54;44;54 49;59;49;59 26074198 Adaptive mutation PB2 D701N promotes nuclear import of influenza vRNPs in mammalian cells. Adaptive mutation PB2 D701N promotes nuclear import of influenza vRNPs in mammalian cells. 2015 European journal of cell biology Title IV D701N 22 27 PB2 18 21 26077257 Influenza A(H7N9) virus acquires resistance-related neuraminidase I222T substitution when infected mallards are exposed to low levels of oseltamivir in water. Influenza A(H7N9) virus acquires resistance-related neuraminidase I222T substitution when infected mallards are exposed to low levels of oseltamivir in water. 2015 Antimicrobial agents and chemotherapy Title IV I222T 66 71 52 65 26089289 Mouse lung-adapted mutation of E190G in hemagglutinin from H5N1 influenza virus contributes to attenuation in mice. Mouse lung-adapted mutation of E190G in hemagglutinin from H5N1 influenza virus contributes to attenuation in mice. 2015 Journal of medical virology Title IV E190G 31 36 HA 40 53 26391278 Dual E627K and D701N mutations in the PB2 protein of A(H7N9) influenza virus increased its virulence in mammalian models. Dual E627K and D701N mutations in the PB2 protein of A(H7N9) influenza virus increased its virulence in mammalian models. 2015 Scientific reports Title IV E627K;D701N;E627K;D701N 5;15;5;15 10;20;10;20 PB2 38 41 26422258 Oseltamivir Resistance in Influenza A(H6N2) Caused by an R292K Substitution in Neuraminidase Is Not Maintained in Mallards without Drug Pressure. Oseltamivir Resistance in Influenza A(H6N2) Caused by an R292K Substitution in Neuraminidase Is Not Maintained in Mallards without Drug Pressure. 2015 PloS one Title IV R292K;R292K 57;57 62;62 79 92 26453960 A PB1 T296R substitution enhance polymerase activity and confer a virulent phenotype to a 2009 pandemic H1N1 influenza virus in mice. A PB1 T296R substitution enhance polymerase activity and confer a virulent phenotype to a 2009 pandemic H1N1 influenza virus in mice. 2015 Virology Title IV T296R;T296R 6;6 11;11 PB1 2 5 26608955 Zanamivir-resistant influenza viruses with Q136K or Q136R neuraminidase residue mutations can arise during MDCK cell culture creating challenges for antiviral susceptibility monitoring. Zanamivir-resistant influenza viruses with Q136K or Q136R neuraminidase residue mutations can arise during MDCK cell culture creating challenges for antiviral susceptibility monitoring. 2015 Euro surveillance Title IV Q136K;Q136R 43;52 48;57 58 71 26621436 Origins of Resistance Conferred by the R292K Neuraminidase Mutation via Molecular Dynamics and Free Energy Calculations. Origins of Resistance Conferred by the R292K Neuraminidase Mutation via Molecular Dynamics and Free Energy Calculations. 2008 Journal of chemical theory and computation Title IV R292K;R292K 39;39 44;44 45 58 26703840 H274Y's Effect on Oseltamivir Resistance: What Happens Before the Drug Enters the Binding Site. H274Y's Effect on Oseltamivir Resistance: What Happens Before the Drug Enters the Binding Site. 2016 Journal of chemical information and modeling Title IV H274Y;H274Y 0;0 5;5 27082171 Crystal structure of the drug-resistant S31N influenza M2 proton channel. Crystal structure of the drug-resistant S31N influenza M2 proton channel. 2016 Protein science Title IV S31N;S31N 40;40 44;44 M2 55 57 27336226 Influenza A(H1N1)pdm09 virus exhibiting enhanced cross-resistance to oseltamivir and peramivir due to a dual H275Y/G147R substitution, Japan, March 2016. Influenza A(H1N1)pdm09 virus exhibiting enhanced cross-resistance to oseltamivir and peramivir due to a dual H275Y/G147R substitution, Japan, March 2016. 2016 Euro surveillance Title IV H275Y;G147R;H275Y;G147R 109;115;109;115 114;120;114;120 27384648 Prevailing PA Mutation K356R in Avian Influenza H9N2 Virus Increases Mammalian Replication and Pathogenicity. Prevailing PA Mutation K356R in Avian Influenza H9N2 Virus Increases Mammalian Replication and Pathogenicity. 2016 Journal of virology Title IV K356R 23 28 PA 11 13 27385729 Pharmacological Characterization of the Spectrum of Antiviral Activity and Genetic Barrier to Drug Resistance of M2-S31N Channel Blockers. Pharmacological Characterization of the Spectrum of Antiviral Activity and Genetic Barrier to Drug Resistance of M2-S31N Channel Blockers. 2016 Molecular pharmacology Title IV S31N 116 120 M2 113 115 27405392 G45R mutation in the nonstructural protein 1 of A/Puerto Rico/8/1934 (H1N1) enhances viral replication independent of dsRNA-binding activity and type I interferon biology. G45R mutation in the nonstructural protein 1 of A/Puerto Rico/8/1934 (H1N1) enhances viral replication independent of dsRNA-binding activity and type I interferon biology. 2016 Virology journal Title IV G45R;G45R 0;0 4;4 27535054 NS1 Protein Mutation I64T Affects Interferon Responses and Virulence of Circulating H3N2 Human Influenza A Viruses. NS1 Protein Mutation I64T Affects Interferon Responses and Virulence of Circulating H3N2 Human Influenza A Viruses. 2016 Journal of virology Title IV I64T;I64T 21;21 25;25 NS1 0 3 27657178 Discovery of Potent Antivirals against Amantadine-Resistant Influenza A Viruses by Targeting the M2-S31N Proton Channel. Discovery of Potent Antivirals against Amantadine-Resistant Influenza A Viruses by Targeting the M2-S31N Proton Channel. 2016 ACS infectious diseases Title IV S31N;S31N 100;100 104;104 M2 97 99 27664027 G45R on nonstructural protein 1 of influenza A virus contributes to virulence by increasing the expression of proinflammatory cytokines in mice. G45R on nonstructural protein 1 of influenza A virus contributes to virulence by increasing the expression of proinflammatory cytokines in mice. 2017 Archives of virology Title IV G45R 0 4 27714494 Role of R292K mutation in influenza H7N9 neuraminidase toward oseltamivir susceptibility: MD and MM/PB(GB)SA study. Role of R292K mutation in influenza H7N9 neuraminidase toward oseltamivir susceptibility: MD and MM/PB(GB)SA study. 2016 Journal of computer-aided molecular design Title IV R292K 8 13 41 54 27830688 [Changes in the phenotypic properties of highly pathogenic influenza A virus of H5N1 subtype induced by N186I and N186T point mutations in hemagglutinin]. [Changes in the phenotypic properties of highly pathogenic influenza A virus of H5N1 subtype induced by N186I and N186T point mutations in hemagglutinin]. 2016 Molekuliarnaia biologiia Title IV N186I;N186T 104;114 109;119 HA 139 152 27849220 Surveillance of antiviral resistance markers in Argentina: detection of E119V neuraminidase mutation in a post-treatment immunocompromised patient. Surveillance of antiviral resistance markers in Argentina: detection of E119V neuraminidase mutation in a post-treatment immunocompromised patient. 2016 Memorias do Instituto Oswaldo Cruz Title IV E119V 72 77 78 91 27886255 Amino acid substitutions V63I or A37S/I61T/V63I/V100A in the PA N-terminal domain increase the virulence of H7N7 influenza A virus. Amino acid substitutions V63I or A37S/I61T/V63I/V100A in the PA N-terminal domain increase the virulence of H7N7 influenza A virus. 2016 Scientific reports Title IV V63I;V63I;A37S;I61T;V100A;V63I;A37S;I61T;V63I;V100A 25;43;33;38;48;25;33;38;43;48 29;47;37;42;53;29;37;42;47;53 PA 61 63 27889648 PB2 substitutions V598T/I increase the virulence of H7N9 influenza A virus in mammals. PB2 substitutions V598T/I increase the virulence of H7N9 influenza A virus in mammals. 2017 Virology Title IV V598T;V598I 18;18 25;25 PB2 0 3 28003482 NS1 Protein Amino Acid Changes D189N and V194I Affect Interferon Responses, Thermosensitivity, and Virulence of Circulating H3N2 Human Influenza A Viruses. NS1 Protein Amino Acid Changes D189N and V194I Affect Interferon Responses, Thermosensitivity, and Virulence of Circulating H3N2 Human Influenza A Viruses. 2017 Journal of virology Title IV D189N;V194I 31;41 36;46 NS1 0 3 28004398 Detection of D151G/N mutations in the neuraminidase gene of influenza A (H3N2) viruses by real-time RT-PCR allelic discrimination assay. Detection of D151G/N mutations in the neuraminidase gene of influenza A (H3N2) viruses by real-time RT-PCR allelic discrimination assay. 2017 Journal of medical virology Title IV D151G;D151N;D151G;D151N 13;13;13;13 20;20;20;20 38 51 28012921 Therapeutic efficacy of peramivir against H5N1 highly pathogenic avian influenza viruses harboring the neuraminidase H275Y mutation. Therapeutic efficacy of peramivir against H5N1 highly pathogenic avian influenza viruses harboring the neuraminidase H275Y mutation. 2017 Antiviral research Title IV H275Y 117 122 103 116 28087313 An M2-V27A channel blocker demonstrates potent in vitro and in vivo antiviral activities against amantadine-sensitive and -resistant influenza A viruses. An M2-V27A channel blocker demonstrates potent in vitro and in vivo antiviral activities against amantadine-sensitive and -resistant influenza A viruses. 2017 Antiviral research Title IV V27A 6 10 M2 3 5 28113045 PAN substitutions A37S, A37S/I61T and A37S/V63I attenuate the replication of H7N7 influenza A virus by impairing the polymerase and endonuclease activities. PAN substitutions A37S, A37S/I61T and A37S/V63I attenuate the replication of H7N7 influenza A virus by impairing the polymerase and endonuclease activities. 2017 The Journal of general virology Title IV A37S;A37S;I61T;A37S;V63I;A37S 18;24;29;38;43;18 22;28;33;42;47;22 28166830 The T160A hemagglutinin substitution affects not only receptor binding property but also transmissibility of H5N1 clade 2.3.4 avian influenza virus in guinea pigs. The T160A hemagglutinin substitution affects not only receptor binding property but also transmissibility of H5N1 clade 2.3.4 avian influenza virus in guinea pigs. 2017 Veterinary research Title IV T160A;T160A 4;4 9;9 HA 10 23 28182419 Expeditious Lead Optimization of Isoxazole-Containing Influenza A Virus M2-S31N Inhibitors Using the Suzuki-Miyaura Cross-Coupling Reaction. Expeditious Lead Optimization of Isoxazole-Containing Influenza A Virus M2-S31N Inhibitors Using the Suzuki-Miyaura Cross-Coupling Reaction. 2017 Journal of medicinal chemistry Title IV S31N;S31N 75;75 79;79 M2 72 74 28279127 In silico prediction of drug resistance due to S247R mutation of Influenza H1N1 neuraminidase protein. In silico prediction of drug resistance due to S247R mutation of Influenza H1N1 neuraminidase protein. 2018 Journal of biomolecular structure & dynamics Title IV S247R 47 52 80 93 28418242 Slow but Steady Wins the Race: Dissimilarities among New Dual Inhibitors of the Wild-Type and the V27A Mutant M2 Channels of Influenza A Virus. Slow but Steady Wins the Race: Dissimilarities among New Dual Inhibitors of the Wild-Type and the V27A Mutant M2 Channels of Influenza A Virus. 2017 Journal of medicinal chemistry Title IV V27A 98 102 M2 110 112 28421062 Identification of Rare PB2-D701N Mutation from a Patient with Severe Influenza: Contribution of the PB2-D701N Mutation to the Pathogenicity of Human Influenza. Identification of Rare PB2-D701N Mutation from a Patient with Severe Influenza: Contribution of the PB2-D701N Mutation to the Pathogenicity of Human Influenza. 2017 Frontiers in microbiology Title IV D701N;D701N 27;104 32;109 PB2;PB2 23;100 26;103 Influenza;Influenza 143;62 158;78 28744280 Amino Acid Substitution K470R in the Nucleoprotein Increases the Virulence of H5N1 Influenza A Virus in Mammals. Amino Acid Substitution K470R in the Nucleoprotein Increases the Virulence of H5N1 Influenza A Virus in Mammals. 2017 Frontiers in microbiology Title IV K470R 24 29 NP 37 50 28750900 Virulence of an H5N8 highly pathogenic avian influenza is enhanced by the amino acid substitutions PB2 E627K and HA A149V. Virulence of an H5N8 highly pathogenic avian influenza is enhanced by the amino acid substitutions PB2 E627K and HA A149V. 2017 Infection, genetics and evolution Title IV E627K;A149V 103;116 108;121 HA;PB2 113;99 115;102 28835506 The K186E Amino Acid Substitution in the Canine Influenza Virus H3N8 NS1 Protein Restores Its Ability To Inhibit Host Gene Expression. The K186E Amino Acid Substitution in the Canine Influenza Virus H3N8 NS1 Protein Restores Its Ability To Inhibit Host Gene Expression. 2017 Journal of virology Title IV K186E 4 9 NS1 69 72 28951584 Identification of neuraminidase inhibitors against dual H274Y/I222R mutant strains. Identification of neuraminidase inhibitors against dual H274Y/I222R mutant strains. 2017 Scientific reports Title IV H274Y;I222R 56;62 61;67 18 31 29118117 A Y161F Hemagglutinin Substitution Increases Thermostability and Improves Yields of 2009 H1N1 Influenza A Virus in Cells. A Y161F Hemagglutinin Substitution Increases Thermostability and Improves Yields of 2009 H1N1 Influenza A Virus in Cells. 2018 Journal of virology Title IV Y161F 2 7 HA 8 21 29159346 Peramivir analogues bearing hydrophilic side chains exhibit higher activities against H275Y mutant than wild-type influenza virus. Peramivir analogues bearing hydrophilic side chains exhibit higher activities against H275Y mutant than wild-type influenza virus. 2017 Organic & biomolecular chemistry Title IV H275Y 86 91 29175013 The PB2-K627E mutation attenuates H3N2 swine influenza virus in cultured cells and in mice. The PB2-K627E mutation attenuates H3N2 swine influenza virus in cultured cells and in mice. 2018 Research in veterinary science Title IV K627E 8 13 PB2 4 7 29199545 The inhibitory performance of flavonoid cyanidin-3-sambubiocide against H274Y mutation in H1N1 influenza virus. The inhibitory performance of flavonoid cyanidin-3-sambubiocide against H274Y mutation in H1N1 influenza virus. 2018 Journal of biomolecular structure & dynamics Title IV H274Y 72 77 29445999 The S190R mutation in the hemagglutinin protein of pandemic H1N1 2009 influenza virus increased its pathogenicity in mice. The S190R mutation in the hemagglutinin protein of pandemic H1N1 2009 influenza virus increased its pathogenicity in mice. 2018 Science China. Life sciences Title IV S190R 4 9 HA 26 39 29491160 Enhanced Human-Type Receptor Binding by Ferret-Transmissible H5N1 with a K193T Mutation. Enhanced Human-Type Receptor Binding by Ferret-Transmissible H5N1 with a K193T Mutation. 2018 Journal of virology Title IV K193T 73 78 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. 2018 Antiviral research Title IV S31N;S31N 88;88 92;92 29541360 Unraveling the Binding, Proton Blockage, and Inhibition of Influenza M2 WT and S31N by Rimantadine Variants. Unraveling the Binding, Proton Blockage, and Inhibition of Influenza M2 WT and S31N by Rimantadine Variants. 2018 ACS medicinal chemistry letters Title IV S31N 79 83 M2 69 71 29574145 Identification of Indonesian clade 2.1 highly pathogenic influenza A(H5N1) viruses with N294S and S246N neuraminidase substitutions which further reduce oseltamivir susceptibility. Identification of Indonesian clade 2.1 highly pathogenic influenza A(H5N1) viruses with N294S and S246N neuraminidase substitutions which further reduce oseltamivir susceptibility. 2018 Antiviral research Title IV N294S;S246N 88;98 93;103 104 117 29593694 Amino Acid Substitutions HA A150V, PA A343T, and PB2 E627K Increase the Virulence of H5N6 Influenza Virus in Mice. Amino Acid Substitutions HA A150V, PA A343T, and PB2 E627K Increase the Virulence of H5N6 Influenza Virus in Mice. 2018 Frontiers in microbiology Title IV A150V;A343T;E627K 28;38;53 33;43;58 HA;PA;PB2 25;35;49 27;37;52 29691337 Identification of the I38T PA Substitution as a Resistance Marker for Next-Generation Influenza Virus Endonuclease Inhibitors. Identification of the I38T PA Substitution as a Resistance Marker for Next-Generation Influenza Virus Endonuclease Inhibitors. 2018 mBio Title IV I38T 22 26 PA 27 29 29885803 PB2 E627K or D701N substitution does not change the virulence of canine influenza virus H3N2 in mice and dogs. PB2 E627K or D701N substitution does not change the virulence of canine influenza virus H3N2 in mice and dogs. 2018 Veterinary microbiology Title IV E627K;D701N 4;13 9;18 PB2 0 3 29997206 Mutation W222L at the Receptor Binding Site of Hemagglutinin Could Facilitate Viral Adaption from Equine Influenza A(H3N8) Virus to Dogs. Mutation W222L at the Receptor Binding Site of Hemagglutinin Could Facilitate Viral Adaption from Equine Influenza A(H3N8) Virus to Dogs. 2018 Journal of virology Title IV W222L;W222L 9;9 14;14 HA 47 60 29999583 A 627K variant in the PB2 protein of H9 subtype influenza virus in wild birds. A 627K variant in the PB2 protein of H9 subtype influenza virus in wild birds. 2018 Influenza and other respiratory viruses Title IV A627K;A627K 0;0 6;6 PB2 22 25 30353004 Genome-wide characterization of the seasonal H3N2 virus in Shanghai reveals natural temperature-sensitive strains conferred by the I668V mutation in the PA subunit. Genome-wide characterization of the seasonal H3N2 virus in Shanghai reveals natural temperature-sensitive strains conferred by the I668V mutation in the PA subunit. 2018 Emerging microbes & infections Title IV I668V;I668V 131;131 136;136 PA 153 155 30365885 Structure-Based Optimization of N-Substituted Oseltamivir Derivatives as Potent Anti-Influenza A Virus Agents with Significantly Improved Potency against Oseltamivir-Resistant N1-H274Y Variant. Structure-Based Optimization of N-Substituted Oseltamivir Derivatives as Potent Anti-Influenza A Virus Agents with Significantly Improved Potency against Oseltamivir-Resistant N1-H274Y Variant. 2018 Journal of medicinal chemistry Title IV H274Y 179 184 30429954 Structure-Property Relationship Studies of Influenza A Virus AM2-S31N Proton Channel Blockers. Structure-Property Relationship Studies of Influenza A Virus AM2-S31N Proton Channel Blockers. 2018 ACS medicinal chemistry letters Title IV S31N;S31N 65;65 69;69 30463209 A PB1-K577E Mutation in H9N2 Influenza Virus Increases Polymerase Activity and Pathogenicity in Mice. A PB1-K577E Mutation in H9N2 Influenza Virus Increases Polymerase Activity and Pathogenicity in Mice. 2018 Viruses Title IV K577E 6 11 PB1 2 5 30569291 The D253N Mutation in the Polymerase Basic 2 Gene in Avian Influenza (H9N2) Virus Contributes to the Pathogenesis of the Virus in Mammalian Hosts. The D253N Mutation in the Polymerase Basic 2 Gene in Avian Influenza (H9N2) Virus Contributes to the Pathogenesis of the Virus in Mammalian Hosts. 2018 Virologica Sinica Title IV D253N 4 9 30787926 Mutation S110L of H1N1 Influenza Virus Hemagglutinin: A Potent Determinant of Attenuation in the Mouse Model. Mutation S110L of H1N1 Influenza Virus Hemagglutinin: A Potent Determinant of Attenuation in the Mouse Model. 2019 Frontiers in immunology Title IV S110L 9 14 HA 39 52 30914078 Influenza A(H3N2) virus exhibiting reduced susceptibility to baloxavir due to a polymerase acidic subunit I38T substitution detected from a hospitalised child without prior baloxavir treatment, Japan, January 2019. Influenza A(H3N2) virus exhibiting reduced susceptibility to baloxavir due to a polymerase acidic subunit I38T substitution detected from a hospitalised child without prior baloxavir treatment, Japan, January 2019. 2019 Euro surveillance Title IV I38T 106 110 PA 80 105 31175183 The L46P mutant confers a novel allosteric mechanism of resistance toward the influenza A virus M2 S31N proton channel blockers. The L46P mutant confers a novel allosteric mechanism of resistance toward the influenza A virus M2 S31N proton channel blockers. 2019 Molecular pharmacology Title IV L46P;S31N 4;99 8;103 M2 96 98 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. 2019 mBio Title IV E627K 75 80 PA;PB2 38;71 40;74 31228489 Effect of influenza H1N1 neuraminidase V116A and I117V mutations on NA activity and sensitivity to NA inhibitors. Effect of influenza H1N1 neuraminidase V116A and I117V mutations on NA activity and sensitivity to NA inhibitors. 2019 Antiviral research Title IV V116A;I117V;V116A;I117V 39;49;39;49 44;54;44;54 NA;NA;NA 68;99;25 70;101;38 31233807 Passaging of an influenza A(H1N1)pdm09 virus in a difluoro sialic acid inhibitor selects for a novel, but unfit I106M neuraminidase mutant. Passaging of an influenza A(H1N1)pdm09 virus in a difluoro sialic acid inhibitor selects for a novel, but unfit I106M neuraminidase mutant. 2019 Antiviral research Title IV I106M;I106M 112;112 117;117 118 131 31267843 Mammalian-adaptive mutation NP-Q357K in Eurasian H1N1 Swine Influenza viruses determines the virulence phenotype in mice. Mammalian-adaptive mutation NP-Q357K in Eurasian H1N1 Swine Influenza viruses determines the virulence phenotype in mice. 2019 Emerging microbes & infections Title IV Q357K 31 36 NP 28 30 31305236 Prevailing I292V PB2 mutation in avian influenza H9N2 virus increases viral polymerase function and attenuates IFN-beta induction in human cells. Prevailing I292V PB2 mutation in avian influenza H9N2 virus increases viral polymerase function and attenuates IFN-beta induction in human cells. 2019 The Journal of general virology Title IV I292V 11 16 PB2 17 20 31323237 The Val430Ile neuraminidase (NA) substitution, identified in influenza B virus isolates, impacts the catalytic 116Arg residue causing reduced susceptibility to NA inhibitors. The Val430Ile neuraminidase (NA) substitution, identified in influenza B virus isolates, impacts the catalytic 116Arg residue causing reduced susceptibility to NA inhibitors. 2019 Antiviral research Title IV V430I;V430I 4;4 13;13 NA;NA;NA 29;160;14 31;162;27 31382442 A Single Mutation N166D in Hemagglutinin Affects Antigenicity and Pathogenesis of H9N2 Avian Influenza Virus. A Single Mutation N166D in Hemagglutinin Affects Antigenicity and Pathogenesis of H9N2 Avian Influenza Virus. 2019 Viruses Title IV N166D;N166D 18;18 23;23 HA 27 40 31669761 Discovery of M2 channel blockers targeting the drug-resistant double mutants M2-S31N/L26I and M2-S31N/V27A from the influenza A viruses. Discovery of M2 channel blockers targeting the drug-resistant double mutants M2-S31N/L26I and M2-S31N/V27A from the influenza A viruses. 2020 European journal of pharmaceutical sciences Title IV S31N;L26I;S31N;V27A 80;85;97;102 84;89;101;106 M2;M2;M2 13;77;94 15;79;96 31773463 Source of oseltamivir resistance due to single E119D and double E119D/H274Y mutations in pdm09H1N1 influenza neuraminidase. Source of oseltamivir resistance due to single E119D and double E119D/H274Y mutations in pdm09H1N1 influenza neuraminidase. 2020 Journal of computer-aided molecular design Title IV E119D;E119D;H274Y;E119D 47;64;70;47 52;69;75;52 109 122 31894969 X-ray Crystal Structures of the Influenza M2 Proton Channel Drug-Resistant V27A Mutant Bound to a Spiro-Adamantyl Amine Inhibitor Reveal the Mechanism of Adamantane Resistance. X-ray Crystal Structures of the Influenza M2 Proton Channel Drug-Resistant V27A Mutant Bound to a Spiro-Adamantyl Amine Inhibitor Reveal the Mechanism of Adamantane Resistance. 2020 Biochemistry Title IV V27A;V27A 75;75 79;79 M2 42 44 31943329 E190V substitution of H6 hemagglutinin is one of key factors for binding to sulfated sialylated glycan receptor and infection to chickens. E190V substitution of H6 hemagglutinin is one of key factors for binding to sulfated sialylated glycan receptor and infection to chickens. 2020 Microbiology and immunology Title IV E190V 0 5 HA 25 38 32064779 Rapid detection of an I38T amino acid substitution in influenza polymerase acidic subunit associated with reduced susceptibility to baloxavir marboxil. Rapid detection of an I38T amino acid substitution in influenza polymerase acidic subunit associated with reduced susceptibility to baloxavir marboxil. 2020 Influenza and other respiratory viruses Title IV I38T 22 26 PA 64 89 32161172 An R195K Mutation in the PA-X Protein Increases the Virulence and Transmission of Influenza A Virus in Mammalian Hosts. An R195K Mutation in the PA-X Protein Increases the Virulence and Transmission of Influenza A Virus in Mammalian Hosts. 2020 Journal of virology Title IV R195K 3 8 PA-X 25 29 32272175 Low replicative fitness of neuraminidase inhibitor-resistant H7N9 avian influenza a virus with R292K substitution in neuraminidase in cynomolgus macaques compared with I222T substitution. Low replicative fitness of neuraminidase inhibitor-resistant H7N9 avian influenza a virus with R292K substitution in neuraminidase in cynomolgus macaques compared with I222T substitution. 2020 Antiviral research Title IV R292K;I222T 95;168 100;173 NA;NA 27;117 40;130 32456831 A D200N hemagglutinin substitution contributes to antigenic changes and increased replication of avian H9N2 influenza virus. A D200N hemagglutinin substitution contributes to antigenic changes and increased replication of avian H9N2 influenza virus. 2020 Veterinary microbiology Title IV D200N 2 7 HA 8 21 32599753 Virtual Screening Identifies Chebulagic Acid as an Inhibitor of the M2(S31N) Viral Ion Channel and Influenza A Virus. Virtual Screening Identifies Chebulagic Acid as an Inhibitor of the M2(S31N) Viral Ion Channel and Influenza A Virus. 2020 Molecules (Basel, Switzerland) Title IV S31N;S31N 71;71 75;75 M2 68 70 32631240 Successful treatment with baloxavir marboxil of a patient with peramivir-resistant influenza A/H3N2 with a dual E119D/R292K substitution after allogeneic hematopoietic cell transplantation: a case report. Successful treatment with baloxavir marboxil of a patient with peramivir-resistant influenza A/H3N2 with a dual E119D/R292K substitution after allogeneic hematopoietic cell transplantation: a case report. 2020 BMC infectious diseases Title IV E119D;R292K 112;118 117;123 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. 2020 Nature communications Title IV I223R;H275Y;I223R;H275Y 58;64;58;64 63;69;63;69 44 57 32721992 Differential Viral-Host Immune Interactions Associated with Oseltamivir-Resistant H275Y and Wild-Type H1N1 A(pdm09) Influenza Virus Pathogenicity. Differential Viral-Host Immune Interactions Associated with Oseltamivir-Resistant H275Y and Wild-Type H1N1 A(pdm09) Influenza Virus Pathogenicity. 2020 Viruses Title IV H275Y;H275Y 82;82 87;87 32746754 A single N342D substitution in Influenza B Virus NA protein determines viral pathogenicity in mice. A single N342D substitution in Influenza B Virus NA protein determines viral pathogenicity in mice. 2020 Emerging microbes & infections Title IV N342D;N342D 9;9 14;14 49 51 32786258 Chemical Probes for Blocking of Influenza A M2 Wild-type and S31N Channels. Chemical Probes for Blocking of Influenza A M2 Wild-type and S31N Channels. 2020 ACS chemical biology Title IV S31N 61 65 M2 44 46 32796071 L226Q Mutation on Influenza H7N9 Virus Hemagglutinin Increases Receptor-Binding Avidity and Leads to Biased Antigenicity Evaluation. L226Q Mutation on Influenza H7N9 Virus Hemagglutinin Increases Receptor-Binding Avidity and Leads to Biased Antigenicity Evaluation. 2020 Journal of virology Title IV L226Q 0 5 HA 39 52 32832869 Investigation of the Drug Resistance Mechanism of M2-S31N Channel Blockers through Biomolecular Simulations and Viral Passage Experiments. Investigation of the Drug Resistance Mechanism of M2-S31N Channel Blockers through Biomolecular Simulations and Viral Passage Experiments. 2020 ACS pharmacology & translational science Title IV S31N 53 57 M2 50 52 32873642 Dynamic PB2-E627K substitution of influenza H7N9 virus indicates the in vivo genetic tuning and rapid host adaptation. Dynamic PB2-E627K substitution of influenza H7N9 virus indicates the in vivo genetic tuning and rapid host adaptation. 2020 Proc Natl Acad Sci U S A Title IV E627K;E627K 12;12 17;17 PB2 8 11 33075446 V292I mutation in PB2 polymerase induces increased effects of E627K on influenza H7N9 virus replication in cells. V292I mutation in PB2 polymerase induces increased effects of E627K on influenza H7N9 virus replication in cells. 2021 Virus research Title IV V292I;E627K 0;62 5;67 PB2 18 21 33142846 A Mutated PB1 Residue 319 Synergizes with the PB2 N265S Mutation of the Live Attenuated Influenza Vaccine to Convey Temperature Sensitivity. A Mutated PB1 Residue 319 Synergizes with the PB2 N265S Mutation of the Live Attenuated Influenza Vaccine to Convey Temperature Sensitivity. 2020 Viruses Title IV N265S 50 55 PB1;PB2 10;46 13;49 33248127 Mechanism and Kinetics of Copper Complexes Binding to the Influenza A M2 S31N and S31N/G34E Channels. Mechanism and Kinetics of Copper Complexes Binding to the Influenza A M2 S31N and S31N/G34E Channels. 2021 Biophysical journal Title IV S31N;S31N;G34E;S31N;S31N;G34E 73;82;87;73;82;87 77;86;91;77;86;91 M2 70 72 33276361 [The Effect of I155T, K156Q, K156E and N186K Mutations in Hemagglutinin on the Virulence and Reproduction of Influenza A/H5N1 Viruses]. [The Effect of I155T, K156Q, K156E and N186K Mutations in Hemagglutinin on the Virulence and Reproduction of Influenza A/H5N1 Viruses]. 2020 Molekuliarnaia biologiia Title IV I155T;K156Q;K156E;N186K 15;22;29;39 20;27;34;44 HA 58 71 33309772 Deep sequencing of the transcriptome from murine lung infected with H5N8 subtype avian influenza virus with combined substitutions I283M and K526R in PB2 gene. Deep sequencing of the transcriptome from murine lung infected with H5N8 subtype avian influenza virus with combined substitutions I283M and K526R in PB2 gene. 2021 Infection, genetics and evolution Title IV I283M;K526R;I283M;K526R 131;141;131;141 136;146;136;146 PB2 150 153 Influenza A virus H5N8 infection 68 72 33351916 Multiple polymerase acidic (PA) I38X substitutions in influenza A(H1N1)pdm09 virus permit polymerase activity and cause reduced baloxavir inhibition. Multiple polymerase acidic (PA) I38X substitutions in influenza A(H1N1)pdm09 virus permit polymerase activity and cause reduced baloxavir inhibition. 2021 The Journal of antimicrobial chemotherapy Title IV I38X;I38X 32;32 36;36 PA;PA 28;9 30;26 33424035 The Effect of I155T, K156Q, K156E and N186K Mutations in Hemagglutinin on the Virulence and Reproduction of Influenza A/H5N1 Viruses. The Effect of I155T, K156Q, K156E and N186K Mutations in Hemagglutinin on the Virulence and Reproduction of Influenza A/H5N1 Viruses. 2020 Molecular biology Title IV I155T;K156Q;K156E;N186K 14;21;28;38 19;26;33;43 HA 57 70 33577807 Development of cycling probe based real-time PCR methodology for influenza A viruses possessing the PA/I38T amino acid substitution associated with reduced baloxavir susceptibility. Development of cycling probe based real-time PCR methodology for influenza A viruses possessing the PA/I38T amino acid substitution associated with reduced baloxavir susceptibility. 2021 Antiviral research Title IV I38T 103 107 PA 100 102 33840358 PB1 S524G mutation of wild bird-origin H3N8 influenza A virus enhances virulence and fitness for transmission in mammals. PB1 S524G mutation of wild bird-origin H3N8 influenza A virus enhances virulence and fitness for transmission in mammals. 2021 Emerging microbes & infections Title IV S524G;S524G 4;4 9;9 PB1 0 3 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. 2021 PloS one Title IV D222G;D222N 17;17 24;24 HA 14 16 33933515 An influenza A(H5N8) virus isolated during an outbreak at a poultry farm in Russia in 2017 has an N294S substitution in the neuraminidase and shows reduced susceptibility to oseltamivir. An influenza A(H5N8) virus isolated during an outbreak at a poultry farm in Russia in 2017 has an N294S substitution in the neuraminidase and shows reduced susceptibility to oseltamivir. 2021 Antiviral research Title IV N294S 98 103 124 137 34068322 Dual R108K and G189D Mutations in the NS1 Protein of A/H1N1 Influenza Virus Counteract Host Innate Immune Responses. Dual R108K and G189D Mutations in the NS1 Protein of A/H1N1 Influenza Virus Counteract Host Innate Immune Responses. 2021 Viruses Title IV R108K;G189D;R108K;G189D 5;15;5;15 10;20;10;20 NS1 38 41 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. 2021 PeerJ Title IV H274Y;H274Y 105;105 110;110 83 96 34358217 Mutation E48K in PB1 Polymerase Subunit Improves Stability of a Candidate Live Attenuated Influenza B Virus Vaccine. Mutation E48K in PB1 Polymerase Subunit Improves Stability of a Candidate Live Attenuated Influenza B Virus Vaccine. 2021 Vaccines Title IV E48K 9 13 PB1 17 20 35045267 Identification of a Permissive Secondary Mutation That Restores the Enzymatic Activity of Oseltamivir Resistance Mutation H275Y. Identification of a Permissive Secondary Mutation That Restores the Enzymatic Activity of Oseltamivir Resistance Mutation H275Y. 2022 Journal of virology Title IV H275Y 122 127 35511288 A novel E198K substitution in the PA gene of influenza A virus with reduced susceptibility to baloxavir acid. A novel E198K substitution in the PA gene of influenza A virus with reduced susceptibility to baloxavir acid. 2022 Archives of virology Title IV E198K;E198K 8;8 13;13 PA 34 36 8787876 Generation and characterization of variants of NWS/G70C influenza virus after in vitro passage in 4-amino-Neu5Ac2en and 4-guanidino-Neu5Ac2en. Generation and characterization of variants of NWS/G70C influenza virus after in vitro passage in 4-amino-Neu5Ac2en and 4-guanidino-Neu5Ac2en. 1996 Antimicrobial agents and chemotherapy Title IV G70C 51 55 9683567 Substrate, inhibitor, or antibody stabilizes the Glu 119 Gly mutant influenza virus neuraminidase. Substrate, inhibitor, or antibody stabilizes the Glu 119 Gly mutant influenza virus neuraminidase. 1998 Virology Title IV E119G 49 60 84 97 9811753 The vaccinia virus 14-kilodalton (A27L) fusion protein forms a triple coiled-coil structure and interacts with the 21-kilodalton (A17L) virus membrane protein through a C-terminal alpha-helix. The vaccinia virus 14-kilodalton (A27L) fusion protein forms a triple coiled-coil structure and interacts with the 21-kilodalton (A17L) virus membrane protein through a C-terminal alpha-helix. 1998 Journal of virology Title IV A27L;A17L;A27L;A17L 34;130;34;130 38;134;38;134 10482558 Mutation of neuraminidase cysteine residues yields temperature-sensitive influenza viruses. Additionally, the C303G and C320G transfectant viruses were found to be attenuated and ts. 1999 Journal of virology Abstract IV C303G;C320G 18;28 23;33 10482558 Mutation of neuraminidase cysteine residues yields temperature-sensitive influenza viruses. Because both the C303G and C320G viruses exhibited stable ts phenotypes, they were tested as helper viruses in reverse genetics experiments. 1999 Journal of virology Abstract IV C303G;C320G 17;27 22;32 10580060 Characterization of Sendai virus M protein mutants that can partially interfere with virus particle production. One of the M mutants (HA-M(30 ), an M protein carrying Thr(112)Met and Val(113) Glu substitutions tagged with an influenza virus haemagglutinin epitope) was characterized further in the context of SeV infection. 1999 The Journal of general virology Abstract IV T112M 54 67 HA;HA;M;M;M 22;129;11;25;36 24;143;12;26;37 10600600 In vitro selection and characterisation of influenza B/Beijing/1/87 isolates with altered susceptibility to zanamivir. Neuraminidase containing the E116G mutation has a 33-fold lower affinity for zanamivir than the wild-type enzyme. 1999 Virology Abstract IV E116G 29 34 0 13 10600600 In vitro selection and characterisation of influenza B/Beijing/1/87 isolates with altered susceptibility to zanamivir. The drug-dependent isolates contained two mutations in the viral haemagglutinin: V90A, close to the proposed secondary sialic acid-binding site, and L240Q, close to the primary sialic acid-binding site. 1999 Virology Abstract IV V90A;L240Q 81;149 85;154 HA 65 79 10600600 In vitro selection and characterisation of influenza B/Beijing/1/87 isolates with altered susceptibility to zanamivir. Virus isolates that were drug resistant contained the same mutations in the haemagglutinin but also contained the mutation E116G in the neuraminidase. 1999 Virology Abstract IV E116G 123 128 HA;NA 76;136 90;149 10604996 Differential requirement for CD80 and CD80/CD86-dependent costimulation in the lung immune response to an influenza virus infection. However, Y100F-Ig treatment had a clear effect on lung effector cell function. 2000 Journal of immunology (Baltimore, Md. Abstract IV Y100F 9 14 10604996 Differential requirement for CD80 and CD80/CD86-dependent costimulation in the lung immune response to an influenza virus infection. Treatment with Y100F-Ig, a mutant form of CTLA4-Ig which selectively binds to CD80 and blocks the CD28-CD80 interaction leaving CD28-CD86 binding intact, did not affect Ab production, spleen cytotoxic precursors, or clearance of virus. 2000 Journal of immunology (Baltimore, Md. Abstract IV Y100F 15 20 10772976 Fusion protein of the paramyxovirus SV5: destabilizing and stabilizing mutants of fusion activation. Compared with the W3A F protein, mutant S443P enhanced the fusion kinetics with a faster rate and greater extent, and had a lower activation temperature. 2000 Virology Abstract IV W3A;S443P 18;40 21;45 10772976 Fusion protein of the paramyxovirus SV5: destabilizing and stabilizing mutants of fusion activation. Mutant P22L did not cause fusion under physiological conditions, but fusion was activated at elevated temperatures. 2000 Virology Abstract IV P22L 7 11 10772976 Fusion protein of the paramyxovirus SV5: destabilizing and stabilizing mutants of fusion activation. Mutant V516A had little effect on F protein-mediated fusion. 2000 Virology Abstract IV V516A 7 12 10772976 Fusion protein of the paramyxovirus SV5: destabilizing and stabilizing mutants of fusion activation. SV5 strains W3A and WR differ by three amino acid residues at positions 22, 443, and 516. 2000 Virology Abstract IV W3A 12 15 10772976 Fusion protein of the paramyxovirus SV5: destabilizing and stabilizing mutants of fusion activation. The double-mutant P22L,S443P was capable of causing fusion, suggesting that the two mutations have opposing effects on fusion activation. 2000 Virology Abstract IV P22L;S443P;P22L,S 18;23;18 22;28;24 10772976 Fusion protein of the paramyxovirus SV5: destabilizing and stabilizing mutants of fusion activation. The fusion (F) protein of the paramyxovirus SV5 strain W3A causes syncytium formation without coexpression of the SV5 hemagglutinin-neuraminidase (HN) glycoprotein, whereas the F protein of the SV5 strain WR requires coexpression of HN for fusion activity. 2000 Virology Abstract IV W3A 55 58 HA;NA 118;132 131;145 10772976 Fusion protein of the paramyxovirus SV5: destabilizing and stabilizing mutants of fusion activation. The W3A F protein residues P22, S443, and V516 were changed to amino acids found in the WR F protein (L22, P443, and A516, respectively). 2000 Virology Abstract IV W3A 4 7 10804744 Influenza-associated encephalopathy in Japan: pathogenesis and treatment. A novel substitution at the receptor-binding site (Tyr 137 to Phe) was reported to be found exclusively in influenza type A (H3N2) viruses isolated from patients with influenza encephalopathy, suggesting that encephalopathy may be caused by a variant influenza type A (H3N2) virus. 2000 Pediatrics international Abstract IV Y137F 51 65 Influenza encephalopathy;Influenza encephalopathy 167;209 191;223 10867989 [Variants of influenza H1N1 virus, adapted to mouse lungs and inhibitors of mouse serum inhibitors differ by hemagglutinin characteristics and structure]. One of glycosylation site (GS) located at the tip of HA spike near the receptor binding site is lost because of mutations in both variants: GS 158 (Asn158Asp substitution) in USSR/90-MS and GS131 (Asp131Asp substitution) in USSR/90-ML. 2000 Voprosy virusologii Abstract IV N158D;D131D 148;197 157;206 HA 53 55 10888619 Antigenic drift in the influenza A virus (H3N2) nucleoprotein and escape from recognition by cytotoxic T lymphocytes. A R384K mutation was found in influenza A viruses isolated during the influenza season 1989-1990 but not in subsequent seasons. 2000 Journal of virology Abstract IV R384K 2 7 10888619 Antigenic drift in the influenza A virus (H3N2) nucleoprotein and escape from recognition by cytotoxic T lymphocytes. Both mutations R384K and R384G abrogated MHC class I presentation and allowed escape from recognition by specific CTLs. 2000 Journal of virology Abstract IV R384K;R384G 15;25 20;30 10888619 Antigenic drift in the influenza A virus (H3N2) nucleoprotein and escape from recognition by cytotoxic T lymphocytes. This R384G mutation proved to be conserved in all influenza A viruses isolated from 1993 onwards. 2000 Journal of virology Abstract IV R384G 5 10 10933681 Analysis of the pore structure of the influenza A virus M(2) ion channel by the substituted-cysteine accessibility method. Extracellular application of MTSEA evoked decreases in the conductances measured from two mutants, M(2)-A30C and M(2)-G34C. 2000 Journal of virology Abstract IV A30C;G34C 104;118 108;122 M;M 99;113 100;114 10933681 Analysis of the pore structure of the influenza A virus M(2) ion channel by the substituted-cysteine accessibility method. However, intracellular application of MTSET caused no change in the conductance of the M(2)-G34C mutant, a result in contrast to that obtained when the reagent was applied extracellularly. 2000 Journal of virology Abstract IV G34C 92 96 M 87 88 10933681 Analysis of the pore structure of the influenza A virus M(2) ion channel by the substituted-cysteine accessibility method. The conductance of the M(2)-W41C mutant was decreased by intracellular injection of a concentrated MTSET solution. 2000 Journal of virology Abstract IV W41C 28 32 M 23 24 10954551 Early alterations of the receptor-binding properties of H1, H2, and H3 avian influenza virus hemagglutinins after their introduction into mammals. For the H2 and H3 strains, a single mutation, 226Q-->L, increased binding to 6'SLN-PAA, while among H1 swine viruses, the 190E-->D and 225G-->E mutations in the HA appeared important for the increased affinity of the viruses for 6'SLN-PAA. 2000 Journal of virology Abstract IV Q226L;G225E 46;135 54;143 HA 161 163 10982377 Recognition of N-glycolylneuraminic acid linked to galactose by the alpha2,3 linkage is associated with intestinal replication of influenza A virus in ducks. A Leu-to-Gln mutation at position 226 and a Ser-to-Gly mutation at position 228 in the HA of human A/Udorn/307/72 (H3N2) permit a reassortant virus [human Udorn HA, with all other genes from A/mallard/New York/6750/78 (H2N2)] to replicate in ducks. 2000 Journal of virology Abstract IV L226Q;S228G 2;44 37;79 HA;HA 87;161 89;163 11021398 Identification of amino acids of influenza virus HA responsible for resistance to a fusion inhibitor, Stachyflin. The amino acid substitutions, lysine to arginine at position 51 or lysine to glutamic acid at position 121 of the HA2 subunit of the HA protein was enough to confer a Stachyflin-resistant phenotype of HA protein. 2000 Microbiology and immunology Abstract IV K51R;K121E 30;67 63;106 HA;HA;HA 114;133;201 116;135;203 11071905 A point mutation in the transmembrane domain of the hemagglutinin of influenza virus stabilizes a hemifusion intermediate that can transit to fusion. A hemagglutinin (HA) of influenza virus having a single semiconserved Gly residue within the transmembrane domain mutated to Leu (G520L) was expressed on cells; these cells were bound to red blood cells. 2000 Molecular biology of the cell Abstract IV G520L 130 135 HA;HA 17;2 19;15 11071905 A point mutation in the transmembrane domain of the hemagglutinin of influenza virus stabilizes a hemifusion intermediate that can transit to fusion. As evidence: 1) increasing temperature to 37 degrees C at neutral pH allowed fusion to proceed; 2) after achieving the intermediate, the two membranes did not separate from each other after proteolytic cleavage of G520L because cells treated with proteinase K could not fuse upon temperature increase but could fuse upon the addition of chlorpromazine; and 3) at the point of the intermediate, adding exogenous lipids known to promote or inhibit the creation of hemifusion did not significantly alter the lipid dye spread that occurred upon increasing temperature, implying that at the intermediate, contacting membrane leaflets had already merged. 2000 Molecular biology of the cell Abstract IV G520L 214 219 11071905 A point mutation in the transmembrane domain of the hemagglutinin of influenza virus stabilizes a hemifusion intermediate that can transit to fusion. The fusion pores generated by G520L did not enlarge, whereas those induced by wild-type HA did. 2000 Molecular biology of the cell Abstract IV G520L 30 35 HA 88 90 11090164 Vaccinia virus F12L protein is required for actin tail formation, normal plaque size, and virulence. A version of the F12L gene with a C-terminal amino acid tag derived from the influenza virus hemagglutinin and that is recognized by a monoclonal antibody was also inserted into the F12L locus of vDeltaF12L. 2000 Journal of virology Abstract IV F12L;F12L 17;182 21;186 HA 93 106 11090164 Vaccinia virus F12L protein is required for actin tail formation, normal plaque size, and virulence. A virus deletion mutant lacking the F12L gene (vDeltaF12L) and a revertant virus with the F12L gene reinserted into the deletion mutant (vF12L-rev) were constructed and analyzed. 2000 Journal of virology Abstract IV F12L;F12L 36;90 40;94 11090164 Vaccinia virus F12L protein is required for actin tail formation, normal plaque size, and virulence. Loss of the F12L protein reduced the formation of IMV 2-fold, but there was a dramatic (99.5%) reduction in actin tail formation, and the levels of cell-associated enveloped virus and extracellular enveloped virus were reduced 8- to 11-fold and 7-fold, respectively. 2000 Journal of virology Abstract IV F12L 12 16 11090164 Vaccinia virus F12L protein is required for actin tail formation, normal plaque size, and virulence. Vaccinia virus gene F12L is shown to encode a 65-kDa protein that is synthesized early and late during infection and that is not modified by glycosylation. 2000 Journal of virology Abstract IV F12L 20 24 11159448 Evolution of intermediates of influenza virus hemagglutinin-mediated fusion revealed by kinetic measurements of pore formation. Cells expressing wild-type influenza virus hemagglutinin (HA) or HA with a point mutation within the transmembrane domain (G520L) were bound to red blood cells and exposed to low pH for short times at suboptimal temperatures followed by reneutralization. 2001 Biophysical journal Abstract IV G520L 123 128 HA;HA;HA 58;65;43 60;67;56 11159448 Evolution of intermediates of influenza virus hemagglutinin-mediated fusion revealed by kinetic measurements of pore formation. For both HA and G520L, the extents of fusion did not depend on the temperature at which pH was lowered, but fusion from the intermediate was extremely sensitive to the temperature to which the cells were raised. 2001 Biophysical journal Abstract IV G520L 16 21 HA 9 11 11159448 Evolution of intermediates of influenza virus hemagglutinin-mediated fusion revealed by kinetic measurements of pore formation. In contrast, generating intermediates in the same way with G520L yielded kinetics of fusion that did not depend on the time intermediates were maintained after reneutralization. 2001 Biophysical journal Abstract IV G520L 59 64 11170976 Selection of influenza virus mutants in experimentally infected volunteers treated with oseltamivir. They bore a substitution His274Tyr in the NA. 2001 The Journal of infectious diseases Abstract IV H274Y 25 34 42 44 11408592 An intact dilysine-like motif in the carboxyl terminus of MAL is required for normal apical transport of the influenza virus hemagglutinin cargo protein in epithelial Madin-Darby canine kidney cells. Ultrastructural analysis indicated that compared with MAL bearing an intact RWKSS sequence, a mutant with lysine -3 substituted by serine showed a twofold increased presence in clathrin-coated cytoplasmic structures and a reduced expression on the plasma membrane. 2001 Molecular biology of the cell Abstract IV K3S 106 137 11413297 A single amino acid alteration in the human parainfluenza virus type 3 hemagglutinin-neuraminidase glycoprotein confers resistance to the inhibitory effects of zanamivir on receptor binding and neuraminidase activity. ZM1 exhibited a markedly fusogenic plaque morphology and harbored two HN gene mutations resulting in two amino acid alterations, T193I and I567V. 2001 Journal of virology Abstract IV T193I;I567V 129;139 134;144 11443933 [Reduction of the functional match of influenza virus hemagglutinin and neuraminidase after reassortation of genes]. Amino acid substitution K156E, which increases a negative charge at the edge of the receptor-binding pocket of HA large subunit (HA1), was revealed in two independent variants. 2001 Molekuliarnaia biologiia Abstract IV K156E 24 29 HA;HA1 111;129 113;132 11504416 Diverged evolution of recent equine-2 influenza (H3N8) viruses in the Western Hemisphere. This low evolution rate was probably due to a unique alternating Ser138 to Ala138 substitutions at antigenic site A. 2001 Archives of virology Abstract IV S138A 65 81 11529559 Mechanism of selective inhibition of respiratory syncytial virus by a benzodithiin compound (RD3-0028). The F gene segment of each of these viruses was sequenced and in each case the mutant RNA segment contained at least one sequence alteration, converting asparagine 276 to tyrosine (F1 protein). 2001 Microbiology and immunology Abstract IV N276Y 153 179 11675142 Characterization of an influenza A (H3N2) virus resistant to the cyclopentane neuraminidase inhibitor RWJ-270201. However, a point mutation resulting in a single amino acid change (Lys189Glu) was found in the resistant viral HA. 2001 Antiviral research Abstract IV K189E 67 76 HA 111 113 11684315 Detection of influenza virus resistance to neuraminidase inhibitors by an enzyme inhibition assay. addition of PO4(3-), Ca2+, DMSO, or EDTA) than wild-type enzymes or a mutant NA with an Arg292-->Lys substitution. 2002 Antiviral research Abstract IV R292K 88 100 77 79 11689658 Amino acids responsible for the absolute sialidase activity of the influenza A virus neuraminidase: relationship to growth in the duck intestine. Using chimeric constructs based on A/Singapore/1/57 and A/England/12/62 NAs, we localized the determinants of high specific NA activity to a region containing six amino acid substitutions in A/England/12/62: Ser331-->Arg, Asp339-->Asn, Asn367-->Ser, Ser370-->Leu, Asn400-->Ser, and Pro431-->Glu. 2001 Journal of virology Abstract IV S331A;D339N;N367S;S370L;N400S;P431E 208;222;236;250;264;282 220;234;248;262;276;294 NA;NA 124;72 126;75 11709315 Comparison of the activities of zanamivir, oseltamivir, and RWJ-270201 against clinical isolates of influenza virus and neuraminidase inhibitor-resistant variants. A zanamivir-resistant variant bearing a Glu119-to-Gly (Glu119-->Gly) or Glu119-->Ala substitution in an NA (N2) remained susceptible to RWJ-270201 and oseltamivir carboxylate. 2001 Antimicrobial agents and chemotherapy Abstract IV E119G;E119G;E119A 40;55;72 53;67;84 104 106 11709315 Comparison of the activities of zanamivir, oseltamivir, and RWJ-270201 against clinical isolates of influenza virus and neuraminidase inhibitor-resistant variants. However, a zanamivir-selected variant with an Arg292-->Lys substitution in an NA (N2) showed a moderate level of resistance to RWJ-270201 (IC(50) = 30 nM) and zanamivir (IC(50) = 20 nM) and a high level of resistance to oseltamivir carboxylate (IC(50) > 3,000 nM). 2001 Antimicrobial agents and chemotherapy Abstract IV R292K 46 58 78 80 11709315 Comparison of the activities of zanamivir, oseltamivir, and RWJ-270201 against clinical isolates of influenza virus and neuraminidase inhibitor-resistant variants. The oseltamivir-selected variant (N1) with the His274-->Tyr substitution exhibited resistance to oseltamivir carboxylate (IC(50) = 400 nM) and to RWJ-270201 (IC(50) = 40 nM) but retained full susceptibility to zanamivir (IC(50) = 1.5 nM). 2001 Antimicrobial agents and chemotherapy Abstract IV H274Y 47 59 11709315 Comparison of the activities of zanamivir, oseltamivir, and RWJ-270201 against clinical isolates of influenza virus and neuraminidase inhibitor-resistant variants. The zanamivir-resistant influenza B virus variant bearing an Arg152-->Lys substitution was resistant to each NA inhibitor (IC(50) = 100 to 750 nM). 2001 Antimicrobial agents and chemotherapy Abstract IV R152K 61 73 109 111 11773097 Detection of amantadine-resistant influenza A virus strains in nursing homes by PCR-restriction fragment length polymorphism analysis with nasopharyngeal swabs. Thirty-one viruses (91.2%) showed a change at position 31 (serine to asparagine), three viruses (8.8%) showed a change at position 30 (alanine to threonine), and none showed a change at position 27. 2002 Journal of clinical microbiology Abstract IV S31N;A30T 55;131 80;156 11773413 Influenza a virus M2 ion channel activity is essential for efficient replication in tissue culture. N31S-M2WSN was amantadine sensitive, whereas A/WSN/33 was amantadine resistant, indicating that the M2 residue N31 is the sole determinant of resistance of A/WSN/33 to amantadine. 2002 Journal of virology Abstract IV N31S 0 4 M2 100 102 11773413 Influenza a virus M2 ion channel activity is essential for efficient replication in tissue culture. We have investigated the effect of amantadine on the growth of four influenza viruses: A/WSN/33; N31S-M2WSN, a mutant in which an asparagine residue at position 31 in the M2 TM domain was replaced with a serine residue; MUd/WSN, which possesses seven RNA segments from WSN plus the RNA segment 7 derived from A/Udorn/72; and A/Udorn/72. 2002 Journal of virology Abstract IV N31S 97 101 M2 171 173 11864740 Use of pseudotyped retroviral vectors to analyze the receptor-binding pocket of hemagglutinin from a pathogenic avian influenza A virus (H7 subtype). The most severely affected mutants contained more than one substitution, with the triple mutant Y88F/E181Q/G219K being the most defective. 2002 Virus research Abstract IV Y88F;E181Q;G219K 96;101;107 100;106;112 11884578 Apical budding of a recombinant influenza A virus expressing a hemagglutinin protein with a basolateral localization signal. C560Y HA was expressed nonpolarly on the surface of infected MDCK cells. 2002 Journal of virology Abstract IV C560Y 0 5 HA 6 8 11884578 Apical budding of a recombinant influenza A virus expressing a hemagglutinin protein with a basolateral localization signal. Interestingly, viral budding remained apical in C560Y virus-infected cells, and so did the location of NP and M1 proteins at late times of infection. 2002 Journal of virology Abstract IV C560Y 48 53 M1;NP 110;103 112;105 11884578 Apical budding of a recombinant influenza A virus expressing a hemagglutinin protein with a basolateral localization signal. We investigated this hypothesis by infecting MDCK cells with a transfectant influenza virus carrying a mutant form of HA (C560Y) with a basolateral sorting signal in its cytoplasmic domain. 2002 Journal of virology Abstract IV C560Y 122 127 HA 118 120 11932243 Polymorphisms and the differential antiviral activity of the chicken Mx gene. On the basis of the comparison among the antiviral activities associated with many Mx variations, a specific amino acid substitution at position 631 (Ser to Asn) was considered to determine the antivirally positive or negative Mx gene. 2002 Genome research Abstract IV S631N 145 161 11932412 New insights into the spring-loaded conformational change of influenza virus hemagglutinin. We analyzed one double mutant, F63P/F70P, as an example. 2002 Journal of virology Abstract IV F63P;F70P 31;36 35;40 11932412 New insights into the spring-loaded conformational change of influenza virus hemagglutinin. We observed that F63P/F70P undergoes key low-pH-induced conformational changes and binds tightly to target membranes. 2002 Journal of virology Abstract IV F63P;F70P 17;22 21;26 11937502 Structural characterizations of fusion peptide analogs of influenza virus hemagglutinin. Implication of the necessity of a helix-hinge-helix motif in fusion activity. Also, the decrease in the C-terminal helix and the reduction of fusion activity in L17A demonstrates the importance of the C-terminal helix in fusion activity. 2002 The Journal of biological chemistry Abstract IV L17A 83 87 11937502 Structural characterizations of fusion peptide analogs of influenza virus hemagglutinin. Implication of the necessity of a helix-hinge-helix motif in fusion activity. E5 exhibits an activity similar to the native fusion peptide, whereas G13L and L17A, which are two point mutants of the E5 analog, possess much less fusion activity. 2002 The Journal of biological chemistry Abstract IV G13L;L17A 70;79 74;83 11937502 Structural characterizations of fusion peptide analogs of influenza virus hemagglutinin. Implication of the necessity of a helix-hinge-helix motif in fusion activity. Furthermore, the decrease of the hinge and the reduction of fusion activity in G13L reveal the importance of the hinge in fusion activity. 2002 The Journal of biological chemistry Abstract IV G13L 79 83 11937502 Structural characterizations of fusion peptide analogs of influenza virus hemagglutinin. Implication of the necessity of a helix-hinge-helix motif in fusion activity. To clarify how the fusion peptide exerts this specific function, we carried out biophysical studies of three fusion peptide analogs of influenza virus hemagglutinin HA2, namely E5, G13L, and L17A. 2002 The Journal of biological chemistry Abstract IV G13L;L17A 181;191 185;195 HA;HA 165;151 167;164 11991966 In vitro selection and characterization of influenza A (A/N9) virus variants resistant to a novel neuraminidase inhibitor, A-315675. By comparison, virus variants recovered from passaging against oseltamivir carboxylate (passage 14) harbored an E119V mutation and displayed a 6,000-fold-lower susceptibility to oseltamivir carboxylate and a 175-fold-lower susceptibility to zanamivir than did wild-type virus. 2002 Journal of virology Abstract IV E119V 112 117 11991966 In vitro selection and characterization of influenza A (A/N9) virus variants resistant to a novel neuraminidase inhibitor, A-315675. However, by passage 10 (2.56 microM A-315675), two mutations (R233K, S339P) in the HA gene appeared in addition to the E119D mutation in the NA gene, resulting in a 310-fold-lower susceptibility to A-315675. 2002 Journal of virology Abstract IV R233K;S339P;E119D 62;69;119 67;74;124 HA;NA 83;141 85;143 11991966 In vitro selection and characterization of influenza A (A/N9) virus variants resistant to a novel neuraminidase inhibitor, A-315675. Sequencing of the viral population identified an E119D mutation in the NA gene, but no mutations were observed in the hemagglutinin (HA) gene. 2002 Journal of virology Abstract IV E119D 49 54 HA;HA;NA 133;118;71 135;131;73 12014958 Structural studies of the resistance of influenza virus neuramindase to inhibitors. Using influenza A/NWS/Tern/Australia/G70C/75 (H1N9), neuraminidase variants E119G and R292K have previously been selected by different inhibitors. 2002 Journal of medicinal chemistry Abstract IV G70C;E119G;R292K 37;76;86 41;81;91 53 66 12062393 Influenza virus carrying neuraminidase with reduced sensitivity to oseltamivir carboxylate has altered properties in vitro and is compromised for infectivity and replicative ability in vivo. Pathogenicity of R292K influenza virus A/Sydney/5/97 was reduced in ferrets as measured by inflammatory and febrile responses at least in parallel to the decrease in replicative ability. 2002 Antiviral research Abstract IV R292K 17 22 12062393 Influenza virus carrying neuraminidase with reduced sensitivity to oseltamivir carboxylate has altered properties in vitro and is compromised for infectivity and replicative ability in vivo. The data indicate that the R292K NA mutation compromises viral fitness such that virus carrying this mutation is unlikely to be of significant clinical consequence in man. 2002 Antiviral research Abstract IV R292K 27 32 33 35 12062393 Influenza virus carrying neuraminidase with reduced sensitivity to oseltamivir carboxylate has altered properties in vitro and is compromised for infectivity and replicative ability in vivo. The infectivity and replicative abilities of R292K mutant virus were reduced by at least 2 logs in a mouse model of influenza infection and by 2 and 4 logs, respectively, in the ferret model. 2002 Antiviral research Abstract IV R292K 45 50 IV infections 116 135 12062393 Influenza virus carrying neuraminidase with reduced sensitivity to oseltamivir carboxylate has altered properties in vitro and is compromised for infectivity and replicative ability in vivo. The predominant mutation seen is the substitution of arginine for lysine at position 292 of the viral NA. 2002 Antiviral research Abstract IV K292R 53 88 102 104 12103431 The H274Y mutation in the influenza A/H1N1 neuraminidase active site following oseltamivir phosphate treatment leave virus severely compromised both in vitro and in vivo. A substitution of the conserved histidine at position 274 for tyrosine in the NA active site has been selected via site directed mutagenesis, serial passage in culture under drug pressure in H1N1 and during the treatment of experimental H1N1 infection in man. 2002 Antiviral research Abstract IV Y274H 32 70 78 80 Influenza A virus H1N1 infection 237 251 12103431 The H274Y mutation in the influenza A/H1N1 neuraminidase active site following oseltamivir phosphate treatment leave virus severely compromised both in vitro and in vivo. Virus carrying a H274Y mutation is unlikely to be of clinical consequence in man. 2002 Antiviral research Abstract IV H274Y 17 22 12103431 The H274Y mutation in the influenza A/H1N1 neuraminidase active site following oseltamivir phosphate treatment leave virus severely compromised both in vitro and in vivo. Virus carrying H274Y NA enzyme selected in vivo has reduced sensitivity to oseltamivir carboxylate. 2002 Antiviral research Abstract IV H274Y 15 20 21 23 12186883 A single amino acid mutation in the PA subunit of the influenza virus RNA polymerase inhibits endonucleolytic cleavage of capped RNAs. A mutant with a histidine-to-alanine change at position 510 (H510A) in the PA protein of influenza A/WSN/33 virus showed a differential effect on transcription and replication. 2002 Journal of virology Abstract IV H510A;H510A 61;16 66;59 PA 75 77 12186883 A single amino acid mutation in the PA subunit of the influenza virus RNA polymerase inhibits endonucleolytic cleavage of capped RNAs. In vitro analyses of the H510A recombinant polymerase, by using transcription initiation, vRNA-binding, capped-RNA-binding, and endonuclease assays, suggest that the primary defect of this mutant polymerase is in its endonuclease activity. 2002 Journal of virology Abstract IV H510A 25 30 12237433 Structure of antigenic sites on the haemagglutinin molecule of H5 avian influenza virus and phenotypic variation of escape mutants. Mutants with the amino acid change K152N, as well as those with the change D126N, showed reduced lethality in mice. 2002 The Journal of general virology Abstract IV K152N;D126N 35;75 40;80 12237433 Structure of antigenic sites on the haemagglutinin molecule of H5 avian influenza virus and phenotypic variation of escape mutants. The substitution D126N, creating a new glycosylation site, was accompanied by an increase in the sensitivity of the mutants to normal mouse serum inhibitors. 2002 The Journal of general virology Abstract IV D126N 17 22 12350356 Contacts between influenza virus N9 neuraminidase and monoclonal antibody NC10. Except for N200L and N329Q, the mutants were inhibited by NC10 to the same extent as wild-type NA although with less affinity. 2002 Virology Abstract IV N200L;N329Q 11;21 16;26 95 97 12350356 Contacts between influenza virus N9 neuraminidase and monoclonal antibody NC10. The enzyme activity (K(cat)) of N200L is 80% reduced, indicating a defect in folding or assembly; therefore, the loss in binding activity due to the missing sugar residue cannot be assessed. 2002 Virology Abstract IV N200L 32 37 12350356 Contacts between influenza virus N9 neuraminidase and monoclonal antibody NC10. The K(d) for N329Q is sixfold higher than for wild-type NA in the inhibition test, but the same as wild-type in ELISA, indicating a change in disposition of the antibody but no loss of affinity. 2002 Virology Abstract IV N329Q 13 18 56 58 12350356 Contacts between influenza virus N9 neuraminidase and monoclonal antibody NC10. The mutations made were N200L (removing an N-linked oligosaccharide), N329Q, N345Q, S370T, S372A, N400L, and K432M. 2002 Virology Abstract IV N200L;N329Q;N345Q;S370T;S372A;N400L;K432M 24;70;77;84;91;98;109 29;75;82;89;96;103;114 12388735 A reverse genetics approach for recovery of recombinant influenza B viruses entirely from cDNA. We adapted the technique for engineering influenza B virus and generated a mutant bearing an amino acid change E116G in the viral neuraminidase which was resistant in vitro to the neuraminidase inhibitor zanamivir. 2002 Journal of virology Abstract IV E116G 111 116 NA;NA 130;180 143;193 12402195 A nontoxic chimeric enterotoxin adjuvant induces protective immunity in both mucosal and systemic compartments with reduced IgE antibodies. A novel nontoxic form of chimeric mucosal adjuvant that combines the A subunit of mutant cholera toxin E112K with the pentameric B subunit of heat-labile enterotoxin from enterotoxigenic Escherichia coli was constructed by use of the Brevibacillus choshinensis expression system (mCTA/LTB). 2002 The Journal of infectious diseases Abstract IV E112K 103 108 12435681 Mechanism by which mutations at his274 alter sensitivity of influenza a virus n1 neuraminidase to oseltamivir carboxylate and zanamivir. An influenza A/H1N1 variant selected in vitro with reduced susceptibility to oseltamivir carboxylate contains a His274Tyr mutation. 2002 Antimicrobial agents and chemotherapy Abstract IV H274Y 112 121 12435681 Mechanism by which mutations at his274 alter sensitivity of influenza a virus n1 neuraminidase to oseltamivir carboxylate and zanamivir. Interestingly, His274Asn, as well as His274Gly, His274Ser, and His274Gln, also displayed reduced sensitivity to zanamivir and its analogue, 4-amino-Neu5Ac2en. 2002 Antimicrobial agents and chemotherapy Abstract IV H274N;H274G;H274S;H274Q 15;37;48;63 24;46;57;72 12435681 Mechanism by which mutations at his274 alter sensitivity of influenza a virus n1 neuraminidase to oseltamivir carboxylate and zanamivir. Loss of this slow-binding inhibition in the His274Tyr and His274Phe mutant NA but not in His274Asn, His274Gly, His274Ser, or His274Gln supports the conclusion that the conformational change of Glu276 is restricted in the His274Tyr and His274Phe mutant NA upon oseltamivir carboxylate binding. 2002 Antimicrobial agents and chemotherapy Abstract IV H274Y;H274F;H274N;H274G;H274S;H274Q;H274Y;H274F 44;58;89;100;111;125;221;235 53;67;98;109;120;134;230;244 NA;NA 75;252 77;254 12435681 Mechanism by which mutations at his274 alter sensitivity of influenza a virus n1 neuraminidase to oseltamivir carboxylate and zanamivir. Substitution of His274 with Tyr in influenza A/Tokyo/3/67 (H3N2) recombinant NA did not affect the susceptibility to oseltamivir carboxylate. 2002 Antimicrobial agents and chemotherapy Abstract IV H274Y 16 31 77 79 12435681 Mechanism by which mutations at his274 alter sensitivity of influenza a virus n1 neuraminidase to oseltamivir carboxylate and zanamivir. To understand the mechanism by which a His274Tyr mutation gives rise to drug resistance, we studied a series of NA variant proteins containing various substitutions at position 274. 2002 Antimicrobial agents and chemotherapy Abstract IV H274Y 39 48 112 114 12438632 Restriction of viral replication by mutation of the influenza virus matrix protein. In contrast, deletion of RKLKR or substitution of Lys with Asn at position 102 or 104 of RKLKR resulted in a lethal mutation. 2002 Journal of virology Abstract IV K102N 50 78 12438632 Restriction of viral replication by mutation of the influenza virus matrix protein. Substitution of Arg with Ser at position 101 or 105 of RKLKR did not have a major impact on nuclear export of RNP or viral replication. 2002 Journal of virology Abstract IV R101S 16 44 RNP 110 113 12477851 Role of protein kinase C betaII in influenza virus entry via late endosomes. Cells expressing a phosphorylation-deficient form of PKCbetaII (T500V), but not an equivalent mutant form of PKCalpha, inhibited successful influenza virus entry-with the virus accumulating in late endosomes. 2003 Journal of virology Abstract IV T500V 64 69 12477851 Role of protein kinase C betaII in influenza virus entry via late endosomes. PKCbetaII T500V expression specifically blocked EGF receptor trafficking and degradation, without affecting transferrin receptor recycling. 2003 Journal of virology Abstract IV T500V 10 15 12477851 Role of protein kinase C betaII in influenza virus entry via late endosomes. SFV, however, believed to enter cells from the early endosome, was unaffected by PKCbetaII T500V expression. 2003 Journal of virology Abstract IV T500V 91 96 12527729 Differences in conductance of M2 proton channels of two influenza viruses at low and high pH. All intermediate mutants possessed one or other property and transformation of the WM2 phenotype into that of RM2 required substitution in all three residues V27I, F38L and D44N; single substitutions in RM2 effected the opposite phenotypic change. 2003 The Journal of physiology Abstract IV V27I;F38L;D44N 158;164;173 162;168;177 12574276 Evaluation of neuraminidase enzyme assays using different substrates to measure susceptibility of influenza virus clinical isolates to neuraminidase inhibitors: report of the neuraminidase inhibitor susceptibility network. Mixing experiments, whereby increasing fractions (0, 20, 40, 60, 80, and 100%) of NA from a known NI-resistant virus were mixed with the corresponding NI-sensitive parental NA, indicated that the resolution of IC(50) values was clearer with the CL assay than with FA-2 for two of the resistant variants (R152K and E119V). 2003 Journal of clinical microbiology Abstract IV R152K;E119V 304;314 309;319 NA;NA 82;173 84;175 12574276 Evaluation of neuraminidase enzyme assays using different substrates to measure susceptibility of influenza virus clinical isolates to neuraminidase inhibitors: report of the neuraminidase inhibitor susceptibility network. We evaluated three NA inhibition assays against a panel of five clinical isolates each of influenza virus A/H1N1, A/H3N2, and B strains and four viruses with a defined resistance genotype (R292K, H274Y, R152K, and E119V). 2003 Journal of clinical microbiology Abstract IV R292K;H274Y;R152K;E119V 189;196;203;214 194;201;208;219 19 21 12663810 A single amino acid mutation in the PA subunit of the influenza virus RNA polymerase promotes the generation of defective interfering RNAs. A C453R mutation in PA can compensate for this defect, suggesting that amino acids C453 and R638 form part of the same domain. 2003 Journal of virology Abstract IV C453R 2 7 PA 20 22 12663810 A single amino acid mutation in the PA subunit of the influenza virus RNA polymerase promotes the generation of defective interfering RNAs. An R638A mutation of the polymerase acidic protein (PA) subunit of the RNA polymerase of influenza A/WSN/33 virus results in severe attenuation of viral growth in cell culture by promoting the synthesis of defective interfering RNAs. 2003 Journal of virology Abstract IV R638A 3 8 PA;PA 52;25 54;42 12663810 A single amino acid mutation in the PA subunit of the influenza virus RNA polymerase promotes the generation of defective interfering RNAs. We propose that R638A is an "elongation" mutant that destabilizes PA-RNA template interactions during elongation. 2003 Journal of virology Abstract IV R638A 16 21 PA 66 68 12692212 Mutations in the N-terminal region of influenza virus PB2 protein affect virus RNA replication but not transcription. Some of the mutations (F130Y, R142A, and R142K) were rescued into infectious virus. 2003 Journal of virology Abstract IV F130Y;R142A;R142K 23;30;41 28;35;46 12692212 Mutations in the N-terminal region of influenza virus PB2 protein affect virus RNA replication but not transcription. The results indicated that the W49A, F130A, and R142A mutations of PB2 reduced or abolished the capacity of mutant RNPs to synthesize RNA in vivo but did not substantially alter their ability to transcribe or carry out cap snatching in vitro. 2003 Journal of virology Abstract IV W49A;F130A;R142A 31;37;48 35;42;53 PB2;RNP 67;115 70;119 12692212 Mutations in the N-terminal region of influenza virus PB2 protein affect virus RNA replication but not transcription. While the F130Y mutant virus replicated faster than the wild type, mutant viruses R142A and R142K showed a delayed accumulation of cRNA and viral RNA during the infection cycle but normal kinetics of primary transcription, as determined by the accumulation of viral mRNA in cells infected in the presence of cycloheximide. 2003 Journal of virology Abstract IV F130Y;R142A;R142K 10;82;92 15;87;97 12719592 Threonine 157 of influenza virus PA polymerase subunit modulates RNA replication in infectious viruses. Finally, recombinant viruses with a T157E mutation in PA protein, which resulted in a drastic reduction of protease and replication activities of RNPs, were not viable. 2003 Journal of virology Abstract IV T157E 36 41 PA;RNP 54;146 56;150 12719592 Threonine 157 of influenza virus PA polymerase subunit modulates RNA replication in infectious viruses. Viruses with a T157A mutation, which presented a severe decrease in protease activity and replication of RNPs, showed a complex phenotype: (i) transport to the nucleus of PAT157A protein was delayed, (ii) virus multiplication was reduced at both low and high multiplicities, (iii) transcriptive synthesis was unaltered while replicative synthesis, especially cRNA, was diminished, and (iv) viral pathogenesis in mice was reduced, as measured by loss of body weight and virus titers in lungs. 2003 Journal of virology Abstract IV T157A 15 20 PA;RNP 171;105 173;109 12719592 Threonine 157 of influenza virus PA polymerase subunit modulates RNA replication in infectious viruses. Viruses with a T162A mutation, which showed a very moderate decrease both in protease and replication activities of reconstituted RNPs, showed a wild-type phenotype. 2003 Journal of virology Abstract IV T162A 15 20 RNP 130 134 12758169 X-ray structure of the hemagglutinin of a potential H3 avian progenitor of the 1968 Hong Kong pandemic influenza virus. We find that structurally significant differences between the avian and the human HAs are restricted to the receptor-binding site particularly the substitutions Q226L and G228S that cause the site to open and residues within it to rearrange, including the conserved residues Y98, W153, and H183. 2003 Virology Abstract IV Q226L;G228S 161;171 166;176 12768027 Basic residues of the helix six domain of influenza virus M1 involved in nuclear translocation of M1 can be replaced by PTAP and YPDL late assembly domain motifs. Among the rescued mutant viruses, R101A and R105K exhibited reduced growth and small-plaque morphology, and all other mutant viruses showed the wild-type phenotype. 2003 Journal of virology Abstract IV R101A;R105K 34;44 39;49 12768027 Basic residues of the helix six domain of influenza virus M1 involved in nuclear translocation of M1 can be replaced by PTAP and YPDL late assembly domain motifs. Deletion (Delta YRKL) or mutation (4A) of YRKL also abolished generation of infectious virus. 2003 Journal of virology Abstract IV 4A;Delta YRKL 35;10 37;20 12768027 Basic residues of the helix six domain of influenza virus M1 involved in nuclear translocation of M1 can be replaced by PTAP and YPDL late assembly domain motifs. Furthermore, mutant M1 proteins (R101A/K102A, Delta YRKL, 4A, PTAP, 4A+PTAP, and YPDL) when expressed alone from cloned cDNAs were only cytoplasmic, whereas the wild-type M1 expressed alone was both nuclear and cytoplasmic as expected. 2003 Journal of virology Abstract IV 4A;4A+PTAP;R101A;K102A;Delta YRKL;PTAP;YPDL 58;68;33;39;46;62;81 60;75;38;44;56;66;85 M1;M1 20;171 22;173 12768027 Basic residues of the helix six domain of influenza virus M1 involved in nuclear translocation of M1 can be replaced by PTAP and YPDL late assembly domain motifs. However, replacement of the YRKL motif with PTAP or YPDL as well as insertion of PTAP after 4A mutation yielded infectious viruses with the wild-type phenotype. 2003 Journal of virology Abstract IV 4A;YRKL;PTAP;YPDL 92;28;44;52 94;32;48;56 12768027 Basic residues of the helix six domain of influenza virus M1 involved in nuclear translocation of M1 can be replaced by PTAP and YPDL late assembly domain motifs. On the other hand, three single mutations (K104A, K105A, and E106A) and three double mutations (R101A/K102A, K104A/K105A, and K102A/R105A) failed to generate infectious virus. 2003 Journal of virology Abstract IV K104A;K105A;E106A;R101A;K102A;K104A;K105A;R105A;K102A 43;50;61;96;102;109;115;132;126 48;55;66;101;107;114;120;137;131 12768027 Basic residues of the helix six domain of influenza virus M1 involved in nuclear translocation of M1 can be replaced by PTAP and YPDL late assembly domain motifs. Our results show that infectious viruses were rescued by reverse genetics from all single alanine mutations of amino acids in the H6 domain and the neighboring region except in three positions (K104A and R105A within the NLS motif and E106A in loop 6 outside the NLS motif). 2003 Journal of virology Abstract IV K104A;R105A;E106A 194;204;235 199;209;240 NLS;NLS 221;263 230;272 12821478 Neuraminidase sequence analysis and susceptibilities of influenza virus clinical isolates to zanamivir and oseltamivir. The drug susceptibilities of known zanamivir- and oseltamivir-resistant viruses with the NA mutations E119V, R292K, H274Y, and R152K fell well outside the 95% confidence limits of the IC(50)s for all natural isolates. 2003 Antimicrobial agents and chemotherapy Abstract IV E119V;R292K;H274Y;R152K 102;109;116;127 107;114;121;132 89 91 12834856 A point mutation in influenza B neuraminidase confers resistance to peramivir and loss of slow binding. In contrast, the P15R enzyme did not display the property of slow binding and was inhibited competitively with a K(i) value of 4.69+/-0.44nM. 2003 Antiviral research Abstract IV P15R 17 21 12834856 A point mutation in influenza B neuraminidase confers resistance to peramivir and loss of slow binding. Passage 15 (P15R) virus contained an additional 3 HA mutations, plus the NA mutation His273Tyr. 2003 Antiviral research Abstract IV P15R;H273Y 12;85 16;94 HA;NA 50;73 52;75 12834856 A point mutation in influenza B neuraminidase confers resistance to peramivir and loss of slow binding. The mechanism of inhibition of WT and P15R NA by peramivir was examined in enzyme assays. 2003 Antiviral research Abstract IV P15R 38 42 43 45 12834856 A point mutation in influenza B neuraminidase confers resistance to peramivir and loss of slow binding. The WT and P15R NAs displayed IC(50) values of 8.4+/-0.4 and 127+/-16 nM, respectively, for peramivir. 2003 Antiviral research Abstract IV P15R 11 15 16 19 1327122 Binding of influenza virus hemagglutinin to analogs of its cell-surface receptor, sialic acid: analysis by proton nuclear magnetic resonance spectroscopy and X-ray crystallography. Although the protein complexed with alpha-2-O-methylsialic acid contains the mutation Gly-135-->Arg near the ligand binding site, the mutation apparently does not affect the ligand's position. 1992 Biochemistry Abstract IV G135R 86 99 1376767 Influenza virus infection elicits class II major histocompatibility complex-restricted T cells specific for an epitope identified in the NS1 non-structural protein. The antigenic determinant was localized by synthetic peptides to amino acids 13 to 32 of NS1, explaining the lack of recognition of A/Udorn/72 virus which has an alanine to valine substitution at position 23 within the determinant. 1992 The Journal of general virology Abstract IV A23V 162 207 NS1 89 92 1413525 Nucleotide sequence changes in the polymerase basic protein 2 gene of temperature-sensitive mutants of influenza A virus. Interestingly, the substitution of aspartic acid for asparagine at position 556 was found to lie within a region that has homology with cap-binding motifs of human and yeast proteins. 1992 Virology Abstract IV N556D 35 79 1448912 Influence of amantadine resistance mutations on the pH regulatory function of the M2 protein of influenza A viruses. A number of amino acid substitutions, e.g., L26H, A30T, S31N and G34E reduced the activity of the M2 protein of A/chicken/Germany/34 (Rostock) and caused a substantial increase in expression of the low-pH form of HA. 1992 Virology Abstract IV L26H;A30T;S31N;G34E 44;50;56;65 48;54;60;69 HA;M2 213;98 215;100 1448912 Influence of amantadine resistance mutations on the pH regulatory function of the M2 protein of influenza A viruses. Furthermore, in double mutants the 127T mutation suppressed the attenuating effects of the A30T and S31N mutations on M2 activity. 1992 Virology Abstract IV A30T;S31N 91;100 95;104 M2 118 120 1448912 Influence of amantadine resistance mutations on the pH regulatory function of the M2 protein of influenza A viruses. The influence of primary structure on the consequences of particular amino acid changes was further emphasized by the contrasting effects of the G34E mutation on the activities of two closely related proteins, causing an increase in the activity of the M2 of A/chicken/Germany/27 (Weybridge) as opposed to the decrease in activity of the Rostock protein. 1992 Virology Abstract IV G34E 145 149 M2 253 255 14505082 Ser624 of the PA subunit of influenza A virus is not essential for viral growth in cells and mice, but required for the maximal viral growth. The growth of S624A virus was less extensive than that of WSN in cells. 2003 Archives of virology Abstract IV S624A 14 19 14505082 Ser624 of the PA subunit of influenza A virus is not essential for viral growth in cells and mice, but required for the maximal viral growth. The LD50 of S624A virus and WSN for intranasal infection in Balb/C mice was 4.0 x 10(4) and 9.3 x 10(3) PFU, respectively. 2003 Archives of virology Abstract IV S624A 12 17 14505082 Ser624 of the PA subunit of influenza A virus is not essential for viral growth in cells and mice, but required for the maximal viral growth. To examine the role of this protease activity in the viral infection cycle, we compared the growth and the pathogenesis of influenza A/WSN/33 (WSN) and the virus encoding a PA with a S624A mutation (S624A virus), which were generated by the plasmid-based rescue system. 2003 Archives of virology Abstract IV S624A;S624A 183;199 188;204 PA 173 175 14533814 Host mediated variation and receptor binding specificity of influenza viruses. Only single amino acid alteration of Leu 226 to Gln made remarkable change of receptor binding specificity 2-6 to 2-3. 2001 Advances in experimental medicine and biology Abstract IV L226Q 37 51 14533814 Host mediated variation and receptor binding specificity of influenza viruses. When Ser 205 is substituted to Tyr, receptor binding specificity become 2-6 predominant rather than 2-3 predominant. 2001 Advances in experimental medicine and biology Abstract IV S205Y 5 34 14645582 A recombinant influenza A virus expressing an RNA-binding-defective NS1 protein induces high levels of beta interferon and is attenuated in mice. Interestingly, passaging in MDCK cells resulted in the selection of a mutant virus containing a third mutation at amino acid residue 42 of the NS1 protein (S42G). 2003 Journal of virology Abstract IV S42G 156 160 NS1 143 146 14689282 Effect of a single mutation in neuraminidase on the properties of Influenza B virus isolates. Both subclones had a common mutation in segment 6 leading to a change from Asp to Asn at position 457 in the NA. 2004 Archives of virology Abstract IV D457N 75 101 109 111 14708223 [Key role of Asp16 in proteolysis of influenza A NP protein by caspases in infected cells]. To verify the above assumption the NP chimeric gene of human influenza virus was developed; Asp16 was replaced by Gly by means of "site-oriented" mutagenesis in the above gene, after that, the A/WSN/33 (H1N1) mutant of human influenza virus with "avian" NP and with point mutation (Gly16) was developed by using the method of "reverse genetics". 2003 Voprosy virusologii Abstract IV D16G 92 117 NP;NP 35;254 37;256 15016548 PB2 amino acid at position 627 affects replicative efficiency, but not cell tropism, of Hong Kong H5N1 influenza A viruses in mice. A single amino acid substitution, from glutamic acid to lysine at position 627 of the PB2 protein, converts a nonlethal H5N1 influenza A virus isolated from a human to a lethal virus in mice. 2004 Virology Abstract IV E627K 39 78 PB2 86 89 15042345 An amino-acid substitution in the influenza-B NB protein affects ion-channel gating. Proton permeability of NB channels, as detected by fluorescence quenching, was also altered by the mutation S20A: channels were no longer proton-permeable. 2004 The Journal of membrane biology Abstract IV S20A 108 112 NB 23 25 15042345 An amino-acid substitution in the influenza-B NB protein affects ion-channel gating. Serine residues at positions 20 and 28, threonine at position 24 and cysteine at position 26 were replaced by alanine. 2004 The Journal of membrane biology Abstract IV S28A;S20A;T24A;C26A 0;0;40;69 38;38;64;117 15042345 An amino-acid substitution in the influenza-B NB protein affects ion-channel gating. The other mutations, S28A, T24A and C26A, did not have any detectable effect on the activity or proton permeability of channels formed by NB. 2004 The Journal of membrane biology Abstract IV S28A;T24A;C26A 21;27;36 25;31;40 NB 138 140 15042345 An amino-acid substitution in the influenza-B NB protein affects ion-channel gating. We found that the mutation S20A gave channels that did not gate and that remained open most of the time. 2004 The Journal of membrane biology Abstract IV S20A 27 31 15113903 A mutation in the HLA-B*2705-restricted NP383-391 epitope affects the human influenza A virus-specific cytotoxic T-lymphocyte response in vitro. Recently, an amino acid substitution (R384G) in an HLA-B*2705-restricted CTL epitope in the influenza A virus nucleoprotein (nucleoprotein containing residues 383 to 391 [NP(383-391)]; SRYWAIRTR, where R is the residue that was mutated) was associated with escape from CTL-mediated immunity. 2004 Journal of virology Abstract IV R384G 38 43 NP;NP;NP 171;110;125 173;123;138 15163496 Sequence variation in the influenza A virus nucleoprotein associated with escape from cytotoxic T lymphocytes. Furthermore, T cell recognition was completely abrogated by the R384G mutation. 2004 Virus research Abstract IV R384G 64 69 15163506 A "universal" human influenza A vaccine. Several adjuvants were tested in conjunction with intraperitoneal vaccine administration, while the non-toxic enterotoxin mutant LT(R192G) was used for intranasal vaccination. 2004 Virus research Abstract IV R192G 132 137 1522584 Crystal structures of two mutant neuraminidase-antibody complexes with amino acid substitutions in the interface. However, two mutants have been found within the site, Ile368 to Arg and Asn329 to Asp selected by antibodies other than NC41, and these mutants bind NC41 antibody with only slightly reduced affinity. 1992 Journal of molecular biology Abstract IV I368R;N329D 54;72 67;85 1522584 Crystal structures of two mutant neuraminidase-antibody complexes with amino acid substitutions in the interface. In the Ile368 to Arg mutant complex, the side-chain of Arg368 is shifted by 2.9 A from its position in the uncomplexed mutant and a shift of 1.3 A in the position of the light chain residue HisL55 with respect to the wild-type complex is also observed. 1992 Journal of molecular biology Abstract IV I368R 7 20 15246273 Binding of influenza viruses to sialic acids: reassortant viruses with A/NWS/33 hemagglutinin bind to alpha2,8-linked sialic acid. Fucosylation of the third sugar and changing the linkage between second and third sugars had little effect on binding by NWS-Tok, but marked effects on A/NWS/33(P227H)(HA)-tern/Australia/G70c/75(NA) (NWS-G70c, H1N9) and NWS-Mem/98. 2004 Virology Abstract IV P227H 161 166 HA;NA 168;195 170;197 15246273 Binding of influenza viruses to sialic acids: reassortant viruses with A/NWS/33 hemagglutinin bind to alpha2,8-linked sialic acid. The P227H mutation in A/NWS/33(P227H)(HA)-A/Memphis/31/98(NA) (NWS-Mem/98, H1N2) results in sevenfold lower affinity for 3' sialyllactose, but binding to 6' sialyllactosamine is unchanged. 2004 Virology Abstract IV P227H;P227H 4;31 9;36 HA;NA 38;58 40;60 15280506 Functional compensation of a detrimental amino acid substitution in a cytotoxic-T-lymphocyte epitope of influenza a viruses by comutations. Introduction of one of the comutations associated with R384G, E375G, partially restored viral fitness and nucleoprotein functionality. 2004 Journal of virology Abstract IV R384G;E375G 55;62 60;67 NP 106 119 15280506 Functional compensation of a detrimental amino acid substitution in a cytotoxic-T-lymphocyte epitope of influenza a viruses by comutations. Introduction of the R384G substitution in the nucleoprotein gene segment of influenza virus A/Hong Kong/2/68 by site-directed mutagenesis was detrimental to viral fitness. 2004 Journal of virology Abstract IV R384G 20 25 NP 46 59 15280506 Functional compensation of a detrimental amino acid substitution in a cytotoxic-T-lymphocyte epitope of influenza a viruses by comutations. The arginine-to-glycine substitution at position 384 of the viral nucleoprotein is associated with escape from CTLs. 2004 Journal of virology Abstract IV R384G 4 52 NP 66 79 15331690 Introduction of a temperature-sensitive phenotype into influenza A/WSN/33 virus by altering the basic amino acid domain of influenza virus matrix protein. Of multiple mutants analyzed, a double mutant, R101S-R105S, of RKLKR resulted in a temperature-sensitive phenotype. 2004 Journal of virology Abstract IV R101S;R105S 47;53 52;58 15331690 Introduction of a temperature-sensitive phenotype into influenza A/WSN/33 virus by altering the basic amino acid domain of influenza virus matrix protein. The R101S-R105S double mutant had a greatly reduced ratio of M1 to NP in viral particles and a weaker binding of M1 to RNPs. 2004 Journal of virology Abstract IV R101S;R105S 4;10 9;15 M1;M1;NP;RNP 61;113;67;119 63;115;69;123 15337401 Resistant influenza A viruses in children treated with oseltamivir: descriptive study. FINDINGS: We found neuraminidase mutations in viruses from nine patients (18%), six of whom had mutations at position 292 (Arg292Lys) and two at position 119 (Glu119Val), which are known to confer resistance to neuraminidase inhibitors. 2004 Lancet (London, England) Abstract IV R292K;E119V 123;159 132;168 NA;NA 19;211 32;224 15337401 Resistant influenza A viruses in children treated with oseltamivir: descriptive study. Sensitivity testing to oseltamivir carboxylate revealed that the neuraminidases of viruses that have an Arg292Lys, Glu119Val, or Asn294Ser mutation were about 10(4)-10(5)-fold, 500-fold, or 300-fold more resistant than their pretreatment neuraminidases, respectively. 2004 Lancet (London, England) Abstract IV R292K;E119V;N294S 104;115;129 113;124;138 NA;NA 65;238 79;252 15337401 Resistant influenza A viruses in children treated with oseltamivir: descriptive study. We also identified another mutation (Asn294Ser) in one patient. 2004 Lancet (London, England) Abstract IV N294S 37 46 15476872 Monoclonal antibodies differentially affect the interaction between the hemagglutinin of H9 influenza virus escape mutants and sialic receptors. A mutant virus with a L226Q substitution showed an increased affinity for the Neu5Acalpha2-3Galbeta1-4Glc. 2004 Virology Abstract IV L226Q 22 27 15476872 Monoclonal antibodies differentially affect the interaction between the hemagglutinin of H9 influenza virus escape mutants and sialic receptors. Several escape mutants viruses carrying the mutation N193D bound to Neu5Acalpha2-6Galbeta1-4GlcNAc considerably stronger than to Neu5Acalpha2-6Galbeta1-4Glc. 2004 Virology Abstract IV N193D 53 58 15479794 Influence of acylation sites of influenza B virus hemagglutinin on fusion pore formation and dilation. However, one of the single-acylation-site mutants, C6, in which Cys581 is replaced with serine, promoted hemifusion but not pore formation. 2004 Journal of virology Abstract IV C581S 64 94 15613301 Involvement of influenza virus PA subunit in assembly of functional RNA polymerase complexes. Sequencing of the gene encoding ts53 PA and recombinant virus rescue experiments revealed that an amino acid change from Leu to Pro at amino acid position 226 is causative of temperature sensitivity. 2005 Journal of virology Abstract IV L226P 121 158 PA 37 39 15650216 Attenuating mutations of the matrix gene of influenza A/WSN/33 virus. In challenge studies, mice immunized by infection with R101S-R105S were fully protected from lethal challenge with A/WSN/33. 2005 Journal of virology Abstract IV R101S;R105S 55;61 60;66 15650216 Attenuating mutations of the matrix gene of influenza A/WSN/33 virus. In contrast, the double mutation R101S-R105S was synergistic and resulted in temperature sensitivity reflected by reduced viral replication at a restrictive temperature. 2005 Journal of virology Abstract IV R101S;R105S 33;39 38;44 15650216 Attenuating mutations of the matrix gene of influenza A/WSN/33 virus. Individual substitution, R101S or R105S, had a minimal effect on viral replication. 2005 Journal of virology Abstract IV R101S;R105S 25;34 30;39 15650216 Attenuating mutations of the matrix gene of influenza A/WSN/33 virus. The replication and attenuating properties of R101S-R105S suggest its potential in development of live influenza virus vaccines. 2005 Journal of virology Abstract IV R101S;R105S 46;52 51;57 15650216 Attenuating mutations of the matrix gene of influenza A/WSN/33 virus. The results from mouse studies indicated that the R101S-R105S double mutant virus was strongly attenuated, while single mutant viruses R101S and R105S were minimally attenuated compared to A/WSN33 Wt under the same conditions. 2005 Journal of virology Abstract IV R101S;R105S;R101S;R105S 50;56;135;145 55;61;140;150 15661833 Hypothalamic growth hormone-releasing hormone (GHRH) deficiency: targeted ablation of GHRH neurons in mice using a viral ion channel transgene. In mammalian cells, (H37A)M2 forms a high conductance monovalent cation channel that can be blocked by the antiviral drug rimantadine. 2005 Molecular endocrinology (Baltimore, Md.) Abstract IV H37A 21 25 M2 26 28 15661833 Hypothalamic growth hormone-releasing hormone (GHRH) deficiency: targeted ablation of GHRH neurons in mice using a viral ion channel transgene. Transgenic mice with (H37A)M2 expression targeted to GHRH neurons developed postweaning dwarfism with hypothalamic GHRH transcripts detectable by RT-PCR but not by in situ hybridization and immunocytochemistry, suggesting that expression of (H37A)M2 had silenced or ablated virtually all the GHRH cells. 2005 Molecular endocrinology (Baltimore, Md.) Abstract IV H37A;H37A 22;242 26;246 M2;M2 27;247 29;249 15661833 Hypothalamic growth hormone-releasing hormone (GHRH) deficiency: targeted ablation of GHRH neurons in mice using a viral ion channel transgene. We have adopted a novel approach to silence or ablate GHRH neurons, using a modified H37A variant of the influenza virus M2 protein ((H37A)M2). 2005 Molecular endocrinology (Baltimore, Md.) Abstract IV H37A;H37A 85;134 89;138 M2;M2 121;139 123;141 15661913 A common polymorphism in the SFTPD gene influences assembly, function, and concentration of surfactant protein D. Genotyping for three single-nucleotide variations altering amino acids in the mature protein in codon 11 (Met(11)Thr), 160 (Ala(160)Thr), and 270 (Ser(270)Thr) of the SP-D gene was performed and related to the SP-D levels in serum. 2005 Journal of immunology (Baltimore, Md. Abstract IV M11T;A160T;S270T 106;124;147 117;136;159 15665027 Characterization of recombinant influenza B viruses with key neuraminidase inhibitor resistance mutations. An arginine to lysine change at position 291 (292 N2 numbering) mimicked that seen frequently in influenza A N2 clinical isolates resistant to oseltamivir. 2005 The Journal of antimicrobial chemotherapy Abstract IV R291K 3 44 15665027 Characterization of recombinant influenza B viruses with key neuraminidase inhibitor resistance mutations. RESULTS AND CONCLUSIONS: With the exception of a virus containing the E116G mutation, mutant viruses were attenuated to different levels in comparison with wild-type virus. 2005 The Journal of antimicrobial chemotherapy Abstract IV E116G 70 75 15665027 Characterization of recombinant influenza B viruses with key neuraminidase inhibitor resistance mutations. Similarly, an arginine to lysine change at position 149 (152 in N2 numbering) was made to reproduce the change found in the only reported zanamivir-resistant clinical isolate of influenza B virus. 2005 The Journal of antimicrobial chemotherapy Abstract IV R149K 14 55 1566586 A single point mutation of the influenza C virus glycoprotein (HEF) changes the viral receptor-binding activity. This mutation at nucleotide position 872 causes an amino acid exchange from threonine to isoleucine at position 284 on the amino acid sequence. 1992 Virology Abstract IV T284I 76 115 15708639 YM-53403, a unique anti-respiratory syncytial virus agent with a novel mechanism of action. Consistent with this result, two YM-53403-resistant viruses have a single point mutation (Y1631H) in the L protein which is a RNA polymerase for both the transcription and replication of the RSV genome. 2005 Antiviral research Abstract IV Y1631H 90 96 15784624 Chemical rescue of histidine selectivity filter mutants of the M2 ion channel of influenza A virus. Buffer molecules that were neutral when protonated (4-morpholineethanesulfonic acid and 3-morpholino-2-hydroxypropanesulfonic acid) did not rescue ion channel activity of the M2-H37G mutant ion channel, but 1-methylimidazole did provide partial rescue of function. 2005 The Journal of biological chemistry Abstract IV H37G 178 182 M2 175 177 15784624 Chemical rescue of histidine selectivity filter mutants of the M2 ion channel of influenza A virus. Chemical rescue was demonstrated for three histidine substitution mutant ion channels (M2-H37G, M2-H37S, and M2-H37T) and for two double mutants in which the Trp-41 channel gate was also mutated (H37G/W41Y and H37G/W41A). 2005 The Journal of biological chemistry Abstract IV H37G;H37G;H37S;H37T;W41Y;H37G;W41A 90;196;99;112;201;210;215 94;200;103;116;205;214;219 M2;M2;M2 87;96;109 89;98;111 15784624 Chemical rescue of histidine selectivity filter mutants of the M2 ion channel of influenza A virus. Currents of the M2-H37G mutant ion channel were inhibited by Cu(II), which has been shown to coordinate with His-37 in the wild-type channel. 2005 The Journal of biological chemistry Abstract IV H37G 19 23 M2 16 18 15784906 Pathogenesis of Hong Kong H5N1 influenza virus NS gene reassortants in mice: the role of cytokines and B- and T-cell responses. Here, in a mouse model, H1N1 A/Puerto Rico/8/34 (PR/8) reassortants that contained the H5N1/97 NS gene, the H5N1/01 NS gene, or an altered H5N1/97 NS gene encoding a Glu92-->Asp substitution in NS1 was studied. 2005 The Journal of general virology Abstract IV E92D 166 177 NS;NS;NS;NS1 95;116;147;194 97;118;149;197 15890915 Improvement of influenza A/Fujian/411/02 (H3N2) virus growth in embryonated chicken eggs by balancing the hemagglutinin and neuraminidase activities, using reverse genetics. Alternatively, recombinant A/Fujian/411/02 virus could be adapted to grow in eggs by two amino acid substitutions in the HA molecule (H183L and V226A), which also resulted in the increased HA receptor-binding activity. 2005 Journal of virology Abstract IV H183L;V226A 134;144 139;149 HA;HA 121;189 123;191 15890915 Improvement of influenza A/Fujian/411/02 (H3N2) virus growth in embryonated chicken eggs by balancing the hemagglutinin and neuraminidase activities, using reverse genetics. It was determined that replication of A/Fujian/411/02 in eggs could be improved by either changing minimum of two HA residues (G186V and V226I) to increase the HA receptor-binding ability or by changing a minimum of two NA residues (E119Q and Q136K) to lower the NA enzymatic activity. 2005 Journal of virology Abstract IV G186V;V226I;E119Q;Q136K 127;137;233;243 132;142;238;248 HA;HA;NA;NA 114;160;220;263 116;162;222;265 15892972 A single amino acid change in the C-terminal domain of the matrix protein M1 of influenza B virus confers mouse adaptation and virulence. Sequencing and characterization of intermediate passages suggested that one change in the C-terminal domain of the M1 protein, an asparagine to a serine at position 221, was responsible for acquisition of virulence and lethality. 2005 Virology Abstract IV N221S 130 168 M1 115 117 15914859 Full restoration of viral fitness by multiple compensatory co-mutations in the nucleoprotein of influenza A virus cytotoxic T-lymphocyte escape mutants. Here, the effect on viral fitness of four other co-mutations associated with R384G was investigated by using plasmid-driven rescue of mutant viruses. 2005 The Journal of general virology Abstract IV R384G 77 82 15914859 Full restoration of viral fitness by multiple compensatory co-mutations in the nucleoprotein of influenza A virus cytotoxic T-lymphocyte escape mutants. One of these is the arginine-to-glycine substitution at position 384 (R384G). 2005 The Journal of general virology Abstract IV R384G;R384G 70;20 75;68 15914859 Full restoration of viral fitness by multiple compensatory co-mutations in the nucleoprotein of influenza A virus cytotoxic T-lymphocyte escape mutants. This substitution alone, however, is detrimental to viral fitness, which is overcome in part by the functionally compensating co-mutation E375G. 2005 The Journal of general virology Abstract IV E375G 138 143 15914859 Full restoration of viral fitness by multiple compensatory co-mutations in the nucleoprotein of influenza A virus cytotoxic T-lymphocyte escape mutants. Whilst none of these alternative co-mutations alone compensated functionally for the detrimental effect of the R384G substitution, the M239V substitution improved viral fitness of viruses containing 375G and 384R. 2005 The Journal of general virology Abstract IV R384G;M239V 111;135 116;140 16081981 Variation of the conserved neutralizing epitope in influenza B virus victoria group isolates in Japan. Amino acid substitutions (D164E or N165K) were observed at the "tip", and the epitope was altered. 2005 Journal of clinical microbiology Abstract IV D164E;N165K 26;35 31;40 16140781 Molecular basis of replication of duck H5N1 influenza viruses in a mammalian mouse model. A single amino acid substitution (Asp to Asn) at position 701 of PB2 enabled DKGX/22 to infect and become lethal for mice. 2005 Journal of virology Abstract IV D701N 33 61 PB2 65 68 16140781 Molecular basis of replication of duck H5N1 influenza viruses in a mammalian mouse model. We find that the PA, NA, and NS genes of DKGX/22 could attenuate DKGX/35 virus to some extent, but PB2 of DKGX/22 virus attenuated the DKGX/35 virus dramatically, and an Asn-to-Asp substitution at position 701 of PB2 plays a key role in this function. 2005 Journal of virology Abstract IV N701D 170 209 NA;NS;PA;PB2;PB2 21;29;17;99;213 23;31;19;102;216 16140782 Membrane structures of the hemifusion-inducing fusion peptide mutant G1S and the fusion-blocking mutant G1V of influenza virus hemagglutinin suggest a mechanism for pore opening in membrane fusion. Abolishment of the kink in G1V results in reduced hydrophobic penetration of the lipid bilayer and an increased propensity to form beta-structures at the membrane surface. 2005 Journal of virology Abstract IV G1V 27 30 16140782 Membrane structures of the hemifusion-inducing fusion peptide mutant G1S and the fusion-blocking mutant G1V of influenza virus hemagglutinin suggest a mechanism for pore opening in membrane fusion. G1S forms a V with a disrupted "glycine edge" on its N-terminal arm and G1V adopts a slightly tilted linear helical structure in membranes. 2005 Journal of virology Abstract IV G1S;G1V 0;72 3;75 16140782 Membrane structures of the hemifusion-inducing fusion peptide mutant G1S and the fusion-blocking mutant G1V of influenza virus hemagglutinin suggest a mechanism for pore opening in membrane fusion. The most N-terminal residue of this domain, a glycine, is highly conserved and is particularly critical for HA function; G1S and G1V mutant HAs cause hemifusion and abolish fusion, respectively. 2005 Journal of virology Abstract IV G1S;G1V 121;129 124;132 HA 108 110 16140782 Membrane structures of the hemifusion-inducing fusion peptide mutant G1S and the fusion-blocking mutant G1V of influenza virus hemagglutinin suggest a mechanism for pore opening in membrane fusion. We have determined the atomic resolution structures of the G1S and G1V mutant fusion domains in membrane environments. 2005 Journal of virology Abstract IV G1S;G1V 59;67 62;70 16189083 Neuraminidase inhibitor-resistant influenza viruses may differ substantially in fitness and transmissibility. Both mutants showed decreased sensitivity to oseltamivir carboxylate, and the RG R292K-NA virus showed cross-resistance to zanamivir. 2005 Antimicrobial agents and chemotherapy Abstract IV R292K 81 86 87 89 16189083 Neuraminidase inhibitor-resistant influenza viruses may differ substantially in fitness and transmissibility. The NA defect caused by the R292K mutation was associated with compromised growth and transmissibility, whereas the growth and transmissibility of the RG E119V-NA virus were comparable to those of RG WT virus. 2005 Antimicrobial agents and chemotherapy Abstract IV R292K;E119V 28;154 33;159 NA;NA 4;160 6;162 16189083 Neuraminidase inhibitor-resistant influenza viruses may differ substantially in fitness and transmissibility. The R292K mutation caused greater reduction of sialidase activity and thermostability than the E119V mutation. 2005 Antimicrobial agents and chemotherapy Abstract IV R292K;E119V 4;95 9;100 16189083 Neuraminidase inhibitor-resistant influenza viruses may differ substantially in fitness and transmissibility. We generated recombinant viruses containing either the wild-type NA (RG WT virus) or a single amino acid change at NA residue 119 (RG E119V-NA virus) or 292 (RG R292K-NA virus) in the A/Wuhan/359/95 (H3N2) influenza virus background by reverse genetics. 2005 Antimicrobial agents and chemotherapy Abstract IV E119V;R292K 134;161 139;166 NA;NA;NA;NA 65;115;140;167 67;117;142;169 16214231 Polymer-bound 6' sialyl-N-acetyllactosamine protects mice infected by influenza virus. Sequencing of the HA gene of the mouse-adapted virus A/NIB/23/89-MA revealed a loss of the glycosylation sites in positions 94 and 163 of HA1 and substitutions 275Asp-->Gly in HA1 and 145Asn-->Asp in HA2. 2005 Antiviral research Abstract IV D275G;N145D 160;184 172;196 HA;HA;HA1;HA1 18;200;138;176 20;202;141;179 16227287 Influenza virus hemagglutinin (H3 subtype) requires palmitoylation of its cytoplasmic tail for assembly: M1 proteins of two subtypes differ in their ability to support assembly. Additionally, a reassortant of strain A/WSN/33 (WSN), containing the Ud HA gene with mutations C555S, C562S, and C565S, produced virus that could form plaques on regular MDCK cells and had only moderately decreased replication, suggesting differences in the interactions between Ud and WSN HA and internal viral proteins. 2005 Journal of virology Abstract IV C555S;C562S;C565S 95;102;113 100;107;118 HA;HA 72;290 74;292 16227287 Influenza virus hemagglutinin (H3 subtype) requires palmitoylation of its cytoplasmic tail for assembly: M1 proteins of two subtypes differ in their ability to support assembly. Mutant viruses containing HA-C562S and HA-C565S mutations had reduced growth and failed to form plaques in MDCK cells but formed wild-type-like plaques in an MDCK cell line expressing wild-type HA. 2005 Journal of virology Abstract IV C562S;C565S 29;42 34;47 HA;HA;HA 26;39;194 28;41;196 16242167 Characterization of a mitochondrial-targeting signal in the PB2 protein of influenza viruses. Recombinant influenza A/WSN/33 viruses expressing PB2 proteins with L7A and/or L10A mutations showed reduced viral titers, but unaffected levels of transcription, replication, and protein expression. 2006 Virology Abstract IV L7A;L10A 68;79 71;83 PB2 50 53 16242167 Characterization of a mitochondrial-targeting signal in the PB2 protein of influenza viruses. The introduction of L7A and/or L10A mutations into recombinant viruses correlated with reduced mitochondrial membrane potential in infected cells, suggesting that mitochondrial localization of PB2 contributes to the preservation of mitochondrial function during influenza virus infection. 2006 Virology Abstract IV L7A;L10A 20;31 23;35 PB2 193 196 IV infections 262 287 16297424 Interaction between a 1998 human influenza virus N2 neuraminidase and monoclonal antibody Mem5. The exceptions were E199A, E199Q, and K221R, in which binding was abrogated. 2006 Virology Abstract IV E199A;E199Q;K221R 20;27;38 25;32;43 16297424 Interaction between a 1998 human influenza virus N2 neuraminidase and monoclonal antibody Mem5. We made mutations D147A, D147N, H150A, H197A, D198A, D198N, E199A, E199Q, K221R, A246K, D251N, and D251A. 2006 Virology Abstract IV D147A;D147N;H150A;H197A;D198A;D198N;E199A;E199Q;K221R;A246K;D251N;D251A 18;25;32;39;46;53;60;67;74;81;88;99 23;30;37;44;51;58;65;72;79;86;93;104 16306596 Genetic analysis of influenza virus NS1 gene: a temperature-sensitive mutant shows defective formation of virus particles. Mutant 11C contained three mutations that led to amino acid exchanges, V18A, R44K, and S195P, all of which were required for the ts phenotype, and was characterized further. 2005 Journal of virology Abstract IV V18A;R44K;S195P 71;77;87 75;81;92 16343533 Glycan microarray analysis of the hemagglutinins from modern and pandemic influenza viruses reveals different receptor specificities. Only one mutation of the NY variant (Asp190Glu) was sufficient to revert the HA receptor preference to that of classical avian strains. 2006 Journal of molecular biology Abstract IV D190E 37 46 HA 77 79 16403603 An avian influenza vaccine for humans targeting the polymerase B2 protein inside the capsid instead of hemagglutinin or neuramidase on the virus surface. Consequently, a publicly available database at the National Center for Biotechnology Information (NCBI) website, and the SYFPEITHI online computer algorithm, were used to generate a hypothesis about a peptide-based vaccine targeted at the E627K mutation in PB2 of the avian influenza virus. 2006 Medical hypotheses Abstract IV E627K 239 244 PB2 257 260 16403603 An avian influenza vaccine for humans targeting the polymerase B2 protein inside the capsid instead of hemagglutinin or neuramidase on the virus surface. However, a recent study has revealed that the 1918 flu virus, like the H5N1 avian flu virus, has an E627K mutation in its polymerase B2 component, which is located inside the virus capsid. 2006 Medical hypotheses Abstract IV E627K 100 105 PB2 122 135 16403603 An avian influenza vaccine for humans targeting the polymerase B2 protein inside the capsid instead of hemagglutinin or neuramidase on the virus surface. It seems reasonable to believe that the constancy, over more than 80 years, of the E627K mutation could be exploited to begin developing a vaccine now, rather than waiting for new mutations. 2006 Medical hypotheses Abstract IV E627K 83 88 16415996 [Antigenic and genetic study of hemagglutinin gene of influenza virus (H3N2) circulated in China in 2004]. There were four important mutant positions, they were 159 Y>F, 189 S>N, 145 K>N, 226 V>I, respectively. 2005 Zhonghua shi yan he lin chuang bing du xue za zhi Abstract IV Y159F;S189N;K145N;V226I 54;63;72;81 61;70;79;88 16479508 Recovery of drug-resistant influenza virus from immunocompromised patients: a case series. Virus variants recovered from 2 patients had mutations in the M2, NA (with a previously recognized Glu119Val NA substitution), and hemagglutinin genes. 2006 The Journal of infectious diseases Abstract IV E119V 99 108 HA;M2;NA;NA 131;62;66;109 144;64;68;111 16479508 Recovery of drug-resistant influenza virus from immunocompromised patients: a case series. We describe a novel Asp198Asn NA mutation in an influenza B virus and its decreased susceptibility to both oseltamivir and zanamivir. 2006 The Journal of infectious diseases Abstract IV D198N 20 29 30 32 16479509 Comparative activities of oseltamivir and A-322278 in immunocompetent and immunocompromised murine models of influenza virus infection. A substitution in the neuraminidase (NA) active site (Arg292Lys) was detected in the cloned virus recovered from an oseltamivir-treated mouse. 2006 The Journal of infectious diseases Abstract IV R292K 54 63 NA;NA 37;22 39;35 1651590 Pneumotropic revertants derived from a pantropic mutant, F1-R, of Sendai virus. Comparative RNA sequence analysis of the F gene of the revertants revealed that the reduced cleavability of the F protein of the revertants was the result of the predicted single amino acid reversion (Pro to Ser) at residue 115 adjacent to the cleavage site. 1991 Virology Abstract IV P115S 200 227 16516984 Combination chemotherapy, a potential strategy for reducing the emergence of drug-resistant influenza A variants. After five sequential passages in MDCK cells, the M2 protein of viruses cultivated with amantadine alone mutated at positions V27A and S31N/I. 2006 Antiviral research Abstract IV V27A;S31N;S31I 126;135;135 130;141;141 M2 50 52 16545416 Molecular changes associated with adaptation of human influenza A virus in embryonated chicken eggs. Changing 2 NA residues (E119Q, Q136K) did not improve growth, and adaptation did not result in the HA changes H183L, D188Y, and V226A found by others. 2006 Virology Abstract IV E119Q;Q136K;H183L;D188Y;V226A 24;31;110;117;128 29;36;115;122;133 HA;NA 99;11 101;13 16545416 Molecular changes associated with adaptation of human influenza A virus in embryonated chicken eggs. During adaptation, 6 amino acid substitutions occurred: 4 in HA (G186V, S219F, V226I, V309I) and 2 in NA (E119Q, Q136K). 2006 Virology Abstract IV G186V;S219F;V226I;V309I;E119Q;Q136K 65;72;79;86;106;113 70;77;84;91;111;118 HA;NA 61;102 63;104 16545416 Molecular changes associated with adaptation of human influenza A virus in embryonated chicken eggs. Two HA substitutions (G186V, V226I) were sufficient to improve growth. 2006 Virology Abstract IV G186V;V226I 22;29 27;34 HA 4 6 1661731 Evidence from lateral mobility studies for dynamic interactions of a mutant influenza hemagglutinin with coated pits. Replacement of cysteine at position 543 by tyrosine in the influenza virus hemagglutinin (HA) protein enables the endocytosis of the mutant protein (Tyr 543) through coated pits (Lazarovits, J., and M. 1991 The Journal of cell biology Abstract IV C543Y 15 51 HA;HA 90;75 92;88 16627618 The primary function of RNA binding by the influenza A virus NS1 protein in infected cells: Inhibiting the 2'-5' oligo (A) synthetase/RNase L pathway. Pretreatment of A549 cells with IFN-beta for 6 h did not inhibit replication of WT Udorn virus, whereas replication of R38A mutant virus was inhibited 1,000-fold. 2006 Proc Natl Acad Sci U S A Abstract IV R38A 119 123 16627618 The primary function of RNA binding by the influenza A virus NS1 protein in infected cells: Inhibiting the 2'-5' oligo (A) synthetase/RNase L pathway. This R38A mutant virus is highly attenuated, and the mutant NS1A protein, like the WT protein, is localized in the nucleus. 2006 Proc Natl Acad Sci U S A Abstract IV R38A 5 9 NS 60 62 16627618 The primary function of RNA binding by the influenza A virus NS1 protein in infected cells: Inhibiting the 2'-5' oligo (A) synthetase/RNase L pathway. Using the R38A mutant virus, we establish that dsRNA binding by the NS1A protein does not inhibit production of IFN-beta mRNA. 2006 Proc Natl Acad Sci U S A Abstract IV R38A 10 14 NS 68 70 16641465 Neuraminidase inhibitor-resistant and -sensitive influenza B viruses isolated from an untreated human patient. Here, we describe the analysis of a mixed viral population that contained a novel D197E amino acid substitution that was responsible for this reduction. 2006 Antimicrobial agents and chemotherapy Abstract IV D197E 82 87 16809934 Amantadine resistance among porcine H1N1, H1N2, and H3N2 influenza A viruses isolated in Germany between 1981 and 2001. Additionally, L27A was detected in two H1N1 strains. 2006 Intervirology Abstract IV L27A 14 18 16809934 Amantadine resistance among porcine H1N1, H1N2, and H3N2 influenza A viruses isolated in Germany between 1981 and 2001. All resistant strains contained the AA substitutions G16E, S31N, and R77Q in the membrane protein 2 (M2). 2006 Intervirology Abstract IV G16E;S31N;R77Q 53;59;69 57;63;73 M2 101 103 16809934 Amantadine resistance among porcine H1N1, H1N2, and H3N2 influenza A viruses isolated in Germany between 1981 and 2001. S31N and/or L27A are well-known amino acid substitutions in M2 that confer amantadine resistance. 2006 Intervirology Abstract IV S31N;L27A 0;12 4;16 M2 60 62 16816857 [Antigenic and genetic study of influenza virus (H1N1) circulated in China in 2004-2005]. The HA1 sequence data showed that the H1N1 virus had the following amino acid mutations such as 54 K > R, 90 T > K, 101 Y > H, 149 R > K, 169 V > A, 190 D > N, 212 R > K, 219 K > R, 245 W > R, 246 Y > F, 258 T > N, 318 V > A and the 54 and 190 amino acids located in antigenic group of HA1. 2006 Zhonghua shi yan he lin chuang bing du xue za zhi Abstract IV T90K;Y101H;R149K;V169A;D190N;R212K;K219R;W245R;Y246F;T258N;V318A 106;116;127;138;149;160;171;182;193;204;215 114;125;136;147;158;169;180;191;202;213;224 HA1;HA1 4;286 7;289 16873236 Amino acid residues in the N-terminal region of the PA subunit of influenza A virus RNA polymerase play a critical role in protein stability, endonuclease activity, cap binding, and virion RNA promoter binding. Both the D108A and K134A mutations completely inhibited endonuclease activity in vitro, explaining their selective defect in transcription. 2006 Journal of virology Abstract IV D108A;K134A 9;19 14;24 16873236 Amino acid residues in the N-terminal region of the PA subunit of influenza A virus RNA polymerase play a critical role in protein stability, endonuclease activity, cap binding, and virion RNA promoter binding. K102A, on the other hand, resulted in a significant decrease in both cap binding and viral RNA promoter-binding activity and consequently inhibited both transcription and replication. 2006 Journal of virology Abstract IV K102A 0 5 16873236 Amino acid residues in the N-terminal region of the PA subunit of influenza A virus RNA polymerase play a critical role in protein stability, endonuclease activity, cap binding, and virion RNA promoter binding. Mutation K102A caused a general decrease both in transcription and replication in vivo, whereas mutations D108A and K134A selectively inhibited transcription. 2006 Journal of virology Abstract IV K102A;D108A;K134A 9;106;116 14;111;121 16873236 Amino acid residues in the N-terminal region of the PA subunit of influenza A virus RNA polymerase play a critical role in protein stability, endonuclease activity, cap binding, and virion RNA promoter binding. Three further PA mutations, K102A, D108A, and K134A, were investigated in detail. 2006 Journal of virology Abstract IV K102A;D108A;K134A 28;35;46 33;40;51 PA 14 16 16891631 Mutations conferring zanamivir resistance in human influenza virus N2 neuraminidases compromise virus fitness and are not stably maintained in vitro. E119V viruses were stable and grew to similar titres as wild-type virus, consistent with their isolation from oseltamivir-treated patients. 2006 The Journal of antimicrobial chemotherapy Abstract IV E119V 0 5 16891631 Mutations conferring zanamivir resistance in human influenza virus N2 neuraminidases compromise virus fitness and are not stably maintained in vitro. Mutations conferring oseltamivir resistance in N1 (H274Y) and B (R152K) NAs also conferred resistance in recombinant G70C N9 NA expressed in insect cells. 2006 The Journal of antimicrobial chemotherapy Abstract IV H274Y;R152K;G70C 51;65;117 56;70;121 N9;NA;NA 122;125;72 124;127;75 16891631 Mutations conferring zanamivir resistance in human influenza virus N2 neuraminidases compromise virus fitness and are not stably maintained in vitro. RESULTS: H3N2 viruses generated by reverse genetics with H274Y, R292K E119V and E119D mutations were rescued. 2006 The Journal of antimicrobial chemotherapy Abstract IV R292K;E119V;H274Y;E119D 64;70;57;80 69;75;62;85 16891631 Mutations conferring zanamivir resistance in human influenza virus N2 neuraminidases compromise virus fitness and are not stably maintained in vitro. The G70C N9 NA may also provide a useful model for understanding the structural basis of subtype-specific drug resistance. 2006 The Journal of antimicrobial chemotherapy Abstract IV G70C 4 8 N9;NA 9;12 11;14 16891631 Mutations conferring zanamivir resistance in human influenza virus N2 neuraminidases compromise virus fitness and are not stably maintained in vitro. Those with E119G, E119A or R152K mutations could only be rescued in the presence of exogenous NA and after passage in the absence of exogenous NA only isolates that had reverted to the wild-type NA or, surprisingly, E119G/A to E119V NA were isolated. 2006 The Journal of antimicrobial chemotherapy Abstract IV E119G;E119A;E119A;R152K;E119G;E119V 11;216;18;27;216;227 16;223;23;32;223;232 NA;NA;NA;NA 94;143;195;233 96;145;197;235 1690775 A dominant Th epitope in influenza nucleoprotein. Analysis of the fine specificity and functional repertoire of T cells recognizing a single determinant. The corresponding sequence of the NP of an equine influenza virus, A/Eq/Prague/56, which has a substitution (leucine to proline) at position 283, was not recognized by the lymph node cells from mice primed with either A/Okuda or A/Eq/Prague. 1990 Journal of immunology (Baltimore, Md. Abstract IV L283P 108 144 NP 34 36 16922680 In silico analysis of genes nucleoprotein, neuraminidase and hemagglutinin: a comparative study on different strains of influenza A (Bird flu) virus sub-type H5N1. None of the mutations was detected as an important change except in NA where K332R was at a PKC phosphorylation site. 2006 In silico biology Abstract IV K332R 77 82 68 70 16963558 Influenza A virus NS1 protein binds p85beta and activates phosphatidylinositol-3-kinase signaling. A mutant influenza virus (A/Udorn/72) expressing NS1 with the Y89F amino acid substitution exhibited a small-plaque phenotype, and grew more slowly in tissue culture than WT virus. 2006 Proc Natl Acad Sci U S A Abstract IV Y89F 62 66 NS1 49 52 1700825 Mechanism of antigenic variation in an individual epitope on influenza virus N9 neuraminidase. Ten mutants had a Ser-to-Phe change at amino acid 372, and six others had mutations at position 367. 1990 Journal of virology Abstract IV S372F 18 53 1700833 Overlapping cytotoxic T-lymphocyte and B-cell antigenic sites on the influenza virus H5 hemagglutinin. A single mutation at residue 168 (Lys to Glu) in the H5 HA variants abolished CTL recognition; this same amino acid was shown previously to be critical for B-cell recognition (M. 1990 Journal of virology Abstract IV K168E 29 45 HA 56 58 1701919 Effect of a Tyr-to-His point-mutation at position 59 in the alpha-1 helix of the HLA-B27 class-I molecule on allospecific and virus-specific cytotoxic T-lymphocyte recognition. HLA-B2703, a mutation of HLA-B2705, is characterized by a Tyr-to-His substitution at position 59 in the alpha 1 domain of the class-I heavy chain. 1990 Scandinavian journal of rheumatology. Supplement Abstract IV Y59H 58 96 17055070 H5N1 Oseltamivir-resistance detection by real-time PCR using two high sensitivity labeled TaqMan probes. A single amino acid substitution, from histidine to tyrosine at position 274 of the neuraminidase gene has converted Oseltamivir sensitive H5N1 influenza A virus into a resistant strain. 2007 Journal of virological methods Abstract IV H274Y 39 76 84 97 17055070 H5N1 Oseltamivir-resistance detection by real-time PCR using two high sensitivity labeled TaqMan probes. Overall, the assay based on real-time PCR with two labeled TaqMan probes described here should be useful for detecting Oseltamivir-resistant H274Y H5N1 influenza A virus in many species and various sources of specimens with high sensitivity and specificity. 2007 Journal of virological methods Abstract IV H274Y 141 146 17142161 Surfactant protein polymorphisms and neonatal lung disease. The main SP-A haplotype, interactively with SP-B Ile131Thr polymorphism and with constitutional and environmental factors, influences the risk of RDS. 2006 Seminars in perinatology Abstract IV I131T 49 58 17207830 Avian-virus-like receptor specificity of the hemagglutinin impedes influenza virus replication in cultures of human airway epithelium. R1 harbored the original HA of the pandemic human virus A/Hong Kong/1/68 (H3N2), whereas R2 was the L226Q/S228G HA mutant with avian-virus-like receptor specificity. 2007 Virology Abstract IV L226Q;S228G 100;106 105;111 HA;HA 25;112 27;114 17251573 Adaptation of an H7N7 equine influenza A virus in mice. It was found that the PB2-E627K substitution in this equine virus contributed to increased viral protein expression and virus replication in mouse cells and enhanced brain invasiveness in mice. 2007 The Journal of general virology Abstract IV E627K 26 31 PB2 22 25 17251573 Adaptation of an H7N7 equine influenza A virus in mice. Of these mutations, the Glu-to-Lys substitution at position 627 of PB2 (PB2-E627K) increased virulence appreciably. 2007 The Journal of general virology Abstract IV E627K;E627K 76;24 81;63 PB2;PB2 67;72 70;75 17251573 Adaptation of an H7N7 equine influenza A virus in mice. These results demonstrate that the importance of the PB2-E627K substitution for mouse adaptation, which was identified previously in human H5N1 isolates, extends to equine influenza A virus. 2007 The Journal of general virology Abstract IV E627K 57 62 PB2 53 56 17294090 Effect of gene constellation and postreassortment amino acid change on the phenotypic features of H5 influenza virus reassortants. A variant of the 7:1 reassortant selected by serial passages in eggs had an amino acid substitution in the hemagglutinin (N244D, H3 numbering). 2007 Archives of virology Abstract IV N244D 122 127 HA 107 120 17338230 [Reassortment and gene interactions in the crossing of low-pathogenic avian influenza H5 virus with human influenza virus]. This variant had one amino acid substitution in hemagglutinin (N244D, H3 numbering) and a lower affinity for fetuin. 2007 Voprosy virusologii Abstract IV N244D 63 68 HA 48 61 17369555 Genomic structure and diversity of the chicken Mx gene. The Mx protein, which confers resistance to orthomyxovirus, has been detected in several organisms, and one nonsynonymous substitution (S631N) of the chicken Mx protein has been shown to affect resistant activities to the avian influenza virus in vitro. 2007 Poultry science Abstract IV S631N 136 141 17384070 Backbone structure of the amantadine-blocked trans-membrane domain M2 proton channel from Influenza A virus. In addition, spectra are shown of the amantadine-resistant mutant, S31N, in the presence and absence of amantadine. 2007 Biophysical journal Abstract IV S31N 67 71 17537859 A mutation on influenza C virus M1 protein affects virion morphology by altering the membrane affinity of the protein. Second, we generated a mutant recombinant virus, rMG96A, which possesses an Ala-->Thr mutation at residue 24 of the M1 protein, a substitution demonstrated to be involved in the morphology (filamentous or spherical) of the influenza C VLPs. 2007 Journal of virology Abstract IV A24T 76 108 M1 116 118 17553873 Molecular changes in the polymerase genes (PA and PB1) associated with high pathogenicity of H5N1 influenza virus in mallard ducks. The HA gene mutations and the PB1 gene K207R mutation did not alter the HP phenotype of the large-plaque virus, whereas constructs with the PA (T515A) and PB1 (Y436H) gene mutations were nonpathogenic in orally inoculated ducks. 2007 Journal of virology Abstract IV K207R;T515A;Y436H 39;144;160 44;149;165 HA;PA;PB1;PB1 4;140;30;155 6;142;33;158 17553873 Molecular changes in the polymerase genes (PA and PB1) associated with high pathogenicity of H5N1 influenza virus in mallard ducks. The PB1 (Y436H) construct was not efficiently transmitted in ducks, whereas the PA (T515A) construct replicated as well as the wild-type virus did and was transmitted efficiently. 2007 Journal of virology Abstract IV Y436H;T515A 9;84 14;89 PA;PB1 80;4 82;7 17553873 Molecular changes in the polymerase genes (PA and PB1) associated with high pathogenicity of H5N1 influenza virus in mallard ducks. There were two differences in the hemagglutinin (HA) gene (K52T and A544V), one in the PA gene (T515A), and two in the PB1 gene (K207R and Y436H). 2007 Journal of virology Abstract IV K52T;A544V;T515A;K207R;Y436H 59;68;96;129;139 63;73;101;134;144 HA;HA;PA;PB1 49;34;87;119 51;47;89;122 17630401 The molecular epidemiology of influenza viruses: a lesson from a highly epidemic season. Moreover, a single K145N substitution in the HA1 site of H3N2 was the starting point of two evolutionary branches. 2008 Journal of clinical pathology Abstract IV K145N 19 24 HA1 45 48 17855542 Neuraminidase inhibitor-resistant recombinant A/Vietnam/1203/04 (H5N1) influenza viruses retain their replication efficiency and pathogenicity in vitro and in vivo. Although the H274Y and N294S mutations did not compromise the replication efficiency of VN1203 or PR8 viruses in vitro, these mutations slightly reduced the lethality of PR8 virus in mice. 2007 Journal of virology Abstract IV H274Y;N294S 13;23 18;28 17855542 Neuraminidase inhibitor-resistant recombinant A/Vietnam/1203/04 (H5N1) influenza viruses retain their replication efficiency and pathogenicity in vitro and in vivo. Four NA mutations (E119G, H274Y, R292K, and N294S) that have been reported to confer resistance to NA inhibitors were each introduced into recombinant A/Vietnam/1203/04 (VN1203) H5N1 influenza virus. 2007 Journal of virology Abstract IV E119G;H274Y;R292K;N294S 19;26;33;44 24;31;38;49 NA;NA 5;99 7;101 17855542 Neuraminidase inhibitor-resistant recombinant A/Vietnam/1203/04 (H5N1) influenza viruses retain their replication efficiency and pathogenicity in vitro and in vivo. However, the VN1203 virus carrying either the H274Y or N294S mutation exhibited lethality similar to that of the wild-type VN1203 virus. 2007 Journal of virology Abstract IV H274Y;N294S 46;55 51;60 17855542 Neuraminidase inhibitor-resistant recombinant A/Vietnam/1203/04 (H5N1) influenza viruses retain their replication efficiency and pathogenicity in vitro and in vivo. In both backgrounds, the H274Y and N294S mutations conferred resistance to oseltamivir carboxylate (50% inhibitory concentration [IC(50)] increases, >250-fold and >20-fold, respectively), and the N294S mutation reduced susceptibility to zanamivir (IC(50) increase, >3.0-fold). 2007 Journal of virology Abstract IV H274Y;N294S;N294S 25;35;196 30;40;201 17855542 Neuraminidase inhibitor-resistant recombinant A/Vietnam/1203/04 (H5N1) influenza viruses retain their replication efficiency and pathogenicity in vitro and in vivo. The E119G and R292K mutations significantly compromised viral growth in vitro, but the H274Y and N294S mutations were stably maintained in VN1203 and PR8 viruses. 2007 Journal of virology Abstract IV E119G;R292K;H274Y;N294S 4;14;87;97 9;19;92;102 17900218 Influence of extracellular and cytoplasmic domains of M2 ion channel of influenza a virus on its activity. Mutational analysis of cytoplasmic domain of M2 protein showed that substitutions C50S, C50P, and H90S did not change the ion channel activity. 2007 Acta virologica Abstract IV C50S;C50P;H90S 82;88;98 86;92;102 M2 45 47 17917748 Homology modeling and examination of the effect of the D92E mutation on the H5N1 nonstructural protein NS1 effector domain. It was found that the D92E mutation could result in weakened interactions of the carboxylate side chain with other phosphorylated residues, thereby activating phosphorylation of NS1. 2007 Journal of molecular modeling Abstract IV D92E 22 26 NS1 178 181 17917748 Homology modeling and examination of the effect of the D92E mutation on the H5N1 nonstructural protein NS1 effector domain. Virulent H5N1 strains of influenza virus often harbor a D92E point mutation in the nonstructural protein NS1. 2007 Journal of molecular modeling Abstract IV D92E 56 60 NS1 105 108 17922571 A single mutation in the PB1-F2 of H5N1 (HK/97) and 1918 influenza A viruses contributes to increased virulence. After comparing viruses from the Hong Kong 1997 H5N1 outbreak, one amino acid change (N66S) was found in the PB1-F2 sequence at position 66 that correlated with pathogenicity. 2007 PLoS pathogens Abstract IV N66S 86 90 PB1F2 109 115 17922571 A single mutation in the PB1-F2 of H5N1 (HK/97) and 1918 influenza A viruses contributes to increased virulence. In addition, both viruses with an S at position 66 (WH N66S and wt 1918) induced elevated levels of cytokines in the lungs of infected mice. 2007 PLoS pathogens Abstract IV N66S 55 59 17922571 A single mutation in the PB1-F2 of H5N1 (HK/97) and 1918 influenza A viruses contributes to increased virulence. In mice infected with WH N66S virus there was increased pathogenicity as measured by weight loss and decreased survival, and a 100-fold increase in virus replication when compared to mice infected with the WH virus. 2007 PLoS pathogens Abstract IV N66S 25 29 17922571 A single mutation in the PB1-F2 of H5N1 (HK/97) and 1918 influenza A viruses contributes to increased virulence. The 1918 pandemic strain A/Brevig Mission/18 was reconstructed with a pathogenicity-reducing mutation in PB1-F2 (S66N). 2007 PLoS pathogens Abstract IV S66N 113 117 PB1F2 105 111 17922571 A single mutation in the PB1-F2 of H5N1 (HK/97) and 1918 influenza A viruses contributes to increased virulence. The resultant 1918 S66N virus was attenuated in mice having a 3-log lower 50% lethal dose and caused less morbidity and mortality in mice than the wild-type virus. 2007 PLoS pathogens Abstract IV S66N 19 23 17922571 A single mutation in the PB1-F2 of H5N1 (HK/97) and 1918 influenza A viruses contributes to increased virulence. This same amino acid change (N66S) was also found in the PB1-F2 protein of the 1918 pandemic A/Brevig Mission/18 virus. 2007 PLoS pathogens Abstract IV N66S 29 33 PB1F2 57 63 17922571 A single mutation in the PB1-F2 of H5N1 (HK/97) and 1918 influenza A viruses contributes to increased virulence. Two isogenic recombinant chimeric viruses were created with an influenza A/WSN/33 virus background containing the PB1 segment from the HK/156/97: WH and WH N66S. 2007 PLoS pathogens Abstract IV N66S 156 160 PB1 114 117 17922571 A single mutation in the PB1-F2 of H5N1 (HK/97) and 1918 influenza A viruses contributes to increased virulence. Viral lung titers were also decreased in 1918 S66N-infected mice compared with wild-type 1918 virus-infected mice. 2007 PLoS pathogens Abstract IV S66N 46 50 17996973 Genetic analysis and evaluation of the reassortment of influenza B viruses isolated in Taiwan during the 2004-2005 and 2006-2007 epidemics. Comparison of isolates from the 2004-2005 and 2006-2007 epidemics revealed four substitutions, N220K, E320D, K343R and E404K in NA genes. 2008 Virus research Abstract IV N220K;E320D;K343R;E404K 95;102;109;119 100;107;114;124 128 130 18032512 A single-amino-acid substitution in the NS1 protein changes the pathogenicity of H5N1 avian influenza viruses in mice. We found that a single-amino-acid substitution of serine for proline at position 42 (P42S) in the NS1 protein dramatically increased the virulence of the DK/12 virus in mice, whereas the substitution of proline for serine at the same position (S42P) completely attenuated the DK/27 virus. 2008 Journal of virology Abstract IV P42S;S42P;P42S 85;244;50 89;248;83 NS1 98 101 18058063 The role of the N-terminal caspase cleavage site in the nucleoprotein of influenza A virus in vitro and in vivo. Insertion of the "human-like" G16-->D mutation into avian NP, which resulted in susceptibility to caspase cleavage, did not rescue virulence, but made the reassortant virus even more attenuated. 2008 Archives of virology Abstract IV G16D 30 37 NP 58 60 18058063 The role of the N-terminal caspase cleavage site in the nucleoprotein of influenza A virus in vitro and in vivo. Introducing the human-like G16-->D substitution into the NP of highly pathogenic A/Vietnam/1203/04 (H5N1) virus decreased lethality in mice. 2008 Archives of virology Abstract IV G16D 27 34 NP 57 59 18058063 The role of the N-terminal caspase cleavage site in the nucleoprotein of influenza A virus in vitro and in vivo. The "avian-like" D16-->G substitution in the NP, which makes this protein resistant to cleavage, did not significantly affect the human A/Puerto Rico/8/34 (H1N1) virus replication in vitro but decreased the lethality of this virus in mice by 68-fold. 2008 Archives of virology Abstract IV D16G 17 24 NP 45 47 18065262 Impact of influenza A virus neuraminidase mutations on the stability, activity, and sensibility of the neuraminidase to neuraminidase inhibitors. RESULTS: Among the viruses detectable through the phenotypic tests, R156K, I222L, H274Y, N294D and E425G viruses presented a NA activity between 70% and 100% of the A/Moscow/10/99 wild type one. 2008 Journal of clinical virology Abstract IV R156K;I222L;H274Y;N294D;E425G 68;75;82;89;99 73;80;87;94;104 125 127 18065262 Impact of influenza A virus neuraminidase mutations on the stability, activity, and sensibility of the neuraminidase to neuraminidase inhibitors. STUDY DESIGN: In the A/Moscow/10/99 (H3N2) virus background, viruses containing mutations in NA framework residues (E119D, R156K, W178L, S179A, D198N, I222L, E227G, H274Y, E277G, N294D, and E425G) were constructed by reverse genetics. 2008 Journal of clinical virology Abstract IV E119D;R156K;W178L;S179A;D198N;I222L;E227G;H274Y;E277G;N294D;E425G 116;123;130;137;144;151;158;165;172;179;190 121;128;135;142;149;156;163;170;177;184;195 93 95 18065262 Impact of influenza A virus neuraminidase mutations on the stability, activity, and sensibility of the neuraminidase to neuraminidase inhibitors. The D198N and the E119D mutations decreased seriously in NA activity compared to the wild-type (>10-fold). 2008 Journal of clinical virology Abstract IV D198N;E119D 4;18 9;23 57 59 18065262 Impact of influenza A virus neuraminidase mutations on the stability, activity, and sensibility of the neuraminidase to neuraminidase inhibitors. The I222L mutation reduced susceptibility to oseltamivir (18-fold). 2008 Journal of clinical virology Abstract IV I222L 4 9 18172752 Genetic characterization of the NS gene indicates co-circulation of two sub-lineages of highly pathogenic avian influenza virus of H5N1 subtype in Northern Europe in 2006. Sub-lineage I isolates contained unique substitutions V194I in NS1 and G63E in Nuclear export protein (NEP). 2008 Virus genes Abstract IV V194I;G63E 54;71 59;75 NEP;NS1;NEP 103;63;79 106;66;101 18188421 Identification of a casein kinase II phosphorylation domain in NS1 protein of H5N1 influenza virus. This domain was formed due to the mutation at position 151 (T151I). 2007 Bioinformation Abstract IV T151I 60 65 18191435 A cluster of conserved basic amino acids near the C-terminus of the PB1 subunit of the influenza virus RNA polymerase is involved in the regulation of viral transcription. Additionally, recombinant viruses containing the K669A or R672A mutations expressed reduced amounts of mRNA compared to cRNA during infection and were attenuated in cell culture. 2008 Virology Abstract IV K669A;R672A 49;58 54;63 18248089 Interaction of polymerase subunit PB2 and NP with importin alpha1 is a determinant of host range of influenza A virus. We show now that adaptive mutations D701N in PB2 and N319K in NP enhance binding of these proteins to importin alpha1 in mammalian cells. 2008 PLoS pathogens Abstract IV D701N;N319K 36;53 41;58 NP;PB2 62;45 64;48 18258312 PA subunit of RNA polymerase as a promising target for anti-influenza virus agents. L-742,001-resistant mutants showed a Thr-20 to Ala substitution in the PA subunit of RNA polymerase. 2008 Antiviral research Abstract IV T20A 37 50 PA 71 73 18299250 Detection of adamantane-resistant influenza on a microarray. Microarray data from a larger set of samples were further analyzed using an artificial neural network and resulted in a correct identification rate of 94% for influenza virus samples that had V27A and S31N mutations. 2008 Journal of clinical virology Abstract IV V27A;S31N 192;201 196;205 18299250 Detection of adamantane-resistant influenza on a microarray. STUDY DESIGN: We have taken advantage of functional genomics and microarray technology to design a DNA microarray that can detect the two most common mutations in the M2 protein associated with adamantane resistance, V27A and S31N. 2008 Journal of clinical virology Abstract IV V27A;S31N 217;226 221;230 M2 167 169 1830112 Intragenic suppression of a deletion mutation of the nonstructural gene of an influenza A virus. Nucleotide sequence analysis revealed the presence of an intragenic mutation in each of the ts+ phenotypic revertant viruses, involving a substitution of valine for alanine at amino acid 23 of the NS1 protein. 1991 Journal of virology Abstract IV A23V 154 189 NS1 197 200 18317917 Virulence of H5N1 avian influenza virus enhanced by a 15-nucleotide deletion in the viral nonstructural gene. Sequence analysis also showed that H5N1 viruses carrying the 15-nt deletion in the NS gene invariably had the D92E shift in their NS1 protein. 2008 Virus genes Abstract IV D92E 110 114 NS;NS1 83;130 85;133 18317917 Virulence of H5N1 avian influenza virus enhanced by a 15-nucleotide deletion in the viral nonstructural gene. The results indicated that the 15-nucleotide deletion of NS gene from site 263 to 277 associated with D92E shift in NS1 protein contributes to the virulence increase of H5N1 viruses in chickens and mice. 2008 Virus genes Abstract IV D92E 102 106 NS;NS1 57;116 59;119 18320820 [Analysis of the amino acid changes of the hemagglutinin of H5 avian influenza virus]. An amino acid change at residue 122 from Trp to Arg and 179 from His to Arg resulted in the loss of hemadsorption activity of the HA protein. 2008 Bing du xue bao Abstract IV W122R;H179R 32;56 51;75 HA 130 132 18325270 Mutations in influenza A virus (H5N1) and possible limited spread, Turkey, 2006. Four novel amino acid changes (Q447L, N556K, and R46K in RNA polymerase and S133A in hemagglutinin) were detected in virus isolates from 2 siblings who died. 2008 Emerging infectious diseases Abstract IV Q447L;N556K;R46K;S133A 31;38;49;76 36;43;53;81 HA 85 98 18353965 Infectivity studies of influenza virus hemagglutinin receptor binding site mutants in mice. Among the mutants examined was a virus containing a Y98F substitution at a conserved position in the receptor binding site that leads to a 20-fold reduction in binding. 2008 Journal of virology Abstract IV Y98F 52 56 18353965 Infectivity studies of influenza virus hemagglutinin receptor binding site mutants in mice. The capacity of the Y98F mutant to induce antibody responses and the structural locations of HA reversion mutations are examined. 2008 Journal of virology Abstract IV Y98F 20 24 HA 93 95 18360902 Evaluation of a virus derived from MDCK cells infected persistently with influenza A virus as a potential live-attenuated vaccine candidate in the mouse model. Upon comparison with the parental influenza A E61-24-P15 strain used to establish persistent infection, amino acid exchanges were found in the M1 protein of IVpi-189 virus; arginine to glutamine at position 72 and threonine to alanine at position 139. 2008 Journal of medical virology Abstract IV R72Q;T139A 173;214 209;250 M1 143 145 18381743 Synthesis of full length PB1-F2 influenza A virus proteins from 'Spanish flu' and 'bird flu'. As the native sequence of BF2 does not contain a cysteine residue two different mutants of BF2 (Y42C) and BF2 (S47C) with appropriate cysteine exchanges were produced. 2008 Journal of peptide science Abstract IV Y42C;S47C 96;111 100;115 18404209 Human-like receptor specificity does not affect the neuraminidase-inhibitor susceptibility of H5N1 influenza viruses. The triple N158S/Q226L/N248D HA mutation (which eliminates a glycosylation site at position 158) caused a switch from avian to human receptor specificity. 2008 PLoS pathogens Abstract IV N158S;Q226L;N248D 11;17;23 16;22;28 HA 29 31 18404209 Human-like receptor specificity does not affect the neuraminidase-inhibitor susceptibility of H5N1 influenza viruses. To gain insight into how combinations of HA and NA mutations can affect the sensitivity of H5N1 virus to NA inhibitors, we also rescued viruses carrying the HA changes together with the H274Y NA substitution, which was reported to confer resistance to the NA inhibitor oseltamivir. 2008 PLoS pathogens Abstract IV H274Y 186 191 HA;HA;NA;NA;NA;NA 41;157;48;105;192;256 43;159;50;107;194;258 18408016 Identification of the pore-lining residues of the BM2 ion channel protein of influenza B virus. It was found that mutation of transmembrane domain residues Ser(9), Ser(12), Phe(13), Ser(16), His(19), and Trp(23) to cysteine were most disruptive for ion channel function. 2008 The Journal of biological chemistry Abstract IV W23C 107 123 18424263 Single-amino-acid mutation in the HA alters the recognition of H9N2 influenza virus by a monoclonal antibody. Substitution of serine for asparagine at the same position (N145S) enables the CK/GX/10 to react with C/B3 in hemaglutinin inhibition, immunofluorescence and neutralization assays. 2008 Biochemical and biophysical research communications Abstract IV N145S 60 65 18424263 Single-amino-acid mutation in the HA alters the recognition of H9N2 influenza virus by a monoclonal antibody. We found that a single-amino-acid substitution of asparagine for serine at position 145 (S145N) in the HA protein prevents the reaction of CK/SD/6 virus with C/B3. 2008 Biochemical and biophysical research communications Abstract IV S145N;S145N 89;50 94;87 HA 103 105 18442378 Application of bioinformatics-coupled experimental analysis reveals a new transport-competent nuclear localization signal in the nucleoprotein of influenza A virus strain. RESULTS: Comparison of the deduced aa sequence of NP of WS/33L strain with the published WS/33 NP sequences revealed that a single amino acid (aa) change (Met to Arg) at position 105 results in converting the flanking regions (between aa position 90-121, a 32-residue stretch) into two classical overlapping bipartite NLS (obpNLS). 2008 BMC cell biology Abstract IV M105R 154 182 NP;NP 50;95 52;97 18453004 In vitro evaluation of neuraminidase inhibitors using the neuraminidase-dependent release assay of hemagglutinin-pseudotyped viruses. The pseudotype virus release assay was used to determine the IC(50) values of Oseltamivir carboxylate, Zanamivir, and the novel phosphonate congeners of Oseltamivir against N1 group neuraminidases and their H274Y Oseltamivir carboxylate-resistant mutants. 2008 Antiviral research Abstract IV H274Y 207 212 182 196 18488446 [Molecular and genetic analysis of influenza A viruses isolated in Russia, based on the neuraminidase and M2 protein gene sequence]. Besides S31N substitution, additional mutations were detected in both proteins. 2008 Molekuliarnaia genetika, mikrobiologiia i virusologiia Abstract IV S31N 8 12 18488446 [Molecular and genetic analysis of influenza A viruses isolated in Russia, based on the neuraminidase and M2 protein gene sequence]. Mutations associated with S31N substitution were detected in each virus subtype, which may be considered as new markers for the identification of remantadin-resistant strains. 2008 Molekuliarnaia genetika, mikrobiologiia i virusologiia Abstract IV S31N 26 30 18488446 [Molecular and genetic analysis of influenza A viruses isolated in Russia, based on the neuraminidase and M2 protein gene sequence]. The M2 sequences analysis among the remantadin resistant viruses demonstrated the S31N substitution in all strains. 2008 Molekuliarnaia genetika, mikrobiologiia i virusologiia Abstract IV S31N 82 86 M2 4 6 18534979 Mechanism of influenza A virus NS1 protein interaction with the p85beta, but not the p85alpha, subunit of phosphatidylinositol 3-kinase (PI3K) and up-regulation of PI3K activity. In reciprocal gain of function experiments with p85alpha, we demonstrated that mutation to Val at Met-582 leads to NS1 binding and increased PI3K activity. 2008 The Journal of biological chemistry Abstract IV V582M 91 105 NS1 115 118 18574690 Ab initio fragment molecular orbital studies of influenza virus hemagglutinin-sialosaccharide complexes toward chemical clarification about the virus host range determination. In the ab initio FMO studies, binding energy of avian Gln226Leu H3-human alpha2-6 was quite similar to that in the human H3-human alpha2-6 complex with amino acid sequence differences at nine positions in the models. 2008 Glycoconjugate journal Abstract IV Q226L 54 63 18574690 Ab initio fragment molecular orbital studies of influenza virus hemagglutinin-sialosaccharide complexes toward chemical clarification about the virus host range determination. Opposite mutation Leu226Gln in the human H3 gave the moderate binding energies to avian alpha2-3 with similarity to avian H3-alpha2-3 complex that supported our previous virus-sialoside binding assay. 2008 Glycoconjugate journal Abstract IV L226Q 18 27 18574690 Ab initio fragment molecular orbital studies of influenza virus hemagglutinin-sialosaccharide complexes toward chemical clarification about the virus host range determination. This similarity indicates that avian Gln226Leu H3 virus can infect human with the same level as human H3 virus. 2008 Glycoconjugate journal Abstract IV Q226L 37 46 18584938 Another look at the molecular mechanism of the resistance of H5N1 influenza A virus neuraminidase (NA) to oseltamivir (OTV). In contrast to the binding free energies, the net charges of Glu276 and Arg224, making charge-charge interactions with Glu276, were established to be more sensitive to detecting subtle conformational differences induced at the key residue Glu276 by the His274X mutations. 2008 Biophysical chemistry Abstract IV H274X 253 260 18584938 Another look at the molecular mechanism of the resistance of H5N1 influenza A virus neuraminidase (NA) to oseltamivir (OTV). The smaller side chain residue mutations of His274 resulted in slightly enhanced or unchanged NA sensitivity to OTV, while His274Phe and His274Tyr reduced the susceptibility of OTV to N1. 2008 Biophysical chemistry Abstract IV H274F;H274Y 123;137 132;146 94 96 18601954 Treatment of influenza A (H1N1) virus infections in mice and ferrets with cyanovirin-N. Recently we created a hybrid (reassortant) influenza A/WSN/33 (H1N1) virus containing the HA gene of A/New Caledonia/20/99 (H1N1) with an Asp225Gly mutation in the HA1, that was lethal to mice yet retained sensitivity to CV-N. 2008 Antiviral research Abstract IV D225G 138 147 HA;HA1 90;164 92;167 18613963 A broad spectrum, one-step reverse-transcription PCR amplification of the neuraminidase gene from multiple subtypes of influenza A virus. The RT-PCR fragment generated includes one of the mutation sites related to oseltamivir resistance, H274Y. 2008 Virology journal Abstract IV H274Y 100 105 18625765 Surveillance for neuraminidase inhibitor resistance among human influenza A and B viruses circulating worldwide from 2004 to 2008. A rise in the incidence of oseltamivir resistance in A(H1N1) viruses carrying the H274Y mutation was detected in the United States and in other countries in the ongoing 2007 to 2008 season. 2008 Antimicrobial agents and chemotherapy Abstract IV H274Y 82 87 18625765 Surveillance for neuraminidase inhibitor resistance among human influenza A and B viruses circulating worldwide from 2004 to 2008. Molecular markers of oseltamivir resistance were found in six A(H1N1) viruses (H274Y) and one A(H3N2) virus (E119V) collected between 2004 and 2007. 2008 Antimicrobial agents and chemotherapy Abstract IV H274Y;E119V 79;109 84;114 18625765 Surveillance for neuraminidase inhibitor resistance among human influenza A and B viruses circulating worldwide from 2004 to 2008. Some outliers contained previously reported mutations (e.g., I222T in the B viruses), while other mutations [e.g., R371K and H274Y in B viruses and H274N in A(H3N2) viruses) were novel. 2008 Antimicrobial agents and chemotherapy Abstract IV I222T;R371K;H274Y;H274N 61;115;125;148 66;120;130;153 18625765 Surveillance for neuraminidase inhibitor resistance among human influenza A and B viruses circulating worldwide from 2004 to 2008. The R371K B virus outlier exhibited high levels of resistance to both inhibitors (>100 nM). 2008 Antimicrobial agents and chemotherapy Abstract IV R371K 4 9 18669647 Functional studies indicate amantadine binds to the pore of the influenza A virus M2 proton-selective ion channel. However, the D44A channel was found to be sensitive to amantadine when measured by electrophysiological recordings in oocytes of Xenopus laevis and in mammalian cells, and when the D44 and R45 mutations were introduced into the influenza virus genome. 2008 Proc Natl Acad Sci U S A Abstract IV D44A 13 17 18684820 Oseltamivir-resistant influenza A viruses are transmitted efficiently among guinea pigs by direct contact but not by aerosol. Here, we demonstrate that recombinant human influenza A/H3N2 viruses without and with oseltamivir resistance mutations (in which NA carries the mutation E119V or the double mutations E119V I222V) have similar in ovo growth kinetics and infectivity in guinea pigs. 2008 Journal of virology Abstract IV E119V;I222V;E119V 153;189;183 158;194;188 129 131 18768984 Mutations at alternative 5' splice sites of M1 mRNA negatively affect influenza A virus viability and growth rate. More M2 mRNA was produced in G11C mutant virus-infected cells than in wild-type-virus-infected cells, and there was little M2 mRNA and none at all in G145A and G52C mutant virus-infected ones, respectively. 2008 Journal of virology Abstract IV G11C;G145A;G52C 29;150;160 33;155;164 M2;M2 5;123 7;125 18768984 Mutations at alternative 5' splice sites of M1 mRNA negatively affect influenza A virus viability and growth rate. On the other hand, mutants with the mutation G11C (at the 3' end of exon of the mRNA3 5' splice site), G52C (for the first nucleotide of the intron for M2 mRNA), or G145A (at the 3' end of the exon of mRNA4) were rescued, although they had significantly attenuated growth rates. 2008 Journal of virology Abstract IV G11C;G52C;G145A 45;103;165 49;107;170 M2 152 154 18768984 Mutations at alternative 5' splice sites of M1 mRNA negatively affect influenza A virus viability and growth rate. Six different mutations at the splice sites were introduced, and viral growth characteristics for those mutants generated by reverse genetics with 12 plasmids were examined, for which G12C (the G-to-C mutation at the first nucleotide of the intron for the mRNA3 5' splice site), C51G (at the 3' end of the exon of the M2 mRNA 5' splice site), and G146C (for the first nucleotide of the intron for mRNA4) are lethal mutations. 2008 Journal of virology Abstract IV G146C;G12C;C51G 347;184;279 352;188;283 M2 318 320 18768984 Mutations at alternative 5' splice sites of M1 mRNA negatively affect influenza A virus viability and growth rate. The production levels of mRNA3 in cells infected with G11C, G52C, and G145A mutant viruses were reduced in comparison with that in wild-type recombinant virus-infected ones. 2008 Journal of virology Abstract IV G11C;G52C;G145A 54;60;70 58;64;75 18769709 Host determinant residue lysine 627 lies on the surface of a discrete, folded domain of influenza virus polymerase PB2 subunit. The structure of the K627E mutated domain shows no structural differences but the charge reversal disrupts a striking basic patch on the domain surface. 2008 PLoS pathogens Abstract IV K627E 21 26 18845822 Emergence of amantadine-resistant H3N2 avian influenza A virus in South Korea. We found a relatively high frequency of unique amantadine-resistant H3N2 and H9N2 avian influenza viruses (Val27Ile on M2 protein) isolated from live poultry markets in South Korea and confirmed that a Val27Ile single substitution in the M2 protein is enough to acquire the amantadine resistance phenotype by using reverse-genetically created human-avian reassortant viruses. 2008 Journal of clinical microbiology Abstract IV V27I;V27I 107;202 115;210 M2;M2 119;238 121;240 18983930 Adaptation of human influenza H3N2 virus in a mouse pneumonitis model: insights into viral virulence, tissue tropism and host pathogenesis. Non-conservative mutations in the hemagglutinin (Gly218Glu) and non-structural 1 (Asp125Gly) proteins were identified in P10 virus which exhibited high virulence. 2009 Microbes and infection Abstract IV G218E;D125G 49;82 58;91 HA;NS 34;64 47;78 18987140 Studies of an influenza A virus temperature-sensitive mutant identify a late role for NP in the formation of infectious virions. Reverse-genetics studies in which A/PR/8/34 segment 7 was swapped with sequences from other strains of virus revealed a profound incompatibility between the M239L mutation and the A/Udorn/72 M1 gene, suggesting that the ts mutation affects M1-NP interactions. 2009 Journal of virology Abstract IV M239L 157 162 M1;M1;NP 191;240;243 193;242;245 18987140 Studies of an influenza A virus temperature-sensitive mutant identify a late role for NP in the formation of infectious virions. Sequence analysis revealed a single mutation, M239L, in NP, consistent with earlier mapping studies assigning the ts lesion to segment 5. 2009 Journal of virology Abstract IV M239L 46 51 NP 56 58 18996090 An in-depth analysis of the biological functional studies based on the NMR M2 channel structure of influenza A virus. To clarify this kind of confusion, an in-depth analysis was performed for these functional studies, particularly for the mutations D44N, D44A and N44D on position 44, and the mutations on positions 27-38. 2008 Biochemical and biophysical research communications Abstract IV D44N;D44A;N44D 131;137;146 135;141;150 18999893 Post-reassortment amino acid change in the hemagglutinin of a human-avian influenza H5N1 reassortant virus alters its antigenic specificity. In this report we demonstrated that the post-reassortment amino acid substitution N244D altered the antigenic specificity of HA as revealed by the loss of reactivity with an anti-H5 monoclonal antibody in hemagglutination-inhibition (HI) test. 2008 Acta virologica Abstract IV N244D 82 87 HA 125 127 18999893 Post-reassortment amino acid change in the hemagglutinin of a human-avian influenza H5N1 reassortant virus alters its antigenic specificity. The variant reassortant had an amino acid substitution in the hemagglutinin N244D (H3 numbering). 2008 Acta virologica Abstract IV N244D 76 81 HA 62 75 19008377 The human H5N1 influenza A virus polymerase complex is active in vitro over a broad range of temperatures, in contrast to the WSN complex, and this property can be attributed to the PB2 subunit. The E627K mutation in the avian PB2 was not required for this effect. 2008 The Journal of general virology Abstract IV E627K 4 9 PB2 32 35 19014974 Aurintricarboxylic acid inhibits influenza virus neuraminidase. ATA was equally potent in inhibiting the NA activity derived from wild-type NA and its H274Y mutant which renders NA resistance to inhibition by oseltamivir. 2009 Antiviral research Abstract IV H274Y 87 92 NA;NA;NA 41;76;114 43;78;116 19015327 Activity of the oral neuraminidase inhibitor A-322278 against the oseltamivir-resistant H274Y (A/H1N1) influenza virus mutant in mice. A-322278 decreased mortality rates and lung virus titers significantly more than oseltamivir in mice infected with the NA H274Y mutant when therapy was started 4 h before or even 48 h after infection. 2009 Antimicrobial agents and chemotherapy Abstract IV H274Y 122 127 119 121 19015327 Activity of the oral neuraminidase inhibitor A-322278 against the oseltamivir-resistant H274Y (A/H1N1) influenza virus mutant in mice. The new oral neuraminidase (NA) inhibitor A-322278 was evaluated in mice infected with influenza A/H1N1 wild-type virus or the oseltamivir-resistant (H274Y mutant) virus. 2009 Antimicrobial agents and chemotherapy Abstract IV H274Y 150 155 NA;NA 28;13 30;26 19019697 Identification of amino acid substitutions in avian influenza virus (H5N1) matrix protein 1 by using nanoelectrospray MS and MS/MS. The specificity of tandem mass spectrometry allowed the identification of six amino acid (AA) substitutions in M1, including R95K, A166V, I168T, N207S, N224S, and R230K. 2009 Journal of the American Society for Mass Spectrometry Abstract IV R95K;A166V;I168T;N207S;N224S;R230K 125;131;138;145;152;163 129;136;143;150;157;168 M1 111 113 19019950 Avian Influenza A virus polymerase association with nucleoprotein, but not polymerase assembly, is impaired in human cells during the course of infection. The NP-polymerase association is restored by a Glu-to-Lys substitution at residue 627 of PB2. 2009 Journal of virology Abstract IV E627K 47 85 NP;PB2 4;89 6;92 19020946 Analysis of a point mutation in H5N1 avian influenza virus hemagglutinin in relation to virus entry into live mammalian cells. Our results revealed that replacing aspartic acid at residue 94 with asparagine enhanced virus fusion activity and increased the binding of HA to sialic acid alpha2,6 galactose, while it decreased pseudotyped virus entry into cells expressing the avian type receptor, sialic acid alpha2,3 galactose. 2008 Archives of virology Abstract IV D94N 36 79 HA 140 142 19035321 [Role of amino acid residues at positions 322 and 329 of hemagglutinin in virulence of H5N1 avian influenza virus]. All recombinant viruses carrying HA gene from Y with Q322L and/or K329-mutations and other seven genes from S were completely attenuated in terms of virulence to ducks whereas all recombinant viruses carrying HA gene from Y with same mutations and other seven genes from Y gained significant virulence. 2008 Bing du xue bao Abstract IV Q322L 53 58 HA;HA 33;209 35;211 19035321 [Role of amino acid residues at positions 322 and 329 of hemagglutinin in virulence of H5N1 avian influenza virus]. Recombinant viruses with S virus backbone were completely attenuated in terms of their virulence to ducks when position 322 (L322Q) and/or position 329 (-329K) of HA gene had been mutated. 2008 Bing du xue bao Abstract IV L322Q 125 130 HA 163 165 19035321 [Role of amino acid residues at positions 322 and 329 of hemagglutinin in virulence of H5N1 avian influenza virus]. Recombinant viruses with Y virus backbone significantly increased their virulence to ducks when position 322 (Q322L) and/or position 329 (K329-) of HA gene had been mutated. 2008 Bing du xue bao Abstract IV Q322L 110 115 HA 148 150 19035321 [Role of amino acid residues at positions 322 and 329 of hemagglutinin in virulence of H5N1 avian influenza virus]. The critical role that L322 and -329 of HA protein from S virus play in the high virulence to ducks were influenced by the entire background of that protein because the recombinant virus with HA gene from Y and other seven genes from S were completely attenuated even if Q322L and K329- mutations of HA gene had been achieved. 2008 Bing du xue bao Abstract IV Q322L 271 276 HA;HA;HA 40;192;300 42;194;302 1904085 Soluble HLA-A2.1 restricted peptides that are recognized by influenza virus specific cytotoxic T lymphocytes. Further substitution of threonine in position 65 with lysine resulted in a soluble antagonist peptide that inhibited sensitization. 1991 Journal of immunological methods Abstract IV T65K 24 60 19052090 PB2 protein of a highly pathogenic avian influenza virus strain A/chicken/Yamaguchi/7/2004 (H5N1) determines its replication potential in pigs. Sequencing of two isolates recovered from the pigs inoculated with rg-Sw-Ck/PB2 revealed either the D256G or the E627K amino acid substitution in the PB2 proteins of the isolates. 2009 Journal of virology Abstract IV D256G;E627K 100;113 105;118 PB2;PB2 76;150 79;153 19052090 PB2 protein of a highly pathogenic avian influenza virus strain A/chicken/Yamaguchi/7/2004 (H5N1) determines its replication potential in pigs. The D256G and E627K mutations enhanced viral polymerase activity in the mammalian cells, correlating with replication of virus in pigs. 2009 Journal of virology Abstract IV D256G;E627K 4;14 9;19 19091818 Cocirculation of antigenic variants and the vaccine-type virus during the 2004-2005 influenza B virus epidemics in Japan. The antigenic variants showed a one-point mutation of a nucleotide in the HA1 gene (C440A or G421A), which resulted in the substitution of one amino acid in the 150 loop of the HA molecule (T147N or G141R). 2009 Journal of clinical microbiology Abstract IV C440A;G421A;T147N;G141R 84;93;190;199 89;98;195;204 HA;HA1 177;74 179;77 19116267 Changes in H5N1 influenza virus hemagglutinin receptor binding domain affect systemic spread. Introduction of an S227N change and removal of N-linked glycosylation at residue 158 increased the alpha2,6-binding affinity of VN1203 HA. 2009 Proc Natl Acad Sci U S A Abstract IV S227N 19 24 HA 135 137 19116267 Changes in H5N1 influenza virus hemagglutinin receptor binding domain affect systemic spread. Recombinant VN1203 virus carrying the S227N change alone or with the residue-158 glycosylation site removed showed reduced lethality and systemic spread in mice but not in domestic chickens. 2009 Proc Natl Acad Sci U S A Abstract IV S227N 38 43 19119420 Transmission of influenza virus in a mammalian host is increased by PB2 amino acids 627K or 627E/701N. Introduction of an asparagine at position 701, in conjunction with the K627E mutation, resulted in a phenotype more similar to that of the parental strains, suggesting that this residue can compensate for the lack of 627K in terms of increasing transmission in mammals. 2009 PLoS pathogens Abstract IV K627E 71 76 19141446 Reverse genetics-generated elastase-dependent swine influenza viruses are attenuated in pigs. Mutant A/SW/SK-R345V carries a mutation from arginine to valine at aa 345 of HA. 2009 The Journal of general virology Abstract IV R345V;R345V 15;45 20;73 HA 77 79 19141446 Reverse genetics-generated elastase-dependent swine influenza viruses are attenuated in pigs. Similarly, mutant A/SW/SK-R345A encodes alanine instead of arginine at aa 345 of HA. 2009 The Journal of general virology Abstract IV R345A;R345A 26;40 31;77 HA 81 83 19146891 Factors responsible for plaque formation of A/duck/Siberia/272/1998 (H13N6) influenza virus on MDCK cells. Genetic and functional analyses of Sib272 and Sib272PF revealed that amino acid substitutions, F3L of the HA2 subunit and T379K of the PB1, were responsible for plaque formation of Sib272PF by enhancing fusion and polymerase activities, respectively. 2009 Virus research Abstract IV F3L;T379K 95;122 98;127 HA;PB1 106;135 108;138 19155268 Interactions between histidine and tryptophan residues in the BM2 proton channel from influenza B virus. Mutation of His19 to Ala almost abolished the channel activity, whereas the His27-to-Ala mutant retained partial activity. 2009 Journal of biochemistry Abstract IV H19A;H27A 12;76 24;88 19155268 Interactions between histidine and tryptophan residues in the BM2 proton channel from influenza B virus. The proton selectivity of the channel was lost upon substitution of Phe for Trp23. 2009 Journal of biochemistry Abstract IV W23F 68 81 19157971 Emergence of oseltamivir-resistant influenza A/H3N2 virus with altered hemagglutination pattern in a hematopoietic stem cell transplant recipient. RESULTS: The emergence of NA oseltamivir-resistance mutation R292K was detected by 12 days of oseltamivir treatment with 44,286-fold increase in oseltamivir IC50. 2009 Journal of clinical virology Abstract IV R292K 61 66 26 28 19157971 Emergence of oseltamivir-resistant influenza A/H3N2 virus with altered hemagglutination pattern in a hematopoietic stem cell transplant recipient. Sequential HA mutations R228S and A138S were identified and associated with a shift in the HA receptor binding pattern reflected by loss of the ability to agglutinate chicken erythrocytes. 2009 Journal of clinical virology Abstract IV R228S;A138S 24;34 29;39 HA;HA 11;91 13;93 19172901 [Site-directed modification of caspase cleavage site regions in avian influenza virus proteins]. Mutation Gly16 --> Asp in avian virus NP made this protein (NPgd) sensitive to caspases, like human virus NP, and permitted its cleavage in infected cells. 2008 Voprosy virusologii Abstract IV G16D 9 22 NP;NP 38;106 40;108 19193808 Amino acid residues in the fusion peptide pocket regulate the pH of activation of the H5N1 influenza virus hemagglutinin protein. Four mutations to residues in the fusion peptide pocket, Y23H and H24Q in the HA1 subunit and E105K and N114K in the HA2 subunit, and a K58I mutation in the HA2 coiled-coil domain significantly altered the pH of activation of the H5 HA protein. 2009 Journal of virology Abstract IV Y23H;H24Q;E105K;N114K;K58I 57;66;94;104;136 61;70;99;109;140 HA;HA;HA;HA1 117;157;233;78 119;159;235;81 19193808 Amino acid residues in the fusion peptide pocket regulate the pH of activation of the H5N1 influenza virus hemagglutinin protein. Introduction of Y23H, H24Q, K58I, and N114K mutations into recombinant viruses resulted in virus-expressed HA proteins with similar shifts in the pH of fusion. 2009 Journal of virology Abstract IV Y23H;H24Q;K58I;N114K 16;22;28;38 20;26;32;43 HA 107 109 19211762 Kinetics of immune responses to influenza virus-like particles and dose-dependence of protection with a single vaccination. In this study, we have investigated the detailed kinetics of immune responses and protective efficacy after a single intranasal immunization with different doses of VLPs alone or in the presence of an Escherichia coli mutant heat-labile enterotoxin [mLT(R192G)] or cholera toxin subunit B as adjuvants. 2009 Journal of virology Abstract IV R192G 254 259 19249874 Recognition of mannosylated ligands and influenza A virus by human surfactant protein D: contributions of an extended site and residue 343. A mutant with valine at 343 (R343V) showed enhanced binding to mannan relative to wild type and R343A. 2009 Biochemistry Abstract IV R343V;R343A 29;96 34;101 19249874 Recognition of mannosylated ligands and influenza A virus by human surfactant protein D: contributions of an extended site and residue 343. Although hNCRDs show negligible binding to influenza A virus (IAV), R343V showed markedly enhanced viral neutralizing activity. 2009 Biochemistry Abstract IV R343V 68 73 19249874 Recognition of mannosylated ligands and influenza A virus by human surfactant protein D: contributions of an extended site and residue 343. Both proteins showed efficient recognition of linear and branched subdomains of high-mannose glycans on carbohydrate microarrays, and R343V showed increased binding to a subset of the oligosaccharides. 2009 Biochemistry Abstract IV R343V 134 139 19249874 Recognition of mannosylated ligands and influenza A virus by human surfactant protein D: contributions of an extended site and residue 343. Crystallographic analysis of an R343V complex with 1,2-DM showed a novel mode of binding. 2009 Biochemistry Abstract IV R343V 32 37 19255111 Morbidity and mortality associated with nosocomial transmission of oseltamivir-resistant influenza A(H1N1) virus. CONCLUSION: Seasonal oseltamivir-resistant influenza A(H1N1) viruses with NA gene H274Y mutation are transmitted and retain significant pathogenicity and lethality in high-risk patients. 2009 JAMA Abstract IV H274Y 82 87 74 76 19255111 Morbidity and mortality associated with nosocomial transmission of oseltamivir-resistant influenza A(H1N1) virus. CONTEXT: The sudden emergence and rapid spread of oseltamivir-resistant influenza A(H1N1) viruses with neuraminidase (NA) gene H274Y amino acid substitution is the hallmark of global seasonal influenza since January 2008. 2009 JAMA Abstract IV H274Y 127 132 NA;NA 118;103 120;116 Influenza 176 201 19255111 Morbidity and mortality associated with nosocomial transmission of oseltamivir-resistant influenza A(H1N1) virus. DESIGN, SETTING, AND PATIENTS: Descriptive outbreak investigation of 2 hematopoietic stem cell transplant recipients and an elderly patient who developed hospital-acquired influenza A virus infection following exposure to an index patient with community-acquired H274Y-mutated influenza A(H1N1) virus infection in a medical ward at a Dutch university hospital in February 2008. 2009 JAMA Abstract IV H274Y 263 268 19255111 Morbidity and mortality associated with nosocomial transmission of oseltamivir-resistant influenza A(H1N1) virus. RESULTS: Viral HA(1) and NA gene sequence analysis from the 4 patients revealed indistinguishable nucleotide sequences and phylogenetic clustering of H274Y-mutated, oseltamivir-resistant influenza A(H1N1) virus, confirming nosocomial transmission. 2009 JAMA Abstract IV H274Y 150 155 HA1;NA 15;25 20;27 19309695 Computational studies of H5N1 influenza virus resistance to oseltamivir. Detailed analyses indicated that conformational change of E276 in the Pocket 1 region of NA is a key source of drug resistance in the H274Y mutant but not in the N294S mutant. 2009 Protein science Abstract IV H274Y;N294S 134;162 139;167 89 91 19309695 Computational studies of H5N1 influenza virus resistance to oseltamivir. We examined two resistant NA mutations, H274Y and N294S, and one non-drug-resistant mutation, E119G. 2009 Protein science Abstract IV H274Y;N294S;E119G 40;50;94 45;55;99 26 28 19331731 Oseltamivir-resistant influenza virus A (H1N1), Europe, 2007-08 season. Neuraminidase genes of ORVs possessing the H275Y substitution formed a homogeneous subgroup closely related to, but distinguishable from, those of oseltamivir-sensitive influenza viruses A (H1N1). 2009 Emerging infectious diseases Abstract IV H275Y 43 48 0 13 19331731 Oseltamivir-resistant influenza virus A (H1N1), Europe, 2007-08 season. Oseltamivir-resistant influenza viruses A (H1N1) (ORVs) with H275Y mutation in the neuraminidase emerged independently of drug use. 2009 Emerging infectious diseases Abstract IV H275Y 61 66 83 96 19342184 Multiple amino acid substitutions are involved in the adaptation of H9N2 avian influenza virus to mice. Functions affected include nuclear localization signals and sites of protein and RNA interaction, while others are known determinants of pathogenicity and host specificity such as the viral polymerase PB2 E627K substitution. 2009 Veterinary microbiology Abstract IV E627K 205 210 PB2 201 204 19367871 Single mutation induced H3N2 hemagglutinin antibody neutralization: a free energy perturbation study. A recent experiment shows that a single mutation in H3N2 HA, T131I, increases the antibody-antigen dissociation constant Kd by a factor of approximately 4000 (equivalent to a binding affinity decrease of approximately 5 kcal/mol), thus introducing an escape of the antibody (Ab) neutralization. 2008 The journal of physical chemistry. B Abstract IV T131I 61 66 HA 57 59 19367871 Single mutation induced H3N2 hemagglutinin antibody neutralization: a free energy perturbation study. As for further validation, we have also modeled another mutation, S157L, with experimental binding affinity available (Kd increasing approximately 500 times), and found a binding affinity decrease of 4.1 +/- 1.0 kcal/mol, which is again in excellent agreement with experiment. 2008 The journal of physical chemistry. B Abstract IV S157L 66 71 19367871 Single mutation induced H3N2 hemagglutinin antibody neutralization: a free energy perturbation study. Detailed analysis reveals that this large binding affinity decrease in the T131I mutant is mainly due to the displacement of two bridge water molecules otherwise present in the wild-type HA/Ab interface. 2008 The journal of physical chemistry. B Abstract IV T131I 75 80 HA 187 189 19367871 Single mutation induced H3N2 hemagglutinin antibody neutralization: a free energy perturbation study. We then simulate all other possible mutations for this specific mutation site T131, and predict a few more mutations with even larger decreases in the binding affinity (i.e., better candidates for antibody neutralization), such as T131W, T131Y, and T131F. 2008 The journal of physical chemistry. B Abstract IV T131W;T131Y;T131F 231;238;249 236;243;254 19383794 Mechanism of drug inhibition and drug resistance of influenza A M2 channel. Mutagenesis and liposomal proton flux assays show that replacing the key residue (Asp-44) in the lipid-facing binding pocket with Ala has a dramatic effect on drug sensitivity, but that the channel remains fully drug sensitive when replacing Ser-31 with Ala. 2009 Proc Natl Acad Sci U S A Abstract IV S31A 242 257 19383794 Mechanism of drug inhibition and drug resistance of influenza A M2 channel. The solution structure of the S31N drug-resistant mutant of M2, a mutant of the highly pathogenic avian influenza subtype H5N1, shows that replacing Ser-31 with Asn has little effect on the structure of the channel pore, but dramatically reduces drug binding to the allosteric site. 2009 Proc Natl Acad Sci U S A Abstract IV S31N;S31N 30;149 34;164 M2 60 62 19393699 Single mutation at the amino acid position 627 of PB2 that leads to increased virulence of an H5N1 avian influenza virus during adaptation in mice can be compensated by multiple mutations at other sites of PB2. Interestingly, one reverse mutation (K627E) took place at the amino acid position 627 of PB2 during passages of MA5 to MA15, indicating that a lysine at position 627 of PB2 is not absolutely needed for virulence and adaptation in mice by H5N1 virus. 2009 Virus research Abstract IV K627E 37 42 PB2;PB2 89;169 92;172 19393699 Single mutation at the amino acid position 627 of PB2 that leads to increased virulence of an H5N1 avian influenza virus during adaptation in mice can be compensated by multiple mutations at other sites of PB2. Taken together, the results suggest that mutations at multiple sites of PB2 contributed to the virulence and adaptation in mice, and the E627K mutation of PB2 is not an indispensable determinant in PB2 for mammalian adaptation by H5N1 avian influenza virus. 2009 Virus research Abstract IV E627K 137 142 PB2;PB2;PB2 72;155;198 75;158;201 19394063 The origin and global emergence of adamantane resistant A/H3N2 influenza viruses. Adamantane resistance is associated with a single amino acid change (S31N) in the M2 protein, which was shown to rapidly disseminate globally in 2005 in association with a genome reassortment event. 2009 Virology Abstract IV S31N 69 73 M2 82 84 19394063 The origin and global emergence of adamantane resistant A/H3N2 influenza viruses. However, the exact origin of influenza A/H3N2 viruses carrying the S31N mutation has not been characterized, particularly in South-East Asia. 2009 Virology Abstract IV S31N 67 71 19394063 The origin and global emergence of adamantane resistant A/H3N2 influenza viruses. We find that although the S31N mutation was independently introduced at least 11 times, the vast majority of resistant viruses now circulating globally descend from a single introduction that was first detected in the summer of 2003 in Hong Kong. 2009 Virology Abstract IV S31N 26 30 19399777 Free energy simulations reveal a double mutant avian H5N1 virus hemagglutinin with altered receptor binding specificity. Moreover, we predict that one double mutation (V135S and A138S) in HA significantly enhances alpha-2,6-linked receptor recognition by the H5 subtype. 2009 Journal of computational chemistry Abstract IV V135S;A138S 47;57 52;62 HA 67 69 19403683 Adaptive mutations resulting in enhanced polymerase activity contribute to high virulence of influenza A virus in mice. An isoleucine-to-leucine change at position 550 in PA further contributed to increased polymerase activity and high virulence, whereas all other mutations in PB1, PB2, and PA were irrelevant. 2009 Journal of virology Abstract IV I550L 3 47 PA;PA;PB1;PB2 51;172;158;163 53;174;161;166 19403683 Adaptive mutations resulting in enhanced polymerase activity contribute to high virulence of influenza A virus in mice. In contrast, the virulent virus selected in the second adaptation experiment had a lysine-to-arginine change at position 208 in PB1 and a glutamate-to-glycine change at position 349 in PA. 2009 Journal of virology Abstract IV K208R;E349G 83;138 124;181 PA;PB1 185;128 187;131 19403683 Adaptive mutations resulting in enhanced polymerase activity contribute to high virulence of influenza A virus in mice. Mutational analyses demonstrated that an isoleucine-to-valine change at position 504 in PB2 was the most critical and strongly enhanced the activity of the reconstituted polymerase complex. 2009 Journal of virology Abstract IV I504V 41 84 PB2 88 91 19403683 Adaptive mutations resulting in enhanced polymerase activity contribute to high virulence of influenza A virus in mice. Surprisingly, the conservative I504V change in PB2 evolved again and was the only mutation present in an aggressive virus variant selected during the first adaptation experiment. 2009 Journal of virology Abstract IV I504V 31 36 PB2 47 50 19436701 Avian Influenza virus glycoproteins restrict virus replication and spread through human airway epithelium at temperatures of the proximal airways. Two of these viruses, A/Victoria/3/75 with L226Q and S228G mutations in hemagglutinin (HA) and neuraminidase (NA) from A/Chick/Italy/1347/99 and A/PR/8/34 containing the H7 and N1 from A/Chick/Italy/1347/99, exhibited temperature restriction approaching that of wholly avian influenza viruses. 2009 PLoS pathogens Abstract IV L226Q;S228G 43;53 48;58 HA;HA;NA;NA 87;72;110;95 89;85;112;108 19451021 Genetic microheterogeneity of emerging H275Y influenza virus A (H1N1) in Toronto, Ontario, Canada from the 2007-2008 respiratory season. BACKGROUND: The H275Y mutation (H274Y in N2 numbering) in the neuraminidase (NA) gene (segment 6) of the influenza virus A (H1N1) genome is linked to oseltamivir resistance. 2009 Journal of clinical virology Abstract IV H275Y;H274Y 16;32 21;37 NA;NA 77;62 79;75 19451021 Genetic microheterogeneity of emerging H275Y influenza virus A (H1N1) in Toronto, Ontario, Canada from the 2007-2008 respiratory season. CONCLUSIONS: During the 2007-2008 influenza season in Toronto, Ontario, Canada, 17% of influenza virus A (H1N1) isolates carried the H275Y mutation associated with oseltamivir resistance. 2009 Journal of clinical virology Abstract IV H275Y 133 138 19451021 Genetic microheterogeneity of emerging H275Y influenza virus A (H1N1) in Toronto, Ontario, Canada from the 2007-2008 respiratory season. H275Y isolates were more likely than H275 isolates to have the mutations A209T and R224G in NS1 (chi(2)=284.9, df=2, p<0.0001). 2009 Journal of clinical virology Abstract IV H275Y;A209T;R224G 0;73;83 5;78;88 NS1 92 95 19451021 Genetic microheterogeneity of emerging H275Y influenza virus A (H1N1) in Toronto, Ontario, Canada from the 2007-2008 respiratory season. OBJECTIVES: To determine the percentage of influenza virus A (H1N1) isolates that carry the H275Y mutation in the NA gene in Toronto, Ontario, Canada and to characterize select oseltamivir resistant and susceptible isolates using sequence analysis. 2009 Journal of clinical virology Abstract IV H275Y 92 97 114 116 19451021 Genetic microheterogeneity of emerging H275Y influenza virus A (H1N1) in Toronto, Ontario, Canada from the 2007-2008 respiratory season. Seventeen percent of these isolates possessed the H275Y NA mutation associated with oseltamivir resistance. 2009 Journal of clinical virology Abstract IV H275Y 50 55 56 58 19451021 Genetic microheterogeneity of emerging H275Y influenza virus A (H1N1) in Toronto, Ontario, Canada from the 2007-2008 respiratory season. Statistical analysis of demographics and proportions of H275 and H275Y isolates with mutations was carried out using chi(2) analyses. 2009 Journal of clinical virology Abstract IV H275Y 65 70 19451021 Genetic microheterogeneity of emerging H275Y influenza virus A (H1N1) in Toronto, Ontario, Canada from the 2007-2008 respiratory season. STUDY DESIGN: Sanger sequencing was used to determine strain type and H275Y mutations based on partial sequencing of the hemagglutinin (HA) (segment 4) and NA genes. 2009 Journal of clinical virology Abstract IV H275Y 70 75 HA;HA;NA 136;121;156 138;134;158 19451021 Genetic microheterogeneity of emerging H275Y influenza virus A (H1N1) in Toronto, Ontario, Canada from the 2007-2008 respiratory season. These H275Y isolates were more likely than H275 isolates to exhibit unique microheterogeneity in the gene encoding the NS1 protein. 2009 Journal of clinical virology Abstract IV H275Y 6 11 NS1 119 122 19454348 Influenza A virus NS1 targets the ubiquitin ligase TRIM25 to evade recognition by the host viral RNA sensor RIG-I. Furthermore, a recombinant influenza A virus expressing an E96A/E97A NS1 mutant is defective in blocking TRIM25-mediated antiviral IFN response and loses virulence in mice. 2009 Cell host & microbe Abstract IV E96A;E97A 59;64 63;68 NS1 69 72 19458903 Functional significance of the hemadsorption activity of influenza virus neuraminidase and its alteration in pandemic viruses. Using this hemadsorption-positive NA, we generated three NA variants with substitutions S370L, N400S and W403R that have been found in the hemadsorption site of human H2N2 viruses. 2009 Archives of virology Abstract IV S370L;N400S;W403R 88;95;105 93;100;110 NA;NA 34;57 36;59 19458903 Functional significance of the hemadsorption activity of influenza virus neuraminidase and its alteration in pandemic viruses. We found that the NA of a representative pandemic virus A/Singapore/1/57 (H2N2) lacks hemadsorption activity and that a single reversion to the avian-virus-like sequence (N367S) restores hemadsorption. 2009 Archives of virology Abstract IV N367S 171 176 18 20 19494001 A complicated message: Identification of a novel PB1-related protein translated from influenza A virus segment 2 mRNA. Removal of the PB1-F2 AUG upregulated N40 synthesis, while truncating PB1-F2 after codon 8 (with a concomitant M40I change in PB1) abolished N40 expression. 2009 Journal of virology Abstract IV M40I 111 115 PB1;PB1F2;PB1F2 126;15;70 129;21;76 19494010 Nuclear factor 90 negatively regulates influenza virus replication by interacting with viral nucleoprotein. This interaction was prevented by a mutation, F412A, in the C-terminal region of the NP, indicating that the C-terminal of NP is required for NF90 binding. 2009 Journal of virology Abstract IV F412A 46 51 NP;NP 85;123 87;125 19502107 Co-circulation of two genetically distinct sub-groups of A/H3N2 influenza strains during the 2006-2007 epidemic season in Corsica Island, France. One of these sub-groups was distinguished by the substitution H156Q whereas the second demonstrated at least one of the 3 other additional mutations (R142G, L157S and K173E) common to the HA1 sequence of A/Nepal/921/2006 reference strain. 2009 Journal of clinical virology Abstract IV H156Q;R142G;L157S;K173E 62;150;157;167 67;155;162;172 HA1 188 191 19517011 Novel genotypes of H9N2 influenza A viruses isolated from poultry in Pakistan containing NS genes similar to highly pathogenic H7N3 and H5N1 viruses. The hemagglutinin (HA) sequences of all isolates were closely related to H9N2 viruses isolated from Iran between 2004 and 2007 and contained leucine instead of glutamine at position 226 in the receptor binding pocket, a recognised marker for the recognition of sialic acids linked alpha2-6 to galactose. 2009 PloS one Abstract IV Q226L 141 185 HA;HA 19;4 21;17 19537916 Amantadine-resistant influenza A (H3N2) viruses in Iran. In investigating the frequency of amantadine-resistant IAVs (H3N2) circulating in Iran in 2005-2008, we found that M2 sequences of recently circulating viruses that were amantadine-resistant contained a Ser31Asn mutation. 2009 Acta virologica Abstract IV S31N 203 211 M2 115 117 19553312 Palmitoylation of the influenza A virus M2 protein is not required for virus replication in vitro but contributes to virus virulence. Recombinant viruses encoding M2 proteins with a serine substituted for the cysteine at position 50 were generated in the A/WSN/33 (H1N1) and A/Udorn/72 (H3N2) genetic backgrounds. 2009 Journal of virology Abstract IV S50C 48 98 M2 29 31 19553505 Mutations in influenza virus replication and transcription: detection of amino acid substitutions in hemagglutinin of an avian influenza virus (H1N1). The comparison of the sequences obtained from analysis of viral genome and peptide found seven variations between HA gene and protein, namely E103K, R130K, T169I, I338V, N387S, S398I/L, and I399S in HA. 2009 FASEB journal Abstract IV E103K;R130K;T169I;I338V;N387S;S398I;S398L;I399S 142;149;156;163;170;177;177;190 147;154;161;168;175;184;184;195 HA;HA 114;199 116;201 19591877 Dynamics of antiviral-resistant influenza viruses in the Netherlands, 2005-2008. For adamantanes, a high proportion (>74%) of A(H3N2) viruses had the S31N mutation in M2 protein, while variation in the HA(1) region of adamantane-sensitive viruses suggested that adamantane-sensitive variants were reseeded into the Dutch population and re-emerged as drug-sensitive due to M-segment reassortment. 2009 Antiviral research Abstract IV S31N 69 73 HA;M;M2 121;291;86 125;292;88 19615420 Molecular and phylogenetic analysis and vaccine strain match of human influenza A(H3N2) viruses isolated in Northern Greece between 2004 and 2008. Receptor binding sites were conserved in 2004-2005 and 2005-2006 strains whereas a variation was observed in all 2006-2007 strains (H195Y). 2009 Virus research Abstract IV H195Y 132 137 19625412 Elastase-dependent live attenuated swine influenza A viruses are immunogenic and confer protection against swine influenza A virus infection in pigs. Based on the immunogenicity results, the R345V virus was further tested in a protection trial in which pigs were vaccinated twice with R345V and then challenged with homologous A/Sw/Saskatchewan/18789/02, H1N1 antigenic variant A/Sw/Indiana/1726/88 or heterologous subtypic H3N2 A/Sw/Texas/4199-2/9/98. 2009 Journal of virology Abstract IV R345V;R345V 41;135 46;140 19625412 Elastase-dependent live attenuated swine influenza A viruses are immunogenic and confer protection against swine influenza A virus infection in pigs. Our data showed that two vaccinations with R345V provided pigs with complete protection from homologous H1N1 SIV infection and partial protection from heterologous subtypic H3N2 SIV infection. 2009 Journal of virology Abstract IV R345V 43 48 19625412 Elastase-dependent live attenuated swine influenza A viruses are immunogenic and confer protection against swine influenza A virus infection in pigs. Previously, we generated two elastase-dependent mutant SIVs derived from A/Sw/Saskatchewan/18789/02(H1N1): A/Sw/Sk-R345V (R345V) and A/Sw/Sk-R345A (R345A). 2009 Journal of virology Abstract IV R345V;R345V;R345A;R345A 115;122;141;148 120;127;146;153 19625412 Elastase-dependent live attenuated swine influenza A viruses are immunogenic and confer protection against swine influenza A virus infection in pigs. We report that intratracheally administrated R345V and R345A induced antigen-specific humoral and cell-mediated immunity characterized by increased production of immunoglobulin G (IgG) and IgA antibodies in the serum and in bronchoalveolar lavage fluid, high hemagglutination inhibition titers in serum, an enhanced level of lymphocyte proliferation, and higher numbers of gamma interferon-secreting cells at the site of infection. 2009 Journal of virology Abstract IV R345V;R345A 45;55 50;60 19626608 Surveillance and oseltamivir resistance of human influenza a virus in Turkey during the 2007-2008 season. H275Y (H274Y according to N2 numbering) mutation, which is known to confer resistance to oseltamivir, was detected in 6 out of 30 (20%) H1N1 isolates from four cities (Istanbul, Bursa, Ankara, and Izmir). 2009 Journal of medical virology Abstract IV H275Y;H274Y 0;7 5;12 19626608 Surveillance and oseltamivir resistance of human influenza a virus in Turkey during the 2007-2008 season. The D354G mutation was observed in all oseltamivir resistant H1N1 isolates but not in the oseltamivir sensitive isolates. 2009 Journal of medical virology Abstract IV D354G 4 9 19646748 The use of a mutant TNF-alpha as a vaccine adjuvant for the induction of mucosal immune responses. Furthermore, intranasal immunization with an antigen from influenza virus plus mTNF-K90R exhibited mucosal adjuvant activity for induction of both systemic and mucosal immune responses. 2009 Biomaterials Abstract IV K90R 84 88 19646748 The use of a mutant TNF-alpha as a vaccine adjuvant for the induction of mucosal immune responses. Here, we examined the potential of mTNF-K90R as a mucosal adjuvant. 2009 Biomaterials Abstract IV K90R 40 44 19646748 The use of a mutant TNF-alpha as a vaccine adjuvant for the induction of mucosal immune responses. Importantly, histopathological examination of the nasal tissue of mTNF-K90R treated mice detected no signs of toxicity. 2009 Biomaterials Abstract IV K90R 71 75 19646748 The use of a mutant TNF-alpha as a vaccine adjuvant for the induction of mucosal immune responses. Initially, we showed that intranasal co-administration of mTNF-K90R with ovalbumin (OVA) potently produced OVA-specific Immunoglobulin (Ig) G antibodies (Abs) in serum and IgA Abs both at local and distal mucosal sites compared to co-administration with wild-type TNF-alpha. 2009 Biomaterials Abstract IV K90R 63 67 19646748 The use of a mutant TNF-alpha as a vaccine adjuvant for the induction of mucosal immune responses. These findings suggest that mTNF-K90R is safe and effective mucosal adjuvant and this system may have potential application as a universal mucosal adjuvant system for mucosal vaccines improving the immune response to a variety of viral antigens. 2009 Biomaterials Abstract IV K90R 33 37 19646748 The use of a mutant TNF-alpha as a vaccine adjuvant for the induction of mucosal immune responses. We have created a mutant tumor necrosis factor-alpha (TNF-alpha), mTNF-K90R, that exhibits high bioactivity and resistance to proteases. 2009 Biomaterials Abstract IV K90R 71 75 19692471 A single-amino-acid substitution in a polymerase protein of an H5N1 influenza virus is associated with systemic infection and impaired T-cell activation in mice. A substitution of glutamic acid for lysine at position 627 of the PB2 protein of H5N1 viruses has been identified as a virulence determinant. 2009 Journal of virology Abstract IV K627E 18 58 PB2 66 69 19696719 Oseltamivir-resistant novel influenza A (H1N1) virus infection in two immunosuppressed patients - Seattle, Washington, 2009. Testing of viral RNA from both patients by pyrosequencing detected a mutation that results in a histidine-to-tyrosine substitution at position 275 (H275Y) in the neuraminidase, known to be associated with oseltamivir resistance. 2009 MMWR. Morbidity and mortality weekly report Abstract IV H275Y;H275Y 148;96 153;146 162 175 19720062 Identification of amino acid residues of influenza A virus H3 HA contributing to the recognition of molecular species of sialic acid. The results indicate that the amino acid substitutions Thr155 to Tyr and Glu158 to Gly in H3 HA facilitate virus binding to N-glycolylneuraminic acid. 2009 FEBS letters Abstract IV T155Y;E158G 55;73 68;86 HA 93 95 19761797 Rapid quantification of single-nucleotide mutations in mixed influenza A viral populations using allele-specific mixture analysis. The FluASMA assays target L26F, V27A, A30T, and S31N mutations in the A/Albany/1/98 (H3N2) M2 gene and H275Y mutation in the A/New Caledonia/20/99 (H1N1) NA gene and have a limit of quantification of 0.25-0.50% mutant. 2010 Journal of virological methods Abstract IV V27A;L26F;A30T;S31N;H275Y 32;26;38;48;103 36;30;42;52;108 M2;NA 91;154 93;156 19763781 Comparison of the activities of BM2 protein and its H19 and W23 mutants of influenza B virus with activities of M2 protein and its H37 and W41 mutants of influenza A virus. Mutation analysis showed that replacement of H19 in BM2 protein by A and L resulted in loss of activity, while M2, with the mutation H37A, remained active, but its severe toxicity was intolerable for cells. 2009 Archives of virology Abstract IV H37A 133 137 BM2;M2 52;111 55;113 19766280 Changes of the receptor-binding properties of influenza B virus B/Victoria/504/2000 during adaptation in chicken eggs. A low-growth virus variant, corresponding to the original egg-derived virus B/Victoria/504/2000 prior to acquisition of amino acid changes G141E, R162M, and D196Y, had a clear preference for the oligosaccharide chains terminated with alpha2-6-linked sialic acid with very weak binding of the glycans terminated with alpha2-3-linked sialic acid. 2009 Virology Abstract IV G141E;R162M;D196Y 139;146;157 144;151;162 19766280 Changes of the receptor-binding properties of influenza B virus B/Victoria/504/2000 during adaptation in chicken eggs. Amino acid substitutions R162M and D196Y had similar effects, resulting in viruses that bound with high efficiency almost all terminally sialylated glycans represented on the array regardless of the type of glycosidic linkage. 2009 Virology Abstract IV R162M;D196Y 25;35 30;40 19766280 Changes of the receptor-binding properties of influenza B virus B/Victoria/504/2000 during adaptation in chicken eggs. In all cases when the effects on virus binding of individual amino acid substitutions differed, the effect of R162M was subordinate to the effect of either G141E or D196Y. 2009 Virology Abstract IV R162M;G141E;D196Y 110;156;165 115;161;170 19766280 Changes of the receptor-binding properties of influenza B virus B/Victoria/504/2000 during adaptation in chicken eggs. In contrast, substitution of G141E alone, or in combinations with the other two amino acid substitutions, significantly restricted virus glycan-binding capabilities. 2009 Virology Abstract IV G141E 29 34 19766280 Changes of the receptor-binding properties of influenza B virus B/Victoria/504/2000 during adaptation in chicken eggs. Linear penta- and heptasaccharide chains represented at the non-reducing end by alpha2-3 sialylated Type-II motif (LacNAc) were the only structures bound with high affinity by the virus variants with G141E substitution. 2009 Virology Abstract IV G141E 200 205 19766280 Changes of the receptor-binding properties of influenza B virus B/Victoria/504/2000 during adaptation in chicken eggs. Selection of high-growth virus variants of strain B/Victoria/504/2000 by serial passage in eggs resulted in three amino acid substitutions, G141E, R162M, and D196Y, in the vicinity of the receptor-binding pocket of viral hemagglutinin. 2009 Virology Abstract IV G141E;R162M;D196Y 140;147;158 145;152;163 HA 221 234 19802744 Stable non-synonymous substitutions on NS gene (NS1 and NS2 proteins) of Qinghai Lake H5N1 influenza virus (Clade 2.2) after successive passages in Muscovy ducks. During the process of serial passages, only the NS gene developed non-synonymous substitutions, which caused two mutations in NS1 protein (Val23Ala and Leu207Pro) and one in NS2 (Phe55Leu). 2009 Science in China. Series C, Life sciences Abstract IV V23A;L207P;F55L 139;152;179 147;161;187 NS;NS1;NS2 48;126;174 50;129;177 1980394 Primary structure of the gene coding for the haemagglutinin of influenza virus A/Leningrad/385/80(H3N2): detection of a point mutation responsible for the antigenic drift. It was shown that a single mutation in an antigenic site (the change from isoleucine to leucine at position 51 of HA1 gene) caused an antigenic drift. 1990 Acta virologica Abstract IV I51L 74 110 HA1 114 117 19837850 Viral aggregating and opsonizing activity in collectin trimers. hSP-D-NCRD/R343V greatly increased viral uptake by neutrophils and monocytes and also potentiated neutrophil respiratory burst responses. 2010 American journal of physiology. Lung cellular and molecular physiology Abstract IV R343V 11 16 19837850 Viral aggregating and opsonizing activity in collectin trimers. The most effective substitution involved replacement of arginine 343 with valine (hSP-D-NCRD/R343V). 2010 American journal of physiology. Lung cellular and molecular physiology Abstract IV R343V;R343V 93;56 98;80 19837850 Viral aggregating and opsonizing activity in collectin trimers. These effects were further increased by cross-linking of hSP-D-NCRD/R343V trimers with MAbs directed against areas of the hSP-D-NCRD not involved in viral binding. 2010 American journal of physiology. Lung cellular and molecular physiology Abstract IV R343V 68 73 19837850 Viral aggregating and opsonizing activity in collectin trimers. Unlike the wild-type human SP-D hSP-D-NCRD, hSP-D-NCRD/R343V also induced viral aggregation. 2010 American journal of physiology. Lung cellular and molecular physiology Abstract IV R343V 55 60 19840674 Influenza virus CTL epitopes, remarkably conserved and remarkably variable. It is of special interest that the R384G substitution in the NP(383-391) epitope was detrimental to virus fitness and was only tolerated in the presence of multiple functionally compensating co-mutations. 2009 Vaccine Abstract IV R384G 35 40 NP 61 63 19850010 Amantadine- and oseltamivir-resistant variants of influenza A viruses in Thailand. All of the amantadine-resistant H3N2 viruses were clustered in one of these three genes and possessed double mutations of S193F and D225N in the HA gene. 2009 Biochemical and biophysical research communications Abstract IV S193F;D225N 122;132 127;137 HA 145 147 19850010 Amantadine- and oseltamivir-resistant variants of influenza A viruses in Thailand. Our results demonstrated that seven out of 32 (22%) of the H1N1 viruses isolated in 2006 in Thailand carried the amino acid S31N substitution, which confers amantadine-resistance, although no isolates in 2007 or 2008 possessed the mutation. 2009 Biochemical and biophysical research communications Abstract IV S31N 124 128 19857993 Evaluation of a rapid molecular algorithm for detection of pandemic influenza A (H1N1) 2009 virus and screening for a key oseltamivir resistance (H275Y) substitution in neuraminidase. In addition, we investigated the performance of a novel discrimination RT-PCR for detection of the H275Y resistance mutation in the neuraminidase gene. 2010 Journal of clinical virology Abstract IV H275Y 99 104 132 145 19857993 Evaluation of a rapid molecular algorithm for detection of pandemic influenza A (H1N1) 2009 virus and screening for a key oseltamivir resistance (H275Y) substitution in neuraminidase. Specificity and discriminative capacities of the H275Y discrimination assay were performed by testing wild type and recombinant H275Y pandemic influenza. 2010 Journal of clinical virology Abstract IV H275Y;H275Y 49;128 54;133 19880155 Loss of function of the influenza A virus NS1 protein promotes apoptosis but this is not due to a failure to activate phosphatidylinositol 3-kinase (PI3K). Surprisingly, given previous reports that NS1 activates PI3K to prevent apoptosis, the mutant viruses rUd-Y89F and rUd-P164/7A that fail to activate PI3K did not induce any more apoptosis than wild-type virus in MRC-5 and A549 cells, even though these cells are highly sensitive to inducers of apoptosis. 2010 Virology Abstract IV Y89F 106 110 NS1 42 45 19882896 [The 24 May, 2009 isolation of the first A/IIV-Moscow/01/2009 (H1N1)swl strain similar to swine A(H1N1) influenza virus from the first Moscow case detected on May 21, 2009, and its deposit in the state collection of viruses (SCV No. 2452 dated May 24, 2009)]. The significant gene substitution of neuraminidase Asp for Gly in position 451, which has been undetectable in any other strain published in the Gen Bank by the present time is unique only to A/IIV-Moscow/01/2009 (H1N1)swl. 2009 Voprosy virusologii Abstract IV G451D 51 78 37 50 19882897 [Amino acid substitutions in the hemagglutinin of H5 influenza virus changing the antigenic specificity and virus virulence]. The results demonstrate that the amino acid change S145F (H3 numbering) in the hemagglutinin ensuring the resistance to a monoclonal antibody can be deleterious to virulence, and that the damaging effect on virulence may be compensated for by additional amino acid changes in position 186 in the hemagglutinin arising in the course of virus passaging in mice. 2009 Voprosy virusologii Abstract IV S145F 51 56 HA;HA 79;296 92;309 19889895 Rapid and specific detection of amantadine-resistant influenza A viruses with a Ser31Asn mutation by the cycling probe method. In the present study, we developed a novel method to detect amantadine-resistant strains harboring the Ser31Asn mutation in the M2 gene based on the cycling probe method and real-time PCR. 2010 Journal of clinical microbiology Abstract IV S31N 103 111 M2 128 130 19893747 Novel pandemic influenza A(H1N1) viruses are potently inhibited by DAS181, a sialidase fusion protein. As inhibition was also observed with oseltamivir-resistant IFV (H274Y), DAS181 may be active against the antigenically novel pandemic influenza A(H1N1) virus should it acquire the H274Y mutation. 2009 PloS one Abstract IV H274Y;H274Y 64;180 69;185 19893747 Novel pandemic influenza A(H1N1) viruses are potently inhibited by DAS181, a sialidase fusion protein. Furthermore, DAS181 antiviral activity against pandemic influenza A(H1N1) strains was comparable to that observed against seasonal influenza virus including the H274Y oseltamivir-resistant influenza virus. 2009 PloS one Abstract IV H274Y 161 166 19893749 Inhibition of neuraminidase inhibitor-resistant influenza virus by DAS181, a novel sialidase fusion protein. Antiviral drug resistance for influenza therapies remains a concern due to the high prevalence of H1N1 2009 seasonal influenza isolates which display H274Y associated oseltamivir-resistance. 2009 PloS one Abstract IV H274Y 150 155 19893749 Inhibition of neuraminidase inhibitor-resistant influenza virus by DAS181, a novel sialidase fusion protein. As expected, all 2007 and 2009 isolates were resistant to oseltamivir, consistent with the identification of the H274Y mutation in the NA gene of all these isolates. 2009 PloS one Abstract IV H274Y 113 118 135 137 19905033 Design and pharmacological characterization of inhibitors of amantadine-resistant mutants of the M2 ion channel of influenza A virus. A lead compound emerging from these investigations, spiro[5.5]undecan-3-amine, is an effective inhibitor of wild-type A/M2 channels and L26F and V27A mutant ion channels in vitro and also inhibits replication of recombinant mutant viruses bearing these mutations in plaque reduction assays. 2009 Biochemistry Abstract IV L26F;V27A 136;145 140;149 M2 120 122 19905033 Design and pharmacological characterization of inhibitors of amantadine-resistant mutants of the M2 ion channel of influenza A virus. The A/M2 proton channel of influenza A virus is a target for the anti-influenza drugs amantadine and rimantadine, whose effectiveness was diminished by the appearance of naturally occurring point mutants in the A/M2 channel pore, among which the most common are S31N, V27A, and L26F. 2009 Biochemistry Abstract IV S31N;V27A;L26F 262;268;278 266;272;282 M2;M2 6;213 8;215 19906934 Mutations in the ectodomain of newcastle disease virus fusion protein confer a hemagglutinin-neuraminidase-independent phenotype. Moreover, the N211A, I463A, and I463F mutants exhibited hemagglutinin-neuraminidase (HN)-independent activity when influenza virus hemagglutinin (HA) was coexpressed as an attachment protein. 2010 Journal of virology Abstract IV N211A;I463A;I463F 14;21;32 19;26;37 HA;HA;HA;NA 146;56;131;70 148;69;144;83 19906934 Mutations in the ectodomain of newcastle disease virus fusion protein confer a hemagglutinin-neuraminidase-independent phenotype. The N211A, L461A, I463A, and I463F mutants showed a hyperfusogenic phenotype both in syncytium and in dye transfer assays. 2010 Journal of virology Abstract IV N211A;L461A;I463A;I463F 4;11;18;29 9;16;23;34 19911968 Clinical effectiveness of oseltamivir and zanamivir for treatment of influenza A virus subtype H1N1 with the H274Y mutation: a Japanese, multicenter study of the 2007-2008 and 2008-2009 influenza seasons. All 49 analyzed H1N1 virus isolates obtained during the 2008-2009 season, but none of the isolates obtained during the 2007-2008 season, contained the H274Y mutation. 2009 Clinical infectious diseases Abstract IV H274Y 151 156 19911968 Clinical effectiveness of oseltamivir and zanamivir for treatment of influenza A virus subtype H1N1 with the H274Y mutation: a Japanese, multicenter study of the 2007-2008 and 2008-2009 influenza seasons. BACKGROUND: Influenza A virus subtype H1N1 with the H274Y mutation emerged and spread worldwide. 2009 Clinical infectious diseases Abstract IV H274Y 52 57 19911968 Clinical effectiveness of oseltamivir and zanamivir for treatment of influenza A virus subtype H1N1 with the H274Y mutation: a Japanese, multicenter study of the 2007-2008 and 2008-2009 influenza seasons. The H274Y neuraminidase mutation status was determined by sequencing the neuraminidase segment. 2009 Clinical infectious diseases Abstract IV H274Y 4 9 NA;NA 10;73 23;86 19917319 Host cell selection of influenza neuraminidase variants: implications for drug resistance monitoring in A(H1N1) viruses. Full NA sequence analysis of a subset of oseltamivir-resistant and sensitive virus isolates from both seasons (n=725) showed that 53 (7.3%) had mutations at residue D151 (D-->E/G/N), while 9 (1.2%) had mutations at Q136 (Q-->K) and 2 (0.3%) had mutations at both residues. 2010 Antiviral research Abstract IV Q136K 215 227 5 7 19917319 Host cell selection of influenza neuraminidase variants: implications for drug resistance monitoring in A(H1N1) viruses. Mutations at D151 without H274Y, did not elevate IC(50) for any tested NAI, however, Q136K alone significantly reduced susceptibility to zanamivir (36-fold), peramivir (80-fold) and A-315675 (114-fold) but not oseltamivir. 2010 Antiviral research Abstract IV H274Y;Q136K 26;85 31;90 NAI 71 74 19917319 Host cell selection of influenza neuraminidase variants: implications for drug resistance monitoring in A(H1N1) viruses. Pyrosequencing analysis confirmed H274Y mutation (H275Y in N1 numbering) in the neuraminidase (NA) gene of oseltamivir-resistant viruses. 2010 Antiviral research Abstract IV H274Y;H275Y 34;50 39;55 NA;NA 95;80 97;93 19917319 Host cell selection of influenza neuraminidase variants: implications for drug resistance monitoring in A(H1N1) viruses. Viruses with very high IC(50) for oseltamivir and peramivir, and elevated IC(50) for zanamivir, had H274Y in addition to mutations at D151 and/or Q136, residues which can potentially confer NAI resistance based on recent N1 NA crystal structure data. 2010 Antiviral research Abstract IV H274Y 100 105 NA;NAI 224;190 226;193 19923184 The pH of activation of the hemagglutinin protein regulates H5N1 influenza virus pathogenicity and transmissibility in ducks. An H24Q mutation that decreased the pH of activation by 0.3 unit resulted in weight loss, mortality, clinical symptoms, and shedding similar to those of the wild type. 2010 Journal of virology Abstract IV H24Q 3 7 19923184 The pH of activation of the hemagglutinin protein regulates H5N1 influenza virus pathogenicity and transmissibility in ducks. An N114K mutation that increased the pH of HA activation by 0.5 unit resulted in decreased replication, genetic stability, and environmental stability. 2010 Journal of virology Abstract IV N114K 3 8 HA 43 45 19923184 The pH of activation of the hemagglutinin protein regulates H5N1 influenza virus pathogenicity and transmissibility in ducks. Changes of +0.4 and -0.5 unit in the pH of activation by Y23H and K58I mutations, respectively, reduced weight loss, mortality, shedding, and transmission in mallards. 2010 Journal of virology Abstract IV Y23H;K58I 57;66 61;70 19934602 A Serine12Stop mutation in PB1-F2 of the 2009 pandemic (H1N1) influenza A: a possible reason for its enhanced transmission and pathogenicity to humans. Genome annotations of this virus identified a stop mutation replacing serine at codon 12 (S12Stop) of the PB1-F2 protein, a virulence factor in influenza A viruses. 2009 Journal of veterinary science Abstract IV S12X 90 97 PB1F2 106 112 19939933 Molecular determinants of adaptation of highly pathogenic avian influenza H7N7 viruses to efficient replication in the human host. These in vitro studies confirmed the roles of the E627K substitution in basic polymerase 2 (PB2) and the A143T substitution in HA in pathogenicity observed in a mouse model previously. 2010 Journal of virology Abstract IV E627K;A143T 50;105 55;110 HA;PB2 127;92 129;95 19939933 Molecular determinants of adaptation of highly pathogenic avian influenza H7N7 viruses to efficient replication in the human host. With the exception of PB2 E627K, all substitutions contributing to enhanced replication of the fatal case virus in vitro were present in poultry viruses prior to transmission to the human fatal case, indicating that viruses with enhanced replication efficiency in the mammalian host can be generated in poultry. 2010 Journal of virology Abstract IV E627K 26 31 PB2 22 25 19943705 Oseltamivir resistance and the H274Y neuraminidase mutation in seasonal, pandemic and highly pathogenic influenza viruses. Fortunately, the current pandemic A(H1N1) 2009 virus, which is circulating globally, remains largely sensitive to both NAIs, although a small number of oseltamivir-resistant viruses have been isolated from patients to date, again with the H274Y mutation. 2009 Drugs Abstract IV H274Y 239 244 NAI 119 123 19943705 Oseltamivir resistance and the H274Y neuraminidase mutation in seasonal, pandemic and highly pathogenic influenza viruses. Recently, however, significant levels of oseltamivir-resistant influenza A(H1) seasonal influenza viruses have also been encountered, which has been associated with a single amino acid change in the viral neuraminidase (H274Y). 2009 Drugs Abstract IV H274Y 220 225 205 218 19946717 Readaptation of a low-virulence influenza H9 escape mutant in mice: the role of changes in hemagglutinin as revealed by site-specific mutagenesis. In our earlier studies, we showed that an escape mutant of mouse-adapted H9N2 influenza virus carrying a T198N amino acid change in heamagglutinin (HA) has a lowered virulence for mice. 2010 Archives of virology Abstract IV T198N 105 110 HA 148 150 19946717 Readaptation of a low-virulence influenza H9 escape mutant in mice: the role of changes in hemagglutinin as revealed by site-specific mutagenesis. The readaptation of this mutant to mice was associated with N198S or N198D reverse mutations. 2010 Archives of virology Abstract IV N198S;N198D 60;69 65;74 19958488 Prediction of avian influenza A binding preference to human receptor using conformational analysis of receptor bound to hemagglutinin. RESULTS: Molecular dynamics simulation was employed to study the interactions between receptor models and hemagglutinin proteins from H5N1 strains A/Duck/Singapore/3/97, mutated A/Duck/Singapore/3/97 (Q222L, G224S, Q222L/G224S), A/Thailand/1(KAN-1)/2004, and mutated A/Thailand/1(KAN-1)/2004 (L129V/A134V). 2009 BMC genomics Abstract IV Q222L;G224S;Q222L;G224S;L129V;A134V 201;208;215;221;293;299 206;213;220;226;298;304 HA 106 119 19962344 Emergence of H274Y oseltamivir-resistant A(H1N1) influenza viruses in Japan during the 2008-2009 season. All oseltamivir-resistant viruses from the 2008-2009 season possessed an A193T substitution in the receptor-binding domain of the hemagglutinin. 2010 Journal of clinical virology Abstract IV A193T 73 78 HA 130 143 19962344 Emergence of H274Y oseltamivir-resistant A(H1N1) influenza viruses in Japan during the 2008-2009 season. CONCLUSIONS: A dramatic surge in oseltamivir-resistant A(H1N1) viruses possessing the NA-H274Y substitution was detected in Japan during the 2008-2009 season. 2010 Journal of clinical virology Abstract IV H274Y 89 94 86 88 19962344 Emergence of H274Y oseltamivir-resistant A(H1N1) influenza viruses in Japan during the 2008-2009 season. Oseltamivir resistance was determined by an H274Y-specific real-time PCR cycling probe assay and a neuraminidase inhibition assay. 2010 Journal of clinical virology Abstract IV H274Y 44 49 99 112 19962344 Emergence of H274Y oseltamivir-resistant A(H1N1) influenza viruses in Japan during the 2008-2009 season. RESULTS: Three of 687 (0.4%) A(H1N1) viruses from the 2007-2008 season and 745 of 745 (100%) viruses from the 2008-2009 season carried the NA-H274Y substitution and demonstrated a >300-fold reduction in oseltamivir susceptibility. 2010 Journal of clinical virology Abstract IV H274Y 142 147 139 141 19995550 X-ray structures of NS1 effector domain mutants. Here we present crystallographic structures of two mutant effector domains, W187Y and W187A, of influenza A/Udorn/72 virus. 2010 Archives of biochemistry and biophysics Abstract IV W187A;W187Y 86;76 91;81 19995550 X-ray structures of NS1 effector domain mutants. The W187Y mutant is able to bind CPSF30 with a binding affinity close to the wild-type protein; that is, it retains a receptor site for aromatic ligands nearly identical to the wild-type. 2010 Archives of biochemistry and biophysics Abstract IV W187Y 4 9 20028826 Detection of molecular markers of drug resistance in 2009 pandemic influenza A (H1N1) viruses by pyrosequencing. We provide a protocol which allows the detection of adamantane resistance markers as well as the I43T change, which is unique to the H1N1pdm M2 protein. 2010 Antimicrobial agents and chemotherapy Abstract IV I43T 97 101 M2 141 143 20028826 Detection of molecular markers of drug resistance in 2009 pandemic influenza A (H1N1) viruses by pyrosequencing. We report on the detection of the first cases of the oseltamivir resistance-conferring mutation H275Y and the I223V change in viruses from the United States using the approach described in this study. 2010 Antimicrobial agents and chemotherapy Abstract IV H275Y;I223V 96;110 101;115 20047917 Laninamivir prodrug CS-8958, a long-acting neuraminidase inhibitor, shows superior anti-influenza virus activity after a single administration. CS-8958 also significantly reduced the titers of an oseltamivir-resistant H1N1 virus with a neuraminidase H274Y substitution in a mouse infection model. 2010 Antimicrobial agents and chemotherapy Abstract IV H274Y 106 111 92 105 20053748 Prophylactic administration of bacterially derived immunomodulators improves the outcome of influenza virus infection in a murine model. Analysis performed 4 days postinfection indicated that prophylactic treatments with CT, LT(R192G), or CpG resulted in significantly increased numbers of CD4 T cells, B cells, and dendritic cells and altered costimulatory marker expression in the airways of infected mice, coinciding with reduced expression of pulmonary chemokines and the appearance of inducible bronchus-associated lymphoid tissue-like structures in the lungs. 2010 Journal of virology Abstract IV R192G 91 96 20053748 Prophylactic administration of bacterially derived immunomodulators improves the outcome of influenza virus infection in a murine model. BALB/c mice were treated nasally with either cholera toxin (CT), a mutant form of the CT-related Escherichia coli heat-labile enterotoxin designated LT(R192G), or CpG oligodeoxynucleotide. 2010 Journal of virology Abstract IV R192G 152 157 20053748 Prophylactic administration of bacterially derived immunomodulators improves the outcome of influenza virus infection in a murine model. Collectively, these results suggest that, despite different immunomodulatory mechanisms, CT, LT(R192G), and CpG induce an initial inflammatory process and enhance the immune response to primary influenza virus challenge while preventing potentially damaging chemokine expression. 2010 Journal of virology Abstract IV R192G 96 101 20053748 Prophylactic administration of bacterially derived immunomodulators improves the outcome of influenza virus infection in a murine model. Treatment with the three immunomodulators prevented or delayed mortality and weight loss, but only CT and LT(R192G) significantly reduced initial lung viral loads as measured by plaque assay. 2010 Journal of virology Abstract IV R192G 109 114 20104769 [An analysis on genetic characterization of HA1 gene of influenza virus subtype H3N2 circulated from 2001 to 2006 in Liaoning local area]. Compared with WHO 2004-2006 H3N2 vaccine A/California/7/2004, 12 bases had changed, 4 positions had amino acid substitution in 62 * > E, 182 T > 1,224 S > A,225 C > Y. 2009 Zhonghua shi yan he lin chuang bing du xue za zhi Abstract IV S224A;C225Y 147;157 156;166 20129961 Genetic makeup of amantadine-resistant and oseltamivir-resistant human influenza A/H1N1 viruses. Phylogenetic analysis revealed that the oseltamivir-resistant strain evolved from a reassortant oseltamivir-susceptible strain (clade 2B) which circulated in the 2007-2008 season by acquiring the H275Y resistance-conferring mutation in the NA gene. 2010 Journal of clinical microbiology Abstract IV H275Y 196 201 240 242 20129961 Genetic makeup of amantadine-resistant and oseltamivir-resistant human influenza A/H1N1 viruses. Therefore, a reassortment event involving two distinct oseltamivir-susceptible lineages, followed by the H275Y substitution in the NA gene and other mutations elsewhere in the genome, contributed to the emergence of the oseltamivir-resistant lineage. 2010 Journal of clinical microbiology Abstract IV H275Y 105 110 131 133 20130063 Introduction of virulence markers in PB2 of pandemic swine-origin influenza virus does not result in enhanced virulence or transmission. Here, using reverse genetics, mutations E627K, D701N, and E677G were introduced into the prototype S-OIV A/Netherlands/602/2009, and their effects on virus replication, virulence, and transmission were investigated. 2010 Journal of virology Abstract IV E627K;D701N;E677G 40;47;58 45;52;63 20130063 Introduction of virulence markers in PB2 of pandemic swine-origin influenza virus does not result in enhanced virulence or transmission. Mutations E627K and D701N caused increased reporter gene expression driven by the S-OIV polymerase complex. 2010 Journal of virology Abstract IV E627K;D701N 10;20 15;25 20130063 Introduction of virulence markers in PB2 of pandemic swine-origin influenza virus does not result in enhanced virulence or transmission. Mutations E627K and D701N in the PB2 protein have previously been identified as determinants of avian and pandemic influenza virus virulence in mammals. 2010 Journal of virology Abstract IV E627K;D701N 10;20 15;25 PB2 33 36 2014635 Mutants and revertants of an avian influenza A virus with temperature-sensitive defects in the nucleoprotein and PB2. This ts defect is due to a single amino acid replacement (R162K) in a completely conserved region of the NP. 1991 Virology Abstract IV R162K 58 63 NP 105 107 20181685 Novel inhibitors of influenza virus fusion: structure-activity relationship and interaction with the viral hemagglutinin. 4c-resistant virus mutants, selected in MDCK cells, contained either a single D112N change in the HA2 subunit of the viral HA or a combination of three substitutions, i.e., R220S (in HA1) and E57K (in HA2) and an A-T substitution at position 43 or 96 of HA2. 2010 Journal of virology Abstract IV D112N;R220S;E57K 78;173;192 83;178;196 HA;HA;HA;HA;HA1 98;123;201;254;183 100;125;203;256;186 20181685 Novel inhibitors of influenza virus fusion: structure-activity relationship and interaction with the viral hemagglutinin. In polykaryon assays with cells expressing single-mutant HA proteins, the E57K, A96T, and D112N mutations resulted in 4c resistance, and the HA proteins containing R220S, A96T, and D112N mutations displayed an increased fusion pH. 2010 Journal of virology Abstract IV E57K;A96T;D112N;R220S;A96T;D112N 74;80;90;164;171;181 78;84;95;169;175;186 HA;HA 57;141 59;143 20181699 PB1-F2 expression by the 2009 pandemic H1N1 influenza virus has minimal impact on virulence in animal models. We have addressed this question by generating two Cal/09 viruses with productive PB1-F2 open reading frames containing either an asparagine at position 66 of PB1-F2 (66N) or a serine at position 66 (66S): this N66S change has previously been shown to be associated with increased virulence in mice. 2010 Journal of virology Abstract IV N66S 210 214 PB1F2;PB1F2 81;158 87;164 20181719 PB2 residue 271 plays a key role in enhanced polymerase activity of influenza A viruses in mammalian host cells. We characterized the activity of avian polymerase complexes containing avian-to-human mutations at these conserved PB2 residues and found that, in addition to the E627K mutation, the PB2 mutation T271A enhances polymerase activity in human cells. 2010 Journal of virology Abstract IV E627K;T271A 163;196 168;201 PB2;PB2 115;183 118;186 20181719 PB2 residue 271 plays a key role in enhanced polymerase activity of influenza A viruses in mammalian host cells. We confirmed the effects of the T271A mutation using recombinant WSN viruses containing avian NP and polymerase genes with wild-type (WT) or mutant PB2. 2010 Journal of virology Abstract IV T271A 32 37 NP;PB2 94;148 96;151 20188682 Rapid generation of a well-matched vaccine seed from a modern influenza A virus primary isolate without recourse to eggs. The L194P mutation was also spontaneously selected during egg propagation of E611/PR8 7:1 recombinant virus. 2010 Vaccine Abstract IV L194P 4 9 20188682 Rapid generation of a well-matched vaccine seed from a modern influenza A virus primary isolate without recourse to eggs. We engineered mutations that affected receptor-binding, G186V or L194P, into the E611 HA gene. 2010 Vaccine Abstract IV G186V;L194P 56;65 61;70 HA 86 88 20188682 Rapid generation of a well-matched vaccine seed from a modern influenza A virus primary isolate without recourse to eggs. Whilst the L194P mutation conferred efficient growth in eggs, G186V did not. 2010 Vaccine Abstract IV L194P;G186V 11;62 16;67 20195900 Shift in oligosaccharide specificities of hemagglutinin and neuraminidase of influenza B viruses resistant to neuraminidase inhibitors. The oligosaccharide specificity of two pairs of field influenza B viruses, namely: i) B/Memphis/20/96 and its NAI-resistant variant, B/Memphis/20-152K/96, containing mutation R152K in the NA and 5 amino acid substitutions in the HA1, and ii) B/Hong Kong/45/2005 and its NAI-resistant variant B/Hong Kong/36/2005, containing a single R371K mutation in the NA, was evaluated. 2010 Glycoconjugate journal Abstract IV R152K;R371K 175;333 180;338 HA1;NA;NA;NAI;NAI 229;188;355;110;270 232;190;357;113;273 20228833 Effects of NS1 variants of H5N1 influenza virus on interferon induction, TNFalpha response and p53 activity. A five-amino-acid (5 aa) deletion at position 80-84 and an aspartic acid to glutamic acid substitution at position 92 (D92E) are two major NS1 mutations that are highly correlated with enhanced virulence. 2010 Cellular & molecular immunology Abstract IV D92E;D92E 119;59 123;117 NS1 139 142 20228833 Effects of NS1 variants of H5N1 influenza virus on interferon induction, TNFalpha response and p53 activity. To investigate the effect of these mutations in H5N1 virulence, three H5N1-NS1 variants were constructed: NS51 (lacking 5 aa at position 80-84), NS51(I) (carrying a 5-aa insertion at position 80-84) and NS51(IM) (carrying both the 5-aa insertion and the D92E mutation). 2010 Cellular & molecular immunology Abstract IV D92E 254 258 NS;NS;NS;NS1 106;145;203;75 108;147;205;78 20228833 Effects of NS1 variants of H5N1 influenza virus on interferon induction, TNFalpha response and p53 activity. We found that the D92E mutation eliminated NS1's repressive effect on IFN induction, while the 5-aa deletion resulted in enhanced resistance to TNFalpha responses. 2010 Cellular & molecular immunology Abstract IV D92E 18 22 NS1 43 46 20237225 Mutations in the NS1 C-terminal tail do not enhance replication or virulence of the 2009 pandemic H1N1 influenza A virus. Adaptation in pigs has led to several changes in the multifunctional viral NS1 protein as compared with the parental 1918 virus, most notably a K217E substitution that abolishes binding to host Crk/CrkL signalling adapters, and an 11 aa C-terminal truncation. 2010 The Journal of general virology Abstract IV K217E 144 149 NS1 75 78 2026879 The 45 pocket of HLA-A2.1 plays a role in presentation of influenza virus matrix peptide and alloantigens. These mutants were transfected into HMy2.C1R cells and assessed for their ability to present influenza virus matrix M1 57-68 peptide and HTLV-I Tax-1 2-25 peptide to HLA-A2.1-restricted, peptide-specific CTL and to present alloantigens to HLA-A2-allospecific CTL lines. 1991 Journal of immunology (Baltimore, Md. Abstract IV C1R 41 44 M1;M 116;109 118;115 2026879 The 45 pocket of HLA-A2.1 plays a role in presentation of influenza virus matrix peptide and alloantigens. Thus, three single amino acid mutants were produced: 24A----S, 45 M----T, and 67V----S. 1991 Journal of immunology (Baltimore, Md. Abstract IV M45T 63 72 20303563 Substitution of lysine at 627 position in PB2 protein does not change virulence of the 2009 pandemic H1N1 virus in mice. To explore the potential role of E627K substitution in PB2 in the pandemic (H1N1) 2009 virus, we compared pathogenicity and growth properties between a recombinant virus containing 627K PB2 gene and the parental A/California/4/2009 strain containing 627E. 2010 Virology Abstract IV E627K 33 38 PB2;PB2 55;186 58;189 20335065 Oseltamivir-induced resistant pandemic A/H1N1 influenza virus in a child with cystic fibrosis and Pseudomonas aeruginosa infection. Infection due to pandemic virus with the H275Y mutation can be associated with a severe clinical course, supporting the systematic monitoring of antiviral susceptibility in pandemic influenza-positive high-risk patients whose influenza is not resolved by oseltamivir treatment. 2010 Journal of clinical virology Abstract IV H275Y 41 46 2033664 Single amino acid substitutions in the hemagglutinin can alter the host range and receptor binding properties of H1 strains of influenza A virus. Those with the mutant phenotype are unchanged at residue 129 but have a Gly to Glu substitution at residue 158, which is close to residue 129 on the HA1 subunit. 1991 Journal of virology Abstract IV G158E 72 110 HA1 149 152 2033664 Single amino acid substitutions in the hemagglutinin can alter the host range and receptor binding properties of H1 strains of influenza A virus. We have previously characterized an influenza A (H1N1) virus which has host-dependent growth and receptor binding properties and have shown that a mutation which removes an oligosaccharide from the tip of the hemagglutinin (HA) by changing Asn-129 to Asp permits this virus to grow to high titer in MDBK cells, (C. 1991 Journal of virology Abstract IV N129D 240 254 HA;HA 224;209 226;222 20336728 Development and implementation of influenza a virus subtyping and detection of genotypic resistance to neuraminidase inhibitors. In the course of implementing the method, two H1N1 isolates with the H274Y mutation in the neuraminidase segment have been detected and their molecular features analyzed. 2010 Journal of medical virology Abstract IV H274Y 69 74 91 104 20367331 Quasispecies of the D225G substitution in the hemagglutinin of pandemic influenza A(H1N1) 2009 virus from patients with severe disease in Hong Kong, China. D225G quasispecies were identified mainly in endotracheal aspirate samples and were identified less frequently in nasopharyngeal aspirate samples from patients with severe disease. 2010 The Journal of infectious diseases Abstract IV D225G 0 5 20367331 Quasispecies of the D225G substitution in the hemagglutinin of pandemic influenza A(H1N1) 2009 virus from patients with severe disease in Hong Kong, China. Direct analysis of polymorphisms in 126 amino acids spanning the receptor-binding site in the hemagglutinin of pandemic H1N1 2009 virus from 117 clinical specimens in Hong Kong found the D225G substitution for 7 (12.5%) of 57 patients with severe disease and for 0 (0%) of 60 patients with mild disease. 2010 The Journal of infectious diseases Abstract IV D225G 187 192 HA 94 107 20367331 Quasispecies of the D225G substitution in the hemagglutinin of pandemic influenza A(H1N1) 2009 virus from patients with severe disease in Hong Kong, China. The D225G (aspartic acid to glycine) substitution in the hemagglutinin of H1N1 influenza virus may alter its receptor-binding specificity. 2010 The Journal of infectious diseases Abstract IV D225G 4 9 HA 57 70 20381552 Challenge and polymorphism analysis of the novel A (H1N1) influenza virus to normal animals. Genome sequence alignment results showed that there was one genetic variation (G408T) in the HA gene of Brandt's vole derived virus and another one (C194A) in the NA gene of BALB/c mice derived virus, and the virulence of these two viruses in MDCK and A549 cells was significantly lower than the virus originally derived from human beings. 2010 Virus research Abstract IV G408T;C194A 79;149 84;154 HA;NA 93;163 95;165 20385168 Detection of the rapid emergence of the H275Y mutation associated with oseltamivir resistance in severe pandemic influenza virus A/H1N1 09 infections. From 25 patients who had been treated with oseltamivir and remained A/H1N1 09 RT-PCR positive, we identified three (12%) individuals with the H275Y mutation: one immuno-suppressed adult, one immuno-competent adult and one child. 2010 Antiviral research Abstract IV H275Y 142 147 20385168 Detection of the rapid emergence of the H275Y mutation associated with oseltamivir resistance in severe pandemic influenza virus A/H1N1 09 infections. Most isolates of the new A/H1N1 09 virus are susceptible to neuraminidase inhibitors, but the H275Y mutation in the neuraminidase gene region associated with high-level oseltamivir resistance has been detected. 2010 Antiviral research Abstract IV H275Y 94 99 NA;NA 60;116 73;129 20385168 Detection of the rapid emergence of the H275Y mutation associated with oseltamivir resistance in severe pandemic influenza virus A/H1N1 09 infections. RCA demonstrates the rapid emergence of the H275Y resistance mutation in individuals with severe A/H1N1 09 infection receiving neuraminidase inhibitors. 2010 Antiviral research Abstract IV H275Y 44 49 127 140 Influenza A virus H1N1 infection 90 116 20385168 Detection of the rapid emergence of the H275Y mutation associated with oseltamivir resistance in severe pandemic influenza virus A/H1N1 09 infections. Using rolling circle amplification (RCA) technology, 96 A/H1N1 09-specific RT-PCR positive clinical samples collected from 80 oseltamivir-treated and untreated patients were screened for the presence of the H275Y mutation. 2010 Antiviral research Abstract IV H275Y 207 212 20447860 First case in Italy of acquired resistance to oseltamivir in an immunocompromised patient with influenza A/H1N1v infection. A pandemic influenza A/H1N1v strain with the neuraminidase H274Y mutation was detected in nasal secretions of a 2-year-old leukemic patient with influenza-like illness after 18 days of treatment with oseltamivir. 2010 Journal of clinical virology Abstract IV H274Y 59 64 45 58 Leukemia 123 131 20459681 Oseltamivir-resistant pandemic (H1N1)2009 in Yemen - case report. Both clinical specimens presented the mutation S31N in the M2 gene associated with resistance to adamantanes and H274Y in NA gene associated with resistance to oseltamivir. 2010 Virology journal Abstract IV S31N;H274Y 47;113 51;118 M2;NA 59;122 61;124 20463064 Functional analysis of the influenza virus H5N1 nucleoprotein tail loop reveals amino acids that are crucial for oligomerization and ribonucleoprotein activities. Although the R267A variant existed as a monomer in vitro, it resumed an oligomeric form upon the addition of RNA and retained a certain degree of RNP activity. 2010 Journal of virology Abstract IV R267A 13 18 RNP 146 149 20463064 Functional analysis of the influenza virus H5N1 nucleoprotein tail loop reveals amino acids that are crucial for oligomerization and ribonucleoprotein activities. Here, by an RNP reconstitution assay, we identified eight NP mutants that had different degrees of defects in forming functional RNPs, with the RNP activities of four mutants being totally abolished (E339A, V408S P410S, R416A, and L418S P419S mutants) and the RNP activities of the other four mutants being more than 50% decreased (R267A, I406S, R422A, and E449A mutants). 2010 Journal of virology Abstract IV V408S;P410S;L418S;P419S;E339A;R416A;R267A;I406S;R422A;E449A 207;213;231;237;200;220;332;339;346;357 212;218;236;242;205;225;337;344;351;362 NP;RNP;RNP;RNP;RNP 58;12;144;260;129 60;15;147;263;133 20463064 Functional analysis of the influenza virus H5N1 nucleoprotein tail loop reveals amino acids that are crucial for oligomerization and ribonucleoprotein activities. The I406S, R422A, and E449A variants existed as a mixture of unstable oligomers, thus resulting in a reduction of RNP activity. 2010 Journal of virology Abstract IV I406S;R422A;E449A 4;11;22 9;16;27 RNP 114 117 20498316 In vitro system for modeling influenza A virus resistance under drug pressure. Sequencing of the M2 gene revealed that mutations appeared at between 48 and 72 h of drug treatment and that the mutations were identical to those identified in the clinic for amantadine-resistant viruses (e.g., V27A, A30T, and S31N). 2010 Antimicrobial agents and chemotherapy Abstract IV V27A;A30T;S31N 212;218;228 216;222;232 M2 18 20 20499646 [Detection of molecular markers of amantadine resistance in swine influenza viruses by pyrosequencing]. RESULTS: All 5 H1N1 swine influenza viruses were adamantine resistance, three mutations were founded in these isolates, namely V27T, V27I and S31N. 2010 Wei sheng wu xue bao Abstract IV V27T;V27I;S31N 127;133;142 131;137;146 20513088 Antiviral drug susceptibilities of seasonal human influenza viruses in Lebanon, 2008-09 season. All the H3N2 viruses were resistant to amantadine but were sensitive to oseltamivir and zanamivir; while all the H1N1 viruses were resistant to oseltamivir (possessed H275Y mutation, N1 numbering, in their NA) but were sensitive to amantadine and zanamivir. 2010 Journal of medical virology Abstract IV H275Y 167 172 206 208 20517627 Molecular dynamics simulation of oseltamivir resistance in neuraminidase of avian influenza H5N1 virus. In addition, there are fewer hydrogen bonds between the oseltamivir and H252Y mutation NA. 2011 Journal of molecular modeling Abstract IV H252Y 72 77 87 89 20517627 Molecular dynamics simulation of oseltamivir resistance in neuraminidase of avian influenza H5N1 virus. tau2 and tau3 torsional angles fluctuation of the oseltamivir are relatively high for the H252Y mutant NA complex. 2011 Journal of molecular modeling Abstract IV H252Y 90 95 103 105 20517627 Molecular dynamics simulation of oseltamivir resistance in neuraminidase of avian influenza H5N1 virus. The carboxylate of Glu276 of H252Y NA faces toward the O-ethyl-propyl group of oseltamivir, Glu276 of wild-type NA adopts a conformation pointing away from the oseltamivir. 2011 Journal of molecular modeling Abstract IV H252Y 29 34 NA;NA 35;112 37;114 20517627 Molecular dynamics simulation of oseltamivir resistance in neuraminidase of avian influenza H5N1 virus. The results show that H252Y mutation NA has high resistance against the drug. 2011 Journal of molecular modeling Abstract IV H252Y 22 27 37 39 20521695 Identification of a dominant epitope in the hemagglutinin of an Asian highly pathogenic avian influenza H5N1 clade 1 virus by selection of escape mutants. An additional substitution K29E in HA2 subunit was also observed and identified with the use of NetChop software as a loss of a proteasomal cleavage site, which seems to be an advantage for H5N1 viruses. 2010 Avian diseases Abstract IV K29E 27 31 HA 35 37 20521695 Identification of a dominant epitope in the hemagglutinin of an Asian highly pathogenic avian influenza H5N1 clade 1 virus by selection of escape mutants. We could detect an amino acid change in our escape mutants at position K189E corresponding to antigenic site 2 of H5 HA1 and site B of H3 HA1. 2010 Avian diseases Abstract IV K189E 71 76 HA1;HA1 117;138 120;141 20521699 Adaptation and transmission of a wild duck avian influenza isolate in chickens. Two consistent amino acid substitutions in the hemagglutinin have been identified, A198V and S274F, and may be important in transmissibility. 2010 Avian diseases Abstract IV A198V;S274F 83;93 88;98 HA 47 60 20521806 How does influenza virus a escape from amantadine? Failure of channel blocking would cause AMT drug resistance in the S31N mutant. 2010 The journal of physical chemistry. B Abstract IV S31N 67 71 20521806 How does influenza virus a escape from amantadine? Mutation experiments indicate that the trans-membrane domain of M2 protein plays an essential role in AMT resistance, especially the S31N mutation. 2010 The journal of physical chemistry. B Abstract IV S31N 133 137 M2 64 66 20521806 How does influenza virus a escape from amantadine? To investigate the details of structure and mechanism, molecular dynamics (MD) simulations and quantum mechanics/molecular mechanics (QM/MM) calculations have been carried out on both the wild-type protein and its S31N mutant. 2010 The journal of physical chemistry. B Abstract IV S31N 214 218 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. However, H5N1 viruses carrying the E119A or the N294S NA mutation were lethal to 1 of 3 inoculated animals and were associated with significantly higher virus titers (P<0.01) and inflammation in the lungs compared to the wild-type virus. 2010 PLoS pathogens Abstract IV E119A;N294S 35;48 40;53 54 56 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. Importantly, the E119A NA mutation (previously reported to confer resistance in the N2 NA subtype) was stable in the clade 2.2 H5N1 virus background and induced cross-resistance to oseltamivir carboxylate and zanamivir. 2010 PLoS pathogens Abstract IV E119A 17 22 NA;NA 23;87 25;89 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. We demonstrated that Y252H NA mutation contributed for decreased susceptibility of clade 2.2 H5N1 viruses to oseltamivir carboxylate as compared to clade 1 viruses. 2010 PLoS pathogens Abstract IV Y252H 21 26 27 29 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. We generated seven genetically stable recombinant clade 2.2 A/Turkey/15/06-like (H5N1) influenza viruses carrying NA mutations located either in the framework residues (E119A, H274Y, N294S) or in close proximity to the NA enzyme active site (V116A, I117V, K150N, Y252H). 2010 PLoS pathogens Abstract IV E119A;H274Y;N294S;V116A;I117V;K150N;Y252H 169;176;183;242;249;256;263 174;181;188;247;254;261;268 NA;NA 114;219 116;221 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. However, the latest surveillance data suggests emergence of a new prominent mutation, E391K, in the hemagglutinin (HA) that is globally on the rise. 2010 PLoS currents Abstract IV E391K 86 91 HA;HA 115;100 117;113 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. We discuss occurrence of HA-E391K in global surveillance data and associated clinical phenotypes from Singapore ranging from mostly mild to few severe symptoms, including sporadic vaccine failure. 2010 PLoS currents Abstract IV E391K 28 33 HA 25 27 20554779 Modifications to the hemagglutinin cleavage site control the virulence of a neurotropic H1N1 influenza virus. In this study we have identified an additional mutation in the P2 position of the WSN HA cleavage site (S328Y) that appears to control virus spread in a plasmin-dependent manner. 2010 Journal of virology Abstract IV S328Y 104 109 HA 86 88 20573832 Tyrosines in the influenza A virus M2 protein cytoplasmic tail are critical for production of infectious virus particles. Recombinant viruses encoding M2 with the Y76A mutation demonstrated replication defects in MDCK cells as well as in primary differentiated airway epithelial cell cultures, defects in the formation of filamentous virus particles, and reduced packaging of nucleoprotein into virus particles. 2010 Journal of virology Abstract IV Y76A 41 45 M2;NP 29;254 31;267 20573832 Tyrosines in the influenza A virus M2 protein cytoplasmic tail are critical for production of infectious virus particles. These defects could all be overcome by a mutation of serine to tyrosine at position 71 of the M2 cytoplasmic tail, which emerged after blind passage of viruses containing the Y76A mutation. 2010 Journal of virology Abstract IV Y76A;S71Y 175;53 179;86 M2 94 96 20591072 Increasing antiviral activity of surfactant protein d trimers by introducing residues from bovine serum collectins: dissociation of mannan-binding and antiviral activity. We now show, however, that combined mutants containing the RAK insertion and R343V or R343I substitutions have greatly increased mannan-binding ability, but lower IAV binding or inhibiting activity than mutants containing R343V or R343I substitutions only. 2010 Scandinavian journal of immunology Abstract IV R343V;R343I;R343V;R343I 77;86;222;231 82;91;227;236 20601494 Monoclonal antibody-assisted structure-function analysis of the carbohydrate recognition domain of surfactant protein D. Conversely, the interspecies substitution of arginine for Lys343 in the rat NCRD (rK343R) conferred binding to two of the mAbs. 2010 American journal of physiology. Lung cellular and molecular physiology Abstract IV K343R 45 64 20601494 Monoclonal antibody-assisted structure-function analysis of the carbohydrate recognition domain of surfactant protein D. Mutations at Glu333 (E333A), Trp340 (W340F), and Phe335 (F335A), which abrogated antiviral activity, were associated with decreased binding to multiple blocking mAbs, consistent with critical structural roles. 2010 American journal of physiology. Lung cellular and molecular physiology Abstract IV E333A;W340F;F335A 21;37;57 26;42;62 20602265 In silico characterization of the functional and structural modules of the hemagglutinin protein from the swine-origin influenza virus A (H1N1)-2009. The D225G/E mutation in HA, which is found in some isolates, may confer dual binding specificity to the 2,3- and 2,6-receptor based on previously reported work. 2010 Science China. Life sciences Abstract IV D225G;D225E 4;4 11;11 HA 24 26 20608076 [Detection of amino acid substitutions of asparaginic acid for glycine and asparagine at the receptor-binding site of hemagglutinin in the variants of pandemic influenza A/H1N1 virus from patients with fatal outcome and moderate form of the disease]. In one patient with the moderate form of the disease, D222G mutation was revealed after the second passage in the developing chick embryos; this mutation was not found in the primary sample from the patient. 2010 Voprosy virusologii Abstract IV D222G 54 59 20608076 [Detection of amino acid substitutions of asparaginic acid for glycine and asparagine at the receptor-binding site of hemagglutinin in the variants of pandemic influenza A/H1N1 virus from patients with fatal outcome and moderate form of the disease]. This site exhibited mutations in 9 samples: D222G (n=3), D222N (n=3), and D222G/D222N (n=3). 2010 Voprosy virusologii Abstract IV D222G;D222N;D222N;D222G;D222N 44;57;80;74;74 49;62;85;79;79 20631125 Evidence for avian and human host cell factors that affect the activity of influenza virus polymerase. Finally, our results strongly suggest that the well-known adaptative mutation E627K on viral protein PB2 facilitates the ability of a human positive factor to enhance replication of influenza virus in human cells. 2010 Journal of virology Abstract IV E627K 78 83 PB2 101 104 20631138 Assessing the viral fitness of oseltamivir-resistant influenza viruses in ferrets, using a competitive-mixtures model. Coinfection of ferrets with mixtures of an oseltamivir-resistant R292K mutant A(H3N2) virus and a R292 oseltamivir-susceptible wild-type virus demonstrated that the R292K mutant virus was rapidly outgrown by the R292 wild-type virus in artificially infected donor ferrets and did not transmit to any of the recipient ferrets. 2010 Journal of virology Abstract IV R292K;R292K 65;165 70;170 20631138 Assessing the viral fitness of oseltamivir-resistant influenza viruses in ferrets, using a competitive-mixtures model. The competitive-mixtures model was also used to investigate the fitness of the seasonal A(H1N1) oseltamivir-resistant H274Y mutant and showed that within infected ferrets the H274Y mutant virus was marginally outgrown by the wild-type strain but demonstrated equivalent transmissibility between ferrets. 2010 Journal of virology Abstract IV H274Y;H274Y 118;175 123;180 20643947 Coexistence of two adamantane binding sites in the influenza A M2 ion channel. Furthermore, by examining drug binding to M2 mutant constructs (V27A, S31N, and D44A), it was possible to probe the location of the two binding sites. 2010 Proc Natl Acad Sci U S A Abstract IV V27A;D44A;S31N 64;80;70 68;84;74 M2 42 44 20657062 Epidemiological, demographic, and molecular characteristics of laboratory-confirmed pandemic influenza A (H1N1) virus infection in Turkey, May 15-November 30, 2009. More than 37% of the isolates had mutation at position D222E/N on HA gene. 2010 Japanese journal of infectious diseases Abstract IV D222E;D222N 55;55 62;62 HA 66 68 20657062 Epidemiological, demographic, and molecular characteristics of laboratory-confirmed pandemic influenza A (H1N1) virus infection in Turkey, May 15-November 30, 2009. There was no isolate harbored mutation at the position H275Y of the NA gene, indicating that the virus isolates currently circulating in Turkey are sensitive to oseltamivir. 2010 Japanese journal of infectious diseases Abstract IV H275Y 55 60 68 70 20660186 Antiviral susceptibility of avian and swine influenza virus of the N1 neuraminidase subtype. In particular, V267I, N307D, and V321I residue changes were found, and structural analyses suggest that these mutations distort hydrophobic pockets and affect residues in the NA active site. 2010 Journal of virology Abstract IV V267I;N307D;V321I 15;22;33 20;27;38 175 177 20660186 Antiviral susceptibility of avian and swine influenza virus of the N1 neuraminidase subtype. Sequence analysis of the outliers did not detect molecular markers of drug-resistance (e.g., H275Y NA mutation [N1 numbering]) but revealed mutations outside the NA active site. 2010 Journal of virology Abstract IV H275Y 93 98 NA;NA 99;162 101;164 20660199 Differential localization and function of PB1-F2 derived from different strains of influenza A virus. Introducing Leu into positions 69 (Q69L) and 75 (H75L) in the C terminus of H5N1 PB1-F2 drove 40.7% of the protein to localize to mitochondria compared with the level of mitochondrial localization of wild-type H5N1 PB1-F2, suggesting that a Leu-rich sequence in the C terminus is important for targeting of mitochondria. 2010 Journal of virology Abstract IV Q69L;H75L 35;49 39;53 PB1F2;PB1F2 81;215 87;221 20661429 Oseltamivir-resistant pandemic A/H1N1 virus is as virulent as its wild-type counterpart in mice and ferrets. A more important perivascular (day 6) and pleural (days 6 and 12) inflammation was noted in the lungs of mice infected with the H274Y mutant, which correlated with increased pulmonary levels of IL-6 and KC. 2010 PLoS pathogens Abstract IV H274Y 128 133 20661429 Oseltamivir-resistant pandemic A/H1N1 virus is as virulent as its wild-type counterpart in mice and ferrets. Furthermore, the H274Y mutant strain was transmitted to ferrets. 2010 PLoS pathogens Abstract IV H274Y 17 22 20661429 Oseltamivir-resistant pandemic A/H1N1 virus is as virulent as its wild-type counterpart in mice and ferrets. In conclusion, viral fitness of the H274Y pH1N1 isolate is not substantially altered and has the potential to induce severe disease and to disseminate. 2010 PLoS pathogens Abstract IV H274Y 36 41 20661429 Oseltamivir-resistant pandemic A/H1N1 virus is as virulent as its wild-type counterpart in mice and ferrets. We describe the characteristics of a pair of oseltamivir-resistant and oseltamivir-susceptible pH1N1 clinical isolates that differed by a single change (H274Y) in the neuraminidase protein. 2010 PLoS pathogens Abstract IV H274Y 153 158 167 180 20667110 Isolation of mixed subtypes of influenza A virus from a bald eagle (Haliaeetus leucocephalus). Further analysis revealed that the PB1-F2 gene sequence of H1N1 virus had the N66S virulence-associated substitution. 2010 Virology journal Abstract IV N66S 78 82 PB1F2 35 41 20668122 Highly sensitive and quantitative detection of the H274Y oseltamivir resistance mutation in seasonal A/H1N1 influenza virus. A C-to-T transition mutation in the neuraminidase gene from seasonal A/H1N1 causes a His-to-Tyr mutation at amino acid position 275 (H274Y, universal N2 numbering), conferring resistance against oseltamivir (Tamiflu). 2010 Journal of clinical microbiology Abstract IV H274Y 133 138 36 49 20668122 Highly sensitive and quantitative detection of the H274Y oseltamivir resistance mutation in seasonal A/H1N1 influenza virus. In samples with mixed populations, it can reliably detect as little as a 1% wild-type or 0.1% H274Y component. 2010 Journal of clinical microbiology Abstract IV H274Y 94 99 20668122 Highly sensitive and quantitative detection of the H274Y oseltamivir resistance mutation in seasonal A/H1N1 influenza virus. Optimization of primers and assay conditions produced a limit of detection of 100 gene copies per reaction for both wild-type and H274Y genotypes. 2010 Journal of clinical microbiology Abstract IV H274Y 130 135 20668122 Highly sensitive and quantitative detection of the H274Y oseltamivir resistance mutation in seasonal A/H1N1 influenza virus. The H274Y mutation was only found in samples from the 2007-2008 season. 2010 Journal of clinical microbiology Abstract IV H274Y 4 9 20668122 Highly sensitive and quantitative detection of the H274Y oseltamivir resistance mutation in seasonal A/H1N1 influenza virus. We developed a highly sensitive and specific quantitative real-time reverse transcriptase PCR assay to detect the H274Y mutation. 2010 Journal of clinical microbiology Abstract IV H274Y 114 119 20686654 Oseltamivir-resistant pandemic H1N1/2009 influenza virus possesses lower transmissibility and fitness in ferrets. The resistant H275Y mutant was derived from a patient on oseltamivir prophylaxis and was the first oseltamivir-resistant isolate of the pandemic virus. 2010 PLoS pathogens Abstract IV H275Y 14 19 20697920 Outbreak of influenza virus A/H1N1 in a hospital ward for immunocompromised patients. Sequencing of the amplified (HA1) haemagglutinin yielded identical nucleotide sequences in isolates from three of the patients, whereas one nucleotide difference was found in the isolate of the fourth patient, resulting in an amino acid substitution (G153R). 2010 Archives of virology Abstract IV G153R 251 256 HA1;HA 29;34 32;48 20702632 PB2 and hemagglutinin mutations are major determinants of host range and virulence in mouse-adapted influenza A virus. In this study, we demonstrate that MA mutations of the PB2 (D701N) and hemagglutinin (HA) (G218W in HA1 and T156N in HA2) genes were the most adaptive genetic determinants for increased growth and virulence in the mouse model. 2010 Journal of virology Abstract IV D701N;G218W;T156N 60;91;108 65;96;113 HA;HA;HA1;HA;PB2 86;117;100;71;55 88;119;103;84;58 20702632 PB2 and hemagglutinin mutations are major determinants of host range and virulence in mouse-adapted influenza A virus. Minigenome transcription assays showed that PB1 and PB2 mutations increased polymerase activity and that the PB2 D701N mutation was comparable in effect to the mammalian adaptive PB2 E627K mutation. 2010 Journal of virology Abstract IV D701N;E627K 113;183 118;188 PB1;PB2;PB2;PB2 44;52;109;179 47;55;112;182 20708697 Immunogenicity and protective efficacy of an elastase-dependent live attenuated swine influenza virus vaccine administered intranasally in pigs. Here we evaluated the immunogenicity and the protective efficacy of R345V against SIV infection by intranasal administration, the more practical route for vaccination of pigs in the field. 2010 Vaccine Abstract IV R345V 68 73 20708697 Immunogenicity and protective efficacy of an elastase-dependent live attenuated swine influenza virus vaccine administered intranasally in pigs. Intranasal vaccination of R345V provided pigs with complete protection not only from parental wild type virus infection, but also from homologous antigenic variant A/Sw/Indiana/1726/88 (H1N1) infection. 2010 Vaccine Abstract IV R345V 26 31 20708697 Immunogenicity and protective efficacy of an elastase-dependent live attenuated swine influenza virus vaccine administered intranasally in pigs. Moreover, intranasal administration of R345V conferred partial protection from heterologous subtypic H3N2 SIV infection in pigs. 2010 Vaccine Abstract IV R345V 39 44 20708697 Immunogenicity and protective efficacy of an elastase-dependent live attenuated swine influenza virus vaccine administered intranasally in pigs. Our data showed that intranasally administered R345V live vaccine is capable of inducing strong antigen-specific IFN-gamma response from local tracheo-bronchial lymphocytes and antibody responses in serum and respiratory mucosa after two applications. 2010 Vaccine Abstract IV R345V 47 52 20708697 Immunogenicity and protective efficacy of an elastase-dependent live attenuated swine influenza virus vaccine administered intranasally in pigs. Previously we reported that an elastase-dependent mutant SIV A/Sw/Sk-R345V (R345V) derived from A/Sw/Saskatchewan/18789/02 (H1N1) (SIV/Sk02) is highly attenuated in pigs. 2010 Vaccine Abstract IV R345V;R345V 69;76 74;81 20708697 Immunogenicity and protective efficacy of an elastase-dependent live attenuated swine influenza virus vaccine administered intranasally in pigs. Thus, R345V elastase-dependent mutant SIV can serve as a live vaccine against antigenically different swine influenza viruses in pigs. 2010 Vaccine Abstract IV R345V 6 11 20708697 Immunogenicity and protective efficacy of an elastase-dependent live attenuated swine influenza virus vaccine administered intranasally in pigs. Two intratracheal administrations of R345V induced strong cell-mediated and humoral immune responses and provided a high degree of protection to antigenically different SIV infection in pigs. 2010 Vaccine Abstract IV R345V 37 42 20738882 Clinical importance and impact on the households of oseltamivir-resistant seasonal A/H1N1 influenza virus in healthy children in Italy. Among the A/H1N1 subtypes, the H275Y mutation was found in 2/126 samples taken in 2007-2008 (1.6%) and in all 17 samples (100%; p < 0.0001) taken in 2008-2009. 2010 Virology journal Abstract IV H275Y 31 36 20738882 Clinical importance and impact on the households of oseltamivir-resistant seasonal A/H1N1 influenza virus in healthy children in Italy. The influenza A virus-positive samples underwent neuraminidase gene analysis using pyrosequencing to identify mutations H275Y and N294 S in A/H1N1, and E119V, R292K, and N294 S in A/H3N2. 2010 Virology journal Abstract IV H275Y;N294S;E119V;R292K;N294S 120;130;152;159;170 125;136;157;164;176 49 62 20738882 Clinical importance and impact on the households of oseltamivir-resistant seasonal A/H1N1 influenza virus in healthy children in Italy. The spread of H275Y-mutated A/H1N1 seasonal influenza virus is a common phenomenon and the clinical importance and impact on the households of the mutated virus is similar to that of the wild-type in an otherwise healthy pediatric population. 2010 Virology journal Abstract IV H275Y 14 19 20739532 Oseltamivir-resistant variants of the 2009 pandemic H1N1 influenza A virus are not attenuated in the guinea pig and ferret transmission models. In vitro, the virus readily acquired a single histidine-to-tyrosine mutation at position 275 (H275Y) in viral neuraminidase when serially passaged in cell culture with increasing concentrations of oseltamivir. 2010 Journal of virology Abstract IV H275Y;H275Y 94;46 99;92 110 123 20739532 Oseltamivir-resistant variants of the 2009 pandemic H1N1 influenza A virus are not attenuated in the guinea pig and ferret transmission models. Unexpectedly, in guinea pigs and ferrets, the fitness of viruses with the H275Y point mutation was not detectably impaired, and both wild-type and mutant viruses were transmitted equally well from animals that were initially inoculated with 1:1 virus mixtures to naive contacts. 2010 Journal of virology Abstract IV H275Y 74 79 2077784 The critical cut-off temperature of avian influenza viruses. This results in a substitution of isoleucine for leucine at amino acid position 512 in the cap-binding protein, PB2. 1990 Virus research Abstract IV L512I 34 83 PB2 112 115 20816700 Amantadine resistance in relation to the evolution of influenza A(H3N2) viruses in Iran. We observed an increase in amantadine resistance, due to a Ser31Asn mutation in the M2 channel protein, among A(H3N2) viruses circulating in Iran during 2005-2007. 2010 Antiviral research Abstract IV S31N 59 67 M2 84 86 20826688 Altered receptor specificity and cell tropism of D222G hemagglutinin mutants isolated from fatal cases of pandemic A(H1N1) 2009 influenza virus. An Asp222Gly (D222G) substitution has been associated with severe or fatal disease. 2010 Journal of virology Abstract IV D222G;D222G 3;14 12;19 20833142 Solution NMR structure of the V27A drug resistant mutant of influenza A M2 channel. Furthermore, due to the high quality NMR data recorded for the V27A mutant, we were able to determine the structured region connecting the channel domain to the C-terminal amphipathic helices that was not determined in the wildtype structure. 2010 Biochemical and biophysical research communications Abstract IV V27A 63 67 20833142 Solution NMR structure of the V27A drug resistant mutant of influenza A M2 channel. Here, we report the solution NMR structure of the highly pathogenic, drug resistant mutant V27A. 2010 Biochemical and biophysical research communications Abstract IV V27A 91 95 20833142 Solution NMR structure of the V27A drug resistant mutant of influenza A M2 channel. Moreover, the V27A structure shows a substantially increased channel opening at the N-terminal end, which may explain the faster proton conduction observed for this mutant. 2010 Biochemical and biophysical research communications Abstract IV V27A 14 18 20833142 Solution NMR structure of the V27A drug resistant mutant of influenza A M2 channel. The V27A mutation significantly decreases hydrophobic packing between the N-terminal ends of the transmembrane helices, which explains the looser, more dynamic tetrameric assembly. 2010 Biochemical and biophysical research communications Abstract IV V27A 4 8 20836794 Oseltamivir-resistant influenza A 2009 H1N1 virus in immunocompromised patients. Four patient specimens (2.1%) were found to carry the H275Y mutation. 2010 Influenza and other respiratory viruses Abstract IV H275Y 54 59 20836794 Oseltamivir-resistant influenza A 2009 H1N1 virus in immunocompromised patients. PyroMark Q24 AQ software (Qiagen, Valencia, CA, USA) was used to allow for quantitative H275Y mutation analysis. 2010 Influenza and other respiratory viruses Abstract IV H275Y 88 93 20836794 Oseltamivir-resistant influenza A 2009 H1N1 virus in immunocompromised patients. Resistance conferred by the H275Y neuraminidase gene mutation is concerning and likely to increase. 2010 Influenza and other respiratory viruses Abstract IV H275Y 28 33 34 47 20836794 Oseltamivir-resistant influenza A 2009 H1N1 virus in immunocompromised patients. RT-PCR and pyrosequencing were used to test for the H275Y mutation (CDC protocol). 2010 Influenza and other respiratory viruses Abstract IV H275Y 52 57 20845746 [Drug-resistant influenza viruses: an overview]. Between 2007 and early 2009, the prevalence of oseltamivir-resistant seasonal H1N1 variants that possess the His274Tyr neuraminidase mutation had dramatically increased, raising concerns regarding the utility of oseltamivir. 2010 Nihon rinsho. Japanese journal of clinical medicine Abstract IV H274Y 109 118 119 132 20852117 Expression analyses and antiviral properties of the Beijing-You and White Leghorn myxovirus resistance gene with different amino acids at position 631. We provide the first report examining the expression level and antiviral activity of different Mx alleles of nucleotide 2216(S631N) genotypes. 2010 Poultry science Abstract IV S631N 125 130 20861597 Treatment options for H5N1: lessons learned from the H1N1 pandemic. Compassionate use of intravenous zanamivir for the treatment of seriously ill patients, including those with H275Y H1N1 infections, has also shown promising results. 2010 Postgraduate medicine Abstract IV H275Y 109 114 Influenza A virus H1N1 infection 115 130 20861597 Treatment options for H5N1: lessons learned from the H1N1 pandemic. Zanamivir is a potent inhibitor of H5N1, attains high lung concentrations immediately on administration, distributes into plasma at antiviral concentrations, has a low propensity for generating resistant virus, and retains activity against H275Y oseltamivir-resistant virus. 2010 Postgraduate medicine Abstract IV H275Y 240 245 20863862 Redundancy of the influenza A virus-specific cytotoxic T lymphocyte response in HLA-B*2705 transgenic mice limits the impact of a mutation in the immunodominant NP(383-391) epitope on influenza pathogenesis. During the 1993-1994 flu season, influenza A/H3N2 viruses emerged with an amino acid substitution (R384G) at the anchor residue of the HLA-B*2705 restricted NP(383-391) epitope located in the nucleoprotein (NP). 2011 Virus research Abstract IV R384G 99 104 NP;NP;NP 157;207;192 159;209;205 20863862 Redundancy of the influenza A virus-specific cytotoxic T lymphocyte response in HLA-B*2705 transgenic mice limits the impact of a mutation in the immunodominant NP(383-391) epitope on influenza pathogenesis. The R384G substitution reached fixation rapidly and abrogated recognition of A/H3N2 viruses by NP(383-391)-specific CD8+ T cytotoxic T lymphocytes (CTL) completely. 2011 Virus research Abstract IV R384G 4 9 NP 95 97 20863862 Redundancy of the influenza A virus-specific cytotoxic T lymphocyte response in HLA-B*2705 transgenic mice limits the impact of a mutation in the immunodominant NP(383-391) epitope on influenza pathogenesis. To test the impact of the R384G substitution in the immunodominant NP(383-391) epitope in vivo, influenza A viruses that differ at position 384 of the NP only were generated by reverse genetics. 2011 Virus research Abstract IV R384G 26 31 NP;NP 67;151 69;153 20881092 Amino acids adjacent to the haemagglutinin cleavage site are relevant for virulence of avian influenza viruses of subtype H5. However, chickens infected with R65-V survived longer than R65-infected animals, indicating that serine 346 in R65 HA contributes to virulence. 2011 The Journal of general virology Abstract IV R65V 32 37 HA 115 117 20881092 Amino acids adjacent to the haemagglutinin cleavage site are relevant for virulence of avian influenza viruses of subtype H5. Moreover, in the R65 HA, serine was replaced with valine at position 346 (R65-V). 2011 The Journal of general virology Abstract IV S346V;R65V 25;74 72;79 HA 21 23 20881092 Amino acids adjacent to the haemagglutinin cleavage site are relevant for virulence of avian influenza viruses of subtype H5. This study generated a virus mutant derived from HPAIV A/Swan/Germany/R65/06 H5N1 (R65) with a monobasic cleavage site, R65(mono)-S-ER, and the following additional mutants: R65(mono)-V-ER with serine changed to valine at position 346, and R65(mono)-S-ETR and R65(mono)-V-ETR with threonine inserted at position 351. 2011 The Journal of general virology Abstract IV S346V 194 234 2088485 The kinetics of peptide binding to HLA-A2 and the conformation of the peptide-A2 complex can be determined by amino acid side chains on the floor of the peptide binding groove. HLA-A2 molecules with naturally occurring single amino acid substitutions of Phe to Tyr at position 9 (HLA-A2.4a, Tyr9) and Tyr to Cys at position 99 (HLA-A2.4b, Cys99) and a site directed mutant with a Val to Leu substitution at position 95 (Leu95) were examined for their ability to present the influenza virus matrix M1 55-73 peptide and several sequence variants of the M1 peptide to a panel of 36 M1 55-73-specific HLA-A2.1-restricted CTL lines. 1990 International immunology Abstract IV F9Y;Y99C;V95L 77;124;203 101;149;241 M1;M1;M1;M 320;374;402;313 322;376;404;319 20886705 [A possible association of fatal pneumonia with mutations of pandemic influenza A/H1N1 sw1 virus in the receptor-binding site of the HA1 subunit]. 70% of the primary materials from the deceased patients were found to have pandemic influenza A(H1N1) v mutants in the lung tissue with D222G (15%), D222N (15%), D222E (2%) substitutions, as well as a mixture of mutants (38%). 2010 Voprosy virusologii Abstract IV D222G;D222N;D222E 136;149;162 141;154;167 20886705 [A possible association of fatal pneumonia with mutations of pandemic influenza A/H1N1 sw1 virus in the receptor-binding site of the HA1 subunit]. Preliminary data from the study of the interaction of the hemagglutinin of two strains having D222G and D222N mutations with 9 oligosaccharides imitating the variants of cell receptors for influenza A virus suggest that there is a double receptor specificity for alpha2'-3' and alpha2'-6'-sialosides with a preponderance of alpha2'-3'-specificity. 2010 Voprosy virusologii Abstract IV D222G;D222N 94;104 99;109 HA 58 71 20920297 Characterization of an H3N2 triple reassortant influenza virus with a mutation at the receptor binding domain (D190A) that occurred upon virus transmission from turkeys to pigs. Here, we characterized an H3N2 triple reassortant (TR) influenza virus (A/turkey/Ohio/313053/04) with a mutation at the receptor binding domain (Asp190Ala) that occurred upon virus transmission from turkeys to pigs in an experimental infection study. 2010 Virology journal Abstract IV D190A 145 154 20926573 Glycine 184 in nonstructural protein NS1 determines the virulence of influenza A virus strain PR8 without affecting the host interferon response. Surprisingly, if CPSF binding was abolished by substituting glycine for arginine at position 184 in the classical NS1-CPSF binding motif, the mutant virus replicated much more slowly in mice, although the mutated NS1 protein continued to repress the IFN response very efficiently. 2010 Journal of virology Abstract IV R184G 60 96 NS1;NS1 114;213 117;216 20931251 Phylogenetic analysis of pandemic 2009 influenza A virus circulating in the South American region: genetic relationships and vaccine strain match. Amino acid substitutions P100S, S220T and I338V were found in almost all HAs of South American H1N1pdm strains. 2011 Archives of virology Abstract IV P100S;S220T;I338V 25;32;42 30;37;47 20934538 Increased prevalence of a rare mutant of pandemic H1N1 influenza virus in a Eurasian region. All the 101 S128P mutants belonged to Clade 7 which has become dominant worldwide since the summer of 2009. 2011 Infection, genetics and evolution Abstract IV S128P 12 17 20934538 Increased prevalence of a rare mutant of pandemic H1N1 influenza virus in a Eurasian region. Among the 3492 viruses, 101 carried a serine to proline substitution at position 128 (S128P) in the viral HA gene. 2011 Infection, genetics and evolution Abstract IV S128P;S128P 86;38 91;84 HA 106 108 20934538 Increased prevalence of a rare mutant of pandemic H1N1 influenza virus in a Eurasian region. Among the 3492 viruses, 1646 were collected before July 25, 2009, and none of these viruses carried the S128P mutation. 2011 Infection, genetics and evolution Abstract IV S128P 104 109 20934538 Increased prevalence of a rare mutant of pandemic H1N1 influenza virus in a Eurasian region. Furthermore, after July 25, 2009, the prevalence of the S128P mutant was 33.56% (99/295) in a region of Eurasia including Russia, Mongolia, mainland China and South Korea, but only 0.11% (2/1846) in the rest of the world. 2011 Infection, genetics and evolution Abstract IV S128P 56 61 20934538 Increased prevalence of a rare mutant of pandemic H1N1 influenza virus in a Eurasian region. The data suggested that the originally rare S128P mutant has become prevalent in the Eurasia region, indicating that the S128P mutant likely transmitted more efficiently than other strains of the virus. 2011 Infection, genetics and evolution Abstract IV S128P;S128P 44;121 49;126 20934538 Increased prevalence of a rare mutant of pandemic H1N1 influenza virus in a Eurasian region. Therefore, it is of significance to observe whether the S128P mutant will be more dominant worldwide in the coming future and investigate the exact effects of the S128P mutation. 2011 Infection, genetics and evolution Abstract IV S128P;S128P 56;163 61;168 20962098 PB2 residue 158 is a pathogenic determinant of pandemic H1N1 and H5 influenza a viruses in mice. Collectively, the data presented in this study demonstrate that PB2-E158G is a novel pathogenic determinant of influenza A viruses in the mouse model. 2011 Journal of virology Abstract IV E158G 68 73 PB2 64 67 20962098 PB2 residue 158 is a pathogenic determinant of pandemic H1N1 and H5 influenza a viruses in mice. Our data also show that PB2-E158G had a much stronger influence on the RNA replication and pathogenesis of H1N1pdm viruses than PB2-E627K, which is a known pathogenic determinant. 2011 Journal of virology Abstract IV E158G;E627K 28;132 33;137 PB2;PB2 24;128 27;131 20962098 PB2 residue 158 is a pathogenic determinant of pandemic H1N1 and H5 influenza a viruses in mice. Remarkably, PB2-E158G substitutions also altered the pathotypes of two avian H5 viruses in mice, indicating that this residue impacts genetically divergent influenza A viruses and suggesting that this region of PB2 could be a new antiviral target. 2011 Journal of virology Abstract IV E158G 16 21 PB2;PB2 12;211 15;214 20962098 PB2 residue 158 is a pathogenic determinant of pandemic H1N1 and H5 influenza a viruses in mice. Results from mini-genome replication assays in human cells and virus titration in mouse tissues demonstrated that PB2-E158G is a pathogenic determinant, because it significantly increases viral replication rates. 2011 Journal of virology Abstract IV E158G 118 123 PB2 114 117 20962098 PB2 residue 158 is a pathogenic determinant of pandemic H1N1 and H5 influenza a viruses in mice. The virus load in PB2-E158G-infected mouse lungs was 1,300-fold higher than that of the wild-type virus. 2011 Journal of virology Abstract IV E158G 22 27 PB2 18 21 20962098 PB2 residue 158 is a pathogenic determinant of pandemic H1N1 and H5 influenza a viruses in mice. We found that a glutamate-to-glycine substitution at residue 158 of the PB2 gene (PB2-E158G) increased the morbidity and mortality of the parental H1N1pdm virus. 2011 Journal of virology Abstract IV E158G;E158G 86;16 91;64 PB2;PB2 72;82 75;85 20962098 PB2 residue 158 is a pathogenic determinant of pandemic H1N1 and H5 influenza a viruses in mice. We speculate that PB2-E158G may be important in the adaptation of avian PB2 genes to other mammals, and BLAST sequence analysis identified a naturally occurring human H1N1pdm isolate that has this substitution. 2011 Journal of virology Abstract IV E158G 22 27 PB2;PB2 18;72 21;75 20970464 Structure-based design of NS2 mutants for attenuated influenza A virus vaccines. We found that simultaneous mutations at three positions (E67S/E74S/E75S) of NS2/NEP were important for inhibition of influenza viral polymerase activity, although the W78S mutant and other glutamate mutants with single substitutions were not. 2011 Virus research Abstract IV E67S;E74S;E75S;W78S 57;62;67;167 61;66;71;171 NEP;NS2 80;76 83;79 20979914 [Impact of avian influenza virus H5N1 neuraminidase mutations on the activity of neuraminidase and the sensibility to neuraminidase inhibitors]. CONCLUSION: It appears that the NA mutations of I117V and I314V can not cause NAIs resistance. 2010 Zhonghua yi xue za zhi Abstract IV I117V;I314V 48;58 53;63 NA;NAI 32;78 34;82 20979914 [Impact of avian influenza virus H5N1 neuraminidase mutations on the activity of neuraminidase and the sensibility to neuraminidase inhibitors]. OBJECTIVE: To study the impact of avian influenza virus H5N1 neuraminidase mutations I117V, I314V and I117V + I314V on the sensibility of neuraminidase inhibitors (NAIs) and the activity of neuraminidase (NA). 2010 Zhonghua yi xue za zhi Abstract IV I117V;I314V;I117V;I314V 85;92;102;110 90;97;107;115 NA;NAI;NA;NA;NA 205;164;61;138;190 207;168;74;151;203 20979914 [Impact of avian influenza virus H5N1 neuraminidase mutations on the activity of neuraminidase and the sensibility to neuraminidase inhibitors]. RESULTS: Compared to the wild-type virus VN1203, the mutation I117V decreased the susceptibility to oseltamivir (17-fold increment of IC(50) value, 20-fold increment of Ki value) and the NA activity (23-fold increment of Km value) while there was little impact on zanamivir sensitivity (2-fold increment of IC(50) value, 3-fold increment of Ki value). 2010 Zhonghua yi xue za zhi Abstract IV I117V 62 67 187 189 20979914 [Impact of avian influenza virus H5N1 neuraminidase mutations on the activity of neuraminidase and the sensibility to neuraminidase inhibitors]. The mutation I314V had no marked influence on either the NA activity or the NAIs susceptibility. 2010 Zhonghua yi xue za zhi Abstract IV I314V 13 18 NA;NAI 57;76 59;80 21047959 Genetic and phylogenetic analyses of influenza A H1N1pdm virus in Buenos Aires, Argentina. The N-4 fragment as well as the hierarchical clustering of samples showed that a consensus sequence prevailed in time but also that different variants, including five H275Y oseltamivir-resistant strains, arose from May to August 2009. 2011 Journal of virology Abstract IV H275Y 167 172 21048522 Oseltamivir-resistant influenza A and B viruses pre- and postantiviral therapy in children and young adults with cancer. One patient was infected with oseltamivir-resistant influenza B virus (IC50, 731.86 +- 155.12 nM) that harbored a N294S NA mutation, the first report of this mutation in influenza B viruses. 2011 The Pediatric infectious disease journal Abstract IV N294S 114 119 120 122 21048522 Oseltamivir-resistant influenza A and B viruses pre- and postantiviral therapy in children and young adults with cancer. Three resistant influenza A (H3N2) viruses shared a common E119V NA mutation. 2011 The Pediatric infectious disease journal Abstract IV E119V 59 64 65 67 21070812 Genotypic and phenotypic resistance of pandemic A/H1N1 influenza viruses circulating in Germany. Eight (0.5%) viruses were resistant to oseltamivir due to the H274Y NA substitution (N2 numbering). 2011 Antiviral research Abstract IV H274Y 62 67 68 70 21070812 Genotypic and phenotypic resistance of pandemic A/H1N1 influenza viruses circulating in Germany. In addition, analysis of 1011 pandemic A/H1N1 virus samples by a PSQ-based assay according to the WHO protocol revealed the presence of mutation S31N in the M2 protein that conferred resistance to M2 ion channel inhibitors. 2011 Antiviral research Abstract IV S31N 145 149 M2;M2 157;197 159;199 21084483 A single N66S mutation in the PB1-F2 protein of influenza A virus increases virulence by inhibiting the early interferon response in vivo. Of note, an N66S amino acid mutation in PB1-F2 has been shown to increase the pathogenesis associated with H5N1 Hong Kong/1997 and H1N1 Brevig Mission/1918 influenza viruses. 2011 Journal of virology Abstract IV N66S 12 16 PB1F2 40 46 21084483 A single N66S mutation in the PB1-F2 protein of influenza A virus increases virulence by inhibiting the early interferon response in vivo. The N66S mutant virus caused increased cellularity in the lungs, as a result of monocyte and neutrophil infiltration. 2011 Journal of virology Abstract IV N66S 4 8 21084483 A single N66S mutation in the PB1-F2 protein of influenza A virus increases virulence by inhibiting the early interferon response in vivo. These data suggest that PB1-F2 N66S may contribute to the delay of innate immune responses, allowing for unchecked viral growth and ultimately severe immunopathology observed in the lungs. 2011 Journal of virology Abstract IV N66S 31 35 PB1F2 24 30 21106781 The I222V neuraminidase mutation has a compensatory role in replication of an oseltamivir-resistant influenza virus A/H3N2 E119V mutant. Based on plaque size, yield assays, and NA activity, the impaired viral fitness of the E119V mutant was partially restored by the I222V NA mutation. 2011 Journal of clinical microbiology Abstract IV E119V;I222V 87;130 92;135 NA;NA 40;136 42;138 21106781 The I222V neuraminidase mutation has a compensatory role in replication of an oseltamivir-resistant influenza virus A/H3N2 E119V mutant. Oseltamivir-resistant A/H3N2 influenza isolates with or without the E119V and I222V neuraminidase (NA) mutations were recovered from an immunocompromised patient. 2011 Journal of clinical microbiology Abstract IV E119V;I222V 68;78 73;83 NA;NA 99;84 101;97 21116343 Does pandemic A/H1N1 virus have the potential to become more pathogenic? These adapted pandemic strains did, however, contain two nonsynonymous mutations (hemagglutinin K154Q and polymerase acidic protein L295P) that conferred a more virulent phenotype, both in cell cultures and in ferrets, than their parental strains. 2010 mBio Abstract IV K154Q;L295P 96;132 101;137 HA;PA 82;106 95;123 21172786 Pandemic H1N1 2009 influenza virus with the H275Y oseltamivir resistance neuraminidase mutation shows a small compromise in enzyme activity and viral fitness. BACKGROUND: Resistance to the neuraminidase inhibitor oseltamivir can be conferred by a well-characterized mutation in the neuraminidase gene, H275Y. 2011 The Journal of antimicrobial chemotherapy Abstract IV H275Y 143 148 NA;NA 30;123 43;136 21172786 Pandemic H1N1 2009 influenza virus with the H275Y oseltamivir resistance neuraminidase mutation shows a small compromise in enzyme activity and viral fitness. CONCLUSIONS: The neuraminidase protein of pandemic influenza isolates tolerates the H275Y mutation and this mutation confers resistance to oseltamivir. 2011 The Journal of antimicrobial chemotherapy Abstract IV H275Y 84 89 17 30 21172786 Pandemic H1N1 2009 influenza virus with the H275Y oseltamivir resistance neuraminidase mutation shows a small compromise in enzyme activity and viral fitness. METHODS: Using reverse genetics we engineered the H275Y mutation into the neuraminidase of a 2009 pandemic H1N1 virus and assessed the ability of this enzyme to desialylate mono- and multivalent substrates. 2011 The Journal of antimicrobial chemotherapy Abstract IV H275Y 50 55 74 87 21172786 Pandemic H1N1 2009 influenza virus with the H275Y oseltamivir resistance neuraminidase mutation shows a small compromise in enzyme activity and viral fitness. RESULTS: The presence of H275Y was associated with a 1.3-fold decrease in the affinity of the neuraminidase for a monovalent substrate and a 4-fold compromise in desialylation of multivalent substrate. 2011 The Journal of antimicrobial chemotherapy Abstract IV H275Y 25 30 94 107 21172786 Pandemic H1N1 2009 influenza virus with the H275Y oseltamivir resistance neuraminidase mutation shows a small compromise in enzyme activity and viral fitness. We examined whether the H275Y mutation affected neuraminidase enzyme activity or replication of the pandemic influenza virus. 2011 The Journal of antimicrobial chemotherapy Abstract IV H275Y 24 29 48 61 21173148 Only two residues are responsible for the dramatic difference in receptor binding between swine and new pandemic H1 hemagglutinin. Modeling of the T200A and E227A substitutions into the crystal structure of the new pandemic human H1 protein revealed the loss of potential hydrogen bond formation with Gln(191), which is part of the 190-loop of the receptor binding site, and with the penultimate galactose, respectively. 2011 The Journal of biological chemistry Abstract IV T200A;E227A 16;26 21;31 21216958 Interaction of the influenza A virus polymerase PB2 C-terminal region with importin alpha isoforms provides insights into host adaptation and polymerase assembly. Two effects were observed: first, adaptive mutations D701N, R702K, and S714R in the nuclear localization signal domain increased 2-4-fold the association rates with avian and human importins; second, measurement of different structural forms of the PB2 C terminus demonstrated that the upstream 627 domain reduced binding affinity, consistent with a steric clash predicted from crystal structures. 2011 The Journal of biological chemistry Abstract IV D701N;R702K;S714R 53;60;71 58;65;76 PB2 249 252 21226922 Influenza A virus NS1 gene mutations F103L and M106I increase replication and virulence. Among eleven mutations selected in the NS1 gene, two mutations F103L and M106I had been previously detected in the highly virulent human H5N1 isolate, A/HK/156/97, suggesting a role for these mutations in virulence in mice and humans. 2011 Virology journal Abstract IV F103L;M106I 63;73 68;78 NS1 39 42 21226922 Influenza A virus NS1 gene mutations F103L and M106I increase replication and virulence. Both F103L and M106I NS1 mutations significantly enhanced growth in vitro (mouse and canine cells) and in vivo (BALB/c mouse lungs) as well as enhanced virulence in the mouse. 2011 Virology journal Abstract IV F103L;M106I 5;15 10;20 NS1 21 24 21226922 Influenza A virus NS1 gene mutations F103L and M106I increase replication and virulence. CONCLUSIONS: The F103L and M106I NS1 mutations were adaptive genetic determinants of growth and virulence in both human and avian NS1 genes in the mouse model. 2011 Virology journal Abstract IV F103L;M106I 17;27 22;32 NS1;NS1 33;130 36;133 21226922 Influenza A virus NS1 gene mutations F103L and M106I increase replication and virulence. Only the M106I NS1 mutation enhanced growth in human cells. 2011 Virology journal Abstract IV M106I 9 14 NS1 15 18 21226922 Influenza A virus NS1 gene mutations F103L and M106I increase replication and virulence. The double mutant, rPR8-HK-NS-F103L + M106I, demonstrated growth attenuation late in infection due to increased IFN-beta induction in mouse cells. 2011 Virology journal Abstract IV F103L;M106I 30;38 35;43 NS 27 29 21226922 Influenza A virus NS1 gene mutations F103L and M106I increase replication and virulence. The rWSN-A/Ck/Beijing/1/95-NS1 gene possessing 103L and 106I demonstrated 100 fold enhanced growth and >10 fold enhanced virulence that was associated with increased tropism for lung alveolar and bronchiolar tissues relative to the corresponding L103F and I106M mutant. 2011 Virology journal Abstract IV L103F;I106M 246;256 251;261 NS1 27 30 21226922 Influenza A virus NS1 gene mutations F103L and M106I increase replication and virulence. We also inserted the avian A/Ck/Beijing/1/95 NS1 gene (the source lineage of the A/HK/156/97 NS1 gene) that possesses 103L + 106I, onto the A/WSN/33 backbone and then generated the L103F + I106M mutant. 2011 Virology journal Abstract IV L103F;I106M 181;189 186;194 NS1;NS1 45;93 48;96 21226922 Influenza A virus NS1 gene mutations F103L and M106I increase replication and virulence. We then generated a rPR8 virus possessing the A/HK/156/97 NS gene that possesses 103L + 106I, and then rescued the L103F + I106M mutant. 2011 Virology journal Abstract IV L103F;I106M 115;123 120;128 NS 58 60 21249207 Nationwide molecular surveillance of pandemic H1N1 influenza A virus genomes: Canada, 2009. One virus that harboured heterozygote coding mutations, including PB2 D567D/G, was attributed to a severe and potentially mixed infection; yet the functional significance of this PB2 mutation remains unknown. 2011 PloS one Abstract IV D567D;D567G 70;70 77;77 PB2;PB2 66;179 69;182 21306576 Influenza and other respiratory viruses in three Central American countries. It also showed that the mutation H274Y conferring resistance to oseltamivir was first detected in Honduran influenza A/H1N1 strains at the beginning of 2008. 2011 Influenza and other respiratory viruses Abstract IV H274Y 33 38 21321237 Broadly neutralizing DNA vaccine with specific mutation alters the antigenicity and sugar-binding activities of influenza hemagglutinin. When we immunized mice with CHA5 harboring individual mutations, the antibodies elicited by CHA5 containing P157S elicited higher neutralizing activity against the clade 2.3 viruses. 2011 Proc Natl Acad Sci U S A Abstract IV P157S 108 113 21343450 Neuraminidase inhibitor sensitivity and receptor-binding specificity of Cambodian clade 1 highly pathogenic H5N1 influenza virus. All viruses were sensitive to both inhibitors; however, we identified a virus with a mildly decreased sensitivity to zanamivir and have predicted that a V149A mutation is responsible. 2011 Antimicrobial agents and chemotherapy Abstract IV V149A 153 158 21343450 Neuraminidase inhibitor sensitivity and receptor-binding specificity of Cambodian clade 1 highly pathogenic H5N1 influenza virus. We also identified a virus with a hemagglutinin A134V mutation, present in a subpopulation amplified directly from a human sample. 2011 Antimicrobial agents and chemotherapy Abstract IV A134V 48 53 HA 34 47 21344749 [Analyses of serological and genetic characteristics on novel H1N1 influenza A virus from the infected patient in Shenzhen]. Further, A His 275 Tyr mutation on NA protein of a virus strain was detected, which induced the oseltamivir resistance of the virus. 2010 Bing du xue bao Abstract IV H275Y 11 22 35 37 21345953 Effects of receptor binding specificity of avian influenza virus on the human innate immune response. To evaluate the role of the viral receptor specificity in promoting innate immune responses in humans, we generated recombinant influenza viruses, one bearing the HA and neuraminidase (NA) genes from the A/Vietnam/1203/2004 H5N1 HPAIV in an influenza A/Puerto Rico/8/1934 (A/PR/8/34) backbone with specificity for SAalpha2,3 and the other a mutant virus (with Q226L and G228S in the HA) with preferential receptor specificity for SAalpha2,6. 2011 Journal of virology Abstract IV Q226L;G228S 360;370 365;375 HA;HA;NA;NA 163;383;185;170 165;385;187;183 21349290 Development of a real-time RT-PCR assay for detection of resistance to oseltamivir in influenza A pandemic (H1N1) 2009 virus using single nucleotide polymorphism probes. The limit of detection was 47.6 copies/reaction for wild-type H275 RNA and 52.9 copies/reaction for the mutant H275Y RNA. 2011 Journal of virological methods Abstract IV H275Y 111 116 21351517 [Establishment of a cell-based 2009 H1N1 influenza neuraminidase inhibitors evaluation system]. A point mutation of H275Y on NA leads oseltamivir-resistance. 2010 Yao xue xue bao Abstract IV H275Y 20 25 29 31 21352864 Palmitoylation of CM2 is dispensable to influenza C virus replication. Furthermore, membrane flotation analysis of the infected cells revealed that equal amount of viral proteins was recovered in the plasma membrane fractions of the rCM2-C65A-infected cells to that in the parental virus-infected cells. 2011 Virus research Abstract IV C65A 167 171 21352864 Palmitoylation of CM2 is dispensable to influenza C virus replication. In the present study, using reverse genetics we generated rCM2-C65A, a recombinant influenza C virus lacking CM2 palmitoylation site, in which cysteine at residue 65 of CM2 was mutated to alanine, and examined viral growth and viral protein synthesis in the recombinant-infected cells. 2011 Virus research Abstract IV C65A 63 67 CM2;CM2 109;169 112;172 21352864 Palmitoylation of CM2 is dispensable to influenza C virus replication. The rCM2-C65A virus grew as efficiently as did the parental virus in cultured HMV-II cells as well as in embryonated chicken eggs. 2011 Virus research Abstract IV C65A 9 13 21352864 Palmitoylation of CM2 is dispensable to influenza C virus replication. The synthesis and biochemical features of HEF, NP, M1 and mutant CM2 in the rCM2-C65A-infected HMV-II cells were similar to those in the parental virus-infected cells. 2011 Virus research Abstract IV C65A 81 85 CM2;M1;NP 65;51;47 68;53;49 21364825 Identification of sequence mutations affecting hemagglutinin specificity to sialic acid receptor in influenza A virus subtypes. Based on our results, we suggest two possible mutation patterns, namely (1) positions 190 and 225 from glutamic acid and glycine to aspartic acid (E190D in A/Brevig Mission/1/18 (H1N1), A/New York/1/18(H1N1) and A/South Carolina/1/1918(H1N1) and G225D in A/South Carolina/1/1918(H1N1), A/South Carolina/1/1918(H1N1), and A/Puerto Rico/8/34(H1N1)), and (2) positions 226 and 228 from glutamine and glycine to leucine and serine, respectively (Q226L and G228S in A/Guiyang/1/1957(H2N2), A/Kayano/57(H2N2), A/Aichi/2/1968(H3N2), A/Hong Kong/1/1968(H3N2) and A/Memphis/1/68(H3N2)) that can potentially contribute to the specificity of hemagglutinin to Sia(alpha2-6)Gal, thereby enabling the replication and transmission of virus within and among humans. 2010 Bioinformation Abstract IV E190D;G225D;Q226L;G228S 147;246;442;452 152;251;447;457 HA 631 644 21367898 Effect of an asparagine-to-serine mutation at position 294 in neuraminidase on the pathogenicity of highly pathogenic H5N1 influenza A virus. Although NA N294S-possessing H5N1 viruses were attenuated in mice and ferrets compared to their oseltamivir-sensitive counterparts, one of the infected ferrets died from systemic infection, demonstrating the potential lethality in ferrets of oseltamivir-resistant H5N1 viruses with the NA N294S substitution. 2011 Journal of virology Abstract IV N294S;N294S 12;289 28;294 NA;NA 9;286 11;288 21367898 Effect of an asparagine-to-serine mutation at position 294 in neuraminidase on the pathogenicity of highly pathogenic H5N1 influenza A virus. Here, we assessed the effect of the NA N294S substitution on the replication and pathogenicity of human H5N1 viruses and on the efficacy of the NA inhibitors oseltamivir and zanamivir in mouse and ferret models. 2011 Journal of virology Abstract IV N294S 39 44 NA;NA 36;144 38;146 21367898 Effect of an asparagine-to-serine mutation at position 294 in neuraminidase on the pathogenicity of highly pathogenic H5N1 influenza A virus. However, unlike viruses with the NA H274Y mutation, the properties of viruses possessing NA N294S are not well understood. 2011 Journal of virology Abstract IV H274Y;N294S 36;92 41;97 NA;NA 33;89 35;91 21367898 Effect of an asparagine-to-serine mutation at position 294 in neuraminidase on the pathogenicity of highly pathogenic H5N1 influenza A virus. Like the histidine-to-tyrosine substitution at position 274 in neuraminidase (NA H274Y), an asparagine-to-serine mutation at position 294 in this protein (NA N294S) confers oseltamivir resistance to highly pathogenic H5N1 influenza A viruses. 2011 Journal of virology Abstract IV H274Y;H274Y;N294S;N294S 9;81;92;158 59;86;137;163 NA;NA;NA 78;155;63 80;157;76 21367898 Effect of an asparagine-to-serine mutation at position 294 in neuraminidase on the pathogenicity of highly pathogenic H5N1 influenza A virus. The efficacy of oseltamivir, but not that of zanamivir, against an NA N294S-possessing virus was substantially impaired both in ferrets and in vitro. 2011 Journal of virology Abstract IV N294S 70 86 67 69 21367898 Effect of an asparagine-to-serine mutation at position 294 in neuraminidase on the pathogenicity of highly pathogenic H5N1 influenza A virus. These results demonstrate the considerable pathogenicity of NA N294S substitution-possessing H5N1 viruses and underscore the importance of monitoring the emergence of the NA N294S mutation in circulating H5N1 viruses. 2011 Journal of virology Abstract IV N294S;N294S 63;174 68;179 NA;NA 60;171 62;173 21367983 PB1-mediated virulence attenuation of H5N1 influenza virus in mice is associated with PB2. Furthermore, the PB1 (T677M) mutation showed a lower replication efficiency, although it had higher polymerase activity. 2011 The Journal of general virology Abstract IV T677M 22 27 PB1 17 20 21367983 PB1-mediated virulence attenuation of H5N1 influenza virus in mice is associated with PB2. In order to assess their effects on pathogenicity in mice, two amino acid changes common to attenuated isolates, one in PB2 (I63T) and the other in PB1 (T677M), were inserted into a wild-type recombinant virus construct. 2011 The Journal of general virology Abstract IV I63T;T677M 125;153 129;158 PB1;PB2 148;120 151;123 21367983 PB1-mediated virulence attenuation of H5N1 influenza virus in mice is associated with PB2. The PB2 (I63T) or PB1 (T677M) mutations alone did not alter the phenotype of H5N1 virus, whereas recombinant virus with both mutations was less pathogenic than the wild-type recombinant virus. 2011 The Journal of general virology Abstract IV I63T;T677M 9;23 13;28 PB1;PB2 18;4 21;7 21406268 Mutations affecting the stability of the haemagglutinin molecule impair the immunogenicity of live attenuated H3N2 intranasal influenza vaccine candidates lacking NS1. Passages of these viruses on Vero cells led to the appearance of single mutations in the HA(1) L194P or HA(2) G75R subunits that impaired virus stability. 2011 Vaccine Abstract IV L194P;G75R 95;110 100;114 HA;HA 104;89 106;93 21407805 A single base-pair change in 2009 H1N1 hemagglutinin increases human receptor affinity and leads to efficient airborne viral transmission in ferrets. Here we report that a single point mutation (Ile219 Lys; a base pair change) in the glycan receptor-binding site (RBS) of a representative 2009 H1N1 influenza A virus, A/California/04/09 or CA04/09, quantitatively increases its human receptor-binding affinity. 2011 PloS one Abstract IV I219K 45 55 21419468 Receptor specificity of the influenza virus hemagglutinin modulates sensitivity to soluble collectins of the innate immune system and virulence in mice. Moreover, infection of mice with viruses bearing the S186I substitution led to severe disease, characterized by enhanced virus replication, lung pathology and pulmonary edema. 2011 Virology Abstract IV S186I 53 58 21419468 Receptor specificity of the influenza virus hemagglutinin modulates sensitivity to soluble collectins of the innate immune system and virulence in mice. Sequence analysis identified a single amino acid substitution (S186I) in the vicinity of the receptor-binding site of HA. 2011 Virology Abstract IV S186I 63 68 HA 118 120 21422222 Combinatorial effect of two framework mutations (E119V and I222L) in the neuraminidase active site of H3N2 influenza virus on resistance to oseltamivir. Among the viruses produced, the E119D+I222L mutant virus was not able to grow without bacterial NA complementation and the D198N+I222L mutant and H274Y+I222L mutant were not stable after passages in MDCK cells. 2011 Antimicrobial agents and chemotherapy Abstract IV E119D;I222L;D198N;I222L;H274Y;I222L 32;38;123;129;146;152 37;43;128;134;151;157 96 98 21422222 Combinatorial effect of two framework mutations (E119V and I222L) in the neuraminidase active site of H3N2 influenza virus on resistance to oseltamivir. In MDCK-SIAT1 cells, the E119V+I222L mutant virus did not present a replicative advantage over the wild-type virus, even in the presence of oseltamivir. 2011 Antimicrobial agents and chemotherapy Abstract IV I222L;E119V 31;25 36;30 21422222 Combinatorial effect of two framework mutations (E119V and I222L) in the neuraminidase active site of H3N2 influenza virus on resistance to oseltamivir. The E119V+I222L mutant was stable after five passages in MDCK cells. 2011 Antimicrobial agents and chemotherapy Abstract IV I222L;E119V 10;4 15;9 21422222 Combinatorial effect of two framework mutations (E119V and I222L) in the neuraminidase active site of H3N2 influenza virus on resistance to oseltamivir. The total NA activity of the E119V+I222L mutant was low (5% compared to that of the wild-type virus). 2011 Antimicrobial agents and chemotherapy Abstract IV I222L;E119V 35;29 40;34 10 12 21422222 Combinatorial effect of two framework mutations (E119V and I222L) in the neuraminidase active site of H3N2 influenza virus on resistance to oseltamivir. This E119V-and-I222L combination had a combinatorial effect on oseltamivir resistance. 2011 Antimicrobial agents and chemotherapy Abstract IV I222L;E119V 15;5 20;10 21422222 Combinatorial effect of two framework mutations (E119V and I222L) in the neuraminidase active site of H3N2 influenza virus on resistance to oseltamivir. To look at the possibility of an increased effect on the resistance phenotype of a combination of framework mutations, known to confer resistance to oseltamivir or zanamivir, with limited effect on virus fitness, we constructed 4 viruses by reverse genetics in the A/Moscow/10/99 H3N2 background containing double mutations in their neuraminidase genes: E119D+I222L, E119V+I222L, D198N+I222L, and H274Y+I222L (N2 numbering). 2011 Antimicrobial agents and chemotherapy Abstract IV E119D;I222L;I222L;E119V;D198N;I222L;H274Y;I222L 354;360;373;367;380;386;397;403 359;365;378;372;385;391;402;408 333 346 21427949 [The 2009 pandemic influenza in Russia. I. Diagnosis and molecular biological characteristics of the virus]. All the test strains contain the S31N substitution in the M2 protein, which determines viral resistance to adamantine, and have no H275Y substitution in neuraminidase, which determines oseltamivir resistance. 2011 Voprosy virusologii Abstract IV S31N;H275Y 33;131 37;136 M2;NA 58;153 60;166 21427949 [The 2009 pandemic influenza in Russia. I. Diagnosis and molecular biological characteristics of the virus]. The substitution of amino acid residue of Asp to Gly at position 222 of HA was found in 8 (73%) of 11 isolates from postmortem lung and trachea samples and in 2 (10%) of 20 isolates from nasopharyngeal swabs. 2011 Voprosy virusologii Abstract IV D222G 42 68 HA 72 74 21455300 Assessing the in vitro fitness of an oseltamivir-resistant seasonal A/H1N1 influenza strain using a mathematical model. Although previous studies had demonstrated that this mutation impaired the replication capacity of the influenza virus in vitro and in vivo, the A/Brisbane/59/2007 H275Y oseltamivir-resistant mutant completely out-competed the wild-type (WT) strain and was, in the 2008-2009 influenza season, the primary A/H1N1 circulating strain. 2011 PloS one Abstract IV H275Y 164 169 21455300 Assessing the in vitro fitness of an oseltamivir-resistant seasonal A/H1N1 influenza strain using a mathematical model. In 2007, the A/Brisbane/59/2007 (H1N1) seasonal influenza virus strain acquired the oseltamivir-resistance mutation H275Y in its neuraminidase (NA) gene. 2011 PloS one Abstract IV H275Y 116 121 NA;NA 144;129 146;142 21455300 Assessing the in vitro fitness of an oseltamivir-resistant seasonal A/H1N1 influenza strain using a mathematical model. In the ST6GalI-MDCK cell line, the latent infection period (i.e., the time for a newly infected cell to start releasing virions) was found to be 1-3 h for the WT strain and more than 7 h for the H275Y mutant. 2011 PloS one Abstract IV H275Y 195 200 21455300 Assessing the in vitro fitness of an oseltamivir-resistant seasonal A/H1N1 influenza strain using a mathematical model. The infecting time (i.e., the time for a single infectious cell to cause the infection of another one) was between 30 and 80 min for the WT, and less than 5 min for the H275Y mutant. 2011 PloS one Abstract IV H275Y 169 174 21455300 Assessing the in vitro fitness of an oseltamivir-resistant seasonal A/H1N1 influenza strain using a mathematical model. These results, though preliminary, suggest that the increased fitness success of the A/Brisbane/59/2007 H275Y mutant may be due to increased infectivity compensating for an impaired or delayed viral release, and are consistent with recent evidence for the mechanistic origins of fitness reduction and recovery in NA expression. 2011 PloS one Abstract IV H275Y 104 109 313 315 21458512 Mutations in PA, NP, and HA of a pandemic (H1N1) 2009 influenza virus contribute to its adaptation to mice. Among these five substitutions, an aspartic acid-to-glutamic acid substitution at position 127 in HA contributed to efficient viral replication in mouse lungs. 2011 Virus research Abstract IV D127E 35 94 HA 98 100 21466220 Exploring the size limit of templates for inhibitors of the M2 ion channel of influenza A virus. Inhibition of the wild-type (wt) M2 channel and the A/M2-S31N and A/M2-V27A mutant ion channels were measured in Xenopus oocytes using two-electrode voltage clamp (TEV) assays. 2011 Journal of medicinal chemistry Abstract IV V27A;S31N 71;57 75;61 M2;M2;M2 33;54;68 35;56;70 21466220 Exploring the size limit of templates for inhibitors of the M2 ion channel of influenza A virus. Only the smallest analogue 8 was found to inhibit the S31N mutant ion channel. 2011 Journal of medicinal chemistry Abstract IV S31N 54 58 21504394 Oseltamivir-resistant influenza viruses get by with a little help from permissive mutations. have solved this riddle by identifying permissive NA mutations that allow viruses to tolerate H274Y. 2011 Expert review of anti-infective therapy Abstract IV H274Y 94 99 50 52 21504394 Oseltamivir-resistant influenza viruses get by with a little help from permissive mutations. However, oseltamivir-resistant H1N1 viruses rapidly spread during the 2007-2008 IAV season and these viruses contained precisely the same exact drug-resistance mutation identified years prior, a histidine to tyrosine substitution at NA residue 274 (H274Y). 2011 Expert review of anti-infective therapy Abstract IV H274Y 249 254 233 235 21504394 Oseltamivir-resistant influenza viruses get by with a little help from permissive mutations. Unlike the experimentally derived NA inhibitor-resistant viruses, 2007-2008 H1N1 viruses containing H274Y replicated efficiently. 2011 Expert review of anti-infective therapy Abstract IV H274Y 100 105 34 36 21520138 Antigenic and genetic variation in the hemagglutinins of H1N1 and H3N2 human influenza a viruses in the Shanghai area from 2005 to 2008. Antigenic differences were detected between circulating A/H1N1 strains isolated from 2005 to 2006 and the epidemic A/H1N1 strains isolated in 2008, which were found to be associated with the amino acid substitution K140E in HA1. 2011 Journal of medical virology Abstract IV K140E 215 220 HA1 224 227 21520138 Antigenic and genetic variation in the hemagglutinins of H1N1 and H3N2 human influenza a viruses in the Shanghai area from 2005 to 2008. The P194L mutation was thought to be responsible for the antigenic evolution of influenza A/H3N2 viruses isolated from Shanghai in 2008. 2011 Journal of medical virology Abstract IV P194L 4 9 21528535 [Genetic characterization of HA1 gene of influenza H3N2 virus isolates during 2008-2009 in Zhuhai, China]. The epitopes of HA1 district of H3N2 influenza strains in Zhuhai in 2009 are different from that of H3N2 influenza vaccine during the same time: K173Q and P194L occur in all of H3N2 influenza strains, N144K, K158N, and N189K occur in the strains except the strain 09-0056. 2011 Bing du xue bao Abstract IV K173Q;P194L;N144K;K158N;N189K 145;155;201;208;219 150;160;206;213;224 HA1 16 19 21528535 [Genetic characterization of HA1 gene of influenza H3N2 virus isolates during 2008-2009 in Zhuhai, China]. When compared with the amino acid sequences of the epitopes of HA1 district of H3N2 influenza vaccine recommended by WHO in 2008, changes were found in those of H3N2 influenza strains in Zhuhai in 2008: K140I in all of H3N2 influenza strains, L157S in 08-0343 and 08-0677, K158R in 08-0466, 08-0620 and 08-0667, K173E in 08-0466 and 08-0620, K173N in 08-0667, and I192T in 08-0667. 2011 Bing du xue bao Abstract IV K140I;L157S;K158R;K173E;K173N;I192T 203;243;273;312;342;364 208;248;278;317;347;369 HA1 63 66 21536025 CL-385319 inhibits H5N1 avian influenza A virus infection by blocking viral entry. Pseudoviruses with M24A mutation in HA1 or F110S mutation in HA2 were resistant to CL-385319, indicating that these two residues in the cavity region may be critical for CL-385319 bindings. 2011 European journal of pharmacology Abstract IV M24A;F110S 19;43 23;48 HA;HA1 61;36 63;39 21537996 Amino acid sequence analysis and identification of mutations in the NS gene of 2009 influenza A (H1N1) isolates from Kenya. A mutation A115T which is a characteristic of clade 5 viruses was noted in the isolates from Lagos, Nigeria. 2011 Virus genes Abstract IV A115T 11 16 21537996 Amino acid sequence analysis and identification of mutations in the NS gene of 2009 influenza A (H1N1) isolates from Kenya. Analysis of the NS1 protein showed only one fixed amino acid change I123V which is one of the characteristics of clade 7 viruses. 2011 Virus genes Abstract IV I123V 68 73 NS1 16 19 21543559 Ultrasensitive detection of drug-resistant pandemic 2009 (H1N1) influenza A virus by rare-variant-sensitive high-resolution melting-curve analysis. Although a majority of 2009 (H1N1) influenza A virus remains oseltamivir susceptible, the threat of resistance due to the His275Tyr mutation is highlighted by the limitations of alternative therapies and the potential for rapid, global fixation of this mutation in the circulating influenza A virus population. 2011 Journal of clinical microbiology Abstract IV H275Y 122 131 21543559 Ultrasensitive detection of drug-resistant pandemic 2009 (H1N1) influenza A virus by rare-variant-sensitive high-resolution melting-curve analysis. In order to better understand the emergence of resistance, we developed a rare-variant-sensitive high-resolution melting-curve analysis method (RVS-HRM) that is able to detect the His275Tyr oseltamivir resistance mutation to 0.5% in a background of susceptible virus. 2011 Journal of clinical microbiology Abstract IV H275Y 180 189 21555520 Biophysical analysis of influenza A virus RNA promoter at physiological temperatures. We also found that a nonfunctional RNA promoter containing the 3'-G3U mutation, as well as a promoter containing the compensatory 3'-G3U/C8A mutations, was able to form a duplex as efficiently as wild type. 2011 The Journal of biological chemistry Abstract IV C8A 137 140 21572517 Mutation analysis of 2009 pandemic influenza A(H1N1) viruses collected in Japan during the peak phase of the pandemic. Oseltamivir resistance-related mutations, i.e., NA-H275Y and NA-N295S, were also detected in sporadic cases in Osaka and Tokyo. 2011 PloS one Abstract IV H275Y;N295S 51;64 56;69 NA;NA 48;61 50;63 21572517 Mutation analysis of 2009 pandemic influenza A(H1N1) viruses collected in Japan during the peak phase of the pandemic. RESULTS AND CONCLUSIONS: Our sequence analysis has revealed that both HA-S220T and NA-N248D are major non-synonymous mutations that clearly discriminate the 2009 pdm influenza viruses identified in the very early phase (May 2009) from those found in the peak phase (October 2009 to January 2010) in Japan. 2011 PloS one Abstract IV S220T;N248D 73;86 78;91 HA;NA 70;83 72;85 21586098 Recent avian influenza virus A/H5N1 evolution in vaccinated and unvaccinated poultry from farms in Southern Vietnam, January-March 2010. The viruses are characterized by a change from isoleucine to valine at position 514 (I514V) and are 1.8% divergent at the nucleotide level from HA sequences sampled in Vietnam in 2007. 2011 Transboundary and emerging diseases Abstract IV I514V;I514V 85;47 90;83 HA 144 146 21617310 Phylogenetic analysis of an off-seasonal influenza virus A (H3N2) in Niigata, Japan, 2010. These viruses exhibited the S31N mutation in M2, which confers resistance to amantadine. 2011 Japanese journal of infectious diseases Abstract IV S31N 28 32 M2 45 47 21628810 Simultaneous detection and subtyping of H274Y-positive influenza A (H1N1) using pyrosequencing. INTRODUCTION: We investigated the frequency of H274Y-positive swine-origin 2009 A (H1N1) influenza virus outbreak in Thailand during May-August 2009.METHODOLOGY: This study sought to find Oseltamivir resistance mutation H274Y by using pyrosequencing. 2011 Journal of infection in developing countries Abstract IV H274Y;H274Y 47;220 61;225 21628810 Simultaneous detection and subtyping of H274Y-positive influenza A (H1N1) using pyrosequencing. RESULTS: From 8,710 real-time RT-PCR swine-origin 2009 A(H1N1) influenza virus-positive specimens, 100 randomly selected samples identified one such virus with H274Y mutationusing pyrosequencing. 2011 Journal of infection in developing countries Abstract IV H274Y 160 165 21645305 Genomic study of the response of chicken to highly pathogenic avian influenza virus. Chickens were genotyped for the Mx polymorphism causing the S631N mutation, and for the Major Histocompatibility Complex (MHC). 2011 BMC proceedings Abstract IV S631N 60 65 21693105 Neuraminidase inhibitor R-125489--a promising drug for treating influenza virus: steered molecular dynamics approach. Based on results obtained by SMD and the molecular mechanics-Poisson-Boltzmann surface area method, we predict that R-125489 can be used to treat not only wild-type but also tamiflu-resistant N294S, H274Y variants of A/H5N1 virus as its binding affinity does not vary much across these systems. 2011 Biochemical and biophysical research communications Abstract IV N294S;H274Y 192;199 197;204 21723574 Isolation and phylogenetic analysis of pandemic H1N1/09 influenza virus from swine in Jiangsu province of China. In addition, some of these viruses had D225G (3/8) mutations in the receptor binding sites of the hemagglutinin (HA) protein, indicating enhancement of their binding affinity to the sialic alpha2, 3Gal receptor. 2012 Research in veterinary science Abstract IV D225G 39 44 HA;HA 113;98 115;111 21730113 Novel genotyping and quantitative analysis of neuraminidase inhibitor resistance-associated mutations in influenza a viruses by single-nucleotide polymorphism analysis. The monoplex assays for the H275Y NA mutation allowed precise and accurate quantification of the proportions of wild-type and mutant genotypes in virus mixtures (5% to 10% discrimination), with results comparable to those of pyrosequencing. 2011 Antimicrobial agents and chemotherapy Abstract IV H275Y 28 33 34 36 21730113 Novel genotyping and quantitative analysis of neuraminidase inhibitor resistance-associated mutations in influenza a viruses by single-nucleotide polymorphism analysis. The multi- or monoplex SNP analysis based on single nucleotide extension assays was developed to detect NA mutations H275Y and I223R/V in pandemic H1N1 viruses, H275Y in seasonal H1N1 viruses, E119V and R292K in seasonal H3N2 viruses, and H275Y and N295S in H5N1 viruses. 2011 Antimicrobial agents and chemotherapy Abstract IV H275Y;I223R;I223V;H275Y;E119V;R292K;H275Y;N295S 117;127;127;161;193;203;239;249 122;134;134;166;198;208;244;254 104 106 21730113 Novel genotyping and quantitative analysis of neuraminidase inhibitor resistance-associated mutations in influenza a viruses by single-nucleotide polymorphism analysis. The SNP analysis revealed the lower growth fitness of an H275Y mutant compared to the wild-type pandemic H1N1 virus by quantitatively genotyping progeny viruses grown in normal human bronchial epithelial cells. 2011 Antimicrobial agents and chemotherapy Abstract IV H275Y 57 62 21734052 Amino acid residues 253 and 591 of the PB2 protein of avian influenza virus A H9N2 contribute to mammalian pathogenesis. Virus with PB2 D253N and Q591K had greater polymerase activity in minireplicon assays, induced more tumor necrosis factor alpha (TNF-alpha) in human macrophages, replicated better in differentiated normal human bronchial epithelial (NHBE) cells, and was more pathogenic for mice. 2011 Journal of virology Abstract IV D253N;Q591K 15;25 20;30 PB2 11 14 21734052 Amino acid residues 253 and 591 of the PB2 protein of avian influenza virus A H9N2 contribute to mammalian pathogenesis. We investigated the tropism, host responses, and virulence of two variants of A/Quail/Hong Kong/G1/1997 (H9N2) (H9N2/G1) with D253N and Q591K in the PB2 protein in primary human macrophages and bronchial epithelium in vitro and in mice in vivo. 2011 Journal of virology Abstract IV D253N;Q591K 126;136 131;141 PB2 149 152 21744829 Molecular dynamics simulation directed rational design of inhibitors targeting drug-resistant mutants of influenza A virus M2. Among these mutations, the V27A mutation was prevalent among transmissible viruses under drug selection pressure. 2011 Journal of the American Chemical Society Abstract IV V27A 27 31 21744829 Molecular dynamics simulation directed rational design of inhibitors targeting drug-resistant mutants of influenza A virus M2. Guided by molecular dynamics (MD) simulation of drug binding and the influence of drug binding on the dynamics of A/M2 from earlier experimental studies, we designed a series of potent spirane amine inhibitors targeting not only WT, but also both A/M2-27A and L26F mutants with IC(50)s similar to that seen for amantadine's inhibition of the WT channel. 2011 Journal of the American Chemical Society Abstract IV L26F 260 264 M2;M2 116;249 118;251 21744829 Molecular dynamics simulation directed rational design of inhibitors targeting drug-resistant mutants of influenza A virus M2. However, most of the current virulent influenza A viruses carry drug-resistant mutations alongside the drug binding site, such as S31N, V27A, and L26F, etc., each of which might be dominant in a given flu season. 2011 Journal of the American Chemical Society Abstract IV S31N;V27A;L26F 130;136;146 134;140;150 21744829 Molecular dynamics simulation directed rational design of inhibitors targeting drug-resistant mutants of influenza A virus M2. Until now, V27A has not been successfully targeted by small molecule inhibitors, despite years of extensive medicinal chemistry research efforts and high throughput screening. 2011 Journal of the American Chemical Society Abstract IV V27A 11 15 21767571 Oseltamivir-resistant pandemic A(H1N1) 2009 influenza viruses detected through enhanced surveillance in the Netherlands, 2009-2010. Of these, 19 cases of oseltamivir-resistant virus harboring the H275Y mutation in the neuraminidase (NA) were detected. 2011 Antiviral research Abstract IV H275Y 64 69 NA;NA 101;86 103;99 21774247 [Etiological and molecular characteristics of pandemic influenza A (H1N1) virus during 2009-2010 in Shandong Province]. No H275Y mutation in NA protein was found. 2011 Bing du xue bao Abstract IV H275Y 3 8 21 23 21808039 Putative amino acid determinants of the emergence of the 2009 influenza A (H1N1) virus in the human population. For example, the alteration S145K (an antigenic position) was found as a characteristic of the pH1N1 strain. 2011 Proc Natl Acad Sci U S A Abstract IV S145K 28 33 21808039 Putative amino acid determinants of the emergence of the 2009 influenza A (H1N1) virus in the human population. Significantly, we showed that the substitutions R133(A)K and R149K, predicted to be pH1N1 characteristics, each altered virus binding to erythrocytes and conferred virulence to A/swine/NC/18161/02 in mice, reinforcing the computational findings. 2011 Proc Natl Acad Sci U S A Abstract IV R149K 61 66 21809641 [Analysis of pandemic influenza in Russia as a part of the global process based on data of an influenza monitoring reference center]. A number of strains contained D222G mutation that is responsible for the expansion of substrate specificity, as well as strain specific substitutions in hemagglutinin and neuraminidase molecules. 2011 Zhurnal mikrobiologii, epidemiologii i immunobiologii Abstract IV D222G 30 35 HA;NA 153;171 166;184 21809641 [Analysis of pandemic influenza in Russia as a part of the global process based on data of an influenza monitoring reference center]. Russian isolates generally were antigenically and genetically similar to the parent pandemic strain--influenza virusA/California/07/09, but contained S203T substitution in hemagglutinin. 2011 Zhurnal mikrobiologii, epidemiologii i immunobiologii Abstract IV S203T 150 155 HA 172 185 21813318 Genotyping of a nosocomial outbreak of pandemic influenza A/H1N1 2009. One of the substitutions (P300S) rendered detection of this variant by the CDC protocol inefficient. 2011 Journal of clinical virology Abstract IV P300S 26 31 21813318 Genotyping of a nosocomial outbreak of pandemic influenza A/H1N1 2009. The other outbreak-specific substitutions (D225E and A189T) were identified at codons that have been analyzed in the context of virulence. 2011 Journal of clinical virology Abstract IV D225E;A189T 43;53 48;58 21813318 Genotyping of a nosocomial outbreak of pandemic influenza A/H1N1 2009. These features involved two silent mutations at N385 and V407 in the NA gene and three amino acid substitutions in the HA gene (D225E, A189T, and P300S). 2011 Journal of clinical virology Abstract IV D225E;A189T;P300S 128;135;146 133;140;151 HA;NA 119;69 121;71 21816827 Biochemical impact of the host adaptation-associated PB2 E627K mutation on the temperature-dependent RNA synthesis kinetics of influenza A virus polymerase complex. 37 and 42C), whereas the human E627K mutant drastically lost activity at these high temperatures. 2011 The Journal of biological chemistry Abstract IV E627K 31 36 21816827 Biochemical impact of the host adaptation-associated PB2 E627K mutation on the temperature-dependent RNA synthesis kinetics of influenza A virus polymerase complex. Importantly, the E627K mutation elevates apparent K(cat) at low temperatures with little effect on K(m), suggesting that the E627K mutation alters the biochemical steps involved in enzyme catalysis rather than the interaction with the incoming NTP. 2011 The Journal of biological chemistry Abstract IV E627K;E627K 17;125 22;130 21816827 Biochemical impact of the host adaptation-associated PB2 E627K mutation on the temperature-dependent RNA synthesis kinetics of influenza A virus polymerase complex. Second, our steady-state kinetics data revealed that the human E627K mutant polymerase is catalytically more active than the avian Glu-627 polymerase at 34C. 2011 The Journal of biological chemistry Abstract IV E627K 63 68 21816827 Biochemical impact of the host adaptation-associated PB2 E627K mutation on the temperature-dependent RNA synthesis kinetics of influenza A virus polymerase complex. Third, this temperature-dependent kinetic impact of the human E627K mutation was also observed with different RNA templates, with different primers and also in the presence of nucleoprotein. 2011 The Journal of biological chemistry Abstract IV E627K 62 67 NP 176 189 21819109 Exploring organosilane amines as potent inhibitors and structural probes of influenza a virus M2 proton channel. Organosilane amine inhibitors were found to be generally as potent as their carbon analogues in targeting WT A/M2 and more potent against the drug-resistant A/M2-V27A mutant. 2011 Journal of the American Chemical Society Abstract IV V27A 162 166 M2;M2 111;159 113;161 21821881 Conservation of a crystallographic interface suggests a role for beta-sheet augmentation in influenza virus NS1 multifunctionality. Introduction of a W187A mutation into the ED abolishes dimer formation; however, strand-strand interactions between mutant NS1 ED monomers have been observed in two previous crystal forms. 2011 Acta crystallographica. Section F, Structural biology and crystallization communications Abstract IV W187A 18 23 NS1 123 126 21834591 Study of Tamiflu sensitivity to variants of A/H5N1 virus using different force fields. GROMOS96 43a1 provides a lower correlation as it supports Oseltamivir to be more resistant to N294S than H274Y. 2011 Journal of chemical information and modeling Abstract IV N294S;H274Y 94;105 99;110 21834591 Study of Tamiflu sensitivity to variants of A/H5N1 virus using different force fields. In this paper, we consider the impact of four main force fields, AMBER99SB, CHARMM27, GROMOS96 43a1, and OPLS-AA/L, on the binding affinity of Oseltamivir carboxylate to the wild-type and Y252H, N294S, and H274Y mutants of glycoprotein neuraminidase from the pandemic A/H5N1 virus. 2011 Journal of chemical information and modeling Abstract IV Y252H;N294S;H274Y 188;195;206 193;200;211 236 249 21834591 Study of Tamiflu sensitivity to variants of A/H5N1 virus using different force fields. They correctly capture the binding ranking Y252H WT N294S H274Y observed in experiments (Collins, P. 2011 Journal of chemical information and modeling Abstract IV N294S;H274Y;Y252H 52;58;43 57;63;48 21849451 Comparative analysis of avian influenza virus diversity in poultry and humans during a highly pathogenic avian influenza A (H7N7) virus outbreak. These include the independent emergence of HA A143T mutants, accumulation of four NA mutations, and farm-to-farm spread of virus variants harboring mammalian host determinants D701N and S714I in PB2. 2011 Journal of virology Abstract IV A143T;D701N;S714I 46;176;186 51;181;191 HA;NA;PB2 43;82;195 45;84;198 21852950 Differential contribution of PB1-F2 to the virulence of highly pathogenic H5N1 influenza A virus in mammalian and avian species. In a mammalian host, the rare N66S polymorphism in PB1-F2 that was previously described to be associated with high lethality of the 1918 influenza A virus showed increased replication and virulence of a recombinant VN1203 H5N1 virus, while deletion of the entire PB1-F2 ORF had negligible effects. 2011 PLoS pathogens Abstract IV N66S 30 34 PB1F2;PB1F2 51;263 57;269 21852950 Differential contribution of PB1-F2 to the virulence of highly pathogenic H5N1 influenza A virus in mammalian and avian species. Interestingly, the N66S substituted virus efficiently invades the CNS and replicates in the brain of Mx+/+ mice. 2011 PLoS pathogens Abstract IV N66S 19 23 21852950 Differential contribution of PB1-F2 to the virulence of highly pathogenic H5N1 influenza A virus in mammalian and avian species. Our data could explain why PB1-F2 is conserved in avian influenza virus isolates and only impacts pathogenicity in mammals when containing certain amino acid motifs such as the rare N66S polymorphism. 2011 PLoS pathogens Abstract IV N66S 182 186 PB1F2 27 33 21865430 High-resolution melting approach to efficient identification and quantification of H275Y mutant influenza H1N1/2009 virus in mixed-virus-population samples. An isolated-probe-asymmetric amplification PCR (Roche LightCycler v2.0) and high-resolution melting (HRM) method using unlabeled probes and amplified products (Idaho LightScanner 32) was designed and optimized to detect and estimate the proportion of H275Y mutants in influenza A/H1N1/2009 virus samples. 2011 Journal of clinical microbiology Abstract IV H275Y 251 256 21865430 High-resolution melting approach to efficient identification and quantification of H275Y mutant influenza H1N1/2009 virus in mixed-virus-population samples. The melting peaks of the H275Y-specific unlabeled probe for the wild-type A/H1N1/2009 and H275Y mutant viruses were clearly distinguishable at 65.5 C and 69.0 C, respectively, at various ratios of wild-type/mutant virus population standards. 2011 Journal of clinical microbiology Abstract IV H275Y;H275Y 25;90 39;95 21865430 High-resolution melting approach to efficient identification and quantification of H275Y mutant influenza H1N1/2009 virus in mixed-virus-population samples. The single-nucleotide variation 823C to T (His275Tyr), responsible for oseltamivir drug resistance has been detected in some isolates of the influenza A/H1N1/2009 virus. 2011 Journal of clinical microbiology Abstract IV H275Y;C823T 43;32 52;41 21874012 Histopathological and immunohistochemical findings of 20 autopsy cases with 2009 H1N1 virus infection. In addition, the D222G amino acid substitution in influenza virus hemagglutinin, which binds to specific cell receptors, was analyzed in formalin-fixed and paraffin-embedded trachea and lung sections by direct sequencing of PCR-amplified products. 2012 Modern pathology Abstract IV D222G 17 22 HA 66 79 21874012 Histopathological and immunohistochemical findings of 20 autopsy cases with 2009 H1N1 virus infection. In one case, the D222G substitution was detected in the lung as a major sequence, although 222D was prominent in the trachea, suggesting that selection of the viral clones occurred in the respiratory tract. 2012 Modern pathology Abstract IV D222G 17 22 21894383 Sequence analysis of the 2009 pandemic influenza A H1N1 virus haemagglutinin gene from 2009-2010 Brazilian clinical samples. A fatal outcome was associated with the D239G mutation (p < 0.0001). 2011 Memorias do Instituto Oswaldo Cruz Abstract IV D239G 40 45 21894383 Sequence analysis of the 2009 pandemic influenza A H1N1 virus haemagglutinin gene from 2009-2010 Brazilian clinical samples. A World Health Organization sequencing protocol allowed us to identify amino acid mutations in the HA protein at positions S220T (71%), D239G/N/S (20%), Y247H (4.5%), E252K (3.3%), M274V (2.2%), Q310H (26.7%) and E391K (12%). 2011 Memorias do Instituto Oswaldo Cruz Abstract IV S220T;D239G;D239N;D239S;Y247H;E252K;M274V;Q310H;E391K 123;136;136;136;153;167;181;195;213 128;145;145;145;158;172;186;200;218 HA 99 101 21899089 [H1N1V influenza epidemic of 2009 in Russia]. 26.7% of the viral isolates obtained in the end of the epidemic had D222G substitution responsible for tropism of viruses to lung tissues. 2011 Vestnik Rossiiskoi akademii meditsinskikh nauk Abstract IV D222G 68 73 21917953 Analysis of influenza virus hemagglutinin receptor binding mutants with limited receptor recognition properties and conditional replication characteristics. A comparison of virus titers in the mouse respiratory tract versus MDCK cells in culture showed that the mutants displayed distinctive replication properties depending on the system, but all were less attenuated in mice than the Y98F virus. 2011 Journal of virology Abstract IV Y98F 229 233 21917953 Analysis of influenza virus hemagglutinin receptor binding mutants with limited receptor recognition properties and conditional replication characteristics. An analysis of receptor binding properties confirmed that the initial Y98F virus bound poorly to several different species of erythrocytes, while all mutants reacquired various degrees of hemagglutination activity. 2011 Journal of virology Abstract IV Y98F 70 74 21917953 Analysis of influenza virus hemagglutinin receptor binding mutants with limited receptor recognition properties and conditional replication characteristics. Interestingly, both the Y98F virus and pseudoreversion mutants were shown to bind very inefficiently to standard glycan microarrays containing an abundance of binding substrates for most influenza viruses that have been characterized to date, provided by the Consortium for Functional Glycomics. 2011 Journal of virology Abstract IV Y98F 24 28 21917953 Analysis of influenza virus hemagglutinin receptor binding mutants with limited receptor recognition properties and conditional replication characteristics. The initial attenuated virus had a tyrosine-to-phenylalanine mutation at HA1 position 98 (Y98F), located in the receptor binding pocket, but viruses that were selected contained second-site pseudoreversion mutations in various structural locations that revealed a range of molecular mechanisms for modulating receptor binding that go beyond the scope that is generally mapped using receptor specificity mutants. 2011 Journal of virology Abstract IV Y98F 90 94 HA1 73 76 21930946 E339...R416 salt bridge of nucleoprotein as a feasible target for influenza virus inhibitors. Consistent with recent work, E339A, R416A, and deletion mutant Delta402-428 were unable to support viral replication in the absence of WT NP. 2011 Proc Natl Acad Sci U S A Abstract IV E339A;R416A 29;36 34;41 NP 138 140 21930946 E339...R416 salt bridge of nucleoprotein as a feasible target for influenza virus inhibitors. However, only E339A and R416A could form hetero complex with WT NP, but the complex was unable to bind the RNA polymerase, leading to inhibition of viral replication. 2011 Proc Natl Acad Sci U S A Abstract IV E339A;R416A 14;24 19;29 NP 64 66 21933546 [Molecular characterization of highly pathogenic avian influenza A (H5N1) viruses isolated from humans in Hunan province, 2006 - 2009]. All 4 viruses had A160T mutation in HA, a 20 amino acid deletion in the neuraminidase (NA) stalk at position 49 - 68, and a 5 amino acid deletion in the non-structural protein 1 (NS1). 2011 Zhonghua liu xing bing xue za zhi Abstract IV A160T 18 23 HA;NA;NA;NS1;NS1 36;87;72;153;179 38;89;85;177;182 21933546 [Molecular characterization of highly pathogenic avian influenza A (H5N1) viruses isolated from humans in Hunan province, 2006 - 2009]. D701N mutation of PB2 that increased the virulence in mice was found in HN/1/08. 2011 Zhonghua liu xing bing xue za zhi Abstract IV D701N 0 5 PB2 18 21 21933546 [Molecular characterization of highly pathogenic avian influenza A (H5N1) viruses isolated from humans in Hunan province, 2006 - 2009]. However, T192I mutation that might enhance the alpha 2, 6-linked sialic acid human influenza receptor binding had emerged in HN/1/09 and HN/2/09. 2011 Zhonghua liu xing bing xue za zhi Abstract IV T192I 9 14 Influenza 77 92 21935413 Genetic structure of human A/H1N1 and A/H3N2 influenza virus on Corsica Island: phylogenetic analysis and vaccine strain match, 2006-2010. It should be noted that Corsican isolates formed a separate sub-clade of clade 7 as a consequence of the presence of the fixed substitution D222E. 2011 PloS one Abstract IV D222E 140 145 21935413 Genetic structure of human A/H1N1 and A/H3N2 influenza virus on Corsica Island: phylogenetic analysis and vaccine strain match, 2006-2010. The A/H1N1 2009 (A/H1N1pdm) strains isolated on Corsica Island were characterized by the S220T mutation specific to clade 7 isolates. 2011 PloS one Abstract IV S220T 89 94 21951678 Comparative safety, immunogenicity, and efficacy of several anti-H5N1 influenza experimental vaccines in a mouse and chicken models (Testing of killed and live H5 vaccine). METHOD: Four experimental live vaccines based on two H5N1 influenza virus strains were tested; two of them had hemagglutinin (HA) of A/Vietnam/1203/04 strain lacking the polybasic HA cleavage site, and two others had hemagglutinins from attenuated H5N1 virus A/Chicken/Kurgan/3/05, with amino acid substitutions of Asp54/Asn and Lys222/Thr in HA1 and Val48/Ile and Lys131/Thr in HA2 while maintaining the polybasic HA cleavage site. 2012 Influenza and other respiratory viruses Abstract IV D54N;K222T;V48I;K131T 315;329;351;365 324;339;360;375 HA;HA;HA;HA;HA1;HA;HA 126;180;379;415;343;111;217 128;182;381;417;346;124;231 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. A dose-dependent glycan array analysis with the D222G virus showed a modest reduction in the binding avidity to human-like (alpha2-6 sialylated glycan) receptors and an increase in the binding to avian-like (alpha2-3 sialylated glycan) receptors in comparison with wild-type virus. 2011 PloS one Abstract IV D222G 48 53 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. In a more relevant human cell model, D222G virus replicated with delayed kinetics compared with wild-type virus but to higher titer in human bronchial epithelial cells. 2011 PloS one Abstract IV D222G 37 42 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. In the ferret pathogenesis model, the D222G mutant virus was found to be similar to wild-type CA/04 virus with respect to lethargy, weight loss and replication efficiency in the upper and lower respiratory tract. 2011 PloS one Abstract IV D222G 38 43 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. The D222G virus failed to productively infect mice inoculated by the ocular route, but exhibited greater viral replication and weight loss than wild-type CA/04 virus in mice inoculated by the intranasal route. 2011 PloS one Abstract IV D222G 4 9 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. The frequency of the amino acid substitution D222G in the hemagglutinin (HA) of 2009 H1N1 viruses isolated from severe but not mild human cases represents the first molecular marker associated with enhanced disease. 2011 PloS one Abstract IV D222G 45 50 HA;HA 73;58 75;71 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. These findings suggest that although the D222G mutation does not influence virus transmission, it may be considered a molecular marker for enhanced replication in certain cell types. 2011 PloS one Abstract IV D222G 41 46 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. To assess the relative contribution of this substitution in virus pathogenesis, transmission, and tropism, we introduced D222G by reverse genetics in the wild-type HA of the 2009 H1N1 virus, A/California/04/09 (CA/04). 2011 PloS one Abstract IV D222G 121 126 HA 164 166 21971186 The influenza A virus protein PB1-F2: killing two birds with one stone? In search for the mechanism by which PB1-F2 N66S increases pathogenicity, we have identified and characterized a novel function of PB1-F2. 2011 Virulence Abstract IV N66S 44 48 PB1F2;PB1F2 37;131 43;137 21980293 Multidrug resistant 2009 A/H1N1 influenza clinical isolate with a neuraminidase I223R mutation retains its virulence and transmissibility in ferrets. Both NL/2631-R223 and a recombinant virus with a single I223R change (recNL/602-I223R), transmitted among ferrets by aerosols, despite observed attenuation of recNL/602-I223R in vitro. 2011 PLoS pathogens Abstract IV I223R;I223R;I223R 56;80;169 61;85;174 21980293 Multidrug resistant 2009 A/H1N1 influenza clinical isolate with a neuraminidase I223R mutation retains its virulence and transmissibility in ferrets. In conclusion, the I223R mutated virus isolate has comparable replicative ability and transmissibility, but lower pathogenicity than the reference virus based on these in vivo studies. 2011 PLoS pathogens Abstract IV I223R 19 24 21980293 Multidrug resistant 2009 A/H1N1 influenza clinical isolate with a neuraminidase I223R mutation retains its virulence and transmissibility in ferrets. In vitro experiments showed that NL/2631-I223R replicated as well as NL/602 in MDCK cells. 2011 PLoS pathogens Abstract IV I223R 41 46 21980293 Multidrug resistant 2009 A/H1N1 influenza clinical isolate with a neuraminidase I223R mutation retains its virulence and transmissibility in ferrets. Recently a novel neuraminidase I223R mutation was identified in an A/H1N1 virus showing cross-resistance to the neuraminidase inhibitors oseltamivir, zanamivir and peramivir. 2011 PLoS pathogens Abstract IV I223R 31 36 NA;NA 17;112 30;125 21980293 Multidrug resistant 2009 A/H1N1 influenza clinical isolate with a neuraminidase I223R mutation retains its virulence and transmissibility in ferrets. This implies that the 2009 pandemic influenza A/H1N1 virus subtype with an isoleucine to arginine change at position 223 in the neuraminidase has the potential to spread in the human population. 2011 PLoS pathogens Abstract IV I223R 75 120 128 141 22001595 Exploring the molecular basis of dsRNA recognition by NS1 protein of influenza A virus using molecular dynamics simulation and free energy calculation. Compared with the wild type NS1A, all the studied mutants S42A, T49A, R38A, R35AR46A have obvious reduced binding free energies with dsRNA reflecting in the reduction of the polar and/or nonpolar interactions. 2011 Antiviral research Abstract IV S42A;T49A;R38A 58;64;70 62;68;74 NS 28 30 22022458 Minor changes in the hemagglutinin of influenza A(H1N1)2009 virus alter its antigenic properties. CONCLUSIONS: According to our results, one to two amino acid changes (N125D and/or N156K) in the major antigenic sites of the hemagglutinin of influenza A(H1N1)2009 virus may lead to significant reduction in the ability of patient and vaccine sera to recognize A(H1N1)2009 viruses. 2011 PloS one Abstract IV N125D;N156K 70;83 75;88 HA 126 139 22056389 In vitro evolution of H5N1 avian influenza virus toward human-type receptor specificity. By in vitro selection for binding alpha2-6 sialosides, we identified four variant viruses with amino acid substitutions in the hemagglutinin (S227N, D187G, E190G, and Q196R) that revealed modestly increased alpha2-6 and minimally decreased alpha2-3 binding by glycan array analysis. 2012 Virology Abstract IV S227N;D187G;E190G;Q196R 142;149;156;167 147;154;161;172 HA 127 140 22056389 In vitro evolution of H5N1 avian influenza virus toward human-type receptor specificity. However, a mutant virus combining Q196R with mutations from previous pandemic viruses (Q226L and G228S) revealed predominantly alpha2-6 binding. 2012 Virology Abstract IV Q196R;Q226L;G228S 34;87;97 39;92;102 22089329 Rapid identification of neuraminidase inhibitor resistance mutations in seasonal influenza virus A(H1N1), A(H1N1)2009, and A(H3N2) subtypes by melting point analysis. We evaluated the use of a procedure involving real-time polymerase chain reaction (PCR) followed by melting point analysis (MPA) of hybrids formed between the PCR product and a specific oligonucleotide probe for the identification of point mutations in the influenza A virus neuraminidase gene (NA) that are associated with oseltamivir resistance [resulting in the amino acid change H275Y for seasonal and pandemic influenza A(H1N1) viruses and E119V for A(H3N2) viruses]. 2012 European journal of clinical microbiology & infectious diseases Abstract IV H275Y;E119V 383;445 388;450 NA;NA 295;275 297;288 22090127 Reassortment and mutation of the avian influenza virus polymerase PA subunit overcome species barriers. Mutational analyses demonstrated that the majority of the enhancing activity in human PA results from a threonine-to-serine change at residue 552. 2012 Journal of virology Abstract IV T552S 104 145 PA 86 88 22090127 Reassortment and mutation of the avian influenza virus polymerase PA subunit overcome species barriers. Reassortant viruses with avian polymerases and human PA subunits, or simply the T552S mutation, displayed faster replication kinetics in culture and increased pathogenicity in mice compared to those containing a wholly avian polymerase complex. 2012 Journal of virology Abstract IV T552S 80 85 PA 53 55 22090127 Reassortment and mutation of the avian influenza virus polymerase PA subunit overcome species barriers. Thus, the acquisition of a human PA subunit, or the signature T552S mutation, is a potential mechanism to overcome the species-specific restriction of avian polymerases and increase virus replication. 2012 Journal of virology Abstract IV T552S 62 67 PA 33 35 22090133 The highly conserved arginine residues at positions 76 through 78 of influenza A virus matrix protein M1 play an important role in viral replication by affecting the intracellular localization of M1. In cells infected with a virus possessing the single substitution with A at position 77 or 78 (R77A or R78A, respectively), the mutated M1 localized in patches at the cell periphery where nucleoprotein and hemagglutinin colocalized more often than the wild-type did. 2012 Journal of virology Abstract IV R77A;R78A 95;103 99;107 HA;M1;NP 206;136;188 219;138;201 22090133 The highly conserved arginine residues at positions 76 through 78 of influenza A virus matrix protein M1 play an important role in viral replication by affecting the intracellular localization of M1. Transmission electron microscopy showed that virus possessing M1 R77A or R78A, but not the wild-type virus, was present in vesicular structures, indicating a defect in virus assembly and/or budding. 2012 Journal of virology Abstract IV R77A;R78A 65;73 69;77 M1 62 64 22090209 Amino acids 473V and 598P of PB1 from an avian-origin influenza A virus contribute to polymerase activity, especially in mammalian cells. In this study, it was found that PB1 from an avian-origin influenza A virus [A/Cambodia/P0322095/2005, H5N1 (Cam)] could enhance the polymerase activity of an attenuated human isolated virus, A/WSN/33, carrying the PB2 K627E mutation (WSN627E) in vitro. 2012 The Journal of general virology Abstract IV K627E 219 224 PB1;PB2 33;215 36;218 22102733 Synergistic adaptive mutations in the hemagglutinin and polymerase acidic protein lead to increased virulence of pandemic 2009 H1N1 influenza A virus in mice. Using reverse genetics, 3 synergistically acting mutations were defined as pathogenicity determinants, comprising 2 mutations in the hemagglutinin (HA[D222G] and HA[K163E]), whereby the HA(D222G) mutation was shown to determine receptor binding specificity and the polymerase acidic (PA) protein F35L mutation increasing polymerase activity. 2012 The Journal of infectious diseases Abstract IV D222G;K163E;D222G;F35L 151;165;189;296 156;170;194;300 HA;HA;HA;HA;PA;PA 148;162;186;133;284;265 150;164;188;146;286;282 22111074 First Fatal Oseltamivir-Resistant 2009 Pandemic Influenza A (H1N1) Case in an Adult in Korea. An H275Y mutation was detected in the neuraminidase gene sequence. 2011 Chonnam medical journal Abstract IV H275Y 3 8 38 51 22138712 The 2008-2009 H1N1 influenza virus exhibits reduced susceptibility to antibody inhibition: Implications for the prevalence of oseltamivir resistant variant viruses. A naturally-occurring H275Y oseltamivir resistant variant of influenza A (H1N1) virus emerged in 2007, subsequently becoming prevalent worldwide, via an undetermined mechanism. 2012 Antiviral research Abstract IV H275Y 22 27 22138712 The 2008-2009 H1N1 influenza virus exhibits reduced susceptibility to antibody inhibition: Implications for the prevalence of oseltamivir resistant variant viruses. To understand the antigenic properties of the H275Y variant, oseltamivir resistant and susceptible strains of H1N1 viruses were analyzed by hemagglutination inhibition (HI) and microneutralization assays. 2012 Antiviral research Abstract IV H275Y 46 51 22138712 The 2008-2009 H1N1 influenza virus exhibits reduced susceptibility to antibody inhibition: Implications for the prevalence of oseltamivir resistant variant viruses. While HA1 and NA phylogenetic trees show that both oseltamivir resistant and susceptible strains belong to clade 2B, NA D354G and HA A189T substitutions were found exclusively, and universally, in oseltamivir resistant variants. 2012 Antiviral research Abstract IV D354G;A189T 120;133 125;138 HA;HA1;NA;NA 130;6;14;117 132;9;16;119 22146492 Two mutations in the C-terminal domain of influenza virus RNA polymerase PB2 enhance transcription by enhancing cap-1 RNA binding activity. Cap-1 RNA-binding activities of D701N/S714R, D701N, and S714R were 262+-25%, 257+-34%, and 315+-9.6% of that of the wt, respectively, and their cap-dependent endonuclease activities were similar to that of the wt. 2012 Biochimica et biophysica acta Abstract IV D701N;S714R;D701N;S714R 32;38;45;56 37;43;50;61 22146492 Two mutations in the C-terminal domain of influenza virus RNA polymerase PB2 enhance transcription by enhancing cap-1 RNA binding activity. Cap-1-dependent transcription activities of D701N/S714R, D701N, and S714R were 348.1+-6.2%, 146.4+-11%, and 250.1+-0.8% of that of the wild type (wt), respectively. 2012 Biochimica et biophysica acta Abstract IV D701N;S714R;D701N;S714R 44;50;57;68 49;55;62;73 22146492 Two mutations in the C-terminal domain of influenza virus RNA polymerase PB2 enhance transcription by enhancing cap-1 RNA binding activity. D701N and S714R mutations enhanced transcription by enhancing cap-1 RNA-binding activity, but they may exhibit decreased efficiency of priming by the cap-1 primer. 2012 Biochimica et biophysica acta Abstract IV D701N;S714R 0;10 5;15 22146492 Two mutations in the C-terminal domain of influenza virus RNA polymerase PB2 enhance transcription by enhancing cap-1 RNA binding activity. The mutant human influenza virus RdRp containing PB2 D701N and D701N/S714R demonstrated enhanced replicon activity in mammalian cells. 2012 Biochimica et biophysica acta Abstract IV D701N;D701N;S714R 53;63;69 58;68;74 PB2 49 52 22155087 Oligomerization paths of the nucleoprotein of influenza A virus. In contrast, preparations of wild-type NP purified in high salt concentrations as well as mutant Y148A engineered for deficiency in nucleic acid binding were partly or totally oligomeric in RNA-free solutions. 2012 Biochimie Abstract IV Y148A 97 102 NP 39 41 22155087 Oligomerization paths of the nucleoprotein of influenza A virus. Recombinant wild-type NP purified in low salt concentrations and a derived mutant engineered for oligomerization deficiency (R416A) were mainly monomeric in RNA-free solutions as shown by biochemical and electron microscopy techniques. 2012 Biochimie Abstract IV R416A 125 130 NP 22 24 22172510 Generation of recombinant pandemic H1N1 influenza virus with the HA cleavable by bromelain and identification of the residues influencing HA bromelain cleavage. Sequence analysis of the pandemic H1N1-like viruses isolated from 2010 revealed emergence of the E374K change. 2012 Vaccine Abstract IV E374K 97 102 22172510 Generation of recombinant pandemic H1N1 influenza virus with the HA cleavable by bromelain and identification of the residues influencing HA bromelain cleavage. The D373N or E374G substitution in the HA2 stalk region of CA09 HA enabled efficient cleavage of CA09 HA by bromelain. 2012 Vaccine Abstract IV D373N;E374G 4;13 9;18 HA;HA;HA 39;64;102 41;66;104 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. All studied mutations reduced the cell surface NA activity compared to WT with the maximum reduction being obtained for the H275Y/Q222R mutant. 2011 PLoS pathogens Abstract IV H275Y;Q222R 124;130 129;135 47 49 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. Comparable infectivity and transmissibility were seen between the WT and the H275Y mutant in ferrets whereas the H275Y/Q222R mutant was associated with significantly lower lung viral titers. 2011 PLoS pathogens Abstract IV H275Y;H275Y;Q222R 77;113;119 82;118;124 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. Here, we rescued a recombinant Bris07-like WT virus and 4 NA mutants/revertants (H275Y, H275Y/Q222R, H275Y/M234V and H275Y/N344D) and characterized them in vitro and in ferrets. 2011 PLoS pathogens Abstract IV H275Y;H275Y;Q222R;H275Y;M234V;H275Y;N344D 81;88;94;101;107;117;123 86;93;99;106;112;122;128 58 60 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. In conclusion, the Q222R reversion mutation compromised Bris07-like H1N1 virus in vitro and in vivo. 2011 PLoS pathogens Abstract IV Q222R 19 24 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. In contrast, the H275Y/Q222R mutant showed a significant decrease of both affinity (40 microM) and activity (7 U/sec). 2011 PLoS pathogens Abstract IV H275Y;Q222R 17;23 22;28 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. Infectivity and contact transmission experiments were evaluated for the WT, H275Y and H275Y/Q222R recombinants in ferrets. 2011 PLoS pathogens Abstract IV H275Y;H275Y;Q222R 76;86;92 81;91;97 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. The H275Y mutation did not significantly alter Km and Vmax values compared to WT. 2011 PLoS pathogens Abstract IV H275Y 4 9 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. The H275Y/N344D mutant had a reduced affinity (Km of 50 vs 12 microM) whereas the H275Y/M234V mutant had a reduced activity (22 vs 28 U/sec). 2011 PLoS pathogens Abstract IV N344D;H275Y;M234V;H275Y 10;4;88;82 15;9;93;87 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. The NA of such variant contained additional NA changes (R222Q, V234M and D344N) that potentially counteracted the detrimental effect of the H275Y mutation on viral fitness. 2011 PLoS pathogens Abstract IV H275Y;R222Q;V234M;D344N 140;56;63;73 145;61;68;78 NA;NA 4;44 6;46 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. The WT, H275Y, H275Y/M234V and H275Y/N344D recombinants had comparable replicative capacities contrasting with H275Y/Q222R mutant whose viral titers were significantly reduced. 2011 PLoS pathogens Abstract IV H275Y;H275Y;M234V;H275Y;N344D;H275Y;Q222R 8;15;21;31;37;111;117 13;20;26;36;42;116;122 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. Thus, the R222Q NA mutation present in the WT virus may have facilitated the emergence of NAI-resistant Bris07 variants. 2011 PLoS pathogens Abstract IV R222Q 10 15 NA;NAI 16;90 18;93 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. Unexpectedly, an oseltamivir-resistant A/Brisbane/59/2007 (Bris07)-like H1N1 H275Y NA variant emerged in 2007 and completely replaced the wild-type (WT) strain in 2008-2009. 2011 PLoS pathogens Abstract IV H275Y 77 82 83 85 22192630 H4N8 subtype avian influenza virus isolated from shorebirds contains a unique PB1 gene and causes severe respiratory disease in mice. The PB1-F2 gene of the isolates consists of a 101-amino acid unique sequence, but lacks the N66S mutation. 2012 Virology Abstract IV N66S 92 96 PB1F2 4 10 22192630 H4N8 subtype avian influenza virus isolated from shorebirds contains a unique PB1 gene and causes severe respiratory disease in mice. The PB2 gene of the H4N8 isolates contains K482R, but not the E627K or D701N substitutions. 2012 Virology Abstract IV K482R;E627K;D701N 43;62;71 48;67;76 PB2 4 7 22194944 Adaption of seasonal H1N1 influenza virus in mice. Genetic analysis indicated that the increased virulence of the mouse-adapted virus was attributed to incremental acquisition of three mutations in the HA protein (T89I, N125T, and D221G). 2011 PloS one Abstract IV T89I;N125T;D221G 163;169;180 167;174;185 HA 151 153 22203589 Impact of mutations at residue I223 of the neuraminidase protein on the resistance profile, replication level, and virulence of the 2009 pandemic influenza virus. As expected, the H275Y mutation conferred resistance to oseltamivir (982-fold) and peramivir (661-fold) compared to the drug-susceptible recombinant WT. 2012 Antimicrobial agents and chemotherapy Abstract IV H275Y 17 22 22203589 Impact of mutations at residue I223 of the neuraminidase protein on the resistance profile, replication level, and virulence of the 2009 pandemic influenza virus. Consequently, I223R and I223V mutations, alone or with H275Y, need to be thoroughly monitored. 2012 Antimicrobial agents and chemotherapy Abstract IV I223R;I223V;H275Y 14;24;55 19;29;60 22203589 Impact of mutations at residue I223 of the neuraminidase protein on the resistance profile, replication level, and virulence of the 2009 pandemic influenza virus. Infectivity and transmissibility in ferrets were comparable between the recombinant WT and the H275Y or I223V-H275Y recombinants. 2012 Antimicrobial agents and chemotherapy Abstract IV H275Y;I223V;H275Y 95;104;110 100;109;115 22203589 Impact of mutations at residue I223 of the neuraminidase protein on the resistance profile, replication level, and virulence of the 2009 pandemic influenza virus. Infectivity and transmission of the WT, H275Y, and I223V-H275Y recombinant viruses were evaluated in ferrets. 2012 Antimicrobial agents and chemotherapy Abstract IV H275Y;H275Y;I223V 40;57;51 45;62;56 22203589 Impact of mutations at residue I223 of the neuraminidase protein on the resistance profile, replication level, and virulence of the 2009 pandemic influenza virus. Interestingly, enhanced levels of resistance to oseltamivir and peramivir and reduced susceptibility to zanamivir (1,647-, 17,347-, and 16-fold increases in IC(50)s, respectively) were observed for the I223R-H275Y recombinant, while the I223V-H275Y mutant exhibited 1,733-, 2,707-, and 2-fold increases in respective IC(50)s. 2012 Antimicrobial agents and chemotherapy Abstract IV H275Y;I223R;H275Y;I223V 208;202;243;237 213;207;248;242 22203589 Impact of mutations at residue I223 of the neuraminidase protein on the resistance profile, replication level, and virulence of the 2009 pandemic influenza virus. The I223R and I223V changes were associated with equivalent or higher viral titers in vitro compared to the recombinant WT. 2012 Antimicrobial agents and chemotherapy Abstract IV I223R;I223V 4;14 9;19 22203589 Impact of mutations at residue I223 of the neuraminidase protein on the resistance profile, replication level, and virulence of the 2009 pandemic influenza virus. The single I223R mutant was associated with reduced susceptibility to oseltamivir (53-fold), zanamivir (7-fold) and peramivir (10-fold), whereas the I223V virus had reduced susceptibility to oseltamivir (6-fold) only. 2012 Antimicrobial agents and chemotherapy Abstract IV I223R;I223V 11;149 16;154 22203589 Impact of mutations at residue I223 of the neuraminidase protein on the resistance profile, replication level, and virulence of the 2009 pandemic influenza virus. We used reverse genetics and site-directed mutagenesis to generate the recombinant A/Quebec/144147/09 pH1N1 wild-type virus (WT) and five (I223R, I223V, H275Y, I223V-H275Y, and I223R-H275Y) NA mutants. 2012 Antimicrobial agents and chemotherapy Abstract IV I223R;I223V;H275Y;I223V;H275Y;I223R;H275Y 139;146;153;160;166;177;183 144;151;158;165;171;182;188 190 192 22217077 Surveillance in Eastern India (2007-2009) revealed reassortment event involving NS and PB1-F2 gene segments among co-circulating influenza A subtypes. RESULTS: Comparative analysis of both nucleotide and deduced amino acid sequences, revealed presence of NS gene with A/PR/8/34(H1N1)-like mutations (H4N, Q21R, A22V, K44R, N53D, C59R, V60A, F103S and M106I) in both RNA-binding and effector domain of NS1 protein, and G63E, the HPAI-H5N1-like mutation in NEP/NS2 of five A/H1N1 strains of 2007 and 2009. 2012 Virology journal Abstract IV H4N;Q21R;A22V;K44R;N53D;C59R;V60A;F103S;M106I;G63E 149;154;160;166;172;178;184;190;200;267 152;158;164;170;176;182;188;195;205;271 NEP;NS;NS1;NS2 304;104;250;308 307;106;253;311 22230322 Highly pathogenic avian influenza virus H5N1 controls type I IFN induction in chicken macrophage HD-11 cells: a polygenic trait that involves NS1 and the polymerase complex. This contrasted with an NS1 mutant Yama virus (Yama-NS1(A144V)) and with the attenuated H5N1 AIV A/duck/Hokkaido/Vac-1/04 (Vac) carrying the haemagglutinin (HA) of the Yama virus (Vac-Yama/HA), that both induced type I IFN in these cells. 2012 Virology journal Abstract IV A144V 56 61 HA;HA;HA;NS1;NS1 157;189;141;24;52 159;191;155;27;55 22235288 Acute respiratory distress syndrome induced by a swine 2009 H1N1 variant in mice. METHODOLOGY PRINCIPAL FINDINGS: Mice were inoculated with A/swine/Shandong/731/2009 (SD/09), which was a 2009 H1N1 influenza variant with a G222D mutation in the hemagglutinin. 2012 PloS one Abstract IV G222D 140 145 HA 162 175 22238617 Mutational analyses of the influenza A virus polymerase subunit PA reveal distinct functions related and unrelated to RNA polymerase activity. We previously reported that a di-codon substitution mutation (G507A-R508A), denoted J10, in the C-terminal half of PA had no apparent effect on viral RNA synthesis but prevented infectious virus production, indicating that PA may have a novel role independent of its polymerase activity. 2012 PloS one Abstract IV G507A;R508A 62;68 67;73 PA;PA 115;223 117;225 22243670 Neuraminidase H275Y and hemagglutinin D222G mutations in a fatal case of 2009 pandemic influenza A (H1N1) virus infection. Further investigations are needed to determine the significance of infection with strains possessing NA-H275Y and HA-D222G. 2012 Influenza and other respiratory viruses Abstract IV H275Y;D222G 104;117 109;122 HA;NA 114;101 116;103 22243670 Neuraminidase H275Y and hemagglutinin D222G mutations in a fatal case of 2009 pandemic influenza A (H1N1) virus infection. Oseltamivir-resistant 2009 H1N1 influenza virus infections associated with neuraminidase (NA) H275Y have been identified sporadically. 2012 Influenza and other respiratory viruses Abstract IV H275Y 94 99 NA;NA 90;75 92;88 Influenza A virus H1N1 infection 32 58 22243670 Neuraminidase H275Y and hemagglutinin D222G mutations in a fatal case of 2009 pandemic influenza A (H1N1) virus infection. Strains possessing the hemagglutinin (HA) D222G mutation have been detected in small numbers of fatal 2009 H1N1 cases. 2012 Influenza and other respiratory viruses Abstract IV D222G 42 47 HA;HA 38;23 40;36 22243670 Neuraminidase H275Y and hemagglutinin D222G mutations in a fatal case of 2009 pandemic influenza A (H1N1) virus infection. We report the first clinical description of 2009 H1N1 virus infection with both NA-H275Y and HA-D222G mutations detected by pyrosequencing of bronchioalveolar lavage fluid obtained on symptom day 19. 2012 Influenza and other respiratory viruses Abstract IV H275Y;D222G 83;96 88;101 HA;NA 93;80 95;82 Influenza A virus H1N1 infection 49 69 22252168 Susceptibility of avian influenza viruses of the N6 subtype to the neuraminidase inhibitor oseltamivir. Two isolates with I222V NA substitution had moderately reduced susceptibility to oseltamivir in vitro (IC(50), 30.0 and 40.0nM). 2012 Antiviral research Abstract IV I222V 18 23 24 26 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. Disruption of the E80-R208 interaction in the triple mutant R361A-E80A-E81A increased its RNA binding affinity and restored its oligomerization back to wt levels in contrast with impaired levels of R361A. 2012 PloS one Abstract IV R361A;E80A;E81A;R361A 60;66;71;198 65;70;75;203 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. In R361A, a salt bridge formed between E80 of loop 1 and R208 of loop 2 driven by hydrophobic contacts between L79 and W207, due to a decreased flexibility of loop 2 and loop 1 unfolding. 2012 PloS one Abstract IV R361A 3 8 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. Thus, RNA could not access its binding groove in R361A; accordingly, R361A had a much lower affinity for RNA than NP. 2012 PloS one Abstract IV R361A;R361A 49;69 54;74 NP 114 116 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. We first performed molecular dynamics simulations of wt NP monomer and trimer in comparison with the R361A protein mutated in the RNA binding groove, using the H1N1 NP as the initial structure. 2012 PloS one Abstract IV R361A 101 106 NP;NP 56;165 58;167 22301136 Residue Y161 of influenza virus hemagglutinin is involved in viral recognition of sialylated complexes from different hosts. Among them, mutant Y161A showed cell-type-dependent viral entry without obvious defects in HA protein expression or viral incorporation. 2012 Journal of virology Abstract IV Y161A 19 24 HA 91 93 22301136 Residue Y161 of influenza virus hemagglutinin is involved in viral recognition of sialylated complexes from different hosts. Rescued mutant Y161A viruses demonstrated a 5- to 10-fold growth defect, but they were robust in viral replication and plaque forming ability. 2012 Journal of virology Abstract IV Y161A 15 20 22312897 [Genetic variability of isolates of pandemic influenza A virus H1N1 isolated in Russia in 2009]. In the hemagglutinin of pandemic A/Salekhard/01/2009(H1N1) isolate a mutation G155E leading to the increase in viral replication in developing chick embryos was detected. 2011 Molekuliarnaia genetika, mikrobiologiia i virusologiia Abstract IV G155E 78 83 HA 7 20 22312897 [Genetic variability of isolates of pandemic influenza A virus H1N1 isolated in Russia in 2009]. The hemagglutinin gene mutation D222G was found in 4 isolates from autopsy material. 2011 Molekuliarnaia genetika, mikrobiologiia i virusologiia Abstract IV D222G 32 37 HA 4 17 22332369 [Oseltamivir resistance depends on the position 273 amino acid of neuraminidase of the type A influenza virus (H1N1), circulating in human population]. Phenylalanine at position 273 in neuraminidase indicates a higher propensity to influenza virus mutation H274Y, leading to the appearance of resistant strains. 2011 Bioorganicheskaia khimiia Abstract IV H274Y 105 110 33 46 22345446 Efficient transmission of pandemic H1N1 influenza viruses with high-level oseltamivir resistance. Here we show that highly oseltamivir-resistant viruses containing both the S247N and H275Y mutations transmit efficiently in the guinea pig transmission model. 2012 Journal of virology Abstract IV S247N;H275Y 75;85 80;90 22345446 Efficient transmission of pandemic H1N1 influenza viruses with high-level oseltamivir resistance. S247N is a novel, naturally occurring N1 neuraminidase mutation that reduces oseltamivir sensitivity and greatly potentiates oseltamivir resistance in the context of the H275Y mutation. 2012 Journal of virology Abstract IV S247N;H275Y 0;170 5;175 41 54 22358415 Virological surveillance and antiviral resistance of human influenza virus in Argentina, 2005-2008. Oseltamivir resistance was observed in 12 (34.3%) of the 35 A(H1N1) strains from 2008; all of them carried the mutation H275Y in their neuraminidase sequence. 2011 Revista panamericana de salud publica Abstract IV H275Y 120 125 135 148 22358415 Virological surveillance and antiviral resistance of human influenza virus in Argentina, 2005-2008. RESULTS: Resistance to amantadine was observed only on A(H3N2) strains (29/33); all of them carried the mutation S31N in their M2 sequence. 2011 Revista panamericana de salud publica Abstract IV S31N 113 117 M2 127 129 22363521 Frequency of D222G and Q223R hemagglutinin mutants of pandemic (H1N1) 2009 influenza virus in Japan between 2009 and 2010. In May 2009, three specimens from mild cases showed D222G and/or Q223R substitutions in a minor subpopulation of viruses infecting these individuals. 2012 PloS one Abstract IV D222G;Q223R 52;65 57;70 22363521 Frequency of D222G and Q223R hemagglutinin mutants of pandemic (H1N1) 2009 influenza virus in Japan between 2009 and 2010. METHODS/RESULTS: To elucidate the existence and transmissibility of alpha2,3 sialic acid-specific viruses in H1N1pdm, amino acid substitutions within viral hemagglutinin molecules were investigated, especially D187E, D222G, and Q223R, which are related to a shift from human to avian receptor specificity. 2012 PloS one Abstract IV D187E;D222G;Q223R 210;217;228 215;222;233 HA 156 169 22363521 Frequency of D222G and Q223R hemagglutinin mutants of pandemic (H1N1) 2009 influenza virus in Japan between 2009 and 2010. The D187E substitution was not widespread in specimens, even in May 2009. 2012 PloS one Abstract IV D187E 4 9 22379077 Decreased neuraminidase activity is important for the adaptation of H5N1 influenza virus to human airway epithelium. Oseltamivir pressure selected a variant of A/Hong Kong/213/03 virus with HA P194S mutation that decreased viral binding to alpha2,6 receptor. 2012 Journal of virology Abstract IV P194S 76 81 HA 73 75 22379077 Decreased neuraminidase activity is important for the adaptation of H5N1 influenza virus to human airway epithelium. Under peramivir pressure, A/Hong Kong/213/03 virus developed a novel NA mutation, R156K, that reduced binding to all three drugs, caused about 90% loss of NA activity, and compromised replication in NHBE cells. 2012 Journal of virology Abstract IV R156K 82 87 NA;NA 69;155 71;157 22379077 Decreased neuraminidase activity is important for the adaptation of H5N1 influenza virus to human airway epithelium. Under pressure of each NA inhibitor, A/Turkey/65-1242/06 developed mutations in the hemagglutinin (HA) (H28R and P194L/T215I) and NA (E119A) proteins that reduced virus binding to alpha2,3-sialyl receptor and NA activity. 2012 Journal of virology Abstract IV H28R;P194L;T215I;E119A 104;113;119;134 108;118;124;139 HA;HA;NA;NA;NA 99;84;23;130;209 101;97;25;132;211 22379895 [Pathogenic aspects of influenza during the epidemics caused by A/H1N1v virus in 2009-2010 according autopsy data]. In the majority of investigated strains was proved the amino acid mutation with replacement D222G. 2011 Arkhiv patologii Abstract IV D222G 92 97 22398284 Recombinant influenza A viruses with enhanced levels of PB1 and PA viral protein expression. Influenza A viruses containing the promoter mutations G3A/C8U in a given segment express increased levels of the corresponding viral protein during infection due to increased levels of mRNA or cRNA species. 2012 Journal of virology Abstract IV G3A 54 57 22398291 Attenuated influenza virus construct with enhanced hemagglutinin protein expression. Finally, mice immunized with rPR8 viruses encoding a truncated NS1 protein and carrying the G3A C8U mutations in the HA segment demonstrated enhanced protection from wild-type virus challenge over that for mice vaccinated with an rPR8 virus encoding the truncated NS1 protein alone. 2012 Journal of virology Abstract IV G3A 92 95 HA;NS1;NS1 117;63;264 119;66;267 22398291 Attenuated influenza virus construct with enhanced hemagglutinin protein expression. For this purpose, we generated an NS1-truncated recombinant influenza A/Puerto Rico/8/34 (rPR8) virus carrying the G3A C8U "superpromoter" mutations in the HA genomic RNA segment. 2012 Journal of virology Abstract IV G3A 115 118 HA;NS1 156;34 158;37 22438920 Mutations in polymerase genes enhanced the virulence of 2009 pandemic H1N1 influenza virus in mice. Here, the variants containing PA-A36T or PB2-H357N observed in the mouse-adapted descendants of 2009 pandemic H1N1 virus (pH1N1), A/Sichuan/1/2009 (SC), were characterized. 2012 PloS one Abstract IV A36T;H357N 33;45 37;50 PA;PB2 30;41 32;44 22438920 Mutations in polymerase genes enhanced the virulence of 2009 pandemic H1N1 influenza virus in mice. PB2-H357N variant demonstrated growth ability comparable to the WT in A549 cells, but replicated well in PK15, LA-4 cells and in mice with an enhanced pathogenic phenotype. 2012 PloS one Abstract IV H357N 4 9 PB2 0 3 22438920 Mutations in polymerase genes enhanced the virulence of 2009 pandemic H1N1 influenza virus in mice. The PA-A36T mutant showed enhanced growth property compared to the WT in both human A549 cells and porcine PK15 cells in vitro, without significant effect on viral propagation in murine LA-4 cells and pathogenicity in mice; however, it did enhance the lung virus titer. 2012 PloS one Abstract IV A36T 7 11 PA 4 6 22449422 Engineering temperature sensitive live attenuated influenza vaccines from emerging viruses. This study demonstrates that engineering key temperature sensitive mutations (PB1-K391E, D581G, A661T; PB2-P112S, N265S, N556D, Y658H) into the genomes of influenza A viruses attenuates divergent human virus lineages and provides an alternative strategy for the generation of LAIVs. 2012 Vaccine Abstract IV K391E;D581G;A661T;P112S;N265S;N556D;Y658H 82;89;96;107;114;121;128 87;94;101;112;119;126;133 PB1;PB2 78;103 81;106 22453134 Antiviral effects of Psidium guajava Linn. (guava) tea on the growth of clinical isolated H1N1 viruses: its role in viral hemagglutination and neuraminidase inhibition. In contrast to both teas, oseltamivir carboxylate (OC) demonstrated high potency against the growth of A/Narita/1/09 (IC(50) of 3.83nM) and A/Yamaguchi/20/06 (IC(50) of 11.57nM) but not against that of A/Kitakyushu/10/06 bearing a His274-to-Tyr substitution (IC(50) of 15.97muM). 2012 Antiviral research Abstract IV H274Y 231 244 22525464 A single point mutation (Y89F) within the non-structural protein 1 of influenza A viruses limits epithelial cell tropism and virulence in mice. In an in vivo mouse model, we observed drastic reductions in weight loss, mortality, and virus titers in lung and bronchoalveolar lavage fluid after infection with the mutant virus PR8 A/NS1-Y89F (PR8 Y89F) when compared with wild-type virus (PR8 wt). 2012 The American journal of pathology Abstract IV Y89F;Y89F 191;201 195;205 NS1 187 190 22525464 A single point mutation (Y89F) within the non-structural protein 1 of influenza A viruses limits epithelial cell tropism and virulence in mice. In marked contrast, the bronchiolar epithelium after infection with the mutant PR8 Y89F virus was entirely intact, and the severity and extent of viral infection was reduced and strongly restricted to alveoli. 2012 The American journal of pathology Abstract IV Y89F 83 87 22535992 Recovery of influenza B virus with the H273Y point mutation in the neuraminidase active site from a human patient. The H273Y influenza B isolate is resistant to oseltamivir and peramivir but sensitive to zanamivir. 2012 Journal of clinical microbiology Abstract IV H273Y 4 9 22535992 Recovery of influenza B virus with the H273Y point mutation in the neuraminidase active site from a human patient. The H275Y oseltamivir resistance mutation confers high-level resistance to oseltamivir in isolates of human A(H1N1) influenza. 2012 Journal of clinical microbiology Abstract IV H275Y 4 9 22535992 Recovery of influenza B virus with the H273Y point mutation in the neuraminidase active site from a human patient. We report the recovery and identification of an influenza B virus with the H273Y neuraminidase point mutation directly from a human patient. 2012 Journal of clinical microbiology Abstract IV H273Y 75 80 81 94 22564359 Effect of receptor specificity of A/Hong Kong/1/68 (H3N2) influenza virus variants on replication and transmission in pigs. OBJECTIVES: Using recombinant viruses R1-HK, which harbored all genes from the original pandemic virus A/Hong Kong/1/68 (H3N2), and R2-HK, which differed by L226Q and S228G mutations in the hemagglutinin and conversion to an avian-virus-like receptor specificity, we assessed the role of receptor specificity on (i) replication in porcine respiratory explants, (ii) pig-to-pig transmission, and (iii) replication and organ tropism in pigs. 2013 Influenza and other respiratory viruses Abstract IV L226Q;S228G 157;167 162;172 HA 190 203 22574858 Long time scale GPU dynamics reveal the mechanism of drug resistance of the dual mutant I223R/H275Y neuraminidase from H1N1-2009 influenza virus. From clinical data, the single I223R (IR(1)) mutant of H1N1-2009 NA reduced efficacy of oseltamivir and zanamivir by 45 and 10 times, (1) respectively. 2012 Biochemistry Abstract IV I223R 31 36 65 67 22574858 Long time scale GPU dynamics reveal the mechanism of drug resistance of the dual mutant I223R/H275Y neuraminidase from H1N1-2009 influenza virus. More seriously, the efficacy of these two inhibitors against the double mutant I223R/H275Y (IRHY(2)) was significantly reduced by a factor of 12 374 and 21 times, respectively, compared to the wild-type.(2) This has led to the question of why the efficacy of the NA inhibitors is reduced by the occurrence of these mutations and, specifically, why the efficacy of oseltamivir against the double mutant IRHY was significantly reduced, to the point where oseltamivir has become an ineffective treatment. 2012 Biochemistry Abstract IV I223R;H275Y 79;85 84;90 263 265 22581100 Molecular mechanism of the enhanced virulence of 2009 pandemic influenza A (H1N1) virus from D222G mutation in the hemagglutinin: a molecular modeling study. D222G mutation of the hemagglutinin (HA) is of special interest because of its close association with the enhanced virulence of 2009 pandemic influenza A (H1N1) virus through the increased binding affinity to alpha2,3-linked sialylated glycan receptors. 2012 Journal of molecular modeling Abstract IV D222G 0 5 HA;HA 37;22 39;35 22581100 Molecular mechanism of the enhanced virulence of 2009 pandemic influenza A (H1N1) virus from D222G mutation in the hemagglutinin: a molecular modeling study. Here, molecular dynamics simulation and binding free energy calculation were performed to explore the altered glycan receptor binding mechanism of HA upon the D222G mutation by studying the interaction of one alpha2,3-linked sialylglycan (sequence: SIA-GAL-NAG) with the wild type and D222G mutated HA. 2012 Journal of molecular modeling Abstract IV D222G;D222G 159;285 164;290 HA;HA 147;299 149;301 22581100 Molecular mechanism of the enhanced virulence of 2009 pandemic influenza A (H1N1) virus from D222G mutation in the hemagglutinin: a molecular modeling study. The binding free energy calculation based on the molecular mechanics generalized Born surface area (MM-GBSA) method indicates that the D222G mutated HA has a much stronger binding affinity with the studied alpha2,3-linked glycan than the wild type. 2012 Journal of molecular modeling Abstract IV D222G 135 140 HA 149 151 22581100 Molecular mechanism of the enhanced virulence of 2009 pandemic influenza A (H1N1) virus from D222G mutation in the hemagglutinin: a molecular modeling study. The increased binding free energy of D222G mutant mainly comes from the increased energy contribution of Gln223. 2012 Journal of molecular modeling Abstract IV D222G 37 42 22615752 Functional analysis of conserved motifs in influenza virus PB1 protein. One exception was mutation K480R, observed in several pandemic (H1N1) 2009 viruses, which slightly increased polymerase activity relative to wild-type. 2012 PloS one Abstract IV K480R 27 32 22621130 The new temperature-sensitive mutation PA-F35S for developing recombinant avian live attenuated H5N1 influenza vaccine. CONCLUSIONS: These findings highlight the potential of the new ts mutation PA (F35S) in developing recombinant avian live attenuated H5N1 influenza vaccine. 2012 Virology journal Abstract IV F35S 79 83 PA 75 77 22621130 The new temperature-sensitive mutation PA-F35S for developing recombinant avian live attenuated H5N1 influenza vaccine. Furthermore, when used as live attenuated vaccine, the recombinant virus with this ts mutation PA (F35S) provided efficient protection for chickens against H5N1 HPAIV infection. 2012 Virology journal Abstract IV F35S 99 103 PA 95 97 Influenza A virus H5N1 infection 156 176 22621130 The new temperature-sensitive mutation PA-F35S for developing recombinant avian live attenuated H5N1 influenza vaccine. The resulting virus acquired ts phenotype and one of its amino acid mutations, PA (F35S), was identified as ts mutation. 2012 Virology journal Abstract IV F35S 83 87 PA 79 81 22644080 Clinical effectiveness of neuraminidase inhibitors--oseltamivir, zanamivir, laninamivir, and peramivir--for treatment of influenza A(H3N2) and A(H1N1)pdm09 infection: an observational study in the 2010-2011 influenza season in Japan. Based on a cycling probe real-time polymerase chain reaction (PCR) assay, none of the A(H1N1)pdm09 strains in this study had the H275Y mutation conferring oseltamivir resistance. 2012 Journal of infection and chemotherapy Abstract IV H275Y 129 134 22647789 Antibody pressure by a human monoclonal antibody targeting the 2009 pandemic H1N1 virus hemagglutinin drives the emergence of a virus with increased virulence in mice. One mutation near the receptor binding site, S186P, increased the binding affinity of the HA to the receptor. 2012 mBio Abstract IV S186P 45 50 HA 90 92 22647789 Antibody pressure by a human monoclonal antibody targeting the 2009 pandemic H1N1 virus hemagglutinin drives the emergence of a virus with increased virulence in mice. Six substitutions greatly reduced MAb binding (K123N, D131E, K133T, G134S, K157N, and G158E). 2012 mBio Abstract IV K123N;D131E;K133T;G134S;K157N;G158E 47;54;61;68;75;86 52;59;66;73;80;91 22661221 Intrahost emergent dynamics of oseltamivir-resistant virus of pandemic influenza A (H1N1) 2009 in a fatally immunocompromised patient. By constructing minimum spanning trees, it is proposed that the H275Y mutant might be generated primarily in the nasopharynx, then spread to the right and left lungs. 2012 Journal of infection and chemotherapy Abstract IV H275Y 64 69 22661221 Intrahost emergent dynamics of oseltamivir-resistant virus of pandemic influenza A (H1N1) 2009 in a fatally immunocompromised patient. Here we detected the uneven distribution of H275Y mutant virus in a patient who received a 21-day long-term administration of oseltamivir. 2012 Journal of infection and chemotherapy Abstract IV H275Y 44 49 22661221 Intrahost emergent dynamics of oseltamivir-resistant virus of pandemic influenza A (H1N1) 2009 in a fatally immunocompromised patient. Intrahost variation of the virus showed that the H275Y mutant virus was the predominant population in both nasopharynx and right lung, whereas the oseltamivir-sensitive virus comprised half the population in the left lung. 2012 Journal of infection and chemotherapy Abstract IV H275Y 49 54 22661221 Intrahost emergent dynamics of oseltamivir-resistant virus of pandemic influenza A (H1N1) 2009 in a fatally immunocompromised patient. The oseltamivir-resistant pandemic influenza virus A (2009 H1N1) with H275Y mutation in neuraminidase (NA) has been sporadically reported, and its wide spread remains a potential threat. 2012 Journal of infection and chemotherapy Abstract IV H275Y 70 75 NA;NA 103;88 105;101 22674977 Structure and receptor complexes of the hemagglutinin from a highly pathogenic H7N7 influenza virus. Glycan microarray and kinetic analysis were performed to compare the receptor binding profile of the wild-type recombinant NL219 HA to a variant with a threonine-to-alanine mutation at position 125, resulting in loss of the glycosylation site at Asn123. 2012 Journal of virology Abstract IV T125A 152 197 HA 129 131 22696672 Persistent oseltamivir-resistant pandemic influenza A/H1N1 infection in an adult with cystic fibrosis. The influenza virus was positive for the H275Y oseltamivir-resistance mutation despite the patient never having received oseltamivir. 2011 BMJ case reports Abstract IV H275Y 41 46 22718825 Analysis by single-gene reassortment demonstrates that the 1918 influenza virus is functionally compatible with a low-pathogenicity avian influenza virus in mice. This attenuation could be corrected by the single E627K amino acid change, further confirming the importance of this change in mammalian adaptation and mouse pathogenicity. 2012 Journal of virology Abstract IV E627K 50 55 22740390 Key molecular factors in hemagglutinin and PB2 contribute to efficient transmission of the 2009 H1N1 pandemic influenza virus. The change from alanine (A) to threonine (T) at position 271 of PB2 also abolished the virus's respiratory droplet transmission in guinea pigs, and this mutation, together with the HA Q226R mutation, abolished the virus's respiratory droplet transmission in ferrets. 2012 Journal of virology Abstract IV A271T;Q226R 15;184 61;189 HA;PB2 181;64 183;67 22764830 Oseltamivir-resistant 2009 H1N1 influenza pneumonia during therapy in a renal transplant recipient. Ongoing surveillance is essential to monitor how oseltamivir-resistant H275Y mutant viruses may evolve in the future. 2012 Pediatric transplantation Abstract IV H275Y 71 76 22764830 Oseltamivir-resistant 2009 H1N1 influenza pneumonia during therapy in a renal transplant recipient. The emergence of oseltamivir-resistant 2009 H1N1 influenza virus (conferred by the H275Y substitution in NA) during therapy or prophylaxis in immunocompromised patients is a serious concern. 2012 Pediatric transplantation Abstract IV H275Y 83 88 105 107 22787231 Roles of the phosphorylation of specific serines and threonines in the NS1 protein of human influenza A viruses. We conclude that attenuation resulting from the T-to-A substitution at position 215 is attributable to a deleterious structural change in the NS1 protein that is not caused by other amino acid substitutions and that phosphorylation of T215 does not affect virus replication. 2012 Journal of virology Abstract IV T215A 48 83 NS1 142 145 22788742 Comprehensive global amino acid sequence analysis of PB1F2 protein of influenza A H5N1 viruses and the influenza A virus subtypes responsible for the 20th-century pandemics. Global database of PB1F2 protein revealed that N66S mutation was present only in 3 8% of the H5N1 strains. 2013 Influenza and other respiratory viruses Abstract IV N66S 47 51 PB1F2 19 24 22788742 Comprehensive global amino acid sequence analysis of PB1F2 protein of influenza A H5N1 viruses and the influenza A virus subtypes responsible for the 20th-century pandemics. We found a novel mutation, N84S in the PB1F2 protein of 9 35% of the highly pathogenic avian influenza H5N1 influenza viruses. 2013 Influenza and other respiratory viruses Abstract IV N84S 27 31 PB1F2 39 44 22796550 Development and evaluation of a line probe assay for rapid typing of influenza viruses and detection of the H274Y mutation. In 49 nasal swabs from a clinical study, the assay showed 100% specificity for virus typing and 88% specificity for detecting the absence of the H274Y mutation, although none of these swabs was PCR-positive for this mutation. 2012 Journal of virological methods Abstract IV H274Y 145 150 22796550 Development and evaluation of a line probe assay for rapid typing of influenza viruses and detection of the H274Y mutation. In examining 354 cultured virus isolates, the LiPA showed 100% specificity for virus typing and 99% specificity for detecting the H274Y mutation. 2012 Journal of virological methods Abstract IV H274Y 130 135 22796550 Development and evaluation of a line probe assay for rapid typing of influenza viruses and detection of the H274Y mutation. LiPA was developed for identification of H1N1 influenza virus subtypes (pandemic 2009 and seasonal types), as well as H3N2 and B subtypes, and to detect the H274Y mutation. 2012 Journal of virological methods Abstract IV H274Y 157 162 22796550 Development and evaluation of a line probe assay for rapid typing of influenza viruses and detection of the H274Y mutation. Reverse hybridization-based line probe assays (LiPA) can be performed using several probes immobilized on nitrocellulose, strips enabling LiPA to determine simultaneously viral subtypes and detect the presence or absence of the H274Y mutation, which confers oseltamivir resistance of H1N1 influenza viruses. 2012 Journal of virological methods Abstract IV H274Y 228 233 22800599 [Analysis of genetic features of influenza B virus in Hunan province from 2007 to 2010]. The major mutations of the strains isolated in year 2007 were found in sites R48K, K88R, P108A, D197N and S230G. 2012 Zhonghua yu fang yi xue za zhi [Chinese journal of preventive medicine] Abstract IV R48K;K88R;P108A;D197N;S230G 77;83;89;96;106 81;87;94;101;111 22800599 [Analysis of genetic features of influenza B virus in Hunan province from 2007 to 2010]. While the major mutations of the strains isolated between year 2009 and 2010 were sited in K88R, S150I, N166Y, D197N and S230G. 2012 Zhonghua yu fang yi xue za zhi [Chinese journal of preventive medicine] Abstract IV K88R;S150I;N166Y;D197N;S230G 91;97;104;111;121 95;102;109;116;126 22808250 Mouse-adapted H9N2 influenza A virus PB2 protein M147L and E627K mutations are critical for high virulence. Although the PB2 E627K amino acid substitution enhanced viral polymerase activity and replication, none of the single mutations of mouse adapted PB2 could confer increased virulence on the SD16 backbone. 2012 PloS one Abstract IV E627K 17 22 PB2;PB2 13;145 16;148 22808250 Mouse-adapted H9N2 influenza A virus PB2 protein M147L and E627K mutations are critical for high virulence. Five amino acid substitutions were found in the genome of SD16-MA compared with SD16 virus: PB2 (M147L, V250G and E627K), HA (L226Q) and M1 (R210K). 2012 PloS one Abstract IV M147L;V250G;E627K;L226Q;R210K 97;104;114;126;141 102;109;119;131;146 HA;M1;PB2 122;137;92 124;139;95 22808250 Mouse-adapted H9N2 influenza A virus PB2 protein M147L and E627K mutations are critical for high virulence. The combination of M147L and E627K significantly enhanced viral replication ability and virulence in mice. 2012 PloS one Abstract IV M147L;E627K 19;29 24;34 22809692 Both influenza hemagglutinin and polymerase acidic genes are important for delayed pandemic 2009 H1N1 virus clearance in the ferret model. In ferrets, H1N1 virus with HA K154Q and PA L295P mutations exhibited significantly higher titers in the upper respiratory tract compared to all other viruses 6 days post-infection. 2012 Virology Abstract IV K154Q;L295P 31;44 36;49 HA;PA 28;41 30;43 22809692 Both influenza hemagglutinin and polymerase acidic genes are important for delayed pandemic 2009 H1N1 virus clearance in the ferret model. Our results suggest that both single mutations HA K154Q and PA L295P are necessary for delayed virus clearance of A/Tennessee/560/09(H1N1) influenza virus in a ferret animal model. 2012 Virology Abstract IV K154Q;L295P 50;63 55;68 HA;PA 47;60 49;62 22809692 Both influenza hemagglutinin and polymerase acidic genes are important for delayed pandemic 2009 H1N1 virus clearance in the ferret model. The HA K154Q mutation reduced the receptor binding affinity of A/Tennessee/560/09 virus to 6-Su-6'SLN and biantennary 6'SLN receptors. 2012 Virology Abstract IV K154Q 7 12 HA 4 6 22809692 Both influenza hemagglutinin and polymerase acidic genes are important for delayed pandemic 2009 H1N1 virus clearance in the ferret model. We previously showed that a pandemic virus, A/Tennessee/560/09(H1N1), had the potential to adapt to human bronchial epithelial cells by the acquisition of hemagglutinin (HA) K154Q and polymerase acidic (PA) protein L295P mutations that conferred a more virulent phenotype. 2012 Virology Abstract IV K154Q;L295P 174;215 179;220 HA;HA;PA;PA 170;155;203;184 172;168;205;201 22809862 Treatment of oseltamivir-resistant influenza A (H1N1) virus infections in mice with antiviral agents. Influenza A/Mississippi/03/2001 (H1N1) and A/Hong Kong/2369/2009 (H1N1) viruses containing the neuraminidase gene mutation H275Y (conferring resistance to oseltamivir) were adapted to mice and evaluated for suitability as models for lethal infection and antiviral treatment. 2012 Antiviral research Abstract IV H275Y 123 128 95 108 22815274 Strain-dependent effects of PB1-F2 of triple-reassortant H3N2 influenza viruses in swine. Ablation of the PB1-F2 ORF (or incorporation of the N66S mutation in the PB1-F2 ORF, Sw/99 N66S) affected the replication in porcine alveolar macrophages of only the Sw/99 KO (PB1-F2 knockout) and Sw/99 N66S variants. 2012 The Journal of general virology Abstract IV N66S;N66S;N66S 52;91;203 56;95;207 PB1F2;PB1F2;PB1F2 16;73;176 22;79;182 22837199 The H275Y neuraminidase mutation of the pandemic A/H1N1 influenza virus lengthens the eclipse phase and reduces viral output of infected cells, potentially compromising fitness in ferrets. A parallel analysis of the H275Y mutation in the prior seasonal A/Brisbane/59/2007 background shows similar changes in the infection kinetic parameters, but in this background, the H275Y mutation also allows the mutant to infect cells five times more rapidly. 2012 Journal of virology Abstract IV H275Y;H275Y 27;181 32;186 22837199 The H275Y neuraminidase mutation of the pandemic A/H1N1 influenza virus lengthens the eclipse phase and reduces viral output of infected cells, potentially compromising fitness in ferrets. The H275Y amino acid substitution of the neuraminidase gene is the most common mutation conferring oseltamivir resistance in the N1 subtype of the influenza virus. 2012 Journal of virology Abstract IV H275Y 4 9 41 54 22837199 The H275Y neuraminidase mutation of the pandemic A/H1N1 influenza virus lengthens the eclipse phase and reduces viral output of infected cells, potentially compromising fitness in ferrets. Using a mathematical model to analyze a set of in vitro experiments that allow for the full characterization of the viral replication cycle, we show that the primary effects of the H275Y substitution on the pandemic H1N1 (H1N1pdm09) strain are to lengthen the mean eclipse phase of infected cells (from 6.6 to 9.1 h) and decrease (by 7-fold) the viral burst size, i.e., the total number of virions produced per cell. 2012 Journal of virology Abstract IV H275Y 181 186 22837199 The H275Y neuraminidase mutation of the pandemic A/H1N1 influenza virus lengthens the eclipse phase and reduces viral output of infected cells, potentially compromising fitness in ferrets. We also find, however, that the infectious-unit-to-particle ratio of the H275Y mutant strain is 12-fold higher than that of the oseltamivir-susceptible strain (0.19 versus 0.016 per RNA copy). 2012 Journal of virology Abstract IV H275Y 73 78 22851656 Emergence of fatal avian influenza in New England harbor seals. These include a D701N mutation in the viral PB2 protein, previously reported in highly pathogenic H5N1 avian influenza viruses infecting people. 2012 mBio Abstract IV D701N 16 21 PB2 44 47 22862843 Detection of haemagglutinin D222 polymorphisms in influenza A(H1N1)pdm09-infected patients by ultra-deep pyrosequencing. D222E, D222G, D222N and D222A were observed in 37.0%, 11.1%, 7.4% and 3.7% of patients, respectively; 10.7% of samples harboured more than two variants. 2013 Clinical microbiology and infection Abstract IV D222G;D222E;D222N;D222A 7;0;14;24 12;5;19;29 22862843 Detection of haemagglutinin D222 polymorphisms in influenza A(H1N1)pdm09-infected patients by ultra-deep pyrosequencing. D222G/N/A were detected, as either minor or predominant variants, only in severe cases, whereas D222E was equally represented in severe and moderate-mild infections. 2013 Clinical microbiology and infection Abstract IV D222N;D222A;D222G;D222E 0;0;0;96 9;9;9;101 22921534 Glycosylation of CM2 is important for efficient replication of influenza C virus. The amount of the genome (GFP-vRNA) in the CM2-N11A-virus-like particles (VLPs) was 13% of that found in WT-VLPs. 2012 Virology Abstract IV N11A 47 51 CM2 43 46 22921534 Glycosylation of CM2 is important for efficient replication of influenza C virus. The incoming GFP-vRNA was less efficiently transported to the nucleus in CM2-N11A-VLP-infected cells than WT-VLP-infected cells, leading to the reduced reporter gene expression in CM2-N11A-VLP-infected cells. 2012 Virology Abstract IV N11A;N11A 77;184 81;188 CM2;CM2 73;180 76;183 22952752 Molecular evolutionary analysis of pH1N1 2009 influenza virus in Reunion Island, South West Indian Ocean region: a cohort study. PRINCIPAL FINDINGS: We found that i) Reunion pH1N1 sequences stemmed from global "clade 7" but shaped two phylogenetic sub-clades; ii) D239E mutation was identified in the hemagglutinin protein of all Reunion sequences, a mutation which has been associated elsewhere with mild-, upper-respiratory tract pH1N1 infecting strains; iii) Date estimates from molecular phylogenies predicted clade emergence some time before the first detection of pH1N1 by the epidemiological surveillance system; iv) Phylogenetic relatedness was observed between Reunion pH1N1 viruses and those from other countries in South-western Indian Ocean area; v) Quasispecies populations were observed within households and individuals of the cohort-study. 2012 PloS one Abstract IV D239E 135 140 HA 172 185 2295311 The structure of a membrane fusion mutant of the influenza virus haemagglutinin. We have determined the neutral pH crystal structure of one such mutant, HA2 112 Asp----Gly. 1990 The EMBO journal Abstract IV D112G 76 90 HA 72 74 22958470 Molecular and phylogenetic analysis of matrix gene of avian influenza viruses isolated from wild birds and live bird markets in the USA. Of these 17 isolates, 16 had S31N change and one isolate had V27A mutation. 2013 Influenza and other respiratory viruses Abstract IV V27A;S31N 61;29 65;33 22978683 Molecular basis of drug resistance in A/H1N1 virus. In this study, free-energy perturbation was used to evaluate the relative binding free energies of Tamiflu and Relenza with H274Y, N294S, and Y252H neuraminidase mutants. 2012 Journal of chemical information and modeling Abstract IV H274Y;N294S;Y252H 124;131;142 129;136;147 148 161 22982118 Design and synthesis of pinanamine derivatives as anti-influenza A M2 ion channel inhibitors. Several imidazole and guanazole derivatives of pinanamine were found to inhibit WT A/M2 to a comparable degree as amantadine and one of these compounds 12 exhibits weak inhibition of A/M2-S31N mutant and it is marginally more effective in inhibiting S31NM2 than amantadine. 2012 Antiviral research Abstract IV S31N 188 192 M2;M2 85;185 87;187 22983300 Bayesian coalescent analysis of pandemic H1N1 influenza A virus circulating in the South American region. HA substitutions D239G/N and Q310H have been observed only in Brazilian patients. 2012 Virus research Abstract IV D239G;D239N;Q310H 17;17;29 24;24;34 HA 0 2 22983300 Bayesian coalescent analysis of pandemic H1N1 influenza A virus circulating in the South American region. While substitution D239G/N is not particularly associated to a specific genetic lineage, all strains bearing substitution Q310H were assigned to clade 6, suggesting a founder effect. 2012 Virus research Abstract IV D239G;D239N;Q310H 19;19;122 26;26;127 22993153 Contribution of NS1 effector domain dimerization to influenza A virus replication and virulence. NS1-W187R protein exhibited lower double-stranded RNA (dsRNA)-binding activity, showed a temporal redistribution during infection, and was minimally compromised for interferon antagonism. 2012 Journal of virology Abstract IV W187R 4 9 NS1 0 3 22993153 Contribution of NS1 effector domain dimerization to influenza A virus replication and virulence. We generated a mutant influenza virus strain expressing NS1-W187R to destabilize this self-interaction. 2012 Journal of virology Abstract IV W187R 60 65 NS1 56 59 23011311 High prevalence of amantadine-resistant influenza A virus isolated in Gyeonggi Province, South Korea, during 2005-2010. Of 308 influenza A viruses examined, 229 had the S31N substitution in the M2 protein. 2013 Archives of virology Abstract IV S31N 49 53 M2 74 76 23015718 Influenza virus neuraminidases with reduced enzymatic activity that avidly bind sialic Acid receptors. Conversely, while wild-type NA shows no detectable binding to sialosides, the D151G NA exhibits avid binding with broad specificity toward alpha2-3 sialosides. 2012 Journal of virology Abstract IV D151G 78 83 NA;NA 28;84 30;86 23015718 Influenza virus neuraminidases with reduced enzymatic activity that avidly bind sialic Acid receptors. D151G NA binds the 3' sialyllactosamine (3'-SLN) and 6'-SLN sialosides with equilibrium dissociation constant (K(D)) values of 30.0 muM and 645 muM, respectively, which correspond to much higher affinities than the corresponding affinities (low mM) of HA to these glycans. 2012 Journal of virology Abstract IV D151G 0 5 HA;NA 252;6 254;8 23015718 Influenza virus neuraminidases with reduced enzymatic activity that avidly bind sialic Acid receptors. Here, we compare the functional and structural properties of a human H3N2 NA from A/Tanzania/205/2010 and its D151G mutant, which supports HA-independent receptor binding. 2012 Journal of virology Abstract IV D151G 110 115 HA;NA 139;74 141;76 23015718 Influenza virus neuraminidases with reduced enzymatic activity that avidly bind sialic Acid receptors. However, NA variants (D151G) of recent human H3N2 viruses have also been reported to bind receptors on red blood cells, but the nature of these receptors and the effect of the mutation on NA activity were not established. 2012 Journal of virology Abstract IV D151G 22 27 NA;NA 9;188 11;190 23015718 Influenza virus neuraminidases with reduced enzymatic activity that avidly bind sialic Acid receptors. The general significance of D151 among influenza virus NAs was further explored by introducing the D151G mutation into three N1 NAs and one N2 NA, which all exhibited reduced enzymatic activity and preferential binding to alpha2-3 sialosides. 2012 Journal of virology Abstract IV D151G 99 104 NA;NA;NA 143;55;128 145;58;131 23019374 Virulence and transmissibility of H1N2 influenza virus in ferrets imply the continuing threat of triple-reassortant swine viruses. Although molecular analysis did not reveal known virulence markers, the Sw/1204 virus acquired mutations in hemagglutinin (HA) (Asp-225-Gly) and neuraminidase (NA) (Ser-315-Asn) proteins during the single ferret passage. 2012 Proc Natl Acad Sci U S A Abstract IV D225G;S315N 128;165 139;176 HA;HA;NA;NA 123;108;160;145 125;121;162;158 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. However, the polar glycerol substituent present in zanamivir, which mimics the natural substrate, is accommodated in the I223R mutant structure in a similar way to wild type, thus explaining the kinetic data. 2012 PLoS pathogens Abstract IV I223R 121 126 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. Oseltamivir inhibition constants (K(I)) increased 48-fold in the single I223R mutant and 7500-fold in the double mutant. 2012 PLoS pathogens Abstract IV I223R 72 77 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. Recently, a novel neuraminidase inhibitor resistance mutation I223R was identified in the neuraminidase of this subtype. 2012 PLoS pathogens Abstract IV I223R 62 67 NA;NA 18;90 31;103 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. Relative to wild type, K(M) values for MUNANA increased only 2-fold for the single I223R mutant and up to 8-fold for the double mutant. 2012 PLoS pathogens Abstract IV I223R 83 88 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. To understand the resistance mechanism of this mutation, the enzymatic properties of the I223R mutant, together with the most frequently observed resistance mutation, H275Y, and the double mutant I223R/H275Y were compared. 2012 PLoS pathogens Abstract IV I223R;H275Y;H275Y;I223R 89;167;202;196 94;172;207;201 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. We find that there is shrinkage of a hydrophobic pocket in the active site as a result of the I223R change. 2012 PLoS pathogens Abstract IV I223R 94 99 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. We have used X-ray crystallography to better understand the effect of mutation I223R on drug binding. 2012 PLoS pathogens Abstract IV I223R 79 84 23029425 Multiple distinct forms of CD8+ T cell cross-reactivity and specificities revealed after 2009 H1N1 influenza A virus infection in mice. Sequences of the immunodominant nucleoprotein (NP) NP366-374 and acid polymerase (PA) PA224-233 CD8 epitopes from X31 each differ from the CA/E3/09 virus by one amino acid: an M371V substitution at position 6 of the NP peptide, and an S224P substitution at position 1 of the PA peptide, raising questions about the role of these epitopes in protection. 2012 PloS one Abstract IV M371V;S224P 176;235 181;240 NP;NP;NP;NP;PA;PA;PA 47;51;216;32;82;86;275 49;53;218;45;84;88;277 23053629 Molecular mechanisms underlying oseltamivir resistance mediated by an I117V substitution in the neuraminidase of subtype H5N1 avian influenza A viruses. An Ile-to-Val change at position 117 in influenza A virus subtype H5N1 NA (NA-I117V) confers a reduction in susceptibility to oseltamivir carboxylate. 2013 The Journal of infectious diseases Abstract IV I117V;I117V 78;3 83;36 NA;NA 71;75 73;77 23053629 Molecular mechanisms underlying oseltamivir resistance mediated by an I117V substitution in the neuraminidase of subtype H5N1 avian influenza A viruses. CONCLUSIONS: Our findings provide new insight into the mechanism of NA-I117V-mediated oseltamivir resistance in highly pathogenic H5N1 avian influenza viruses. 2013 The Journal of infectious diseases Abstract IV I117V 71 76 68 70 23053629 Molecular mechanisms underlying oseltamivir resistance mediated by an I117V substitution in the neuraminidase of subtype H5N1 avian influenza A viruses. METHODS: We created single-point-mutant viruses with 3 genetically different backgrounds (ie, 1 belonging to clade 1 and 2 belonging to clade 2.3.4) and evaluated the effects of the I117V mutation on oseltamivir susceptibility in vitro, in vivo, and in silico. 2013 The Journal of infectious diseases Abstract IV I117V 182 187 23053629 Molecular mechanisms underlying oseltamivir resistance mediated by an I117V substitution in the neuraminidase of subtype H5N1 avian influenza A viruses. Mice infected with I117V virus exhibited reduced susceptibility to oseltamivir and decreased survival in 2 of 3 virus pairs tested. 2013 The Journal of infectious diseases Abstract IV I117V 19 24 23053629 Molecular mechanisms underlying oseltamivir resistance mediated by an I117V substitution in the neuraminidase of subtype H5N1 avian influenza A viruses. Molecular dynamics simulations revealed that I117V caused the loss of hydrogen bonds between an arginine at position 118 and the carboxyl group of oseltamivir, leading to a lower binding affinity for oseltamivir. 2013 The Journal of infectious diseases Abstract IV I117V 45 50 23053629 Molecular mechanisms underlying oseltamivir resistance mediated by an I117V substitution in the neuraminidase of subtype H5N1 avian influenza A viruses. RESULTS: The NA-I117V mutation conferred a slight reduction in susceptibility to oseltamivir in vitro (1.3- to 6.3-fold changes), although it did not substantially compromise NA enzymatic activity. 2013 The Journal of infectious diseases Abstract IV I117V 16 21 NA;NA 13;175 15;177 23055004 Molecular characterization of avian-like H1N1 swine influenza a viruses isolated in Eastern China, 2011. The M2 proteins of the isolates have the mutation (S31N), a characteristic marker of the European avian-like swine viruses since about 1987, which may confer resistance to amantadine and rimantadine antivirals. 2012 Virologica Sinica Abstract IV S31N 51 55 M2 4 6 23071861 Emergence of HA mutants during influenza virus pneumonia. An infection model utilizing guinea pigs, which was chosen in order to best simulate the sialic acid distribution of severe pneumonia in human patients, demonstrated an increase of D222G mutants and a delay in the diminution of mutants in the lower respiratory tract in comparison to the upper respiratory tract. 2012 International journal of clinical and experimental pathology Abstract IV D222G 181 186 Pneumonia 124 133 23071861 Emergence of HA mutants during influenza virus pneumonia. Mutations at amino acid 222 (D222G mutations) in the virus hemagglutinin (HA) molecule, known to alter the receptor-recognition properties of the virus, were detected in a number of the more severely-affected patients in the early phases of the pandemic. 2012 International journal of clinical and experimental pathology Abstract IV D222G 29 34 HA;HA 74;59 76;72 23071861 Emergence of HA mutants during influenza virus pneumonia. To understand the background for the emergence of the mutant amino acid D222G in human lungs, we conducted histological examinations on lung specimens of patients from Mexico who had succumbed in the pandemic. 2012 International journal of clinical and experimental pathology Abstract IV D222G 72 77 23077313 Investigation of influenza virus polymerase activity in pig cells. We also investigated in pig cells the consequences of some known mammalian host range determinants that enhance influenza virus polymerase activity in human cells, such as PB2 mutations E627K, D701N, G590S/Q591R, and T271A. 2013 Journal of virology Abstract IV E627K;D701N;G590S;Q591R;T271A 186;193;200;206;217 191;198;205;211;222 PB2 172 175 23077315 The compensatory G88R change is essential in restoring the normal functions of influenza A/WSN/33 virus matrix protein 1 with a disrupted nuclear localization signal. Computational modeling suggested that the compensatory G88R change could reestablish the integrity of the M1 layer through new salt bridges between adjacent M1 subunits when the original interactions were interrupted by simultaneous R101S and R105S replacements in the NLS. 2013 Journal of virology Abstract IV G88R;R101S;R105S 55;233;243 59;238;248 M1;M1 106;157 108;159 23077315 The compensatory G88R change is essential in restoring the normal functions of influenza A/WSN/33 virus matrix protein 1 with a disrupted nuclear localization signal. G88R emerged as a compensatory mutation in matrix protein 1 (M1) of influenza virus A/WSN/33 when its nuclear localization signal (NLS) was disrupted by R101S and R105S substitutions. 2013 Journal of virology Abstract IV G88R;R101S;R105S 0;153;163 4;158;168 M1;M 61;43 63;49 23077315 The compensatory G88R change is essential in restoring the normal functions of influenza A/WSN/33 virus matrix protein 1 with a disrupted nuclear localization signal. The G88R compensatory mutation not only restored normal functions of M1 in the presence of a disrupted NLS but also resulted in a strong association of M1 with viral ribonucleoprotein. 2013 Journal of virology Abstract IV G88R 4 8 M1;M1 69;152 71;154 23077315 The compensatory G88R change is essential in restoring the normal functions of influenza A/WSN/33 virus matrix protein 1 with a disrupted nuclear localization signal. To understand why G88R was favored by the virus as a compensatory change for the NLS loss and resultant replication deficiency, three more M1 triple mutants with an alternative G88K, G88V, or G88E change in addition to R101S and R105S substitutions in the NLS were generated. 2013 Journal of virology Abstract IV G88R;G88K;G88V;G88E;R101S;R105S 18;177;183;192;219;229 22;181;187;196;224;234 M1 139 141 23114374 Community outbreak of macrolide-resistant Mycoplasma pneumoniae in Yamagata, Japan in 2009. An A2063T mutation in domain V of the 23S rRNA gene, which is associated with macrolide resistance, was identified in 39 (83.0%) isolates. 2013 The Pediatric infectious disease journal Abstract IV A2063T 3 9 23114374 Community outbreak of macrolide-resistant Mycoplasma pneumoniae in Yamagata, Japan in 2009. The minimum inhibitory concentrations for isolates with an A2063T transversion showed high resistance to clarithromycin (minimum inhibitory concentration, 16-64 mg/L), and clarithromycin prescribed initially was clinically ineffective. 2013 The Pediatric infectious disease journal Abstract IV A2063T 59 65 23115299 Unstable polymerase-nucleoprotein interaction is not responsible for avian influenza virus polymerase restriction in human cells. Avian-origin influenza virus polymerase activity can be dramatically increased in human cells with the PB2 E627K mutation. 2013 Journal of virology Abstract IV E627K 107 112 PB2 103 106 23115299 Unstable polymerase-nucleoprotein interaction is not responsible for avian influenza virus polymerase restriction in human cells. However, we demonstrate here that a variety of PB2 adaptive mutations, including E627K, do not enhance the stability of the vRNP but rather increase the amount of replicated RNA that results in more PB2-NP coprecipitation. 2013 Journal of virology Abstract IV E627K 81 86 NP;PB2;PB2 203;47;199 205;50;202 23124793 Methionine-101 from one strain of H5N1 NS1 protein determines its IFN-antagonizing ability and subcellular distribution pattern. H5-M101I gained the ability to specifically inhibit IFN-beta promoter activity, translocate to the cytoplasm, and release CPSF30. 2012 Science China. Life sciences Abstract IV M101I 3 8 23124793 Methionine-101 from one strain of H5N1 NS1 protein determines its IFN-antagonizing ability and subcellular distribution pattern. The M101I mutation of H5N1 NS1, namely H5-M101I, fully reversed its functions. 2012 Science China. Life sciences Abstract IV M101I;M101I 4;42 9;47 NS1 27 30 23131559 A single E105K mutation far from the active site of influenza B virus neuraminidase contributes to reduced susceptibility to multiple neuraminidase-inhibitor drugs. A sequence analysis of viruses propagated in MDCK cells revealed that the isolate contained a mutation (E105K) not previously associated with reduced susceptibility to NA inhibitors. 2012 Biochemical and biophysical research communications Abstract IV E105K 104 109 168 170 23131559 A single E105K mutation far from the active site of influenza B virus neuraminidase contributes to reduced susceptibility to multiple neuraminidase-inhibitor drugs. Analysis of the three-dimensional model of E105 and K105 NAs with peramivir suggested that the E105K mutation at the monomer-monomer interface of the NA tetramer may destabilize the tetrameric form of NA, leading to decreased susceptibility to NA inhibitors. 2012 Biochemical and biophysical research communications Abstract IV E105K 95 100 NA;NA;NA;NA 150;201;244;57 152;203;246;60 23131559 A single E105K mutation far from the active site of influenza B virus neuraminidase contributes to reduced susceptibility to multiple neuraminidase-inhibitor drugs. However, pyrosequencing analysis showed that the NA E105K mutation was below a detectable level in the original clinical specimens, suggesting that the mutant virus may be preferably selected during propagation in MDCK cells. 2012 Biochemical and biophysical research communications Abstract IV E105K 52 57 49 51 23152521 Systematic identification of H274Y compensatory mutations in influenza A virus neuraminidase by high-throughput screening. Compensatory mutations contribute to the appearance of the oseltamivir resistance substitution H274Y in the neuraminidase (NA) gene of H1N1 influenza viruses. 2013 Journal of virology Abstract IV H274Y 95 100 NA;NA 123;108 125;121 23152521 Systematic identification of H274Y compensatory mutations in influenza A virus neuraminidase by high-throughput screening. Here, we describe a high-throughput screening method utilizing error-prone PCR and next-generation sequencing to comprehensively screen NA genes for H274Y compensatory mutations. 2013 Journal of virology Abstract IV H274Y 149 154 136 138 23152521 Systematic identification of H274Y compensatory mutations in influenza A virus neuraminidase by high-throughput screening. The compensatory effect of E214D is applicable in both seasonal influenza virus strain A/New Caledonia/20/1999 and 2009 pandemic swine influenza virus strain A/California/04/2009. 2013 Journal of virology Abstract IV E214D 27 32 23152521 Systematic identification of H274Y compensatory mutations in influenza A virus neuraminidase by high-throughput screening. We found four mutations that can either fully (R194G, E214D) or partially (L250P, F239Y) compensate for the fitness deficiency of the H274Y mutant. 2013 Journal of virology Abstract IV R194G;E214D;L250P;F239Y;H274Y 47;54;75;82;134 52;59;80;87;139 23169971 Molecular characterization and phylogenetic analysis of the hemagglutinin 1 protein of human influenza A virus subtype H1N1 circulating in Kenya during 2007-2008. However, the majority of 2008 viruses from Kenya also had R192K and R226Q substitutions, compared with A/Solomon Islands/3/2006 (H1N1)-like virus. 2012 The Journal of infectious diseases Abstract IV R192K;R226Q 58;68 63;73 23169971 Molecular characterization and phylogenetic analysis of the hemagglutinin 1 protein of human influenza A virus subtype H1N1 circulating in Kenya during 2007-2008. RESULTS: We found that, similar to A/Brisbane/59/2007 (H1N1)-like virus, which was included in the southern hemisphere vaccine for the 2009 influenza season, all 2007 Kenyan viruses had D39N, R77K, T132V, K149R, and E277K amino acid substitutions, compared with A/Solomon Islands/3/2006 (H1N1)-like virus, a component of the southern hemisphere vaccine for the 2008 influenza season. 2012 The Journal of infectious diseases Abstract IV D39N;R77K;T132V;K149R;E277K 186;192;198;205;216 190;196;203;210;221 23169971 Molecular characterization and phylogenetic analysis of the hemagglutinin 1 protein of human influenza A virus subtype H1N1 circulating in Kenya during 2007-2008. The A193T substitution is involved in binding the sialic acid receptor. 2012 The Journal of infectious diseases Abstract IV A193T 4 9 23169971 Molecular characterization and phylogenetic analysis of the hemagglutinin 1 protein of human influenza A virus subtype H1N1 circulating in Kenya during 2007-2008. The main cluster contained viruses with N187S and A193T changes; residue 187 is involved in receptor binding, whereas residue 193 is at antigenic site Sb. 2012 The Journal of infectious diseases Abstract IV N187S;A193T 40;50 45;55 23169971 Molecular characterization and phylogenetic analysis of the hemagglutinin 1 protein of human influenza A virus subtype H1N1 circulating in Kenya during 2007-2008. The majority of the 2008 Kenyan isolates contained N187S, G189N, and A193T mutations, which differed from A/Brisbane/59/2007 (H1N1)-like virus. 2012 The Journal of infectious diseases Abstract IV N187S;G189N;A193T 51;58;69 56;63;74 23192869 Pandemic 2009 H1N1 influenza A virus carrying a Q136K mutation in the neuraminidase gene is resistant to zanamivir but exhibits reduced fitness in the guinea pig transmission model. Interestingly, the Q136K mutation strongly impairs viral fitness in the guinea pig transmission model. 2013 Journal of virology Abstract IV Q136K 19 24 23192869 Pandemic 2009 H1N1 influenza A virus carrying a Q136K mutation in the neuraminidase gene is resistant to zanamivir but exhibits reduced fitness in the guinea pig transmission model. We show here that a Q136K mutation in the NA of the 2009 pandemic H1N1 virus confers a high degree of resistance to zanamivir. 2013 Journal of virology Abstract IV Q136K 20 25 42 44 23201406 Both antiviral activity and intracellular localization of chicken Mx protein depend on a polymorphism at amino acid position 631. Furthermore, we found that replacing Ser with Asn at 631 aa provided Mx with antiviral activity against VSV, with Mx showing granular-like distribution in the cytoplasm. 2013 Biochemical and biophysical research communications Abstract IV S631N 37 56 23201406 Both antiviral activity and intracellular localization of chicken Mx protein depend on a polymorphism at amino acid position 631. In chickens, a polymorphism at amino acid position 631 (631 aa) of Mx protein has been suggested to be involved in the antiviral ability against vesicular stomatitis virus (VSV) and influenza virus, indicating that a Ser-to-Asn substitution at 631 aa is the source of this antiviral ability. 2013 Biochemical and biophysical research communications Abstract IV S631N 217 247 23201459 Evaluation of influenza virus antiviral susceptibility testing in Europe: results from the first external quality assessment exercise. CONCLUSIONS: Detection of NA-H275Y in A(H1N1) viruses was achieved by most laboratories. 2013 Journal of clinical virology Abstract IV H275Y 29 34 26 28 23211197 [National Influenza Surveillance Programme: results of influenza activity in Portugal in the 2010/2011 season]. To date, the LNRVG detected the presence of the H275Y substitution in the neuraminidase gene, associated with oseltamivir resistance, in three virus A(H1)pdm09.For one of them, oseltamivir resistance was confirmed by phenotypic assays. 2012 Acta medica portuguesa Abstract IV H275Y 48 53 74 87 23211427 Characterization of mutations associated with the adaptation of a low-pathogenic H5N1 avian influenza virus to chicken embryos. The relevance of these changes, except H103Y in HA, to viral replication remains unknown. 2013 Veterinary microbiology Abstract IV H103Y 39 44 HA 48 50 23215782 Influenza virus subpopulations: exchange of lethal H5N1 virus NS for H1N1 virus NS triggers de novo generation of defective-interfering particles and enhances interferon-inducing particle efficiency. In this study, we demonstrated that the specific exchange of the NS gene segment from highly pathogenic A/HK/156/97 (H5N1) [E92 or E92D NS1] virus for the cognate NS gene segment of A/PR/834(H1N1) [D92 NS1] virus did not cause a significant change in the sizes of infectious particle subpopulations. 2013 Journal of interferon & cytokine research Abstract IV E92D 131 135 NS;NS;NS1;NS1 65;163;136;202 67;165;139;205 23242536 A cluster of patients infected with I221V influenza b virus variants with reduced oseltamivir susceptibility--North Carolina and South Carolina, 2010-2011. Among patients who completed oseltamivir, those with B/I221V infection reported a longer duration until illness resolution (5 vs 3 days; P = .02). 2013 The Journal of infectious diseases Abstract IV I221V 55 60 23242536 A cluster of patients infected with I221V influenza b virus variants with reduced oseltamivir susceptibility--North Carolina and South Carolina, 2010-2011. B/I221V infection was not associated with differences in underlying conditions or illness severity, compared with B/WT infection. 2013 The Journal of infectious diseases Abstract IV I221V 0 7 23242536 A cluster of patients infected with I221V influenza b virus variants with reduced oseltamivir susceptibility--North Carolina and South Carolina, 2010-2011. BACKGROUND: During 2010-2011, influenza B viruses with a novel neuraminidase substitution, denoted I221V (B/I221V), associated with reduced in vitro oseltamivir susceptibility were detected in North Carolina. 2013 The Journal of infectious diseases Abstract IV I221V;I221V 99;106 104;113 63 76 23242536 A cluster of patients infected with I221V influenza b virus variants with reduced oseltamivir susceptibility--North Carolina and South Carolina, 2010-2011. CONCLUSIONS: B/I221V cocirculated with B/WT in North Carolina and South Carolina during 2010-2011. 2013 The Journal of infectious diseases Abstract IV I221V 13 20 23242536 A cluster of patients infected with I221V influenza b virus variants with reduced oseltamivir susceptibility--North Carolina and South Carolina, 2010-2011. I221V did not alter illness severity but may have reduced oseltamivir effectiveness. 2013 The Journal of infectious diseases Abstract IV I221V 0 5 23242536 A cluster of patients infected with I221V influenza b virus variants with reduced oseltamivir susceptibility--North Carolina and South Carolina, 2010-2011. METHODS: We determined the prevalence of I221V among B viruses submitted to the Centers for Disease Control and Prevention for antiviral resistance surveillance, including all B viruses submitted to North Carolina and South Carolina state laboratories, during October 2010-September 2011.We conducted chart reviews and telephone interviews to characterize North Carolina and South Carolina patients with B/I221V vs wild-type B virus infection (B/WT). 2013 The Journal of infectious diseases Abstract IV I221V;I221V 41;404 46;411 23242536 A cluster of patients infected with I221V influenza b virus variants with reduced oseltamivir susceptibility--North Carolina and South Carolina, 2010-2011. No patients with B/I221V infection received oseltamivir prior to specimen collection. 2013 The Journal of infectious diseases Abstract IV I221V 17 24 23242536 A cluster of patients infected with I221V influenza b virus variants with reduced oseltamivir susceptibility--North Carolina and South Carolina, 2010-2011. RESULTS: We detected I221V in 45 (22%) of 209 B viruses from North Carolina and 8 (10%) of 82 B viruses from South Carolina. 2013 The Journal of infectious diseases Abstract IV I221V 21 26 23242536 A cluster of patients infected with I221V influenza b virus variants with reduced oseltamivir susceptibility--North Carolina and South Carolina, 2010-2011. Thus, global surveillance for I221V is important. 2013 The Journal of infectious diseases Abstract IV I221V 30 35 23242536 A cluster of patients infected with I221V influenza b virus variants with reduced oseltamivir susceptibility--North Carolina and South Carolina, 2010-2011. We detected I221V in 3 (0.3%) of 881 B viruses tested from 45 other states. 2013 The Journal of infectious diseases Abstract IV I221V 12 17 23247916 Attenuation of an influenza A virus due to alteration of its hemagglutinin-neuraminidase functional balance in mice. A reverse genetics study revealed that the single mutation HA E190K, which occurs infrequently in naturally isolated H1N1 viruses, was responsible for the phenotype of this variant. 2013 Archives of virology Abstract IV E190K 62 67 HA 59 61 23267831 Neuraminidase inhibitor susceptibility testing of influenza type B viruses in China during 2010 and 2011 identifies viruses with reduced susceptibility to oseltamivir and zanamivir. Additionally, a single virus with reduced susceptibility to both oseltamivir and zanamivir was identified and contained an amino acid substitution D197N (GAC AAC) at another conserved residue in the NA active site (D198N in N2 numbering). 2013 Antiviral research Abstract IV D197N;D198N 147;215 152;220 199 201 23267831 Neuraminidase inhibitor susceptibility testing of influenza type B viruses in China during 2010 and 2011 identifies viruses with reduced susceptibility to oseltamivir and zanamivir. Four influenza B viruses exhibited reduced susceptibilities to oseltamivir, but not zanamivir, and shared the amino acid substitution I221T (ATC ACC), at this conserved residue in the NA active site (I222T in N2 numbering). 2013 Antiviral research Abstract IV I221T;I222T 134;200 139;205 184 186 23269805 Amino acid 316 of hemagglutinin and the neuraminidase stalk length influence virulence of H9N2 influenza virus in chickens and mice. H9N2 influenza viruses with an A316S substitution in hemagglutinin (HA) and a shorter neuraminidase (NA) stalk have become predominant in China. 2013 Journal of virology Abstract IV A316S 31 36 HA;HA;NA;NA 68;53;101;86 70;66;103;99 23269805 Amino acid 316 of hemagglutinin and the neuraminidase stalk length influence virulence of H9N2 influenza virus in chickens and mice. The A316S was shown to increase HA cleavage efficiency when combined with short stalk NA, and the short stalk NA improved NA enzyme activity and release of virus from erythrocytes. 2013 Journal of virology Abstract IV A316S 4 9 HA;NA;NA;NA 32;86;110;122 34;88;112;124 23280098 Genetic characterization of influenza virus circulating in Brazilian pigs during 2009 and 2010 reveals a high prevalence of the pandemic H1N1 subtype. Genetic diversity was higher in the HA than in the NA gene, and the amino acid substitution S203T in one of HA's antigenic sites was found in most of the samples. 2013 Influenza and other respiratory viruses Abstract IV S203T 92 97 HA;HA;NA 36;108;51 38;110;53 23280524 Clinical and molecular characteristics of the 2009 pandemic influenza H1N1 infection with severe or fatal disease from 2009 to 2011 in Shenzhen, China. Both D222G and D222N were associated statistically with severe disease. 2013 Journal of medical virology Abstract IV D222G;D222N 5;15 10;20 23280524 Clinical and molecular characteristics of the 2009 pandemic influenza H1N1 infection with severe or fatal disease from 2009 to 2011 in Shenzhen, China. Four substitutions (D222G, D222N, D222E, and Q223R) were observed on the 220-loop of the receptor-binding sites of the HA gene. 2013 Journal of medical virology Abstract IV D222G;D222N;D222E;Q223R 20;27;34;45 25;32;39;50 HA 119 121 23289789 Genetic analysis of influenza B viruses isolated in Uganda during the 2009-2010 seasons. The Ugandan B/Victoria-lineage isolates grouped in clade 1 which was defined by the N75K, N165K and S172P substitutions in hemagglutinin (HA) protein clustered together with the B/Brisbane/60/2008 vaccine strain. 2013 Virology journal Abstract IV N75K;N165K;S172P 84;90;100 88;95;105 HA;HA 138;123 140;136 23289789 Genetic analysis of influenza B viruses isolated in Uganda during the 2009-2010 seasons. The Yamagata-like Ugandan strain, B/Uganda/MUWRP-053/2009, clustered with clade 3 Yamagata viruses such as B/Bangladesh/3333/2007 which is characterized by S150I and N166Y substitutions in HA. 2013 Virology journal Abstract IV S150I;N166Y 156;166 161;171 HA 189 191 23302696 Structure and inhibition of the drug-resistant S31N mutant of the M2 ion channel of influenza A virus. Among the handful of drug-resistant mutants, S31N is found in more than 95% of the currently circulating viruses and shows greatly decreased inhibition by amantadine. 2013 Proc Natl Acad Sci U S A Abstract IV S31N 45 49 23302696 Structure and inhibition of the drug-resistant S31N mutant of the M2 ion channel of influenza A virus. Nevertheless, we have discovered small-molecule drugs that inhibit S31N with potencies greater than amantadine's potency against WT M2. 2013 Proc Natl Acad Sci U S A Abstract IV S31N 67 71 M2 132 134 23302696 Structure and inhibition of the drug-resistant S31N mutant of the M2 ion channel of influenza A virus. The discovery of inhibitors of S31N has been hampered by the limited size, polarity, and dynamic nature of its amantadine-binding site. 2013 Proc Natl Acad Sci U S A Abstract IV S31N 31 35 23302696 Structure and inhibition of the drug-resistant S31N mutant of the M2 ion channel of influenza A virus. This S31N inhibitor, like other potent M2 inhibitors, contains a charged ammonium group. 2013 Proc Natl Acad Sci U S A Abstract IV S31N 5 9 M2 39 41 23307364 A serine-to-asparagine mutation at position 314 of H5N1 avian influenza virus NP is a temperature-sensitive mutation that interferes with nuclear localization of NP. This mutant NP contains a serine-to-asparagine mutation at position 314 (S314N). 2013 Archives of virology Abstract IV S314N;S314N 73;26 78;71 NP 12 14 23307376 Pathobiology and virus shedding of low-pathogenic avian influenza virus (A/H1N1) infection in mallards exposed to oseltamivir. The ducks were subjected to three low concentrations (80 ng/L, 1 mug/L, and 80 mug/L) of the active metabolite of oseltamivir (Tamiflu( )), oseltamivir carboxylate (OC), which resulted in the development of the viral resistance mutation H274Y at 1 and 80 mug/L. 2013 Journal of wildlife diseases Abstract IV H274Y 237 242 23307376 Pathobiology and virus shedding of low-pathogenic avian influenza virus (A/H1N1) infection in mallards exposed to oseltamivir. There was no obvious difference in the course of the infection in artificial versus contact infection, when the level of OC was increased from 80 ng/L to 1 mug/L (based on IHC and q-PCR), when the level of OC was increased to 80 mug/L, or when the resistance mutation H274Y developed (based on q-PCR). 2013 Journal of wildlife diseases Abstract IV H274Y 268 273 23326573 An assay suitable for high throughput screening of anti-influenza drugs. Two potential inhibitors for M2 (V27A) mutant were verified using this method, which inhibit both the mutant and wild-type M2 channels. 2013 PloS one Abstract IV V27A 33 37 M2;M2 29;123 31;125 23351651 Within-patient emergence of the influenza A(H1N1)pdm09 HA1 222G variant and clear association with severe disease, Norway. In most of the D222G cases (11/13), the mutant virus was found as a quasispecies. 2013 Euro surveillance Abstract IV D222G 15 20 23351651 Within-patient emergence of the influenza A(H1N1)pdm09 HA1 222G variant and clear association with severe disease, Norway. No D222G mutations were found among the 381 mild cases. 2013 Euro surveillance Abstract IV D222G 3 8 23351651 Within-patient emergence of the influenza A(H1N1)pdm09 HA1 222G variant and clear association with severe disease, Norway. The association between a particular mutation in the HA1 subunit of the influenza virus haemagglutinin, D222G, and severe and fatal disease in cases of influenza A(H1N1)pdm09 in Norway during the 2009 pandemic was investigated using pyrosequencing. 2013 Euro surveillance Abstract IV D222G 104 109 HA1;HA 53;88 56;102 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. Alanine mutation at amino acid 8 (R8A) caused a significant reduction in the nuclear localization and binding to the three importin isoforms. 2013 PloS one Abstract IV R8A 34 37 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. By contrast, another mutant, S9A NP, which localized in the nucleus, caused a reduction in viral growth and vRNA transcription, suggesting that the unconventional NLS within NP may be associated with nuclear transport, vRNA transcription and viral replication through independent pathways. 2013 PloS one Abstract IV S9A 29 32 NP;NP 33;174 35;176 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. Furthermore, activities of vRNA transcription and replication of S9A NP mutants were decreased by silencing Qip1 in without changing nuclear localization, indicating that Qip1 involves in multiplication of S9A mutant virus independently of nuclear transport function. 2013 PloS one Abstract IV S9A;S9A 65;206 68;209 NP 69 71 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. Interestingly, the N-terminal 110-amino acid region, which contained the unconventional NLS with S9A mutation, mainly bound to Qip1. 2013 PloS one Abstract IV S9A 97 100 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. The R8A NP mutant virus did not generate by reverse-genetics approach. 2013 PloS one Abstract IV R8A 4 7 NP 8 10 23383318 Inhibitors of the influenza A virus M2 proton channel discovered using a high-throughput yeast growth restoration assay. Despite progress in designing inhibitors of V27A and L26F M2, there are currently no drugs targeting these mutated channels in clinical trials. 2013 PloS one Abstract IV V27A;L26F 44;53 48;57 M2 58 60 23383318 Inhibitors of the influenza A virus M2 proton channel discovered using a high-throughput yeast growth restoration assay. The effectiveness of these drugs has been dramatically limited by the rapid spread of drug resistant mutations, mainly at sites S31N, V27A and L26F in the pore of the channel. 2013 PloS one Abstract IV V27A;S31N;L26F 134;128;143 138;132;147 23385316 Analysis of oseltamivir resistance substitutions in influenza virus glycoprotein neuraminidase using a lentivirus-based surrogate assay system. In contrast, a mutant NA (H274Y) is more resistant to oseltamivir treatment. 2013 Virologica Sinica Abstract IV H274Y 26 31 22 24 23397331 Influenza virus A(H1N1)pdm09 hemagglutinin polymorphism and associated disease in southern Germany during the 2010/11 influenza season. The D222G mutation, which had previously been observed in severe cases, was not detected. 2013 Archives of virology Abstract IV D222G 4 9 23397331 Influenza virus A(H1N1)pdm09 hemagglutinin polymorphism and associated disease in southern Germany during the 2010/11 influenza season. The H275Y mutation in the influenza virus neuraminidase gene, known to confer resistance to the neuraminidase inhibitor oseltamivir, was detected in one patient. 2013 Archives of virology Abstract IV H275Y 4 9 NA;NA 42;96 55;109 23408613 Identification of critical residues in the hemagglutinin and neuraminidase of influenza virus H1N1pdm for vaccine virus replication in embryonated chicken eggs. In 2009, we successfully produced a high-yield live attenuated H1N1pdm A/California/7/2009 vaccine (CA/09 LAIV) by substitution of three residues (K119E, A186D, and D222G) in the hemagglutinin (HA) protein. 2013 Journal of virology Abstract IV K119E;A186D;D222G 147;154;165 152;159;170 HA;HA 194;179 196;192 23408613 Identification of critical residues in the hemagglutinin and neuraminidase of influenza virus H1N1pdm for vaccine virus replication in embryonated chicken eggs. The 2010 strains with the new HA substitutions near the HA receptor binding site (N125D and D127E or D127E and K209E) grew well in eggs and formed large plaques in Madin-Darby canine kidney (MDCK) cells. 2013 Journal of virology Abstract IV N125D;D127E;D127E;K209E 82;92;101;111 87;97;106;116 HA;HA 30;56 32;58 23408622 A single amino acid at the hemagglutinin cleavage site contributes to the pathogenicity but not the transmission of Egyptian highly pathogenic H5N1 influenza virus in chickens. The R325G substitution significantly reduced pathogenicity without altering the transmission efficiency of HPAI H5N1 virus. 2013 Journal of virology Abstract IV R325G 4 9 23418535 Evolutionary characterization of the pandemic H1N1/2009 influenza virus in humans based on non-structural genes. Strains of the 2009 H1N1 pandemic influenza A virus could be divided into two categories based on the V123I mutation in the NS1 gene: G1 (characterized as 123 Val) and G2 (characterized as 123 Ile). 2013 PloS one Abstract IV V123I 102 107 NS1 124 127 23436652 Structural and functional characterization of K339T substitution identified in the PB2 subunit cap-binding pocket of influenza A virus. Our statistical analysis of PB2 sequences showed that residue Lys(339) located in the cap-binding pocket of H5N1 PB2cap was gradually replaced by Thr(339) over the past decade. 2013 The Journal of biological chemistry Abstract IV K339T 62 154 23436652 Structural and functional characterization of K339T substitution identified in the PB2 subunit cap-binding pocket of influenza A virus. The K339T substitution in the cap-binding pocket of PB2 modulates the polymerase activity and virulence by regulating the cap binding activity. 2013 The Journal of biological chemistry Abstract IV K339T 4 9 PB2 52 55 23436652 Structural and functional characterization of K339T substitution identified in the PB2 subunit cap-binding pocket of influenza A virus. The structures showed that Lys(339) contributes to binding the gamma-phosphate group of m(7)GTP, and the replacement of Lys(339) by Thr eliminates this interaction. 2013 The Journal of biological chemistry Abstract IV K339T 119 136 23436652 Structural and functional characterization of K339T substitution identified in the PB2 subunit cap-binding pocket of influenza A virus. The structures showed that Lys(339) contributes to binding the 纬-phosphate group of m(7)GTP, and the replacement of Lys(339) by Thr eliminates this interaction. 2013 The Journal of biological chemistry Abstract IV K339T 115 132 23437033 Quantitative description of glycan-receptor binding of influenza A virus H7 hemagglutinin. Furthermore, we have demonstrated for the first time that two specific mutations; Gln226 Leu and Gly228 Ser in glycan receptor-binding site of H7 HA substantially increase its binding affinity to human receptor. 2013 PloS one Abstract IV Q226L;G228S 82;97 92;107 HA 146 148 23437217 Parallel screening of wild-type and drug-resistant targets for anti-resistance neuraminidase inhibitors. Importantly, a dual H275Y/I223R mutation detected in the pandemic influenza A 2009 virus strain results in multidrug resistance to current neuraminidase (NA) drugs. 2013 PloS one Abstract IV H275Y;I223R;H275Y 20;26;20 25;31;27 NA;NA 154;139 156;152 23437217 Parallel screening of wild-type and drug-resistant targets for anti-resistance neuraminidase inhibitors. Initially, we analyzed the subsite of the dual H275Y/I223R NA mutant. 2013 PloS one Abstract IV H275Y;I223R 47;53 54;58 59 61 23437533 [Cuban strategy for the molecular characterization of the pandemic influenza A virus (H1N1)]. RESULTS: The third strategy provided the most comprehensive results such as differential diagnosis, the surveillance of the D222G/E mutation in hemagglutinin and Tamiflu-resistant H275Y viral variants. 2011 Revista cubana de medicina tropical Abstract IV D222G;D222E;H275Y 124;124;180 131;131;185 HA 144 157 23437766 Discovery of novel dual inhibitors of the wild-type and the most prevalent drug-resistant mutant, S31N, of the M2 proton channel from influenza A virus. However, the S31N mutant presents a huge challenge to drug discovery, and it has been considered undruggable for several decades. 2013 Journal of medicinal chemistry Abstract IV S31N 13 17 23437766 Discovery of novel dual inhibitors of the wild-type and the most prevalent drug-resistant mutant, S31N, of the M2 proton channel from influenza A virus. S31N is the predominant and amantadine-resistant M2 mutant, present in almost all of the circulating influenza A strains as well as in the pandemic 2009 H1N1 and the highly pathogenic H5N1 flu strains. 2013 Journal of medicinal chemistry Abstract IV S31N 0 4 M2 49 51 23437766 Discovery of novel dual inhibitors of the wild-type and the most prevalent drug-resistant mutant, S31N, of the M2 proton channel from influenza A virus. These inhibitors demonstrate that S31N is a druggable target and provide a new starting point to design novel M2 inhibitors that address the problem of drug-resistant influenza A infections. 2013 Journal of medicinal chemistry Abstract IV S31N 34 38 M2 110 112 IAV infections 167 189 23437766 Discovery of novel dual inhibitors of the wild-type and the most prevalent drug-resistant mutant, S31N, of the M2 proton channel from influenza A virus. Thus, there is an urgent need to develop second-generation M2 inhibitors targeting the S31N mutant. 2013 Journal of medicinal chemistry Abstract IV S31N 87 91 M2 59 61 23437766 Discovery of novel dual inhibitors of the wild-type and the most prevalent drug-resistant mutant, S31N, of the M2 proton channel from influenza A virus. Using structural information, classical medicinal chemistry approaches, and M2-specific biological testing, we discovered benzyl-substituted amantadine derivatives with activity against both S31N and WT, among which 4-(adamantan-1-ylaminomethyl)-benzene-1,3-diol (44) is the most potent dual inhibitor. 2013 Journal of medicinal chemistry Abstract IV S31N 191 195 M2 76 78 23449784 The pH of activation of the hemagglutinin protein regulates H5N1 influenza virus replication and pathogenesis in mice. The HA-K582I mutant virus had greater growth and virulence in DBA/2J mice than the wild type did, although the mutant virus was highly attenuated in ducks. 2013 Journal of virology Abstract IV K582I 7 12 HA 4 6 23449784 The pH of activation of the hemagglutinin protein regulates H5N1 influenza virus replication and pathogenesis in mice. The HA-Y231H mutant virus was highly susceptible to acid inactivation in vitro and was attenuated for growth and virulence in mice, suggesting that an H5N1 HA protein triggered at pH 6.3 is too unstable for the virus to remain fit. 2013 Journal of virology Abstract IV Y231H 7 12 HA;HA 4;156 6;158 23449784 The pH of activation of the hemagglutinin protein regulates H5N1 influenza virus replication and pathogenesis in mice. To investigate how mutations that alter the activation pH of the HA protein influence the fitness of an avian H5N1 influenza virus in a mammalian model, we infected C57BL/6J or DBA/2J mice and compared the replication and virulence of recombinant A/chicken/Vietnam/C58/04 (H5N1) HA-Y231H mutant, wild-type, and HA-H241Q and HA-K582I mutant viruses that have HA activation pH values of 6.3, 5.9, 5.6, and 5.4, respectively. 2013 Journal of virology Abstract IV Y231H;H241Q;K582I 282;314;327 287;319;332 HA;HA;HA;HA;HA 65;279;311;324;358 67;281;313;326;360 23449784 The pH of activation of the hemagglutinin protein regulates H5N1 influenza virus replication and pathogenesis in mice. Wild-type and HA-H241Q viruses were similar in pathogenicity and grew to similar levels in mice, ducks, and cell cultures derived from both avian and mammalian tissues, suggesting that H5N1 HA proteins triggered at pH values in the range of 5.9 to 5.6 broadly support replication. 2013 Journal of virology Abstract IV H241Q 17 22 HA;HA 14;190 16;192 23450341 A case of recurrent acute encephalopathy with febrile convulsive status epilepticus with carnitine palmitoyltransferase II variation. The patient had a thermolabile genotype of carnitine palmitoyltransferase II (CPT II) variations consisting of three single nucleotide polymorphisms in exons 4 [1055T > G/F352C and 1102G > A/V368I] and 5 [1939A > G/M647V]. 2013 Neuropediatrics Abstract IV F352C;V368I;M647V 171;191;215 176;196;220 23451169 Simultaneous detection of oseltamivir- and amantadine-resistant influenza by oligonucleotide microarray visualization. Consequently, a cost-effective oligonucleotide microarray visualization method, which was based on quantum dot-catalyzed silver deposition, was developed and evaluated for the simultaneous detection of neuraminidase H275Y and E119V; matrix protein 2 V27A and S31N mutations of influenza A (H3N2), seasonal influenza A (H1N1), and 2009 influenza A (H1N1). 2013 PloS one Abstract IV H275Y;E119V;V27A;S31N 216;226;250;259 221;231;254;263 M;NA 233;202 249;215 23459475 Effect of oseltamivir carboxylate consumption on emergence of drug-resistant H5N2 avian influenza virus in Mallard ducks. These results indicate that consumption by wild waterfowl of OC in drinking water may promote selection of the E119V resistance mutation in some strains of H5N2 AIV that could contribute to viruses infecting human populations. 2013 Antimicrobial agents and chemotherapy Abstract IV E119V 111 116 23459475 Effect of oseltamivir carboxylate consumption on emergence of drug-resistant H5N2 avian influenza virus in Mallard ducks. Virus isolates carrying the E119V mutation displayed in vitro replication kinetics similar to those of the wild-type virus, but in vivo, the E119V virus rapidly reverted back to wild type in the absence of OC, and only the wild-type parental strain was transmitted to contact ducks. 2013 Antimicrobial agents and chemotherapy Abstract IV E119V;E119V 28;141 33;146 23459475 Effect of oseltamivir carboxylate consumption on emergence of drug-resistant H5N2 avian influenza virus in Mallard ducks. We detected development of virus variants carrying a known molecular marker of oseltamivir resistance (neuraminidase E119V) in 4 out of 6 mallards infected with A/Mallard/Minnesota/182742/1998 (H5N2) and exposed to 1,000 ng/liter OC. 2013 Antimicrobial agents and chemotherapy Abstract IV E119V 117 122 103 116 23459490 Structure-based discovery of the novel antiviral properties of naproxen against the nucleoprotein of influenza A virus. The predicted naproxen binding sites were tested using the Y148A, R152A, R355A, and R361A proteins carrying single-point mutations. 2013 Antimicrobial agents and chemotherapy Abstract IV Y148A;R152A;R355A;R361A 59;66;73;84 64;71;78;89 23473485 Fusion peptides promote formation of bilayer cubic phases in lipid dispersions. An x-ray diffraction study. Comparative measurements were made on a series of three peptides, a 20-residue wild-type X-31 influenza virus fusion peptide, GLFGAIAGFIENGWEGMIDG, and its two point-mutant, fusion-incompetent peptides G1E and G13L, in mixtures with hydrated phospholipids, either dipalmitoleoylphosphatidylethanolamine (DPoPE), or monomethylated dioleoyl phosphatidylethanolamine (DOPE-Me), at lipid/peptide molar ratios of 200:1 and 50:1. 2013 Biophysical journal Abstract IV G1E;G13L 202;210 205;214 23473485 Fusion peptides promote formation of bilayer cubic phases in lipid dispersions. An x-ray diffraction study. The wild-type fusion peptide, WT-20, was distinguished from G1E and G13L by the markedly greater magnitude of its effect. 2013 Biophysical journal Abstract IV G1E;G13L 60;68 63;72 23483248 Molecular and serological investigations of the Influenza A(H1N1) 2009 pandemic virus in Turkey. Additional substitutions, I216V, V321I, E374K, S203T in HA, V655I in PB2, and I163V in NA, were detected. 2013 Medical microbiology and immunology Abstract IV I216V;V321I;E374K;S203T;V655I;I163V 26;33;40;47;60;78 31;38;45;52;65;83 HA;NA;PB2 56;87;69 58;89;72 23483248 Molecular and serological investigations of the Influenza A(H1N1) 2009 pandemic virus in Turkey. D222G was detected in nasal samples from two severe cases. 2013 Medical microbiology and immunology Abstract IV D222G 0 5 23483248 Molecular and serological investigations of the Influenza A(H1N1) 2009 pandemic virus in Turkey. Thirteen rRT-PCR positive samples were analyzed for presence of mutations that have been associated with host range, virulence, and antiviral resistance: substitution D222G in the HA, E627K in the PB2, and H275Y in the neuraminidase (NA). 2013 Medical microbiology and immunology Abstract IV D222G;E627K;H275Y 167;184;206 172;189;211 HA;NA;NA;PB2 180;234;219;197 182;236;232;200 23493002 Molecular characterization of influenza A(H1N1)pdm09 virus circulating during the 2009 outbreak in Thua Thien Hue, Vietnam. The NA amino acid substitutions identified did not include the oseltamivir-resistant H275Y substitution. 2013 Journal of infection in developing countries Abstract IV H275Y 85 90 4 6 23493558 Preemptive priming readily overcomes structure-based mechanisms of virus escape. Engineered viruses with a substitution at a critical residue (position 6, P6M) all evaded recognition by WT D(b)NP366-specific CD8(+) T cells, but only the NPM6I and NPM6T mutants altered the topography of a key residue (His155) in the MHC class I binding site. 2013 Proc Natl Acad Sci U S A Abstract IV P6M 74 77 NP;NP;NP 112;156;166 114;158;168 23514882 Molecular basis of the receptor binding specificity switch of the hemagglutinins from both the 1918 and 2009 pandemic influenza A viruses by a D225G substitution. A single D225G mutation in both H1s switches receptor binding specificity from alpha2,6 linkage binding to dual receptor binding. 2013 Journal of virology Abstract IV D225G 9 14 23514882 Molecular basis of the receptor binding specificity switch of the hemagglutinins from both the 1918 and 2009 pandemic influenza A viruses by a D225G substitution. Here, we show via H1-ligand complex structures that the D225G substitution results in a loss of a salt bridge between amino acids D225 and K222, enabling the key residue Q226 to interact with the avian receptor, thereby obtaining dual receptor binding. 2013 Journal of virology Abstract IV D225G 56 61 23514882 Molecular basis of the receptor binding specificity switch of the hemagglutinins from both the 1918 and 2009 pandemic influenza A viruses by a D225G substitution. This is further confirmed by a D225E mutant that retains human receptor binding specificity with the salt bridge intact. 2013 Journal of virology Abstract IV D225E 31 36 23529501 Mutations at the monomer-monomer interface away from the active site of influenza B virus neuraminidase reduces susceptibility to neuraminidase inhibitor drugs. A sequence analysis of viruses propagated in MDCK cells revealed that all three isolates contained a single mutation (Q138R, P139S, or G140R) in NA not previously associated with reduced susceptibility to NA inhibitors. 2013 Journal of infection and chemotherapy Abstract IV Q138R;P139S;G140R 118;125;135 123;130;140 NA;NA 145;205 147;207 23529501 Mutations at the monomer-monomer interface away from the active site of influenza B virus neuraminidase reduces susceptibility to neuraminidase inhibitor drugs. However, pyrosequencing analyses showed that the Q138R and G140R mutations were below a detectable level in the original clinical specimens; the P139S mutation was detected at a very low level, suggesting that the mutant viruses may be preferably selected during propagation in MDCK cells. 2013 Journal of infection and chemotherapy Abstract IV Q138R;G140R;P139S 49;59;145 54;64;150 23536663 Substitutions T200A and E227A in the hemagglutinin of pandemic 2009 influenza A virus increase lethality but decrease transmission. We report that swine influenza virus-like substitutions T200A and E227A in the hemagglutinin (HA) of the 2009 pandemic influenza virus alter its pathogenesis and transmission. 2013 Journal of virology Abstract IV T200A;E227A 56;66 61;71 HA;HA 94;79 96;92 23555270 Monomeric nucleoprotein of influenza A virus. The S165D mutant that mimics phosphorylation is monomeric and displays a lowered affinity for RNA compared with wt monomeric NP. 2013 PLoS pathogens Abstract IV S165D 4 9 NP 125 127 23555270 Monomeric nucleoprotein of influenza A virus. We therefore crystallized the obligate monomeric R416A mutant nucleoprotein and observed how the domain exchange loop that leads over to a neighbouring protomer in the trimer structure interacts with equivalent sites on the mutant monomer surface, avoiding polymerisation. 2013 PLoS pathogens Abstract IV R416A 49 54 NP 62 75 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. Influenza B viruses (n = 346) were sensitive to all NAIs, except two (0.6%) with H273Y (N1 numbering; H274Y in N2 numbering) substitution, exhibiting reduced susceptibility to oseltamivir and peramivir, and one with previously unreported G140R and N144K substitutions, exhibiting reduced susceptibility to oseltamivir, zanamivir, and peramivir. 2013 Influenza and other respiratory viruses Abstract IV H273Y;H274Y;G140R;N144K 81;102;238;248 86;107;243;253 NAI 52 56 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. It is unknown whether substitutions N325K, G140R, and N144K were present in the virus prior to culturing because clinical specimens were unavailable for testing. 2013 Influenza and other respiratory viruses Abstract IV N325K;G140R;N144K 36;43;54 41;48;59 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. RESULTS: Influenza A(H1N1)pdm09 viruses (n = 326) were sensitive to all NAIs, except for two (0.6%) with H275Y (N1 numbering; H274Y in N2 numbering) substitution, which exhibited elevated IC50 s for oseltamivir and peramivir, and a third with previously unreported N325K substitution, exhibiting reduced susceptibility to oseltamivir. 2013 Influenza and other respiratory viruses Abstract IV H275Y;H274Y;N325K 105;126;265 110;131;270 NAI 72 76 23588737 Comparison of influenza virus replication fidelity in vitro using selection pressure with monoclonal antibodies. The results showed A/Wyoming/3/03(H3N2) possessed lower fidelity relative to the A/California/7/04(H3N2) and A/Wisconsin/57/05(H3N2) viruses through the emergence of mutant viruses carrying H156Q hemagglutinin mutation which allows antibody escape. 2013 Journal of medical virology Abstract IV H156Q 190 195 HA 196 209 23593230 Effect of cysteine mutations in the extracellular domain of CM2 on the influenza C virus replication. Analyses of one-step grown virions and virus-infected cells could not provide evidence for any difference in growth between rC1620A and rWT. 2013 PloS one Abstract IV C1620A 124 131 23593230 Effect of cysteine mutations in the extracellular domain of CM2 on the influenza C virus replication. In the present study, to examine the effect of CM2 oligomerization on virus replication, we generated a mutant recombinant virus, rC1620A, in which all three cysteines on CM2 were substituted to alanines. 2013 PloS one Abstract IV C1620A 130 137 CM2;CM2 47;171 50;174 23593230 Effect of cysteine mutations in the extracellular domain of CM2 on the influenza C virus replication. On the other hand, the amount of genome present in VLPs possessing the mutant CM2 (C1620A-VLPs) was approximately 31% of that in VLPs possessing wild-type CM2 (WT-VLPs). 2013 PloS one Abstract IV C1620A 83 94 CM2;CM2 78;155 81;158 23593230 Effect of cysteine mutations in the extracellular domain of CM2 on the influenza C virus replication. The amount of CM2 protein incorporated into the rC1620A virions was comparable to that into the rWT virions, although the main CM2 species in the rC1620A virions was in the form of a dimer. 2013 PloS one Abstract IV C1620A 48 55 23593230 Effect of cysteine mutations in the extracellular domain of CM2 on the influenza C virus replication. The CM2 protein synthesized in rC1620A-infected cells could not apparently be detected as a tetramer and was transported to the cell surface less efficiently than was authentic CM2. 2013 PloS one Abstract IV C1620A 31 38 CM2;CM2 4;177 7;180 23593230 Effect of cysteine mutations in the extracellular domain of CM2 on the influenza C virus replication. The incoming genome from VLPs was less efficiently transported to the nucleus in the C1620A-VLP-infected cells than in WT-VLP-infected cells, leading to reduced reporter gene expression in the C1620A-VLP-infected cells. 2013 PloS one Abstract IV C1620A;C1620A 85;193 104;212 23593230 Effect of cysteine mutations in the extracellular domain of CM2 on the influenza C virus replication. The rC1620A virus was more attenuated than the recombinant wild-type (rWT) virus in cultured cells. 2013 PloS one Abstract IV C1620A 4 11 23597879 Molecular assays for quantitative and qualitative detection of influenza virus and oseltamivir resistance mutations. Four assays are included for detection of oseltamivir resistance mutations H275Y in prepandemic and pandemic influenza A/H1N1 and E119V and R292K in influenza A/H3N2 neuraminidase. 2013 The Journal of molecular diagnostics Abstract IV H275Y;E119V;R292K 75;130;140 80;135;145 166 179 23601520 [Analysis of evolution features of whole genome of influenza virus H3N2 in Qingdao between year 2007 and 2011]. The sequence analysis of M2 protein showed that the isolated influenza virus H3N2 mutated in amino acid site 31, from serine to asparagine (S31N). 2013 Zhonghua yu fang yi xue za zhi [Chinese journal of preventive medicine] Abstract IV S31N 140 144 M2 25 27 23615615 Receptor binding by a ferret-transmissible H5 avian influenza virus. The structure of the complex also explains how the change in preference from avian to human receptors arises from the Gln226Leu substitution, which facilitates binding to human receptor but restricts binding to avian receptor. 2013 Nature Abstract IV Q226L 118 127 23626667 Quantitative characterization of glycan-receptor binding of H9N2 influenza A virus hemagglutinin. Further we show that alpha2 6 glycan receptor-binding affinity of a mutant H9 HA carrying Thr-189 Ala amino acid change correlates with the respiratory droplet transmission in ferrets conferred by this change. 2013 PloS one Abstract IV T189A 90 101 HA 78 80 23628410 Genomic signature and protein sequence analysis of a novel influenza A (H7N9) virus that causes an outbreak in humans in China. The HA protein has the Q226L mutation, which is associated with increased binding to mammalian-like receptors bearing alpha 2,6 receptor in the human upper airway. 2013 Microbes and infection Abstract IV Q226L 23 28 HA 4 6 23628410 Genomic signature and protein sequence analysis of a novel influenza A (H7N9) virus that causes an outbreak in humans in China. The M2 protein contains the N31S mutation, suggesting its resistance to the M2 channel blockers amantadine and rimantadine. 2013 Microbes and infection Abstract IV N31S 28 32 M2;M2 4;76 6;78 23638404 Virtual screening for oseltamivir-resistant a (H5N1) influenza neuraminidase from traditional Chinese medicine database: a combined molecular docking with molecular dynamics approach. Most importantly, H274Y mutation in neuraminidase exhibits high levels of resistance to oseltamivir. 2013 SpringerPlus Abstract IV H274Y 18 23 36 49 23640582 Genetic diversity of early (1998) and recent (2010) avian influenza H9N2 virus strains isolated from poultry in Iran. An analysis of the viral amino acid sequence of the M2 protein of the recent strain revealed a V27A mutation, which is associated with amantadine resistance in avian influenza virus. 2013 Archives of virology Abstract IV V27A 95 99 M2 52 54 23640582 Genetic diversity of early (1998) and recent (2010) avian influenza H9N2 virus strains isolated from poultry in Iran. The deduced amino acid sequence of the new isolate contained the mutation Q226L, which is a characteristic of human-type sialic acid influenza receptor binding. 2013 Archives of virology Abstract IV Q226L 74 79 23646055 Occurrence and characterization of oseltamivir-resistant influenza virus in children between 2007-2008 and 2008-2009 seasons. However, phenotypic analysis of the virus revealed a high oseltamivir IC50 range and that H275Y substitution of the neuraminidase (NA) gene and partial variation of the hemagglutinin (HA) gene did not affect its antigenicity to the HA vaccine even though group A had a shorter hospitalization duration and fewer lower respiratory tract complications than group B. 2013 Korean journal of pediatrics Abstract IV H275Y 90 95 HA;HA;HA;NA;NA 184;232;169;131;116 186;234;182;133;129 23657795 Environmental connections of novel avian-origin H7N9 influenza virus infection and virus adaptation to the human. One of the Hangzhou viruses had gained a novel amino acid substitution (Q226I) in the receptor binding region of hemagglutinin. 2013 Science China. Life sciences Abstract IV Q226I 72 77 HA 113 126 23665848 Molecular detection of human H7N9 influenza A virus causing outbreaks in China. The virus is a reassortant of avian viruses, but these human isolates contain mutations [hemagglutinin (HA) Q226L and PB2 E627K] that might make it easier for the virus to adapt to mammalian hosts. 2013 Clinical chemistry Abstract IV Q226L;E627K 108;122 113;127 HA;HA;PB2 104;89;118 106;102;121 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. Glycan binding assays demonstrated the N156K escape mutant had altered receptor binding preferences compared to wildtype virus, which was supported by computational modeling predictions. 2013 PLoS pathogens Abstract IV N156K 39 44 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. In this study, sequential passaging of A(H1N1)pdm09 virus by contact transmission through two independent series of suboptimally vaccinated ferrets resulted in selection of variant viruses with an amino acid substitution (N156K, H1 numbering without signal peptide; N159K, H3 numbering without signal peptide; N173K, H1 numbering from first methionine) in a known antigenic site of the viral HA. 2013 PLoS pathogens Abstract IV N156K;N159K;N173K 222;266;310 227;271;315 HA 392 394 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. In vitro, in a range of cell culture systems, the N156K variant rapidly adapted, acquiring additional mutations in the viral HA that also potentially affected antigenic properties. 2013 PLoS pathogens Abstract IV N156K 50 55 HA 125 127 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. The N156K escape mutant was antigenically distinct from wildtype virus as shown by binding of HA-specific antibodies. 2013 PLoS pathogens Abstract IV N156K 4 9 HA 94 96 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. The N156K HA variant replicated and transmitted efficiently between naive ferrets and outgrew wildtype virus in vivo in ferrets in the presence and absence of immune pressure. 2013 PLoS pathogens Abstract IV N156K 4 9 HA 10 12 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. The N156K substitution, and culture adaptations, have been detected in human A(H1N1)pdm09 viruses with N156K preferentially reported in sequences from original clinical samples rather than cultured isolates. 2013 PLoS pathogens Abstract IV N156K;N156K 4;103 9;108 23683998 Molecular characterization of a H5N1 highly pathogenic avian influenza virus clade 2.3.2.1b circulating in Vietnam in 2011. Additionally, we identified numerous mutations with amino acid substitutions in the hemagglutinin: M226I, I239S located at N-link glycosylation site and 2H, 45N, 53K 120D, 133A and 14N mutations at antigenic site, which can affect receptor specificity as well as viral pathogenicity. 2013 Veterinary microbiology Abstract IV M226I;I239S 99;106 104;111 HA 84 97 23683998 Molecular characterization of a H5N1 highly pathogenic avian influenza virus clade 2.3.2.1b circulating in Vietnam in 2011. Notably, I239S and S133A mutations are unique to A/Duck/QuangNgai/1037/2011, suggesting that it may involve in the virus' ability to evade the host immune system. 2013 Veterinary microbiology Abstract IV I239S;S133A 9;19 14;24 23717200 Prolonged influenza virus shedding and emergence of antiviral resistance in immunocompromised patients and ferrets. Given the inherent difficulties in studying antiviral efficacy in immunocompromised patients, we have infected immunocompromised ferrets with either wild-type, or oseltamivir-resistant (H275Y) 2009 pandemic virus. 2013 PLoS pathogens Abstract IV H275Y 186 191 23717200 Prolonged influenza virus shedding and emergence of antiviral resistance in immunocompromised patients and ferrets. In 5 out of these 11 (45%) cases oseltamivir resistant H275Y viruses emerged. 2013 PLoS pathogens Abstract IV H275Y 55 60 23717200 Prolonged influenza virus shedding and emergence of antiviral resistance in immunocompromised patients and ferrets. In wild-type virus infected animals treated with oseltamivir, H275Y resistant variants emerged within a week after infection. 2013 PLoS pathogens Abstract IV H275Y 62 67 23759670 Virological self-sampling to monitor influenza antiviral susceptibility in a community cohort. Influenza A(H1N1)pdm09 RT-PCR-positive samples were screened for the oseltamivir resistance-inducing H275Y substitution, and a subset of samples also underwent phenotypic antiviral susceptibility testing by enzyme inhibition assay. 2013 The Journal of antimicrobial chemotherapy Abstract IV H275Y 101 106 23759670 Virological self-sampling to monitor influenza antiviral susceptibility in a community cohort. No reduction in phenotypic susceptibility to neuraminidase inhibitors was detected, but five cases with minority quasi-species of oseltamivir-resistant virus (an H275Y amino acid substitution in neuraminidase) were detected. 2013 The Journal of antimicrobial chemotherapy Abstract IV H275Y 162 167 NA;NA 45;195 58;208 23771788 Epidemiology and full genome sequence analysis of H1N1pdm09 from Northeast China. Three HA amino acid site substitutions occurred at the HA receptor-binding sites and antigenic determinant, including S179N and K180T (located at antigenic site Sa) in A/Tianjinhedong/SWL44/2011(H1) and A/Tianjinjinnan/SWL41/2011(H1), and D239N (located at antigenic site Ca) in A/Tianjinninghe/SWL49/2009(H1). 2013 Virus genes Abstract IV S179N;K180T;D239N 118;128;239 123;133;244 HA;HA 6;55 8;57 23778667 Oseltamivir-resistant influenza A(H1N1)pdm09 virus in southern Brazil. Clinical samples were collected in the state of Rio Grande do Sul (RS) from 2009-2011 and two NA inhibitor-resistant mutants were identified, one in 2009 (H275Y) and the other in 2011 (S247N). 2013 Memorias do Instituto Oswaldo Cruz Abstract IV H275Y;S247N 155;185 160;190 94 96 23779115 Factors responsible for pathogenicity in chickens of a low-pathogenic H7N7 avian influenza virus isolated from a feral duck. Six amino acid substitutions were identified by comparison of the Vac2sub-P3 and Vac2sub-P0 genomic sequences: Lys123Glu in PB2, Asn16Asp in PB1, Glu227Gly and Ile388Thr in HA, Gly228Arg in M1, and Leu46Pro in M2. 2013 Archives of virology Abstract IV K123E;N16D;E227G;I388T;G228R;L46P 111;129;146;160;177;198 120;137;155;169;186;206 HA;M1;M2;PB1;PB2 173;190;210;141;124 175;192;212;144;127 23779115 Factors responsible for pathogenicity in chickens of a low-pathogenic H7N7 avian influenza virus isolated from a feral duck. The results of intravenous inoculations of chickens with recombinant virus indicated that all six amino acid substitutions were required to varying degrees for Vac2sub-P3 pathogenicity, with Glu227Gly and Ile388Thr in HA being particularly essential. 2013 Archives of virology Abstract IV E227G;I388T 191;205 200;214 HA 218 220 23787694 Receptor binding by an H7N9 influenza virus from humans. The human-receptor-binding properties of human H7 probably arise from the introduction of two bulky hydrophobic residues by the substitutions Gln226Leu and Gly186Val. 2013 Nature Abstract IV Q226L;G186V 142;156 151;165 23791870 Neuraminidase inhibitor susceptibility profile of pandemic and seasonal influenza viruses during the 2009-2010 and 2010-2011 influenza seasons in Japan. Among influenza A(H1N1)pdm09 viruses, the prevalence of H274Y viruses increased from 0% in the 2009-2010 season to 3% in the 2010-2011 season. 2013 Antiviral research Abstract IV H274Y 56 61 23791870 Neuraminidase inhibitor susceptibility profile of pandemic and seasonal influenza viruses during the 2009-2010 and 2010-2011 influenza seasons in Japan. Among influenza A(H3N2) viruses, two outliers were identified with D151G and T148I mutations, which exhibited a reduction in susceptibility to oseltamivir and zanamivir, respectively. 2013 Antiviral research Abstract IV D151G;T148I 67;77 72;82 23791870 Neuraminidase inhibitor susceptibility profile of pandemic and seasonal influenza viruses during the 2009-2010 and 2010-2011 influenza seasons in Japan. For paired samples that were collected before and after drug treatment, three (3/11; 27.3%) H274Y viruses were identified among A(H1N1)pdm09 viruses after oseltamivir treatment but no outliers were found in the laninamivir-treatment group (n=3). 2013 Antiviral research Abstract IV H274Y 92 97 23791870 Neuraminidase inhibitor susceptibility profile of pandemic and seasonal influenza viruses during the 2009-2010 and 2010-2011 influenza seasons in Japan. Other mutations in NA, such as I222T and M241I were identified among the outliers. 2013 Antiviral research Abstract IV I222T;M241I 31;41 36;46 19 21 23791870 Neuraminidase inhibitor susceptibility profile of pandemic and seasonal influenza viruses during the 2009-2010 and 2010-2011 influenza seasons in Japan. These H274Y viruses were resistant to oseltamivir and peramivir with 200-300 fold increase in IC50 values but remained sensitive to zanamivir and laninamivir. 2013 Antiviral research Abstract IV H274Y 6 11 23794001 Structure and receptor-binding properties of an airborne transmissible avian influenza A virus hemagglutinin H5 (VN1203mut). As the Q226L substitution is shown important for obtaining human receptor binding, we suspect that the newly emerged H7N9 binds human receptor as H7 has a Q226L substitution. 2013 Protein & cell Abstract IV Q226L;Q226L 7;155 12;160 23794010 Insight into the oseltamivir resistance R292K mutation in H5N1 influenza virus: a molecular docking and molecular dynamics approach. In particular, influenza strains with a R292K NA mutation are highly resistant to the oseltamivir. 2014 Cell biochemistry and biophysics Abstract IV R292K 40 45 46 48 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. In addition, compared to the NY1682-WT virus, the NY1682-D701N mutant virus induced less IFN-lambda and replicated to a higher titer in primary human alveolar epithelial cells. 2013 PloS one Abstract IV D701N 57 62 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. Mini-genome replication assay, in vitro replication characteristics in cell lines, and analysis in the mouse and ferret models demonstrated that PB2-D701N increased virus replication rates and resulted in more severe pathogenicity in mice and more efficient transmission in ferrets. 2013 PloS one Abstract IV D701N 149 154 PB2 145 148 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. Previous studies have shown that PB2-627K is not necessary because of a compensatory Q591R substitution. 2013 PloS one Abstract IV Q591R 85 90 PB2 33 36 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. The 2009/2010 pandemic influenza virus (H1N1pdm) contains an avian-lineage PB2 gene that lacks E627K and D701N substitutions important in the pathogenesis and transmission of avian-origin viruses in humans or other mammals. 2013 PloS one Abstract IV E627K;D701N 95;105 100;110 PB2 75 78 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. Therefore, PB2-D701N was introduced into an H1N1pdm virus (A/New York/1682/2009 (NY1682)) and analyzed in vitro and in vivo. 2013 PloS one Abstract IV D701N 15 20 PB2 11 14 23824808 Functional and structural analysis of influenza virus neuraminidase N3 offers further insight into the mechanisms of oseltamivir resistance. Furthermore, we found that members of NA serotype N3 also possess Y252, raising the key question as to whether or not H274Y resistance may also be possible for some group 2 NAs. 2013 Journal of virology Abstract IV H274Y 118 123 NA;NA 38;173 40;176 23824808 Functional and structural analysis of influenza virus neuraminidase N3 offers further insight into the mechanisms of oseltamivir resistance. Here, we demonstrate that the H274Y substitution results in mild oseltamivir resistance for N3. 2013 Journal of virology Abstract IV H274Y 30 35 23824808 Functional and structural analysis of influenza virus neuraminidase N3 offers further insight into the mechanisms of oseltamivir resistance. However, H274Y has only been reported in N1 subtypes, which indicates that there must be additional key residues that determine H274Y resistance. 2013 Journal of virology Abstract IV H274Y;H274Y 9;128 14;133 23824808 Functional and structural analysis of influenza virus neuraminidase N3 offers further insight into the mechanisms of oseltamivir resistance. Previous structural studies suggest that the group specific 252 residue (Y252 in group 1 and T252 in group 2) might be a key factor underlying H274Y resistance. 2013 Journal of virology Abstract IV H274Y 143 148 23824808 Functional and structural analysis of influenza virus neuraminidase N3 offers further insight into the mechanisms of oseltamivir resistance. The influenza virus neuraminidase H274Y substitution is a highly prevalent amino acid substitution associated with resistance to the most heavily used influenza drug, oseltamivir. 2013 Journal of virology Abstract IV H274Y 34 39 20 33 23824816 Single hemagglutinin mutations that alter both antigenicity and receptor binding avidity influence influenza virus antigenic clustering. Enzyme-linked immunosorbent assays (ELISA) revealed that the N145K HA mutation does not prevent antibody binding; rather, viruses possessing this mutation escape antisera in HAI assays simply by attaching to cells more efficiently. 2013 Journal of virology Abstract IV N145K 61 66 HA 67 69 23824816 Single hemagglutinin mutations that alter both antigenicity and receptor binding avidity influence influenza virus antigenic clustering. Reverse-genetics experiments demonstrated that the N145K HA mutation increases viral receptor binding avidity. 2013 Journal of virology Abstract IV N145K 51 56 HA 57 59 23824816 Single hemagglutinin mutations that alter both antigenicity and receptor binding avidity influence influenza virus antigenic clustering. Unexpectedly, we found an asymmetric antigenic effect of the N145K HA mutation. 2013 Journal of virology Abstract IV N145K 61 66 HA 67 69 23824816 Single hemagglutinin mutations that alter both antigenicity and receptor binding avidity influence influenza virus antigenic clustering. We experimentally focused on an antigenic cluster associated with a single N145K hemagglutinin (HA) substitution that occurred between 1992 and 1995. 2013 Journal of virology Abstract IV N145K 75 80 HA;HA 96;81 98;94 23824818 Increased acid stability of the hemagglutinin protein enhances H5N1 influenza virus growth in the upper respiratory tract but is insufficient for transmission in ferrets. The acid-stabilizing HA2-K58I mutation, which diminishes H5N1 replication and transmission in ducks, increased the virus load in the ferret nasal cavity early during infection while simultaneously reducing the virus load in the lungs. 2013 Journal of virology Abstract IV K58I 25 29 HA 21 23 23824818 Increased acid stability of the hemagglutinin protein enhances H5N1 influenza virus growth in the upper respiratory tract but is insufficient for transmission in ferrets. The VN1203-HA2-K58I virus had replication kinetics similar to those of wild-type VN1203 in MDCK and normal human bronchial epithelial cells and yet had reduced growth in human alveolar A549 cells, which were found to have a higher endosomal pH than MDCK cells. 2013 Journal of virology Abstract IV K58I 15 19 HA 11 13 23824818 Increased acid stability of the hemagglutinin protein enhances H5N1 influenza virus growth in the upper respiratory tract but is insufficient for transmission in ferrets. We generated isogenic A/Vietnam/1203/2004 (H5N1) (VN1203) viruses containing either wild-type HA protein (activation pH 6.0) or an HA2-K58I point mutation (K to I at position 58) (activation pH 5.5). 2013 Journal of virology Abstract IV K58I 135 139 HA;HA 94;131 96;133 23824818 Increased acid stability of the hemagglutinin protein enhances H5N1 influenza virus growth in the upper respiratory tract but is insufficient for transmission in ferrets. Wild-type and HA2-K58I viruses promoted similar levels of morbidity and mortality in C57BL/6J mice and ferrets, and neither virus transmitted efficiently to naive contact cage-mate ferrets. 2013 Journal of virology Abstract IV K58I 18 22 HA 14 16 23824822 Mutational analysis of the binding pockets of the diketo acid inhibitor L-742,001 in the influenza virus PA endonuclease. Marked (up to 20-fold) resistance to L-742,001 was observed for the H41A, I120T, and G81F/V/T mutant forms of PA. 2013 Journal of virology Abstract IV H41A;I120T;G81F;G81V;G81T 68;74;85;85;85 72;79;93;93;93 PA 110 112 23824822 Mutational analysis of the binding pockets of the diketo acid inhibitor L-742,001 in the influenza virus PA endonuclease. Two- to 3-fold resistance was seen for the T20A, L42T, and V122T mutants, and the R124Q and Y130A mutants were 3-fold more sensitive to L-742,001. 2013 Journal of virology Abstract IV T20A;L42T;V122T;R124Q;Y130A 43;49;59;82;92 47;53;64;87;97 23843641 The amphipathic helix of influenza A virus M2 protein is required for filamentous bud formation and scission of filamentous and spherical particles. Electron microscopy showed that with the 5PM and the I51A-Y52A A/Udorn/72 and WSN viruses, scission failed, and emerging virus particles exhibited a "beads-on-a-string" morphology. 2013 Journal of virology Abstract IV I51A;Y52A 53;58 57;62 23843641 The amphipathic helix of influenza A virus M2 protein is required for filamentous bud formation and scission of filamentous and spherical particles. When the 5PM and a representative double mutant (I51A-Y52A) were introduced into A/WSN/33 M2, a strain that produces spherical particles, similar debilitation in viral growth occurred. 2013 Journal of virology Abstract IV I51A;Y52A 49;54 53;58 M2 90 92 23843645 The effect of the PB2 mutation 627K on highly pathogenic H5N1 avian influenza virus is dependent on the virus lineage. Intriguingly, PB2 628R and/or A1869G appeared to improve the genetic stability of 50-92 PB2 627K. 2013 Journal of virology Abstract IV A1869G 30 36 PB2;PB2 14;88 17;91 23843645 The effect of the PB2 mutation 627K on highly pathogenic H5N1 avian influenza virus is dependent on the virus lineage. The 50-92 PB2 627K was genetically unstable during virus propagation, resulting in reversion to PB2 627E or the accumulation of the additional mutation PB2 628R and/or a synonymous mutation from an A to a G nucleotide at nucleotide position 1869 (PB2 A1869G). 2013 Journal of virology Abstract IV A1869G 251 257 PB2;PB2;PB2;PB2 10;96;152;247 13;99;155;250 23860768 Resistance to neuraminidase inhibitors conferred by an R292K mutation in a human influenza virus H7N9 isolate can be masked by a mixed R/K viral population. IMPORTANCE: The neuraminidase (NA) inhibitors oseltamivir and zanamivir are currently the front-line therapeutic options against the novel H7N9 influenza viruses, which possess an S31N mutation that confers resistance to the M2 ion channel blockers. 2013 mBio Abstract IV S31N 180 184 M2;NA;NA 225;31;16 227;33;29 23860768 Resistance to neuraminidase inhibitors conferred by an R292K mutation in a human influenza virus H7N9 isolate can be masked by a mixed R/K viral population. Our results confirmed that the NA R292K mutation confers resistance to oseltamivir, peramivir, and zanamivir in the novel human H7N9 viruses. 2013 mBio Abstract IV R292K 34 39 31 33 23860768 Resistance to neuraminidase inhibitors conferred by an R292K mutation in a human influenza virus H7N9 isolate can be masked by a mixed R/K viral population. Resistance to NA inhibitors conferred by the R292K mutation in a human influenza virus H7N9 isolate can be masked by a mixed R/K viral population, and this should be taken into consideration while monitoring antiviral resistance in patients with H7N9 infection. 2013 mBio Abstract IV R292K 45 50 14 16 Influenza A virus H7N9 infection 246 260 23876206 Genetic diversity of influenza B virus in 2009-2010 and 2010-2011 in Tunisia. This study allowed identifying amino acid substitutions: T121A, S150I, N165Y, T181A, G183R, D196N, S229D, M251V and K253R in the B/Yamagata lineage; L58P, N75K, K109N, N165K, S172P and K257R into the B/Victoria lineage. 2013 Medecine et maladies infectieuses Abstract IV T121A;S150I;N165Y;T181A;G183R;D196N;S229D;M251V;K253R;L58P;N75K;K109N;N165K;S172P;K257R 57;64;71;78;85;92;99;106;116;149;155;161;168;175;185 62;69;76;83;90;97;104;111;121;153;159;166;173;180;190 23886034 Influenza A/Hong Kong/156/1997(H5N1) virus NS1 gene mutations F103L and M106I both increase IFN antagonism, virulence and cytoplasmic localization but differ in binding to RIG-I and CPSF30. CONCLUSIONS: The F103L and M106I mutations in the H5N1 NS1 protein each increased IFN antagonism and mediated interstitial pneumonia in mice that was associated with increased cytoplasmic localization and altered host factor binding. 2013 Virology journal Abstract IV F103L;M106I 17;27 22;32 NS1 55 58 Pneumonia 110 132 23886034 Influenza A/Hong Kong/156/1997(H5N1) virus NS1 gene mutations F103L and M106I both increase IFN antagonism, virulence and cytoplasmic localization but differ in binding to RIG-I and CPSF30. Each of the F103L and M106I mutations restored a defect in cytoplasmic localization of H5N1 NS1 in mouse cells. 2013 Virology journal Abstract IV F103L;M106I 12;22 17;27 NS1 92 95 23886034 Influenza A/Hong Kong/156/1997(H5N1) virus NS1 gene mutations F103L and M106I both increase IFN antagonism, virulence and cytoplasmic localization but differ in binding to RIG-I and CPSF30. Human H1N1 and H3N2 NS1 proteins bound to the CARD, helicase and RD RIG-I domains, whereas the H5N1 NS1 with the same consensus 103F and 106M mutations did not bind these domains, which was totally or partially restored by the M106I or F103L mutations respectively. 2013 Virology journal Abstract IV M106I;F103L 227;236 232;241 NS1;NS1 20;100 23;103 23886034 Influenza A/Hong Kong/156/1997(H5N1) virus NS1 gene mutations F103L and M106I both increase IFN antagonism, virulence and cytoplasmic localization but differ in binding to RIG-I and CPSF30. RESULTS: Each of the F103L and M106I mutations contributes additively to virulence to reduce the lethal dose by >800 and >3,200 fold respectively by mediating alveolar tissue infection with >100 fold increased infectious yields. 2013 Virology journal Abstract IV F103L;M106I 21;31 26;36 23886034 Influenza A/Hong Kong/156/1997(H5N1) virus NS1 gene mutations F103L and M106I both increase IFN antagonism, virulence and cytoplasmic localization but differ in binding to RIG-I and CPSF30. The human A/HK/156/1997 (H5N1) virus that transmitted from poultry possesses NS1 gene mutations F103L + M106I that are virulence determinants in the mouse model of pneumonia; however their individual roles have not been determined. 2013 Virology journal Abstract IV F103L;M106I 96;104 101;109 NS1 77 80 Pneumonia 164 173 23894575 Analysis of adaptation mutants in the hemagglutinin of the influenza A(H1N1)pdm09 virus. Finally, variant 4 (E374K) altered hemagglutinin stability in the vicinity of the fusion peptide. 2013 PloS one Abstract IV E374K 20 25 HA 35 48 23894575 Analysis of adaptation mutants in the hemagglutinin of the influenza A(H1N1)pdm09 virus. Variant 2 (A134T), and variant 3 (D222E, P297S) had an increased binding affinity for the receptor. 2013 PloS one Abstract IV A134T;D222E;P297S 11;34;41 16;39;46 23894575 Analysis of adaptation mutants in the hemagglutinin of the influenza A(H1N1)pdm09 virus. We found that variant 1 (S143G, S185T) likely arose to avoid immune recognition. 2013 PloS one Abstract IV S143G;S185T 25;32 30;37 23895699 A novel reassortant H3N8 influenza virus isolated from drinking water for duck in a domestic duck farm in Poyang Lake area. The mutations of Asn30Asp, and Thr215Ala of the M1 protein implied the potential of pathogenicity increase in mice. 2013 Biomedical and environmental sciences Abstract IV N30D;T215A 17;31 25;40 M1 48 50 23902660 Frequency of D222G haemagglutinin mutant of pandemic (H1N1) pdm09 influenza virus in Tunisia between 2009 and 2011. CONCLUSIONS: A specific mutation in the viral haemagglutinin (D222G) was found in fatal, severe and mild case. 2013 Diagnostic pathology Abstract IV D222G 62 67 HA 46 60 23902660 Frequency of D222G haemagglutinin mutant of pandemic (H1N1) pdm09 influenza virus in Tunisia between 2009 and 2011. D222E substitution was found in virus taken from one patient with severe clinical syndrome (2%) out of 42 severe cases analyzed and E374K substitution was found in two severe cases (4%) out of 42 severe cases studied. 2013 Diagnostic pathology Abstract IV D222E;E374K 0;132 5;137 23902660 Frequency of D222G haemagglutinin mutant of pandemic (H1N1) pdm09 influenza virus in Tunisia between 2009 and 2011. METHODS: To monitor the genetic polymorphisms at position 222 of Haemagglutinin of influenza A(H1N1)pdm09 viruses from both outpatients with mild influenza and individuals with severe disease requiring hospitalization, during 2009-2010 and 2010-2011 seasons, a sequence-based genotypic assessment of viral populations to understand the prevalence of D222G mutation. 2013 Diagnostic pathology Abstract IV D222G 350 355 HA 65 79 23902660 Frequency of D222G haemagglutinin mutant of pandemic (H1N1) pdm09 influenza virus in Tunisia between 2009 and 2011. RESULTS: The D222G was identified in clinical specimens from 3 out of 42 cases analyzed in Tunisia with severe outcome (7%). 2013 Diagnostic pathology Abstract IV D222G 13 18 23907396 Mutations in hepatitis C virus p7 reduce both the egress and infectivity of assembled particles via impaired proton channel function. Here, we showed that proton channel activity alone, provided in trans by either influenza virus M2 or genotype 1b HCV p7, was both necessary and sufficient to restore infectious particle production to genotype 2a HCV (JFH-1 isolate) carrying deleterious p7 alanine substitutions within the p7 dibasic loop (R33A, R35A), and the N-terminal trans-membrane region (N15 : C16 : H17/AAA). 2013 The Journal of general virology Abstract IV R33A;R35A 307;313 311;317 M2 96 98 23908028 Preliminary crystallographic analysis of neuraminidase N2 from a new influenza A virus. In this study, a Q136K mutant N2 protein was expressed in a baculovirus system and crystals were obtained. 2013 Acta crystallographica. Section F, Structural biology and crystallization communications Abstract IV Q136K 17 22 23908028 Preliminary crystallographic analysis of neuraminidase N2 from a new influenza A virus. Q136K is a novel mutation in NA which confers resistance to zanamivir. 2013 Acta crystallographica. Section F, Structural biology and crystallization communications Abstract IV Q136K 0 5 29 31 23908945 Tracking oseltamivir-resistance in New Zealand influenza viruses during a medicine reclassification in 2007, a resistant-virus importation in 2008 and the 2009 pandemic. Sequencing of the neuraminidase gene showed that the resistant viruses contained an H275Y mutation, and S247N was also identified in the neuraminidase gene of one seasonal influenza A(H1N1) virus that exhibited enhanced resistance. 2012 Western Pacific surveillance and response journal Abstract IV H275Y;S247N 84;104 89;109 NA;NA 18;137 31;150 23917311 Bioluminescence-based neuraminidase inhibition assay for monitoring influenza virus drug susceptibility in clinical specimens. Notably, the QFlu assay identified oseltamivir-resistant A(H1N1)pdm09 viruses carrying the H275Y marker directly in clinical specimens, which is not feasible with the other two phenotypic assays, which required prior virus culturing in cells. 2013 Antimicrobial agents and chemotherapy Abstract IV H275Y 91 96 23917311 Bioluminescence-based neuraminidase inhibition assay for monitoring influenza virus drug susceptibility in clinical specimens. To provide proof of principle, clinical specimens (n = 235) confirmed by real-time reverse transcription (RT)-PCR to contain influenza virus A(H1N1)pdm09 and prescreened for the oseltamivir resistance marker H275Y using pyrosequencing were subsequently tested in the QFlu assay. 2013 Antimicrobial agents and chemotherapy Abstract IV H275Y 208 213 23917311 Bioluminescence-based neuraminidase inhibition assay for monitoring influenza virus drug susceptibility in clinical specimens. Unless the antigenic types were first identified, certain NA variants (e.g., H3N2 with E119V) could be detected among seasonal viruses using the FL assays only. 2013 Antimicrobial agents and chemotherapy Abstract IV E119V 87 92 58 60 23926340 The PA and HA gene-mediated high viral load and intense innate immune response in the brain contribute to the high pathogenicity of H5N1 avian influenza virus in mallard ducks. Moreover, the K237E mutation in the GS10 PA gene increased PA nuclear accumulation. 2013 Journal of virology Abstract IV K237E 14 19 PA;PA 41;59 43;61 23941842 [Clinical characteristics and molecular epidemiology of the novel influenza A (H1N1) infection in children in Shanghai]. OBJECTIVE: To investigate the epidemiological features, genetic drift in the epitopes of hemagglutinin (HA) of the novel influenza A (H1N1) virus and oseltamivir-resistant variants characterized by H275Y and N295S mutations in children in Shanghai since the outbreak. 2013 Zhonghua er ke za zhi Abstract IV H275Y;N295S 198;208 203;213 HA;HA 104;89 106;102 23941842 [Clinical characteristics and molecular epidemiology of the novel influenza A (H1N1) infection in children in Shanghai]. The H275Y and N295S amino acid mutations associated with oseltamivir resistance were not found in the circulating novel influenza (H1N1) strains. 2013 Zhonghua er ke za zhi Abstract IV H275Y;N295S 4;14 9;19 23941842 [Clinical characteristics and molecular epidemiology of the novel influenza A (H1N1) infection in children in Shanghai]. The nucleotide sequences of HA1 gene were highly homologous between the vaccine strain A/California/07/2009 and Shanghai circulating novel influenza A (H1N1) strains and only S83P mutation in epitope E of HA was detected inclusively in the circulating strains. 2013 Zhonghua er ke za zhi Abstract IV S83P 175 179 HA;HA1 205;28 207;31 23951116 Resistance mutation R292K is induced in influenza A(H6N2) virus by exposure of infected mallards to low levels of oseltamivir. After 4 days with 12 microg/L of OC exposure, the resistance mutation R292K emerged and then persisted. 2013 PloS one Abstract IV R292K 70 75 23951116 Resistance mutation R292K is induced in influenza A(H6N2) virus by exposure of infected mallards to low levels of oseltamivir. Reduced neuraminidase activity and decrease in recovered virus after propagation in embryonated hen eggs was observed in R292K viruses. 2013 PloS one Abstract IV R292K 121 126 8 21 23951116 Resistance mutation R292K is induced in influenza A(H6N2) virus by exposure of infected mallards to low levels of oseltamivir. The initial, but not the later R292K isolates reverted to wild-type during egg-propagation, suggesting a stabilization of the mutation, possibly through additional mutations in the neuraminidase (D113N or D141N) or hemagglutinin (E216K). 2013 PloS one Abstract IV R292K;D113N;D141N;E216K 31;196;205;230 36;201;210;235 HA;NA 215;181 228;194 23951116 Resistance mutation R292K is induced in influenza A(H6N2) virus by exposure of infected mallards to low levels of oseltamivir. Viral shedding was similar when comparing R292K and wild-type virus indicating sustained replication and transmission. 2013 PloS one Abstract IV R292K 42 47 23951116 Resistance mutation R292K is induced in influenza A(H6N2) virus by exposure of infected mallards to low levels of oseltamivir. We previously demonstrated that an influenza A(H1N1) virus in mallards (Anas platyrhynchos) exposed to 1 microg/L of OC developed oseltamivir resistance through the mutation H274Y (N2-numbering). 2013 PloS one Abstract IV H274Y 174 179 23958122 [Analysis of genetic variation of hemagglutinin and three internal genes of influenza B virus isolated in Zhejiang province from 1999 to 2012]. Determined amino acid sequences of NP of Victoria-like influenza B isolates were similar to Yamagata-like isolates after 2010 and variations happened on four characteristic amino acid sites, naming A60D, I233V, N513S and V5341, compared with previous Victoria-like influenza B isolates. 2013 Zhonghua yu fang yi xue za zhi [Chinese journal of preventive medicine] Abstract IV A60D;I233V;N513S 198;204;211 202;209;216 NP 35 37 23958122 [Analysis of genetic variation of hemagglutinin and three internal genes of influenza B virus isolated in Zhejiang province from 1999 to 2012]. Variations of amino acid of HAl domain of Victoria-like isolates mainly included K48E ,L58P ,N75K,K80R,K129N/S,N165K,S172P ,Sl97N/D and A202V; while those in Yamagata-like isolates were R48K, S1501, N166Y, N203S, G230D and D233N. 2013 Zhonghua yu fang yi xue za zhi [Chinese journal of preventive medicine] Abstract IV K48E;L58P;N75K;K80R;K129N;K129S;N165K;S172P;A202V;R48K;N166Y;N203S;G230D;D233N;N165K,S 81;87;93;98;103;103;111;117;136;186;199;206;213;223;111 85;91;97;102;110;110;116;122;141;190;204;211;218;228;116 23966381 Fecal influenza in mammals: selection of novel variants. Most of the novel genotypes emerged as PB2(E627K), HA(F128V), HA(F454L), or HA(H300P) variations, and double mutations frequently occurred in the same isolate. 2013 Journal of virology Abstract IV E627K;F128V;F454L;H300P 43;54;65;79 48;59;70;84 HA;HA;HA;PB2 51;62;76;39 53;64;78;42 23969554 Study of immunogenicity of recombinant proteins based on hemagglutinin and neuraminidase conservative epitopes of influenza A virus. Substitutions were made: typical for Russian virus isolates (in HA - S220T, NA - D248N) and in active centers of molecules - R118L, R293L, R368L; C92S, C417S to increase recombinant proteins stability in E. 2013 Medical science monitor basic research Abstract IV S220T;D248N;R118L;R293L;R368L;C92S;C417S 69;81;125;132;139;146;152 74;86;130;137;144;150;157 HA;NA 64;76 66;78 23990570 Novel avian-origin human influenza A(H7N9) can be transmitted between ferrets via respiratory droplets. There were 4 mutations in the virus isolated from the contact ferret: D678Y in the gene encoding PB2, R157K in the gene encoding hemagglutinin (H3 numbering), I109T in the gene encoding nucleoprotein, and T10I in the gene encoding neuraminidase. 2014 The Journal of infectious diseases Abstract IV D678Y;R157K;I109T;T10I 70;102;159;205 75;107;164;209 HA;NA;NP;PB2 129;231;186;97 142;244;199;100 23994833 Mutation tryptophan to leucine at position 222 of haemagglutinin could facilitate H3N2 influenza A virus infection in dogs. In this study, reassortant viruses rH3N2-222L (canine-like) and rH3N2-222W (avian-like) with HA mutation L222W were generated using reverse genetics to evaluate the significance of the L222W mutation on receptor binding and host tropism of H3N2 IAV. 2013 The Journal of general virology Abstract IV L222W;L222W 105;185 110;190 HA 93 95 24020758 Effects of the Q223R mutation in the hemagglutinin (HA) of egg-adapted pandemic 2009 (H1N1) influenza A virus on virus growth and binding of HA to human- and avian-type cell receptors. In this study, the Q223R mutation was shown to change the viral HA binding preference from the human-type receptor, alpha2,6-linked sialic acid, to the avian-type receptor, alpha2,3-linked sialic acid; and to enhance the viral growth in embryonated eggs but not in cell culture. 2013 Acta virologica Abstract IV Q223R 19 24 HA 64 66 24020758 Effects of the Q223R mutation in the hemagglutinin (HA) of egg-adapted pandemic 2009 (H1N1) influenza A virus on virus growth and binding of HA to human- and avian-type cell receptors. The glutamine to arginine mutation at the amino acid position 223 (Q223R) of the hemagglutinin (HA) gene is the major mutation previously found in egg-adapted 2009 H1N1 strains and shown to enhance viral growth in embryonated eggs. 2013 Acta virologica Abstract IV Q223R 67 72 HA;HA 96;81 98;94 24027333 A mutant influenza virus that uses an N1 neuraminidase as the receptor-binding protein. Although the G147R NA receptor-binding mutant virus that we characterize is a laboratory creation, this same mutation is found in several natural clusters of H1N1 and H5N1 viruses. 2013 Journal of virology Abstract IV G147R 13 18 19 21 24027333 A mutant influenza virus that uses an N1 neuraminidase as the receptor-binding protein. However, the NAs of some recent human H3N2 isolates have acquired receptor-binding activity via the mutation D151G, although these isolates also appear to retain the ability to bind receptors via HA. 2013 Journal of virology Abstract IV D151G 109 114 HA;NA 196;13 198;16 24027333 A mutant influenza virus that uses an N1 neuraminidase as the receptor-binding protein. We report here the laboratory generation of a mutation (G147R) that enables an N1 NA to completely co-opt the receptor-binding function normally performed by HA. 2013 Journal of virology Abstract IV G147R 56 61 HA;NA 158;82 160;84 24055835 Insights into susceptibility of antiviral drugs against the E119G mutant of 2009 influenza A (H1N1) neuraminidase by molecular dynamics simulations and free energy calculations. However, for ZNV, the E119G mutation has both direct and indirect influences on the drug binding. 2013 Antiviral research Abstract IV E119G 22 27 24055835 Insights into susceptibility of antiviral drugs against the E119G mutant of 2009 influenza A (H1N1) neuraminidase by molecular dynamics simulations and free energy calculations. In this study, molecular dynamics (MD) simulations and Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) were applied to investigate the different sensitivities of oseltamivir (OTV), zanamivir (ZNV), and peramivir (PRV) against the E119G mutant of 2009 A/H1N1 neuraminidase. 2013 Antiviral research Abstract IV E119G 242 247 270 283 24055835 Insights into susceptibility of antiviral drugs against the E119G mutant of 2009 influenza A (H1N1) neuraminidase by molecular dynamics simulations and free energy calculations. The indirectly conformational variations of the inhibitors, which caused by the E119G mutation, are responsible for the loss of the binding free energies. 2013 Antiviral research Abstract IV E119G 80 85 24055835 Insights into susceptibility of antiviral drugs against the E119G mutant of 2009 influenza A (H1N1) neuraminidase by molecular dynamics simulations and free energy calculations. The predicted binding free energies indicate that the E119G mutation in NA confers resistance to all of the three studied inhibitors. 2013 Antiviral research Abstract IV E119G 54 59 72 74 24057757 Evaluation of neutralizing efficacy of monoclonal antibodies specific for 2009 pandemic H1N1 influenza A virus in vitro and in vivo. We mapped the antigenic epitopes of the HA by characterizing escape mutants of a 2009 H1N1 vaccine strain (NYMC X-179A). 2014 Archives of virology Abstract IV X179A 112 118 HA 40 42 24074585 Mutation from arginine to lysine at the position 189 of hemagglutinin contributes to the antigenic drift in H3N2 swine influenza viruses. A consistent mutation was observed at the position 189 of hemagglutinin (R189K) between H3N2SIV-alpha and H3N2SIV-beta fair isolates. 2013 Virology Abstract IV R189K 73 78 HA 58 71 24074585 Mutation from arginine to lysine at the position 189 of hemagglutinin contributes to the antigenic drift in H3N2 swine influenza viruses. The antigenic cartography demonstrated that the R189K mutation in the hemagglutinin of H3N2 IAV contributed to the antigenic drift, separating these viruses into H3N2SIV-alpha to H3N2SIV-beta. 2013 Virology Abstract IV R189K 48 53 HA 70 83 24074585 Mutation from arginine to lysine at the position 189 of hemagglutinin contributes to the antigenic drift in H3N2 swine influenza viruses. This R189K mutation was also found to contribute to the cross-reaction with several ferret sera raised against historical human IAVs with hemagglutinin carrying 189K. 2013 Virology Abstract IV R189K 5 10 HA 138 151 24074585 Mutation from arginine to lysine at the position 189 of hemagglutinin contributes to the antigenic drift in H3N2 swine influenza viruses. This study suggests that the R189K mutation plays a vital role in the antigenicity of swine and human H3N2 IAVs and identification of this antigenic determinant will help us rapidly identify antigenic variants in influenza surveillance. 2013 Virology Abstract IV R189K 29 34 24074585 Mutation from arginine to lysine at the position 189 of hemagglutinin contributes to the antigenic drift in H3N2 swine influenza viruses. To evaluate the contribution of R189K mutation to the antigenic drift from H3N2SIV-alpha to H3N2SIV-beta, four reassortant viruses with 189R or 189K were generated. 2013 Virology Abstract IV R189K 32 37 24080660 Cell culture-selected substitutions in influenza A(H3N2) neuraminidase affect drug susceptibility assessment. Sequence analysis of its NA gene revealed a known oseltamivir-resistance marker, the glutamic acid-to-valine substitution at position 119 (E119V), and an additional change, threonine to isoleucine at position 148 (T148I). 2013 Antimicrobial agents and chemotherapy Abstract IV E119V;T148I;E119V;T148I 139;214;85;173 144;219;137;212 25 27 24080660 Cell culture-selected substitutions in influenza A(H3N2) neuraminidase affect drug susceptibility assessment. The T148I substitution reduced NA activity by 50%, most likely by affecting the positioning of the 150 loop at the NA catalytic site. 2013 Antimicrobial agents and chemotherapy Abstract IV T148I 4 9 NA;NA 31;115 33;117 24080660 Cell culture-selected substitutions in influenza A(H3N2) neuraminidase affect drug susceptibility assessment. Unlike E119V, T148I was not detected in the clinical sample but acquired during viral propagation in MDCK cells. 2013 Antimicrobial agents and chemotherapy Abstract IV E119V;T148I 7;14 12;19 24080660 Cell culture-selected substitutions in influenza A(H3N2) neuraminidase affect drug susceptibility assessment. Using recombinant proteins, T148I by itself was shown to cause only a 6-fold increase in the zanamivir 50% inhibitory concentration (IC50) and had no effect on inhibition by other drugs. 2013 Antimicrobial agents and chemotherapy Abstract IV T148I 28 33 24088848 Emergence of an oseltamivir-resistant influenza A/H3N2 virus in an elderly patient receiving a suboptimal dose of antiviral prophylaxis. In neuraminidase inhibition assays, the E119V variant showed a 413-fold increase in the 50% inhibitory oseltamivir concentration and grew at titers comparable to those of the wild type in vitro. 2013 Journal of clinical microbiology Abstract IV E119V 40 45 3 16 24088848 Emergence of an oseltamivir-resistant influenza A/H3N2 virus in an elderly patient receiving a suboptimal dose of antiviral prophylaxis. We report the emergence of an influenza virus A/H3N2-E119V neuraminidase variant from an elderly patient with renal dysfunction who received a suboptimal dose of oseltamivir prophylaxis. 2013 Journal of clinical microbiology Abstract IV E119V 53 58 59 72 24109242 Evolution of the hemagglutinin protein of the new pandemic H1N1 influenza virus: maintaining optimal receptor binding by compensatory substitutions. Strikingly, two major variants harbor combinations of substitutions (S186P/A137T and S188T/A200T, respectively) with opposite individual effects on binding. 2013 Journal of virology Abstract IV S186P;A137T;S188T;A200T 69;75;85;91 74;80;90;96 24109242 Evolution of the hemagglutinin protein of the new pandemic H1N1 influenza virus: maintaining optimal receptor binding by compensatory substitutions. Two changes (S186P and S188T) were shown to increase the receptor-binding avidity of HA, whereas two others (A137T and A200T) decreased binding avidity. 2013 Journal of virology Abstract IV S186P;S188T;A137T;A200T 13;23;109;119 18;28;114;124 HA 85 87 24120936 Pathogenicity in domestic ducks and mice of highly pathogenic H5N1 clade 2.3.2.1 influenza viruses recently circulating in Eastern Asia. The three viruses had K deletion at the -2 position of the HA1-connecting peptide (PQRERRRK-R), which is associated with increased virulence in domestic ducks and harbored NA stalk deletion, NS1 deletion and mutation of P42S in NS1, and full length (90aa) in PB1-F2, which confer increased virulence in mice. 2013 Veterinary microbiology Abstract IV P42S 220 224 HA1;NA;NS1;NS1;PB1F2 59;172;191;228;259 62;174;194;231;265 24125614 [Genomic sequences of human infection of avian-origin influenza A(H7N9)virus in Zhejiang province]. The E627K mutation was shared by all the other novel H7N9 viruses resulted in human infections through analysis on the currently available sequences. 2013 Zhonghua liu xing bing xue za zhi Abstract IV E627K 4 9 24125614 [Genomic sequences of human infection of avian-origin influenza A(H7N9)virus in Zhejiang province]. The sequenced virus showed Q226L mutation in HA protein, but E627K was not presented in PB2 protein of this virus. 2013 Zhonghua liu xing bing xue za zhi Abstract IV Q226L;E627K 27;61 32;66 HA;PB2 45;88 47;91 24125614 [Genomic sequences of human infection of avian-origin influenza A(H7N9)virus in Zhejiang province]. The virus showed Q226L mutation on HA protein but E627K did not present on PB2 protein of this virus. 2013 Zhonghua liu xing bing xue za zhi Abstract IV Q226L;E627K 17;50 22;55 HA;PB2 35;75 37;78 24136722 Origin and molecular characterization of the human-infecting H6N1 influenza virus in Taiwan. Furthermore, compared to avian isolates, a single P186L (H3 numbering) substitution in the hemagglutinin H6 of the human isolate might increase the mammalian receptor binding and, hence, this strain's pathogenicity in humans. 2013 Protein & cell Abstract IV P186L 50 55 HA 91 104 24139991 Asp44 stabilizes the Trp41 gate of the M2 proton channel of influenza A virus. Here, we show that the proton currents recorded for mutants of Asp44, including D44N found in the A/FPV/Rostock/34 strain, lose this asymmetry. 2013 Structure (London, England Abstract IV D44N 80 84 24140051 A monoclonal antibody targeting a highly conserved epitope in influenza B neuraminidase provides protection against drug resistant strains. Moreover, the growth and NA enzymatic activity of two drug resistant influenza B strains (E117D and D197E) are also inhibited by the antibody even though these two mutations are conformationally proximal to the universal epitope. 2013 Biochemical and biophysical research communications Abstract IV E117D;D197E 90;100 95;105 25 27 24147093 Emerging antigenic variants at the antigenic site Sb in pandemic A(H1N1)2009 influenza virus in Japan detected by a human monoclonal antibody. 5E4 escape mutants harbored amino acid substitutions (A189T and D190E) in the hemagglutinin (HA) protein, suggesting that 5E4 recognized the antigenic site Sb in the HA protein. 2013 PloS one Abstract IV A189T;D190E 54;64 59;69 HA;HA;HA 93;166;78 95;168;91 24150926 Hemagglutinin and neuraminidase genes of influenza B viruses circulating in Riyadh, Saudi Arabia during 2010-2011: evolution and sequence analysis. In NA gene, a unique common substitution (D53G) was found in all Riyadh strains, while two unique substitutions (L38P, G233R) were recognized only in B/Vic-like Riyadh strains. 2014 Journal of medical virology Abstract IV D53G;L38P;G233R 42;113;119 46;117;124 3 5 24150926 Hemagglutinin and neuraminidase genes of influenza B viruses circulating in Riyadh, Saudi Arabia during 2010-2011: evolution and sequence analysis. Three unique substitutions (T182A, D196N, and K254R) were identified in HA gene of the B/Yam-like Riyadh strains. 2014 Journal of medical virology Abstract IV T182A;D196N;K254R 28;35;46 33;40;51 HA 72 74 24155392 Evolution of the influenza A virus genome during development of oseltamivir resistance in vitro. Following drug treatment, the H274Y resistance mutation fixed reproducibly within the population. 2014 Journal of virology Abstract IV H274Y 30 35 24155392 Evolution of the influenza A virus genome during development of oseltamivir resistance in vitro. In addition, once evolved, the H274Y mutation persisted after the withdrawal of the drug, even when not fixed in viral populations. 2014 Journal of virology Abstract IV H274Y 31 36 24155392 Evolution of the influenza A virus genome during development of oseltamivir resistance in vitro. The presence of the H274Y mutation in the viral population, at either a low or a high frequency, led to measurable changes in the neuraminidase inhibition assay. 2014 Journal of virology Abstract IV H274Y 20 25 130 143 24155392 Evolution of the influenza A virus genome during development of oseltamivir resistance in vitro. We conclude that only selection of H274Y is required for oseltamivir resistance and that H274Y is not deleterious in the absence of the drug. 2014 Journal of virology Abstract IV H274Y;H274Y 35;89 40;94 24155392 Evolution of the influenza A virus genome during development of oseltamivir resistance in vitro. While the neighboring K248E mutation was also a target of positive selection prior to H274Y fixation, H274Y was the primary beneficial mutation in the population. 2014 Journal of virology Abstract IV K248E;H274Y;H274Y 22;86;102 27;91;107 24162312 Adaptation of novel H7N9 influenza A virus to human receptors. These differences could be attributed to substitutions Q226L and G186V. 2013 Scientific reports Abstract IV Q226L;G186V 55;65 60;70 24165891 Characterization of two distinct neuraminidases from avian-origin human-infecting H7N9 influenza viruses. In this study, we show that an R294K substitution results in multidrug resistance with extreme oseltamivir resistance (over 100 000-fold) using protein- and virus-based assays. 2013 Cell research Abstract IV R294K 31 36 24165891 Characterization of two distinct neuraminidases from avian-origin human-infecting H7N9 influenza viruses. Moreover, we found that R294K substitution results in reduced NA catalytic efficiency along with lower viral fitness. 2013 Cell research Abstract IV R294K 24 29 62 64 24165891 Characterization of two distinct neuraminidases from avian-origin human-infecting H7N9 influenza viruses. NAs from these two viruses are distinct as the A/Shanghai/1/2013 NA has an R294K substitution that can confer NA inhibitor oseltamivir resistance. 2013 Cell research Abstract IV R294K 75 80 NA;NA;NA 65;110;0 67;112;3 24165891 Characterization of two distinct neuraminidases from avian-origin human-infecting H7N9 influenza viruses. R294K substitution results in an unfavorable E276 conformation for oseltamivir binding, and consequently loss of inhibitor carboxylate interactions, which compromises the binding of all classical NA ligands/inhibitors. 2013 Cell research Abstract IV R294K 0 5 196 198 24173220 A novel cytotoxic sequence contributes to influenza A viral protein PB1-F2 pathogenicity and predisposition to secondary bacterial infection. When administered to mice, a 27-mer PB1-F2-derived C-terminal peptide with this amino acid motif caused significantly greater weight loss and pulmonary inflammation than the peptide without it (due to I68T, L69Q, and V70G mutations). 2014 Journal of virology Abstract IV I68T;L69Q;V70G 201;207;217 205;211;221 PB1F2 36 42 2417413 Loss of enzyme activity in a site-directed mutant of influenza neuraminidase compared to expressed wild-type protein. Full-length double-stranded DNA copies of the neuraminidase (NA) gene of influenza virus A/Tokyo/3/67 (N2) and a mutant generated in vitro by site-specific, oligonucleotide-directed mutagenesis with a substitution of leucine for tryptophan at position 178 were cloned into an SV40 late replacement expression vector. 1986 Virology Abstract IV W178L 217 255 NA;NA 61;46 63;59 24174280 Loss and gain of N-linked glycosylation sites in globular head and stem of HA found in A/H3N2 flu fatal and severe cases during 2013 Tunisia flu seasonal survey. Also the mutation N145S was presented in the receptor-binding site of all segments analyzed. 2014 Virus genes Abstract IV N145S 18 23 2420611 Conformational-dependent recognition of influenza virus hemagglutinin by murine T helper clones. Five HA-specific Th clones failed to recognize X31 mutant viruses R19 and R20 each with a His to Arg substitution at position 17 of HA1. 1986 European journal of immunology Abstract IV H17R 90 128 HA;HA1 5;132 7;135 2420611 Conformational-dependent recognition of influenza virus hemagglutinin by murine T helper clones. In addition, four of the five clones failed to recognize variant virus Eng-72 which has Arg to Gly substitution at position 208 in the interface antibody-binding region. 1986 European journal of immunology Abstract IV R208G 88 127 24211668 A novel pyrosequencing assay for the detection of neuraminidase inhibitor resistance-conferring mutations among clinical isolates of avian H7N9 influenza virus. One strain (A/shanghai/1/2013) contained the R294K substitution in the neuraminidase (NA) gene, indicating resistance to oseltamivir. 2014 Virus research Abstract IV R294K 45 50 NA;NA 86;71 88;84 24211668 A novel pyrosequencing assay for the detection of neuraminidase inhibitor resistance-conferring mutations among clinical isolates of avian H7N9 influenza virus. Only one isolate containing the E120V heterogenic mutation was detected by pyrosequencing and confirmed by Sanger sequencing. 2014 Virus research Abstract IV E120V 32 37 24215378 Detection and management of antiviral resistance for influenza viruses. Recent studies have shown that, in the presence of the appropriate permissive mutations, the H275Y variant can retain virulence and transmissibility in some viral backgrounds. 2013 Influenza and other respiratory viruses Abstract IV H275Y 93 98 24215378 Detection and management of antiviral resistance for influenza viruses. The most frequently reported change conferring oseltamivir resistance in that viral context is the H275Y neuraminidase mutation (N1 numbering). 2013 Influenza and other respiratory viruses Abstract IV H275Y 99 104 105 118 24218291 Mutation effects of neuraminidases and their docking with ligands: a molecular dynamics and free energy calculation study. Susceptibility of influenza virus to NA inhibitors can be reinforced by some mutations; e.g., the binding free energies of ligands with N2 subtype increase from -18.0 to -42.1 kcal mol(-1) by the E119D mutation. 2013 Journal of computer-aided molecular design Abstract IV E119D 196 201 37 39 24222196 Adaptive mutation in nuclear export protein allows stable transgene expression in a chimaeric influenza A virus vector. Although improved vector fitness was associated with the appearance of four coding mutations in the polymerase (PB2), haemagglutinin and non-structural (NS) segments, the stability of the transgene expression was dependent primarily on the single mutation Q20R in the nuclear export protein (NEP). 2014 The Journal of general virology Abstract IV Q20R 256 260 HA;NEP;NS;NS;NEP;PB2 118;292;137;153;268;112 132;295;151;155;290;115 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. Furthermore, the blocking mechanism of HA differs for WT and D325A+R343V because of alternate glycan binding modes. 2013 Biochemistry Abstract IV D325A;R343V 61;67 66;72 HA 39 41 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. On the basis of the D325A+R343V-Man9 structure and other crystallographic data, models of complexes between HA and WT or D325A+R343V were produced and subjected to molecular dynamics. 2013 Biochemistry Abstract IV D325A;R343V;D325A;R343V 20;26;121;127 25;31;126;132 HA 108 110 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. Simulations reveal that whereas WT and D325A+R343V both block the sialic acid receptor site of HA, the D325A+R343V complex is more stable, with stronger binding caused by additional hydrogen bonds and hydrophobic interactions with HA residues. 2013 Biochemistry Abstract IV D325A;R343V;D325A;R343V 39;45;103;109 44;50;108;114 HA;HA 95;231 97;233 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. To elucidate the mechanism for these biochemical observations, we have determined crystal structures of D325A+R343V in the presence and absence of a viral nonamannoside (Man9). 2013 Biochemistry Abstract IV D325A;R343V 104;110 109;115 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. Two truncated human SP-D forms, wild-type (WT) and double mutant D325A+R343V, representing neck and carbohydrate recognition domains are compared in this study. 2013 Biochemistry Abstract IV D325A;R343V 65;71 70;76 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. Whereas both WT and D325A+R343V bind to isolated glycosylated HA, WT does not inhibit IAV in neutralization assays; in contrast, D325A+R343V neutralization compares well with that of full-length native SP-D. 2013 Biochemistry Abstract IV D325A;R343V;D325A;R343V 20;26;129;135 25;31;134;140 HA 62 64 24224816 Swine influenza in Norway: a distinct lineage of influenza A(H1N1)pdm09 virus. Viruses detected in pigs by the end of 2011 had acquired four characteristic amino acid substitutions (N31D, S84I S164F, and N473D) and formed a distinct phylogenetic group. 2013 Influenza and other respiratory viruses Abstract IV N31D;S84I;S164F;N473D 103;109;114;125 107;113;119;130 24237039 3-Azatetracyclo[5.2.1.1(5,8).0(1,5)]undecane derivatives: from wild-type inhibitors of the M2 ion channel of influenza A virus to derivatives with potent activity against the V27A mutant. Inhibition of the wild-type (WT) M2 channel and the amantadine-resistant A/M2-S31N and A/M2-V27A mutant ion channels were measured in Xenopus oocytes using two-electrode voltage clamp (TEV) assays. 2013 Journal of medicinal chemistry Abstract IV V27A;S31N 92;78 96;82 M2;M2;M2 33;75;89 35;77;91 24237039 3-Azatetracyclo[5.2.1.1(5,8).0(1,5)]undecane derivatives: from wild-type inhibitors of the M2 ion channel of influenza A virus to derivatives with potent activity against the V27A mutant. None of the compounds was found to inhibit the S31N mutant ion channel. 2013 Journal of medicinal chemistry Abstract IV S31N 47 51 24237039 3-Azatetracyclo[5.2.1.1(5,8).0(1,5)]undecane derivatives: from wild-type inhibitors of the M2 ion channel of influenza A virus to derivatives with potent activity against the V27A mutant. Of note, several compounds inhibited the A/M2 V27A mutant ion channel, one of them with submicromolar IC50. 2013 Journal of medicinal chemistry Abstract IV V27A 46 50 M2 43 45 24237039 3-Azatetracyclo[5.2.1.1(5,8).0(1,5)]undecane derivatives: from wild-type inhibitors of the M2 ion channel of influenza A virus to derivatives with potent activity against the V27A mutant. The antiviral activity of three novel dual WT and A/M2-V27A channels inhibitors was confirmed by influenza virus yield assays. 2013 Journal of medicinal chemistry Abstract IV V27A 55 59 M2 52 54 24257603 Emergence of the virulence-associated PB2 E627K substitution in a fatal human case of highly pathogenic avian influenza virus A(H7N7) infection as determined by Illumina ultra-deep sequencing. During a large influenza A(H7N7) virus outbreak in the Netherlands in 2003, the A(H7N7) virus isolated from a fatal human case contained the PB2 E627K mutation as well as a hemagglutinin (HA) K416R mutation. 2014 Journal of virology Abstract IV E627K;K416R 145;192 150;197 HA;HA;PB2 188;173;141 190;186;144 24257603 Emergence of the virulence-associated PB2 E627K substitution in a fatal human case of highly pathogenic avian influenza virus A(H7N7) infection as determined by Illumina ultra-deep sequencing. In both the avian influenza A(H5N1) and the recently emerging avian influenza A(H7N9) viruses, the polymerase basic 2 protein (PB2) E627K mutation appears to be of key importance for human adaptation. 2014 Journal of virology Abstract IV E627K 132 137 PB2;PB2 127;99 130;125 24257603 Emergence of the virulence-associated PB2 E627K substitution in a fatal human case of highly pathogenic avian influenza virus A(H7N7) infection as determined by Illumina ultra-deep sequencing. In the human samples, the PB2 E627K mutation was identified with increasing frequency during infection. 2014 Journal of virology Abstract IV E627K 30 35 PB2 26 29 24257603 Emergence of the virulence-associated PB2 E627K substitution in a fatal human case of highly pathogenic avian influenza virus A(H7N7) infection as determined by Illumina ultra-deep sequencing. Our results strongly suggest that human adaptation marker PB2 E627K has emerged during virus infection of a single human host, emphasizing the importance of reducing human exposure to avian influenza viruses to reduce the likelihood of viral adaptation to humans. 2014 Journal of virology Abstract IV E627K 62 67 PB2 58 61 24257603 Emergence of the virulence-associated PB2 E627K substitution in a fatal human case of highly pathogenic avian influenza virus A(H7N7) infection as determined by Illumina ultra-deep sequencing. Results showed that the PB2 E627K mutation was not present in any of the chicken samples tested. 2014 Journal of virology Abstract IV E627K 28 33 PB2 24 27 24312396 Conformational polymorphism of m7GTP in crystal structure of the PB2 middle domain from human influenza A virus. Here we report the crystal structure of the middle domain of H1N1 PB2 with or without m(7)GTP at 1.9 A and 2.0 A resolution, respectively, which has two mutations (P453H, I471T) to increase electrostatic potential and solubility. 2013 PloS one Abstract IV P453H;I471T 164;171 169;176 PB2 66 69 24323790 Egg- or cell culture-derived hemagglutinin mutations impair virus stability and antigen content of inactivated influenza vaccines. The subsequent propagation of H3N2 and H1N1 egg-derived seed viruses in MDCK and Vero cells induced HA2 N50K (H1N1) and D160E (H3N2) mutations, improving virus growth in cell culture but further impairing virus stability. 2014 Biotechnology journal Abstract IV N50K;D160E 104;120 108;125 HA 100 102 24323790 Egg- or cell culture-derived hemagglutinin mutations impair virus stability and antigen content of inactivated influenza vaccines. This phenotype was associated with HA1 (A138S, L194P) and HA2 (D160N) substitutions, and strongly related to decreased virus stability towards acidic pH and elevated temperature. 2014 Biotechnology journal Abstract IV A138S;L194P;D160N 40;47;63 45;52;68 HA;HA1 58;35 60;38 24335306 PB2-588I enhances 2009 H1N1 pandemic influenza virus virulence by increasing viral replication and exacerbating PB2 inhibition of beta interferon expression. Comparing the consensus sequences of the PB2 subunit of human isolates of pdm/09 viruses with those of the four swine isolate viruses revealed one consensus mutation: T588I. 2014 Journal of virology Abstract IV T588I 167 172 PB2 41 44 24335306 PB2-588I enhances 2009 H1N1 pandemic influenza virus virulence by increasing viral replication and exacerbating PB2 inhibition of beta interferon expression. These findings indicate that the pdm/09 influenza virus has increased pathogenicity upon the acquisition of the PB2-T588I mutation and highlight the need for the continued surveillance of the genetic variation of molecular markers in influenza viruses because of their potential effects on pathogenicity and threats to human health. 2014 Journal of virology Abstract IV T588I 116 121 PB2 112 115 24335306 PB2-588I enhances 2009 H1N1 pandemic influenza virus virulence by increasing viral replication and exacerbating PB2 inhibition of beta interferon expression. To investigate whether the PB2 with the T5581 mutation (PB2-T558I) has an effect on the increased pathogenicity, we rescued a variant containing PB2-588I (Mex_PB2-588I) in the pdm/09 virus, A/Mexico/4486/2009(H1N1), referred to as Mex_WT (where WT is wild type), and characterized the variant in vitro and in vivo. 2014 Journal of virology Abstract IV T558I 60 65 PB2;PB2;PB2 27;56;145 30;59;148 24350808 Emergence of a novel drug resistant H7N9 influenza virus: evidence based clinical potential of a natural IFN-alpha for infection control and treatment. The emerging H7N9 viruses are resistant to the M2-ion channel blockers because of a S31N mutation in the M2 protein; additionally, some H7N9 isolates have gained neuraminidase R292K substitution resulting in broad resistance to neuraminidase inhibitors. 2014 Expert review of anti-infective therapy Abstract IV S31N;R292K 84;176 88;181 M2;M2;NA;NA 47;105;162;228 49;107;175;241 24350809 Host immunological response and factors associated with clinical outcome in patients with the novel influenza A H7N9 infection. Genetic characterization of the H7N9 virus revealed an Arg292Lys mutation in the neuraminidase gene associated with oseltamivir-resistance. 2014 Clinical microbiology and infection Abstract IV R292K 55 64 81 94 24366752 A conformational restriction in the influenza A virus neuraminidase binding site by R152 results in a combinational effect of I222T and H274Y on oseltamivir resistance. Furthermore, the I222K and I222T substitutions had a combinational effect of further increasing resistance in the presence of H274Y, which might result from a conformational restriction in the NA binding site. 2014 Antimicrobial agents and chemotherapy Abstract IV I222K;I222T;H274Y 17;27;126 22;32;131 193 195 24366752 A conformational restriction in the influenza A virus neuraminidase binding site by R152 results in a combinational effect of I222T and H274Y on oseltamivir resistance. Moreover, significantly attenuated NA function and viral growth abilities were found in the I222K+H274Y double mutant, while the I222T+H274Y double mutant exhibited slightly delayed growth but had a peak viral titer similar to that of the wild-type virus in MDCK cells. 2014 Antimicrobial agents and chemotherapy Abstract IV I222K;H274Y;H274Y;I222T 92;98;135;129 97;103;140;134 35 37 24366752 A conformational restriction in the influenza A virus neuraminidase binding site by R152 results in a combinational effect of I222T and H274Y on oseltamivir resistance. Of note, by using molecular dynamics simulations, R152, the neighbor of T222, was observed to translate to a position closer to T222, resulting in the narrowing of the binding pocket, which otherwise only subtends the residue substitution of H274Y. 2014 Antimicrobial agents and chemotherapy Abstract IV H274Y 242 247 24366752 A conformational restriction in the influenza A virus neuraminidase binding site by R152 results in a combinational effect of I222T and H274Y on oseltamivir resistance. Reduced sensitivities to oseltamivir were observed in all three mutants (I222K, I222R, and I222T). 2014 Antimicrobial agents and chemotherapy Abstract IV I222K;I222R;I222T 73;80;91 78;85;96 24366752 A conformational restriction in the influenza A virus neuraminidase binding site by R152 results in a combinational effect of I222T and H274Y on oseltamivir resistance. The effects of these substitutions, together with the most frequently observed resistance-related substitution, H274Y, on viral fitness and resistance mechanisms were further investigated in this study. 2014 Antimicrobial agents and chemotherapy Abstract IV H274Y 112 117 24366752 A conformational restriction in the influenza A virus neuraminidase binding site by R152 results in a combinational effect of I222T and H274Y on oseltamivir resistance. The I222K, I222R, and I222T substitutions in neuraminidase (NA) have been found in clinically derived 2009 pandemic influenza A/H1N1 viruses with altered susceptibilities to NA inhibitors (NAIs). 2014 Antimicrobial agents and chemotherapy Abstract IV I222K;I222R;I222T 4;11;22 9;16;27 NA;NA;NAI;NA 60;174;189;45 62;176;193;58 24366752 A conformational restriction in the influenza A virus neuraminidase binding site by R152 results in a combinational effect of I222T and H274Y on oseltamivir resistance. The relative growth advantage of the I222T mutant versus the I222K mutant and the higher frequency of I222T emerging in N1 subtype influenza viruses raise concerns necessitating close monitoring of the dual substitutions I222T and H274Y. 2014 Antimicrobial agents and chemotherapy Abstract IV I222T;I222K;I222T;I222T;H274Y 37;61;102;221;231 42;66;107;226;236 24368278 HA222 polymorphism in Influenza A(H1N1) 2009 isolates from Intensive Care Units and ambulatory patients during three influenza seasons. Amino acid substitutions which can affect the receptor binding specificity of the influenza virus, like the substitution of aspartic acid with glycine in position 222 of the haemagglutinin (HA) of influenza virus A(H1N1) 2009, have been associated with increased viral pathogenicity and increased tropism for the lower respiratory tract. 2014 Virus research Abstract IV D222G 124 166 HA;HA 190;174 192;188 24391498 A single amino acid in the stalk region of the H1N1pdm influenza virus HA protein affects viral fusion, stability and infectivity. The 2009 H1N1 pandemic (H1N1pdm) viruses have evolved to contain an E47K substitution in the HA2 subunit of the stalk region of the hemagglutinin (HA) protein. 2014 PLoS pathogens Abstract IV E47K 68 72 HA;HA;HA 93;147;132 95;149;145 24391498 A single amino acid in the stalk region of the H1N1pdm influenza virus HA protein affects viral fusion, stability and infectivity. The E47K change was found to reduce the threshold pH for membrane fusion from 5.4 to 5.0. 2014 PLoS pathogens Abstract IV E47K 4 8 24391498 A single amino acid in the stalk region of the H1N1pdm influenza virus HA protein affects viral fusion, stability and infectivity. The higher structural and acid stability of the HA trimer caused by the E47K change also conferred higher viral thermal stability and infectivity in ferrets, suggesting a fitness advantage for the E47K evolutionary change in humans. 2014 PLoS pathogens Abstract IV E47K;E47K 72;197 76;201 HA 48 50 24391972 Identification of adaptive mutations in the influenza A virus non-structural 1 gene that increase cytoplasmic localization and differentially regulate host gene expression. Several adaptive mutations increased the proportion of NS1 in the cytoplasm of mouse cells with the greatest effects for mutations M106I and D125G. 2013 PloS one Abstract IV M106I;D125G 131;141 136;146 NS1 55 58 24391972 Identification of adaptive mutations in the influenza A virus non-structural 1 gene that increase cytoplasmic localization and differentially regulate host gene expression. While host genes were predominantly down regulated for the HGR group of mutants (D2N, V23A, F103L, M106I+L98S, L98S, M106V, and M106V+M124I), the LGR phenotype mutants (D125G, M106I, V180A, V226I, and R227K) were characterized by a predominant up regulation of host genes. 2013 PloS one Abstract IV D2N;V23A;F103L;M106I;L98S;L98S;M106V;M106V;M124I;D125G;M106I;V180A;V226I;R227K 81;86;92;99;105;111;117;128;134;169;176;183;190;201 84;90;97;104;109;115;122;133;139;174;181;188;195;206 24394699 The PB2 E627K mutation contributes to the high polymerase activity and enhanced replication of H7N9 influenza virus. In this study, we demonstrate that the PB2 E627K mutation, which occurs in over 70 % of the H7N9 patient isolates, promotes the replication of H7N9 virus by enhancing PB2 polymerase activity and enhances virulence in mice. 2014 The Journal of general virology Abstract IV E627K 43 48 PB2;PB2 39;167 42;170 24394699 The PB2 E627K mutation contributes to the high polymerase activity and enhanced replication of H7N9 influenza virus. Our results show the PB2 E627K mutation has played an important role in this H7N9 influenza outbreak and in the pathogenicity of the H7N9 virus. 2014 The Journal of general virology Abstract IV E627K 25 30 PB2 21 24 24403580 Specific residues of PB2 and PA influenza virus polymerase subunits confer the ability for RNA polymerase II degradation and virus pathogenicity in mice. Three changes in the PB2 sequence (I105M, N456D, and I504V) and two in PA (Q193H and I550L) differentiate PA and PB2 of lvPR8 from those of hvPR8. 2014 Journal of virology Abstract IV I105M;N456D;I504V;Q193H;I550L 35;42;53;75;85 40;47;58;80;90 PA;PA;PB2;PB2 71;106;21;113 73;108;24;116 24403592 Amino acid substitutions in polymerase basic protein 2 gene contribute to the pathogenicity of the novel A/H7N9 influenza virus in mammalian hosts. In addition, the compensatory role of the PB2 mutations T271A, Q591K, and D701N in H7N9 virus was investigated. 2014 Journal of virology Abstract IV T271A;Q591K;D701N 56;63;74 61;68;79 PB2 42 45 24403592 Amino acid substitutions in polymerase basic protein 2 gene contribute to the pathogenicity of the novel A/H7N9 influenza virus in mammalian hosts. In this study, we determined the contribution of PB2-E627K in H7N9 virus to its pathogenicity in mammalian hosts. 2014 Journal of virology Abstract IV E627K 53 58 PB2 49 52 24403592 Amino acid substitutions in polymerase basic protein 2 gene contribute to the pathogenicity of the novel A/H7N9 influenza virus in mammalian hosts. Since many human (but not avian) H7N9 virus isolates have an amino acid substitution at position E627K in the polymerase basic protein 2 (PB2) gene, we investigated the role of this and other functionally related mutations for polymerase activity in vitro, virus replication competence, and pathogenicity in the mouse model. 2014 Journal of virology Abstract IV E627K 97 102 PB2 138 141 24403592 Amino acid substitutions in polymerase basic protein 2 gene contribute to the pathogenicity of the novel A/H7N9 influenza virus in mammalian hosts. We found that E627K and functionally related mutations are associated with increased polymerase activity, increased viral replication competence, and increased disease severity in mice. 2014 Journal of virology Abstract IV E627K 14 19 24419622 Crystallization and preliminary X-ray diffraction studies of a surface mutant of the middle domain of PB2 from human influenza A (H1N1) virus. To improve the solubility, a surface double mutant (P453H and I471T) was prepared. 2014 Acta crystallographica. Section F, Structural biology communications Abstract IV P453H;I471T 52;62 57;67 24426284 Genetic Analysis of the Neuraminidase (NA) Gene of Equine Influenza Virus (H3N8) from Epizootic of 2008-2009 in India. Amino acid (aa) sequence analysis also revealed five consistent aa residue changes viz, Gly/Arg40Glu, Tyr66His, Val191Ile, Val209Ile and Asp235Asn in Asian including Indian isolates, Spain/07 and Spain/09 isolates in comparison to other EIVs circulating worldwide. 2013 Indian journal of virology Abstract IV R40E;Y66H;V191I;V209I;D235N;G40E 88;102;112;123;137;88 100;110;121;132;146;100 24426284 Genetic Analysis of the Neuraminidase (NA) Gene of Equine Influenza Virus (H3N8) from Epizootic of 2008-2009 in India. Among Indian isolates, two amino acid (aa) changes each in Mysore/12/08 (Asn67Tyr & Asp396Gly), Gopeshwar/1/09 (Ile49Val & Asp396Gly), and Uttarkashi/1/09 (Ile49Val & Asp396Gly) isolates were observed in respect to Jammu-Katra/06/08 isolate. 2013 Indian journal of virology Abstract IV N67Y;D396G;I49V;D396G;I49V;D396G 73;84;112;123;156;167 81;93;120;132;164;176 24461756 Human infection with avian influenza A H6N1 virus: an epidemiological analysis. A unique clade of H6N1 viruses with a G228S substitution of haemagglutinin have circulated persistently in poultry in Taiwan. 2013 The Lancet. Respiratory medicine Abstract IV G228S 38 43 HA 60 74 24461756 Human infection with avian influenza A H6N1 virus: an epidemiological analysis. Notably, the virus had a G228S substitution in the haemagglutinin protein that might increase its affinity for the human alpha2-6 linked sialic acid receptor. 2013 The Lancet. Respiratory medicine Abstract IV G228S 25 30 HA 51 65 24480583 Development of a surveillance scheme for equine influenza in the UK and characterisation of viruses isolated in Europe, Dubai and the USA from 2010-2012. Two subpopulations of clade 2 viruses were isolated, with either substitution A144V or I179V. 2014 Veterinary microbiology Abstract IV A144V;I179V 78;87 83;92 24501410 Flow cytometry reveals that H5N1 vaccination elicits cross-reactive stem-directed antibodies from multiple Ig heavy-chain lineages. Incorporation of a previously described mutation (Y98F) to the receptor binding site (RBS) causes HA to bind only those B cells that express HA-specific Abs, but it does not bind nonspecifically to B cells, and this mutation has no effect on the binding of broadly neutralizing Abs to the RBS. 2014 Journal of virology Abstract IV Y98F 50 54 HA;HA 98;141 100;143 24501410 Flow cytometry reveals that H5N1 vaccination elicits cross-reactive stem-directed antibodies from multiple Ig heavy-chain lineages. To test the specificity of the Y98F mutation, we first demonstrated that previously described HA nanoparticles mediate hemagglutination and then determined that the Y98F mutation eliminates this activity. 2014 Journal of virology Abstract IV Y98F;Y98F 31;165 35;169 HA 94 96 24503069 The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus. Here we demonstrate that the mutation Phe95 Tyr in influenza B virus HA restores all three hydrogen bonds made by Tyr-98 in influenza A/H1-15 HA and has the potential to enhance receptor binding. 2014 Virology Abstract IV F95Y 38 47 HA;HA 69;142 71;144 24521884 Mass spectrometry analysis coupled with de novo sequencing reveals amino acid substitutions in nucleocapsid protein from influenza A virus. Thus, LC-MS/MS analyses, coupled with manual de novo sequencing, allowed the determination of three substituted amino acid residues R452K, T423A and N430T in two tryptic peptides. 2014 International journal of molecular sciences Abstract IV R452K;T423A;N430T 132;139;149 137;144;154 24522908 Naturally occurring mutations in the PA gene are key contributors to increased virulence of pandemic H1N1/09 influenza virus in mice. In particular, the PA-P224S mutation when combined with PA-A70V in CA04 drastically reduced the virus's 50% mouse lethal dose (LD50), by almost 1,000-fold. 2014 Journal of virology Abstract IV P224S;A70V 22;59 27;63 PA;PA 19;56 21;58 24522908 Naturally occurring mutations in the PA gene are key contributors to increased virulence of pandemic H1N1/09 influenza virus in mice. We found that four amino acid mutations (P224S in the PA protein [PA-P224S], PB2-T588I, NA-V106I, and NS1-I123V) contributed to the lethal phenotype of SD731. 2014 Journal of virology Abstract IV P224S;P224S;T588I;V106I;I123V 41;69;81;91;106 46;74;86;96;111 NA;NS1;PA;PA;PB2 88;102;54;66;77 90;105;56;68;80 24524021 Generation and Characterization of Recombinant Influenza A(H1N1) Viruses Resistant to Neuraminidase Inhibitors. RESULTS: NA-inhibition assays showed that all the single and double mutants containing the Y275 except the single Y275-E119V mutant conferred important levels of resistance to oseltamivir, whereas all the single, double, and triple mutants containing the E119V mutation were associated with the resistance to zanamivir. 2013 Osong public health and research perspectives Abstract IV E119V;E119V 119;255 124;260 9 11 24531414 Characterization of an enhanced antigenic change in the pandemic 2009 H1N1 influenza virus haemagglutinin. However, one of these isolates (A/Extremadura/RR6530/2010) lacked reactivity with the mAbs and carried two unique mutations in the HA head (S88Y and K136N) that were required simultaneously to eliminate reactivity with the murine antibodies. 2014 The Journal of general virology Abstract IV S88Y;K136N 140;149 144;154 HA 131 133 2453566 Fine specificity of murine class II-restricted T cell clones for synthetic peptides of influenza virus hemagglutinin. Heterogeneity of antigen interaction with the T cell and the Ia molecule. Peptide analogs or mutant viruses with a single amino acid substitution at position 63 (Asp to Asn or Tyr) reduced the responses of the T cell clones to variable extents, suggesting that Asp63 may form part of overlapping T cell determinants. 1988 Journal of immunology (Baltimore, Md. Abstract IV D63N 84 99 24558492 Study of oseltamivir and zanamivir resistance-related mutations in influenza viruses isolated from wild mallards in Sweden. Furthermore, both wild types (WTs) in the N6 and one WT in the N9 subtype were less sensitive to ZA than were genotypically related mutants with R152K and R118K change in the respective subtypes. 2014 PloS one Abstract IV R152K;R118K 145;155 150;160 N9 63 65 24558492 Study of oseltamivir and zanamivir resistance-related mutations in influenza viruses isolated from wild mallards in Sweden. The R118K mutation was the most recurrent, as it was observed in all subtypes except for N6. 2014 PloS one Abstract IV R118K 4 9 24560697 Cleavage site stability of Egyptian highly pathogenic avian influenza viruses in backyard chickens during 2009-2011. The divergence of four sequences with classic and variant lineages is 2-2.7% and 2.3-3%, respectively, with two amino acid substitutions (A249P and N251Y). 2015 Journal of microbiology, immunology, and infection Abstract IV A249P;N251Y 138;148 143;153 24563658 Synergistic combinations of favipiravir and oseltamivir against wild-type pandemic and oseltamivir-resistant influenza A virus infections in mice. Against the H275Y virus infection, oseltamivir alone was only 30% protective from death at 100 mg/kg/day, but combinations of the two compounds produced a synergistic improvement in survival rate. 2013 Future virology Abstract IV H275Y 12 17 24563658 Synergistic combinations of favipiravir and oseltamivir against wild-type pandemic and oseltamivir-resistant influenza A virus infections in mice. MATERIALS & METHODS: Mice infected with pandemic influenza A/California/04/2009 (H1N1pdm) virus or an oseltamivir-resistant (H275Y neuraminidase mutation) influenza A/Mississippi/ 3/2001 (H1N1) virus were treated orally with inhibitors twice a day for 5 days starting 4 h after infection. 2013 Future virology Abstract IV H275Y 125 130 131 144 24566185 Fitness costs for Influenza B viruses carrying neuraminidase inhibitor-resistant substitutions: underscoring the importance of E119A and H274Y. All NA substitutions, except for D198Y and R371K, were genetically stable after seven passages in MDCK cells. 2014 Antimicrobial agents and chemotherapy Abstract IV D198Y;R371K 33;43 38;48 4 6 24566185 Fitness costs for Influenza B viruses carrying neuraminidase inhibitor-resistant substitutions: underscoring the importance of E119A and H274Y. Cell surface NA protein expression was significantly increased by H274Y and N294S substitutions. 2014 Antimicrobial agents and chemotherapy Abstract IV H274Y;N294S 66;76 71;81 13 15 24566185 Fitness costs for Influenza B viruses carrying neuraminidase inhibitor-resistant substitutions: underscoring the importance of E119A and H274Y. Our results showed that four NA substitutions (D198E, I222T, H274Y, and N294S) conferred reduced inhibition by oseltamivir and three (E119A, D198Y, and R371K) conferred highly reduced inhibition by oseltamivir, zanamivir, and peramivir. 2014 Antimicrobial agents and chemotherapy Abstract IV D198E;I222T;H274Y;N294S;E119A;D198Y;R371K 47;54;61;72;134;141;152 52;59;66;77;139;146;157 29 31 24566185 Fitness costs for Influenza B viruses carrying neuraminidase inhibitor-resistant substitutions: underscoring the importance of E119A and H274Y. Overall, viruses with the E119A or H274Y NA substitution possess fitness comparable to NAI-susceptible virus, and the acquisition of these substitutions by influenza B viruses should be closely monitored. 2014 Antimicrobial agents and chemotherapy Abstract IV E119A;H274Y 26;35 31;40 NA;NAI 41;87 43;90 24566185 Fitness costs for Influenza B viruses carrying neuraminidase inhibitor-resistant substitutions: underscoring the importance of E119A and H274Y. Viruses with the E119A, I222T, H274Y, or N294S substitution were not attenuated in replication efficiency in vitro or in NHBE cells. 2014 Antimicrobial agents and chemotherapy Abstract IV E119A;I222T;H274Y;N294S 17;24;31;41 22;29;36;46 24566185 Fitness costs for Influenza B viruses carrying neuraminidase inhibitor-resistant substitutions: underscoring the importance of E119A and H274Y. We generated recombinant viruses containing either wild-type (WT) NA or NA with a substitution in the catalytic (R371K) or framework (E119A, D198E, D198Y, I222T, H274Y, and N294S) residues. 2014 Antimicrobial agents and chemotherapy Abstract IV R371K;E119A;D198E;D198Y;I222T;H274Y;N294S 113;134;141;148;155;162;173 118;139;146;153;160;167;178 NA;NA 66;72 68;74 24569063 An investigational antiviral drug, DAS181, effectively inhibits replication of zoonotic influenza A virus subtype H7N9 and protects mice from lethality. Here we show that DAS181 (Fludase), an antiviral drug with sialidase activity, potently inhibited replication of wild-type influenza A(H7N9) and its oseltamivir-resistant R292K variants in mice. 2014 The Journal of infectious diseases Abstract IV R292K 171 176 24576826 Unique reassortant of influenza A(H7N9) virus associated with severe disease emerging in Hong Kong. A unique PA L336M mutation, associated with increased polymerase activity, was found. 2014 The Journal of infection Abstract IV L336M 12 17 PA 9 11 24576826 Unique reassortant of influenza A(H7N9) virus associated with severe disease emerging in Hong Kong. The unique mutation PA L336M may enhance viral replication and therefore disease severity. 2014 The Journal of infection Abstract IV L336M 23 28 PA 20 22 2460997 Amino acid substitution at position 226 of the hemagglutinin molecule of influenza (H1N1) virus affects receptor binding activity but not fusion activity. Two mutant HA proteins containing single amino acid substitutions of Asn and Met for Gln at position 226 retained their receptor binding activity, but others with amino acid substitutions Glu, His, Leu, Val, and Thr for Gln at position 226 lost this activity. 1988 Virology Abstract IV Q226M;Q226T 77;212 104;239 HA 11 13 24632455 Complex reassortment of polymerase genes in Asian influenza A virus H7 and H9 subtypes. Furthermore, the most recent reassortments occurred multiply on the polymerase genes of the newly emerging H7N9 isolated from human in South China, evolving E627K mutation in PB2 independently. 2014 Infection, genetics and evolution Abstract IV E627K 157 162 PB2 175 178 24657788 Mammalian pathogenesis of oseltamivir-resistant pandemic (H1N1) 2009 influenza virus isolated in South Korea. To better understand the differences between oseltamivir-susceptible and oseltamivir-resistant virus, we compared the replication and pathogenesis of the NA H275Y mutant virus, A/Gyeongnam/1820/2009, in ferrets and mice with those of oseltamivir-susceptible A/Korea/01/2009 virus. 2014 Virus research Abstract IV H275Y 157 162 154 156 24662294 Interleukin-1 receptor-associated kinase-2 genetic variant rs708035 increases NF-kappaB activity through promoting TRAF6 ubiquitination. Here, we found that the non-synonymous IRAK2 variant rs708035 (coding D431E) increases NF-kappaB activity and leads to more expression of NF-kappaB-dependent proinflammatory cytokines compared with IRAK2 wild type. 2014 The Journal of biological chemistry Abstract IV D431E 70 75 24662294 Interleukin-1 receptor-associated kinase-2 genetic variant rs708035 increases NF-kappaB activity through promoting TRAF6 ubiquitination. Moreover, when IRAK2 knockdown cells reconstituted with siRNA-resistant WT-IRAK2 or D431E-IRAK2 were infected with influenza virus, a more obvious induction of IL-6 and a stronger anti-apoptosis effect were observed in D431E-IRAK2 expressing cells. 2014 The Journal of biological chemistry Abstract IV D431E;D431E 84;219 89;224 24662294 Interleukin-1 receptor-associated kinase-2 genetic variant rs708035 increases NF-kappaB activity through promoting TRAF6 ubiquitination. Notably, we also found that the levels of proinflammatory cytokine-IL-6 were indeed higher in people carrying D431E-IRAK2 than those carrying WT-IRAK2. 2014 The Journal of biological chemistry Abstract IV D431E 110 115 24667168 Low 2012-13 influenza vaccine effectiveness associated with mutation in the egg-adapted H3N2 vaccine strain not antigenic drift in circulating viruses. The egg-adapted strain was itself antigenically distinct from the WHO-recommended prototype, and bore three AA mutations at antigenic sites B [H156Q, G186V] and D [S219Y]. 2014 PloS one Abstract IV H156Q;G186V;S219Y 143;150;164 148;155;169 24696271 A nonpathogenic duck-origin H9N2 influenza A virus adapts to high pathogenicity in mice. Except for HA-L80F, the other seven substitutions were all located in known functional regions involved in interaction of viral proteins or interaction between the virus and host factors. 2014 Archives of virology Abstract IV L80F 11 18 HA 11 13 24696271 A nonpathogenic duck-origin H9N2 influenza A virus adapts to high pathogenicity in mice. Genomic sequence alignment revealed eight amino acid substitutions (HA-L80F, HA-N193D, NA-A27T, PB2-F404L, PA-D3V, PA-S225R, NP-V105M, M1-A166V) in six viral proteins of DK1-MA compared with DK1 virus. 2014 Archives of virology Abstract IV L80F;N193D;A27T;F404L;D3V;S225R;V105M;A166V 68;77;87;100;110;118;128;138 75;85;94;105;113;123;133;143 HA;HA;M1;NA;NP;PA;PA;PB2 68;77;135;87;125;107;115;96 70;79;137;89;127;109;117;99 24696487 Airborne transmission of highly pathogenic H7N1 influenza virus in ferrets. Four amino acid mutations (PB2 T81I, NP V284M, and M1 R95K and Q211K) in the internal genes and a minimal amino acid mutation (K/R313R) in the stalk region of the hemagglutinin protein were associated with airborne transmission. 2014 Journal of virology Abstract IV K313R;T81I;V284M;R95K;Q211K;R313R 127;31;40;54;63;127 134;35;45;58;68;134 HA;M1;NP;PB2 163;51;37;27 176;53;39;30 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. Furthermore, using reverse engineered viruses we demonstrate that a pair of permissive secondary NA mutations, V241I and N369K, confers robust fitness on recent H275Y A(H1N1)pdm09 viruses, which correlated with enhanced surface expression and enzymatic activity of the A(H1N1)pdm09 NA protein. 2014 PLoS pathogens Abstract IV V241I;N369K;H275Y 111;121;161 116;126;166 NA;NA 97;282 99;284 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. However, a cluster of OR A(H1N1)pdm09 viruses, encoding the neuraminidase (NA) H275Y oseltamivir resistance mutation, was detected in Australia in 2011 amongst community patients that had not been treated with oseltamivir. 2014 PLoS pathogens Abstract IV H275Y 79 84 NA;NA 75;60 77;73 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. In conjunction with data from in vitro analyses of NA expression and activity we demonstrate that contemporary A(H1N1)pdm09 viruses are now more capable of acquiring H275Y without compromising their fitness, than earlier A(H1N1)pdm09 viruses circulating in 2009. 2014 PLoS pathogens Abstract IV H275Y 166 171 51 53 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. Our findings suggest that recent A(H1N1)pdm09 viruses are now more permissive to the acquisition of H275Y than earlier A(H1N1)pdm09 viruses, increasing the risk that OR A(H1N1)pdm09 will emerge and spread worldwide. 2014 PLoS pathogens Abstract IV H275Y 100 105 24705721 Mutations flanking the carbohydrate binding site of surfactant protein D confer antiviral activity for pandemic influenza A viruses. D325A+R343V and D325S+R343V also strongly inhibited HA activity, and markedly aggregated, the 1968 pandemic H3N2 strain, Aichi68. 2014 American journal of physiology. Lung cellular and molecular physiology Abstract IV D325A;R343V;R343V;D325S 0;6;22;16 5;11;27;21 HA 52 54 24705721 Mutations flanking the carbohydrate binding site of surfactant protein D confer antiviral activity for pandemic influenza A viruses. D325S+R343V significantly reduced viral loads and mortality of mice infected with Aichi68, whereas wild-type SP-D NCRD did not. 2014 American journal of physiology. Lung cellular and molecular physiology Abstract IV R343V;D325S 6;0 11;5 24705721 Mutations flanking the carbohydrate binding site of surfactant protein D confer antiviral activity for pandemic influenza A viruses. Importantly, we now show that D325A+R343V and D325S+R343V inhibited Cal09 H1N1 and related strains, and reduced uptake of Cal09 by epithelial cells. 2014 American journal of physiology. Lung cellular and molecular physiology Abstract IV D325A;R343V;R343V;D325S 30;36;52;46 35;41;57;51 24705721 Mutations flanking the carbohydrate binding site of surfactant protein D confer antiviral activity for pandemic influenza A viruses. The activity of the double mutants was significantly greater than that of either single mutant (D325A/S or R343V). 2014 American journal of physiology. Lung cellular and molecular physiology Abstract IV D325A;D325S;R343V 96;96;107 103;103;112 24705721 Mutations flanking the carbohydrate binding site of surfactant protein D confer antiviral activity for pandemic influenza A viruses. We now show that replacement of D325 with serine to create D325S+R343V provided equal or increased neutralizing activity compared with D325A+R343V. 2014 American journal of physiology. Lung cellular and molecular physiology Abstract IV R343V;D325S;D325A;R343V 65;59;135;141 70;64;140;146 24705721 Mutations flanking the carbohydrate binding site of surfactant protein D confer antiviral activity for pandemic influenza A viruses. We recently reported that a trimeric neck and carbohydrate recognition domain (NCRD) fragment of human surfactant protein D (SP-D), a host defense lectin, with combinatorial substitutions at the 325 and 343 positions (D325A+R343V) exhibits markedly increased antiviral activity for seasonal strains of influenza A virus (IAV). 2014 American journal of physiology. Lung cellular and molecular physiology Abstract IV D325A;R343V 218;224 223;229 24719414 Development of a high-yield live attenuated H7N9 influenza virus vaccine that provides protection against homologous and heterologous H7 wild-type viruses in ferrets. The selected vaccine virus containing two amino acid changes (N133D/G198E) in the HA improved viral titer by more than 10-fold (reached a titer of 10(8.6) fluorescent focus units/ml) without affecting viral antigenicity. 2014 Journal of virology Abstract IV N133D;G198E 62;68 67;73 HA 82 84 24745625 The antigenic drift molecular basis of the H5N1 influenza viruses in a novel branch of clade 2.3.4. The results of cross-HI assay, micro-neutralization assay and the antigen map of the mutated recombinant viruses showed that three substitutions in antigenic site B, especially D205K, are the major contributors to the antigenic drift of the novel branch of clade 2.3.4. 2014 Veterinary microbiology Abstract IV D205K 177 182 24751348 PCR for detection of oseltamivir resistance mutation in influenza A(H7N9) virus. Sensitive molecular techniques are needed for rapid detection of the R292K oseltamivir-resistant mutant of influenza A(H7/N9) virus strain to monitor its transmission and guide antiviral treatment. 2014 Emerging infectious diseases Abstract IV R292K 69 74 N9 122 124 24760887 Residue 41 of the Eurasian avian-like swine influenza a virus matrix protein modulates virion filament length and efficiency of contact transmission. Moreover, the P41A change altered virion morphology, reducing the number and length of filamentous virions, as well as reducing the neuraminidase activity of virions. 2014 Journal of virology Abstract IV P41A 14 18 132 145 2476569 Single-amino-acid substitution in an antigenic site of influenza virus hemagglutinin can alter the specificity of binding to cell membrane-associated gangliosides. The majority of variants, including one with a substitution near the receptor-binding site (Asn-133----Lys), did not differ from the parent in specificity for receptor molecules. 1989 Journal of virology Abstract IV N133K 92 106 24772896 [Characteristics of complete genome of pandemic A/H1N1/2009 influenza virus isolated in Fujian Province, China]. Compared with the vaccine strain, the influenza strains from Fujian had relatively large variation, and variation was identified at 11 amino acid sites of the HA gene of A/Fujiangulou/SWL1155/2012 strain, including 4 sites (H138R, L161I, S185T, and S203T) involved inthree antigen determinants (Ca, Sa, and Sb). 2014 Bing du xue bao Abstract IV H138R;L161I;S185T;S203T 224;231;238;249 229;236;243;254 HA 159 161 24777528 Molecular characterization of circulating pandemic strains of influenza A virus during 2012 to 2013 in Lucknow (India). In mutational analysis, 33 strains had the S220T mutation, which is at an antigenic site and characteristic of clade seven along with few minor mutations; K180I/T/Q, V190I, S200P, S202T, A203T, A214T, S220T, V251I, and A273T. 2014 Journal of medical virology Abstract IV S220T;K180I;K180T;K180Q;V190I;S200P;S202T;A203T;A214T;S220T;V251I;A273T 43;155;155;155;166;173;180;187;194;201;208;219 48;164;164;164;171;178;185;192;199;206;213;224 24790833 Isolation and characterization of H9N2 influenza virus isolates from poultry respiratory disease outbreak. Isolate 1 has the S31N substitution in the M2 gene that has been associated with drug resistance as well as R57Q and C241Y mutations in the NP gene which are associated with human adaptation. 2014 SpringerPlus Abstract IV S31N;R57Q;C241Y 18;108;117 22;112;122 M2;NP 43;140 45;142 24795482 A novel I221L substitution in neuraminidase confers high-level resistance to oseltamivir in influenza B viruses. CONCLUSIONS: Enzyme kinetic and NA structural analyses provide an explanation for the high level of resistance to oseltamivir while retaining good fitness of viruses carrying I221L variant NA. 2014 The Journal of infectious diseases Abstract IV I221L 175 180 NA;NA 32;189 34;191 24795482 A novel I221L substitution in neuraminidase confers high-level resistance to oseltamivir in influenza B viruses. METHODS: Enzymatic characterization of the NAs (Km, Ki) and the in vitro fitness of viruses carrying wild-type or mutated (I221L) NA genes were evaluated. 2014 The Journal of infectious diseases Abstract IV I221L 123 128 NA;NA 130;43 132;46 24795482 A novel I221L substitution in neuraminidase confers high-level resistance to oseltamivir in influenza B viruses. RESULTS: The Km and Ki revealed that the I221L variant NA had approximately 84 and 51 times lower affinity for oseltamivir carboxylate and zanamivir, respectively, compared with wild-type NA. 2014 The Journal of infectious diseases Abstract IV I221L 41 46 NA;NA 55;188 57;190 24795482 A novel I221L substitution in neuraminidase confers high-level resistance to oseltamivir in influenza B viruses. Structural characterizations by X-ray crystallography of a wild-type and I221L variant NA were performed. 2014 The Journal of infectious diseases Abstract IV I221L 73 78 87 89 24795482 A novel I221L substitution in neuraminidase confers high-level resistance to oseltamivir in influenza B viruses. The crystal structure of the I221L NA and oseltamivir complex showed that the leucine side chain protrudes into the hydrophobic pocket of the active site that accommodates the pentyloxy substituent of oseltamivir. 2014 The Journal of infectious diseases Abstract IV I221L 29 34 35 37 24795482 A novel I221L substitution in neuraminidase confers high-level resistance to oseltamivir in influenza B viruses. UNLABELLED: Influenza B viruses with a novel I221L substitution in neuraminidase (NA) conferring high-level resistance to oseltamivir were isolated from an immunocompromised patient after prolonged oseltamivir treatment. 2014 The Journal of infectious diseases Abstract IV I221L 45 50 NA;NA 82;67 84;80 24795482 A novel I221L substitution in neuraminidase confers high-level resistance to oseltamivir in influenza B viruses. Viruses with a wild-type or I221L variant NA had similar growth kinetics in Madin-Darby canine kidney (MDCK) cells, and 5 passages in MDCK cells revealed no reversion of the I221L substitution. 2014 The Journal of infectious diseases Abstract IV I221L;I221L 28;174 33;179 42 44 24818619 Hemagglutinin mutation D222N of the 2009 pandemic H1N1 influenza virus alters receptor specificity without affecting virulence in mice. A dose-dependent glycan array analysis with the D222N virus showed a modest increase in the binding avidity to human-like (alpha-2,6 sialylated glycan) receptors and avian-like (alpha-2,3 sialylated glycan) receptors than the WT virus. 2014 Virus research Abstract IV D222N 48 53 24818619 Hemagglutinin mutation D222N of the 2009 pandemic H1N1 influenza virus alters receptor specificity without affecting virulence in mice. The D222N HA mutation resulted in slight weight loss, lower lung titers, inflammatory cytokines and alveolar inflammation in mice than the WT virus. 2014 Virus research Abstract IV D222N 4 9 HA 10 12 24818619 Hemagglutinin mutation D222N of the 2009 pandemic H1N1 influenza virus alters receptor specificity without affecting virulence in mice. The D222N hemagglutinin (HA) mutation within the receptor-binding site was detected with higher frequencies in severe cases of 2009 pandemic H1N1 (pdmH1N1) infections. 2014 Virus research Abstract IV D222N 4 9 HA;HA 25;10 27;23 Influenza A virus H1N1 infection 132 166 24818619 Hemagglutinin mutation D222N of the 2009 pandemic H1N1 influenza virus alters receptor specificity without affecting virulence in mice. The recombinant D222N virus grew to significantly lower viral titers than the WT in A549 but not in MDCK cells. 2014 Virus research Abstract IV D222N 16 21 24820460 Passaging impact of H9N2 avian influenza virus in hamsters on its pathogenicity and genetic variability. The amino acid sequence of the neuraminidase in the third passaged H9N2 virus recovered from lungs showed a R46P mutation that might have a role in the pathogenic adaptability of P3 viruses in hamsters' lungs. 2014 Journal of infection in developing countries Abstract IV R46P 108 112 31 44 24824345 Effects of a hemagglutinin D222G substitution on the pathogenicity of 2009 influenza A (H1N1) virus in mice. Altogether, our data suggest that the HA D222G substitution in the K/09 virus might be deleterious to viral fitness. 2014 Archives of virology Abstract IV D222G 41 46 HA 38 40 24824345 Effects of a hemagglutinin D222G substitution on the pathogenicity of 2009 influenza A (H1N1) virus in mice. Compared with the A/Korea/01/2009 (K/09) virus, the HA D222G mutant showed reduced growth in cells and reduced binding avidity to human and turkey red blood cells. 2014 Archives of virology Abstract IV D222G 55 60 HA 52 54 24824345 Effects of a hemagglutinin D222G substitution on the pathogenicity of 2009 influenza A (H1N1) virus in mice. In a BALB/c mouse infection model, infection with the HA D222G mutant virus resulted in less body weight loss when compared to the parental K/09 virus. 2014 Archives of virology Abstract IV D222G 57 62 HA 54 56 24824345 Effects of a hemagglutinin D222G substitution on the pathogenicity of 2009 influenza A (H1N1) virus in mice. In this study, we have investigated the pathogenic effects of the HA D222G substitution in a 2009 pandemic H1N1 virus in mice. 2014 Archives of virology Abstract IV D222G 69 74 HA 66 68 24824345 Effects of a hemagglutinin D222G substitution on the pathogenicity of 2009 influenza A (H1N1) virus in mice. Recently, there have been multiple cases of severe human infections associated with an HA D222G mutant influenza virus. 2014 Archives of virology Abstract IV D222G 90 95 HA 87 89 24838853 Analysis of the phylogeny of Chinese H9N2 avian influenza viruses and their pathogenicity in mice. A T300I mutation in three strains resulted in the loss of a potential glycosylation site. 2014 Archives of virology Abstract IV T300I 2 7 24838853 Analysis of the phylogeny of Chinese H9N2 avian influenza viruses and their pathogenicity in mice. The P315S mutation in seven strains added a potential glycosylation site in HA. 2014 Archives of virology Abstract IV P315S 4 9 HA 76 78 24854981 Solid phase assay for comparing reactivation rates of neuraminidases of influenza wild type and resistant mutants after inhibitor removal. Dissociation of zanamivir and oseltamivir were faster from the D197E mutant, but not of peramivir. 2014 Antiviral research Abstract IV D197E 63 68 24854981 Solid phase assay for comparing reactivation rates of neuraminidases of influenza wild type and resistant mutants after inhibitor removal. Viruses with H274Y, E119V and E119G mutations demonstrated faster dissociation of the inhibitor to which they were resistant. 2014 Antiviral research Abstract IV H274Y;E119V;E119G 13;20;30 18;25;35 24858683 Human monoclonal antibodies derived from a patient infected with 2009 pandemic influenza A virus broadly cross-neutralize group 1 influenza viruses. Furthermore, Ile45Phe and Glu47Gly double substitutions in the alpha-helix region made the HA unrecognizable by the HuMAbs. 2014 Biochemical and biophysical research communications Abstract IV I45F;E47G 13;26 21;34 HA 91 93 24889237 Enhanced human receptor binding by H5 haemagglutinins. In contrast, a double mutant, Delta133/Ile155Thr, isolated in Egypt has greater avidity for human receptor while retaining wild-type avidity for avian receptor. 2014 Virology Abstract IV I155T 39 48 24909420 Research/review: Structure and linkage disequilibrium analysis of adamantane resistant mutations in influenza virus m2 proton channel. After evolutionary and linkage disequilibrium analyses, we found that the some residues in the C-terminal were associated with the famed resistant mutation S31N. 2014 Current drug metabolism Abstract IV S31N 156 160 24923162 [Complete genome phylogenetic analysis of five H9N2 avian influenza viruses isolated from poultry flocks in Qinghai lake region]. The HA receptor-binding site had the Q226L mutation. 2014 Bing du xue bao Abstract IV Q226L 37 42 HA 4 6 24923162 [Complete genome phylogenetic analysis of five H9N2 avian influenza viruses isolated from poultry flocks in Qinghai lake region]. The M1 gene segment had the N30D and T215A mutations. 2014 Bing du xue bao Abstract IV N30D;T215A 28;37 32;42 M1 4 6 24928037 The R35 residue of the influenza A virus NS1 protein has minimal effects on nuclear localization but alters virus replication through disrupting protein dimerization. Recombinant viruses encoding NS1 R35A were not recovered but viruses containing second site mutations at position D39 in addition to the R35A mutation were isolated. 2014 Virology Abstract IV R35A;R35A 33;137 37;141 NS1 29 32 24940441 Analysis of the full-length genome of a novel strain of the H7N9 avian influenza virus. Molecular characterization demonstrated that 52 novel H7N9 viruses sequenced to date contain the G228S and G186V mutations in the receptor binding site of the HA protein. 2014 Experimental and therapeutic medicine Abstract IV G228S;G186V 97;107 102;112 HA 159 161 24941437 Easily accessible polycyclic amines that inhibit the wild-type and amantadine-resistant mutants of the M2 channel of influenza A virus. Inhibition of the wild-type M2 channel and the A/M2-S31N, A/M2-V27A, and A/M2-L26F mutant forms of the channel were measured in Xenopus oocytes using two-electrode voltage clamp assays. 2014 Journal of medicinal chemistry Abstract IV V27A;S31N;L26F 63;52;78 67;56;82 M2;M2;M2;M2 28;49;60;75 30;51;62;77 24941437 Easily accessible polycyclic amines that inhibit the wild-type and amantadine-resistant mutants of the M2 channel of influenza A virus. None of the compounds was found to inhibit the S31N mutant ion channel. 2014 Journal of medicinal chemistry Abstract IV S31N 47 51 24941437 Easily accessible polycyclic amines that inhibit the wild-type and amantadine-resistant mutants of the M2 channel of influenza A virus. Of note, two of the compounds inhibited the amantadine-resistant A/M2-V27A and A/M2-L26F mutant ion channels with submicromolar and low micromolar IC50, respectively. 2014 Journal of medicinal chemistry Abstract IV V27A;L26F 70;84 74;88 M2;M2 67;81 69;83 24951535 Mutations in the chikungunya virus non-structural proteins cause resistance to favipiravir (T-705), a broad-spectrum antiviral. Reverse-engineering of this K291R mutation into an infectious clone of CHIKV confirmed the link between the mutant genotype and the resistant phenotype. 2014 The Journal of antimicrobial chemotherapy Abstract IV K291R 28 33 24951535 Mutations in the chikungunya virus non-structural proteins cause resistance to favipiravir (T-705), a broad-spectrum antiviral. Several favipiravir-resistant CHIKV variants were independently selected and all of them in particular acquired the unique K291R mutation in the RNA-dependent RNA polymerase (RdRp). 2014 The Journal of antimicrobial chemotherapy Abstract IV K291R 123 128 24951824 The R292K mutation that confers resistance to neuraminidase inhibitors leads to competitive fitness loss of A/Shanghai/1/2013 (H7N9) influenza virus in ferrets. An NA-R292K mutation that confers broad-spectrum resistance to NA inhibitors has been documented in H7N9 patients after treatment. 2014 The Journal of infectious diseases Abstract IV R292K 6 11 NA;NA 3;63 5;65 24951824 The R292K mutation that confers resistance to neuraminidase inhibitors leads to competitive fitness loss of A/Shanghai/1/2013 (H7N9) influenza virus in ferrets. CONCLUSIONS: The NA inhibitor-resistant H7N9 virus with the NA-R292K mutation may transmit among ferrets but showed compromised fitness in vivo while in competition with the wild-type virus. 2014 The Journal of infectious diseases Abstract IV R292K 63 68 NA;NA 17;60 19;62 24951824 The R292K mutation that confers resistance to neuraminidase inhibitors leads to competitive fitness loss of A/Shanghai/1/2013 (H7N9) influenza virus in ferrets. In ferrets inoculated with the plaque-purified A/Shanghai/1/2013 NA-R292K virus with dominant K292 (94%), the resistant K292 genotype was outgrown by the wild-type R292 genotype during the course of infection. 2014 The Journal of infectious diseases Abstract IV R292K 68 73 65 67 24951824 The R292K mutation that confers resistance to neuraminidase inhibitors leads to competitive fitness loss of A/Shanghai/1/2013 (H7N9) influenza virus in ferrets. METHODS: We evaluated the transmission potential of a human influenza A H7N9 isolate with a NA-R292K mutation in the ferret model followed by genotyping assay to monitor its competitive fitness in vivo. 2014 The Journal of infectious diseases Abstract IV R292K 95 100 92 94 Influenza 54 69 24951824 The R292K mutation that confers resistance to neuraminidase inhibitors leads to competitive fitness loss of A/Shanghai/1/2013 (H7N9) influenza virus in ferrets. RESULTS: Plaque-purified A/Shanghai/1/2013 wild-type and NA-R292K viruses transmitted at comparable efficiency to direct or respiratory droplet contact ferrets. 2014 The Journal of infectious diseases Abstract IV R292K 60 65 57 59 24957832 Characterization of drug-resistant influenza virus A(H1N1) and A(H3N2) variants selected in vitro with laninamivir. In the A/Brisbane/10/2007 A(H3N2) background, a large NA deletion accompanied by S138A/P194L HA substitutions was selected. 2014 Antimicrobial agents and chemotherapy Abstract IV S138A;P194L 81;87 86;92 HA;NA 93;54 95;56 24957832 Characterization of drug-resistant influenza virus A(H1N1) and A(H3N2) variants selected in vitro with laninamivir. In vitro, laninamivir pressure selected the E119A NA substitution in the A/Solomon Islands/3/2006 A(H1N1) background, whereas E119K and G147E NA changes along with a K133E hemagglutinin (HA) substitution were selected in the A/Quebec/144147/2009 A(H1N1)pdm09 strain. 2014 Antimicrobial agents and chemotherapy Abstract IV E119A;E119K;G147E;K133E 44;126;136;166 49;131;141;171 HA;HA;NA;NA 187;172;50;142 189;185;52;144 24957832 Characterization of drug-resistant influenza virus A(H1N1) and A(H3N2) variants selected in vitro with laninamivir. More specifically, it retained activity against oseltamivir-resistant H275Y and N295S A(H1N1) variants and the E119V A(H3N2) variant. 2014 Antimicrobial agents and chemotherapy Abstract IV H275Y;N295S;E119V 70;80;111 75;85;116 24965464 High-throughput identification of loss-of-function mutations for anti-interferon activity in the influenza A virus NS segment. Mechanistic characterization further showed that a single substitution, D92Y, resulted in the inability of NS to inhibit RIG-I ubiquitination. 2014 Journal of virology Abstract IV D92Y 72 76 NS 107 109 24993865 Characterization of the amantadine-resistant H5N1 highly pathogenic avian influenza variants isolated from quails in Southern China. Molecular analysis suggested that QA viruses and clade 4 H5N1 viruses carried consistent residue signatures, such as the characteristic M2 Ser31Asn amantadine-resistance mutation, implying a common origin of these viruses. 2014 Virus genes Abstract IV S31N 139 147 M2 136 138 24993865 Characterization of the amantadine-resistant H5N1 highly pathogenic avian influenza variants isolated from quails in Southern China. Results from amantadine sensitivity tests of wild-type QA viruses and their reverse genetic viruses demonstrated that all QA viruses were resistant to amantadine, and the M2 Ser31Asn mutation was determined as the most likely cause of the increased amantadine-resistance of H5N1 QA viruses. 2014 Virus genes Abstract IV S31N 174 182 M2 171 173 2499887 Two murine natural polyreactive autoantibodies are encoded by nonmutated germ-line genes. Compared with the germ-line VH 1210.7 gene, E7 has a single nucleotide difference leading to a silent mutation at position 15, whereas D23 seems to be encoded by germ-line VH 101 with one nucleotide difference causing replacement of Ser-84 by Ala. 1989 Proc Natl Acad Sci U S A Abstract IV S84A 233 246 25024224 Recent evolution of equine influenza and the origin of canine influenza. Analyses of site-specific mutant HAs indicate that a single amino acid substitution, Thr-30 Ser, influences interactions between N-terminal and C-terminal regions of the subdomain that are important in the structural changes required for membrane fusion activity. 2014 Proc Natl Acad Sci U S A Abstract IV T30S 85 95 25024224 Recent evolution of equine influenza and the origin of canine influenza. HAs of canine viruses are distinct in containing a Trp-222 Leu substitution in the receptor binding site that influences specificity for receptor analogs. 2014 Proc Natl Acad Sci U S A Abstract IV W222L 51 62 25031333 Amino acid substitutions in PB1 of avian influenza viruses influence pathogenicity and transmissibility in chickens. In the present study, we introduced a C38Y substitution into WB PB1 and demonstrated that this substitution increased both polymerase activity in DF-1 cells in vitro and the pathogenicity of the recombinant viruses in chickens. 2014 Journal of virology Abstract IV C38Y 38 42 PB1 64 67 25031333 Amino acid substitutions in PB1 of avian influenza viruses influence pathogenicity and transmissibility in chickens. Interestingly, the V14A substitution reduced viral shedding and transmissibility. 2014 Journal of virology Abstract IV V14A 19 23 25031333 Amino acid substitutions in PB1 of avian influenza viruses influence pathogenicity and transmissibility in chickens. The V14A substitution in LP PB1 reduced polymerase activity but did not affect pathogenicity in chickens. 2014 Journal of virology Abstract IV V14A 4 8 PB1 28 31 25033052 Y155H amino acid substitution in influenza A(H1N1)pdm09 viruses does not confer a phenotype of reduced susceptibility to neuraminidase inhibitors. Contrary to what was observed in the seasonal A(H1N1) viruses, neither of the Y155H A(H1N1) pdm09 viruses described here showed a phenotype of reduced inhibition by NAIs as determined by the neuraminidase enzyme inhibition assay (MUNANA). 2014 Euro surveillance Abstract IV Y155H 78 83 NAI;NA 165;191 169;204 25033052 Y155H amino acid substitution in influenza A(H1N1)pdm09 viruses does not confer a phenotype of reduced susceptibility to neuraminidase inhibitors. During the 2012/13 epidemic season in Spain, two A(H1N1) pdm09 viruses bearing the specific Y155H substitution in the NA were detected and isolated from two patients diagnosed with severe respiratory syndrome and pneumonia requiring admission to the intensive care unit. 2014 Euro surveillance Abstract IV Y155H 92 97 118 120 Acute respiratory distress syndrome;Pneumonia 181;213 208;222 25033052 Y155H amino acid substitution in influenza A(H1N1)pdm09 viruses does not confer a phenotype of reduced susceptibility to neuraminidase inhibitors. High-throughput sequencing of the NA of both Y155H viruses showed that they were composed to >99% of H155 variants. 2014 Euro surveillance Abstract IV Y155H 45 50 34 36 25033052 Y155H amino acid substitution in influenza A(H1N1)pdm09 viruses does not confer a phenotype of reduced susceptibility to neuraminidase inhibitors. The Y155H amino acid substitution in the neuraminidase gene (NA) has previously been associated with highly reduced inhibition by neuraminidase inhibitors in the seasonal H1N1 influenza A virus which circulated in humans before the 2009 pandemic. 2014 Euro surveillance Abstract IV Y155H 4 9 NA;NA;NA 61;41;130 63;54;143 25037995 Adaptation of a natural reassortant H5N2 avian influenza virus in mice. Only five amino acid mutations in four viral proteins (HA-S227N, PB2-Q591K, PB2-D701N, PA-I554V and NP-R351K) of HB10-MA virus were found when compared with those of HB10, indicating that they may be responsible for the adaptation of the novel reassortant H5N2 avian influenza virus in mice with increased virulence and replication efficiency. 2014 Veterinary microbiology Abstract IV S227N;Q591K;D701N;I554V;R351K 58;69;80;90;103 63;74;85;95;108 HA;NP;PA;PB2;PB2 55;100;87;65;76 57;102;89;68;79 25043638 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2012-2013. The emergence and global spread in 2007/2008 of A(H1N1) influenza viruses showing clinical resistance to oseltamivir due to neuraminidase (NA) H275Y substitution, in the absence of drug pressure, warrants continued vigilance and monitoring for similar viruses. 2014 Antiviral research Abstract IV H275Y 143 148 NA;NA 139;124 141;137 25043638 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2012-2013. Those showing HRI were A(H1N1)pdm09 with NA H275Y (n=18), A(H3N2) with NA E119V (n=3) or NA R292K (n=1) and B/Victoria-lineage with NA H273Y (n=2); amino acid position numbering is A subtype and B type specific. 2014 Antiviral research Abstract IV H275Y;E119V;R292K;H273Y 44;74;92;135 49;79;97;140 NA;NA;NA;NA 41;71;89;132 43;73;91;134 25066276 Development and clinical testing of a simple, low-density gel element array for influenza identification, subtyping, and H275Y detection. Seasonal H275Y variants were detectable in a mixed population when present at >5% with wild type virus, while the 2009 pandemic H1N1 H275Y variant was detectable at <=1% in a mixture with pandemic wild type virus. 2014 Journal of virological methods Abstract IV H275Y;H275Y 9;133 14;138 25078301 Epitope mapping of the 2009 pandemic and the A/Brisbane/59/2007 seasonal (H1N1) influenza virus haemagglutinins using mAbs and escape mutants. Among the six HA mutations that were part of predicted antigenic sites (Ca1, Ca2, Cb, Sa or Sb), three (G172E, N173D and K180E) were within the Sa site. 2014 The Journal of general virology Abstract IV G172E;N173D;K180E 104;111;121 109;116;126 HA 14 16 25078301 Epitope mapping of the 2009 pandemic and the A/Brisbane/59/2007 seasonal (H1N1) influenza virus haemagglutinins using mAbs and escape mutants. Eight escape mutations (H54N, N55D, N55K, L60H, N203D, A231T, V314I and K464E) were obtained for Bris07 HA, and all but one (N203D, Sb site) were outside the predicted antigenic sites. 2014 The Journal of general virology Abstract IV H54N;N55D;N55K;L60H;N203D;A231T;V314I;K464E;N203D 24;30;36;42;48;55;62;72;125 28;34;40;46;53;60;67;77;130 HA 104 106 25078301 Epitope mapping of the 2009 pandemic and the A/Brisbane/59/2007 seasonal (H1N1) influenza virus haemagglutinins using mAbs and escape mutants. Our results suggest that the Sa antigenic site is immunodominant in pdm09 HA, whereas the N203D mutation (Sb site), present in three different Bris07 escape mutants, appears as the immunodominant epitope in that strain. 2014 The Journal of general virology Abstract IV N203D 90 95 HA 74 76 25078301 Epitope mapping of the 2009 pandemic and the A/Brisbane/59/2007 seasonal (H1N1) influenza virus haemagglutinins using mAbs and escape mutants. The resulting epitope mapping of the pdm09 HA protein revealed 11 escape mutations including three that were previously described (G172E, N173D and K256E) and eight novel ones (T89R, F128L, G157E, K180E, A212E, R269K, N311T and G478E). 2014 The Journal of general virology Abstract IV G172E;N173D;K256E;T89R;F128L;G157E;K180E;A212E;R269K;N311T;G478E 131;138;148;177;183;190;197;204;211;218;228 136;143;153;181;188;195;202;209;216;223;233 HA 43 45 25078692 A single amino acid substitution in the novel H7N9 influenza A virus NS1 protein increases CPSF30 binding and virulence. An I106M substitution in H7N9 NS1 can restore CPSF30 binding together with the ability to block host gene expression. 2014 Journal of virology Abstract IV I106M 3 8 NS1 30 33 25078692 A single amino acid substitution in the novel H7N9 influenza A virus NS1 protein increases CPSF30 binding and virulence. Furthermore, a recombinant virus expressing H7N9 NS1-I106M replicates to higher titers in vivo, and is subtly more virulent, than the parental virus. 2014 Journal of virology Abstract IV I106M 53 58 NS1 49 52 25081940 Prolonged shedding of pandemic influenza A (H1N1) 2009 virus in a pancreas-after-kidney transplant recipient. Pyrosequencing analysis detected the H275Y mutation, which is associated with resistance to oseltamivir. 2014 Journal of clinical virology Abstract IV H275Y 37 42 25100840 Influenza A virus acquires enhanced pathogenicity and transmissibility after serial passages in swine. Crucially, one mutant viral clone with the five consensus mutations, which also carried D187E, K211E, and S289N mutations in its HA, additionally was able to infect ferrets by airborne transmission as effectively as the pandemic virus. 2014 Journal of virology Abstract IV D187E;K211E;S289N 88;95;106 93;100;111 HA 129 131 25100840 Influenza A virus acquires enhanced pathogenicity and transmissibility after serial passages in swine. Deep sequencing of viral quasispecies from the ninth passage found five consensus amino acid mutations: PB1 A469T, PA 1129T, NA N329D, NS1 N205K, and NEP T48N. 2014 Journal of virology Abstract IV A469T;N329D;N205K;T48N 108;128;139;154 113;133;144;158 NA;NEP;NS1;PA;PB1 125;150;135;115;104 127;153;138;117;107 25100840 Influenza A virus acquires enhanced pathogenicity and transmissibility after serial passages in swine. Specifically, two mutants of rH1N1 (PB1 A469T and a combination of NS1 N205K and NEP T48N) were identified as determinants of transmissibility in guinea pigs. 2014 Journal of virology Abstract IV A469T;N205K;T48N 40;71;85 45;76;89 NEP;NS1;PB1 81;67;36 84;70;39 25119465 Functional balance between the hemagglutinin and neuraminidase of influenza A(H1N1)pdm09 HA D222 variants. D222G/N substitutions in A(H1N1)pdm09 hemagglutinin may be associated with increased binding of viruses causing low respiratory tract infections and human pathogenesis. 2014 PloS one Abstract IV D222G;D222N 0;0 7;7 HA 38 51 25124927 Characterization of drug-resistant influenza A(H7N9) variants isolated from an oseltamivir-treated patient in Taiwan. METHODS: Four NA variants of A/Taiwan/1/2013(H7N9) virus containing a single substitution (NA-E119V, NA-I222K, NA-I222R, or NA-R292K) recovered from an oseltamivir-treated patient were tested for NAI susceptibility in vitro; their replicative fitness was evaluated in cell culture, mice, and ferrets. 2015 The Journal of infectious diseases Abstract IV E119V;I222K;I222R;R292K 94;104;114;127 99;109;119;132 NA;NA;NA;NA;NA;NAI 14;91;101;111;124;196 16;93;103;113;126;199 25124927 Characterization of drug-resistant influenza A(H7N9) variants isolated from an oseltamivir-treated patient in Taiwan. NA-I222K virus was the most virulent in mice, whereas virus lacking NA change (NA-WT) and NA-R292K virus seemed the least virulent. 2015 The Journal of infectious diseases Abstract IV I222K;R292K 3;93 8;98 NA;NA;NA;NA 0;68;79;90 2;70;81;92 25124927 Characterization of drug-resistant influenza A(H7N9) variants isolated from an oseltamivir-treated patient in Taiwan. NA-R292K virus, showed reduced replicative fitness in this animal model. 2015 The Journal of infectious diseases Abstract IV R292K 3 8 0 2 25124927 Characterization of drug-resistant influenza A(H7N9) variants isolated from an oseltamivir-treated patient in Taiwan. RESULTS: NA-R292K led to highly reduced inhibition by oseltamivir and peramivir, while NA-E119V, NA-I222K, and NA-I222R caused reduced inhibition by oseltamivir. 2015 The Journal of infectious diseases Abstract IV R292K;E119V;I222K;I222R 12;90;100;114 17;95;105;119 NA;NA;NA;NA 9;87;97;111 11;89;99;113 25124927 Characterization of drug-resistant influenza A(H7N9) variants isolated from an oseltamivir-treated patient in Taiwan. Sequence analysis suggests that PB2-S714N increased virulence of NA-I222K virus in mice; NS1-K126R, alone or in combination with PB2-V227M, produced contrasting effects in NA-WT and NA-R292K viruses. 2015 The Journal of infectious diseases Abstract IV S714N;I222K;K126R;V227M;R292K 36;68;93;133;185 41;73;98;138;190 NA;NA;NA;NS1;PB2;PB2 65;172;182;89;32;129 67;174;184;92;35;132 25135885 Two amino acid substitutions in the haemagglutinin of the 2009 pandemic H1N1 virus decrease direct-contact transmission in guinea pigs. In this study, we report that a combination of two mutations (N159D and Q226R) in the haemagglutinin (HA) protein of the representative 2009 H1N1 influenza virus A/California/04/2009 (CA04) caused a switch in receptor binding preference from the alpha2,6-sialoglycan to the alpha2,3-sialoglycan receptor, and decreased the binding intensities for both glycans. 2014 The Journal of general virology Abstract IV N159D;Q226R 62;72 67;77 HA;HA 102;86 104;100 25142579 Influenza A virus polymerase is a site for adaptive changes during experimental evolution in bat cells. Adaptation of an avian virus-like virus resulted in the canonical PB2 E627K mutation that is required for efficient replication in other mammals. 2014 Journal of virology Abstract IV E627K 70 75 PB2 66 69 25142579 Influenza A virus polymerase is a site for adaptive changes during experimental evolution in bat cells. Deep sequencing of adapted human influenza A virus revealed a mutation in the PA polymerase subunit not previously described, M285K. 2014 Journal of virology Abstract IV M285K 126 131 PA 78 80 25142579 Influenza A virus polymerase is a site for adaptive changes during experimental evolution in bat cells. Recombinant virus with the PA M285K mutation completely phenocopied the adapted virus. 2014 Journal of virology Abstract IV M285K 30 35 PA 27 29 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. The H5N1 PB1-V43I-recombinant virus replicates to comparable titres as the wild-type virus in vitro or in the mouse lungs. 2014 Nature communications Abstract IV V43I 13 17 PB1 9 12 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. We demonstrate that a single PB1-V43I mutation increases selectivity to guanosine in A/Wuhan/359/95 (H3N2) and A/Vietnam/1203/04 (H5N1) viruses. 2014 Nature communications Abstract IV V43I 33 37 PB1 29 32 25187542 A histidine residue of the influenza virus hemagglutinin controls the pH dependence of the conformational change mediating membrane fusion. The HA of highly pathogenic H5N1 viruses carries a Glu-to-Arg mutation at position 216 close to His184. 2014 Journal of virology Abstract IV E216R 51 86 HA 4 6 25191344 Prevalence of Oseltamivir-Resistant 2009 H1N1 Influenza Virus among Patients with Pandemic 2009 H1N1 Influenza infection in NRITLD, Tehran, Iran. MATERIALS AND METHODS: In a retrospective cross-sectional study, respiratory tract specimens of confirmed cases of 2009 H1N1 influenza referred to the Masih Daneshvari Hospital were analyzed for presence of H275Y mutation. 2011 Tanaffos Abstract IV H275Y 207 212 25191344 Prevalence of Oseltamivir-Resistant 2009 H1N1 Influenza Virus among Patients with Pandemic 2009 H1N1 Influenza infection in NRITLD, Tehran, Iran. RESULTS: From November 2009 through March 2010, oseltamivir-resistant 2009 H1N1 infection was observed and confirmed in 4 patients (including 2 immunocompromised patients) by performing H275Y mutation molecular testing. 2011 Tanaffos Abstract IV H275Y 186 191 Influenza A virus H1N1 infection 75 89 25191344 Prevalence of Oseltamivir-Resistant 2009 H1N1 Influenza Virus among Patients with Pandemic 2009 H1N1 Influenza infection in NRITLD, Tehran, Iran. The H275Y mutation (oseltamivir-resistant genotype) could appear in the absence or presence of selective drug pressure. 2011 Tanaffos Abstract IV H275Y 4 9 25194918 PB2-E627K and PA-T97I substitutions enhance polymerase activity and confer a virulent phenotype to an H6N1 avian influenza virus in mice. Our results demonstrate that PB2-E627K and PA-T97I enhance the ability of H6N1 virus to replicate and cause disease in mammals. 2014 Virology Abstract IV E627K;T97I 33;46 38;50 PA;PB2 43;29 45;32 25194918 PB2-E627K and PA-T97I substitutions enhance polymerase activity and confer a virulent phenotype to an H6N1 avian influenza virus in mice. Polymerase complexes possessing either PB2-E627K, PA-T97I, and PB2-E627K/PA-T97I displayed higher virus polymerase activity when compared to the wild-type virus, which may account for the increased replication kinetics and enhanced virulence of variant viruses. 2014 Virology Abstract IV E627K;T97I;E627K;T97I 43;53;67;76 48;57;72;80 PA;PA;PB2;PB2 50;73;39;63 52;75;42;66 25194918 PB2-E627K and PA-T97I substitutions enhance polymerase activity and confer a virulent phenotype to an H6N1 avian influenza virus in mice. We found that the recombinant H6N1 viruses possessing both the PA-T97I and PB2-E627K substitutions displayed the greatest enhancement of replication in vitro and in vivo. 2014 Virology Abstract IV E627K;T97I 79;66 84;70 PA;PB2 63;75 65;78 25204499 A human monoclonal antibody derived from a vaccinated volunteer recognizes heterosubtypically a novel epitope on the hemagglutinin globular head of H1 and H9 influenza A viruses. Furthermore, Phe114Ile substitution in the epitope made the HA unrecognizable by the HuMAb. 2014 Biochemical and biophysical research communications Abstract IV F114I 13 22 HA 60 62 25210166 Accumulation of human-adapting mutations during circulation of A(H1N1)pdm09 influenza virus in humans in the United Kingdom. A mutation in PA (N321K) enhanced polymerase activity of third-wave viruses and also provided a replicative advantage in HAE cells. 2014 Journal of virology Abstract IV N321K 18 23 PA 14 16 25210184 Mutations to PB2 and NP proteins of an avian influenza virus combine to confer efficient growth in primary human respiratory cells. In addition, minimal combinations of three (PB2 Q236H, E627K, and NP N309K) or two (PB2 Q591K and NP S50G) mutations were sufficient to recapitulate the efficient growth in HTBE cells of dk/AB/76 viruses isolated after 10 passages in this substrate. 2014 Journal of virology Abstract IV Q236H;E627K;N309K;Q591K;S50G 48;55;69;88;101 53;60;74;93;105 NP;NP;PB2;PB2 66;98;44;84 68;100;47;87 25210184 Mutations to PB2 and NP proteins of an avian influenza virus combine to confer efficient growth in primary human respiratory cells. The results indicate that coupling of the mammalian-adaptive mutation PB2 E627K or Q591K to selected mutations in NP further augments the growth of the corresponding viruses. 2014 Journal of virology Abstract IV E627K;Q591K 74;83 79;88 NP;PB2 114;70 116;73 25211283 Effect of cytosolic pH on inward currents reveals structural characteristics of the proton transport cycle in the influenza A protein M2 in cell-free membrane patches of Xenopus oocytes. Transport activity through the mutant D44A of the M2 proton channel from influenza virus A was measured in excised inside-out macro-patches of Xenopus laevis oocytes at cytosolic pH values of 5.5, 7.5 and 8.2. 2014 PloS one Abstract IV D44A 38 42 M2 50 52 25231317 Amino acid changes in the influenza A virus PA protein that attenuate avian H5N1 viruses in mammals. Specifically, we found that an arginine-to-lysine substitution at position 185 of an H5N1 virus PA protein significantly affected that virus's virulence and pathogenicity in mice. 2014 Journal of virology Abstract IV R185K 31 78 PA 96 98 25234090 Dextran sulfate-resistant A/Puerto Rico/8/34 influenza virus is associated with the emergence of specific mutations in the neuraminidase glycoprotein. In addition, R430L, K432E or K435E in the 430-435 region was a common mutation in all resistant NA genes. 2014 Antiviral research Abstract IV R430L;K432E;K435E 13;20;29 18;25;34 96 98 25246391 Multiple influenza A (H3N2) mutations conferring resistance to neuraminidase inhibitors in a bone marrow transplant recipient. In addition, a combination of a 4-amino-acid deletion at residues 245 to 248 (Delta245-248) accompanied by the E119V substitution occurred, causing resistance to or reduced inhibition by NAIs (oseltamivir, zanamivir, and peramivir). 2014 Antimicrobial agents and chemotherapy Abstract IV E119V 111 116 NAI 187 191 25246391 Multiple influenza A (H3N2) mutations conferring resistance to neuraminidase inhibitors in a bone marrow transplant recipient. In-depth analysis by deep gene sequencing revealed that various known markers of antiviral resistance, including transient R292K and Q136K substitutions and a sustained E119K (N2 numbering) substitution in the NA protein emerged during prolonged antiviral therapy. 2014 Antimicrobial agents and chemotherapy Abstract IV R292K;Q136K;E119K 123;133;169 128;138;174 210 212 25262472 Influenza A viruses with different amino acid residues at PB2-627 display distinct replication properties in vitro and in vivo: revealing the sequence plasticity of PB2-627 position. Of these, PB2-D309N was identified as a novel one. 2014 Virology Abstract IV D309N 14 19 PB2 10 13 25275121 A combination of HA and PA mutations enhances virulence in a mouse-adapted H6N6 influenza A virus. Amino acid substitutions in PB2 (E627K), PA (I38M), and hemagglutinin ([HA] L111F, H156N, and S263R) occurred in GDK6-MA. 2014 Journal of virology Abstract IV H156N;S263R;E627K;I38M;L111F 83;94;33;45;76 88;99;38;49;81 HA;HA;PA;PB2 72;56;41;28 74;69;43;31 25275121 A combination of HA and PA mutations enhances virulence in a mouse-adapted H6N6 influenza A virus. HA with the H156N mutation [HA(H156N)] resulted in enlarged plaque sizes on MDCK cells and enhanced early-stage viral replication in mammalian cells. 2014 Journal of virology Abstract IV H156N;H156N 12;31 17;36 HA;HA 0;28 2;30 25275121 A combination of HA and PA mutations enhances virulence in a mouse-adapted H6N6 influenza A virus. PA(I38M) raised polymerase activity in vitro but did not change virus replication in either mammalian cells or mice. 2014 Journal of virology Abstract IV I38M 3 7 PA 0 2 25275121 A combination of HA and PA mutations enhances virulence in a mouse-adapted H6N6 influenza A virus. Specific mutations were found in PB2 (E627K), PA (I38M), and HA (L111F, H156N, and S263R) and were assessed for their virulence in mice. 2014 Journal of virology Abstract IV E627K;I38M;L111F;H156N;S263R 38;50;65;72;83 43;54;70;77;88 HA;PA;PB2 61;46;33 63;48;36 25275121 A combination of HA and PA mutations enhances virulence in a mouse-adapted H6N6 influenza A virus. The combination of HA(H156N S263R) and PA(I38M) compensated for the lack of PB2(627K) and showed increased pathogenicity in mice, revealing a novel mechanism that can affect the virulence of influenza viruses. 2014 Journal of virology Abstract IV H156N;S263R;I38M 22;28;42 27;33;46 HA;PA;PB2 19;39;76 21;41;79 25275121 A combination of HA and PA mutations enhances virulence in a mouse-adapted H6N6 influenza A virus. These single substitutions had only limited effects on virulence; however, a combination of HA(H156N S263R) with PA(I38M) in the GDK6 backbone led to a significantly more virulent variant. 2014 Journal of virology Abstract IV S263R;H156N;I38M 101;95;116 106;100;120 HA;PA 92;113 94;115 25301400 Characterization of human Influenza Viruses in Lebanon during 2010-2011 and 2011-2012 post-pandemic seasons. Nonetheless, all 2011-2012 H1N1p isolates had three mutations (V241I, N369K, and N386S) in the NA gene that were suggested to be permissive of the H275Y mutation, which confers resistance to oseltamivir. 2014 Intervirology Abstract IV V241I;N369K;N386S;H275Y 63;70;81;147 68;75;86;152 95 97 25301400 Characterization of human Influenza Viruses in Lebanon during 2010-2011 and 2011-2012 post-pandemic seasons. We also detected one H1N1p virus during the 2010-2011 season with a 4-fold decrease in susceptibility to oseltamivir due to an NA-S247N mutation. 2014 Intervirology Abstract IV S247N 130 135 127 129 25320319 Profiling and characterization of influenza virus N1 strains potentially resistant to multiple neuraminidase inhibitors. Furthermore, E119D and E119D-H274Y mutants in the pH1N1 background maintained overall fitness properties in vitro and in vivo. 2015 Journal of virology Abstract IV E119D;H274Y;E119D 13;29;23 18;34;34 25320319 Profiling and characterization of influenza virus N1 strains potentially resistant to multiple neuraminidase inhibitors. Of the 14 single and double mutant viruses recovered in the backbone of pH1N1, four variants (E119D, E119A/D/G-H274Y) exhibited reduced inhibition by all of the NAIs and two variants (E119D and E119D-H274Y) retained the overall properties of gene stability, replicative efficiency, pathogenicity, and transmissibility in vitro and in vivo. 2015 Journal of virology Abstract IV E119D;E119A;E119D;E119G;H274Y;E119D;H274Y;E119D 94;101;101;101;101;184;200;194 99;110;110;110;110;189;205;205 NAI 161 165 25320319 Profiling and characterization of influenza virus N1 strains potentially resistant to multiple neuraminidase inhibitors. Of the nine recombinant H5N1 viruses, four variants (E119D, E119A/D/G-H274Y) also showed reduced inhibition by all of the NAIs, though their overall viral fitness was impaired in vitro and/or in vivo. 2015 Journal of virology Abstract IV E119D;H274Y;E119A;E119D;E119G 53;70;60;60;60 58;75;69;69;69 NAI 122 126 25320319 Profiling and characterization of influenza virus N1 strains potentially resistant to multiple neuraminidase inhibitors. We found that recombinant E119D and E119A/D/G/-H274Y mutant viruses demonstrated reduced inhibition by all of the NAIs tested in both the backbone of the 2009 H1N1 pandemic (pH1N1) and highly pathogenic avian influenza H5N1 viruses. 2015 Journal of virology Abstract IV E119D;E119A;E119D;E119G;H274Y 26;36;36;36;36 31;45;45;45;45 NAI 114 118 25320319 Profiling and characterization of influenza virus N1 strains potentially resistant to multiple neuraminidase inhibitors. We therefore screened a known mutation(s) that could confer multidrug resistance to the currently approved NAIs oseltamivir, zanamivir, and peramivir by assessing recombinant viruses with mutant NA-encoding genes (catalytic residues R152K and R292K, framework residues E119A/D/G, D198N, H274Y, and N294S) in the backbones of the 2009 pandemic H1N1 (pH1N1) and highly pathogenic avian influenza (HPAI) H5N1 viruses. 2015 Journal of virology Abstract IV R152K;R292K;E119A;E119D;E119G;D198N;H274Y;N294S 233;243;269;269;269;280;287;298 238;248;278;278;278;285;292;303 NA;NAI 195;107 197;111 25328558 Influenza A H1N1pdm 2009 Virus in Paraguay: Nucleotide Point Mutations in Hemagglutinin and Neuraminidase Genes are not Associated with Drug Resistance. Neither the mutation related to exacerbation of disease (D239G in hemagglutinin) nor that related to antiviral resistance (H275Y in neuraminidase), both detected in neighboring countries, were found. 2014 The open virology journal Abstract IV D239G;H275Y 57;123 62;128 HA;NA 66;132 79;145 25339773 Virulence determinants in the PB2 gene of a mouse-adapted H9N2 virus. Here, we show that a mouse-adapted PB2 gene with a phenylalanine-to-leucine mutation (F404L) mainly contributes to enhanced polymerase activity, replication, and pathogenicity of H9N2 in mice and also increases the virulence of the H5N1 and 2009 pandemic H1N1 influenza viruses. 2015 Journal of virology Abstract IV F404L 86 91 PB2 35 38 25342196 Viral M2 ion channel protein: a promising target for anti-influenza drug discovery. The biologically important compounds discovered using the scaffolds such as bisnoradmantane, noradamantane, triazine, spiroadamantane, isoxazole, amino alcohol, azaspiro, spirene, pinanamine, etc are reported to exhibit anti-influenza activity against wild or mutant type (S31N and V27A) of M2 proton channel protein. 2014 Mini reviews in medicinal chemistry Abstract IV V27A;S31N 282;273 286;277 M2 291 293 25409547 The K526R substitution in viral protein PB2 enhances the effects of E627K on influenza virus replication. Here we show that mutation PB2-K526R is present in some human H7N9 influenza isolates, in nearly 80% of H5N1 human isolates from Indonesia and, in conjunction with E627K, in almost all seasonal H3N2 viruses since 1970. 2014 Nature communications Abstract IV K526R;E627K 31;164 36;169 PB2 27 30 25409547 The K526R substitution in viral protein PB2 enhances the effects of E627K on influenza virus replication. Host-adaptive strategies, such as the E627K substitution in the PB2 protein, are critical for replication of avian influenza A viruses in mammalian hosts. 2014 Nature communications Abstract IV E627K 38 43 PB2 64 67 25409547 The K526R substitution in viral protein PB2 enhances the effects of E627K on influenza virus replication. PB2-K526R interacts with nuclear export protein and our results suggest that it contributes to enhance replication for certain influenza virus subtypes, particularly in combination with 627K. 2014 Nature communications Abstract IV K526R 4 9 NEP;PB2 25;0 47;3 25418970 Tetrahydrobiopterin deficiency among Serbian patients presenting with hyperphenylalaninemia. Genetic analyses showed that the patient does not have disease-causing variants of the PAH gene and carries a p.Asp136Val mutation in homozygous state in the PTS gene. 2015 Journal of pediatric endocrinology & metabolism Abstract IV D136V 110 121 25457364 Multiple amino acid substitutions involved in the adaptation of H6N1 avian influenza virus in mice. Sequencing of the variants revealed amino acid changes in the PB2 (E627K), PA (T97I), and HA (N394T) proteins. 2014 Veterinary microbiology Abstract IV E627K;T97I;N394T 67;79;94 72;83;99 HA;PA;PB2 90;75;62 92;77;65 25470189 Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel. For example, the wild-type (WT) influenza A viruses, such as the seasonal H1N1, tend to be sensitive to antiviral drugs, amantadine and rimantadine, while the S31N mutant viruses, such as the pandemic 2009 H1N1 (H1N1pdm09) and seasonal H3N2, are resistant to this class of drugs. 2014 Journal of the American Chemical Society Abstract IV S31N 159 163 25470189 Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel. Solution NMR studies and molecular dynamics (MD) simulations of drug-M2 interactions supported our design hypothesis: namely, the dual inhibitor binds in the WT M2 channel with an aromatic group facing down toward the C-terminus, while the same drug binds in the S31N M2 channel with its aromatic group facing up toward the N-terminus. 2014 Journal of the American Chemical Society Abstract IV S31N 263 267 M2;M2;M2 69;161;268 71;163;270 25470189 Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel. The potency of the most active compound 11 in inhibiting WT and the S31N mutant influenza viruses is comparable with that of amantadine in inhibiting WT influenza virus. 2014 Journal of the American Chemical Society Abstract IV S31N 68 72 25470189 Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel. Thus, drugs targeting both WT and the S31N mutant are highly desired. 2014 Journal of the American Chemical Society Abstract IV S31N 38 42 25479596 Phylogenetic analysis of the neuraminidase gene of pandemic H1N1 influenza A virus circulating in the South American region. 3.4% of the strains enrolled in these studies carried the H275Y substitution that confers resistance to oseltamivir. 2015 Virus research Abstract IV H275Y 58 63 25480165 Effects of different NS genes of avian influenza viruses and amino acid changes on pathogenicity of recombinant A/Puerto Rico/8/34 viruses. The novel single mutations of 0028 NS1 to corresponding amino acid of PR8 NS1, G139D and S151T increased the pathogenicity of rPR8-NS(0028). 2015 Veterinary microbiology Abstract IV G139D;S151T 79;89 84;94 NS;NS1;NS1 131;35;74 133;38;77 25505067 The nucleoprotein of newly emerged H7N9 influenza A virus harbors a unique motif conferring resistance to antiviral human MxA. Accordingly, two substitutions in the NP of PR/8 [PR/8(mut)] to the Mx-sensitive amino acids (P283L and Y313F) led to attenuation in Mx1-positive mice. 2015 Journal of virology Abstract IV P283L;Y313F 94;104 99;109 NP 38 40 25505067 The nucleoprotein of newly emerged H7N9 influenza A virus harbors a unique motif conferring resistance to antiviral human MxA. N52Y substitution in NP results in increased sensitivity of the H7N9 virus to human Mx, indicating that this residue is a determinant of Mx resistance in mammals. 2015 Journal of virology Abstract IV N52Y 0 4 NP 21 23 25505067 The nucleoprotein of newly emerged H7N9 influenza A virus harbors a unique motif conferring resistance to antiviral human MxA. Serial lung passages of PR/8(mut) in Mx1 mice resulted in a single exchange of tyrosine to asparagine at position 52 in NP (in close proximity to the amino acid cluster at positions 100, 283, and 313), which partially compensates loss of Mx resistance in PR/8(mut). 2015 Journal of virology Abstract IV Y52N 79 116 NP 120 122 25505461 D701N mutation in the PB2 protein contributes to the pathogenicity of H5N1 avian influenza viruses but not transmissibility in guinea pigs. Interestingly, virus isolates from co-caged guinea pigs had the D701N mutation in the PB2 protein. 2014 Frontiers in microbiology Abstract IV D701N 64 69 PB2 86 89 25555151 Adaptive amino acid substitutions enhance the virulence of a reassortant H7N1 avian influenza virus isolated from wild waterfowl in mice. Analysis of the variant virus genomes revealed amino acid changes in the PB2 (E627K), HA (H3 numbering; E114K, G205E, and G218E), and NA (S350N) proteins. 2015 Virology Abstract IV E627K;E114K;G205E;G218E;S350N 78;104;111;122;138 83;109;116;127;143 HA;NA;PB2 86;134;73 88;136;76 25588658 Detection of a transient R292K mutation in influenza A/H3N2 viruses shed for several weeks by an immunocompromised patient. The R292K mutation was identified by direct testing in 3 of 11 respiratory specimens collected throughout the patient's illness but in none of the cultures from those specimens. 2015 Journal of clinical microbiology Abstract IV R292K 4 9 25588658 Detection of a transient R292K mutation in influenza A/H3N2 viruses shed for several weeks by an immunocompromised patient. We describe the case of an immunocompromised patient, positive for influenza A virus (H3N2), in whom the neuraminidase R292K mutation was transiently detected during oseltamivir treatment. 2015 Journal of clinical microbiology Abstract IV R292K 119 124 105 118 25601799 Comparative virulence of wild-type H1N1pdm09 influenza A isolates in swine. A/Swine/IL/5265/2010 (IL/10), with substitutions I120M, S146G, S186P, V252M, had lower viral titers in the lungs and nasal secretions and fewer lung lesions. 2015 Veterinary microbiology Abstract IV I120M;S146G;S186P;V252M 49;56;63;70 54;61;68;75 Lung lesions 144 156 25601799 Comparative virulence of wild-type H1N1pdm09 influenza A isolates in swine. The other two swine viruses caused respiratory pathology and replicated to titers similar to the human CA/09, although MN/10 (with mutations D45Y, K304E, A425S) had lower nasal shedding. 2015 Veterinary microbiology Abstract IV D45Y;K304E;A425S 141;147;154 145;152;159 25609803 Influenza viruses with receptor-binding N1 neuraminidases occur sporadically in several lineages and show no attenuation in cell culture or mice. Furthermore, the G147R virus had modestly enhanced resistance to neutralization by the Fab of an antibody against the receptor-binding pocket of HA, although it remained completely sensitive to the full-length IgG. 2015 Journal of virology Abstract IV G147R 17 22 HA 145 147 25609803 Influenza viruses with receptor-binding N1 neuraminidases occur sporadically in several lineages and show no attenuation in cell culture or mice. G147R also occurs at low frequencies in the reported sequences of viruses from three different lineages: human 2009 pandemic H1N1 (pdmH1N1), human seasonal H1N1, and chicken H5N1. 2015 Journal of virology Abstract IV G147R 0 5 25609803 Influenza viruses with receptor-binding N1 neuraminidases occur sporadically in several lineages and show no attenuation in cell culture or mice. Here we reconstructed a representative G147R NA from each of these lineages and found that all of the proteins have acquired the ability to bind an unknown cellular receptor while retaining substantial sialidase activity. 2015 Journal of virology Abstract IV G147R 39 44 45 47 25609803 Influenza viruses with receptor-binding N1 neuraminidases occur sporadically in several lineages and show no attenuation in cell culture or mice. One of these mutations, D151G, appears to arise in the NA of recent human H3N2 viruses upon passage in tissue culture. 2015 Journal of virology Abstract IV D151G 24 29 55 57 25609803 Influenza viruses with receptor-binding N1 neuraminidases occur sporadically in several lineages and show no attenuation in cell culture or mice. Overall, our results suggest that circulating N1 viruses occasionally may acquire the G147R NA receptor-binding mutation without impairment of replicative capacity. 2015 Journal of virology Abstract IV G147R 86 91 92 94 25609803 Influenza viruses with receptor-binding N1 neuraminidases occur sporadically in several lineages and show no attenuation in cell culture or mice. We inadvertently isolated the second of these mutations, G147R, in the NA of the lab-adapted A/WSN/33 (H1N1) strain while we were passaging a heavily engineered virus in the lab. 2015 Journal of virology Abstract IV G147R 57 62 71 73 25609803 Influenza viruses with receptor-binding N1 neuraminidases occur sporadically in several lineages and show no attenuation in cell culture or mice. We then reconstructed a virus with the HA and NA of a reported G147R pdmH1N1 variant and found no attenuation of viral replication in cell culture or change in pathogenesis in mice. 2015 Journal of virology Abstract IV G147R 63 68 HA;NA 39;46 41;48 25613667 Isolation and characteristic analysis of a novel strain H7N9 of avian influenza virus A from a patient with influenza-like symptoms in China. Mutations of Q226L and G186V were found in the hemagglutinin protein (HA). 2015 International journal of infectious diseases Abstract IV Q226L;G186V 13;23 18;28 HA;HA 70;47 72;60 25616792 Oseltamivir-resistant influenza A (H1N1) virus strain with an H274Y mutation in neuraminidase persists without drug pressure in infected mallards. In this in vivo mallard (Anas platyrhynchos) study, we tested whether an OC-resistant avian IAV (H1N1) strain with an H274Y mutation in the neuraminidase (NA-H274Y) could retain resistance while drug pressure was gradually removed. 2015 Applied and environmental microbiology Abstract IV H274Y;H274Y 118;158 123;163 NA;NA 155;140 157;153 25631084 Mammalian adaptive mutations of the PA protein of highly pathogenic avian H5N1 influenza virus. Here, we report that five amino acid substitutions in PA (V44I, V127A, C241Y, A343T, and I573V) contribute to the replicative efficiency of H5N1 viruses in human lung cells and to high virulence in mice. 2015 Journal of virology Abstract IV V44I;V127A;C241Y;A343T;I573V 58;64;71;78;89 62;69;76;83;94 PA 54 56 25631084 Mammalian adaptive mutations of the PA protein of highly pathogenic avian H5N1 influenza virus. The five PA amino acid substitutions V44I, V127A, C241Y, A343T, and I573V, which are rare in H5N1 viruses from human and avian sources, enhanced the growth capability of this virus in A549 cells. 2015 Journal of virology Abstract IV V44I;V127A;C241Y;A343T;I573V 37;43;50;57;68 41;48;55;62;73 PA 9 11 25641917 Identification of potential virulence determinants associated H9N2 avian influenza virus PB2 E627K mutation by comparative proteomics. By iTRAQ method, we found that the mutated K627E contributed to a set of differentially expressed lung proteins, including five upregulated proteins and nine downregulated proteins at 12 h postinfection; ten upregulated proteins and 25 downregulated proteins at 72 h postinfection. 2015 Proteomics Abstract IV K627E 43 48 25641917 Identification of potential virulence determinants associated H9N2 avian influenza virus PB2 E627K mutation by comparative proteomics. Further, three upregulated proteins (moesin, ezrin, and sp-A) caused by PB2 K627E were also confirmed in A549 cells. 2015 Proteomics Abstract IV K627E 76 81 PB2 72 75 25641917 Identification of potential virulence determinants associated H9N2 avian influenza virus PB2 E627K mutation by comparative proteomics. In this study, sp-A as a potential virulence determinant associated H9N2 AIV PB2 E627K mutation was identified using comparative proteomics. 2015 Proteomics Abstract IV E627K 81 86 PB2 77 80 25641917 Identification of potential virulence determinants associated H9N2 avian influenza virus PB2 E627K mutation by comparative proteomics. To investigate the mechanism of increased pathogenicity for H9N2 AIV PB2 627K, we analyzed the difference in mouse lung proteins expression response to PB2 K627E. 2015 Proteomics Abstract IV K627E 156 161 PB2;PB2 69;152 72;155 25645906 Identification of NS1 domains of avian H5N1 influenza virus which influence the interaction with the NOLC1 protein. Only the mutant D120A or R195A showed reduced binding with NOLC1, suggesting that D120 and R195 were crucial to the binding of NS1 to NOLC1. 2015 Virus genes Abstract IV D120A;R195A 16;25 21;30 NS1 127 130 25653452 Influenza hemagglutinin (HA) stem region mutations that stabilize or destabilize the structure of multiple HA subtypes. Furthermore, the K58I mutants, in particular, may be of interest for potential use in the development of vaccines with improved stability profiles. 2015 Journal of virology Abstract IV K58I 17 21 25653452 Influenza hemagglutinin (HA) stem region mutations that stabilize or destabilize the structure of multiple HA subtypes. We demonstrate that a K58I mutation confers an acid-stable phenotype for nearly all HAs examined, whereas a D112G mutation consistently leads to elevated fusion pH. 2015 Journal of virology Abstract IV K58I;D112G 22;108 26;113 25659818 Assessment of transmission, pathogenesis and adaptation of H2 subtype influenza viruses in ferrets. The avian H2 viruses isolated from ferret nasal washes contained mutations in the HA1, including a Gln226Leu substitution, which is a mutation associated with alpha2,6 sialic acid (human-like) binding preference. 2015 Virology Abstract IV Q226L 99 108 HA1 82 85 25673705 Competitive fitness of influenza B viruses with neuraminidase inhibitor-resistant substitutions in a coinfection model of the human airway epithelium. Based on the lack of attenuated replication of rg-E119A in NHBE cells in the presence of oseltamivir or zanamivir and the fitness advantage of rg-H274Y over rg-WT, we emphasize the importance of these substitutions in the NA glycoprotein. 2015 Journal of virology Abstract IV E119A;H274Y 50;146 55;151 222 224 25673705 Competitive fitness of influenza B viruses with neuraminidase inhibitor-resistant substitutions in a coinfection model of the human airway epithelium. Human infections with influenza B viruses carrying the E119A or H274Y substitution could limit the therapeutic options for those infected; the emergence of such viruses should be closely monitored. 2015 Journal of virology Abstract IV E119A;H274Y 55;64 60;69 25673705 Competitive fitness of influenza B viruses with neuraminidase inhibitor-resistant substitutions in a coinfection model of the human airway epithelium. In a fluorescence-based assay, detection of rg-E119A was easily masked by the presence of NAI-susceptible virus. 2015 Journal of virology Abstract IV E119A 47 52 NAI 90 93 25673705 Competitive fitness of influenza B viruses with neuraminidase inhibitor-resistant substitutions in a coinfection model of the human airway epithelium. The replication in NHBE cells of viruses with reduced inhibition by oseltamivir (recombinant virus with the E119A mutation generated by reverse genetics [rg-E119A], rg-D198E, rg-I222T, rg-H274Y, rg-N294S, and rg-R371K, N2 numbering) or zanamivir (rg-E119A and rg-R371K) failed to be inhibited by the presence of the respective NAI. 2015 Journal of virology Abstract IV E119A;E119A;D198E;I222T;H274Y;N294S;R371K;E119A;R371K 108;157;168;178;188;198;212;250;263 113;162;173;183;193;203;217;255;268 NAI 327 330 25673705 Competitive fitness of influenza B viruses with neuraminidase inhibitor-resistant substitutions in a coinfection model of the human airway epithelium. We coinfected NHBE cells with NAI-susceptible and -resistant viruses and used next-generation deep sequencing to reveal the order of relative fitness compared to that of recombinant wild-type (WT) virus generated by reverse genetics (rg-WT): rg-H274Y > rg-WT > rg-I222T > rg-N294S > rg-D198E > rg-E119A >> rg-R371K. 2015 Journal of virology Abstract IV H274Y;I222T;N294S;D198E;E119A;R371K 245;264;275;286;297;309 250;269;280;291;302;314 NAI 30 33 25673705 Competitive fitness of influenza B viruses with neuraminidase inhibitor-resistant substitutions in a coinfection model of the human airway epithelium. We show that virus with an E119A NA substitution can replicate efficiently in NHBE cells in the presence of oseltamivir or zanamivir and that virus with the H274Y NA substitution has a relative fitness greater than that of the wild-type NAI-susceptible virus. 2015 Journal of virology Abstract IV E119A;H274Y 27;157 32;162 NA;NA;NAI 33;163;237 35;165;240 25676826 Molecular epidemiology and evolution of influenza A and B viruses during winter 2013-2014 in Beijing, China. All six A(H1N1)pdm09 strains fell into the 6B genetic group with amino acid substitutions D97N, S185T, K163Q, and A256T; the four H3N2 strains fell into genetic group 3C.3 with substitutions T128A, R142G, N145S, and V186G, and the eight influenza B strains were categorized into subgroup 3.1 and harbored an N217S mutation. 2015 Archives of virology Abstract IV D97N;S185T;K163Q;A256T;T128A;R142G;N145S;V186G;N217S 90;96;103;114;191;198;205;216;308 94;101;108;119;196;203;210;221;313 25676826 Molecular epidemiology and evolution of influenza A and B viruses during winter 2013-2014 in Beijing, China. Mutations N131K, S165I, N181Y, and D212N in HA of influenza B mapped to the 120-loop, 150-loop, 160-loop, and 190-helix, respectively. 2015 Archives of virology Abstract IV N131K;S165I;N181Y;D212N 10;17;24;35 15;22;29;40 HA 44 46 25676826 Molecular epidemiology and evolution of influenza A and B viruses during winter 2013-2014 in Beijing, China. Two new mutations (K180Q and G187E at the Sa and Ca antigenic sites of the H1 segment, respectively), which were not detected during the preceding influenza season, were identified. 2015 Archives of virology Abstract IV K180Q;G187E 19;29 24;34 25691568 The crystal structure of the PB2 cap-binding domain of influenza B virus reveals a novel cap recognition mechanism. Replacement of FluB PB2 Glu(325) by Phe, the corresponding residue of FluA PB2, increased the binding affinity of FluB PB2cap for m(7)GDP to a level approximate to that of FluA PB2cap and caused a significant higher affinity to GDP. 2015 The Journal of biological chemistry Abstract IV E325F 24 39 PB2;PB2 20;75 23;78 25691568 The crystal structure of the PB2 cap-binding domain of influenza B virus reveals a novel cap recognition mechanism. To detect the feature of cap-dependent transcription of influenza B virus (FluB) polymerase, we determined the crystal structures of the wild-type FluB polymerase PB2 subunit cap-binding domain (PB2cap) with bound GDP and the mutant FluB Q325F PB2cap with bound m(7)GDP or GDP. 2015 The Journal of biological chemistry Abstract IV Q325F 238 243 PB2 163 166 25701593 Influenza A viruses of swine circulating in the United States during 2009-2014 are susceptible to neuraminidase inhibitors but show lineage-dependent resistance to adamantanes. (1930-2014) showed 0.03% (1/3396) sequences with clinically relevant H274Y-NA substitution. 2015 Antiviral research Abstract IV H274Y 69 74 75 77 25701593 Influenza A viruses of swine circulating in the United States during 2009-2014 are susceptible to neuraminidase inhibitors but show lineage-dependent resistance to adamantanes. (2009-2011) confirmed amantadine resistance caused by the S31N-M2 and revealed an intermediate level of resistance caused by the I27T-M2. 2015 Antiviral research Abstract IV S31N;I27T 58;129 62;133 M2;M2 63;134 65;136 25701593 Influenza A viruses of swine circulating in the United States during 2009-2014 are susceptible to neuraminidase inhibitors but show lineage-dependent resistance to adamantanes. All IAV-S of the Eurasian avian M lineage were amantadine-resistant and possessed either a single S31N-M2 substitution (78%, 585/747) or its combination with the V27A-M2 (22%, 162/747). 2015 Antiviral research Abstract IV V27A;S31N 162;98 166;102 M2;M2 103;167 105;169 25701593 Influenza A viruses of swine circulating in the United States during 2009-2014 are susceptible to neuraminidase inhibitors but show lineage-dependent resistance to adamantanes. Phylogenetic analysis showed that both S31N-M2 and I27T-M2 emerged stochastically but appeared to be fixed in the U.S. 2015 Antiviral research Abstract IV S31N;I27T 39;51 43;55 M2;M2 44;56 46;58 25701593 Influenza A viruses of swine circulating in the United States during 2009-2014 are susceptible to neuraminidase inhibitors but show lineage-dependent resistance to adamantanes. The I27T-M2 substitution accounted for 43% (429/993) of amantadine resistance in classic swine M lineage. 2015 Antiviral research Abstract IV I27T 4 8 M2 9 11 25701593 Influenza A viruses of swine circulating in the United States during 2009-2014 are susceptible to neuraminidase inhibitors but show lineage-dependent resistance to adamantanes. The majority (96.7%, 589/609) of IAV-S with the I27T-M2 in the influenza database were isolated from pigs in the U.S. 2015 Antiviral research Abstract IV I27T 48 52 M2 53 55 25713566 PB2 segment promotes high-pathogenicity of H5N1 avian influenza viruses in mice. The mutation Ser715Asn in PB2 sharply attenuated the virulence of rgDK212 in mice (2710-fold). 2015 Frontiers in microbiology Abstract IV S715N 13 22 PB2 26 29 25721488 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2013-2014. Although approximately 98% of circulating viruses tested during the 2013-2014 period were sensitive to all four NAIs, a large community cluster of A(H1N1)pdm09 viruses with the NA H275Y substitution from patients with no previous exposure to antivirals was detected in Hokkaido, Japan. 2015 Antiviral research Abstract IV H275Y 180 185 NA;NAI 177;112 179;116 25721488 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2013-2014. Significant numbers of A(H1N1)pdm09 NA H275Y viruses were also detected in China and the United States: phylogenetic analyses showed that the Chinese viruses were similar to those from Japan, while the United States viruses clustered separately from those of the Hokkaido outbreak, indicative of multiple resistance-emergence events. 2015 Antiviral research Abstract IV H275Y 39 44 36 38 25721488 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2013-2014. Those showing HRI were A(H1N1)pdm09 with NA H275Y (n=169), A(H3N2) with NA E119V (n=1), B/Victoria-lineage with NA E117G (n=1) and B/Yamagata-lineage with NA H273Y (n=1); amino acid position numbering is A subtype and B type specific. 2015 Antiviral research Abstract IV H275Y;E119V;E117G;H273Y 44;75;115;158 49;80;120;163 NA;NA;NA;NA 41;72;112;155 43;74;114;157 25740987 Mutational analysis of vaccinia virus E3 protein: the biological functions do not correlate with its biochemical capacity to bind double-stranded RNA. Although the majority of the mutants defective in dsRNA binding also showed defective replication in HeLa cells, nine mutants (I105A, Y125A, E138A, F148A, F159A, K171A, L182A, L183A, and I187/188A) retained the host range function to various degrees. 2015 Journal of virology Abstract IV I105A;Y125A;E138A;F148A;F159A;K171A;L182A;L183A 127;134;141;148;155;162;169;176 132;139;146;153;160;167;174;181 25740987 Mutational analysis of vaccinia virus E3 protein: the biological functions do not correlate with its biochemical capacity to bind double-stranded RNA. Further examination of a set of representative E3L mutants showed that residues essential for dsRNA binding are not essential for the biological functions of E3 protein, such as inhibition of protein kinase R (PKR) activation, suppression of cytokine expression, and apoptosis. 2015 Journal of virology Abstract IV E3L 47 50 25740997 Neuraminidase Mutations Conferring Resistance to Oseltamivir in Influenza A(H7N9) Viruses. A small reduction of viral titers was detected on day 5 in ferrets infected with the I222K virus. 2015 Journal of virology Abstract IV I222K 85 90 25740997 Neuraminidase Mutations Conferring Resistance to Oseltamivir in Influenza A(H7N9) Viruses. Collectively, we demonstrate that R292K, E119V, and I222K reduced the inhibitory activity of oseltamivir, not only in the NI assay, but also in infected ferrets, judged particularly by viral loads in nasal washes, and may signal the need for alternative therapeutics. 2015 Journal of virology Abstract IV R292K;E119V;I222K 34;41;52 39;46;57 25740997 Neuraminidase Mutations Conferring Resistance to Oseltamivir in Influenza A(H7N9) Viruses. Conversely, treatment failed to significantly inhibit the replication of R292K or E119V virus. 2015 Journal of virology Abstract IV R292K;E119V 73;82 78;87 25740997 Neuraminidase Mutations Conferring Resistance to Oseltamivir in Influenza A(H7N9) Viruses. In the NA inhibition (NI) assay, R292K conferred highly reduced inhibition by oseltamivir, while E119V and I222K each caused reduced inhibition. 2015 Journal of virology Abstract IV R292K;E119V;I222K 33;97;107 38;102;112 7 9 25740997 Neuraminidase Mutations Conferring Resistance to Oseltamivir in Influenza A(H7N9) Viruses. The propensity for oseltamivir resistance emergence was assessed in oseltamivir-treated animals infected with wild-type virus; emergence of R292K virus was detected in 3 of 6 ferrets within 5 to 7 days postinfection. 2015 Journal of virology Abstract IV R292K 140 145 25740997 Neuraminidase Mutations Conferring Resistance to Oseltamivir in Influenza A(H7N9) Viruses. The rapid emergence of viruses with R292K in treated ferrets correlates well with the multiple reports on this NA variant in treated human patients. 2015 Journal of virology Abstract IV R292K 36 41 111 113 25742269 Oseltamivir-resistant influenza A(H1N1)pdm2009 strains found in Brazil are endowed with permissive mutations, which compensate the loss of fitness imposed by antiviral resistance. Consequently, OST-resistant strains, carrying the mutation H275Y, emerged in the years after the pandemics, with a prevalence of 1-2%. 2015 Memorias do Instituto Oswaldo Cruz Abstract IV H275Y 59 64 25742269 Oseltamivir-resistant influenza A(H1N1)pdm2009 strains found in Brazil are endowed with permissive mutations, which compensate the loss of fitness imposed by antiviral resistance. Importantly, the change D344N, also predicted to compensate loss of fitness imposed by H275Y mutation, was found in Brazil, but not in other countries in 2013. 2015 Memorias do Instituto Oswaldo Cruz Abstract IV D344N;H275Y 24;87 29;92 25742269 Oseltamivir-resistant influenza A(H1N1)pdm2009 strains found in Brazil are endowed with permissive mutations, which compensate the loss of fitness imposed by antiviral resistance. Some previously predicted permissive mutations, such as V241I and N369K, found in different countries, were also detected in Brazil. 2015 Memorias do Instituto Oswaldo Cruz Abstract IV V241I;N369K 56;66 61;71 25742269 Oseltamivir-resistant influenza A(H1N1)pdm2009 strains found in Brazil are endowed with permissive mutations, which compensate the loss of fitness imposed by antiviral resistance. To spread in community settings, H275Y mutants must contain additional mutations, collectively called permissive mutations. 2015 Memorias do Instituto Oswaldo Cruz Abstract IV H275Y 33 38 25766295 Structure and receptor binding of the hemagglutinin from a human H6N1 influenza virus. We find that, although the H6 HA RBS contains D190V and G228S substitutions that potentially promote human receptor binding, recombinant H6 HA preferentially binds alpha2-3-linked sialosides, indicating no adaptation to human receptors. 2015 Cell host & microbe Abstract IV D190V;G228S 46;56 51;61 HA;HA 30;140 32;142 25768797 Adamantane-resistant influenza a viruses in the world (1902-2013): frequency and distribution of M2 gene mutations. To investigate the frequency and distribution of M2 gene mutations in adamantane-resistant influenza variants circulated in the world between 1902 and 2013, 31251 available M2 protein sequences from different HA-subtype influenza A viruses (H1-H17) were analyzed and adamantane resistance-associated mutations were compared (L26F, V27A, A30T, A30V, S31N, G34E, and L38F). 2015 PloS one Abstract IV V27A;L26F;A30T;A30V;S31N;G34E;L38F 331;325;337;343;349;355;365 335;329;341;347;353;359;369 HA;M2;M2 209;49;173 211;51;175 25768797 Adamantane-resistant influenza a viruses in the world (1902-2013): frequency and distribution of M2 gene mutations. We find that 45.2% (n = 14132) of influenza A (H1-H17) viruses circulating globally were resistant to adamantanes, and the vast majority of resistant viruses (95%) bear S31N mutations. 2015 PloS one Abstract IV S31N 169 173 25768797 Adamantane-resistant influenza a viruses in the world (1902-2013): frequency and distribution of M2 gene mutations. Whereas, only about 1% have V27A mutations and other mutations (L26F, A30T, G34E, and L38F) were extremely rare (their prevalence appeared to be < 0.2%). 2015 PloS one Abstract IV V27A;L26F;A30T;G34E;L38F 28;64;70;76;86 32;68;74;80;90 25769645 Adaptive amino acid substitutions enhance the virulence of an H7N7 avian influenza virus isolated from wild waterfowl in mice. Genomic analysis of the adapted variant viruses revealed amino acid changes in the PB2 (E627K), PB1 (R118I), PA (L550M), HA (G214R), and NA (S372N) proteins. 2015 Veterinary microbiology Abstract IV E627K;R118I;L550M;G214R;S372N 88;101;113;125;141 93;106;118;130;146 HA;NA;PA;PB1;PB2 121;137;109;96;83 123;139;111;99;86 25782865 Rapid emergence of a PB2-E627K substitution confers a virulent phenotype to an H9N2 avian influenza virus during adoption in mice. Polymerase complexes possessing PB2-E627K displayed 16.1-fold higher viral polymerase activity when compared to the wild-type virus, which may account for enhanced virulence of this virus. 2015 Archives of virology Abstract IV E627K 36 41 PB2 32 35 25782865 Rapid emergence of a PB2-E627K substitution confers a virulent phenotype to an H9N2 avian influenza virus during adoption in mice. The other two substitutions (HA-N313D and HA-N496S) enhanced binding to both alpha2,3-linked and alpha2,6-linked sialic acid receptors; however, the HA-N313D and N496S substitutions alone decreased the virulence of mouse-adapted virus. 2015 Archives of virology Abstract IV N313D;N496S;N313D;N496S 32;45;152;162 37;50;157;167 HA;HA;HA 29;42;149 31;44;151 25782865 Rapid emergence of a PB2-E627K substitution confers a virulent phenotype to an H9N2 avian influenza virus during adoption in mice. The PB2-E627K substitution rapidly appeared at the second passage and played a decisive role in virulence. 2015 Archives of virology Abstract IV E627K 8 13 PB2 4 7 25784728 Integrated Sentinel Surveillance Linking Genetic, Antigenic, and Epidemiologic Monitoring of Influenza Vaccine-Virus Relatedness and Effectiveness During the 2013-2014 Influenza Season. A(H1N1)pdm09 viruses belonged to clade 6B, distinguished by a K163Q substitution, but remained antigenically similar to the A/California/07/2009-like vaccine strain, with an adjusted VE of 71% (95% confidence interval [CI], 58%-80%). 2015 The Journal of infectious diseases Abstract IV K163Q 62 67 25786478 Influenza viruses with B/Yamagata- and B/Victoria-like neuraminidases are differentially affected by mutations that alter antiviral susceptibility. Mutations E105K, P139S and G140R of the monomeric interface were also found to cause highly reduced inhibition, but, interestingly, their effect was substantially greater in a B/Victoria-like neuraminidase than in a B/Yamagata-like neuraminidase, with some susceptibility values being up to 1000-fold different between lineages. 2015 The Journal of antimicrobial chemotherapy Abstract IV E105K;P139S;G140R 10;17;27 15;22;32 NA;NA 192;232 205;245 25786478 Influenza viruses with B/Yamagata- and B/Victoria-like neuraminidases are differentially affected by mutations that alter antiviral susceptibility. RESULTS: Framework residue mutations E117A and E117G conferred highly reduced inhibition to three of the four NAIs, but substantially reduced neuraminidase activity, whereas other framework mutations retained a greater level of NA activity. 2015 The Journal of antimicrobial chemotherapy Abstract IV E117A;E117G 37;47 42;52 NA;NAI;NA 228;110;142 230;114;155 25787277 Phosphorylation controls the nuclear-cytoplasmic shuttling of influenza A virus nucleoprotein. However, at later stages of infection, it was weakened by the Y10F mutation. 2015 Journal of virology Abstract IV Y10F 62 66 25793397 Characterization of a novel mutation in NS1 protein of influenza A virus induced by a chemical substance for the attenuation of pathogenicity. Sequencing analysis revealed that a novel mutation, C490U in ns gene (P164S in NS1), was detected in all MFPTr virus clones tested. 2015 PloS one Abstract IV P164S 70 75 NS1 79 82 25793397 Characterization of a novel mutation in NS1 protein of influenza A virus induced by a chemical substance for the attenuation of pathogenicity. Therefore, NS1 might be a main target of MFPT, and it was suggested that the P164S mutation contributed to the attenuated pathogenicity of the mutants. 2015 PloS one Abstract IV P164S 77 82 NS1 11 14 25817403 A single NS2 mutation of K86R promotes PR8 vaccine donor virus growth in Vero cells. Because the NS2(K86R) mutation does not increase PR8 virulence in either mice or embryonated eggs, the PR8-NS2(K86R) virus could serve as a promising vaccine donor strain in Vero cells. 2015 Virology Abstract IV K86R;K86R 16;111 20;115 NS2;NS2 12;107 15;110 25817403 A single NS2 mutation of K86R promotes PR8 vaccine donor virus growth in Vero cells. Further analysis showed that the later steps in the virus replication cycle were accelerated by NS2(K86R) mutation, which may relate to an enhanced interaction between NS2(K86R) and the components of host factor F1Fo-ATPase, FoB and F1beta. 2015 Virology Abstract IV K86R;K86R 100;172 104;176 NS2;NS2 96;168 99;171 25817403 A single NS2 mutation of K86R promotes PR8 vaccine donor virus growth in Vero cells. In this study, a single mutation of K86R in the NS2 protein can sufficiently render the high-yielding property to the PR8 virus in Vero cells. 2015 Virology Abstract IV K86R 36 40 NS2 48 51 25839842 New genetic variants of influenza A(H1N1)pdm09 detected in Cuba during 2011-2013. Mutations were detected in the antigenic site or in the receptor-binding domains of HA1 segment, including S174P, S179N, K180Q, S202T, S220T and R222K. 2015 Infection, genetics and evolution Abstract IV S174P;S179N;K180Q;S202T;S220T;R222K 107;114;121;128;135;145 112;119;126;133;140;150 HA1 84 87 25839842 New genetic variants of influenza A(H1N1)pdm09 detected in Cuba during 2011-2013. Substitutions S174P, S179N, K180Q and R222K were detected in Cuban strains for the first time. 2015 Infection, genetics and evolution Abstract IV S174P;S179N;K180Q;R222K 14;21;28;38 19;26;33;43 25861376 Molecular docking of potential inhibitors for influenza H7N9. Further analyses showed that R294K mutation in neuraminidase could remarkably decrease the binding energies for oseltamivir, while other small molecules showed stable binding abilities with mutated neuraminidase. 2015 Computational and mathematical methods in medicine Abstract IV R294K 29 34 NA;NA 47;198 60;211 25861376 Molecular docking of potential inhibitors for influenza H7N9. Furthermore, H7N9 has already generated various mutations such as neuraminidase R294K mutation which could make the anti-influenza oseltamivir less effective or ineffective. 2015 Computational and mathematical methods in medicine Abstract IV R294K 80 85 66 79 25876137 SNPer: an R library for quantitative variant analysis on single nucleotide polymorphisms among influenza virus populations. More minor genetic alterations in genetic drift can lead to influenza drug resistance such as the H274Y mutation associated with oseltamivir resistance. 2015 PloS one Abstract IV H274Y 98 103 25899336 New polycyclic dual inhibitors of the wild type and the V27A mutant M2 channel of the influenza A virus with unexpected binding mode. However, some of the 14-azaheptacyclo[8.6.1.0(2,5).0(3,11).0(4,9).0(6,17).0(12,16)]heptadecane derivatives were dual inhibitors of the wild-type and the V27A mutant M2 channels. 2015 European journal of medicinal chemistry Abstract IV V27A 153 157 M2 165 167 25899336 New polycyclic dual inhibitors of the wild type and the V27A mutant M2 channel of the influenza A virus with unexpected binding mode. Their binding mode was analysed through molecular dynamics simulations, which showed the existence of distinct binding modes in the wild type M2 channel and its V27A variant. 2015 European journal of medicinal chemistry Abstract IV V27A 161 165 M2 142 144 25928577 Amino acid substitutions in the neuraminidase protein of an H9N2 avian influenza virus affect its airborne transmission in chickens. The results show that airborne transmission of A/Chicken/Shandong/01/2008 (SD01) virus was related to the neuraminidase (NA) gene, and four amino acid mutations (D368E, S370L, E313K and G381D) within the head region of the SD01 NA, reduced virus replication in the respiratory tract of chickens, reduced virus NA activity, and resulted in a loss of airborne transmission ability in chickens. 2015 Veterinary research Abstract IV D368E;S370L;E313K;G381D 162;169;176;186 167;174;181;191 NA;NA;NA;NA 121;228;310;106 123;230;312;119 25929033 [Epitope analysis of the hemagglutinin molecule of the Victoria lineage influenza B viruses]. In addition, AAS N197S was detected in three EMs. 2014 Voprosy virusologii Abstract IV N197S 17 22 25929033 [Epitope analysis of the hemagglutinin molecule of the Victoria lineage influenza B viruses]. Three EMs had single, two--double and one--triple amino acid substitutions (AAS) in HA1 (H122N, A202E, K203T, K2031, K203N or A317V). 2014 Voprosy virusologii Abstract IV H122N;A202E;K203T;K203N;A317V 89;96;103;117;126 94;101;108;122;131 HA1 84 87 25934533 Identification and characterization of a novel antigenic epitope in the hemagglutinin of the escape mutants of H9N2 avian influenza viruses. Our study suggests that G92R mutation together with other identified antigenic sites may serve as molecular markers for H9N2 virus evolution, and may aid improving AIV vaccine effectiveness. 2015 Veterinary microbiology Abstract IV G92R 24 28 25939747 Two polar residues within C-terminal domain of M1 are critical for the formation of influenza A Virions. M1 point mutants suggest that single S183A or T185A substitution could result in the production of morphologically filamentous particles, while double substitutions, M1-S183A/T185A, totally disrupted the fourfold symmetry and resulted in the failure of virus production. 2015 Cellular microbiology Abstract IV S183A;T185A;S183A;T185A 37;46;169;175 42;51;174;180 M1;M1 0;166 2;168 25942938 [Analysis of influenza A/H3N2 neuraminidase genes obtained from influenza patients in the 2011/12 and 2012/13 seasons in Japan]. RESULTS: One putative amino acid mutation, D151N, was found in an NA activity-related cite in five of ninety-six tested isolate. 2015 Fukuoka igaku zasshi Abstract IV D151N 43 48 66 68 25948745 Cross-Reactive Neuraminidase-Inhibiting Antibodies Elicited by Immunization with Recombinant Neuraminidase Proteins of H5N1 and Pandemic H1N1 Influenza A Viruses. Cross-reactive NI antibodies were further dissected via pH1N1 rNA protein immunizations with I149V (NA with a change of Ile to Val at position 149), N344Y, and I365T/S366N NA mutations. 2015 Journal of virology Abstract IV I149V;I149V;N344Y;I365T;S366N 93;120;149;160;166 98;146;154;165;171 NA;NA;NA 100;172;62 102;174;65 25948745 Cross-Reactive Neuraminidase-Inhibiting Antibodies Elicited by Immunization with Recombinant Neuraminidase Proteins of H5N1 and Pandemic H1N1 Influenza A Viruses. Our results indicate that H5N1 rNA immunization induced more potent cross-protective immunity than pH1N1 rNA immunization, and three mutated residues, I149V, I365T, and S366N, near the NA enzyme active site(s) are linked to enhanced cross-reactive NA-inhibiting antibodies against heterologous and heterosubtypic influenza A viruses. 2015 Journal of virology Abstract IV I149V;I365T;S366N 151;158;169 156;163;174 NA;NA;NA;NA 185;248;31;105 187;250;34;108 25948745 Cross-Reactive Neuraminidase-Inhibiting Antibodies Elicited by Immunization with Recombinant Neuraminidase Proteins of H5N1 and Pandemic H1N1 Influenza A Viruses. The I365T/S366N mutation of pH1N1 rNA enhanced cross-reactive NI antibodies against H5N1, H3N2, and H7N9 viruses. 2015 Journal of virology Abstract IV I365T;S366N 4;10 9;15 34 37 25966032 Virological characterization of influenza H1N1pdm09 in Vietnam, 2010-2013. Five isolates (8 2%) had substitutions G155E and N156K in the HA, which were associated with reduced HI titers by antiserum raised against the vaccine virus A/California/07/2009. 2015 Influenza and other respiratory viruses Abstract IV G155E;N156K 39;49 44;54 HA 62 64 25966032 Virological characterization of influenza H1N1pdm09 in Vietnam, 2010-2013. One isolate from 2011 and one isolate from 2013 had a predicted H275Y substitution in the neuraminidase molecule, which was associated with reduced susceptibility to oseltamivir in a NAI assay. 2015 Influenza and other respiratory viruses Abstract IV H275Y 64 69 NAI;NA 183;90 186;103 25966032 Virological characterization of influenza H1N1pdm09 in Vietnam, 2010-2013. We also identified a D222N change in the HA of a virus isolated from a fatal case in 2013. 2015 Influenza and other respiratory viruses Abstract IV D222N 21 26 HA 41 43 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. Cells infected by H1N1pdm09 virus carrying the I223V mutation display a disadvantageous, shorter infectious lifespan (17 h shorter) than those infected with the wild-type or MUT-H275Y strains. 2015 PloS one Abstract IV I223V;H275Y 47;174 52;183 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. In terms of compensating traits, the H275Y mutation in the H1N1pdm09 background results in increased virus infectiousness, as we reported previously, whereas the I223V exhibits none, leaving it overall less fit than both its wild-type counterpart and the MUT-H275Y strain. 2015 PloS one Abstract IV H275Y;I223V;H275Y 37;162;255 42;167;264 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. The H275Y and I223V amino acid substitutions in the NA of the H1N1pdm09 influenza strain have been separately observed in patients exhibiting oseltamivir-resistance. 2015 PloS one Abstract IV H275Y;I223V 4;14 9;19 52 54 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. The H275Y mutation should therefore be more commonly observed than the I223V mutation in circulating H1N1pdm09 strains, assuming both mutations have a similar impact or no significant impact on between-host transmission. 2015 PloS one Abstract IV H275Y;I223V 4;71 9;76 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. Using computer simulated competition experiments, we determine that in the presence of oseltamivir at doses even below standard therapy, both the MUT-H275Y and MUT-I223V dominate their wild-type counterpart in all aspects, and the MUT-H275Y outcompetes the MUT-I223V. 2015 PloS one Abstract IV H275Y;I223V;H275Y;I223V 146;160;231;257 155;169;240;266 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. We find that both the H275Y and I223V mutations in the H1N1pdm09 background significantly lengthen the duration of the eclipse phase (by 2.5 h and 3.6 h, respectively), consistent with these NA mutations delaying the release of viral progeny from newly infected cells. 2015 PloS one Abstract IV H275Y;I223V 22;32 27;37 191 193 25998916 H5N1 influenza A virus with K193E and G225E double mutations in haemagglutinin is attenuated and immunogenic in mice. Importantly, in vivo virulence assessment demonstrated that rVN-K193E/G225E was significantly attenuated in mice. 2015 The Journal of general virology Abstract IV G225E;K193E 70;64 75;69 25998916 H5N1 influenza A virus with K193E and G225E double mutations in haemagglutinin is attenuated and immunogenic in mice. In the present study, serial passage of H5N1 virus A/Vietnam/1194/2004 in Madin-Darby canine kidney cells resulted in the generation of adapted variants with large-plaque morphology, and genomic sequencing of selected variants revealed two specific amino acid substitutions (K193E and G225E) in the RBD. 2015 The Journal of general virology Abstract IV K193E;G225E 275;285 280;290 25998916 H5N1 influenza A virus with K193E and G225E double mutations in haemagglutinin is attenuated and immunogenic in mice. Microneutralization and haemagglutination inhibition assays demonstrated that immunization with rVN-K193E/G225E efficiently induced a robust antibody response against WT H5N1 virus in mice. 2015 The Journal of general virology Abstract IV K193E;G225E 100;106 105;111 25998916 H5N1 influenza A virus with K193E and G225E double mutations in haemagglutinin is attenuated and immunogenic in mice. Taken together, our experiments demonstrated that K193E and G225E mutations synergistically attenuated H5N1 virus without enhancing the receptor-binding avidity, and that the RG virus rVN-K193E/G225E represents a potential H5N1 LAIV strategy that deserves further development. 2015 The Journal of general virology Abstract IV K193E;G225E;K193E;G225E 50;60;188;194 55;65;193;199 25998916 H5N1 influenza A virus with K193E and G225E double mutations in haemagglutinin is attenuated and immunogenic in mice. The RG virus containing K193E and G225E mutations (rVN-K193E/G225E) demonstrated large-plaque morphology, enhanced replication and genetic stability after serial passage, without changing the receptor-binding preference. 2015 The Journal of general virology Abstract IV K193E;G225E;K193E;G225E 24;34;55;61 29;39;60;66 25999284 Egg-adaptive mutations in H3N2v vaccine virus enhance egg-based production without loss of antigenicity or immunogenicity. Here we demonstrate that the respective combined HA substitutions G1861V+N2461K, N1651K+G1861V, T1281N+N1651K+R762G, and T1281N+N1651K+I102M, all identified after egg passage, enhanced the replication of the CVVs in eggs without substantially affecting their antigenicity or immunogenicity. 2015 Vaccine Abstract IV N2461K;G1861V;G1861V;N1651K;N1651K;R762G;T1281N;N1651K;T1281N;I102M 73;66;88;81;103;110;96;128;121;135 79;72;94;87;109;115;102;134;127;140 HA 49 51 25999284 Egg-adaptive mutations in H3N2v vaccine virus enhance egg-based production without loss of antigenicity or immunogenicity. We found two crucial mutations, G186V, which was previously defined, and N246K, which in combination improved virus yield in eggs without significantly impacting antigenicity or immunogenicity. 2015 Vaccine Abstract IV G186V;N246K 32;73 37;78 26018156 Identification of Influenza A Virus PB2 Residues Involved in Enhanced Polymerase Activity and Virus Growth in Mammalian Cells at Low Temperatures. The PB2 T271A mutation, which we previously reported, also contributed to enhanced activity. 2015 Journal of virology Abstract IV T271A 8 13 PB2 4 7 26018156 Identification of Influenza A Virus PB2 Residues Involved in Enhanced Polymerase Activity and Virus Growth in Mammalian Cells at Low Temperatures. Using a reporter gene assay, we identified novel mutations, PB2 V661A and V683T/A684S, which are involved in enhanced Cal polymerase activity at low temperature. 2015 Journal of virology Abstract IV V661A;V683T;A684S 64;74;80 69;79;85 PB2 60 63 26033540 Steered molecular dynamics approach for promising drugs for influenza A virus targeting M2 channel proteins. We have used steered molecular dynamics simulation to investigate the molecular interactions between four M2 inhibitors (amantadine, rimantadine, and two other amantadine derivatives) and the M2 protein channels of influenza A virus H5N1, including the wild type (WT) and three previously identified drug-resistant variants (G34A, S31N, and V27A). 2015 European biophysics journal Abstract IV V27A;G34A;S31N 341;325;331 345;329;335 M2;M2 106;192 108;194 26038410 Adaptive mutation in influenza A virus non-structural gene is linked to host switching and induces a novel protein by alternative splicing. Here we show that the non-structural protein1 nucleotide substitution, A374G, encoding the D125G(GAT GGT) mutation, which evolved during the adaptation of a human virus within a mouse host, activates a novel donor splice site in the non-structural gene, hence producing a novel influenza A viral protein, NS3. 2012 Emerging microbes & infections Abstract IV A374G;D125G 71;91 76;96 NS;NS;NS 22;233;305 36;247;307 26038484 Human H7N9 avian influenza virus infection: a review and pandemic risk assessment. Infection in Ratitae species may lead to the selection of PB2-E627K and PB2-D701N mutants and the conversion of nH7N9 to a highly pathogenic avian influenza virus. 2013 Emerging microbes & infections Abstract IV E627K;D701N 62;76 67;81 PB2;PB2 58;72 61;75 26038484 Human H7N9 avian influenza virus infection: a review and pandemic risk assessment. nH7N9 isolated from humans contains features related to adaptation to humans, including a Q226L mutation in the hemagglutinin cleavage site and E627K and D701N mutations in the PB2 protein. 2013 Emerging microbes & infections Abstract IV Q226L;E627K;D701N 90;144;154 95;149;159 HA;PB2 112;177 125;180 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. A combination of NAIs and non-NAIs did not exhibit a marked synergistic effect against the R292K variant. 2014 Emerging microbes & infections Abstract IV R292K 91 96 NAI;NAI 17;30 21;34 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. In this study, by using limited serial passage and plaque purification, an R292K variant of the Anhui1 lineage was isolated from a patient with clinical evidence of resistance to oseltamivir. 2014 Emerging microbes & infections Abstract IV R292K 75 80 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. In vitro and cell-based assays confirmed a high level of resistance conferred by the R292K mutation to oseltamivir carboxylate and a moderate level of resistance to zanamivir and peramivir. 2014 Emerging microbes & infections Abstract IV R292K 85 90 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. The emergence of NAI-resistant variants of H7N9viruses with an NA R292K mutation poses a therapeutic challenge. 2014 Emerging microbes & infections Abstract IV R292K 66 71 NA;NAI 63;17 65;20 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. The pathogenicity and transmissibility of the R292K H7N9 variant should be further assessed with genetically well-characterized pairs of viruses and, most-desirably, with competitive fitness experiments. 2014 Emerging microbes & infections Abstract IV R292K 46 51 26044768 A 3D-RISM/RISM study of the oseltamivir binding efficiency with the wild-type and resistance-associated mutant forms of the viral influenza B neuraminidase. For E119G and R152K, reduction of the direct drug-target interaction, especially at the mutated residue, is the main source of high-level oseltamivir resistance. 2016 Protein science Abstract IV E119G;R152K 4;14 9;19 26044768 A 3D-RISM/RISM study of the oseltamivir binding efficiency with the wild-type and resistance-associated mutant forms of the viral influenza B neuraminidase. The binding affinity of oseltamivir to the influenza B neuraminidase and to its variants with three single substitutions, E119G, R152K, and D198N, is investigated by the MM/3D-RISM method. 2016 Protein science Abstract IV E119G;R152K;D198N 122;129;140 127;134;145 55 68 26044768 A 3D-RISM/RISM study of the oseltamivir binding efficiency with the wild-type and resistance-associated mutant forms of the viral influenza B neuraminidase. The theoretical results of the binding affinity of the drug to the mutants reproduced the observed trend in the resistivity, measured by IC50 ; the high-level resistance of E119G and R152K, and the low-level resistance of D198N. 2016 Protein science Abstract IV E119G;R152K;D198N 173;183;222 178;188;227 26044768 A 3D-RISM/RISM study of the oseltamivir binding efficiency with the wild-type and resistance-associated mutant forms of the viral influenza B neuraminidase. This phenomenon, however, is not found in the D198N strain, which is located in the framework of the active-site. 2016 Protein science Abstract IV D198N 46 51 26055368 Emergence of H7N9 Influenza A Virus Resistant to Neuraminidase Inhibitors in Nonhuman Primates. NA inhibitors (oseltamivir and peramivir) barely reduced the total virus amount because of the emergence of resistant variants with R289K or I219T in NA [residues 289 and 219 in N9 of A/Anhui/1/2013 (H7N9) correspond to 292 and 222 in N2, respectively] in three of the six treated macaques, whereas subcutaneous immunization of an inactivated vaccine derived from A/duck/Mongolia/119/2008 (H7N9) prevented propagation of A/Anhui/1/2013 (H7N9) in all vaccinated macaques. 2015 Antimicrobial agents and chemotherapy Abstract IV R289K;I219T 132;141 137;146 N9;NA;NA 178;0;150 180;2;152 26055368 Emergence of H7N9 Influenza A Virus Resistant to Neuraminidase Inhibitors in Nonhuman Primates. The virus with R289K in NA was reported in samples from human patients, whereas that with I219T in NA was identified for the first time in this study using macaques, though no variant H7N9 virus was reported in previous studies using mice. 2015 Antimicrobial agents and chemotherapy Abstract IV R289K;I219T 15;90 20;95 NA;NA 24;99 26;101 26056814 Molecular Characterisation of the Haemagglutinin Glycan-Binding Specificity of Egg-Adapted Vaccine Strains of the Pandemic 2009 H1N1 Swine Influenza A Virus. Collectively, the glycan binding data inform future vaccine design strategies to introduce the D225G or Q226R amino acid substitutions into recombinant H1N1 viruses. 2015 Molecules (Basel, Switzerland) Abstract IV D225G;Q226R 95;104 100;109 26056814 Molecular Characterisation of the Haemagglutinin Glycan-Binding Specificity of Egg-Adapted Vaccine Strains of the Pandemic 2009 H1N1 Swine Influenza A Virus. In contrast, the vaccine virus strains and recombinant HA harboring the Q226R HA mutation displayed a comparable pattern of highly specific binding to alpha2,3-linked sialyl-glycans, with a negligible affinity for alpha2,6-linked sialyl-glycans. 2015 Molecules (Basel, Switzerland) Abstract IV Q226R 72 77 HA;HA 55;78 57;80 26056814 Molecular Characterisation of the Haemagglutinin Glycan-Binding Specificity of Egg-Adapted Vaccine Strains of the Pandemic 2009 H1N1 Swine Influenza A Virus. The D225G A/California/07/09 recombinant HA displayed an enhanced binding affinity for both alpha2,6- and alpha2,3-linked sialyl-glycans in the array. 2015 Molecules (Basel, Switzerland) Abstract IV D225G 4 9 HA 41 43 26056814 Molecular Characterisation of the Haemagglutinin Glycan-Binding Specificity of Egg-Adapted Vaccine Strains of the Pandemic 2009 H1N1 Swine Influenza A Virus. The K123N mutation which introduces a glycosylation site proximal to the receptor binding site, did not impact the alpha2,3/alpha2,6 glycan selectivity, however, it lowered the overall glycan binding affinity of the HA; suggesting glycosylation may interfere with receptor binding. 2015 Molecules (Basel, Switzerland) Abstract IV K123N 4 9 HA 216 218 26056814 Molecular Characterisation of the Haemagglutinin Glycan-Binding Specificity of Egg-Adapted Vaccine Strains of the Pandemic 2009 H1N1 Swine Influenza A Virus. This study integrates glycan binding data with structure-recognition models to examine the impact of the K123N, D225G and Q226R mutations (as seen in the HA of vaccine strains of the pandemic 2009 H1N1 swine influenza A virus). 2015 Molecules (Basel, Switzerland) Abstract IV K123N;D225G;Q226R 105;112;122 110;117;127 HA 154 156 26071346 Quantitative analysis of influenza A (H3N2) E119V and R292K variants in clinical specimens by real-time reverse transcription polymerase chain reaction. CONCLUSIONS: Discrepancies in the proportion of R292K variants between clinical samples and isolates should be suspected in clinical settings. 2015 Journal of clinical virology Abstract IV R292K 48 53 26071346 Quantitative analysis of influenza A (H3N2) E119V and R292K variants in clinical specimens by real-time reverse transcription polymerase chain reaction. Prior to treatment, R292K variants were detected in all clinical samples; however, they comprised only a small fraction of the total population. 2015 Journal of clinical virology Abstract IV R292K 20 25 26071346 Quantitative analysis of influenza A (H3N2) E119V and R292K variants in clinical specimens by real-time reverse transcription polymerase chain reaction. RESULTS: The E119V variant was detected in only one patient during oseltamivir therapy, exhibiting decreased susceptibility to oseltamivir. 2015 Journal of clinical virology Abstract IV E119V 13 18 26071346 Quantitative analysis of influenza A (H3N2) E119V and R292K variants in clinical specimens by real-time reverse transcription polymerase chain reaction. STUDY DESIGN: We measured the populations of the low-susceptibility influenza A H3N2 variants E119V and R292K by qRT-PCR using 305 nasal aspiration samples collected over time from 13, 16, and 11 patients treated with no neuraminidase inhibitors, oseltamivir, and zanamivir, respectively. 2015 Journal of clinical virology Abstract IV E119V;R292K 94;104 99;109 221 234 26071346 Quantitative analysis of influenza A (H3N2) E119V and R292K variants in clinical specimens by real-time reverse transcription polymerase chain reaction. The proportion of the R292K variant in clinical samples increased for 6/27 (22.2%) patients treated with oseltamivir or zanamivir, whereas an increase in the proportion of the R292K variant in virus isolates was observed in only one patient. 2015 Journal of clinical virology Abstract IV R292K;R292K 22;176 27;181 26074198 Adaptive mutation PB2 D701N promotes nuclear import of influenza vRNPs in mammalian cells. To throw light on the role of the NLSs of NP and PB2 in nuclear transport, we have analysed the effect of mutation D701N, responsible for the exposure of the NLS domain of PB2, on the intracellular localisation of vRNPs. 2015 European journal of cell biology Abstract IV D701N 115 120 NP;PB2;PB2 42;49;172 44;52;175 26077257 Influenza A(H7N9) virus acquires resistance-related neuraminidase I222T substitution when infected mallards are exposed to low levels of oseltamivir in water. Following mallard exposure to 2.5 mug/liter OC, the resistance-related neuraminidase (NA) I222T substitution, was detected within 2 days during the first passage and was found in all viruses sequenced from subsequently introduced ducks. 2015 Antimicrobial agents and chemotherapy Abstract IV I222T 90 95 NA;NA 86;71 88;84 26089289 Mouse lung-adapted mutation of E190G in hemagglutinin from H5N1 influenza virus contributes to attenuation in mice. Moreover, the virulence assessment demonstrated that rVN-E190G was attenuated in mice. 2015 Journal of medical virology Abstract IV E190G 53 62 26089289 Mouse lung-adapted mutation of E190G in hemagglutinin from H5N1 influenza virus contributes to attenuation in mice. Results demonstrated that rVN-E190G virus increased the binding avidity to alpha2,6 SA (sialic acid) and reduced the affinity to alpha2,3 SA, meanwhile weakened the viral replication in vitro. 2015 Journal of medical virology Abstract IV E190G 26 35 26089289 Mouse lung-adapted mutation of E190G in hemagglutinin from H5N1 influenza virus contributes to attenuation in mice. The mouse lung-adapted variants were isolated and the mutation of E190G (H3 numbering) in the RBD was recognized. 2015 Journal of medical virology Abstract IV E190G 66 71 26089289 Mouse lung-adapted mutation of E190G in hemagglutinin from H5N1 influenza virus contributes to attenuation in mice. The receptor binding activity, growth curve and pathogenicity in mice of the rVN-E190G were investigated. 2015 Journal of medical virology Abstract IV E190G 77 86 26089289 Mouse lung-adapted mutation of E190G in hemagglutinin from H5N1 influenza virus contributes to attenuation in mice. The recombinant virus, rVN-E190G carrying E190G in hemagglutinin (HA) was designed and rescued using reverse genetics techniques. 2015 Journal of medical virology Abstract IV E190G;E190G 23;42 32;47 HA;HA 66;51 68;64 26089289 Mouse lung-adapted mutation of E190G in hemagglutinin from H5N1 influenza virus contributes to attenuation in mice. These results indicated that the mutation E190G in HA decreases H5N1 viral replication in vitro and significantly attenuates virulence in vivo. 2015 Journal of medical virology Abstract IV E190G 42 47 HA 51 53 2609643 [Antigenic variability of avian influenza virus A/H13, isolated in the USSR]. Two replacements of arginine by lysine and asparagine by serine in positions 15 and 16, respectively, are the most significant. 1989 Voprosy virusologii Abstract IV N15S 43 79 26160744 Outcomes and Susceptibility to Neuraminidase Inhibitors in Individuals Infected With Different Influenza B Lineages: The Influenza Resistance Information Study. Of 15 predefined resistance mutations, 2 were detected by neuraminidase sequencing: I221T had reduced sensitivity to oseltamivir, and I221V was sensitive to NAI inhibition. 2016 The Journal of infectious diseases Abstract IV I221T;I221V 84;134 89;139 NAI;NA 157;58 160;71 26164939 [Genetic Diversity and Evolution of the M Gene of Human Influenza A Viruses from 2009 to 2013 in Hangzhou, China]. All strains contained the adamantine-resistant mutation S31N in its M2 protein. 2015 Bing du xue bao Abstract IV S31N 56 60 M2 68 70 26164939 [Genetic Diversity and Evolution of the M Gene of Human Influenza A Viruses from 2009 to 2013 in Hangzhou, China]. One of the seasonal A(H3N2) viruses had another form of double-mutant R45H/S31N. 2015 Bing du xue bao Abstract IV R45H;S31N 70;75 74;79 26164939 [Genetic Diversity and Evolution of the M Gene of Human Influenza A Viruses from 2009 to 2013 in Hangzhou, China]. Two of the A(H1N1)pdm09 strains had double mutants of V27A/S31N or V271/S31N. 2015 Bing du xue bao Abstract IV V27A;S31N;S31N 54;59;72 58;63;76 26188087 Quantifying relative within-host replication fitness in influenza virus competition experiments. Results are consistent with those of our previous analysis, suggesting that the within-host replication fitness of these OR viruses is not compromised relative to that of related oseltamivir-susceptible (OS) strains, and that potentially permissive mutations in the neuraminidase gene (V241I and N369K) significantly enhance the fitness of H1N1pdm09 OR viruses. 2015 Journal of theoretical biology Abstract IV V241I;N369K 286;296 291;301 266 279 26211889 Amphipathic alpha-helices and putative cholesterol binding domains of the influenza virus matrix M1 protein are crucial for virion structure organisation. The M1 mutations included F32Y in the CRAC of alpha-helix 2, W45Y and W45F in the CRAC of alpha-helix 3, Y100S in the CRAC of alpha-helix 6, M128A and M128S in the CRAC of alpha-helix 8 and a double L103I/L130I mutation in both a putative cholesterol consensus motif and the nuclear localisation signal. 2015 Virus research Abstract IV F32Y;W45Y;W45F;Y100S;M128A;M128S;L103I;L130I 26;61;70;105;141;151;199;205 30;65;74;110;146;156;204;210 M1 4 6 26224460 Molecular characterization of mammalian-adapted Korean-type avian H9N2 virus and evaluation of its virulence in mice. Moreover, reverse genetic studies established that an E627K substitution in PB2 and the loss of the N-glycosylation site in the HA protein (aa166) are critical virulence markers in the mouse-adapted H9N2 virus. 2015 Journal of microbiology (Seoul, Korea) Abstract IV E627K 54 59 HA;PB2 128;76 130;79 26246579 Hemagglutinin-Neuraminidase Balance Influences the Virulence Phenotype of a Recombinant H5N3 Influenza A Virus Possessing a Polybasic HA0 Cleavage Site. Although introducing the R293K mutation into the original low-pathogenicity rH5N3 increased its virulence, transmission to naive contact birds was inefficient, suggesting that one or more of the remaining changes that had accumulated in the passage number six virus also play an important role in transmissibility. 2015 Journal of virology Abstract IV R293K 25 30 26246579 Hemagglutinin-Neuraminidase Balance Influences the Virulence Phenotype of a Recombinant H5N3 Influenza A Virus Possessing a Polybasic HA0 Cleavage Site. One of these involved the catalytic site of the neuraminidase (NA; R293K) and is associated with decreased neuraminidase activity and resistance to oseltamivir. 2015 Journal of virology Abstract IV R293K 67 72 NA;NA;NA 63;48;107 65;61;120 26247418 Difluorosialic acids, potent novel influenza virus neuraminidase inhibitors, induce fewer drug resistance-associated neuraminidase mutations than does oseltamivir. Among the 12 oseltamivir-resistant passaged lines, five gained NA mutations and four of these were the well-defined H275Y mutation that causes oseltamivir resistance. 2015 Virus research Abstract IV H275Y 116 121 63 65 26263554 Phenotypic and Genetic Characterization of Avian Influenza H5N2 Viruses with Intra- and Inter-Duck Variations in Taiwan. Both p518-L and p518-S strains had the N170D substitution in HA, which might be related to their greater binding to MDCK cells. 2015 PloS one Abstract IV N170D 39 44 HA 61 63 26263554 Phenotypic and Genetic Characterization of Avian Influenza H5N2 Viruses with Intra- and Inter-Duck Variations in Taiwan. Moreover, three amino acid substitutions in PA (P224S), PB2 (E72D), and M1 (A128T) were identified in intra-duck variations (p518-L vs p518-S), whereas other changes in HA (N170D), NA (I56T), and NP (Y289H) were present in inter-duck variations (DV518 vs DV413). 2015 PloS one Abstract IV P224S;E72D;A128T;N170D;I56T;Y289H 48;61;76;173;185;200 53;65;81;178;189;205 HA;M1;NA;NP;PA;PB2 169;72;181;196;44;56 171;74;183;198;46;59 26292325 Unique Determinants of Neuraminidase Inhibitor Resistance among N3, N7, and N9 Avian Influenza Viruses. In a fluorescence-based NA inhibition assay, we identified three categories of NA substitutions associated with reduced inhibition by NAIs (oseltamivir, zanamivir, and peramivir): (i) novel subtype-specific substitutions in or near the enzyme catalytic site (R152W, A246T, and D293N, N2 numbering), (ii) subtype-independent substitutions (E119G/V and/or D and R292K), and (iii) substitutions previously reported in other subtypes (Q136K, I222M, and E276D). 2015 Journal of virology Abstract IV R152W;A246T;D293N;E119G;E119V;R292K;Q136K;I222M;E276D 259;266;277;339;339;360;431;438;449 264;271;282;346;346;365;436;443;454 NA;NA;NAI 24;79;134 26;81;138 26310893 Synthesis and inhibitory effects of novel pyrimido-pyrrolo-quinoxalinedione analogues targeting nucleoproteins of influenza A virus H1N1. Recombinant WSN carrying the S377G NP is resistant to PPQ in anti-influenza and RNA polymerase assays. 2015 European journal of medicinal chemistry Abstract IV S377G 29 34 NP 35 37 26315318 Optimization of Droplet Digital PCR from RNA and DNA extracts with direct comparison to RT-qPCR: Clinical implications for quantification of Oseltamivir-resistant subpopulations. Well-characterized RNA purified from H275-wild type (WT) and H275Y-point mutated (MUT) neuraminidase of influenza A (H1N1) pandemic 2009 virus was used to demonstrate a ddPCR optimization workflow to assure robust data for downstream analysis. 2015 Journal of virological methods Abstract IV H275Y 61 66 87 100 26315686 Adaptive mutations in PB2 gene contribute to the high virulence of a natural reassortant H5N2 avian influenza virus in mice. Genomic sequencing revealed five mutations (HA-S227N, PB2-Q591K, PB2-D701N, PA-I554V and NP-R351K) that distinguished HB10-MA virus from its parental HB10 virus. 2015 Virus research Abstract IV S227N;Q591K;D701N;I554V;R351K 47;58;69;79;92 52;63;74;84;97 HA;NP;PA;PB2;PB2 44;89;76;54;65 46;91;78;57;68 26315686 Adaptive mutations in PB2 gene contribute to the high virulence of a natural reassortant H5N2 avian influenza virus in mice. Therefore, our results collectively emphasized the crucial role of PB2 gene, particularly the paired mutations of Q591K and D701N in the host adaptation of the novel reassortant H5N2 AIV in mammals, which may provide helpful insights into the pathogenic potential of emerging AIV in human beings. 2015 Virus research Abstract IV Q591K;D701N 114;124 119;129 PB2 67 70 IAV infections 276 279 26321885 Analysis of the Contrasting Pathogenicities Induced by the D222G Mutation in 1918 and 2009 Pandemic Influenza A Viruses. Accumulated mutations at positions 183 and 224 that alter the size of the binding pocket are identified with the fitness of the 2009 pandemic virus carrying the D222G mutation. 2015 Journal of chemical theory and computation Abstract IV D222G 161 166 26321885 Analysis of the Contrasting Pathogenicities Induced by the D222G Mutation in 1918 and 2009 Pandemic Influenza A Viruses. In 2009, the D222G mutation in the hemagglutinin (HA) glycoprotein of pandemic H1N1 influenza A virus was found to correlate with fatal and severe human infections. 2015 Journal of chemical theory and computation Abstract IV D222G 13 18 HA;HA 50;35 52;48 26339046 Molecular Determinants of Virulence and Stability of a Reporter-Expressing H5N1 Influenza A Virus. We also found that a single mutation in PB2 (V25A) or in PA (R443K) increased the virulence of the WT-Venus-H5N1 virus in mice and that the presence of both of these mutations substantially enhanced the pathogenicity of the virus. 2015 Journal of virology Abstract IV V25A;R443K 45;61 49;66 PA;PB2 57;40 59;43 26339046 Molecular Determinants of Virulence and Stability of a Reporter-Expressing H5N1 Influenza A Virus. We found that mutations in PB2 (V25A) and PA (R443K) play crucial roles in the stable maintenance of a foreign protein as an NS1 fusion protein in influenza A virus and in the virulence of influenza virus in mice. 2015 Journal of virology Abstract IV V25A;R443K 32;46 36;51 NS1;PA;PB2 125;42;27 128;44;30 26341387 Computational assay of Zanamivir binding affinity with original and mutant influenza neuraminidase 9 using molecular docking. The docking scores obtained after Zanamivir was bound to all mutant molecules of NA9 revealed 3 notable mutations R292W, R118P, and R292K that could greatly reduce the binding affinity of the medicine. 2015 Journal of theoretical biology Abstract IV R292W;R118P;R292K 114;121;132 119;126;137 81 83 26345289 Influenza virus surveillance in Argentina during the 2012 season: antigenic characterization, genetic analysis and antiviral susceptibility. This isolate, an A(H1N1)pdm09 virus possessing the substitution NA-N295S, showed highly reduced inhibition by oseltamivir and reduced inhibition by zanamivir. 2016 Epidemiology and infection Abstract IV N295S 67 72 64 66 26378170 Role of Substitutions in the Hemagglutinin in the Emergence of the 1968 Pandemic Influenza Virus. Substitutions Q226L and G228S are known to be essential for adaptation of avian HA to mammals. 2015 Journal of virology Abstract IV Q226L;G228S 14;24 19;29 HA 80 82 26422258 Oseltamivir Resistance in Influenza A(H6N2) Caused by an R292K Substitution in Neuraminidase Is Not Maintained in Mallards without Drug Pressure. AIM AND METHODS: In a previous in vivo Mallard experiment, an influenza A(H6N2) virus developed oseltamivir resistance by the R292K substitution in the neuraminidase (NA), when the birds were exposed to oseltamivir. 2015 PloS one Abstract IV R292K 126 131 NA;NA 167;152 169;165 26422258 Oseltamivir Resistance in Influenza A(H6N2) Caused by an R292K Substitution in Neuraminidase Is Not Maintained in Mallards without Drug Pressure. Three variants of resistant H6N2/R292K virus were each propagated during 17 days in five successive pairs of naive Mallards, while oseltamivir exposure was decreased and removed. 2015 PloS one Abstract IV R292K 33 38 26453960 A PB1 T296R substitution enhance polymerase activity and confer a virulent phenotype to a 2009 pandemic H1N1 influenza virus in mice. Analysis of the variants genomes revealed 6 amino acid changes in the PB1 (T296R), PA (I94V), HA (H3 numbering; N159D, D225G, and R226Q), and NP (D375N). 2015 Virology Abstract IV T296R;I94V;N159D;D225G;R226Q;D375N 75;87;112;119;130;146 80;91;117;124;135;151 HA;NP;PA;PB1 94;142;83;70 96;144;85;73 26453960 A PB1 T296R substitution enhance polymerase activity and confer a virulent phenotype to a 2009 pandemic H1N1 influenza virus in mice. Using reverse genetics, we found that a PB1-T296R substitution found in all adapted viral variants enhanced viral replication kinetics in vitro and vivo, increased viral polymerase activity in human cells, and was sufficient for enhanced virulence of the 2009 pandemic H1N1 virus in mice. 2015 Virology Abstract IV T296R 44 49 PB1 40 43 26468540 PB1-F2 Protein Does Not Impact the Virulence of Triple-Reassortant H3N2 Swine Influenza Virus in Pigs but Alters Pathogenicity and Transmission in Turkeys. Further, turkeys infected with SIV 1145-N66S displayed poor infectivity and transmissibility. 2016 Journal of virology Abstract IV N66S 40 44 26468540 PB1-F2 Protein Does Not Impact the Virulence of Triple-Reassortant H3N2 Swine Influenza Virus in Pigs but Alters Pathogenicity and Transmission in Turkeys. Using the eight-plasmid reverse genetics system, we rescued wild-type SIV A/swine/Minnesota/1145/2007 (H3N2) (SIV 1145-WT), a PB1-F2 knockout mutant (SIV 1145-KO), and its N66S variant (SIV 1145-N66S). 2016 Journal of virology Abstract IV N66S;N66S 172;195 176;199 PB1F2 126 132 26477933 Deep sequencing reveals the viral adaptation process of environment-derived H10N8 in mice. Using Illumina high-throughput data, we detected the gradual mutations of F277S, C278Q, F611S and L653P in the polymerase acidic (PA) protein, and of L207V and E627K in the PB2 protein during adaptation. 2016 Infection, genetics and evolution Abstract IV C278Q;F277S;F611S;L653P;L207V;E627K 81;74;88;98;150;160 86;79;93;103;155;165 PA;PB2;PA 130;173;111 132;176;128 26491158 A Unique Multibasic Proteolytic Cleavage Site and Three Mutations in the HA2 Domain Confer High Virulence of H7N1 Avian Influenza Virus in Chickens. A436T and/or K536R restored viral replication in vitro and in vivo. 2016 Journal of virology Abstract IV A436T;K536R 0;13 5;18 26491158 A Unique Multibasic Proteolytic Cleavage Site and Three Mutations in the HA2 Domain Confer High Virulence of H7N1 Avian Influenza Virus in Chickens. In addition to the mCS, Q450L was required for full virulence and transmissibility of the virus. 2016 Journal of virology Abstract IV Q450L 24 29 26491158 A Unique Multibasic Proteolytic Cleavage Site and Three Mutations in the HA2 Domain Confer High Virulence of H7N1 Avian Influenza Virus in Chickens. Nonetheless, it was detrimental to virus replication and required A436T and/or K536R to restore replication, systemic spread, and stability. 2016 Journal of virology Abstract IV A436T;K536R 66;79 71;84 26491158 A Unique Multibasic Proteolytic Cleavage Site and Three Mutations in the HA2 Domain Confer High Virulence of H7N1 Avian Influenza Virus in Chickens. Q450L in the HA2 stem domain increased virulence and transmission but was detrimental to replication in cell culture, probably due to low-pH activation of HA. 2016 Journal of virology Abstract IV Q450L 0 5 HA;HA 13;155 15;157 26491158 A Unique Multibasic Proteolytic Cleavage Site and Three Mutations in the HA2 Domain Confer High Virulence of H7N1 Avian Influenza Virus in Chickens. Viruses possessing A436T and K536R were observed early in the HPAI outbreak but were later superseded by viruses carrying all three mutations. 2016 Journal of virology Abstract IV A436T;K536R 19;29 24;34 26506405 Isocyanides as Influenza A Virus Subtype H5N1 Wild-Type M2 Channel Inhibitors. Furthermore, the isocyanide analogues synthesized in this study did not inhibit the V27A or S31N mutant M2 ion channels, according to electrophysiology experiments, and did not exhibit activity against amantadine-resistant virus strains. 2015 ChemMedChem Abstract IV V27A;S31N 84;92 88;96 M2 104 106 26583707 Influenza A(H6N1) Virus in Dogs, Taiwan. Molecular analysis indicated that this isolate was closely related to influenza A(H6N1) viruses circulating in Taiwan and harbored the E627K substitution in the polymerase basic 2 protein, which indicated its ability to replicate in mammalian species. 2015 Emerging infectious diseases Abstract IV E627K 135 140 PB1F2 161 187 26608319 H1N1 Swine Influenza Viruses Differ from Avian Precursors by a Higher pH Optimum of Membrane Fusion. Eight amino acid substitutions in the HA were found to separate the EAsw viruses from their putative avian precursor; four substitutions-T492S, N722D, R752K, and S1132F-were located in the structural regions of the HA2 subunit known to play a role in acid-induced conformational transition of the HA. 2016 Journal of virology Abstract IV T492S;N722D;R752K;S1132F 137;144;151;162 142;149;156;168 HA;HA;HA 38;215;297 40;217;299 26608955 Zanamivir-resistant influenza viruses with Q136K or Q136R neuraminidase residue mutations can arise during MDCK cell culture creating challenges for antiviral susceptibility monitoring. The effect of Q136K, Q136R, Q136H and Q136L substitutions in NA subtypes N1 and N2 on NAI susceptibility and in vitro viral fitness was assessed. 2015 Euro surveillance Abstract IV Q136K;Q136R;Q136H;Q136L 14;21;28;38 19;26;33;43 NA;NAI 61;86 63;89 26608955 Zanamivir-resistant influenza viruses with Q136K or Q136R neuraminidase residue mutations can arise during MDCK cell culture creating challenges for antiviral susceptibility monitoring. We showed that variant viruses containing the Q136K and Q136R NA mutations were preferentially selected in Madin-Darby canine kidney epithelial (MDCK) cells, but were less well supported in MDCK-SIAT1 cells and embryonated eggs. 2015 Euro surveillance Abstract IV Q136K;Q136R 46;56 51;61 62 64 26609523 Phylogenetic Analysis of Hemagglutinin Genes of H9N2 Avian Influenza Viruses Isolated from Chickens in Shandong, China, between 1998 and 2013. Importantly, 29 out of these 35 isolates had an amino acid exchange (Q226L) in the receptor-binding site. 2015 BioMed research international Abstract IV Q226L 69 74 26621436 Origins of Resistance Conferred by the R292K Neuraminidase Mutation via Molecular Dynamics and Free Energy Calculations. Notably, in every case, the simulation results correctly predict that loss of binding occurs as a result of the R292K mutation. 2008 Journal of chemical theory and computation Abstract IV R292K 112 117 26621436 Origins of Resistance Conferred by the R292K Neuraminidase Mutation via Molecular Dynamics and Free Energy Calculations. Per-residue binding footprints reveal that changes in DeltaDeltaEcoul for R292K-wildtype at position 292 parallel the change in experimental fold resistance energies (DeltaDeltaGR292K-WT) with S03 < S00 < S02 < S01. 2008 Journal of chemical theory and computation Abstract IV R292K;R292K 74;177 79;183 26621436 Origins of Resistance Conferred by the R292K Neuraminidase Mutation via Molecular Dynamics and Free Energy Calculations. The goal is to elucidate which structural and energetic properties change as a result of a mutation at position R292K. 2008 Journal of chemical theory and computation Abstract IV R292K 112 117 26623630 Characterization of H5N1 influenza A virus that caused the first highly pathogenic avian influenza outbreak in Saudi Arabia. Additionally, a few mutations with amino acid substitutions such as M226I at N-link glycosylation site were identified in two of these isolates. 2015 Journal of infection in developing countries Abstract IV M226I 68 73 26630841 [Analysis of the Neuraminidase Amino Acid Sequences of Influenza A/H1N1pdm09, A/H3N2, and B Viruses Isolated from Influenza Patients in the 2013/14 Japanese Influenza Season]. CONCLUSION: The previously reported H275Y mutation that causes oseltamivir resistance was found in the two A/H1N1pdm09 viruses that showed a very high IC50 for oseltamivir. 2015 Fukuoka igaku zasshi Abstract IV H275Y 36 41 26630841 [Analysis of the Neuraminidase Amino Acid Sequences of Influenza A/H1N1pdm09, A/H3N2, and B Viruses Isolated from Influenza Patients in the 2013/14 Japanese Influenza Season]. RESULTS: Two A/H1N1pdm09 viruses that showed very high IC50 for oseltamivir (150 nM and 130 nM) contained the H275Y mutation. 2015 Fukuoka igaku zasshi Abstract IV H275Y 110 115 26639679 Amantadine resistance among highly pathogenic avian influenza viruses (H5N1) isolated from India. Results of the study revealed resistance to amantadine in antiviral assay among four H5N1 viruses out of which two viruses had Serine 31 Asparagine (AGT-AAT i.e., S31N) mutation and two had Valine 27 Alanine (GTT-GCT i.e., V27A) mutation. 2016 Microbial pathogenesis Abstract IV V27A;S31N;S31N;V27A 223;163;127;190 227;167;147;207 26639679 Amantadine resistance among highly pathogenic avian influenza viruses (H5N1) isolated from India. The four resistant viruses not only exhibited significant difference in effective concentration 50% (EC50) values of amantadine hydrochloride from that of susceptible viruses (P < 0.0001) but also showed significant difference between two different types (S31N and V27A) of mutant viruses (P < 0.05). 2016 Microbial pathogenesis Abstract IV V27A;S31N 265;256 269;260 26645808 Residue-based design of small molecule inhibitor for H1N1, H5N1 and H7N1 mutants. Our in silico findings suggest that saussureamine C can inhibit H274Y and N294S mutants, and that diiodotyrosine can also inhibit N294S mutants. 2016 Journal of molecular modeling Abstract IV H274Y;N294S;N294S 64;74;130 69;79;135 26645808 Residue-based design of small molecule inhibitor for H1N1, H5N1 and H7N1 mutants. Point mutations H274Y and N294S can lead to resistance of influenza virus strains to some drug molecules. 2016 Journal of molecular modeling Abstract IV H274Y;N294S 16;26 21;31 26656922 A Balance between Inhibitor Binding and Substrate Processing Confers Influenza Drug Resistance. Furthermore, two NA mutations, K221N and Y276F, each reduce susceptibility to oseltamivir by increasing NA activity without altering drug binding. 2016 Journal of molecular biology Abstract IV K221N;Y276F 31;41 36;46 NA;NA 17;104 19;106 26656922 A Balance between Inhibitor Binding and Substrate Processing Confers Influenza Drug Resistance. NA mutations previously known to confer oseltamivir resistance in N1 strains, including H275Y and N295S, were adaptive in the presence of drug, indicating that our experimental system captured salient features of real-world selection pressures acting on NA. 2016 Journal of molecular biology Abstract IV H275Y;N295S 88;98 93;103 NA;NA 0;254 2;256 26665435 [Testing of apathogenic influenza virus H5N3 as a poultry live vaccine]. The hemagglutinin of the Ku-at has the amino acid substitutions Asp54/Asn and Lys222/Thr in HA1 and Val48/Ile and Lys131/Thr in HA2, while maintaining the polybasic HA cleavage site at an invariable level. 2015 Voprosy virusologii Abstract IV D54N;K222T;V48I;K131T 64;78;100;114 73;88;109;124 HA;HA;HA1;HA 128;165;92;4 130;167;95;17 26703222 Recombinant influenza virus with a pandemic H2N2 polymerase complex has a higher adaptive potential than one with seasonal H2N2 polymerase complex. We further identified three mutations (PB2-I114V, PB1-S261N and PA-D383N) responsible for the reduced activity. 2016 The Journal of general virology Abstract IV I114V;S261N;D383N 43;54;67 48;59;72 PA;PB1;PB2 64;50;39 66;53;42 26703840 H274Y's Effect on Oseltamivir Resistance: What Happens Before the Drug Enters the Binding Site. However, most of the reported studies on H274Y focused only on the drug-bound system, so the direct effects of the mutation on NA itself prior to drug binding still remain unclear. 2016 Journal of chemical information and modeling Abstract IV H274Y 41 46 127 129 26703840 H274Y's Effect on Oseltamivir Resistance: What Happens Before the Drug Enters the Binding Site. Increased reports of oseltamivir (OTV)-resistant strains of the influenza virus, such as the H274Y mutation on its neuraminidase (NA), have created some cause for concern. 2016 Journal of chemical information and modeling Abstract IV H274Y 93 98 NA;NA 130;115 132;128 26703840 H274Y's Effect on Oseltamivir Resistance: What Happens Before the Drug Enters the Binding Site. It was observed that the disruption of the NA binding site due to the H274Y mutation was initiated by the repulsive effect of Y274 on the 250-loop, which in turn altered the hydrogen-bonding network around residue 274. 2016 Journal of chemical information and modeling Abstract IV H274Y 70 75 43 45 26703840 H274Y's Effect on Oseltamivir Resistance: What Happens Before the Drug Enters the Binding Site. Many studies have been conducted in the attempt to uncover the mechanism of OTV resistance in H274Y NA. 2016 Journal of chemical information and modeling Abstract IV H274Y 94 99 100 102 26703840 H274Y's Effect on Oseltamivir Resistance: What Happens Before the Drug Enters the Binding Site. Therefore, molecular dynamics simulations of NA in apo form, followed by principal component analysis and interaction energy calculations, were performed to investigate the structural changes of the NA binding site as a result of the H274Y mutation. 2016 Journal of chemical information and modeling Abstract IV H274Y 234 239 NA;NA 45;199 47;201 26722757 Imidazole-based pinanamine derivatives: Discovery of dual inhibitors of the wild-type and drug-resistant mutant of the influenza A virus. We previously reported potent hit compound 4 inhibiting the wild-type influenza A virus A/HK/68 (H3N2) and A/M2-S31N mutant viruses A/WS/33 (H1N1), with its latter activity quite weak. 2016 European journal of medicinal chemistry Abstract IV S31N 112 116 M2 109 111 26738596 Species difference in ANP32A underlies influenza A virus polymerase host restriction. Substitutions, such as PB2(E627K), were rapidly selected upon infection of humans with avian H5N1 or H7N9 influenza viruses, adapting the viral polymerase for the shorter mammalian ANP32A. 2016 Nature Abstract IV E627K 27 32 PB2 23 26 26739054 Deep Sequencing Reveals Potential Antigenic Variants at Low Frequencies in Influenza A Virus-Infected Humans. These mutations included two substitutions in H1N1pdm viruses, G158K and N159K, which were recently found to confer escape from virus-specific antibodies. 2016 Journal of virology Abstract IV G158K;N159K 63;73 68;78 26754751 Coupling high-throughput genetics with phylogenetic information reveals an epistatic interaction on the influenza A virus M segment. Comparison with natural sequence variation showed that a deleterious substitution M1 Q214H was prevalent in circulating strains. 2016 BMC genomics Abstract IV Q214H 85 90 M1 82 84 26754751 Coupling high-throughput genetics with phylogenetic information reveals an epistatic interaction on the influenza A virus M segment. In particular, we were able to identify an epistatic interaction between M1 substitutions A209T and Q214H. 2016 BMC genomics Abstract IV A209T;Q214H 90;100 95;105 M1 73 75 26754751 Coupling high-throughput genetics with phylogenetic information reveals an epistatic interaction on the influenza A virus M segment. Subsequently, we experimentally validated that M1 A209T was a compensatory substitution for M1 Q214H. 2016 BMC genomics Abstract IV A209T;Q214H 50;95 55;100 M1;M1 47;92 49;94 26782141 PB2-588 V promotes the mammalian adaptation of H10N8, H7N9 and H9N2 avian influenza viruses. Taken together, our results suggest that the substitution PB2-A588V may be a new strategy for an avian influenza virus to adapt mammalian hosts. 2016 Scientific reports Abstract IV A588V 62 67 PB2 58 61 26802558 Antiviral activity of SA-2 against influenza A virus in vitro/vivo and its inhibition of RNA polymerase. In a cytopathic effect assay, SA-2 dose dependently inhibited H1N1, H3N2 and the oseltamivir-resistant mutant H1N1-H275Y influenza viruses in both virus-infected MDCK and A549 cells, with 50% effective concentrations (EC50) in MDCK cells of 9.6, 19.2 and 19.8 muM respectively, and 50% cytotoxic concentration (CC50) of 444.5 muM, showing competitive antiviral activity with oseltamivir in vitro. 2016 Antiviral research Abstract IV H275Y 115 120 26802558 Antiviral activity of SA-2 against influenza A virus in vitro/vivo and its inhibition of RNA polymerase. Orally administered SA-2 effectively protected mice infected with lethal doses of H1N1 or oseltamivir-resistant strain H1N1-H275Y, conferring 70% or 50% survival at a dosage of 100 mg/kg/d, reducing body weight loss, alleviating the influenza-induced acute lung injury, and reducing lung virus titer. 2016 Antiviral research Abstract IV H275Y 124 129 Lung lesions 251 268 26811446 Molecular requirements for a pandemic influenza virus: An acid-stable hemagglutinin protein. A ferret-adapted revertant (HA1-H17Y/HA2-R106K) regained airborne transmissibility by stabilizing HA to an activation pH of 5.3, similar to that of human-adapted isolates from late 2009-2014. 2016 Proc Natl Acad Sci U S A Abstract IV H17Y;R106K 32;41 38;46 HA;HA;HA1 37;98;28 39;100;31 26811446 Molecular requirements for a pandemic influenza virus: An acid-stable hemagglutinin protein. A loss-of-function pH1N1 virus with a destabilizing HA1-Y17H mutation (pH 6.0) was less pathogenic in mice and ferrets, less transmissible by contact, and no longer airborne-transmissible. 2016 Proc Natl Acad Sci U S A Abstract IV Y17H 56 60 HA1 52 55 26813086 Variability of tropism and replicative capacity of two naturally occurring influenza A H9N2 viruses in cell cultures from different tissues. We described the results of a comparative analysis of replication efficiency of two naturally occurring influenza A H9N2 variants isolated from poultry and wild birds, differing by only two substitutions Q226L and T384N, in the receptor-binding site of haemagglutinin and the 380 loop region of NA proteins, respectively. 2016 Avian pathology Abstract IV Q226L;T384N 204;214 209;219 HA;NA 253;295 267;297 26845764 Genomic Signatures for Avian H7N9 Viruses Adapting to Humans. An RNP activity assay showed that Q591K, D701N, and M535L restored the polymerase activity in human cells when 627K transformed to an avian-like E. 2016 PloS one Abstract IV Q591K;D701N;M535L 34;41;52 39;46;57 RNP 3 6 26845764 Genomic Signatures for Avian H7N9 Viruses Adapting to Humans. An RNP assay suggested Q591K, D701N, and M535L as potential markers for an H7N9 virus capable of infecting humans. 2016 PloS one Abstract IV Q591K;D701N;M535L 23;30;41 28;35;46 RNP 3 6 26845764 Genomic Signatures for Avian H7N9 Viruses Adapting to Humans. We discovered 10 PB2 substitutions that covaried with K627E. 2016 PloS one Abstract IV K627E 54 59 PB2 17 20 26847414 Amino acid changes in PB2 and HA affect the growth of a recombinant influenza virus expressing a fluorescent reporter protein. Here, we demonstrate that the enhanced viral replication and virulence in mice of this Venus-expressing influenza virus are primarily conferred by the PB2-E712D mutation, with only a minor contribution by the HA-T380A mutation. 2016 Scientific reports Abstract IV E712D;T380A 155;212 160;217 HA;PB2 209;151 211;154 26874012 Enhancement of the safety of live influenza vaccine by attenuating mutations from cold-adapted hemagglutinin. We examined their phenotypes and found a major attenuating mutation, N81K. 2016 Virology Abstract IV N81K 69 73 26912622 Neuraminidase Activity and Resistance of 2009 Pandemic H1N1 Influenza Virus to Antiviral Activity in Bronchoalveolar Fluid. The oseltamivir resistance mutation H275Y rendered the pandemic H1N1 virus but not the seasonal H1N1 virus more sensitive to BAL fluid. 2016 Journal of virology Abstract IV H275Y 36 41 26912622 Neuraminidase Activity and Resistance of 2009 Pandemic H1N1 Influenza Virus to Antiviral Activity in Bronchoalveolar Fluid. The resistance to the pulmonary innate antiviral activity of the pandemic virus was determined by its neuraminidase (NA) gene, and it was shown that the NA inhibitor resistance mutation H275Y abolished this resistance of the pandemic H1N1 but not the seasonal H1N1 virus, which had compensatory mutations that maintained the fitness of drug-resistant strains. 2016 Journal of virology Abstract IV H275Y 186 191 NA;NA;NA 117;153;102 119;155;115 26914510 Genetic characterization of an adapted pandemic 2009 H1N1 influenza virus that reveals improved replication rates in human lung epithelial cells. The increased replication rate was pinpointed to two mutations within the hemagglutinin (HA) gene segment (HA1 D130E, HA2 I91L), near the receptor binding site and the stem domain. 2016 Virology Abstract IV D130E;I91L 111;122 116;126 HA;HA;HA1;HA 89;118;107;74 91;120;110;87 26935590 The significance of naturally occurring neuraminidase quasispecies of H5N1 avian influenza virus on resistance to oseltamivir: a point of concern. The results revealed that the mutant populations, S236F mutant, S236F/C278Y mutant, A250V/V266A/P271H/G285S mutant and C278Y mutant, had a lower binding affinity with OTV as compared with the WT virus due to rearrangement of amino acid residues and increased flexibility in the 150-loop. 2016 The Journal of general virology Abstract IV S236F;S236F;C278Y;A250V;V266A;P271H;G285S;C278Y 50;64;70;84;90;102;102;119 55;69;75;89;95;107;107;124 26951014 [Analysis of HA and NA Genes of Influenza A H1N1 Virus in Yunnan Province during 2009-2014]. The sequencing result showed that HA and NA gene were divided into 3 groups, one was detected with H275Y mutation strains. 2015 Bing du xue bao Abstract IV H275Y 99 104 HA;NA 34;41 36;43 26974849 Effects of egg-adaptation on receptor-binding and antigenic properties of recent influenza A (H3N2) vaccine viruses. Results show that viruses with egg-adaptive HA substitutions R156Q, S219Y, and I226N, have increased binding avidity to alpha2,3-linked receptor-analogues and decreased binding avidity to alpha2,6-linked receptor-analogues. 2016 The Journal of general virology Abstract IV R156Q;S219Y;I226N 61;68;79 66;73;84 HA 44 46 26997612 Amino acid substitutions occurring during adaptation of an emergent H5N6 avian influenza virus to mammals. We provide evidence that the mutations HA A150V, NA R143K and G147E, PB2 E627K, and PA A343T may be important for adaptation of H5N6 AIVs to mammals. 2016 Archives of virology Abstract IV A150V;R143K;G147E;E627K;A343T 42;52;62;73;87 47;57;67;78;92 HA;NA;PA;PB2 39;49;84;69 41;51;86;72 27020673 Interim estimates of 2015/16 vaccine effectiveness against influenza A(H1N1)pdm09, Canada, February 2016. Among the 67 A(H1N1)pdm09-positive specimens that were successfully sequenced, 62 (> 90%) belonged to the emerging genetic 6B.1 subclade, defined by S162N (potential gain of glycosylation) and I216T mutations in the haemagglutinin protein. 2016 Euro surveillance Abstract IV S162N;I216T 149;193 154;198 HA 216 230 27066703 Adaptive amino acid substitutions enhance the virulence of a novel human H7N9 influenza virus in mice. Analysis of adapted viral genomes revealed a total of 14 amino acid changes among the three variant viruses in the PA (T97I, K328R, P332T, and Q556R), HA (H3 numbering; A107T, R220I, L226Q, and R354K), NP (A284T and M352I), NA (M26I, N142S, and G389D), and M1 (M128R) proteins. 2016 Veterinary microbiology Abstract IV T97I;K328R;P332T;Q556R;A107T;R220I;L226Q;R354K;A284T;M352I;M26I;N142S;G389D;M128R 119;125;132;143;169;176;183;194;206;216;228;234;245;261 123;130;137;148;174;181;188;199;211;221;232;239;250;266 HA;M1;NA;NP;PA 151;257;224;202;115 153;259;226;204;117 27076644 Multiple Natural Substitutions in Avian Influenza A Virus PB2 Facilitate Efficient Replication in Human Cells. Although substitutions like E627K in the PB2 polymerase subunit can facilitate polymerase activity to allow replication in mammals, many human H5N1 and H7N9 viruses lack this adaptive substitution. 2016 Journal of virology Abstract IV E627K 28 33 PB2 41 44 27082171 Crystal structure of the drug-resistant S31N influenza M2 proton channel. Here we report the first crystal structure of the S31N mutant crystallized using lipidic cubic phase crystallization techniques and solved to 1.59 A resolution. 2016 Protein science Abstract IV S31N 50 54 27082171 Crystal structure of the drug-resistant S31N influenza M2 proton channel. In recent decades mutations have arisen in M2 that prevent the adamantanes from binding to the channel pore, with the most prevalent of these mutations being S31N. 2016 Protein science Abstract IV S31N 158 162 M2 43 45 27089319 The Molecular Epidemiology and Evolutionary Dynamics of Influenza B Virus in Two Italian Regions during 2010-2015: The Experience of Sicily and Liguria. D197N in 190-helix was found in almost all viruses collected. 2016 International journal of molecular sciences Abstract IV D197N 0 5 27089319 The Molecular Epidemiology and Evolutionary Dynamics of Influenza B Virus in Two Italian Regions during 2010-2015: The Experience of Sicily and Liguria. The most represented amino-acid substitutions were N116K in the 120-loop (83.9% of B/Yamagata clade 3 strains) and I146V in the 150-loop (89.6% of B/Victoria clade 1 strains). 2016 International journal of molecular sciences Abstract IV N116K;I146V 51;115 56;120 27095056 A Novel Potent and Highly Specific Inhibitor against Influenza Viral N1-N9 Neuraminidases: Insight into Neuraminidase-Inhibitor Interactions. Like zanamivir, it is highly effective against N1-N9 avian and N1-N2 human viNAs, including H274Y oseltamivir-resistant N1 viNA, due to its C-6 portion still being anchored in the active site, different from the disruption of oseltamivir's C-6 anchoring by H274Y mutation. 2016 Journal of medicinal chemistry Abstract IV H274Y;H274Y 92;257 97;262 N9 50 52 27097026 Novel Polymerase Gene Mutations for Human Adaptation in Clinical Isolates of Avian H5N1 Influenza Viruses. A major determinant in the change of the avian influenza virus host range to humans is the E627K substitution in the PB2 polymerase protein. 2016 PLoS pathogens Abstract IV E627K 91 96 PB2 117 120 27097026 Novel Polymerase Gene Mutations for Human Adaptation in Clinical Isolates of Avian H5N1 Influenza Viruses. However, the polymerase activity of avian influenza viruses with a single PB2-E627K mutation is still lower than that of seasonal human influenza viruses, implying that avian viruses require polymerase mutations in addition to PB2-627K for human adaptation. 2016 PLoS pathogens Abstract IV E627K 78 83 PB2;PB2 74;227 77;230 27105450 Residues in the PB2 and PA genes contribute to the pathogenicity of avian H7N3 influenza A virus in DBA/2 mice. Analysis of individual residues in the PB2 and PA genes identified position 358 (E358V) in PB2 and positions 190 (P190S) and 400 (Q400P) in PA that reduced the virulence of H7N3 virus. 2016 Virology Abstract IV E358V;P190S;Q400P 81;114;130 86;119;135 PA;PA;PB2;PB2 47;140;39;91 49;142;42;94 27105450 Residues in the PB2 and PA genes contribute to the pathogenicity of avian H7N3 influenza A virus in DBA/2 mice. The E358V and P190S substitutions also caused reduced inflammation after infection. 2016 Virology Abstract IV E358V;P190S 4;14 9;19 27138550 Virulence of a novel reassortant canine H3N2 influenza virus in ferret, dog and mouse models. We found that the PA and NS gene segments of VC378 were introduced from pdmH1N1, and these genes included the amino acid substitutions PA-P224S and NS-I123V, which were previously found to be associated with increased virulence in mice. 2016 Archives of virology Abstract IV P224S;I123V 138;151 143;156 NS;NS;PA;PA 25;148;18;135 27;150;20;137 27145596 [AVIAN RECOMBINANT VIRUS H5N1 INFLUENZA (A/VIETNAM/1203/04) AND ITS ESCAPE-MUTANT m13(13) INDUCE EARLY SIGNALING REACTIONS OF THE IMMUNITY IN HUMAN LYMPHOCYTES]. The mutant virus A/Vietnam/1203/04 (HA S145F), stimulated an increase in the transcription level of the membrane receptor gene TLR4 and a decrease in the level of activation of TNF-alpha gene. 2016 Voprosy virusologii Abstract IV S145F 39 44 HA 36 38 27146707 Design of Broad-Spectrum Inhibitors of Influenza A Virus M2 Proton Channels: A Molecular Modeling Approach. CONCLUSION: Using the molecular dynamics and molecular docking techniques, we have refined the dynamic dimer-ofdimers structures of the WT, S31N and V27A variants of the M2 proton channel of the influenza A virus, analyzed the inhibitor binding sites, identified a number of potential broad-spectrum inhibitor structures targeting them, and clarified the binding modes and probable mechanisms of action of one promising compound. 2016 Current computer-aided drug design Abstract IV V27A;S31N 149;140 153;144 M2 170 172 27146707 Design of Broad-Spectrum Inhibitors of Influenza A Virus M2 Proton Channels: A Molecular Modeling Approach. METHOD: The dynamic dimer-of-dimers structures of the three primary M2 target variants, wild-type, S31N and V27A, were modeled by molecular dynamics and thoroughly analyzed in order to define the inhibitor binding sites. 2016 Current computer-aided drug design Abstract IV V27A;S31N 108;99 112;103 M2 68 70 27186639 In-Depth Analysis of HA and NS1 Genes in A(H1N1)pdm09 Infected Patients. Known polymorphisms, S203T (HA) and I123V (NS1), were observed as dominant variants (>98%) in almost all patients; three HA and two NS1 further variants were observed at frequency >40%; a number of additional variants were detected at frequency <6% (minority variants), of which three HA and four NS1 variants were novel. 2016 PloS one Abstract IV S203T;I123V 21;36 26;41 HA;HA;HA;NS1;NS1;NS1 28;121;285;43;132;297 30;123;287;46;135;300 27188368 [Genomic characteristics of 2 strains of influenza A(H9N2)virus isolated from human infection cases in Anhui province]. The amino acid sequence alignment results showed that several mutations for human infection tropism presented in the two virus strains, including Q226L, H183N and E190T in HA; S31N in M2; 63-65 deletion in NA. 2016 Zhonghua liu xing bing xue za zhi Abstract IV Q226L;H183N;E190T;S31N 146;153;163;176 151;158;168;180 HA;M2;NA 172;184;206 174;186;208 27193582 Mechanisms of Action of Novel Influenza A/M2 Viroporin Inhibitors Derived from Hexamethylene Amiloride. In addition, tert-butyl 4'-(carbamimidoylcarbamoyl)-2',3-dinitro-[1,1'-biphenyl]-4-carboxylate ( 27: ) acts both on adamantane-sensitive and a resistant M2 variant encoding a serine to asparagine 31 mutation (S31N) with improved efficacy over amantadine and HMA (IC50 = 0.6 microM and 4.4 microM, respectively). 2016 Molecular pharmacology Abstract IV S31N;S31N 209;175 213;198 M2 153 155 27193582 Mechanisms of Action of Novel Influenza A/M2 Viroporin Inhibitors Derived from Hexamethylene Amiloride. Whereas 9: inhibited in vitro replication of influenza virus encoding wild-type M2 (EC50 = 2.3 microM), both 27: and tert-butyl 4'-(carbamimidoylcarbamoyl)-2',3-dinitro-[1,1'-biphenyl]-4-carboxylate ( 26: ) preferentially inhibited viruses encoding M2(S31N) (respective EC50 = 18.0 and 1.5 microM). 2016 Molecular pharmacology Abstract IV S31N 252 256 M2;M2 80;249 82;251 27194759 Mosaic H5 Hemagglutinin Provides Broad Humoral and Cellular Immune Responses against Influenza Viruses. Compared to a MVA construct expressing hemagglutinin (HA) from influenza virus A/VN/1203/04 (MVA-HA), the MVA-H5M vaccine markedly increased and broadened B cell and T cell responses against H5N1 virus. 2016 Journal of virology Abstract IV H5M 110 113 HA;HA;HA 54;97;39 56;99;52 27194759 Mosaic H5 Hemagglutinin Provides Broad Humoral and Cellular Immune Responses against Influenza Viruses. Finally, expression of the H5M gene as either a DNA vaccine or a subunit protein protected mice against H5N1 challenge, indicating the effectiveness of the mosaic sequence without viral vectors for the development of a universal influenza vaccine. 2016 Journal of virology Abstract IV H5M 27 30 27194759 Mosaic H5 Hemagglutinin Provides Broad Humoral and Cellular Immune Responses against Influenza Viruses. In addition, MVA-H5M induced CD8(+) T cell responses that play a major role in heterosubtypic protection (H1N1). 2016 Journal of virology Abstract IV H5M 17 20 27194759 Mosaic H5 Hemagglutinin Provides Broad Humoral and Cellular Immune Responses against Influenza Viruses. The MVA-H5M also provided effective protection with no morbidity against H5N1 challenge, whereas MVA-HA-vaccinated mice showed clinical signs and experienced significant weight loss. 2016 Journal of virology Abstract IV H5M 8 11 HA 101 103 27194759 Mosaic H5 Hemagglutinin Provides Broad Humoral and Cellular Immune Responses against Influenza Viruses. This MVA-H5M construct protected mice against multiple clades of H5N1 and H1N1 viruses. 2016 Journal of virology Abstract IV H5M 9 12 27203354 Drug-Resistant and Genetic Evolutionary Analysis of Influenza Virus from Patients During the 2013 and 2014 Influenza Season in Beijing. All of the 23 samples with influenza A viruses harbored amantadine resistance mutation S31N in M2 matrix protein. 2017 Microbial drug resistance (Larchmont, N.Y.) Abstract IV S31N 87 91 M2;M 95;98 97;104 27203354 Drug-Resistant and Genetic Evolutionary Analysis of Influenza Virus from Patients During the 2013 and 2014 Influenza Season in Beijing. V241I, a compensatory NAI resistance mutation, was detected in all of the 19 A(H1N1)pdm09 viruses. 2017 Microbial drug resistance (Larchmont, N.Y.) Abstract IV V241I 0 5 NAI 22 25 27215706 Neuroinvasive influenza virus A(H5N8) in fattening ducks, Hungary, 2015. A number of unique or rarely detected amino acid changes was detected in the HA (T220I, R512G), the M2 (I39M), the NA (T211I), the NS1 (P85T), and the PB2 (I261V) proteins of the Hungarian strain. 2016 Infection, genetics and evolution Abstract IV T220I;R512G;I39M;T211I;P85T;I261V 81;88;104;119;136;156 86;93;108;124;140;161 HA;M2;NA;NS1;PB2 77;100;115;131;151 79;102;117;134;154 27226365 A Role of Influenza Virus Exposure History in Determining Pandemic Susceptibility and CD8+ T Cell Responses. Our study, however, identified potential CTL immune evasion from pH2N2 irrespective of age, within HLA-A*03:01(+) individuals for PB1471-L473V/N476I variants and HLA-B*15:01(+) population for NP404-414-V408I mutant. 2016 Journal of virology Abstract IV L473V;N476I;V408I 137;143;202 142;148;207 NP 192 194 27268229 Detection of reassortant avian influenza A (H11N9) virus in environmental samples from live poultry markets in China. The Asn30Asp and Thr215Ala substitutions in the M1 protein implied a potentially increased pathogenicity in mice. 2016 Infectious diseases of poverty Abstract IV N30D;T215A 4;17 12;26 M1 48 50 27309069 Susceptibility and Status of Avian Influenza in Ostriches. Ostriches maintain a low upper- to midtracheal temperature as part of their adaptive physiology for desert survival, which may explain the selection in ratites for E627K or its compensatory mutations-markers that facilitate AIV replication at lower temperatures. 2016 Avian diseases Abstract IV E627K 164 169 27309069 Susceptibility and Status of Avian Influenza in Ostriches. Seventeen of 27 (63%) ostrich viruses contained the polymerase basic 2 (PB2) E627K marker, and 2 of the ostrich isolates that lacked E627K contained the compensatory Q591K mutation, whereas a third virus had a D701N mutation. 2016 Avian diseases Abstract IV E627K;E627K;Q591K;D701N 77;133;166;210 82;138;171;215 PB2 72 75 27336226 Influenza A(H1N1)pdm09 virus exhibiting enhanced cross-resistance to oseltamivir and peramivir due to a dual H275Y/G147R substitution, Japan, March 2016. An influenza A(H1N1)pdm09 virus carrying a G147R substitution in combination with an H275Y substitution in the neuraminidase protein, which confers cross-resistance to oseltamivir and peramivir, was detected from an immunocompromised inpatient in Japan, March 2016. 2016 Euro surveillance Abstract IV H275Y;G147R 85;43 90;48 111 124 27336226 Influenza A(H1N1)pdm09 virus exhibiting enhanced cross-resistance to oseltamivir and peramivir due to a dual H275Y/G147R substitution, Japan, March 2016. This dual H275Y/G147R mutant virus exhibited enhanced cross-resistance to both drugs compared with the single H275Y mutant virus and reduced susceptibility to zanamivir, although it showed normal inhibition by laninamivir. 2016 Euro surveillance Abstract IV G147R;H275Y;H275Y 16;10;110 21;15;115 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. The Gln387Lys mutation completely abolishes binding of the antibody to the HA stalk epitope. 2016 PLoS pathogens Abstract IV Q387K 4 13 HA 75 77 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. The other two mutations, Asp391Tyr and Asp391Gly, do not affect antibody binding at neutral pH and only slightly reduce binding at low pH. 2016 PLoS pathogens Abstract IV D391Y;D391G 25;39 34;48 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. The three resistant viruses harbor three different mutations in the HA stalk: (1) Gln387Lys; (2) Asp391Tyr; (3) Asp391Gly. 2016 PLoS pathogens Abstract IV Q387K;D391Y;D391G 82;97;112 91;106;121 HA 68 70 27369428 Genetic characterization of highly pathogenic avian influenza H5N1 viruses isolated from naturally infected pigeons in Egypt. Several unique mutations, not reported before in any Egyptian isolates, were detected in the internal genes (i.e., polymerase residues PB1-V3D, PB1-K363R, PA-A369V, and PA-V602I; nucleoprotein residue NP-R38K; and nonstructural protein residues NS1-D120N and NS2-F55C). 2016 Virus genes Abstract IV V3D;K363R;A369V;V602I;R38K;D120N;F55C 139;148;158;172;204;249;263 142;153;163;177;208;254;267 NP;NS1;NS2;NP;PA;PA;PB1;PB1 201;245;259;179;155;169;135;144 203;248;262;192;157;171;138;147 27374689 Persistent Infection of Drug-resistant Influenza A Virus during Chemotherapy for Malignant Lymphoma. Virological analyses revealed that he was infected with the NA inhibitor-resistant A (H3N2) virus possessing an R292K substitution in the NA protein. 2016 Internal medicine (Tokyo, Japan) Abstract IV R292K 112 117 NA;NA 60;138 62;140 27376632 Threonine 80 phosphorylation of non-structural protein 1 regulates the replication of influenza A virus by reducing the binding affinity with RIG-I. In further study, the T80E mutant decreased the binding capacity between NS1 and viral nucleoprotein (NP), leading to impaired viral ribonucleoprotein (vRNP)-mediated viral transcription. 2017 Cellular microbiology Abstract IV T80E 22 26 NP;NS1;NP 102;73;87 104;76;100 27376632 Threonine 80 phosphorylation of non-structural protein 1 regulates the replication of influenza A virus by reducing the binding affinity with RIG-I. The T80E (phosphomimetic) mutant attenuated virus replication, whereas the T80A (non-phosphorylatable) mutant did not. 2017 Cellular microbiology Abstract IV T80E;T80A 4;75 8;79 27376632 Threonine 80 phosphorylation of non-structural protein 1 regulates the replication of influenza A virus by reducing the binding affinity with RIG-I. The T80E mutant was also unable to inhibit interferon (IFN) production by reducing the binding affinity between NS1 and retinoic acid-induced gene 1 protein (RIG-I), causing attenuation of virus replication. 2017 Cellular microbiology Abstract IV T80E 4 8 NS1 112 115 27380821 Genetic analysis of neuraminidase gene of influenza A(H1N1)pdm09 virus circulating in Southwest India from 2009 to 2012. Similarly, mutations in the antigenic sites (K217E, K254E, V267A, and D451E except I263V) are discussed for the first time through this article. 2017 Journal of medical virology Abstract IV K217E;K254E;V267A;D451E;I263V 45;52;59;70;83 50;57;64;75;88 27380821 Genetic analysis of neuraminidase gene of influenza A(H1N1)pdm09 virus circulating in Southwest India from 2009 to 2012. The catalytic site consisting of 8 functional and 11 framework residues were found conserved in 20 isolates and mutated in three (E228G, E278G, and N295T) isolates. 2017 Journal of medical virology Abstract IV E228G;E278G;N295T 130;137;148 135;142;153 27384648 Prevailing PA Mutation K356R in Avian Influenza H9N2 Virus Increases Mammalian Replication and Pathogenicity. Avian H9N2 virus with the PA-K356R mutation in human A549 cells showed increased nuclear accumulation of PA and increased viral polymerase activity that resulted in elevated levels of viral transcription and virus output. 2016 Journal of virology Abstract IV K356R 29 34 PA;PA 26;105 28;107 27384648 Prevailing PA Mutation K356R in Avian Influenza H9N2 Virus Increases Mammalian Replication and Pathogenicity. In addition, combined mutation of PA-K356R and PB2-E627K, a well-known mammalian adaptive marker, in the H9N2 virus showed further cooperative increases in virus production and severity of infection in vitro and in vivo In summary, PA-K356R behaves as a novel mammalian tropism mutation, which, along with other mutations such as PB2-E627K, might render avian H9N2 viruses adapted for human infection. 2016 Journal of virology Abstract IV K356R;E627K;K356R;E627K 37;51;235;334 42;56;240;339 PA;PA;PB2;PB2 34;232;47;330 36;234;50;333 27384648 Prevailing PA Mutation K356R in Avian Influenza H9N2 Virus Increases Mammalian Replication and Pathogenicity. This study reports a novel and predominant mammalian adaptive mutation, PA-K356R, in avian H9N2 viruses and human isolates of emergent H7N9 and H10N8 viruses. 2016 Journal of virology Abstract IV K356R 75 80 PA 72 74 27384648 Prevailing PA Mutation K356R in Avian Influenza H9N2 Virus Increases Mammalian Replication and Pathogenicity. We found that PA mutation K356R (PA-K356R) has become predominant since 2014 in avian H9N2 viruses in China as with seasonal human H1N1 viruses. 2016 Journal of virology Abstract IV K356R;K356R 26;36 31;41 PA;PA 14;33 16;35 27384648 Prevailing PA Mutation K356R in Avian Influenza H9N2 Virus Increases Mammalian Replication and Pathogenicity. We found that PA-356R in H9N2 viruses causes significant increases in virus replication and severity of infection in human cells and mice and that PA-K356R cooperates with the PB2-E627K mutation, a well-characterized human adaptive marker, to exacerbate mammalian infection in vitro and in vivo Therefore, the PA-K356R mutation is a significant adaptation in H9N2 viruses and related H7N9 and H10N8 reassortants toward human infectivity. 2016 Journal of virology Abstract IV K356R;E627K;K356R 150;180;313 155;185;318 PA;PA;PA;PB2 14;147;310;176 16;149;312;179 27384648 Prevailing PA Mutation K356R in Avian Influenza H9N2 Virus Increases Mammalian Replication and Pathogenicity. We further demonstrated the mammalian adaptive functionality of the PA-K356R mutation. 2016 Journal of virology Abstract IV K356R 71 76 PA 68 70 27385729 Pharmacological Characterization of the Spectrum of Antiviral Activity and Genetic Barrier to Drug Resistance of M2-S31N Channel Blockers. Among a handful of drug-resistant mutants, M2-S31N is the predominant mutation and persists in more than 95% of currently circulating influenza A strains. 2016 Molecular pharmacology Abstract IV S31N 46 50 M2 43 45 27385729 Pharmacological Characterization of the Spectrum of Antiviral Activity and Genetic Barrier to Drug Resistance of M2-S31N Channel Blockers. In addition, M2-S31N inhibitors display a higher in vitro genetic barrier to drug resistance than amantadine. 2016 Molecular pharmacology Abstract IV S31N 16 20 M2 13 15 27385729 Pharmacological Characterization of the Spectrum of Antiviral Activity and Genetic Barrier to Drug Resistance of M2-S31N Channel Blockers. In this report, we evaluated the therapeutic potential of these two classes of M2-S31N inhibitors (WJ379 and BC035) by profiling their antiviral efficacy against multidrug-resistant influenza A viruses, in vitro drug resistance barrier, and synergistic effect with oseltamivir. 2016 Molecular pharmacology Abstract IV S31N 82 86 M2 79 81 27385729 Pharmacological Characterization of the Spectrum of Antiviral Activity and Genetic Barrier to Drug Resistance of M2-S31N Channel Blockers. Overall, these results reaffirm that M2-S31N inhibitors are promising antiviral drug candidates that warrant further development. 2016 Molecular pharmacology Abstract IV S31N 40 44 M2 37 39 27385729 Pharmacological Characterization of the Spectrum of Antiviral Activity and Genetic Barrier to Drug Resistance of M2-S31N Channel Blockers. We found that M2-S31N inhibitors were active against several influenza A viruses that are resistant to one or both classes of Food and Drug Administration-approved anti-influenza drugs. 2016 Molecular pharmacology Abstract IV S31N 17 21 M2 14 16 27385729 Pharmacological Characterization of the Spectrum of Antiviral Activity and Genetic Barrier to Drug Resistance of M2-S31N Channel Blockers. We recently designed two classes of M2-S31N inhibitors, S31N-specific inhibitors and S31N/WT dual inhibitors, which are represented by N-[(5-cyclopropyl-1,2-oxazol-3-yl)methyl]adamantan-1-amine (WJ379) and N-[(5-bromothiophen-2-yl)methyl]adamantan-1-amine (BC035), respectively. 2016 Molecular pharmacology Abstract IV S31N;S31N;S31N 39;56;85 43;60;89 M2 36 38 27405392 G45R mutation in the nonstructural protein 1 of A/Puerto Rico/8/1934 (H1N1) enhances viral replication independent of dsRNA-binding activity and type I interferon biology. As G45R/NS1 virus induced the type I IFN induction and response in infected A549 cells, it is also interesting to investigate virus virulence for further studies. 2016 Virology journal Abstract IV G45R 3 7 NS1 8 11 27405392 G45R mutation in the nonstructural protein 1 of A/Puerto Rico/8/1934 (H1N1) enhances viral replication independent of dsRNA-binding activity and type I interferon biology. G45R/NS1 slightly decreased NS1 binding to dsRNA but did not interfere with its suppression of RIG-I-mediated type I IFN production. 2016 Virology journal Abstract IV G45R 0 4 NS1;NS1 5;28 8;31 27405392 G45R mutation in the nonstructural protein 1 of A/Puerto Rico/8/1934 (H1N1) enhances viral replication independent of dsRNA-binding activity and type I interferon biology. Likewise, replication of G45R/NS1 virus was increased in comparison to wild type virus in both wild type and type I interferon receptor null Let1 cells. 2016 Virology journal Abstract IV G45R 25 29 NS1 30 33 27405392 G45R mutation in the nonstructural protein 1 of A/Puerto Rico/8/1934 (H1N1) enhances viral replication independent of dsRNA-binding activity and type I interferon biology. RESULTS: The G45R mutation in the NS1 of PR8 (G45R/NS1) virus is critical for the enhanced viral replication in A549 cells. 2016 Virology journal Abstract IV G45R;G45R 13;46 17;50 NS1;NS1 34;51 37;54 27405649 Identification of specific residues in avian influenza A virus NS1 that enhance viral replication and pathogenicity in mammalian systems. Here, we show that efficient replication of FPV-NSMA-derived mutants was linked to the presence of a single substitution (D74N) and more prominently to a triple substitution (P3S+R41K+D74N) in the NS1MA protein. 2016 The Journal of general virology Abstract IV P3S;D74N;D74N;R41K 175;122;184;179 178;126;188;183 NS 197 199 27413002 Pulmonary changes in Norwegian fatal cases of pandemic influenza H1N1 (2009) infection: a morphologic and molecular genetic study. In addition to a possible role for the HA D222G mutation, our findings indicate that host factors and underlying conditions in the infected individuals are fundamental for disease outcome in many cases. 2016 Influenza and other respiratory viruses Abstract IV D222G 42 47 HA 39 41 27413002 Pulmonary changes in Norwegian fatal cases of pandemic influenza H1N1 (2009) infection: a morphologic and molecular genetic study. The HA D222G mutation was detected in six cases, 3 of which had no underlying illness. 2016 Influenza and other respiratory viruses Abstract IV D222G 7 12 HA 4 6 27440882 Reversion of Cold-Adapted Live Attenuated Influenza Vaccine into a Pathogenic Virus. Sequencing of the variant identified seven nonsynonymous mutations, PB1-E51K, PB1-I171V, PA-N350K, PA-L366I, NP-N125Y, NP-V186I, and NS2-G63E. 2016 Journal of virology Abstract IV E51K;I171V;N350K;L366I;N125Y;V186I;G63E 72;82;92;102;112;122;137 76;87;97;107;117;127;141 NP;NP;NS2;PA;PA;PB1;PB1 109;119;133;89;99;68;78 111;121;136;91;101;71;81 27440889 Unmasking Stem-Specific Neutralizing Epitopes by Abolishing N-Linked Glycosylation Sites of Influenza Virus Hemagglutinin Proteins for Vaccine Design. Only H5 N484A HA2 stem mutant protein immunization increased the numbers of antibody-secreting cells, germinal center B cells, and memory B cells targeting the stem helix A epitopes in splenocytes. 2016 Journal of virology Abstract IV N484A 8 13 HA 14 16 27440889 Unmasking Stem-Specific Neutralizing Epitopes by Abolishing N-Linked Glycosylation Sites of Influenza Virus Hemagglutinin Proteins for Vaccine Design. Unmasking N-glycans in the HA2 stem region (H5 N484A and H1 N503A) was found to elicit more potent neutralizing antibody titers against homologous, heterologous, and heterosubtypic viruses. 2016 Journal of virology Abstract IV N484A;N503A 47;60 52;65 HA 27 29 27486041 Discovery of Potential, Non-Toxic Influenza Virus Inhibitor by Computational Techniques. However, S31N mutation in M2 proton channel diminishes the efficiency of rimantadine and creates resistance. 2014 Molecular informatics Abstract IV S31N 9 13 M2 26 28 27515172 Dynamic patterns of circulating influenza virus from 2005 to 2012 in Shandong Province, China. Influenza A(H1N1)pdm09 strains isolated in Shandong Province were characterized by an S203T mutation that is specific to clade 7 isolates. 2016 Archives of virology Abstract IV S203T 86 91 27525812 Novel residues in the PA protein of avian influenza H7N7 virus affect virulence in mammalian hosts. A mini-genome assay demonstrated that PA mutations P103H and S659L can cooperatively decrease polymerase activity. 2016 Virology Abstract IV P103H;S659L 51;61 56;66 PA 38 40 27525812 Novel residues in the PA protein of avian influenza H7N7 virus affect virulence in mammalian hosts. Actually, PA with double mutation P103H-S659L cannot sustain the generation of live virus by reverse genetics. 2016 Virology Abstract IV P103H;S659L 34;40 39;45 PA 10 12 27525812 Novel residues in the PA protein of avian influenza H7N7 virus affect virulence in mammalian hosts. In conclusion, we demonstrated that PA mutations P103H and S659L can cooperatively reduce polymerase activity and viral replication in mammalian cells and attenuate pathogenicity in mice. 2016 Virology Abstract IV P103H;S659L 49;59 54;64 PA 36 38 27535054 NS1 Protein Mutation I64T Affects Interferon Responses and Virulence of Circulating H3N2 Human Influenza A Viruses. Surprisingly, a previously unidentified mutation in the double-stranded RNA (dsRNA)-binding domain (I64T) decreased NS1-mediated general inhibition of host protein synthesis by decreasing its interaction with cleavage and polyadenylation specificity factor 30 (CPSF30), leading to increased innate immune responses after viral infection. 2016 Journal of virology Abstract IV I64T 100 104 NS1 116 119 27539435 Identification of single amino acid substitutions (SAAS) in neuraminidase from influenza a virus (H1N1) via mass spectrometry analysis coupled with de novo peptide sequencing. RESULTS: LC-MS/MS analyses, coupled with manual de novo sequencing, allowed the determination of three amino acid substitutions: R346K, S349 N, and S370I/L, in the neuraminidase from the influenza virus (A/Puerto Rico/8/1934 H1N1), which were located in three mutated peptides of the neuraminidase: YGNGVWIGK, TKNHSSR, and PNGWTETDI/LK, respectively. 2016 Rapid communications in mass spectrometry Abstract IV R346K;S349N;S370I;S370L 129;136;148;148 134;142;155;155 NA;NA 164;284 177;297 27565992 Antiviral activity of KR-23502 targeting nuclear export of influenza B virus ribonucleoproteins. Interestingly, it was observed that proteasome-mediated degradation of M1(D54G) was attenuated by KR-23502. 2016 Antiviral research Abstract IV D54G 74 78 M1 71 73 27565992 Antiviral activity of KR-23502 targeting nuclear export of influenza B virus ribonucleoproteins. Moreover, a single mutation (aspartate to glycine) at amino acid position 54 in M1 [M1(D54G)] was detected after 18 passages in the presence of KR-23502 with a 2-fold increase in 50% effective concentration indicating that this compound has a relatively high genetic barrier to resistance. 2016 Antiviral research Abstract IV D54G 87 91 M1;M1 80;84 82;86 27572837 The hemifusion structure induced by influenza virus haemagglutinin is determined by physical properties of the target membranes. Here, influenza virus-like particles(4) carrying wild-type haemagglutinin or haemagglutinin hemifusion mutant G1S(5) and liposome mixtures were studied at low pH by Volta phase plate cryo-electron tomography, which improves the signal-to-noise ratio close to focus. 2016 Nature microbiology Abstract IV G1S 110 113 HA;HA 59;77 73;91 27572837 The hemifusion structure induced by influenza virus haemagglutinin is determined by physical properties of the target membranes. The rupture frequency and hemifusion diaphragm diameter were not affected by G1S mutation, but decreased when the cholesterol level in the liposomes was close to physiological concentrations. 2016 Nature microbiology Abstract IV G1S 77 80 27586413 Effects of hemagglutinin amino acid substitutions in H9 influenza A virus escape mutants. Four HA changes, S133N, T189A, N198D, and L226Q, were associated with a significant increase in HA thermostability compared to the wild-type virus. 2016 Archives of virology Abstract IV S133N;T189A;N198D;L226Q 17;24;31;42 22;29;36;47 HA;HA 5;96 7;98 27586413 Effects of hemagglutinin amino acid substitutions in H9 influenza A virus escape mutants. The N198S mutation significantly increased the optimum pH of fusion. 2016 Archives of virology Abstract IV N198S 4 9 27587808 H9N2 Influenza A Virus Isolated from a Greater White-Fronted Wild Goose (Anser albifrons) in Alaska Has a Mutation in the PB2 Gene, Which Is Associated with Pathogenicity in Human Pandemic 2009 H1N1. Both strains contain a G590S mutation in the polymerase basic 2 (PB2) gene, which is a pathogenicity marker in the pandemic 2009 H1N1 virus when combined with R591. 2016 Genome announcements Abstract IV G590S 23 28 PB2 65 68 27596738 Mutations at highly conserved residues in influenza A(H1N1)pdm09 virus affect neuraminidase activity. NA mutations N386K and P431S together or separately, and in the presence or absence of H275Y were further evaluated using recombinant influenza A/California/04/2009 (pH1N1) viruses containing single, double, or triple mutations. 2016 Virus research Abstract IV N386K;P431S;H275Y 13;23;87 18;28;92 0 2 27596738 Mutations at highly conserved residues in influenza A(H1N1)pdm09 virus affect neuraminidase activity. This study reports two amino acid substitutions (N386K and P431S) in the NA of the influenza A(H1N1)pdm09 virus that emerged in 2009 in Mexico. 2016 Virus research Abstract IV N386K;P431S 49;59 54;64 73 75 27596738 Mutations at highly conserved residues in influenza A(H1N1)pdm09 virus affect neuraminidase activity. Viral growth was reduced in the presence of mutation P431S alone or combined with N386K and/or H275Y. 2016 Virus research Abstract IV P431S;N386K;H275Y 53;82;95 58;87;100 27630240 Human Monoclonal Antibody 81.39a Effectively Neutralizes Emerging Influenza A Viruses of Group 1 and 2 Hemagglutinins. Among group 2 HA viruses tested, a single A(H7N9) virus was not neutralized at 50 mug/ml; it contained HA2-Asp19Gly, an amino acid position previously associated with resistance to neutralization by the group 2 HA-neutralizing MAb CR8020. 2016 Journal of virology Abstract IV D19G 107 115 HA;HA;HA 14;103;211 16;105;213 27630240 Human Monoclonal Antibody 81.39a Effectively Neutralizes Emerging Influenza A Viruses of Group 1 and 2 Hemagglutinins. Conversely, H9 viruses harboring HA2-Asp19Ala were fully susceptible to neutralization. 2016 Journal of virology Abstract IV D19A 37 45 HA 33 35 27630240 Human Monoclonal Antibody 81.39a Effectively Neutralizes Emerging Influenza A Viruses of Group 1 and 2 Hemagglutinins. Furthermore, 81.39a protected mice infected with A(H7N9) harboring HA2-Asp19Gly, although the antiviral effect was lessened. 2016 Journal of virology Abstract IV D19G 71 79 HA 67 69 27630240 Human Monoclonal Antibody 81.39a Effectively Neutralizes Emerging Influenza A Viruses of Group 1 and 2 Hemagglutinins. Notably, among group 1 HA viruses, H11-H13 and H16 subtypes were not neutralized at 50 mug/ml; they shared the substitution HA2-Asp19Asn/Ala. 2016 Journal of virology Abstract IV D19N 128 140 HA;HA 23;124 25;126 27654285 Influenza Virus Susceptibility of Wild-Derived CAST/EiJ Mice Results from Two Amino Acid Changes in the MX1 Restriction Factor. Especially the A222V mutation reduced GTPase activity of purified MX1 and diminished the inhibitory effect of MX1 in influenza A virus polymerase activity assays. 2016 Journal of virology Abstract IV A222V 15 20 27654285 Influenza Virus Susceptibility of Wild-Derived CAST/EiJ Mice Results from Two Amino Acid Changes in the MX1 Restriction Factor. Further, MX1 protein was substantially less abundant in organs of interferon-treated mice carrying the CAST Mx1 allele than in those of mice carrying the A2G Mx1 allele. 2016 Journal of virology Abstract IV A2G 154 157 27654285 Influenza Virus Susceptibility of Wild-Derived CAST/EiJ Mice Results from Two Amino Acid Changes in the MX1 Restriction Factor. Sequencing revealed that CAST-derived MX1 differs from A2G-derived MX1 by two amino acids (G83R and A222V) in the GTPase domain. 2016 Journal of virology Abstract IV A2G;G83R;A222V 55;91;100 58;95;105 27654285 Influenza Virus Susceptibility of Wild-Derived CAST/EiJ Mice Results from Two Amino Acid Changes in the MX1 Restriction Factor. The interferon-regulated Mx1 gene of the A2G mouse strain confers a high degree of resistance against influenza A and Thogoto viruses. 2016 Journal of virology Abstract IV A2G 41 44 27654293 Resistance to Mutant Group 2 Influenza Virus Neuraminidases of an Oseltamivir-Zanamivir Hybrid Inhibitor. A previous report showed that an N2 E119V/I222L dual mutant conferred drug resistance to seasonal influenza virus. 2016 Journal of virology Abstract IV E119V;I222L 36;42 41;47 27654293 Resistance to Mutant Group 2 Influenza Virus Neuraminidases of an Oseltamivir-Zanamivir Hybrid Inhibitor. We further elucidate the molecular mechanism underlying N2 drug resistance by solving crystal structures of the N2 E119V and I222L mutants and the dual mutant. 2016 Journal of virology Abstract IV E119V;I222L 115;125 120;130 27657178 Discovery of Potent Antivirals against Amantadine-Resistant Influenza A Viruses by Targeting the M2-S31N Proton Channel. In this study, we report the development of a late-stage diversification strategy for the expeditious synthesis of M2-S31N inhibitors. 2016 ACS infectious diseases Abstract IV S31N 118 122 M2 115 117 27657178 Discovery of Potent Antivirals against Amantadine-Resistant Influenza A Viruses by Targeting the M2-S31N Proton Channel. Several M2-S31N inhibitors were identified to have potent M2-S31N channel blockage and micromolar antiviral efficacy against several M2-S31N-containing influenza A viruses. 2016 ACS infectious diseases Abstract IV S31N;S31N;S31N 11;61;136 15;65;140 M2;M2;M2 8;58;133 10;60;135 27657178 Discovery of Potent Antivirals against Amantadine-Resistant Influenza A Viruses by Targeting the M2-S31N Proton Channel. We chose the influenza A virus M2-S31N mutant proton channel as the drug target to address this need as it is one of the most conserved viral proteins and persist in >95% of currently circulating influenza A viruses. 2016 ACS infectious diseases Abstract IV S31N 34 38 M2 31 33 27658193 Sensitive Detection and Simultaneous Discrimination of Influenza A and B Viruses in Nasopharyngeal Swabs in a Single Assay Using Next-Generation Sequencing-Based Diagnostics. Of the influenza A viruses, 66.7% of A(H3N2) viruses tested had a E627K mutation in the PB2 protein, and 87.8% of the influenza A viruses contained the S31N mutation in the M2 protein. 2016 PloS one Abstract IV E627K;S31N 66;152 71;156 M2;PB2 173;88 175;91 27659246 Platform for determining the inhibition profile of neuraminidase inhibitors in an influenza virus N1 background. Besides confirming the inhibition profile of zanamivir and oseltamivir, the distinct effect of I427Q/M on the activity of both NAIs was shown. 2016 Journal of virological methods Abstract IV I427M;I427Q 95;95 102;102 NAI 127 131 27659246 Platform for determining the inhibition profile of neuraminidase inhibitors in an influenza virus N1 background. Employing reverse genetics, a set of influenza virus variants containing an amino acid substitution associated with oseltamivir resistance in N1 isolates (H274Y, N294S, Y155H or Q136L) was generated. 2016 Journal of virological methods Abstract IV H274Y;N294S;Y155H;Q136L 155;162;169;178 160;167;174;183 27659246 Platform for determining the inhibition profile of neuraminidase inhibitors in an influenza virus N1 background. For 5-amidino and 5-guanidino analogs of oseltamivir a significantly stronger inhibition of virus variants carrying a NA-H274Y was confirmed, and additionally shown for NA-N294S and NA-Y155H substitutions as compared to the parent compound. 2016 Journal of virological methods Abstract IV H274Y;N294S;Y155H 121;172;185 126;177;190 NA;NA;NA 118;169;182 120;171;184 27659246 Platform for determining the inhibition profile of neuraminidase inhibitors in an influenza virus N1 background. In parallel, so far unreported mutations of I427 (I427Q and I427M) were investigated. 2016 Journal of virological methods Abstract IV I427Q;I427M 50;60 55;65 27659246 Platform for determining the inhibition profile of neuraminidase inhibitors in an influenza virus N1 background. Novel NAIs should in particular be also effective against seasonal and/or pandemic N1 that carry a H274Y or N294S substitution (N2 numbering), which are most commonly linked to oseltamivir resistance. 2016 Journal of virological methods Abstract IV H274Y;N294S 99;108 104;113 NAI 6 10 27663652 Amino acid substitutions involved in the adaptation of a novel highly pathogenic H5N2 avian influenza virus in mice. FINDINGS: Amino acid changes were identified in the MA-DK19 PB2 (E627K), PB1 (I181T), HA (A150S), NS1 (seven amino acid extension "WRNKVAD" at the C-terminal), and NS2 (E69G) proteins. 2016 Virology journal Abstract IV E627K;I181T;A150S;E69G;extension "WRNKVAD" 65;78;90;169;120 70;83;95;173;139 HA;NS1;NS2;PB1;PB2 86;98;164;73;60 88;101;167;76;63 27664027 G45R on nonstructural protein 1 of influenza A virus contributes to virulence by increasing the expression of proinflammatory cytokines in mice. In A549 cells, the majority of G45R/NS1 protein was localized in the cytoplasm whereas the majority of WT/NS1 protein was localized in the nucleus. 2017 Archives of virology Abstract IV G45R 31 35 NS1;NS1 36;106 39;109 27664027 G45R on nonstructural protein 1 of influenza A virus contributes to virulence by increasing the expression of proinflammatory cytokines in mice. In this study, we investigated the effect of the amino acid substitution G45R on the NS1 of A/Puerto Rico/8/1934 (H1N1) (G45R/NS1) on viral virulence and host gene expression in a mouse model and the human lung cell line A549. 2017 Archives of virology Abstract IV G45R;G45R 73;121 77;125 NS1;NS1 85;126 88;129 27664027 G45R on nonstructural protein 1 of influenza A virus contributes to virulence by increasing the expression of proinflammatory cytokines in mice. Mice infected with the G45R/NS1 virus lost more body weight and had lower survival rates than mice infected with the wild type (WT/NS1) virus. 2017 Archives of virology Abstract IV G45R 23 27 NS1;NS1 28;131 31;134 27664027 G45R on nonstructural protein 1 of influenza A virus contributes to virulence by increasing the expression of proinflammatory cytokines in mice. Microarray analysis revealed that A549 cells infected with the G45R/NS1 virus had higher expression of genes encoding proteins associated with the innate immune response and cytokine activity than cells infected with the WT/NS1 virus. 2017 Archives of virology Abstract IV G45R 63 67 NS1;NS1 68;224 71;227 27664027 G45R on nonstructural protein 1 of influenza A virus contributes to virulence by increasing the expression of proinflammatory cytokines in mice. Our findings suggest that G45R on NS1 protein contributes to viral virulence by increasing the expression of inflammatory cytokines early in infection. 2017 Archives of virology Abstract IV G45R 26 30 NS1 34 37 27664027 G45R on nonstructural protein 1 of influenza A virus contributes to virulence by increasing the expression of proinflammatory cytokines in mice. Replication of the G45R/NS1 virus was higher than that of the WT/NS1 virus in vitro, but the replication of both viruses was similar in mouse lungs. 2017 Archives of virology Abstract IV G45R 19 23 NS1;NS1 24;65 27;68 27664027 G45R on nonstructural protein 1 of influenza A virus contributes to virulence by increasing the expression of proinflammatory cytokines in mice. The G45R/NS1 virus had increased virulence by inducing an earlier and robust proinflammatory cytokine response in mice. 2017 Archives of virology Abstract IV G45R 4 8 NS1 9 12 27713074 An influenza A virus (H7N9) anti-neuraminidase monoclonal antibody with prophylactic and therapeutic activity in vivo. Affinity analysis also revealed that 3c10-3 binds equally well to recombinant NA of wild-type A/Anhui/1/2013 and to a variant NA carrying a R289K mutation known to infer NAI resistance. 2016 Antiviral research Abstract IV R289K 140 145 NA;NA;NAI 78;126;170 80;128;173 27714494 Role of R292K mutation in influenza H7N9 neuraminidase toward oseltamivir susceptibility: MD and MM/PB(GB)SA study. However, some H7N9 strains that have been isolated from patient after drug treatment have a R292K mutation in neuraminidase. 2016 Journal of computer-aided molecular design Abstract IV R292K 92 97 110 123 27714494 Role of R292K mutation in influenza H7N9 neuraminidase toward oseltamivir susceptibility: MD and MM/PB(GB)SA study. In addition, oseltamivir does not bind well to the R292K mutant complex as shown by the high degree of fluctuation in ligand RMSD during the simulation and the change in angular distribution of bulky side chain groups. 2016 Journal of computer-aided molecular design Abstract IV R292K 51 56 27714496 Community- and hospital-acquired infections with oseltamivir- and peramivir-resistant influenza A(H1N1)pdm09 viruses during the 2015-2016 season in Japan. Overall, the prevalence of the H275Y A(H1N1)pdm09 viruses was 1.8 % (5/282). 2017 Virus genes Abstract IV H275Y 31 36 27714496 Community- and hospital-acquired infections with oseltamivir- and peramivir-resistant influenza A(H1N1)pdm09 viruses during the 2015-2016 season in Japan. The resistant viruses possessed the V241I, N369 K, and N386 K substitutions in the NA that have been previously reported among A(H1N1)pdm09 to alter transmission fitness. 2017 Virus genes Abstract IV V241I;N369K;N386K 36;43;55 41;49;61 83 85 27714496 Community- and hospital-acquired infections with oseltamivir- and peramivir-resistant influenza A(H1N1)pdm09 viruses during the 2015-2016 season in Japan. We report five cases of community- and hospital-acquired infections with oseltamivir- and peramivir-resistant A(H1N1)pdm09 viruses possessing the neuraminidase (NA) H275Y mutation during January-February 2016 in Japan. 2017 Virus genes Abstract IV H275Y 165 170 NA;NA 161;146 163;159 27733236 Risk of resistant avian influenza A virus in wild waterfowl as a result of environmental release of oseltamivir. In an A(H1N1)/H274Y virus, the OC resistance mutation persisted without selective drug pressure, demonstrating the potential of an IAV with a permissive genetic background to acquire and maintain OC resistance, potentially allowing circulation of the resistant variant among wild birds. 2016 Infection ecology & epidemiology Abstract IV H274Y 14 19 27741319 Cross-Neutralising Nanobodies Bind to a Conserved Pocket in the Hemagglutinin Stem Region Identified Using Yeast Display and Deep Mutational Scanning. In addition, our deep sequence analysis predicted that binding to the emerging H1N1 strain (A/Christchurch/16/2010) carrying the HA2-E47K mutation would not affect binding was confirmed experimentally. 2016 PloS one Abstract IV E47K 133 137 HA 129 131 27741319 Cross-Neutralising Nanobodies Bind to a Conserved Pocket in the Hemagglutinin Stem Region Identified Using Yeast Display and Deep Mutational Scanning. We have shown that a D46N mutation in the HA2 stem domain uniquely interferes with binding of R2b-E8. 2016 PloS one Abstract IV D46N 21 25 HA 42 44 27805571 Pharmacokinetics and safety of intravenous peramivir, neuraminidase inhibitor of influenza virus, in healthy Japanese subjects. The peramivir plasma and upper respiratory tract fluid levels were significantly higher than the 50% inhibition concentrations for NA enzyme activity (IC50) of epidemic influenza viruses, including those harbouring the H274Y mutation. 2017 Antiviral therapy Abstract IV H274Y 219 224 131 133 27816637 Co-expression of sialic acid receptors compatible with avian and human influenza virus binding in emus (Dromaius novaehollandiae). Since 2006, several reports of IAV isolations from emus have surfaced and avian influenza infection of emus can lead to the selection of mammalian like PB2-E627K and PB2-D701N mutants. 2017 Virology Abstract IV E627K;D701N 156;170 161;175 PB2;PB2 152;166 155;169 IV infections 80 99 27830688 [Changes in the phenotypic properties of highly pathogenic influenza A virus of H5N1 subtype induced by N186I and N186T point mutations in hemagglutinin]. N186I and N186T mutations in the HA protein increased the virulence of the original virus in mice. 2016 Molekuliarnaia biologiia Abstract IV N186I;N186T 0;10 5;15 HA 33 35 27849220 Surveillance of antiviral resistance markers in Argentina: detection of E119V neuraminidase mutation in a post-treatment immunocompromised patient. One of the most frequent substitutions in the neuraminidase (NA) protein of influenza A(H3N2) viruses during or soon after oseltamivir administration is E119V mutation. 2016 Memorias do Instituto Oswaldo Cruz Abstract IV E119V 153 158 NA;NA 61;46 63;59 27849220 Surveillance of antiviral resistance markers in Argentina: detection of E119V neuraminidase mutation in a post-treatment immunocompromised patient. Out of 888 A(H3N2) samples, 842 were tested for the E119V substitution by quantitative RT-PCR: 841 A(H3N2) samples had the wild-type E119 genotype and in one sample, a mixture of viral E119/ V119 subpopulations was detected. 2016 Memorias do Instituto Oswaldo Cruz Abstract IV E119V 52 57 27849220 Surveillance of antiviral resistance markers in Argentina: detection of E119V neuraminidase mutation in a post-treatment immunocompromised patient. We describe the emergence of a mixed viral population with the E119E/V mutation in the NA protein sequence in a post-treatment influenza sample collected from an immunocompromised patient in Argentina. 2016 Memorias do Instituto Oswaldo Cruz Abstract IV E119E;E119V 63;63 70;70 87 89 2786093 Class II-restricted T-cell clones to a synthetic peptide of influenza virus hemagglutinin differ in their fine specificities and in the ability to respond to virus. The response of the clones to peptide analogs identified certain residues within the sites that were critical for recognition, with the substitution Gln-311----Ser having a differential effect on clones responding to the N-terminal site. 1989 Journal of virology Abstract IV Q311S 149 163 27862840 Differential nucleocytoplasmic shuttling of the nucleoprotein of influenza a viruses and association with host tropism. In addition, an F253I substitution in the NP of WSN altered the survival ratio of infected mice and the growth curve in infected avian-origin cells (DF-1). 2017 Cellular microbiology Abstract IV F253I 16 21 NP 42 44 27862840 Differential nucleocytoplasmic shuttling of the nucleoprotein of influenza a viruses and association with host tropism. The current data indicate that the F253I mutation results in attenuated pathogenicity of the virus in mice and altered cell tropism. 2017 Cellular microbiology Abstract IV F253I 35 40 27869615 Highly Pathogenic Influenza A(H5Nx) Viruses with Altered H5 Receptor-Binding Specificity. In contrast to ancestral clade 2.3.4 H5 proteins, novel clade 2.3.4.4 H5 proteins bind to fucosylated sialosides because of substitutions K222Q and S227R, which are unique for highly pathogenic influenza virus H5 proteins. 2017 Emerging infectious diseases Abstract IV K222Q;S227R 138;148 143;153 27869615 Highly Pathogenic Influenza A(H5Nx) Viruses with Altered H5 Receptor-Binding Specificity. North American clade 2.3.4.4 virus isolates have retained only the K222Q substitution but still bind fucosylated sialosides. 2017 Emerging infectious diseases Abstract IV K222Q 67 72 27886255 Amino acid substitutions V63I or A37S/I61T/V63I/V100A in the PA N-terminal domain increase the virulence of H7N7 influenza A virus. Collectively, our findings demonstrated that the PA-Nter substitutions V63I and Mfour enhanced IAV pathogenicity through modification of the polymerase activity and the endonuclease activity, which added to the evolving knowledge of IAV virulence determinants. 2016 Scientific reports Abstract IV V63I 71 75 PA 49 51 27886255 Amino acid substitutions V63I or A37S/I61T/V63I/V100A in the PA N-terminal domain increase the virulence of H7N7 influenza A virus. Here we identified PA-Nter substitutions A37S, I61T, V63I and V100A in recently emerged avian influenza A viruses (IAVs) with potential effect on virus pathogenicity and/or host adaptation. 2016 Scientific reports Abstract IV A37S;I61T;V63I;V100A 41;47;53;62 45;51;57;67 PA 19 21 27886255 Amino acid substitutions V63I or A37S/I61T/V63I/V100A in the PA N-terminal domain increase the virulence of H7N7 influenza A virus. Notably, substitutions V63I and Mfour strongly increased virus replication and virulence in mice. 2016 Scientific reports Abstract IV V63I 23 27 27886255 Amino acid substitutions V63I or A37S/I61T/V63I/V100A in the PA N-terminal domain increase the virulence of H7N7 influenza A virus. Our results showed that single substitution V63I and combined substitutions, I61T/V63I and A37S/I61T/V63I/V100A (Mfour), significantly increased virus growth capacity in mammalian cells. 2016 Scientific reports Abstract IV V63I;I61T;V63I;A37S;I61T;V100A;V63I 44;77;82;91;96;106;101 48;81;86;95;100;111;105 27889648 PB2 substitutions V598T/I increase the virulence of H7N9 influenza A virus in mammals. Notably, the PB2-V598T/I substitutions substantially increased virus replication and virulence in mice. 2017 Virology Abstract IV V598T;V598I 17;17 24;24 PB2 13 16 27889648 PB2 substitutions V598T/I increase the virulence of H7N9 influenza A virus in mammals. To evaluate the biological significance of these substitutions, PB2-K389R and -V598T/I mutant viruses of avian H7N9 IAVs were generated by reverse genetics. 2017 Virology Abstract IV K389R;V598T;V598I 68;79;79 73;86;86 PB2 64 67 27889648 PB2 substitutions V598T/I increase the virulence of H7N9 influenza A virus in mammals. Together, we demonstrated that the substitutions PB2-V598T/I contributed to higher IAV replication and virulence in mammals, which added to the knowledge of IAV virulence determinants and benefited the surveillance of IAVs. 2017 Virology Abstract IV V598T;V598I 53;53 60;60 PB2 49 52 27902899 Endemic Variation of H9N2 Avian Influenza Virus in China. A total of 96.8% (337/348) of the viruses had three amino-acid deletions at 63-65 in the NA stalk, associated with enhanced virulence in chickens and mice; 97.1% (338/348) of M2 proteins had the S31N mutation associated with adamantane resistance in humans. 2016 Avian diseases Abstract IV S31N 195 199 M2;NA 175;89 177;91 27902899 Endemic Variation of H9N2 Avian Influenza Virus in China. Meanwhile, 99.6% (443/445) of lineage 9.4.2.5 viruses had PSRSSR GLF instead of PARSSR GLF motifs in the HA cleavage sites; 98.2% (444/452) of HA genes showed human receptor binding associated mutation Q226L. 2016 Avian diseases Abstract IV Q226L 202 207 HA;HA 105;143 107;145 27914930 Biological fitness and natural selection of amantadine resistant variants of avian influenza H5N1 viruses. Here, using reverse genetics we investigated the biological impact of Ser31Asn in M2 commonly seen in viruses in clade 2.2.1.1 in farmed poultry in Egypt. 2017 Virus research Abstract IV S31N 70 78 M2 82 84 27914930 Biological fitness and natural selection of amantadine resistant variants of avian influenza H5N1 viruses. The prevalence of the amantadine resistance marker at position 31 (Ser31Asn) of the M2 protein increased over time. 2017 Virus research Abstract IV S31N 67 75 M2 84 86 27926816 Identification of polymerase gene mutations that affect viral replication in H5N1 influenza viruses isolated from pigeons. In contrast, the PB2-K627E and PA-K158R mutations had moderate effects: PB2-K627E decreased and PA-K158R increased polymerase activity. 2017 The Journal of general virology Abstract IV K627E;K158R;K627E;K158R 21;34;76;99 26;39;81;104 PA;PA;PB2;PB2 31;96;17;72 33;98;20;75 27926816 Identification of polymerase gene mutations that affect viral replication in H5N1 influenza viruses isolated from pigeons. Structural homology modelling indicated that the PB1-V3D residue was located in the PB1 core region that interacts with PA, predicting that the PB1 mutation would produce a stronger interaction between PB1 and PA that results in decreased replication of pigeon-derived H5N1 viruses. 2017 The Journal of general virology Abstract IV V3D 53 56 PA;PA;PB1;PB1;PB1;PB1 120;210;49;84;144;202 122;212;52;87;147;205 27926816 Identification of polymerase gene mutations that affect viral replication in H5N1 influenza viruses isolated from pigeons. The results showed that the PB1-V3D mutation significantly decreased polymerase activity and viral growth in both mammalian and avian cells. 2017 The Journal of general virology Abstract IV V3D 32 35 PB1 28 31 27933797 Nuclear Magnetic Resonance and Molecular Dynamics Simulation of the Interaction between Recognition Protein H7 of the Novel Influenza Virus H7N9 and Glycan Cell Surface Receptors. This highlighted aspects that could affect glycan-HA recognition, including the mutation H7 G228S, which increases H2 and H3 specificity for the human receptor. 2016 Biochemistry Abstract IV G228S 92 97 HA 50 52 27933932 Mechanism of the Pseudoirreversible Binding of Amantadine to the M2 Proton Channel. Finally, the results reveal that the thermodynamics and kinetics of Amt (un)binding is very sensitive to the V27A mutation, providing a quantitative rationale to the drastic decrease in inhibitory potency against the V27A variant. 2016 Journal of the American Chemical Society Abstract IV V27A;V27A 109;217 113;221 27933932 Mechanism of the Pseudoirreversible Binding of Amantadine to the M2 Proton Channel. To this end, we have investigated the binding of amantadine (Amt) to the wild type (wt) M2 channel and its V27A variant using multiple independent molecular dynamics simulations, exploratory conventional metadynamics, and multiple-walkers well-tempered metadynamics calculations. 2016 Journal of the American Chemical Society Abstract IV V27A 107 111 M2 88 90 27993855 Obatoclax Inhibits Alphavirus Membrane Fusion by Neutralizing the Acidic Environment of Endocytic Compartments. Characterization of escape mutants revealed that the L369I mutation in the SFV E1 fusion protein was sufficient to confer partial resistance against obatoclax. 2017 Antimicrobial agents and chemotherapy Abstract IV L369I 53 58 28003482 NS1 Protein Amino Acid Changes D189N and V194I Affect Interferon Responses, Thermosensitivity, and Virulence of Circulating H3N2 Human Influenza A Viruses. A recombinant A/Puerto Rico/8/34 (PR8) H1N1 virus encoding the H3N2 NS1-D189N protein was slightly attenuated, whereas the virus encoding the H3N2 NS1-V194I protein was further attenuated in mice. 2017 Journal of virology Abstract IV D189N;V194I 72;151 77;156 NS1;NS1 68;147 71;150 28003482 NS1 Protein Amino Acid Changes D189N and V194I Affect Interferon Responses, Thermosensitivity, and Virulence of Circulating H3N2 Human Influenza A Viruses. In fact, we showed that the virus encoding the H3N2 NS1-V194I protein demonstrated a temperature-sensitive (ts) phenotype, providing a most likely explanation for the stronger attenuation observed. 2017 Journal of virology Abstract IV V194I 56 61 NS1 52 55 28003482 NS1 Protein Amino Acid Changes D189N and V194I Affect Interferon Responses, Thermosensitivity, and Virulence of Circulating H3N2 Human Influenza A Viruses. Interestingly, a virus encoding the H3N2 NS1-V194I protein demonstrated a temperature-sensitive phenotype, further attenuating the virus in vivo. 2017 Journal of virology Abstract IV V194I 45 50 NS1 41 44 28003482 NS1 Protein Amino Acid Changes D189N and V194I Affect Interferon Responses, Thermosensitivity, and Virulence of Circulating H3N2 Human Influenza A Viruses. NS1 mutations D189N and V194I impaired the ability of the NS1 protein to inhibit general gene expression, and recombinant viruses harboring these mutations were attenuated in a mouse model of influenza infection. 2017 Journal of virology Abstract IV D189N;V194I 14;24 19;29 NS1;NS1 0;58 3;61 IV infections 192 211 28003482 NS1 Protein Amino Acid Changes D189N and V194I Affect Interferon Responses, Thermosensitivity, and Virulence of Circulating H3N2 Human Influenza A Viruses. The consequences of these mutations for the NS1-mediated inhibition of IFN responses and the pathogenesis of the virus were evaluated, showing that NS1 mutations D189N and V194I impaired the ability of the NS1 protein to inhibit general gene expression, most probably because these mutations decreased the binding of NS1 to the cleavage and polyadenylation specificity factor 30 (CPSF30). 2017 Journal of virology Abstract IV D189N;V194I 162;172 167;177 NS1;NS1;NS1;NS1 44;148;206;317 47;151;209;320 28004398 Detection of D151G/N mutations in the neuraminidase gene of influenza A (H3N2) viruses by real-time RT-PCR allelic discrimination assay. It is important to consider and exclude D151G/N mutants after isolation of influenza virus in MDCK cell line; since, the substitutions can highly influence the results of experimental research. 2017 Journal of medical virology Abstract IV D151G;D151N 40;40 47;47 28004398 Detection of D151G/N mutations in the neuraminidase gene of influenza A (H3N2) viruses by real-time RT-PCR allelic discrimination assay. NA-D151G/N-substitutions of influenza A (H3N2) viruses are frequently induced and selected by culturing in Madin-Darby canine kidney (MDCK) cell lines. 2017 Journal of medical virology Abstract IV D151G;D151N 3;3 10;10 0 2 28004398 Detection of D151G/N mutations in the neuraminidase gene of influenza A (H3N2) viruses by real-time RT-PCR allelic discrimination assay. The study aims to develop an allelic discrimination real-time reverse transcriptase polymerase chain reaction (RT-PCR) for the screening of D151G/N mutants. 2017 Journal of medical virology Abstract IV D151G;D151N 140;140 147;147 28004398 Detection of D151G/N mutations in the neuraminidase gene of influenza A (H3N2) viruses by real-time RT-PCR allelic discrimination assay. Thirty-six influenza A (H3N2) virus isolates were included and screened for D151G/N mutants using allelic discrimination assay. 2017 Journal of medical virology Abstract IV D151G;D151N 76;76 83;83 28008819 Effects of PB1-F2 on the pathogenicity of H1N1 swine influenza virus in mice and pigs. KS07_K/O showed similar pathogenicity in mice to the KS07_WT, whereas KS07_N66S displayed enhanced virulence when compared to the other two viruses. 2017 The Journal of general virology Abstract IV N66S 75 79 28008819 Effects of PB1-F2 on the pathogenicity of H1N1 swine influenza virus in mice and pigs. Using reverse genetics, we generated the wild-type KS07 (KS07_WT), a PB1-F2 knockout mutant (KS07_K/O) and its N66S variant (KS07_N66S). 2017 The Journal of general virology Abstract IV N66S;N66S 111;130 115;134 PB1F2 69 75 28012921 Therapeutic efficacy of peramivir against H5N1 highly pathogenic avian influenza viruses harboring the neuraminidase H275Y mutation. Evaluation of the in vivo antiviral activity showed that a single intravenous treatment of peramivir (10 mg/kg) prevented lethality in mice infected with wild-type H5N1 virus and also following infection with H5N1 virus with the H275Y mutation after a 5 day administration of peramivir (30 mg/kg). 2017 Antiviral research Abstract IV H275Y 229 234 28012921 Therapeutic efficacy of peramivir against H5N1 highly pathogenic avian influenza viruses harboring the neuraminidase H275Y mutation. In H5N1 viruses containing the NA H275Y mutation, the antiviral activity of peramivir against the variant was lower than that against the wild-type. 2017 Antiviral research Abstract IV H275Y 34 39 31 33 28012921 Therapeutic efficacy of peramivir against H5N1 highly pathogenic avian influenza viruses harboring the neuraminidase H275Y mutation. These results suggest that peramivir has therapeutic activity against HPAI viruses even if the virus harbors the NA H275Y mutation. 2017 Antiviral research Abstract IV H275Y 116 121 113 115 28026814 [Prediction of selective inhibition of neuraminidase from various influenza virus strains by potential inhibitors]. It is based on known 3D data for neuraminidases from three influenza virus strains (A/Tokyo/3/67, A/tern/Australia/G70C/75, B/Lee/40) and modeling of 3D structure of neuraminidases from other strains (A/PR/8/34 e A/Aichi/2/68). 2016 Biomeditsinskaia khimiia Abstract IV G70C 115 119 NA;NA 33;166 47;180 28053101 Generation of a Genetically Stable High-Fidelity Influenza Vaccine Strain. Here, we describe the generation of a high-fidelity and high-growth influenza vaccine master virus strain with a single V43I amino acid change in the PB1 polymerase of the high-growth A/Puerto Rico/8/1934 (PR8) master virus. 2017 Journal of virology Abstract IV V43I 120 124 PB1 150 153 28053101 Generation of a Genetically Stable High-Fidelity Influenza Vaccine Strain. In order to compare the efficiency of egg adaptation and the occurrence of gene mutations leading to antigenic alterations, we constructed 6:2 genetic reassortant viruses between the A(H1N1)pdm09 and the PR8-PB1-V43I viruses; hemagglutinin (HA) and neuraminidase (NA) were from the A(H1N1)pdm09 virus, and the other genes were from the PR8 virus. 2017 Journal of virology Abstract IV V43I 212 216 HA;HA;NA;NA;PB1 241;226;264;249;208 243;239;266;262;211 28053101 Generation of a Genetically Stable High-Fidelity Influenza Vaccine Strain. Mutations responsible for egg adaptation mutations occurred in the HA of the PB1-V43I reassortant virus during serial egg passages; however, in contrast, antigenic mutations were introduced into the HA gene of the 6:2 reassortant virus possessing the wild-type PB1. 2017 Journal of virology Abstract IV V43I 81 85 HA;HA;PB1;PB1 67;199;77;261 69;201;80;264 28053101 Generation of a Genetically Stable High-Fidelity Influenza Vaccine Strain. The PB1-V43I mutation was introduced to increase replication fidelity in order to design an H1N1 vaccine strain with a low error rate. 2017 Journal of virology Abstract IV V43I 8 12 PB1 4 7 28053101 Generation of a Genetically Stable High-Fidelity Influenza Vaccine Strain. The PR8-PB1-V43I virus exhibited good replication compared with that of the parent PR8 virus. 2017 Journal of virology Abstract IV V43I 12 16 PB1 8 11 28053101 Generation of a Genetically Stable High-Fidelity Influenza Vaccine Strain. This study shows that the mutant PR8 virus possessing the PB1 polymerase with the V43I substitution may be utilized as a master virus for the generation of high-growth vaccine viruses with high polymerase fidelity, low error rates of gene replication, and reduced antigenic diversity during virus propagation in eggs for vaccine production.IMPORTANCE Vaccination represents the most effective prophylactic option against influenza. 2017 Journal of virology Abstract IV V43I 82 86 PB1 58 61 28084423 Single PA mutation as a high yield determinant of avian influenza vaccines. Of the four mutations, the PA E31K showed the greatest effect on the replication property of reverse genetically-rescued viruses. 2017 Scientific reports Abstract IV E31K 30 34 PA 27 29 28084423 Single PA mutation as a high yield determinant of avian influenza vaccines. Taken all together, our results suggest the PA E31K mutation as a single, substantial growth determinant of avian influenza CVVs and for the establishment of a high-yield avian influenza vaccine backbone. 2017 Scientific reports Abstract IV E31K 47 51 PA 44 46 28084423 Single PA mutation as a high yield determinant of avian influenza vaccines. The passaged CVV harbored the four amino acid mutations (R136K in PB2; E31K in PA; A172T in HA; and R80Q in M2) without changing its antigenicity, compared with the parental CVV. 2017 Scientific reports Abstract IV R136K;E31K;A172T;R80Q 57;71;83;100 62;75;88;104 HA;M2;PA;PB2 92;108;79;66 94;110;81;69 28084423 Single PA mutation as a high yield determinant of avian influenza vaccines. When applied to different avian influenza CVVs (H7N9 and H9N2 subtypes), the PA E31K mutation resulted in the increases of viral replication in the Vero cell again. 2017 Scientific reports Abstract IV E31K 80 84 PA 77 79 28087313 An M2-V27A channel blocker demonstrates potent in vitro and in vivo antiviral activities against amantadine-sensitive and -resistant influenza A viruses. Among the limited number of M2 mutants that confer amantadine resistance, the M2-V27A mutant was found to be the predominant mutant under drug selection pressure, thereby representing a high profile antiviral drug target. 2017 Antiviral research Abstract IV V27A 81 85 M2;M2 28;78 30;80 28087313 An M2-V27A channel blocker demonstrates potent in vitro and in vivo antiviral activities against amantadine-sensitive and -resistant influenza A viruses. Compound 3 not only had single to sub-micromolar EC50 values against M2-WT- and M2-V27A-containing influenza A viruses in antiviral assays, but also rescued mice from lethal viral infection by either M2-WT- or M2-V27A-containing influenza A viruses. 2017 Antiviral research Abstract IV V27A;V27A 83;213 87;217 M2;M2;M2;M2 69;80;200;210 71;82;202;212 28087313 An M2-V27A channel blocker demonstrates potent in vitro and in vivo antiviral activities against amantadine-sensitive and -resistant influenza A viruses. Guided by molecular dynamics simulations, we previously designed first-in-class M2-V27A inhibitors. 2017 Antiviral research Abstract IV V27A 83 87 M2 80 82 28087313 An M2-V27A channel blocker demonstrates potent in vitro and in vivo antiviral activities against amantadine-sensitive and -resistant influenza A viruses. One of the potent lead compounds, spiroadamantane amine (3), inhibits both the M2-WT and M2-V27A mutant with IC50 values of 18.7 and 0.3 muM, respectively, in in vitro electrophysiological assays. 2017 Antiviral research Abstract IV V27A 92 96 M2;M2 79;89 81;91 28100622 Glycosylation of the Hemagglutinin Protein of H5N1 Influenza Virus Increases Its Virulence in Mice by Exacerbating the Host Immune Response. We further found that the G158N mutation introduced an N-linked glycosylation at positions 158 to 160 of the HA protein and that this N-linked glycosylation enhanced viral productivity in infected mammalian cells and induced stronger host immune and inflammatory responses to viral infection. 2017 Journal of virology Abstract IV G158N 26 31 HA 109 111 28102191 A broadly protective therapeutic antibody against influenza B virus with two mechanisms of action. After passage of the B/Brisbane/60/2008 virus in the presence of 46B8, we isolated three resistant clones, all harbouring the same mutation (Ser301Phe) in HA that abolishes 46B8 binding to HA at low pH. 2017 Nature communications Abstract IV S301F 141 150 HA;HA 155;189 157;191 28113045 PAN substitutions A37S, A37S/I61T and A37S/V63I attenuate the replication of H7N7 influenza A virus by impairing the polymerase and endonuclease activities. At the same time, the PAN-A37S, -A37S/I61T and -A37S/V63I mutant viruses displayed decreased viral transcription and replication by diminishing virus RNA synthesis activity. 2017 The Journal of general virology Abstract IV A37S;I61T;A37S;A37S;V63I 26;38;33;48;53 30;42;37;52;57 28113045 PAN substitutions A37S, A37S/I61T and A37S/V63I attenuate the replication of H7N7 influenza A virus by impairing the polymerase and endonuclease activities. Biochemical assays indicated that the substitutions PAN-A37S, -A37S/I61T and -A37S/V63I suppressed the polymerase and endonuclease activities when compared with those of the wild-type. 2017 The Journal of general virology Abstract IV A37S;A37S;I61T;A37S;V63I 56;63;68;78;83 60;67;72;82;87 28113045 PAN substitutions A37S, A37S/I61T and A37S/V63I attenuate the replication of H7N7 influenza A virus by impairing the polymerase and endonuclease activities. During our previous study, which identified PAN-V63I and -A37S/I61T/V63I/V100A substitutions as virulence determinants, we observed a severe decrease in virus growth and transcription/replication capacity posed by PAN-A37S/V100A substitution. 2017 The Journal of general virology Abstract IV A37S;V63I;A37S;I61T;V63I;V100A;V100A 218;48;58;63;68;73;223 222;52;62;67;72;78;228 28113045 PAN substitutions A37S, A37S/I61T and A37S/V63I attenuate the replication of H7N7 influenza A virus by impairing the polymerase and endonuclease activities. Our results showed that all mutant viruses except PAN-V100A showed a significantly reduced growth capability in infected cells. 2017 The Journal of general virology Abstract IV V100A 54 59 28113045 PAN substitutions A37S, A37S/I61T and A37S/V63I attenuate the replication of H7N7 influenza A virus by impairing the polymerase and endonuclease activities. To further delineate the significance of substitutions at these positions, we generated mutant H7N7 viruses bearing the substitutions PAN-A37S, -A37S/I61T, -A37S/V63I, -V100A, -I61T/V100A and -V63I/V100A by reverse genetics. 2017 The Journal of general virology Abstract IV A37S;A37S;A37S;I61T;V63I;V100A;I61T;V100A;V63I;V100A 138;157;145;150;162;169;177;182;193;198 142;161;149;154;166;174;181;187;197;203 28113045 PAN substitutions A37S, A37S/I61T and A37S/V63I attenuate the replication of H7N7 influenza A virus by impairing the polymerase and endonuclease activities. Together, our results demonstrated that the PAN-A37S, -A37S/I61T and -A37S/V63I substitutions contributed to a decreased pathogenicity of avian H7N7 influenza A virus. 2017 The Journal of general virology Abstract IV A37S;A37S;I61T;V63I;A37S 48;55;60;75;70 52;59;64;79;74 28116526 Genetic properties and pathogenicity of a novel reassortant H10N5 influenza virus from wild birds. After sequential passage in mice, mouse-adapted viruses bearing mutations PB2-E627K and HA-G218E were generated. 2017 Archives of virology Abstract IV E627K;G218E 78;91 83;96 HA;PB2 88;74 90;77 28125233 Depth-Dependent Membrane Ordering by Hemagglutinin Fusion Peptide Promotes Fusion. We report here the effect of the wild type, G1S, G1V, and W14A mutants of hemagglutinin fusion peptide on depth-dependent ordering of model membranes along the bilayer normal. 2017 The journal of physical chemistry. B Abstract IV G1S;G1V;W14A 44;49;58 47;52;62 HA 74 87 28125233 Depth-Dependent Membrane Ordering by Hemagglutinin Fusion Peptide Promotes Fusion. Wild type peptide uniquely ordered a region ~12 A from the bilayer midpoint, W14A and G1S mutants mainly ordered the bilayer interface, while G1V had little ordering influence. 2017 The journal of physical chemistry. B Abstract IV W14A;G1S;G1V 77;86;142 81;89;145 28128091 Development of oseltamivir and zanamivir resistance in influenza A(H1N1)pdm09 virus, Denmark, 2014. Day 149 when the patient had almost completed the second zanamivir treatment, mixes of the following resistance mutations were detected; H275Y(65.1%), I223R(9.2%), and E119G(89.6%), accompanied by additional mutations, showing a more complex viral population in the long-term treated patient. 2017 Euro surveillance Abstract IV H275Y;I223R;E119G 137;151;168 142;156;173 28128091 Development of oseltamivir and zanamivir resistance in influenza A(H1N1)pdm09 virus, Denmark, 2014. In a sample collected 15 days after the end of the first treatment with oseltamivir (Day 20 post-symptom onset), oseltamivir resistance was detected (mutation H275Y with 60.3% frequency by NGS). 2017 Euro surveillance Abstract IV H275Y 159 164 28132927 Antigenic and genetic characterization of influenza viruses circulating in Bulgaria during the 2015/2016 season. They contained unique HA1 substitutions N171K, S312R and HA2 substitutions I77V and G155E compared to Bulgarian 3C.2a viruses of the previous season. 2017 Infection, genetics and evolution Abstract IV N171K;S312R;I77V;G155E 40;47;75;84 45;52;79;89 HA;HA1 57;22 59;25 28148793 Mutations during the Adaptation of H9N2 Avian Influenza Virus to the Respiratory Epithelium of Pigs Enhance Sialic Acid Binding Activity and Virulence in Mice. The HA mutations, A190V and T212I, were characterized by generating recombinant viruses containing either one or both amino acid exchanges. 2017 Journal of virology Abstract IV A190V;T212I 18;28 23;33 HA 4 6 28162820 Manipulation of neuraminidase packaging signals and hemagglutinin residues improves the growth of A/Anhui/1/2013 (H7N9) influenza vaccine virus yield in eggs. The HA of the passaged CVV, did, however, exhibit egg-adaptive mutations and one of them (HA-G218E) improved CVV growth in eggs without significantly changing antigenicity. 2017 Vaccine Abstract IV G218E 93 98 HA;HA 4;90 6;92 28162820 Manipulation of neuraminidase packaging signals and hemagglutinin residues improves the growth of A/Anhui/1/2013 (H7N9) influenza vaccine virus yield in eggs. The HA-G218E substitution and a chimeric NA, thus, combine to provide an Anhui/1 CVV with properties more favorable for vaccine manufacture. 2017 Vaccine Abstract IV G218E 7 12 HA;NA 4;41 6;43 28166830 The T160A hemagglutinin substitution affects not only receptor binding property but also transmissibility of H5N1 clade 2.3.4 avian influenza virus in guinea pigs. The results show that the T160A substitution resulted in the loss of a glycosylation site at 158N and led not only to enhanced binding specificity for human-type receptors but also transmissibility among guinea pigs, which could be considered as an important molecular marker for assessing pandemic potential of H5 subtype avian influenza isolates. 2017 Veterinary research Abstract IV T160A 26 31 28182419 Expeditious Lead Optimization of Isoxazole-Containing Influenza A Virus M2-S31N Inhibitors Using the Suzuki-Miyaura Cross-Coupling Reaction. As the AM2-S31N mutant persists in more than 95% of current circulating influenza A viruses, targeting the AM2-S31N proton channel appears to be a logical and valid approach to combating drug resistance. 2017 Journal of medicinal chemistry Abstract IV S31N;S31N 11;111 15;115 28182419 Expeditious Lead Optimization of Isoxazole-Containing Influenza A Virus M2-S31N Inhibitors Using the Suzuki-Miyaura Cross-Coupling Reaction. Starting from compound 1, an isoxazole compound with potent AM2-S31N channel blockage and antiviral activity, in this study we report an expeditious synthetic strategy that allows us to promptly explore the structure-activity relationships of isoxazole-containing AM2-S31N inhibitors. 2017 Journal of medicinal chemistry Abstract IV S31N;S31N 64;268 68;272 28182988 Design, in silico studies, synthesis and in vitro evaluation of oseltamivir derivatives as inhibitors of neuraminidase from influenza A virus H1N1. The emergence of NA mutations, such as H275Y, has led to great resistance against neuraminidase inhibitors, including oseltamivir and zanamivir. 2017 European journal of medicinal chemistry Abstract IV H275Y 39 44 NA;NA 17;82 19;95 28202753 Mutation of the Second Sialic Acid-Binding Site, Resulting in Reduced Neuraminidase Activity, Preceded the Emergence of H7N9 Influenza A Virus. Mutational analysis showed that these differences resulted from substitution T401A in the 2nd SIA-binding site, indicating that substrate binding via this site enhances NA catalytic activity. 2017 Journal of virology Abstract IV T401A 77 82 169 171 28202753 Mutation of the Second Sialic Acid-Binding Site, Resulting in Reduced Neuraminidase Activity, Preceded the Emergence of H7N9 Influenza A Virus. Our phylogenetic analyses show that substitution T401A occurred prior to substitutions in hemagglutinin (HA), causing the altered receptor-binding properties mentioned above. 2017 Journal of virology Abstract IV T401A 49 54 HA;HA 105;90 107;103 28202753 Mutation of the Second Sialic Acid-Binding Site, Resulting in Reduced Neuraminidase Activity, Preceded the Emergence of H7N9 Influenza A Virus. Substitution T401A in the novel N9 protein appears to functionally mimic the substitutions that are found in the 2nd SIA-binding site of NA proteins of avian-derived IAVs that became human pandemic viruses. 2017 Journal of virology Abstract IV T401A 13 18 N9;NA 32;137 34;139 28205506 Prospective surveillance of antiviral resistance in hospitalized infants less than 12 months of age with A(H3N2) influenza infection and treated with oseltamivir. Sanger sequencing revealed the selection of the NA-R292K substitution in both instances (after dose number 10 on day 6). 2017 Antiviral therapy Abstract IV R292K 51 56 48 50 28250123 Influenza A Virus Virulence Depends on Two Amino Acids in the N-Terminal Domain of Its NS1 Protein To Facilitate Inhibition of the RNA-Dependent Protein Kinase PKR. Significantly, this corresponded with restoration of viral virulence for NS1 R35A and R46A mutant viruses in PKR-/- mice. 2017 Journal of virology Abstract IV R35A;R46A 77;86 81;90 NS1 73 76 28250123 Influenza A Virus Virulence Depends on Two Amino Acids in the N-Terminal Domain of Its NS1 Protein To Facilitate Inhibition of the RNA-Dependent Protein Kinase PKR. The strong attenuation conferred by NS1 mutation R35A or R46A was substantially alleviated by stable knockdown of PKR in human cells. 2017 Journal of virology Abstract IV R35A;R46A 49;57 53;61 NS1 36 39 28251891 Mid-season real-time estimates of seasonal influenza vaccine effectiveness in persons 65 years and older in register-based surveillance, Stockholm County, Sweden, and Finland, January 2017. Most (68%) of the samples collected from vaccinated patients belonged to the 3C.2a1 subclade with the additional amino acid substitution T135K in haemagglutinin (64%) or to subclade 3C.2a with the additional haemagglutinin substitutions T131K and R142K (36%). 2017 Euro surveillance Abstract IV T135K;T131K;R142K 137;237;247 142;242;252 HA;HA 146;208 160;222 28252002 NEDDylation of PB2 Reduces Its Stability and Blocks the Replication of Influenza A Virus. In addition, we observed that overexpression of NEDD8 significantly inhibited the replication of WSN, but not WSN-PB2 K699R. 2017 Scientific reports Abstract IV K699R 118 123 PB2 114 117 28252002 NEDDylation of PB2 Reduces Its Stability and Blocks the Replication of Influenza A Virus. The infection assay in mice showed that WSN-PB2 K699R exhibited enhanced virulence in mice compared to WSN, suggesting that NEDDylation of PB2 reduced IAV replication in vivo. 2017 Scientific reports Abstract IV K699R 48 53 PB2;PB2 44;139 47;142 28252002 NEDDylation of PB2 Reduces Its Stability and Blocks the Replication of Influenza A Virus. We found that NEDDylation deficient PB2 mutant (PB2 K699R) has a longer half-life than wild-type PB2, indicating that NEDDylation of PB2 reduces its stability. 2017 Scientific reports Abstract IV K699R 52 57 PB2;PB2;PB2;PB2 36;48;97;133 39;51;100;136 28252002 NEDDylation of PB2 Reduces Its Stability and Blocks the Replication of Influenza A Virus. We generated an IAV mutant in which PB2 was mutated to PB2 K699R (WSN-PB2 K699R) and examined the replication of WSN and WSN-PB2 K699R viruses in both MDCK and A549 cells and found that the replication of WSN-PB2 K699R was more efficient than wild-type WSN. 2017 Scientific reports Abstract IV K699R;K699R;K699R;K699R 59;74;129;213 64;79;134;218 PB2;PB2;PB2;PB2;PB2 36;55;70;125;209 39;58;73;128;212 28279127 In silico prediction of drug resistance due to S247R mutation of Influenza H1N1 neuraminidase protein. Another mutation (S247N) was already known to confer resistance to oseltamivir. 2018 Journal of biomolecular structure & dynamics Abstract IV S247N 18 23 28279127 In silico prediction of drug resistance due to S247R mutation of Influenza H1N1 neuraminidase protein. Our analysis shows that S247R may have high probability of being resistant. 2018 Journal of biomolecular structure & dynamics Abstract IV S247R 24 29 28279127 In silico prediction of drug resistance due to S247R mutation of Influenza H1N1 neuraminidase protein. We did a comparative study of these two mutations vis-a-vis the drug-sensitive wild type NA to understand the mechanism of drug resistance of S247N and to predict the probability of the novel S247R mutation to become resistant to the currently available drugs, oseltamivir and zanamivir. 2018 Journal of biomolecular structure & dynamics Abstract IV S247N;S247R 142;192 147;197 89 91 28279127 In silico prediction of drug resistance due to S247R mutation of Influenza H1N1 neuraminidase protein. We performed molecular docking- and molecular dynamics-based analysis of both the mutant proteins and showed that mutation of S247R affects drug binding to the protein by positional displacement due to altered active site cavity architecture, which in turn reduces the affinity of the drug molecules to the NA active site. 2018 Journal of biomolecular structure & dynamics Abstract IV S247R 126 131 307 309 28279127 In silico prediction of drug resistance due to S247R mutation of Influenza H1N1 neuraminidase protein. We report here a novel mutation (S247R) in the NA protein that was sequenced earlier from the nasopharyngeal swab from Sri Lanka and Thailand in the year 2009 and 2011, respectively. 2018 Journal of biomolecular structure & dynamics Abstract IV S247R 33 38 47 49 28282440 H1N1 influenza viruses varying widely in hemagglutinin stability transmit efficiently from swine to swine and to ferrets. Using an early 2009 pandemic H1N1 (pH1N1) virus backbone, we generated three viruses differing by one HA residue that only altered HA stability: WT (pH 5.5), HA1-Y17H (pH 6.0), and HA2-R106K (pH 5.3). 2017 PLoS pathogens Abstract IV Y17H;R106K 162;185 166;190 HA;HA;HA;HA1 102;131;181;158 104;133;183;161 28282440 H1N1 influenza viruses varying widely in hemagglutinin stability transmit efficiently from swine to swine and to ferrets. Y17H (pH 6.0) acquired HA mutations that stabilized the HA protein to pH 5.8 after transmission to pigs and 5.5 after transmission to ferrets. 2017 PLoS pathogens Abstract IV Y17H 0 4 HA;HA 23;56 25;58 28323816 An NS-segment exonic splicing enhancer regulates influenza A virus replication in mammalian cells. G540A supports virus replication in mammalian cells while retaining replication ability in avian cells. 2017 Nature communications Abstract IV G540A 0 5 28323816 An NS-segment exonic splicing enhancer regulates influenza A virus replication in mammalian cells. Host splicing regulator, SF2, interacts with this ESE to regulate splicing of NEP/NS1 mRNA and G540A substitution affects SF2-ESE interaction. 2017 Nature communications Abstract IV G540A 95 100 NEP;NS1 78;82 81;85 28323816 An NS-segment exonic splicing enhancer regulates influenza A virus replication in mammalian cells. Through genetic analysis and functional characterization, we here show that the NS segment of H7N9 virus contains a unique G540A substitution, located within a previously undefined exonic splicing enhancer (ESE) motif present in the NEP mRNA of influenza A viruses. 2017 Nature communications Abstract IV G540A 123 128 NEP;NS 233;80 236;82 28331993 Molecular characterization and phylogenetic analysis of human influenza A viruses isolated in Iran during the 2014-2015 season. Analysis of the A/H3N2 viruses showed a genetic drift from the vaccine strain A/Texas/50/2012 with 5 mutations (T128A, R142G, N145S, P198S and S219F) belonging to the antigenic sites A, B, and D of the HA protein. 2017 Archives of virology Abstract IV T128A;R142G;N145S;P198S;S219F 112;119;126;133;143 117;124;131;138;148 HA 202 204 28331993 Molecular characterization and phylogenetic analysis of human influenza A viruses isolated in Iran during the 2014-2015 season. Phylogenetic analysis of the HA genes of the A/H1N1pdm09 viruses revealed the circulation of clade 6C, characterized by amino acid substitutions D97N, V234I and K283E. 2017 Archives of virology Abstract IV D97N;V234I;K283E 145;151;161 149;156;166 HA 29 31 28338150 Stereoselective synthesis of novel adamantane derivatives with high potency against rimantadine-resistant influenza A virus strains. Biological assays of the prepared compounds were performed on the rimantadine-resistant S31N mutated strains of influenza A - A/California/7/2009(H1N1)pdm09 and modern pandemic strain A/IIV-Orenburg/29-L/2016(H1N1)pdm09. 2017 Organic & biomolecular chemistry Abstract IV S31N 88 92 28371631 Single nucleoprotein residue determines influenza A virus sensitivity to an intertypic suppression mechanism. An avian IAV polymerase carrying an NP-V343L mutation switched from being highly BNP-sensitive to moderately BNP-resistant, and vice versa for a human IAV polymerase carrying a reverse mutation. 2017 Virology Abstract IV V343L 39 44 NP 36 38 28381577 Understanding the Mechanism of the Broad-Spectrum Antiviral Activity of Favipiravir (T-705): Key Role of the F1 Motif of the Viral Polymerase. A mutagenesis analysis at position K159 identified the K159M variant as the only other viable variant which had also acquired the A239G substitution. 2017 Journal of virology Abstract IV K159M;A239G 55;130 60;135 28381577 Understanding the Mechanism of the Broad-Spectrum Antiviral Activity of Favipiravir (T-705): Key Role of the F1 Motif of the Viral Polymerase. Furthermore, the K159R A239G variant was found to be highly attenuated in mice. 2017 Journal of virology Abstract IV K159R;A239G 17;23 22;28 28381577 Understanding the Mechanism of the Broad-Spectrum Antiviral Activity of Favipiravir (T-705): Key Role of the F1 Motif of the Viral Polymerase. Introduction of the corresponding K-to-R substitution in the CVB3 RdRp (K159R) resulted in a nonviable virus. 2017 Journal of virology Abstract IV K159R 72 77 28381577 Understanding the Mechanism of the Broad-Spectrum Antiviral Activity of Favipiravir (T-705): Key Role of the F1 Motif of the Viral Polymerase. Replication competence of the K159R variant was restored by spontaneous acquisition of an A239G substitution in the RdRp. 2017 Journal of virology Abstract IV K159R;A239G 30;90 35;95 28381577 Understanding the Mechanism of the Broad-Spectrum Antiviral Activity of Favipiravir (T-705): Key Role of the F1 Motif of the Viral Polymerase. The K159 substitutions markedly decreased the processivity of the purified viral RdRp, which was restored by the introduction of the A239G mutation. 2017 Journal of virology Abstract IV A239G 133 138 28381577 Understanding the Mechanism of the Broad-Spectrum Antiviral Activity of Favipiravir (T-705): Key Role of the F1 Motif of the Viral Polymerase. The K159R A239G and K159M A239G variants proved, surprisingly, more susceptible than the wild-type virus to T-705 and exhibited lower fidelity in polymerase assays. 2017 Journal of virology Abstract IV K159R;A239G;K159M;A239G 4;10;20;26 9;15;25;31 28381577 Understanding the Mechanism of the Broad-Spectrum Antiviral Activity of Favipiravir (T-705): Key Role of the F1 Motif of the Viral Polymerase. We demonstrated earlier that the K291R mutation in the F1 motif of the RNA-dependent RNA polymerase (RdRp) of CHIKV is responsible for low-level resistance to T-705. 2017 Journal of virology Abstract IV K291R 33 38 28385598 Discovery of acylguanidine oseltamivir carboxylate derivatives as potent neuraminidase inhibitors. Among them, compounds 9 and 17 were potent NA inhibitors that exhibited a 5 and 11-fold increase in activity comparing with oseltamivir carboxylate (2, OC) against the H259Y mutant, respectively. 2017 Bioorganic & medicinal chemistry Abstract IV H259Y 168 173 43 45 28385598 Discovery of acylguanidine oseltamivir carboxylate derivatives as potent neuraminidase inhibitors. Furthermore, the effect against influenza virus H259Y mutant (H1N1) replication and cytotoxicity assays indicated that compounds 9 and 17 exhibited a 20 and 6-fold increase than the parent compound 2, and had no obvious cytotoxicity in vitro. 2017 Bioorganic & medicinal chemistry Abstract IV H259Y 48 53 28385598 Discovery of acylguanidine oseltamivir carboxylate derivatives as potent neuraminidase inhibitors. The representative compounds with strong inhibitory activities (IC50 <40nM) against neuraminidase (NA) were further tested against the NA from oseltamivir-resistant strain (H259Y). 2017 Bioorganic & medicinal chemistry Abstract IV H259Y 173 178 NA;NA;NA 99;135;84 101;137;97 28402848 The 150-Loop Restricts the Host Specificity of Human H10N8 Influenza Virus. Mutation of the 150-loop on the background of Q226L and G228S mutations, which arose in the receptor-binding site of human pandemic H2 and H3 viruses, resulted in acquisition of human-type receptor specificity. 2017 Cell reports Abstract IV Q226L;G228S 46;56 51;61 28410396 Evolution of the neuraminidase gene of seasonal influenza A and B viruses in Thailand between 2010 and 2015. We initially examined oseltamivir resistance (characterized by the H275Y mutation in the NA gene) in 485 A(H1N1)pdm09 strains circulating in Thailand and found that 0.82% (4/485) had this substitution. 2017 PloS one Abstract IV H275Y 67 72 89 91 28418242 Slow but Steady Wins the Race: Dissimilarities among New Dual Inhibitors of the Wild-Type and the V27A Mutant M2 Channels of Influenza A Virus. In addition, electrophysiology experiments revealed two interesting findings: (i) these inhibitors display a different behavior against the wild-type versus V27A mutant A/M2 channels, and (ii) the compounds display antiviral activity when they have kd equal or smaller than 10-6 while they do not exhibit antiviral activity when kd is 10-5 or higher although they may show blocking activity in the TEV assay. 2017 Journal of medicinal chemistry Abstract IV V27A 157 161 M2 171 173 28418242 Slow but Steady Wins the Race: Dissimilarities among New Dual Inhibitors of the Wild-Type and the V27A Mutant M2 Channels of Influenza A Virus. New insights on the amantadine resistance mechanism of the V27A mutant were obtained through the study of novel, easily accessible 4-(1- and 2-adamantyl)piperidines, identified as dual binders of the wild-type and V27A mutant M2 channels of influenza A virus. 2017 Journal of medicinal chemistry Abstract IV V27A;V27A 59;214 63;218 M2 226 228 28418242 Slow but Steady Wins the Race: Dissimilarities among New Dual Inhibitors of the Wild-Type and the V27A Mutant M2 Channels of Influenza A Virus. These findings provide experimental evidence of the resistance mechanism of the V27A mutation to wild-type inhibitors, previously predicted in silico, offer an explanation for the lack of antiviral activity of compounds active in the TEV assay, and may help design new and more effective drugs. 2017 Journal of medicinal chemistry Abstract IV V27A 80 84 28421062 Identification of Rare PB2-D701N Mutation from a Patient with Severe Influenza: Contribution of the PB2-D701N Mutation to the Pathogenicity of Human Influenza. An exhaustive search has revealed PB2-D701 as a highly conserved position in all available H1N1 human virus sequences in NCBI database, showing a very low prevalence of PB2-D701N change. 2017 Frontiers in microbiology Abstract IV D701N 173 178 PB2;PB2 34;169 37;172 28421062 Identification of Rare PB2-D701N Mutation from a Patient with Severe Influenza: Contribution of the PB2-D701N Mutation to the Pathogenicity of Human Influenza. Several amino acid changes have been previously implicated in adaptation of avian influenza viruses to human hosts, among them the D701N change in the PB2 polymerase subunit that also is the main determinant of avian virus pathogenesis in animal models. 2017 Frontiers in microbiology Abstract IV D701N 131 136 PB2 151 154 28421062 Identification of Rare PB2-D701N Mutation from a Patient with Severe Influenza: Contribution of the PB2-D701N Mutation to the Pathogenicity of Human Influenza. This study helps to clarify a debate that has arisen regarding the role of PB2-D701N in human influenza virus pathogenicity. 2017 Frontiers in microbiology Abstract IV D701N 79 84 PB2 75 78 28433777 Design and expeditious synthesis of organosilanes as potent antivirals targeting multidrug-resistant influenza A viruses. Since more than 95% of current circulating influenza A viruses carry the S31N mutation in their M2 genes, the AM2-S31N mutant proton channel represents an attractive target for the development of broad-spectrum antivirals. 2017 European journal of medicinal chemistry Abstract IV S31N;S31N 73;114 77;118 M2 96 98 28455649 Human parainfluenza virus type 2 V protein inhibits induction of tetherin. Furthermore, hPIV-2 V protein but not P and VW178H/W182E/W192A suppressed tetherin induction. 2017 Medical microbiology and immunology Abstract IV W182E;W192A;V178H;W178H 51;57;44;44 56;62;50;50 28455649 Human parainfluenza virus type 2 V protein inhibits induction of tetherin. In contrast, robust tetherin induction was observed by infection of rPIV-2s carrying V mutants, in which either three Trp residues (W178H/W182E/W192A) or Cys residues (C209/211/214A) that are important for decreasing cell surface tetherin are mutated. 2017 Medical microbiology and immunology Abstract IV W178H;W182E;W192A 132;138;144 137;143;149 28465552 A reassortant H9N2 influenza virus containing 2009 pandemic H1N1 internal-protein genes acquired enhanced pig-to-pig transmission after serial passages in swine. The broader tissue tropism and the increased post-transmission replication after seven passages were associated with the HA-D225G substitution. 2017 Scientific reports Abstract IV D225G 124 129 HA 121 123 28477572 Host dihydrofolate reductase (DHFR)-directed cycloguanil analogues endowed with activity against influenza virus and respiratory syncytial virus. Activity was also observed for two influenza A strains, including a virus with the S31N mutant form of M2 proton channel, which is the most prevalent resistance mutation for amantadine. 2017 European journal of medicinal chemistry Abstract IV S31N 83 87 M2 103 105 28498306 A Conserved Residue, Tyrosine (Y) 84, in H5N1 Influenza A Virus NS1 Regulates IFN Signaling Responses to Enhance Viral Infection. Cells infected with rWSN-GH-NS1-Y84F express higher levels of IFN stimulated genes (ISGs) associated with an antiviral response compared with cells infected with rWSN-GH-NS1-wt. 2017 Viruses Abstract IV Y84F 32 36 NS1;NS1 28;170 31;173 28498306 A Conserved Residue, Tyrosine (Y) 84, in H5N1 Influenza A Virus NS1 Regulates IFN Signaling Responses to Enhance Viral Infection. IFN-beta treatment of mice infected with rWSN-GH-NS1-Y84F reduced lung viral titers and increased lung ISG expression, but did not alter viral titers and ISG expression in mice infected with rWSN-GH-NS1-wt. 2017 Viruses Abstract IV Y84F 53 57 NS1;NS1 49;199 52;202 28498306 A Conserved Residue, Tyrosine (Y) 84, in H5N1 Influenza A Virus NS1 Regulates IFN Signaling Responses to Enhance Viral Infection. In mice, intranasal infection with rWSN-GH-NS1-Y84F resulted in a delay in onset of weight loss, reduced lung pathology, lower lung viral titers and higher ISG expression, compared with mice infected with rWSN-GH-NS1-wt. 2017 Viruses Abstract IV Y84F 47 51 NS1;NS1 43;213 46;216 28498306 A Conserved Residue, Tyrosine (Y) 84, in H5N1 Influenza A Virus NS1 Regulates IFN Signaling Responses to Enhance Viral Infection. Recombinant IAV (rIAV) [H1N1] expressing A/Grey Heron/Hong Kong/837/2004 [H5N1] NS1-Y84F (rWSN-GH-NS1-Y84F) replicates to lower titers in human lung epithelial cells and is more susceptible to the antiviral effects of IFN-beta treatment compared with rIAV expressing the intact H5N1 NS1 (rWSN-GH-NS1-wt). 2017 Viruses Abstract IV Y84F;Y84F 84;102 88;106 NS1;NS1;NS1;NS1 80;98;283;296 83;101;286;299 28530165 Basic amino acids in the N-terminal half of the PB2 subunit of influenza virus RNA polymerase are involved in both transcription and replication. Cross-linking studies suggested that a reduction of the polymerase activity in the R124A mutant was due to a significant decrease in binding to the viral RNA promoter. 2017 The Journal of general virology Abstract IV R124A 83 88 28530165 Basic amino acids in the N-terminal half of the PB2 subunit of influenza virus RNA polymerase are involved in both transcription and replication. Notably, R124A mutation remarkably reduced the synthesis of mRNA, cRNA and vRNA in vivo, which was in good agreement with the data obtained in vitro. 2017 The Journal of general virology Abstract IV R124A 9 14 28537245 [Impact of mutations in nucleoprotein on replication of influenza virus A/Hong Kong/1/68/162/35 reassortants at different temperatures]. It has been shown that reverse mutation Gly292Glu in the NP reduced virus ability to replicate at low temperature, the introduction of the second reverse mutation Arg102Gly completely abolished virus cold adaptation. 2017 Molekuliarnaia biologiia Abstract IV G292E;R102G 40;163 49;172 NP 57 59 28537245 [Impact of mutations in nucleoprotein on replication of influenza virus A/Hong Kong/1/68/162/35 reassortants at different temperatures]. Two mutations occurred in the NP: Gly102Arg and Glu292Gly. 2017 Molekuliarnaia biologiia Abstract IV G102R;E292G 34;48 43;57 NP 30 32 28554059 Residues F103 and M106 within the influenza A virus NS1 CPSF4-binding region regulate interferon-stimulated gene translation initiation. Recombinant (r) IAVs encoding F103L and M106I mutations in NS1 replicate to significantly lower viral titers in human A549 lung epithelial cells and primary type II alveolar cells. 2017 Virology Abstract IV F103L;M106I 30;40 35;45 NS1 59 62 28588133 Novel Nonreplicating Vaccinia Virus Vector Enhances Expression of Heterologous Genes and Suppresses Synthesis of Endogenous Viral Proteins. Expression of heterologous proteins mediated by the A23R deletion vector equaled that of a replicating VACV, was higher than that of a nonreplicating modified vaccinia virus Ankara (MVA) vector used for candidate vaccines in vitro and in vivo, and was similarly immunogenic in mice. 2017 mBio Abstract IV A23R 52 56 28588133 Novel Nonreplicating Vaccinia Virus Vector Enhances Expression of Heterologous Genes and Suppresses Synthesis of Endogenous Viral Proteins. Unlike the MVA vector, the A23R deletion vector still expresses numerous early genes that can restrict immunogenicity as demonstrated here by the failure of the prototype vector to induce interferon alpha. 2017 mBio Abstract IV A23R 27 31 28588133 Novel Nonreplicating Vaccinia Virus Vector Enhances Expression of Heterologous Genes and Suppresses Synthesis of Endogenous Viral Proteins. We describe a vaccinia virus (VACV) vector that uses an early promoter to express the bacteriophage T7 RNA polymerase; has the A23R intermediate transcription factor gene deleted, thereby restricting virus replication to complementing cells; and has a heterologous gene regulated by a T7 promoter. 2017 mBio Abstract IV A23R 127 131 28597818 Enhanced pathogenicity and neurotropism of mouse-adapted H10N7 influenza virus are mediated by novel PB2 and NA mutations. K110E mutation in NA, on the other hand, significantly promoted NA enzymatic activity. 2017 The Journal of general virology Abstract IV K110E 0 5 NA;NA 18;64 20;66 28597818 Enhanced pathogenicity and neurotropism of mouse-adapted H10N7 influenza virus are mediated by novel PB2 and NA mutations. Mutations M631L and E158G of PB2 and K110E of NA were required to mediate increased virus replication and severity of infection in mice and mammalian cells. 2017 The Journal of general virology Abstract IV M631L;E158G;K110E 10;20;37 15;25;42 NA;PB2 46;29 48;32 28597818 Enhanced pathogenicity and neurotropism of mouse-adapted H10N7 influenza virus are mediated by novel PB2 and NA mutations. PB2-M631L was functionally the most dominant mutation in that it strongly upregulated viral polymerase activity and played a critical role in the enhancement of virus replication and disease severity in mice. 2017 The Journal of general virology Abstract IV M631L 4 9 PB2 0 3 28597818 Enhanced pathogenicity and neurotropism of mouse-adapted H10N7 influenza virus are mediated by novel PB2 and NA mutations. Sequencing showed the absence of the widely recognized mammalian adaptation markers of E627K and D701N in PB2 in the mouse-adapted strain; instead, five amino acid mutations were identified: E158G and M631L in PB2; G218E in haemagglutinin (H3 numbering); and K110E and S453I in neuraminidase (NA). 2017 The Journal of general virology Abstract IV E627K;D701N;E158G;M631L;G218E;K110E;S453I 87;97;191;201;215;259;269 92;102;196;206;220;264;274 HA;NA;NA;PB2;PB2 224;293;278;106;210 238;295;291;109;213 28633988 A cross-clade H5N1 influenza A virus neutralizing monoclonal antibody binds to a novel epitope within the vestigial esterase domain of hemagglutinin. Interestingly, MAb 9F4 retained neutralizing efficacy against a clade 2.3.2.1a H5N1 virus consisting of an arginine to lysine substitution at position 62 in HA. 2017 Antiviral research Abstract IV R62K 107 153 HA 157 159 28637754 Functional Evolution of Influenza Virus NS1 Protein in Currently Circulating Human 2009 Pandemic H1N1 Viruses. Here we show that the NS1 protein from currently circulating pH1N1 viruses has evolved to encode 6 amino acid changes (E55K, L90I, I123V, E125D, K131E, and N205S) with respect to the original protein. 2017 Journal of virology Abstract IV E55K;L90I;I123V;E125D;K131E;N205S 119;125;131;138;145;156 123;129;136;143;150;161 NS1 22 25 28637754 Functional Evolution of Influenza Virus NS1 Protein in Currently Circulating Human 2009 Pandemic H1N1 Viruses. However, currently circulating pH1N1 viruses have evolved to encode 6 amino acid changes (E55K, L90I, I123V, E125D, K131E, and N205S) that allow the NS1 protein of contemporary pH1N1 strains to inhibit host gene expression, which correlates with its ability to interact with CPSF30. 2017 Journal of virology Abstract IV E55K;L90I;I123V;E125D;K131E;N205S 90;96;102;109;116;127 94;100;107;114;121;132 NS1 149 152 28659482 Complete Genome Sequencing of Influenza A Viruses within Swine Farrow-to-Wean Farms Reveals the Emergence, Persistence, and Subsidence of Diverse Viral Genotypes. Additionally, 3 out of 5 farms contained IAV isolates (n = 5) with gene segments from more than one VG, and 79% of all the IAVs sequenced contained a signature mutation (S31N) in the matrix gene that has been associated with resistance to the antiviral amantadine. 2017 Journal of virology Abstract IV S31N 170 174 M 183 189 28664296 Rapid virulence shift of an H5N2 avian influenza virus during a single passage in mice. Our molecular analysis revealed that two amino acid changes in the polymerase complex (a glutamate-to-lysine substitution at position 627 of PB2 and a threonine-to-isoleucine substitution at position 97 of PA) were associated with the increased pathogenicity; the PB2 E627K mutation was responsible for the initial virulence conversion (0 to 100% lethality), while the PA T97I mutation acted as an accessory for the increased virulence. 2017 Archives of virology Abstract IV E627K;T97I;E627K;T97I 268;372;89;151 273;376;137;202 PA;PA;PB2;PB2 206;369;141;264 208;371;144;267 28694323 A single mutation in Taiwanese H6N1 influenza hemagglutinin switches binding to human-type receptors. However, we show here that a single nucleotide substitution, resulting in a change from Gly to Asp at position 225 (G225D), completely switches specificity to human-type (NeuAcalpha2-6Gal) receptors. 2017 EMBO molecular medicine Abstract IV G225D;G225D 116;88 121;114 28694323 A single mutation in Taiwanese H6N1 influenza hemagglutinin switches binding to human-type receptors. Significantly, G225D H6 loses binding to chicken trachea epithelium and is now able to bind to human tracheal tissue. 2017 EMBO molecular medicine Abstract IV G225D 15 20 28697450 Changes in genetically drifted H3N2 influenza A viruses and vaccine effectiveness in adults 65 years and older during the 2016/17 season in Denmark. RESULTS: The genetic characterization revealed several genetically drifted viruses, which could be divided into four main clusters by the defining amino acid substitutions: 3C.2a/N121K/S144K, 3C.2a/T131K/R142K, 3C.2a1, and 3C.2a1/N121K. 2017 Journal of clinical virology Abstract IV N121K;T131K;S144K;R142K;N121K 179;198;185;204;230 184;203;190;209;235 28697450 Changes in genetically drifted H3N2 influenza A viruses and vaccine effectiveness in adults 65 years and older during the 2016/17 season in Denmark. VE for the four main virus clusters was; cluster 3C.2a1: 38.8% (95% CI: -29.8-71.1), cluster 3C.2a/N121K/S144K: 9.2% (95% CI: -63.0-49.4), cluster 3C.2a/T131K/R142K: 19.0% (95% CI: -85.3-64.6), and cluster 3C.2a1/N121K: -12.2% (95%CI: -129.7-45.2). 2017 Journal of clinical virology Abstract IV N121K;T131K;S144K;R142K;N121K 99;153;105;159;213 104;158;110;164;218 28744280 Amino Acid Substitution K470R in the Nucleoprotein Increases the Virulence of H5N1 Influenza A Virus in Mammals. A mini-genome assay demonstrated that the NP mutations K91R and K198R significantly decreased the polymerase activity. 2017 Frontiers in microbiology Abstract IV K91R;K198R 55;64 59;69 NP 42 44 28744280 Amino Acid Substitution K470R in the Nucleoprotein Increases the Virulence of H5N1 Influenza A Virus in Mammals. Of these, K227R, K229R, and K470R viruses were successfully rescued by reverse genetic, but the K91R and K198R viruses were not viable. 2017 Frontiers in microbiology Abstract IV K227R;K229R;K470R;K91R;K198R 10;17;28;96;105 15;22;33;100;110 28750900 Virulence of an H5N8 highly pathogenic avian influenza is enhanced by the amino acid substitutions PB2 E627K and HA A149V. Substitutions in the HA (A149V) and PB2 (E627K) proteins led to enhanced viral virulence in mice, the viruses displayed expanded tissue tropism, and increased replication kinetics in mammalian cells. 2017 Infection, genetics and evolution Abstract IV A149V;E627K 25;41 30;46 HA;PB2 21;36 23;39 28750900 Virulence of an H5N8 highly pathogenic avian influenza is enhanced by the amino acid substitutions PB2 E627K and HA A149V. The virulence of mouse-adapted virus was increased and adaptive mutations, HA (A149V) and PB2 (E627K), were detected after the ninth passage in each series of mice. 2017 Infection, genetics and evolution Abstract IV A149V;E627K 79;95 84;100 HA;PB2 75;90 77;93 28754164 Data-driven interdisciplinary mathematical modelling quantitatively unveils competition dynamics of co-circulating influenza strains. CONCLUSIONS: We conclude that interdisciplinary data-driven mathematical modelling could bring to light the transmission dynamics of the A/H1N1 H275Y strains during the 2007-2009 influenza seasons worldwide and may inspire us to tackle the continually emerging drug-resistant A/H1N1pdm09 strains. 2017 Journal of translational medicine Abstract IV H275Y 144 149 28754164 Data-driven interdisciplinary mathematical modelling quantitatively unveils competition dynamics of co-circulating influenza strains. We found that, during the 2008-2009 influenza season, the annual effective reproductive number of the succeeding A/H1N1 clade 2B-2, carrying H275Y mutation in the neuraminidase, was estimated around 1.65. 2017 Journal of translational medicine Abstract IV H275Y 141 146 163 176 28757037 Multiple amino acid substitutions involved in the virulence enhancement of an H3N2 avian influenza A virus isolated from wild waterfowl in mice. Genomic analysis revealed mutations in the PB2 (E192K and D701N), PB1 (F269S, I475V, and L598P), HA (V242E), NA (G170R), and M1 (M192V) proteins. 2017 Veterinary microbiology Abstract IV E192K;D701N;F269S;I475V;L598P;V242E;G170R;M192V 48;58;71;78;89;101;113;129 53;63;76;83;94;106;118;134 HA;M1;NA;PB1;PB2 97;125;109;66;43 99;127;111;69;46 28757046 Rapid acquisition adaptive amino acid substitutions involved in the virulence enhancement of an H1N2 avian influenza virus in mice. Sequence analysis revealed multiple amino acid substitutions in the PB2 (L134H, I647L, and D701N), HA (G228S), and M1 (D231N) proteins. 2017 Veterinary microbiology Abstract IV L134H;I647L;D701N;G228S;D231N 73;80;91;103;119 78;85;96;108;124 HA;M1;PB2 99;115;68 101;117;71 28768203 Avian-to-Human Receptor-Binding Adaptation by Influenza A Virus Hemagglutinin H4. The Q226L and G228S substitutions are pivotal for the receptor-binding switch, which resulted in similar human receptor-binding features to the pandemic H2 and H3, implying that H4 has the potential to cause human infections. 2017 Cell reports Abstract IV Q226L;G228S 4;14 9;19 28780426 Characterization of oseltamivir-resistant influenza virus populations in immunosuppressed patients using digital-droplet PCR: Comparison with qPCR and next generation sequencing analysis. Discrimination performance and sensitivity of the RT-ddPCR assay were evaluated using mixes of wild type (WT) and mutated H275Y-NA-coding segments. 2017 Antiviral research Abstract IV H275Y 122 127 128 130 28780426 Characterization of oseltamivir-resistant influenza virus populations in immunosuppressed patients using digital-droplet PCR: Comparison with qPCR and next generation sequencing analysis. For the first patient, the H275Y-NA substitution was selected by oseltamivir treatment and reached about 50% of the IV population before dropping to less than 2% after treatment discontinuation which was under the lower limit of quantification by RT-qPCR and RT-ddPCR (<2%) after treatment stop. 2017 Antiviral research Abstract IV H275Y 27 32 33 35 28780426 Characterization of oseltamivir-resistant influenza virus populations in immunosuppressed patients using digital-droplet PCR: Comparison with qPCR and next generation sequencing analysis. For the second patient, the H275Y-NA substitution reached about 30% two days after oseltamivir discontinuation. 2017 Antiviral research Abstract IV H275Y 28 33 34 36 28780426 Characterization of oseltamivir-resistant influenza virus populations in immunosuppressed patients using digital-droplet PCR: Comparison with qPCR and next generation sequencing analysis. INTRODUCTION: The H275Y substitution in neuraminidase (NA) confers oseltamivir-resistance in A(H1N1) influenza viruses (IV). 2017 Antiviral research Abstract IV H275Y 18 23 NA;NA 55;40 57;53 28780426 Characterization of oseltamivir-resistant influenza virus populations in immunosuppressed patients using digital-droplet PCR: Comparison with qPCR and next generation sequencing analysis. Then, five days after oseltamivir was re-introduced, the H275Y-NA substitution rose up to 100%. 2017 Antiviral research Abstract IV H275Y 57 62 63 65 28780426 Characterization of oseltamivir-resistant influenza virus populations in immunosuppressed patients using digital-droplet PCR: Comparison with qPCR and next generation sequencing analysis. This technique could be used to detect earlier emergence of H275Y-NA substitution. 2017 Antiviral research Abstract IV H275Y 60 65 66 68 28780426 Characterization of oseltamivir-resistant influenza virus populations in immunosuppressed patients using digital-droplet PCR: Comparison with qPCR and next generation sequencing analysis. We also analyzed the proportions of H275Y-NA substitution for two immunosuppressed patients with sustained shedding of A(H1N1)pdm09 IV. 2017 Antiviral research Abstract IV H275Y 36 41 42 44 28790432 Conformational modulation of influenza virus hemagglutinin: characterization and in vivo efficacy of monomeric form. Two mutants, F88E and V91W, were characterized to form a monomer and their double mutant F88E/V91W monomer was selected as an antigen. 2017 Scientific reports Abstract IV F88E;F88E;V91W;V91W 13;89;22;94 17;93;26;98 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. A single B/Victoria-lineage virus harboured NA G104E, which was associated with HRI by all four NAIs. 2017 Antiviral research Abstract IV G104E 47 52 NA;NAI 44;96 46;100 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. As in previous seasons, the most common NA AAS was H275Y in A(H1N1)pdm09 viruses, which confers HRI by oseltamivir and peramivir. 2017 Antiviral research Abstract IV H275Y 51 56 40 42 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. Three B/Victoria-lineage viruses contained a new AAS, NA H134N, which conferred HRI by zanamivir and laninamivir, and borderline HRI by peramivir. 2017 Antiviral research Abstract IV H134N 57 62 54 56 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. Two A(H1N1)pdm09 viruses carried a rare NA AAS, S247R, shown in this study to confer RI/HRI by the four NAIs. 2017 Antiviral research Abstract IV S247R 48 53 NA;NAI 40;104 42;108 28814518 A Single-Amino-Acid Substitution at Position 225 in Hemagglutinin Alters the Transmissibility of Eurasian Avian-Like H1N1 Swine Influenza Virus in Guinea Pigs. We found that a single-amino-acid substitution of glycine (G) for glutamic acid (E) at position 225 (E225G) in the HA1 protein completely abolished the respiratory droplet transmission of GX/18, whereas the substitution of E for G at the same position (G225E) in HA1 enabled HLJ/27 to transmit in guinea pigs. 2017 Journal of virology Abstract IV E225G;G225E 101;253 106;258 HA1;HA1 115;263 118;266 28814737 Susceptibility of influenza A(H1N1)/pdm2009, seasonal A(H3N2) and B viruses to Oseltamivir in Guangdong, China between 2009 and 2014. MutationsV241I, N369K, N386K and K432E, alone or in conjunction with H275Y, had a significant impact on the binding pattern and affinity of oseltamivir for neuraminidase, rendering neuraminidase less susceptible. 2017 Scientific reports Abstract IV N369K;N386K;K432E;H275Y 16;23;33;69 21;28;38;74 NA;NA 156;181 169;194 28814737 Susceptibility of influenza A(H1N1)/pdm2009, seasonal A(H3N2) and B viruses to Oseltamivir in Guangdong, China between 2009 and 2014. We found that 2013/2014 oseltamivir-resistant strains and 2012/2013/2014 oseltamivir-sensitive strains had all or some of the following mutations: N44S, N200S,V241I, I321V,N369K, N386 K and K432E. 2017 Scientific reports Abstract IV N44S;N200S;V241I;I321V;N369K;N386K;K432E 147;153;159;166;172;179;190 151;158;164;171;177;185;195 28815216 Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity. A second drug-selected mutation, PA T97I, interacts epistatically with PB1 T123A to mediate high-level mutagen resistance, predominantly by limiting the inhibitory effect of nucleosides on polymerase activity. 2017 mSphere Abstract IV T97I;T123A 36;75 40;80 PA;PB1 33;71 35;74 28815216 Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity. Two previously identified ribavirin {1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1H-1,2,4-triazole-3-carboxamide} resistance mutations, PB1 V43I and PB1 D27N, do not confer drug resistance in the PR8 background, and the PR8-PB1 V43I polymerase exhibits a normal baseline mutation rate. 2017 mSphere Abstract IV V43I;D27N;V43I 157;170;245 161;174;249 PB1;PB1;PB1 153;166;241 156;169;244 28815216 Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity. We find that PB1 T123A has higher replicative fitness than the wild type, PR8, and maintains its level of genome production during 5-fluorouracil (2,4-dihydroxy-5-fluoropyrimidine) treatment. 2017 mSphere Abstract IV T123A 17 22 PB1 13 16 28835506 The K186E Amino Acid Substitution in the Canine Influenza Virus H3N8 NS1 Protein Restores Its Ability To Inhibit Host Gene Expression. Such ability was restored by a single amino acid substitution in position 186 (K186E) that resulted in NS1 binding to the 30-kDa subunit of the cleavage and polyadenylation specificity factor (CPSF30), a cellular protein involved in pre-mRNA processing. 2017 Journal of virology Abstract IV K186E 79 84 NS1 103 106 28835506 The K186E Amino Acid Substitution in the Canine Influenza Virus H3N8 NS1 Protein Restores Its Ability To Inhibit Host Gene Expression. The H3N8 CIV NS1 did not block host gene expression, but this activity was restored by a single amino acid substitution (K186E), which was responsible for NS1 binding to the host factor CPSF30. 2017 Journal of virology Abstract IV K186E 121 126 NS1;NS1 13;155 16;158 28837667 Influenza NS1 directly modulates Hedgehog signaling during infection. We identified a point mutation in NS1, A122V, that modulates this activity in a context-dependent fashion. 2017 PLoS pathogens Abstract IV A122V 39 44 NS1 34 37 28837667 Influenza NS1 directly modulates Hedgehog signaling during infection. When the A122V mutation was incorporated into a mouse-adapted influenza A virus, it cell-autonomously enhanced expression of some Hh targets in the mouse lung, including IL6, and hastened lethality. 2017 PLoS pathogens Abstract IV A122V 9 14 28860593 Prerequisites for the acquisition of mammalian pathogenicity by influenza A virus with a prototypic avian PB2 gene. Here, we demonstrated that key amino acid mutations (I66M, I109V, and I133V, collectively referred to as MVV) of this prototypic avian PB2 increase the replication efficiency of recombinant PR8 virus carrying the mutated PB2 in both avian and mammalian hosts. 2017 Scientific reports Abstract IV I66M;I109V;I133V 53;59;70 57;64;75 PB2;PB2 135;221 138;224 28860593 Prerequisites for the acquisition of mammalian pathogenicity by influenza A virus with a prototypic avian PB2 gene. The MVV mutations caused no weight loss in mice, but they did allow replication in infected lungs, and the viruses acquired fatal mammalian pathogenic mutations such as Q591R/K, E627K, or D701N in the infected lungs. 2017 Scientific reports Abstract IV Q591R;Q591K;E627K;D701N 169;169;178;188 176;176;183;193 28860626 Topological N-glycosylation and site-specific N-glycan sulfation of influenza proteins in the highly expressed H1N1 candidate vaccines. In this report, we have systematically evaluated the glycan composition, structural distribution and topology of glycosylation for two high-yield candidate reassortant vaccines (NIBRG-121xp and NYMC-X181A) by combining various enzymatic digestions with high performance liquid chromatography and multiple-stage mass spectrometry. 2017 Scientific reports Abstract IV X181A 199 204 28878070 Effect of Phosphorylation of CM2 Protein on Influenza C Virus Replication. Furthermore, the virus growth of the recombinant viruses possessing CM2 with a serine-to-aspartic acid change at position 78, to mimic constitutive phosphorylation, was virtually identical to that of the wild-type virus. 2017 Journal of virology Abstract IV S78D 79 124 CM2 68 71 28878070 Effect of Phosphorylation of CM2 Protein on Influenza C Virus Replication. The virus production of the recombinant influenza C virus possessing CM2 mutants containing a serine-to-alanine change at residue 78 was significantly lower than that of wild-type recombinant influenza C virus. 2017 Journal of virology Abstract IV S78A 94 132 CM2 69 72 28886889 Anti-influenza activity of diazaadamantanes combined with monoterpene moieties. Modelling these compounds against an influenza virus M2 ion channel predicted plausible binding modes to both the wild-type and the mutant (S31N). 2017 Bioorganic & medicinal chemistry letters Abstract IV S31N 140 144 M2 53 55 28889970 Genomic signature analysis of the recently emerged highly pathogenic A(H5N8) avian influenza virus: implying an evolutionary trend for bird-to-human transmission. Furthermore, the HA protein had S137A and S227R substitutions in the receptor-binding site and A160T in the glycosylation site, potentially increasing viral ability to bind human-type receptors. 2017 Microbes and infection Abstract IV S137A;S227R;A160T 32;42;95 37;47;100 HA 17 19 28940727 Whole-genome sequencing and antigenic analysis of the first equine influenza virus identified in Turkey. Whole-genome sequencing indicated that A/equine/Ankara/1/2013 is most closely related to the viruses described as the 179 group based on the substitution I179V in HA1, for example A/equine/East Renfrewshire/2/2011, A/equine/Cambremer/1/2012 and A/equine/Saone et Loire/1/2015. 2018 Influenza and other respiratory viruses Abstract IV I179V 154 159 HA1 163 166 28951584 Identification of neuraminidase inhibitors against dual H274Y/I222R mutant strains. The experimental results identified inhibitors with similar activities against both wild-type and dual H274Y/I222R mutant neuraminidases and showed little cytotoxic effects. 2017 Scientific reports Abstract IV H274Y;I222R 103;109 108;114 122 136 28966609 Amino Acid Substitutions Associated with Avian H5N6 Influenza A Virus Adaptation to Mice. Using genome sequencing and alignment, multiple amino acid substitutions, including PB2 E627K, PB2 T23I, PA T97I, and HA R239H, were found in the adaptation of H5N6 to mice. 2017 Frontiers in microbiology Abstract IV E627K;T23I;T97I;R239H 88;99;108;121 93;103;112;126 HA;PA;PB2;PB2 118;105;84;95 120;107;87;98 2897244 A single amino acid change in the cytoplasmic domain allows the influenza virus hemagglutinin to be endocytosed through coated pits. However, one of these mutations, substituting tyrosine for cysteine at amino acid 543, changed HA from a protein that was endocytosed at a very low rate to a protein that readily entered coated pits, was internalized, and apparently recycled to the cell surface. 1988 Cell Abstract IV C543Y 46 85 HA 95 97 28993123 Single mutation in the matrix gene of seasonal influenza A viruses critically affects the performance of diagnostic molecular assay. A single mutation, G189T, in the conserved region of influenza virus matrix gene was detected by Sanger sequencing. 2018 Journal of virological methods Abstract IV G189T 19 24 M 69 75 29019145 Phylogenetic and genetic characterization of a 2017 clinical isolate of H7N9 virus in Guangzhou, China during the fifth epidemic wave. The 2017 isolate also possesses an R292K substitution in the neuraminidase (NA) protein, which confers oseltamivir resistance. 2017 Science China. Life sciences Abstract IV R292K 35 40 NA;NA 76;61 78;74 29023600 Reduced accumulation of defective viral genomes contributes to severe outcome in influenza virus infected patients. Looking for potential virulence factors, we have identified a polymerase PA D529N mutation detected in a fatal IAV case, whose introduction into two different recombinant virus backbones, led to reduced defective viral genomes (DVGs) production. 2017 PLoS pathogens Abstract IV D529N 76 81 PA 73 75 29046451 Mutations in the Influenza A Virus M1 Protein Enhance Virus Budding To Complement Lethal Mutations in the M2 Cytoplasmic Tail. Mutations in the distal cytoplasmic tail region of M2, and in particular a tyrosine-to-alanine mutation at residue 76 (Y76A), were essential for infectious virus production and filament formation while having limited effects on total virus particle budding. 2018 Journal of virology Abstract IV Y76A;Y76A 119;75 123;117 M2 51 53 29046464 Screening for Neuraminidase Inhibitor Resistance Markers among Avian Influenza Viruses of the N4, N5, N6, and N8 Neuraminidase Subtypes. In addition, two substitutions, H274Y and R292K (N2 numbering), were introduced into each NA gene for comparison. 2018 Journal of virology Abstract IV H274Y;R292K 32;42 37;47 90 92 29046464 Screening for Neuraminidase Inhibitor Resistance Markers among Avian Influenza Viruses of the N4, N5, N6, and N8 Neuraminidase Subtypes. Substitutions conferring NAI resistance were mainly categorized as either novel NA subtype specific (G/N147V/I, A246V, and I427L) or previously reported in other subtypes (E119A/D/V, Q136K, E276D, R292K, and R371K). 2018 Journal of virology Abstract IV G147V;G147I;N147V;N147I;A246V;I427L;E119A;E119D;E119V;Q136K;E276D;R292K;R371K 101;101;101;101;112;123;172;172;172;183;190;197;208 110;110;110;110;117;128;181;181;181;188;195;202;213 NA;NAI 80;25 82;28 29070694 Emergence and Adaptation of a Novel Highly Pathogenic H7N9 Influenza Virus in Birds and Humans from a 2013 Human-Infecting Low-Pathogenic Ancestor. Notably, human-origin viruses were more pathogenic in mice than avian viruses, and the mutations in the PB2 gene associated with adaptation to mammals (E627K, A588V, and D701N) were identified by next-generation sequencing (NGS) and Sanger sequencing of the isolates from infected mice. 2018 Journal of virology Abstract IV E627K;A588V;D701N 152;159;170 157;164;175 PB2 104 107 29090366 PB2 and HA mutations increase the virulence of highly pathogenic H5N5 clade 2.3.4.4 avian influenza virus in mice. After two passages, we obtained a mouse-adapted H5N5 virus that contained single amino acid substitutions in the PB2 (E627K) and hemagglutinin (HA) (F430L) proteins. 2018 Archives of virology Abstract IV E627K;F430L 118;149 123;154 HA;HA;PB2 144;129;113 146;142;116 29090366 PB2 and HA mutations increase the virulence of highly pathogenic H5N5 clade 2.3.4.4 avian influenza virus in mice. Furthermore, we found that PB2-E627K enhanced viral replication kinetics in vitro and in vivo. 2018 Archives of virology Abstract IV E627K 31 36 PB2 27 30 29090366 PB2 and HA mutations increase the virulence of highly pathogenic H5N5 clade 2.3.4.4 avian influenza virus in mice. The 50% mouse lethal dose (MLD50) of the H5N5 virus containing the PB2-E627K substitution or the HA-F430L substitution was reduced 1000-fold or 3.16-fold, respectively. 2018 Archives of virology Abstract IV E627K;F430L 71;100 76;105 HA;PB2 97;67 99;70 29090366 PB2 and HA mutations increase the virulence of highly pathogenic H5N5 clade 2.3.4.4 avian influenza virus in mice. These results suggest that the PB2-E627K and HA-F430L substitutions are important for adaptation of H5N5 AIVs to mammals. 2018 Archives of virology Abstract IV E627K;F430L 35;48 40;53 HA;PB2 45;31 47;34 29097654 Role of influenza A virus NP acetylation on viral growth and replication. Interestingly, release deficiency is also observed mimicking constant acetylation at this site (K229Q), whereas virus encoding NP-K113Q could not be generated. 2017 Nature communications Abstract IV K229Q;K113Q 96;130 101;135 NP 127 129 29097654 Role of influenza A virus NP acetylation on viral growth and replication. Viral growth of mutant virus encoding K229R, mimicking a non-acetylated NP lysine residue, is severely impaired compared to wildtype or the mutant viruses encoding K77R or K113R. 2017 Nature communications Abstract IV K229R;K77R;K113R 38;164;172 43;168;177 NP 72 74 29100932 Evolution of equine influenza viruses (H3N8) during a Brazilian outbreak, 2015. Two of them were in antigenic site A (A138S and G142R), one in antigenic site E (R62K) and another not in antigenic site (K304E). 2018 Brazilian journal of microbiology Abstract IV A138S;G142R;R62K;K304E 38;48;81;122 43;53;85;127 29107426 Synthesis and biological evaluation of NH2-acyl oseltamivir analogues as potent neuraminidase inhibitors. Moreover, 11b showed moderate inhibitions against mutant neuraminidases from H5N1-H274Y and H1N1-H274Y with IC50 values of 2075 nM and 1382 nM, which were inferior to those of oseltamivir carboxylate (6095 nM and 4071 nM). 2017 European journal of medicinal chemistry Abstract IV H274Y;H274Y 82;97 87;102 57 71 29113821 Multiple adaptive amino acid substitutions increase the virulence of a wild waterfowl-origin reassortant H5N8 avian influenza virus in mice. Sequence analysis revealed four amino acid substitutions in the PB2 (E627K), PA (F35S), HA (R227H), and NA (I462V) proteins. 2018 Virus research Abstract IV E627K;F35S;R227H;I462V 69;81;92;108 74;85;97;113 HA;NA;PA;PB2 88;104;77;64 90;106;79;67 29118117 A Y161F Hemagglutinin Substitution Increases Thermostability and Improves Yields of 2009 H1N1 Influenza A Virus in Cells. Compared with A(H1N1)pdm09, the Y161F mutant had significantly higher avidity for avian-like and human-like receptor analogs. 2018 Journal of virology Abstract IV Y161F 32 37 29118117 A Y161F Hemagglutinin Substitution Increases Thermostability and Improves Yields of 2009 H1N1 Influenza A Virus in Cells. In this study, we identified a molecular signature, Y161F, in hemagglutinin (HA) that resulted in increased virus growth in Madin-Darby canine kidney and Vero cells, two cell lines commonly used for influenza vaccine manufacturing. 2018 Journal of virology Abstract IV Y161F 52 57 HA;HA 77;62 79;75 29118117 A Y161F Hemagglutinin Substitution Increases Thermostability and Improves Yields of 2009 H1N1 Influenza A Virus in Cells. Of note, the introduction of the Y161F mutation into HA of seasonal H3N2 influenza A virus (IAV) and canine H3N8 IAV also increased yields and thermostability in MDCK cells and chicken embryotic eggs. 2018 Journal of virology Abstract IV Y161F 33 38 HA 53 55 29118117 A Y161F Hemagglutinin Substitution Increases Thermostability and Improves Yields of 2009 H1N1 Influenza A Virus in Cells. The vaccine produced from the Y161F mutant fully protected mice against lethal challenge with wild-type A(H1N1)pdm09. 2018 Journal of virology Abstract IV Y161F 30 35 29118117 A Y161F Hemagglutinin Substitution Increases Thermostability and Improves Yields of 2009 H1N1 Influenza A Virus in Cells. These results suggest that a vaccine strain bearing the Y161F mutation in HA could potentially increase vaccine yields in mammalian cell culture systems. 2018 Journal of virology Abstract IV Y161F 56 61 HA 74 76 29118117 A Y161F Hemagglutinin Substitution Increases Thermostability and Improves Yields of 2009 H1N1 Influenza A Virus in Cells. This Y161F mutation not only increased HA thermostability but also enhanced its binding affinity for alpha2,6- and alpha2,3-linked Neu5Ac. 2018 Journal of virology Abstract IV Y161F 5 10 HA 39 41 29118117 A Y161F Hemagglutinin Substitution Increases Thermostability and Improves Yields of 2009 H1N1 Influenza A Virus in Cells. Using influenza A(H1N1)pdm09 virus as the testing platform and an integrating error-prone PCR-based mutagenesis strategy, we identified a Y161F mutation in hemagglutinin (HA) that not only enhanced the infectivity of the resultant virus by more than 300-fold but also increased its thermostability without changing its original antigenic properties. 2018 Journal of virology Abstract IV Y161F 138 143 HA;HA 171;156 173;169 29128380 Low influenza vaccine effectiveness and the effect of previous vaccination in preventing admission with A(H1N1)pdm09 or B/Victoria-Lineage in patients 60 years old or older during the 2015/2016 influenza season. The majority of A(H1N1)pdm09 sequenced viruses belonged to the emerging 6B.1 subclade, defined by S162N and I216T mutations in the hemagglutinin protein. 2017 Vaccine Abstract IV S162N;I216T 98;108 103;113 HA 131 144 29139346 In vivo mallard experiments indicate that zanamivir has less potential for environmental influenza A virus resistance development than oseltamivir. Our study also adds further evidence regarding the stability of the oseltamivir-induced substitution H275Y without drug pressure, and demonstrates the ability of a H275Y-carrying virus to acquire secondary mutations, further boosting oseltamivir resistance when exposed to zanamivir. 2017 The Journal of general virology Abstract IV H275Y;H275Y 101;164 106;169 29139346 In vivo mallard experiments indicate that zanamivir has less potential for environmental influenza A virus resistance development than oseltamivir. This conclusion is based on: (1) the lower increase in zanamivir IC50 conferred by the mutations caused by zanamivir exposure (2-17-fold); (2) the higher zanamivir water concentration needed to induce resistance (at least 10 microg l-1); (3) the lack of zanamivir resistance persistence without drug pressure; and (4) the multiple resistance-related substitutions seen during zanamivir exposure (V116A, A138V, R152K, T157I and D199G) suggesting lack of one straight-forward evolutionary path to resistance. 2017 The Journal of general virology Abstract IV V116A;A138V;R152K;T157I;D199G 396;403;410;417;427 401;408;415;422;432 29145498 Antigenicity of the 2015-2016 seasonal H1N1 human influenza virus HA and NA proteins. The circulating strains belonged to subclade 6B.1, defined by HA amino acid substitutions S101N, S179N, and I233T. 2017 PloS one Abstract IV S101N;S179N;I233T 90;97;108 95;102;113 HA 62 64 29159346 Peramivir analogues bearing hydrophilic side chains exhibit higher activities against H275Y mutant than wild-type influenza virus. In contrast, zanamivir having a hydrophilic glycerol side chain still possesses high affinity toward the H275Y NA. 2017 Organic & biomolecular chemistry Abstract IV H275Y 105 110 111 113 29159346 Peramivir analogues bearing hydrophilic side chains exhibit higher activities against H275Y mutant than wild-type influenza virus. Notably, the peramivir analogue bearing a glycerol side chain inhibits the H275Y mutant with an IC50 value of 35 nM, which is better than the WSN virus by 9 fold. 2017 Organic & biomolecular chemistry Abstract IV H275Y 75 80 29159346 Peramivir analogues bearing hydrophilic side chains exhibit higher activities against H275Y mutant than wild-type influenza virus. Peramivir is an effective anti-influenza drug in the clinical treatment of influenza, but its efficacy toward the H275Y mutant is reduced. 2017 Organic & biomolecular chemistry Abstract IV H275Y 114 119 29159346 Peramivir analogues bearing hydrophilic side chains exhibit higher activities against H275Y mutant than wild-type influenza virus. The molecular docking experiments reveal that the hydrophilic side chain can provide extra hydrogen bonding with the translocated Glu-276 residue in the H275Y NA active site. 2017 Organic & biomolecular chemistry Abstract IV H275Y 153 158 159 161 29159346 Peramivir analogues bearing hydrophilic side chains exhibit higher activities against H275Y mutant than wild-type influenza virus. Thus, the H275Y mutant may be even more sensitive than wild-type virus toward the peramivir analogues bearing hydrophilic side chains. 2017 Organic & biomolecular chemistry Abstract IV H275Y 10 15 29159346 Peramivir analogues bearing hydrophilic side chains exhibit higher activities against H275Y mutant than wild-type influenza virus. We thus designed five peramivir analogues (5-9) carrying hydrophilic glycol or glycerol side chains, and evaluated their roles in anti-influenza activity, especially for the H275Y mutant. 2017 Organic & biomolecular chemistry Abstract IV H275Y 174 179 29164401 Isolation and molecular characterization of an H5N1 swine influenza virus in China in 2015. A Glu627Lys mutation associated with pathogenicity was observed in the PB2 protein. 2018 Archives of virology Abstract IV E627K 2 11 PB2 71 74 29167343 Ubiquitination of the Cytoplasmic Domain of Influenza A Virus M2 Protein Is Crucial for Production of Infectious Virus Particles. An M2-K78R (Lys78 Arg78) mutant, which produces ubiquitination-deficient M2, showed a severe defect in the production of infectious virus particles. 2018 Journal of virology Abstract IV K78R 6 10 M2;M2 3;73 5;75 29167343 Ubiquitination of the Cytoplasmic Domain of Influenza A Virus M2 Protein Is Crucial for Production of Infectious Virus Particles. Finally, we found that the M2-K78R mutant virus induced autophagy and apoptosis earlier than did the wild-type virus. 2018 Journal of virology Abstract IV K78R 30 34 M2 27 29 29167343 Ubiquitination of the Cytoplasmic Domain of Influenza A Virus M2 Protein Is Crucial for Production of Infectious Virus Particles. Furthermore, most of the M2-K78R mutant viral particles lacked viral ribonucleoproteins upon examination by electron microscopy and exhibited slightly lower densities. 2018 Journal of virology Abstract IV K78R 28 32 M2 25 27 29167343 Ubiquitination of the Cytoplasmic Domain of Influenza A Virus M2 Protein Is Crucial for Production of Infectious Virus Particles. M2-K78R mutant progeny contained more hemagglutinin (HA) proteins, less viral RNAs, and less internal viral proteins, including M1 and NP, than the wild-type virus. 2018 Journal of virology Abstract IV K78R 3 7 HA;HA;M1;M2;NP 53;38;128;0;135 55;51;130;2;137 29175013 The PB2-K627E mutation attenuates H3N2 swine influenza virus in cultured cells and in mice. For the first time, our results showed that PB2-K627E mutation attenuates H3N2 swine influenza virus in mammalian cells and in mice, suggesting that PB2-627K is required for viral replication and pathogenicity of H3N2 swine influenza virus. 2018 Research in veterinary science Abstract IV K627E 48 53 PB2;PB2 44;149 47;152 29175013 The PB2-K627E mutation attenuates H3N2 swine influenza virus in cultured cells and in mice. To explore the potential role of PB2-K627E substitution in H3N2 swine influenza virus, the growth properties and pathogenicity between H3N2 swine influenza virus and its PB2-K627E mutant were compared. 2018 Research in veterinary science Abstract IV K627E;K627E 37;174 42;179 PB2;PB2 33;170 36;173 29199545 The inhibitory performance of flavonoid cyanidin-3-sambubiocide against H274Y mutation in H1N1 influenza virus. A single H274Y mutation induces the conformational changes in the 150th loop which leads to produce more resistance to oseltamivir. 2018 Journal of biomolecular structure & dynamics Abstract IV H274Y 9 14 29199545 The inhibitory performance of flavonoid cyanidin-3-sambubiocide against H274Y mutation in H1N1 influenza virus. C3S has more binding affinity with WT and MT proteins. 2018 Journal of biomolecular structure & dynamics Abstract IV C3S 0 4 29199545 The inhibitory performance of flavonoid cyanidin-3-sambubiocide against H274Y mutation in H1N1 influenza virus. Few H1N1 influenza strains with the H274Y mutation creates drug resistance to oseltamivir. 2018 Journal of biomolecular structure & dynamics Abstract IV H274Y 36 41 29199545 The inhibitory performance of flavonoid cyanidin-3-sambubiocide against H274Y mutation in H1N1 influenza virus. In this study, we report that flavonoid cyanidin-3-sambubiocide (C3S) compound acts as a potential inhibitor against H274Y mutation. 2018 Journal of biomolecular structure & dynamics Abstract IV C3S;H274Y 65;117 68;122 29199545 The inhibitory performance of flavonoid cyanidin-3-sambubiocide against H274Y mutation in H1N1 influenza virus. The 150th cavity is more attractive target for C3S to stop the conformational changes in the MT, than 430th cavity of NA protein. 2018 Journal of biomolecular structure & dynamics Abstract IV C3S 47 50 118 120 29199545 The inhibitory performance of flavonoid cyanidin-3-sambubiocide against H274Y mutation in H1N1 influenza virus. The C3S is stabilized with MT by more number of hydrogen bonds than oseltamivir. 2018 Journal of biomolecular structure & dynamics Abstract IV C3S 4 7 29199545 The inhibitory performance of flavonoid cyanidin-3-sambubiocide against H274Y mutation in H1N1 influenza virus. The drug resistance mechanism and inhibitory activity of C3S and oseltamivir against wild-type (WT) and H274Y mutant-type (MT) have been studied and compared based on the results of molecular docking, molecular dynamics, and quantum chemical methods. 2018 Journal of biomolecular structure & dynamics Abstract IV C3S;H274Y 57;104 60;109 29199545 The inhibitory performance of flavonoid cyanidin-3-sambubiocide against H274Y mutation in H1N1 influenza virus. The electrostatic interaction energy shows a stronger C3S binding with MT and this compound may be more effective against oseltamivir-resistant virus strains. 2018 Journal of biomolecular structure & dynamics Abstract IV C3S 54 57 29209052 Maintaining pH-dependent conformational flexibility of M1 is critical for efficient influenza A virus replication. Crystallographic analysis indicated that M(NLS-88R) M1, like wild-type M1, is able to switch from a face-to-back-oriented conformation to a face-to-face-oriented conformation when pH drops from neutral to acidic, whereas G88E mutation causes M(NLS-88E) M1 to be trapped in a face-to-face-arranged conformation regardless of environmental pH. 2017 Emerging microbes & infections Abstract IV G88E 221 225 M;M;M1;M1;M1 41;242;52;71;253 42;243;54;73;255 29209052 Maintaining pH-dependent conformational flexibility of M1 is critical for efficient influenza A virus replication. G88R but not G88E was the compensatory mutation naturally selected by the virus after its nuclear localization signal was disrupted. 2017 Emerging microbes & infections Abstract IV G88R;G88E 0;13 4;17 29209052 Maintaining pH-dependent conformational flexibility of M1 is critical for efficient influenza A virus replication. M(NLS-88R) and M(NLS-88E) are two M1 mutants differing by only a single amino acid: G88R vs G88E. 2017 Emerging microbes & infections Abstract IV G88R;G88E 84;92 88;96 M;M;M1 0;15;34 1;16;36 29210473 Analysis by metadynamics simulation of binding pathway of influenza virus M2 channel blockers. The most prevalent resistant mutation is a substitution from Ser31 to Asn31 in M2. 2018 Microbiology and immunology Abstract IV S31N 61 75 M2 79 81 29212927 Mutations in the PA Protein of Avian H5N1 Influenza Viruses Affect Polymerase Activity and Mouse Virulence. Further studies revealed that the PA-S343A/E347D (PA with the S-to-A change at position 343 and the E-to-D change at position 347) mutations reduced viral polymerase activity and mouse virulence when tested in the genetic background of QT1728 virus. 2018 Journal of virology Abstract IV S343A;E347D 37;43 42;48 PA;PA 34;50 36;52 29212936 Structural Insight into a Human Neutralizing Antibody against Influenza Virus H7N9. Meanwhile, dual mutations at V186G and L226Q in RBS were able to disrupt viral HA1 binding with the antibody. 2018 Journal of virology Abstract IV V186G;L226Q 29;39 34;44 HA1 79 82 29278832 An epidemic surge of influenza A(H3N2) virus at the end of the 2016-2017 season in Taiwan with an increased viral genetic heterogeneity. New genetic variants were detected, including clade 3C.2a.1 with additional N121 K, K92R or T135 K mutations, 3C.2a.3a with T135 K and R150 K mutations and 3C.2a.4. 2018 Journal of clinical virology Abstract IV N121K;K92R;T135K;T135K;R150K 76;84;92;124;135 82;88;98;130;141 29278832 An epidemic surge of influenza A(H3N2) virus at the end of the 2016-2017 season in Taiwan with an increased viral genetic heterogeneity. The proportions of N121 K and T135 K mutations were continuously increasing. 2018 Journal of clinical virology Abstract IV N121K;T135K 19;30 25;36 29288584 Oseltamivir-resistant influenza A(H1N1)pdm09 virus associated with high case fatality, India 2015. Amino acid substitution analysis of complete NA gene revealed V241I, N369K, N386K substitution in all strains playing synergistic role in oseltamivir drug resistance. 2018 Journal of medical virology Abstract IV V241I;N369K;N386K 62;69;76 67;74;81 45 47 29288584 Oseltamivir-resistant influenza A(H1N1)pdm09 virus associated with high case fatality, India 2015. Out of 22 fatal cases, 6 (27.27%) were found to harbor oseltamivir resistant virus strains, whereas the H275Y mutation was not observed among the 20 non fatal cases. 2018 Journal of medical virology Abstract IV H275Y 104 109 29288584 Oseltamivir-resistant influenza A(H1N1)pdm09 virus associated with high case fatality, India 2015. Samples were investigated through RT-PCR/RFLP analysis, followed by nucleotide cycle sequencing of whole NA gene for detection of H275Y amino acid substitution in NA gene responsible for oseltamivir drug resistance. 2018 Journal of medical virology Abstract IV H275Y 130 135 NA;NA 105;163 107;165 29299528 Human Clade 2.3.4.4 A/H5N6 Influenza Virus Lacks Mammalian Adaptation Markers and Does Not Transmit via the Airborne Route between Ferrets. This A/H5N6 virus possessed high polymerase activity, mediated by the E627K substitution in the PB2 protein, which corresponds to only one biological trait out of the three that were previously shown to confer airborne transmissibility to A/H5N1 viruses between ferrets. 2018 mSphere Abstract IV E627K 70 75 PB2 96 99 29299533 Cooperating H3N2 Influenza Virus Variants Are Not Detectable in Primary Clinical Samples. However, it is unclear whether selection for the cooperative benefits of D151G is a cell culture phenomenon or whether the mutation is also sometimes present at appreciable frequency in virus populations sampled directly from infected humans. 2018 mSphere Abstract IV D151G 73 78 29299533 Cooperating H3N2 Influenza Virus Variants Are Not Detectable in Primary Clinical Samples. Prior work has not detected D151G in unpassaged clinical samples, but those studies have used methods like Sanger sequencing and pyrosequencing, which are relatively insensitive to low-frequency variation. 2018 mSphere Abstract IV D151G 28 33 29299533 Cooperating H3N2 Influenza Virus Variants Are Not Detectable in Primary Clinical Samples. The D151G mutation reaches a stable frequency of about 50% when virus is passaged in cell culture. 2018 mSphere Abstract IV D151G 4 9 29299533 Cooperating H3N2 Influenza Virus Variants Are Not Detectable in Primary Clinical Samples. The frequency of D151G did not exceed the frequency of library preparation and sequencing errors in any of the sequenced samples. 2018 mSphere Abstract IV D151G 17 22 29299533 Cooperating H3N2 Influenza Virus Variants Are Not Detectable in Primary Clinical Samples. These variants differ by a single mutation, D151G, in the neuraminidase protein. 2018 mSphere Abstract IV D151G 44 49 58 71 29299533 Cooperating H3N2 Influenza Virus Variants Are Not Detectable in Primary Clinical Samples. We conclude that passage in cell culture is primarily responsible for the frequent observations of D151G in recent H3N2 influenza virus strains. 2018 mSphere Abstract IV D151G 99 104 29299533 Cooperating H3N2 Influenza Virus Variants Are Not Detectable in Primary Clinical Samples. We identified nine samples of human H3N2 influenza virus collected between 2013 and 2015 in which Sanger sequencing had detected a high frequency of the D151G mutation following one to three passages in cell culture. 2018 mSphere Abstract IV D151G 153 158 29308074 Neuraminidase Gene Variations in Influenza A(H1N1)pdm09 Virus among Patients Admitted to Refferal Pulmonary Hospital, Tehran, Iran in 2009-2013. Meanwhile, H275Y substitution, related to oseltamivir resistance, was detected in 3 isolates. 2017 Tanaffos Abstract IV H275Y 11 16 29308074 Neuraminidase Gene Variations in Influenza A(H1N1)pdm09 Virus among Patients Admitted to Refferal Pulmonary Hospital, Tehran, Iran in 2009-2013. Some of these substitutions (N248D, V241I, N369K, N44S, and N200S) were important in terms of phylogenetic relationship, while the rest (D103N, V106I, R130T, N200S, G201E, and G414R) influenced the antigenic indices of B-cell epitopes. 2017 Tanaffos Abstract IV N248D;V241I;N369K;N44S;N200S;D103N;V106I;R130T;N200S;G201E;G414R 29;36;43;50;60;137;144;151;158;165;176 34;41;48;54;65;142;149;156;163;170;181 29312300 Histone Deacetylase 1 Plays an Acetylation-Independent Role in Influenza A Virus Replication. Compared with wild-type protein, two K103 NP mutants, K103A and K103R, enhanced replication efficiency of the recombinant viruses in vitro. 2017 Frontiers in immunology Abstract IV K103A;K103R 54;64 59;69 NP 42 44 29315673 Surveillance for antiviral resistance among influenza viruses circulating in Algeria during five consecutive influenza seasons (2009-2014). Influenza season 2007/2008 was marked by a worldwide emergence of oseltamivir-resistant A(H1N1) viruses possessing a mutation in the neuraminidase gene causing His-to-Tyr substitution at amino acid position 275 (H275Y). 2018 Journal of medical virology Abstract IV H275Y;H275Y 212;160 217;210 133 146 29315673 Surveillance for antiviral resistance among influenza viruses circulating in Algeria during five consecutive influenza seasons (2009-2014). These strains were isolated in Algeria where 30% of seasonal A(H1N1) viruses harbored the H275Y mutation. 2018 Journal of medical virology Abstract IV H275Y 90 95 29315673 Surveillance for antiviral resistance among influenza viruses circulating in Algeria during five consecutive influenza seasons (2009-2014). To detect the H275Y mutation in the neuraminidase of the A(H1N1) strains we performed a real-time RT-PCR allelic discrimination analysis. 2018 Journal of medical virology Abstract IV H275Y 14 19 36 49 29324781 Neuraminidase inhibitor susceptibility and neuraminidase enzyme kinetics of human influenza A and B viruses circulating in Thailand in 2010-2015. All introduced substitutions were stable except for B/YAM-D342S and B/YAM-A395V which reverted to WT sequences after three passages. 2018 PloS one Abstract IV D342S;A395V 58;74 63;79 29324781 Neuraminidase inhibitor susceptibility and neuraminidase enzyme kinetics of human influenza A and B viruses circulating in Thailand in 2010-2015. The Km and Vmax for the NAs of A/PR8-S331G and A/PR8-S331R viruses were higher than for the NA of WT virus, and the corresponding values for the B/YAM-D342S virus were lower than for the NA of WT virus. 2018 PloS one Abstract IV S331G;S331R;D342S 37;53;151 42;58;156 NA;NA;NA 92;187;24 94;189;27 29324781 Neuraminidase inhibitor susceptibility and neuraminidase enzyme kinetics of human influenza A and B viruses circulating in Thailand in 2010-2015. To study the effect of these substitutions on the enzymatic properties of NA and on virus characteristics, we generated recombinant influenza viruses possessing either a wild type (WT) NA or an NA with a single I222V, S331G, or S331R substitution [in influenza A(H3N2) viruses] or a single D342S, A395T, A395V, or A395D NA substitution (in influenza B viruses). 2018 PloS one Abstract IV I222V;S331G;S331R;D342S;A395T;A395V;A395D 211;218;228;290;297;304;314 216;223;233;295;302;309;319 NA;NA;NA;NA 74;185;194;320 76;187;196;322 29331671 The molecular characteristics of avian influenza viruses (H9N2) derived from air samples in live poultry markets. The N30D and T215A mutations in the M1 gene and amino acid residues L89V in PB2, P42S in NS1 and S31N in M2 were retained in these 9 strains of H9N2 isolates, which could enhance the virus's virulence. 2018 Infection, genetics and evolution Abstract IV N30D;T215A;L89V;P42S;S31N 4;13;68;81;97 8;18;72;85;101 M1;M2;NS1;PB2 36;105;89;76 38;107;92;79 29331671 The molecular characteristics of avian influenza viruses (H9N2) derived from air samples in live poultry markets. The PA gene of ZS201503 and ZS201602 exhibited an L336M mutation. 2018 Infection, genetics and evolution Abstract IV L336M 50 55 PA 4 6 29355500 Influenza Hemifusion Phenotype Depends on Membrane Context: Differences in Cell-Cell and Virus-Cell Fusion. Here, we show that a well-described fusion peptide mutant, G1S, has a phenotype that depends strongly on the viral membrane context. 2018 Journal of molecular biology Abstract IV G1S 59 62 29355500 Influenza Hemifusion Phenotype Depends on Membrane Context: Differences in Cell-Cell and Virus-Cell Fusion. The G1S mutant is well known to cause a "hemifusion" phenotype based on experiments in transfected cells, where cells expressing G1S hemagglutinin can undergo lipid mixing in a pH-triggered fashion similar to virus but will not support fusion pores. 2018 Journal of molecular biology Abstract IV G1S;G1S 4;129 7;132 HA 133 146 29355500 Influenza Hemifusion Phenotype Depends on Membrane Context: Differences in Cell-Cell and Virus-Cell Fusion. We compare fusion by the G1S hemagglutinin mutant expressed either in cells or in influenza virions and show that this hemifusion phenotype occurs in transfected cells but that native virions are able to support full fusion, albeit at a slower rate and 10-100x reduced infectious titer. 2018 Journal of molecular biology Abstract IV G1S 25 28 HA 29 42 29355500 Influenza Hemifusion Phenotype Depends on Membrane Context: Differences in Cell-Cell and Virus-Cell Fusion. We explain this with a quantitative model where the G1S mutant, instead of causing an absolute block of fusion, alters the protein stoichiometry required for fusion. 2018 Journal of molecular biology Abstract IV G1S 52 55 29407952 Discovery of C-1 modified oseltamivir derivatives as potent influenza neuraminidase inhibitors. And its potency against mutant H5N1-H274Y NA was just 7-fold weaker than OSC. 2018 European journal of medicinal chemistry Abstract IV H274Y 36 41 42 44 29409570 Early season co-circulation of influenza A(H3N2) and B(Yamagata): interim estimates of 2017/18 vaccine effectiveness, Canada, January 2018. Adjusted VE for influenza A(H3N2), driven by a predominant subgroup of clade 3C.2a viruses with T131K + R142K + R261Q substitutions, was low at 17% (95% confidence interval (CI): -14 to 40). 2018 Euro surveillance Abstract IV T131K;R142K;R261Q 96;104;112 101;109;117 29433792 Clinical characteristics of influenza virus-induced lower respiratory infection during the 2015 to 2016 season. In the six PB cases, we found one patient with H275Y mutation in neuraminidase. 2018 Journal of infection and chemotherapy Abstract IV H275Y 47 52 65 78 29445999 The S190R mutation in the hemagglutinin protein of pandemic H1N1 2009 influenza virus increased its pathogenicity in mice. In this study, we detected an egg-adapted HA S190R mutation in the pandemic H1N1 virus 2009 (pdmH1N1), and evaluated the effects of this mutation on receptor binding affinity and pathogenicity in mice. 2018 Science China. Life sciences Abstract IV S190R 45 50 HA 42 44 29445999 The S190R mutation in the hemagglutinin protein of pandemic H1N1 2009 influenza virus increased its pathogenicity in mice. Our study demonstrated that the S190R mutation resulted in earlier death and higher weight loss in mice compared with the wild-type virus. 2018 Science China. Life sciences Abstract IV S190R 32 37 29453856 Defective RNA sensing by RIG-I in severe influenza virus infection. By whole exome sequencing we identified two variants, p.R71H and p.P885S, located in the caspase activation and recruitment domain (CARD) and RNA binding domains, respectively, of DExD/H-box helicase 58 (DDX58) encoding the RNA sensor retinoic acid inducible gene 1 (RIG-I). 2018 Clinical and experimental immunology Abstract IV R71H;P885S 54;65 60;72 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. In addition, sequence analysis confirmed the several substitutions of internal genes and gene substitutions associated with drug resistance (I222V in NA and S31N in M2) in the fatal cases. 2018 Influenza and other respiratory viruses Abstract IV I222V;S31N 141;157 146;161 M2;NA 165;150 167;152 29489903 Design and synthesis of constrained bicyclic molecules as candidate inhibitors of influenza A neuraminidase. This allowed the efficient preparation of a small library of new bicyclic ligands that were characterized by enzyme inhibition assays against influenza A neuraminidases N1, its H274Y mutant, and N2. 2018 PloS one Abstract IV H274Y 177 182 154 168 29491160 Enhanced Human-Type Receptor Binding by Ferret-Transmissible H5N1 with a K193T Mutation. Indeed, the addition of the K193T mutation to the H5 HA of a respiratory-droplet-transmissible virus dramatically improves both binding to human trachea epithelial cells and specificity for extended alpha2-6-sialylated N-linked glycans recognized by human influenza viruses.IMPORTANCE Infections by avian H5N1 viruses are associated with a high mortality rate in several species, including humans. 2018 Journal of virology Abstract IV K193T 28 33 HA 53 55 29491160 Enhanced Human-Type Receptor Binding by Ferret-Transmissible H5N1 with a K193T Mutation. K193T seems to be a common receptor specificity determinant, as it increases human-type receptor binding in multiple subtypes. 2018 Journal of virology Abstract IV K193T 0 5 29491160 Enhanced Human-Type Receptor Binding by Ferret-Transmissible H5N1 with a K193T Mutation. The K193T mutation can now be used as a marker during surveillance of emerging viruses to assess potential pandemic risk. 2018 Journal of virology Abstract IV K193T 4 9 29491160 Enhanced Human-Type Receptor Binding by Ferret-Transmissible H5N1 with a K193T Mutation. Thus, we hypothesized that a K193T mutation would improve binding to branched N-linked receptors. 2018 Journal of virology Abstract IV K193T 29 34 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. AM2-S31N/V27I and AM2-S31N/L26I channels achieved similar specific proton conductance as AM2-S31N, but the AM2-S31N/L26I/A30T triple mutant had drastically reduced specific proton conductance. 2018 Antiviral research Abstract IV S31N;V27I;L26I;S31N;S31N;S31N;L26I;A30T 4;9;27;22;93;111;116;121 8;13;31;26;97;115;120;125 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. However, AM2-S31N/L26I/A30T viruses displayed attenuated growth as well as inability to compete with AM2-S31N viruses. 2018 Antiviral research Abstract IV S31N;L26I;A30T;S31N 13;18;23;105 17;22;27;109 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. Passage with a higher drug concentration of compound 2 selected higher level resistant viruses with a double mutant L26I + A30T. 2018 Antiviral research Abstract IV L26I;A30T 116;123 120;127 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. The majority of human influenza A viruses currently in circulation carry the amantadine-resistant AM2-S31N channel mutation. 2018 Antiviral research Abstract IV S31N 102 106 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. The results herein offer insight regarding the resistance mechanism of AM2-S31N inhibitors, and may help guide the design of the next-generation of AM2-S31N inhibitors with a higher genetic barrier to drug resistance. 2018 Antiviral research Abstract IV S31N;S31N 75;152 79;156 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. To understand the drug-resistance mechanism of AM2-S31N inhibitors, we performed serial viral passage experiments using the influenza virus A/California/07/2009 (H1N1) to select drug-resistant AM2 mutations against two representative AM2-S31N channel blockers (1 and 2). 2018 Antiviral research Abstract IV S31N;S31N 51;238 55;242 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. Unlike amantadine, which gives rise to resistance after a single passage, compounds 1 and 2 selected for partially resistant viruses at passages 05 and 04 with a V27I and L26I mutation, respectively. 2018 Antiviral research Abstract IV L26I;V27I 171;162 175;166 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. Viral replication fitness of AM2-S31N/V27I and AM2-S31N/L26I double mutant viruses were similar to AM2-S31N containing viruses in cell culture. 2018 Antiviral research Abstract IV V27I;S31N;L26I;S31N;S31N 38;33;56;51;103 42;37;60;55;107 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. We previously discovered a series of AM2-S31N inhibitors with potent antiviral activity against both oseltamivir-sensitive and -resistant influenza A viruses. 2018 Antiviral research Abstract IV S31N 41 45 29522492 Challenge for One Health: Co-Circulation of Zoonotic H5N1 and H9N2 Avian Influenza Viruses in Egypt. The H5N1 viruses acquired enhanced bird-to-human transmissibility by (1) altering amino acids in hemagglutinin (HA) that enable binding affinity to human-type receptors, (2) loss of the glycosylation site and 130 loop in the HA protein and (3) mutation of E627K in the PB2 protein to enhance viral replication in mammalian hosts. 2018 Viruses Abstract IV E627K 256 261 HA;HA;HA;PB2 112;225;97;269 114;227;110;272 29522492 Challenge for One Health: Co-Circulation of Zoonotic H5N1 and H9N2 Avian Influenza Viruses in Egypt. The receptor binding site of HA of Egyptian H9N2 viruses has been shown to contain the Q234L substitution along with a H191 mutation, which can increase human-like receptor specificity. 2018 Viruses Abstract IV Q234L 87 92 HA 29 31 29530659 Emergence of novel reassortant H6N2 avian influenza viruses in ducks in India. However, Kerala14 had V27I mutation marker for amantadine resistance in M2. 2018 Infection, genetics and evolution Abstract IV V27I 22 26 M2 72 74 29540597 Antigenically Diverse Swine Origin H1N1 Variant Influenza Viruses Exhibit Differential Ferret Pathogenesis and Transmission Phenotypes. A substitution in the H1 hemagglutinin (G155E) was identified that likely impacted antigenicity, and reverse genetics was employed to understand the molecular mechanism of antibody escape. 2018 Journal of virology Abstract IV G155E 40 45 HA 25 38 29540597 Antigenically Diverse Swine Origin H1N1 Variant Influenza Viruses Exhibit Differential Ferret Pathogenesis and Transmission Phenotypes. Reverse genetics was employed to identify a single antigenic site substitution (HA G155E) responsible for antigenic variation of A/Ohio/09/2015 compared to related classical swine influenza A(H1N1) viruses. 2018 Journal of virology Abstract IV G155E 83 88 HA 80 82 29541360 Unraveling the Binding, Proton Blockage, and Inhibition of Influenza M2 WT and S31N by Rimantadine Variants. Here, we investigate these concepts to explain binding and proton blockage of rimantadine variants bearing progressively larger alkyl groups to influenza A virus M2 wild type (WT) and M2 S31N protein proton channel. 2018 ACS medicinal chemistry letters Abstract IV S31N 187 191 M2;M2 162;184 164;186 29541360 Unraveling the Binding, Proton Blockage, and Inhibition of Influenza M2 WT and S31N by Rimantadine Variants. This is due to the fact that, in M2 S31N, the loss of the V27 pocket for the adamantyl cage resulted in low residence time inside the M2 pore. 2018 ACS medicinal chemistry letters Abstract IV S31N 36 40 M2;M2 33;134 35;136 29541360 Unraveling the Binding, Proton Blockage, and Inhibition of Influenza M2 WT and S31N by Rimantadine Variants. We showed that resistance of M2 S31N to rimantadine analogues compared to M2 WT resulted from their higher koff rates compared to the kon rates according to electrophysiology (EP) measurements. 2018 ACS medicinal chemistry letters Abstract IV S31N 32 36 M2;M2 29;74 31;76 29542264 Molecular design of antimicrobial peptides based on hemagglutinin fusion domain to combat antibiotic resistance in bacterial infection. Conversion of the native HAfp1-23 to a positively charged peptide HAfp1-23 _KK by E11K/D19K mutation can promote the peptide-membrane interaction substantially; this confers to the peptide a moderate antibacterial potency against antibiotic-resistant bacterial strains. 2018 Journal of peptide science Abstract IV E11K;D19K 82;87 86;91 29563296 New Threats from H7N9 Influenza Virus: Spread and Evolution of High- and Low-Pathogenicity Variants with High Genomic Diversity in Wave Five. Importantly, neuraminidase (NA) inhibitor (NAI) resistance (R292K in NA) and mammalian adaptation (e.g., E627K and A588V in PB2) mutations were found in a few non-human-derived HP-H7N9 strains. 2018 Journal of virology Abstract IV R292K;E627K;A588V 60;105;115 65;110;120 NA;NA;NAI;NA;PB2 28;69;43;13;124 30;71;46;26;127 29563296 New Threats from H7N9 Influenza Virus: Spread and Evolution of High- and Low-Pathogenicity Variants with High Genomic Diversity in Wave Five. Notably, the NAI drug-resistant (R292K in NA) and mammalian-adapted (e.g., E627K in PB2) mutations were found in HP-H7N9 not only from human isolates but also from poultry and environmental isolates, indicating increased risks for human infections. 2018 Journal of virology Abstract IV R292K;E627K 33;75 38;80 NA;NAI;PB2 42;13;84 44;16;87 29572682 The inhibitory effect of sodium baicalin on oseltamivir-resistant influenza A virus via reduction of neuraminidase activity. Direct interactions between sodium baicalin and NA were observed, and we simulated the interactions of sodium baicalin with N9-R294K and N9 near the active sites of OC-N9-R294K and OC-N9. 2018 Archives of pharmacal research Abstract IV R294K;R294K 127;171 132;176 N9;N9;N9;N9;NA 124;137;168;184;48 126;139;170;186;50 29572682 The inhibitory effect of sodium baicalin on oseltamivir-resistant influenza A virus via reduction of neuraminidase activity. Intravenous administration of sodium baicalin at 100 mg/kg/d enabled the survival of 20% of H1N1-H275Y-infected mice. 2018 Archives of pharmacal research Abstract IV H275Y 97 102 29572682 The inhibitory effect of sodium baicalin on oseltamivir-resistant influenza A virus via reduction of neuraminidase activity. Its efficacy against oseltamivir-resistant mutant A/FM/1/47-H275Y (H1N1-H275Y) was evaluated in vitro and in vivo. 2018 Archives of pharmacal research Abstract IV H275Y;H275Y 60;72 65;77 29572682 The inhibitory effect of sodium baicalin on oseltamivir-resistant influenza A virus via reduction of neuraminidase activity. Results showed that 10 muM of sodium baicalin inhibited A/FM/1/47 (H1N1), A/Beijing/32/92 (H3N2) and H1N1-H275Y in MDCK cells in a dose-dependent manner, with inhibitory rates of 83.9, 75.9 and 47.7%, respectively. 2018 Archives of pharmacal research Abstract IV H275Y 106 111 29572682 The inhibitory effect of sodium baicalin on oseltamivir-resistant influenza A virus via reduction of neuraminidase activity. The IC50 values of sodium baicalin against H1N1-H275Y and cells-expressing A/Anhui/1/2013-R294K (H7N9-R294K) NA protein (N9-R294K) were 214.4 muM and 216.3 muM. 2018 Archives of pharmacal research Abstract IV H275Y;R294K;R294K;R294K 48;90;102;124 53;95;107;129 N9;NA 121;109 123;111 29572682 The inhibitory effect of sodium baicalin on oseltamivir-resistant influenza A virus via reduction of neuraminidase activity. The residues responsible for the sodium baicalin-N9-R294K and sodium baicalin-N9 interactions were the same, confirming that sodium baicalin exerts effects on wild-type and oseltamivir-resistant viral strains. 2018 Archives of pharmacal research Abstract IV R294K 52 57 N9;N9 49;78 51;80 29574145 Identification of Indonesian clade 2.1 highly pathogenic influenza A(H5N1) viruses with N294S and S246N neuraminidase substitutions which further reduce oseltamivir susceptibility. The NAs of two of these viruses from Sumatra and Aceh, had an N294S substitution, while one virus from Sulawesi had an S246N NA substitution. 2018 Antiviral research Abstract IV N294S;S246N 62;119 67;124 NA;NA 125;4 127;7 29582231 Amino acid substitutions in low pathogenic avian influenza virus strains isolated from wild birds in Korea. We found substitution rates of 71.7% at the C38Y amino acid site within the polymerase basic protein 1 (PB1) gene, 66.7% at the D222G site within the hemagglutinin (HA) 1 gene, and 75.6% at the A184 site within the nucleoprotein (NP) gene. 2018 Virus genes Abstract IV C38Y;D222G 44;128 48;133 HA;HA;NP;NP;PB1 165;150;230;215;104 167;163;232;228;107 29587786 Effects of the S42 residue of the H1N1 swine influenza virus NS1 protein on interferon responses and virus replication. METHODS: To study the effects of the key amino acids of NS1, we rescued NS1 mutants (S42P, D92E, and S42P/D92E) of the A/swine/Shanghai/3/2014(H1N1) strain and compared their replication ability and cytokine production as well as the intracellular localization in cultured cells. 2018 Virology journal Abstract IV S42P;D92E;S42P;D92E 85;91;101;106 89;95;105;110 NS1;NS1 56;72 59;75 29587786 Effects of the S42 residue of the H1N1 swine influenza virus NS1 protein on interferon responses and virus replication. RESULTS: We found that the S42P and D92E mutation displayed no changes on NS1 nuclear localization. 2018 Virology journal Abstract IV S42P;D92E 27;36 31;40 NS1 74 77 29587786 Effects of the S42 residue of the H1N1 swine influenza virus NS1 protein on interferon responses and virus replication. The S42P (but not D92E) mutation suppressed protein synthesis and reduced virus growth properties, and there was an inability to antagonize host cell interferon production and IRF3 activation, which led to high levels of IFN-alpha and IFN-beta production. 2018 Virology journal Abstract IV S42P;D92E 4;18 8;22 29587792 Major contribution of the RNA-binding domain of NS1 in the pathogenicity and replication potential of an avian H7N1 influenza virus in chickens. RESULTS: The double substitution R38A-K41A in the RBD dramatically reduced the pathogenicity and replication potential of the virus, whereas the substitution A149V that was considered to abrogate the IFN-antagonistic activity of the effector domain entailed much less effects. 2018 Virology journal Abstract IV R38A;K41A;A149V 33;38;158 37;42;163 29587792 Major contribution of the RNA-binding domain of NS1 in the pathogenicity and replication potential of an avian H7N1 influenza virus in chickens. Unexpectedly, the R38A-K41A substitution in the recombinant RBD did not alter its in vitro affinity for a model dsRNA. 2018 Virology journal Abstract IV R38A;K41A 18;23 22;27 29587792 Major contribution of the RNA-binding domain of NS1 in the pathogenicity and replication potential of an avian H7N1 influenza virus in chickens. When overexpressed in avian cells, both the wt- and A149V-NS1s, as well as the individually expressed wt-RBD to a lesser extent, enhanced the activity of the reconstituted viral RNA-polymerase in a minireplicon assay. 2018 Virology journal Abstract IV A149V 52 57 NS1 58 62 29587792 Major contribution of the RNA-binding domain of NS1 in the pathogenicity and replication potential of an avian H7N1 influenza virus in chickens. When overexpressed in avian lung epithelial cells, both the wt-NS1 and 3841AA-NS1, but not the A149V-NS1, reduced the poly(I:C)-induced activation of the IFN-sensitive chicken Mx promoter. 2018 Virology journal Abstract IV A149V 95 100 NS1;NS1;NS1 63;78;101 66;81;104 29587792 Major contribution of the RNA-binding domain of NS1 in the pathogenicity and replication potential of an avian H7N1 influenza virus in chickens. While all three viruses initiated the viral life cycle in avian cells, replication of the R38A-K41A virus was severely impaired. 2018 Virology journal Abstract IV R38A;K41A 90;95 94;99 29593694 Amino Acid Substitutions HA A150V, PA A343T, and PB2 E627K Increase the Virulence of H5N6 Influenza Virus in Mice. However, HA A150V and PA A343T seemed to attenuate PB2 E627K in vivo, which implies the difference between mixed viral populations under natural condition and single population under experiment, specialization and cooperation in quasispecies is important in the process of adaption. 2018 Frontiers in microbiology Abstract IV A150V;A343T;E627K 12;25;55 17;30;60 HA;PA;PB2 9;22;51 11;24;54 29593694 Amino Acid Substitutions HA A150V, PA A343T, and PB2 E627K Increase the Virulence of H5N6 Influenza Virus in Mice. In addition, we show that PA A343T dramatically exacerbates the effect of PB2 E627K on viral polymerase activity; when combined, these two substitutions work synergistically. 2018 Frontiers in microbiology Abstract IV A343T;E627K 29;78 34;83 PA;PB2 26;74 28;77 29593694 Amino Acid Substitutions HA A150V, PA A343T, and PB2 E627K Increase the Virulence of H5N6 Influenza Virus in Mice. The PA A343T substitution mildly enhanced viral polymerase activity but the reduced survival rate in mice indicates this substitution may change the immunoreaction of the host. 2018 Frontiers in microbiology Abstract IV A343T 7 12 PA 4 6 29593694 Amino Acid Substitutions HA A150V, PA A343T, and PB2 E627K Increase the Virulence of H5N6 Influenza Virus in Mice. The results demonstrate that HA A150V greatly altered the receptor binding preference of 6D2. 2018 Frontiers in microbiology Abstract IV A150V 32 37 HA 29 31 29593694 Amino Acid Substitutions HA A150V, PA A343T, and PB2 E627K Increase the Virulence of H5N6 Influenza Virus in Mice. The well-known PB2 E627K substitution increased eight folds the relative polymerase activity compared to PA A343T and resulted in 100% death rate in mice. 2018 Frontiers in microbiology Abstract IV E627K;A343T 19;108 24;113 PA;PB2 105;15 107;18 29593694 Amino Acid Substitutions HA A150V, PA A343T, and PB2 E627K Increase the Virulence of H5N6 Influenza Virus in Mice. This study suggests that HA A150V, PA A343T, and PB2 E627K are crucial in the adaption and increased pathogenicity of H5N6 in mammalian hosts. 2018 Frontiers in microbiology Abstract IV A150V;A343T;E627K 28;38;53 33;43;58 HA;PA;PB2 25;35;49 27;37;52 29593694 Amino Acid Substitutions HA A150V, PA A343T, and PB2 E627K Increase the Virulence of H5N6 Influenza Virus in Mice. Three amino acid substitutions (HA A150V, PA A343T, PB2 E627K) are observed in H5N6 virus A/duck/Zhejiang/6D2/2013 (6D2) in lung-to-lung passage in mice. 2018 Frontiers in microbiology Abstract IV A150V;A343T;E627K 35;45;56 40;50;61 HA;PA;PB2 32;42;52 34;44;55 29607359 Molecular analysis of hemagglutinin, neuraminidase, matrix genes provide insight into the genetic diversity of seasonal H3N2 human influenza a viruses in Bangladesh during July-August, 2012. Despite these findings, we found N161S substitution in all four H3N2 influenza stains resulting in the gain of NSS160-162 glycosylation site. 2018 Virusdisease Abstract IV N161S 33 38 NS 111 113 29630683 The use of plant lectins to regulate H1N1 influenza A virus receptor binding activity. Consecutive passages of the A/California/04/09 virus with or without lectins in human lung epithelial Calu-3 cells led to development of three HA1 amino acid substitutions, N129D, G155E, and S183P, and one mutation in the neuraminidase (NA), G201E. 2018 PloS one Abstract IV N129D;G155E;S183P;G201E 173;180;191;242 178;185;196;247 HA1;NA;NA 143;237;222 146;239;235 29630683 The use of plant lectins to regulate H1N1 influenza A virus receptor binding activity. Furthermore, the G201E mutation in NA reduced the NA enzyme activity ( 2.3-fold). 2018 PloS one Abstract IV G201E 17 22 NA;NA 35;50 37;52 29630683 The use of plant lectins to regulate H1N1 influenza A virus receptor binding activity. In addition, the HA1 N129D and HA1 G155E substitutions were identified as antigenic mutations. 2018 PloS one Abstract IV N129D;G155E 21;35 26;40 HA1;HA1 17;31 20;34 29630683 The use of plant lectins to regulate H1N1 influenza A virus receptor binding activity. The S183P mutation significantly increased binding to several alpha2,6 SA-linked glycans, including YDS, 6'SL(N), and 6-Su-6'SLN, compared to the wild-type virus ( 3.6-fold, P < 0.05). 2018 PloS one Abstract IV S183P 4 9 29630683 The use of plant lectins to regulate H1N1 influenza A virus receptor binding activity. Two other HA1 mutations, N129D and G155E, were sufficient to significantly increase binding to alpha2,6-linked glycans, 6'SLN and 6-Su-6'SLN, compared to S183P ( 4.1-fold, P < 0.05). 2018 PloS one Abstract IV N129D;G155E;S183P 25;35;154 30;40;159 HA1 10 13 29643248 A Single Amino Acid in the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses. In a subsequent minireplicon assay, the effect of PA K338R was highlighted by the enhancement of viral polymerase complex activity of both Vc_BR60 and Ym_WI01 viruses. 2018 Journal of virology Abstract IV K338R 53 58 PA 50 52 29643248 A Single Amino Acid in the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses. Several amino acid mutations were identified in the PB2, PB1, PA, BM2, and/or NS1 protein-coding regions, and one concurrent lysine (K)-to-arginine (R) mutation in PA residue 338 (PA K338R) was found in both maVc_BR60 and maYm_WI01 viruses. 2018 Journal of virology Abstract IV K338R 183 188 BM2;NS1;PA;PA;PA;PB1;PB2 66;78;62;164;180;57;52 69;81;64;166;182;60;55 29643248 A Single Amino Acid in the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses. These results suggest that the PA K338R mutation may be a molecular determinant of IBV pathogenicity via modulating the viral polymerase function of IBVs.IMPORTANCE To investigate molecular pathogenic determinants of IBVs, which are one of the targets of seasonal influenza vaccines, we adapted both Victoria and Yamagata lineage IBVs independently in mice. 2018 Journal of virology Abstract IV K338R 34 39 PA 31 33 29643248 A Single Amino Acid in the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses. When analyzed using viruses rescued through reverse genetics, it was shown that PA K338R alone could increase the pathogenicity of both IBVs in mice and viral replication in the respiratory tracts of ferrets. 2018 Journal of virology Abstract IV K338R 83 88 PA 80 82 29677653 Three amino acid substitutions in the NS1 protein change the virus replication of H5N1 influenza virus in human cells. Furthermore, a recombinant HN01 virus expressing either NS1-C133F or the triple mutation replicate with higher titers in human A549 cells and macrophages compared to the parent virus. 2018 Virology Abstract IV C133F 60 65 NS1 56 59 29677653 Three amino acid substitutions in the NS1 protein change the virus replication of H5N1 influenza virus in human cells. This capability was restored by three amino acid substitutions on the NS1 protein: K55E, K66E, and C133F, resulting in recovered binding to CPSF30 and decreased interferon response activity. 2018 Virology Abstract IV K55E;K66E;C133F 83;89;99 87;93;104 NS1 70 73 29688498 Dynamic Variation and Reversion in the Signature Amino Acids of H7N9 Virus During Human Infection. Dual D701N and E627K mutations emerged but failed to achieve predominance in any of the samples. 2018 The Journal of infectious diseases Abstract IV D701N;E627K 5;15 10;20 29688498 Dynamic Variation and Reversion in the Signature Amino Acids of H7N9 Virus During Human Infection. Neuraminidase (NA) R292K, basic polymerase 2 (PB2) E627K, and D701N were the 3 most dynamic mutations. 2018 The Journal of infectious diseases Abstract IV R292K;E627K;D701N 19;51;62 24;56;67 NA;NA;PB2 15;0;46 17;13;49 29688498 Dynamic Variation and Reversion in the Signature Amino Acids of H7N9 Virus During Human Infection. The oseltamivir resistance-related NA R292K mutation was present in 9 samples from 5 patients, including 1 sample obtained before antiviral therapy. 2018 The Journal of infectious diseases Abstract IV R292K 38 43 35 37 29688498 Dynamic Variation and Reversion in the Signature Amino Acids of H7N9 Virus During Human Infection. The PB2 E627K substitution was present in 18 samples from 8 patients, among which 12 samples demonstrated a mixture of E/K and the 627K frequency exhibited dynamic variation. 2018 The Journal of infectious diseases Abstract IV E627K 8 13 PB2 4 7 29691337 Identification of the I38T PA Substitution as a Resistance Marker for Next-Generation Influenza Virus Endonuclease Inhibitors. However, the change does not lead to a complete loss of replication activity in vitro Our results predict that RO-7-resistant influenza viruses carrying the I38T substitution may emerge under treatment. 2018 mBio Abstract IV I38T 157 161 29691337 Identification of the I38T PA Substitution as a Resistance Marker for Next-Generation Influenza Virus Endonuclease Inhibitors. I38T emerged between 5 and 10 passages, and when introduced into recombinant influenza A(H1N1) viruses, alone conferred RO-7 resistance (up to an 81-fold change in EC50). 2018 mBio Abstract IV I38T 0 4 29691337 Identification of the I38T PA Substitution as a Resistance Marker for Next-Generation Influenza Virus Endonuclease Inhibitors. Through serial passage of influenza A(H1N1) viruses in MDCK cells under selective pressure of RO-7, we identified an I38T substitution within the PA endonuclease domain that conferred in vitro resistance to RO-7 (up to a 287-fold change in 50% effective concentration [EC50]). 2018 mBio Abstract IV I38T 117 121 PA 146 148 29743603 Unexpected infection outcomes of China-origin H7N9 low pathogenicity avian influenza virus in turkeys. However, the amino acid change L235Q in the haemagglutinin gene occurred in directly-infected turkeys and transmitted to the contacts, including those that died and the two which resolved infection to survive to the end of the study. 2018 Scientific reports Abstract IV L235Q 31 36 HA 44 58 29750015 Symmetric dimeric adamantanes for exploring the structure of two viroporins: influenza virus M2 and hepatitis C virus p7. The lack of channel blockage of the dimeric amantadine and rimantadine analogs against M2 wild type and M2-S31N mutant was consistent with previously proposed drug-binding mechanisms and further confirmed that the pore-binding model is the pharmacologically relevant drug-binding model. 2018 Drug design, development and therapy Abstract IV S31N 107 111 M2;M2 87;104 89;106 29753891 Pleiotropic effects of hemagglutinin amino acid substitutions of influenza A(H1N1)pdm09 virus escape mutants. Our potential antigenic variants, except readapted variant, which contained A198E mutation, did not reach fixation in infected people. 2018 Virus research Abstract IV A198E 76 81 29753891 Pleiotropic effects of hemagglutinin amino acid substitutions of influenza A(H1N1)pdm09 virus escape mutants. Our results showed that N133D (H3 numbering) mutation significantly lowered the pH of fusion optimum. 2018 Virus research Abstract IV N133D 24 29 29753891 Pleiotropic effects of hemagglutinin amino acid substitutions of influenza A(H1N1)pdm09 virus escape mutants. Several amino acid substitutions, including K163 N, Q192 L, D190E, G228E, and K285 M, reduced the stability of HA as determined by heat inactivation, whereas A198E substitution is associated with significant increase in HA thermostability compared to the wild-type virus. 2018 Virus research Abstract IV K163N;Q192L;D190E;G228E;K285M;A198E 44;52;60;67;78;158 50;58;65;72;84;163 HA;HA 111;220 113;222 29753891 Pleiotropic effects of hemagglutinin amino acid substitutions of influenza A(H1N1)pdm09 virus escape mutants. We found that amino acid change D190 N was associated with a significant decrease in viral growth in eggs and mice. 2018 Virus research Abstract IV D190N 32 38 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. Furthermore, we observed that the NS1 R38A/K41A virus triggered high-level of IFN-alpha/beta production in lung tissues and was eliminated from the host in a relatively short period of time. 2018 Frontiers in cellular and infection microbiology Abstract IV R38A;K41A 38;43 42;47 NS1 34 37 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. Here, RIG-I-knockout 293T cells were used to package the IFN-sensitive influenza A/WSN/33 (H1N1) virus expressing the mutant NS1 R38A/K41A. 2018 Frontiers in cellular and infection microbiology Abstract IV R38A;K41A 129;134 133;138 NS1 125 128 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. In a mouse model, the NS1 R38A/K41A virus showed more than a 4-log reduction in lung virus titers compared to the WT virus at 3 and 5 days post infection. 2018 Frontiers in cellular and infection microbiology Abstract IV R38A;K41A 26;31 30;35 NS1 22 25 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. Moreover, the NS1 R38A/K41A virus almost lost its IFN antagonist activity and could no longer replicate in A549, MDCK, and Vero cells after 3-6 passages. 2018 Frontiers in cellular and infection microbiology Abstract IV R38A;K41A 18;23 22;27 NS1 14 17 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. The NS1 R38A/K41A virus was able to steadily propagate in this IFN-deficient cell line for at least 20 passages. 2018 Frontiers in cellular and infection microbiology Abstract IV R38A;K41A 8;13 12;17 NS1 4 7 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. This indicated that the replication of NS1 R38A/K41A virus is limited in conventional cells. 2018 Frontiers in cellular and infection microbiology Abstract IV R38A;K41A 43;48 47;52 NS1 39 42 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. Thus, we found that the replication of the NS1 R38A/K41A virus was limited in IFN-competent cells and mice. 2018 Frontiers in cellular and infection microbiology Abstract IV R38A;K41A 47;52 51;56 NS1 43 46 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. We found that the packaging efficiency of the NS1 R38A/K41A virus in RIG-I-knockout 293T cells was much higher than that in 293T cells. 2018 Frontiers in cellular and infection microbiology Abstract IV R38A;K41A 50;55 54;59 NS1 46 49 29783694 Adaptive Mutations in Influenza A/California/07/2009 Enhance Polymerase Activity and Infectious Virion Production. Among mutations that emerged during mouse-adaptation, we focused on amino acid substitutions in polymerase subunits: polymerase basic-1 (PB1) T156A and F740L and polymerase acidic (PA) E349G. 2018 Viruses Abstract IV T156A;F740L;E349G 142;152;185 147;157;190 PA;PB1;PA 181;137;162 183;140;179 29783694 Adaptive Mutations in Influenza A/California/07/2009 Enhance Polymerase Activity and Infectious Virion Production. These mutations were evaluated singly and in combination in minigenome replicon assays, which revealed that PA E349G increased polymerase activity. 2018 Viruses Abstract IV E349G 111 116 PA 108 110 29866491 Neuraminidase inhibitor susceptibility profile of human influenza viruses during the 2016-2017 influenza season in Mainland China. One B/Victoria-lineage virus contained dual amino acid substitution NA P124T and V422I, which confers HRI by zanamivir. 2018 Journal of infection and chemotherapy Abstract IV P124T;V422I 71;81 76;86 68 70 29866491 Neuraminidase inhibitor susceptibility profile of human influenza viruses during the 2016-2017 influenza season in Mainland China. The most common neuraminidase (NA) amino acid substitution was H275Y in A (H1N1)pdm09 virus, which confers HRI by oseltamivir. 2018 Journal of infection and chemotherapy Abstract IV H275Y 63 68 NA;NA 31;16 33;29 29866491 Neuraminidase inhibitor susceptibility profile of human influenza viruses during the 2016-2017 influenza season in Mainland China. Two A (H1N1)pdm09 viruses contained a new NA amino acid substitution respectively, S110F and D151E, which confers RI by oseltamivir or/and zanamivir. 2018 Journal of infection and chemotherapy Abstract IV S110F;D151E 83;93 88;98 42 44 29866491 Neuraminidase inhibitor susceptibility profile of human influenza viruses during the 2016-2017 influenza season in Mainland China. Two B/Victoria-lineage viruses harbored a new NA amino acid substitution respectively, H134Q and S246P, which confers RI by zanamivir. 2018 Journal of infection and chemotherapy Abstract IV H134Q;S246P 87;97 92;102 46 48 29882021 Lethal Influenza in Two Related Adults with Inherited GATA2 Deficiency. Patients were heterozygous for a novel, hypomorphic, R396L mutation leading to haplo-insufficiency. 2018 Journal of clinical immunology Abstract IV R396L 53 58 29885803 PB2 E627K or D701N substitution does not change the virulence of canine influenza virus H3N2 in mice and dogs. Here, we constructed recombinant viruses by introducing E627K or D701N into the PB2 gene in the genetic background of A/Canine/Guangdong/02/2011H3N2 using a reverse-genetic system. 2018 Veterinary microbiology Abstract IV E627K;D701N 56;65 61;70 PB2 80 83 29885803 PB2 E627K or D701N substitution does not change the virulence of canine influenza virus H3N2 in mice and dogs. However, how the E627K and D701N substitutions in the PB2 subunit might affect the virulence of CIV H3N2 is unclear. 2018 Veterinary microbiology Abstract IV E627K;D701N 17;27 22;32 PB2 54 57 29885803 PB2 E627K or D701N substitution does not change the virulence of canine influenza virus H3N2 in mice and dogs. Previous studies have reported that the E627K and D701N substitutions in the PB2 subunit enhanced viral pathogenicity to mammals in various influenza viruses. 2018 Veterinary microbiology Abstract IV E627K;D701N 40;50 45;55 PB2 77 80 29885803 PB2 E627K or D701N substitution does not change the virulence of canine influenza virus H3N2 in mice and dogs. The results showed that the E627K or D701N substitutions in the PB2 subunit of CIV H3N2 enhanced polymerase activity, but these substitutions did not impact viral pathogenicity in mice or beagles. 2018 Veterinary microbiology Abstract IV E627K;D701N 28;37 33;42 PB2 64 67 29899096 Directed Evolution of an Influenza Reporter Virus To Restore Replication and Virulence and Enhance Noninvasive Bioluminescence Imaging in Mice. rPB2-MA9/PA-D479N has increased mRNA transcription, which helps restore wild-type-like phenotypes in DBA/2 and BALB/c mice. 2018 Journal of virology Abstract IV D479N 12 17 PA 9 11 29899096 Directed Evolution of an Influenza Reporter Virus To Restore Replication and Virulence and Enhance Noninvasive Bioluminescence Imaging in Mice. Using reverse genetics, we discovered fitness was restored in virus rPB2-MA9/PA-D479N by a combination of PA-D479N and PB2-E158G amino acid mutations and PB2 noncoding mutations C1161T and C1977T. 2018 Journal of virology Abstract IV D479N;D479N;E158G;C1161T;C1977T 80;109;123;178;189 85;114;128;184;195 PA;PA;PB2;PB2 77;106;119;154 79;108;122;157 29899096 Directed Evolution of an Influenza Reporter Virus To Restore Replication and Virulence and Enhance Noninvasive Bioluminescence Imaging in Mice. Virus rPB2-MA9/PA-D479N is expected to be a useful tool for noninvasive imaging of pH1N1 influenza virus infection and clearance while analyzing virus-host interactions and developing new therapeutics and vaccines.IMPORTANCE Influenza viruses contribute to 290,000 to 650,000 deaths globally each year. 2018 Journal of virology Abstract IV D479N 18 23 PA 15 17 Influenza A virus H1N1 infection 89 114 29927982 Influenza D virus M2 protein exhibits ion channel activity in Xenopus laevis oocytes. Compared with intact DM2, DM2 variants with mutation in the YxxxK motif, namely Y72A and K76A DM2, showed lower Vmid values while showing no change in reversal potential. 2018 PloS one Abstract IV Y72A;K76A 80;89 84;93 29933553 Kinetic, Thermodynamic, and Structural Analysis of Drug Resistance Mutations in Neuraminidase from the 2009 Pandemic Influenza Virus. Combination of H275Y with an I223V or S247N mutation results in extreme impairment of oseltamivir's inhibition potency. 2018 Viruses Abstract IV H275Y;I223V;S247N 15;29;38 20;34;43 29933553 Kinetic, Thermodynamic, and Structural Analysis of Drug Resistance Mutations in Neuraminidase from the 2009 Pandemic Influenza Virus. In contrast, the major oseltamivir resistance mutation H275Y causes a significant decrease in the enzyme's ability to bind this drug. 2018 Viruses Abstract IV H275Y 55 60 29933553 Kinetic, Thermodynamic, and Structural Analysis of Drug Resistance Mutations in Neuraminidase from the 2009 Pandemic Influenza Virus. Our crystal structures also helped explain the augmenting effect on resistance of combining H275Y with both substitutions. 2018 Viruses Abstract IV H275Y 92 97 29933553 Kinetic, Thermodynamic, and Structural Analysis of Drug Resistance Mutations in Neuraminidase from the 2009 Pandemic Influenza Virus. Our results reveal that the I223V or S247N substitution alone confers only a moderate reduction in oseltamivir affinity. 2018 Viruses Abstract IV I223V;S247N 28;37 33;42 29933553 Kinetic, Thermodynamic, and Structural Analysis of Drug Resistance Mutations in Neuraminidase from the 2009 Pandemic Influenza Virus. Our structural analyses revealed that the H275Y substitution has a major effect on the oseltamivir binding pose within the active site while the influence of other studied mutations is much less prominent. 2018 Viruses Abstract IV H275Y 42 47 29933553 Kinetic, Thermodynamic, and Structural Analysis of Drug Resistance Mutations in Neuraminidase from the 2009 Pandemic Influenza Virus. The resistance substitutions I223V and S247N, alone or in combination with the major oseltamivir-resistance mutation H275Y, have been observed in 2009 pandemic H1N1 viruses. 2018 Viruses Abstract IV I223V;S247N;H275Y 29;39;117 34;44;122 29933553 Kinetic, Thermodynamic, and Structural Analysis of Drug Resistance Mutations in Neuraminidase from the 2009 Pandemic Influenza Virus. We overexpressed and purified the ectodomain of wild-type neuraminidase from the A/California/07/2009 (H1N1) influenza virus, as well as variants containing H275Y, I223V, and S247N single mutations and H275Y/I223V and H275Y/S247N double mutations. 2018 Viruses Abstract IV H275Y;I223V;S247N;H275Y;I223V;H275Y;S247N 157;164;175;202;208;218;224 162;169;180;207;213;223;229 58 71 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. A reduced affinity to the I38T mutant is supported by the lower stability of the BXA-bound endonuclease. 2018 Scientific reports Abstract IV I38T 26 30 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. Co-crystal structures of wild-type and I38T influenza A and B endonucleases bound to BXA show that the mutation reduces van der Waals contacts with the inhibitor. 2018 Scientific reports Abstract IV I38T 39 43 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. The viruses harboring the I38T substitution show severely impaired replicative fitness in cells, and correspondingly reduced endonuclease activity in vitro. 2018 Scientific reports Abstract IV I38T 26 30 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. We find that the PA I38T substitution is a major pathway for reduced susceptibility to BXA, with 30- to 50-fold and 7-fold EC50 changes in A and B viruses, respectively. 2018 Scientific reports Abstract IV I38T 20 24 PA 17 19 29945131 Changes in Hemagglutinin and Neuraminidase Genes of pH1N1 Influenza Virus Strains Collected from a North Indian Tertiary Care Hospital during 2015. Four of HA1(K180Q, S202T, S220T, and A273T) and NA1 (N200S, V241I, N248D, and N270K) mutations were observed in all pH1N1 study strains. 2017 Intervirology Abstract IV K180Q;S202T;S220T;A273T;N200S;V241I;N248D;N270K 12;19;26;37;53;60;67;78 17;24;31;42;58;65;72;83 HA1;NA 8;48 11;50 29965752 Optimization of N-Substituted Oseltamivir Derivatives as Potent Inhibitors of Group-1 and -2 Influenza A Neuraminidases, Including a Drug-Resistant Variant. They also showed greater inhibitory activity than OSC toward H274Y and E119V variant. 2018 Journal of medicinal chemistry Abstract IV H274Y;E119V 61;71 66;76 29976861 Anti-Influenza A Viral Butenolide from Streptomyces sp. Smu03 Inhabiting the Intestine of Elephas maximus. In addition, 1 was also active against oseltamivir-resistant influenza virus strain of A/PR/8/34 with NA-H274Y mutation. 2018 Viruses Abstract IV H274Y 105 110 102 104 29981696 Novel mutations in avian PA in combination with an adaptive mutation in PR8 NP exacerbate the virulence of PR8-derived recombinant influenza A viruses in mice. The PR8-PA(0028)-E684G mutant showed significantly higher viral replication in mammalian cells as compared to PR8-PA(0028) and led to 100% mortality in mice, with significantly increased interferon beta expression. 2018 Veterinary microbiology Abstract IV E684G 17 22 PA;PA 8;114 10;116 29981696 Novel mutations in avian PA in combination with an adaptive mutation in PR8 NP exacerbate the virulence of PR8-derived recombinant influenza A viruses in mice. Thus, the E684G mutation in the PA gene may play an important role in viral pathogenicity in mice by increasing viral replication and the host immune response. 2018 Veterinary microbiology Abstract IV E684G 10 15 PA 32 34 29981696 Novel mutations in avian PA in combination with an adaptive mutation in PR8 NP exacerbate the virulence of PR8-derived recombinant influenza A viruses in mice. To minimize the differences due to NP mutations, we generated 0028-PA mutants with an E375G mutation, not affecting viral replication and pathogenicity, in the NP gene. 2018 Veterinary microbiology Abstract IV E375G 86 91 NP;NP;PA 35;160;67 37;162;69 29997206 Mutation W222L at the Receptor Binding Site of Hemagglutinin Could Facilitate Viral Adaption from Equine Influenza A(H3N8) Virus to Dogs. Findings from this study suggest that an equine-origin A(H3N8) IAV with mutation W222L at its hemagglutinin increased binding to canine-specific receptors with sialyl Lewis X and Neu5Gc motifs and, thereby, may have facilitated viral adaption from horses to dogs. 2018 Journal of virology Abstract IV W222L 81 86 HA 94 107 29997206 Mutation W222L at the Receptor Binding Site of Hemagglutinin Could Facilitate Viral Adaption from Equine Influenza A(H3N8) Virus to Dogs. Our findings suggest that a substitution of W222L in the hemagglutinin of the equine-origin A(H3N8) virus facilitated its host adaption to dogs. 2018 Journal of virology Abstract IV W222L 44 49 HA 57 70 29999583 A 627K variant in the PB2 protein of H9 subtype influenza virus in wild birds. Most importantly, two viruses harbored the E627K mutation in the polymerase PB2 (PB2) protein. 2018 Influenza and other respiratory viruses Abstract IV E627K 43 48 PB2;PB2 76;81 79;84 30021892 Functional Evolution of the 2009 Pandemic H1N1 Influenza Virus NS1 and PA in Humans. DeDiego, J Virol 91:e00721-17, 2017, https://doi.org/10.1128/JVI.00721-17), and amino acid changes in the PA-X protein (V100I, N204S, R221Q, and L229S). 2018 Journal of virology Abstract IV V100I;N204S;R221Q;L229S 120;127;134;145 125;132;139;150 PA-X 106 110 30021892 Functional Evolution of the 2009 Pandemic H1N1 Influenza Virus NS1 and PA in Humans. In addition, currently circulating pH1N1 viruses have acquired amino acid changes in the PA protein (V100I, P224S, N321K, I330V, and R362K). 2018 Journal of virology Abstract IV V100I;P224S;N321K;I330V;R362K 101;108;115;122;133 106;113;120;127;138 PA 89 91 30021892 Functional Evolution of the 2009 Pandemic H1N1 Influenza Virus NS1 and PA in Humans. Recent pH1N1 viruses contain amino acid changes in the NS1 protein (E55K, L90I, I123V, E125D, K131E, and N205S), as previously described (A. 2018 Journal of virology Abstract IV E55K;L90I;I123V;E125D;K131E;N205S 68;74;80;87;94;105 72;78;85;92;99;110 NS1 55 58 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. Although Oseltamivir reduced the total amount of virus shedding from the nose and throat of treated ferrets, it also resulted in the emergence of the neuraminidase R292K resistance substitution in all these animals, as determined by mutation specific RT-PCR and next-generation sequencing. 2018 PloS one Abstract IV R292K 164 169 150 163 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. No additional mutations that could be associated with the emergence of the R292K resistance mutation were detected. 2018 PloS one Abstract IV R292K 75 80 3003392 Variant influenza virus hemagglutinin that induces fusion at elevated pH. This substitution, asparagine for aspartic acid at position 132, disrupted a highly conserved interchain salt bridge between adjacent HA2 subunits. 1986 Journal of virology Abstract IV D132N 19 63 HA 134 136 30050898 Structurally Diverse Polyketides From the Mangrove-Derived Fungus Diaporthe sp. SCSIO 41011 With Their Anti-influenza A Virus Activities. Antiviral evaluation results revealed that compounds 14, 15, 26, and 5-chloroisorotiorin displayed significant anti-IAV activities against three influenza A virus subtypes, including A/Puerto Rico/8/34 H274Y (H1N1), A/FM-1/1/47 (H1N1), and A/Aichi/2/68 (H3N2), with IC50 values in the range of 2.52-39.97 muM. 2018 Frontiers in chemistry Abstract IV H274Y 202 207 30084768 Exchange of amino acids in the H1-haemagglutinin to H3 residues is required for efficient influenza A virus replication and pathology in Tmprss2 knock-out mice. However, exchange of a distant amino acid from H1 to H3 sequence (E31D) in addition to the HA-loop substitution resulted in virus replication in Tmprss2-/- knock-out mice that was comparable to WT mice. 2018 The Journal of general virology Abstract IV E31D 66 70 HA 91 93 30102858 A Small-Molecule Compound Has Anti-influenza A Virus Activity by Acting as a ''PB2 Inhibitor". Our results revealed that D715-2441 possessed antiviral activities against multiple subtypes of influenza A viruses (IAVs) strains, including H1N1, H5N1, H7N9, H3N2, the clinical isolate 690 (H3), and oseltamivir-resistant strains with the H274Y NA mutation, and suppressed the early steps in the virus replication cycle. 2018 Molecular pharmaceutics Abstract IV H274Y 240 245 246 248 30111290 Development of a quadruple qRT-PCR assay for simultaneous identification of highly and low pathogenic H7N9 avian influenza viruses and characterization against oseltamivir resistance. Moreover, a neuraminidase inhibitor (NAI) resistance (R292K in NA) mutation was found in H7N9 isolates from humans, poultry and the environment. 2018 BMC infectious diseases Abstract IV R292K 54 59 NA;NAI;NA 63;37;12 65;40;25 30113030 [Mutations in Hemagglutinin and Polymerase Alter the Virulence of Pandemic A(H1N1) Influenza Virus]. Thus, (1) substitutions in HA (Asp225Gly or Gln226Arg) and compensatory mutation decreasing the charge of HA (Lys123Asn, Lys157Asn, Gly158Glu, Asn159Asp, or Lys212Met) altered viral receptor-binding specificity and restored the functional balance between HA and NA; (2) Phe35Leu substitution in the PA protein increased viral polymerase activity. 2018 Molekuliarnaia biologiia Abstract IV D225G;Q226R;K123N;K157N;G158E;N159D;K212M;F35L 31;44;110;121;132;143;157;270 40;53;119;130;141;152;166;278 HA;HA;HA;NA;PA 27;106;255;262;299 29;108;257;264;301 30141905 The Stabilities of the Soluble Ectodomain and Fusion Peptide Hairpins of the Influenza Virus Hemagglutinin Subunit II Protein Are Positively Correlated with Membrane Fusion. Circular dichroism for HA2 and FHA2 FP+SE constructs shows dramatic losses of stability for the mutants, including a Tm reduced by 40C for I173E-FHA2. 2018 Biochemistry Abstract IV I173E 139 144 HA 23 25 30141905 The Stabilities of the Soluble Ectodomain and Fusion Peptide Hairpins of the Influenza Virus Hemagglutinin Subunit II Protein Are Positively Correlated with Membrane Fusion. The G1E mutant may have disrupted FP hairpins, with consequent non-native FP binding to dissociated SE strands. 2018 Biochemistry Abstract IV G1E 4 7 30141905 The Stabilities of the Soluble Ectodomain and Fusion Peptide Hairpins of the Influenza Virus Hemagglutinin Subunit II Protein Are Positively Correlated with Membrane Fusion. This study compares wild-type HA2 (WT-HA2) with G1E(FP) and I173E(SE strand) mutants. 2018 Biochemistry Abstract IV G1E;I173E 48;60 51;65 HA;HA 30;38 32;40 30165308 Selection of influenza virus resistant to the novel camphor-based antiviral camphecene results in loss of pathogenicity. This was associated with the emergence of a V458L mutation in the HA2 subunit of HA and with a decrease in viral pathogenicity. 2018 Virology Abstract IV V458L 44 49 HA;HA 66;81 68;83 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. In particular, specific mutations acted synergistically with the PB2-D701N mutation and showed synergistic effects on viral replication both in human airway cells and mice compared with the corresponding single mutations. 2018 Scientific reports Abstract IV D701N 69 74 PB2 65 68 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. Several of these mutations acted either alone or together to increase viral polymerase activity in human airway cells to levels similar to the PB2-D701N and PB2-E627K single mutations and to increase progeny virus yields in infected mouse lungs to levels similar to the PB2-D701N single mutation. 2018 Scientific reports Abstract IV D701N;E627K;D701N 147;161;274 152;166;279 PB2;PB2;PB2 143;157;270 146;160;273 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. The role of the influenza virus polymerase complex in host range restriction has been well-studied and several host range determinants, such as the polymerase PB2-E627K and PB2-D701N mutations, have been identified. 2018 Scientific reports Abstract IV E627K;D701N 163;177 168;182 PB2;PB2 159;173 162;176 30186261 Acquisition of Innate Inhibitor Resistance and Mammalian Pathogenicity During Egg Adaptation by the H9N2 Avian Influenza Virus. As a result of this process, the virus developed highly replicative and pathogenic traits within the ECEs through adaptive mutations in hemagglutinin (HA: T133N, V216G, and E439D) and neuraminidase (NA: 18-amino acid deletion and E54D). 2018 Frontiers in microbiology Abstract IV T133N;V216G;E439D;E54D 155;162;173;230 160;167;178;234 HA;HA;NA;NA 151;136;199;184 153;149;201;197 30186261 Acquisition of Innate Inhibitor Resistance and Mammalian Pathogenicity During Egg Adaptation by the H9N2 Avian Influenza Virus. By using a loss-of-function mutant and receptor-binding assay, we demonstrated that a T133N site directed mutation created an additional N-glycosite at position 133 in rH20N20. 2018 Frontiers in microbiology Abstract IV T133N 86 91 30201817 Characterization of Influenza B Virus Variants with Reduced Neuraminidase Inhibitor Susceptibility. Although a D197N variant is yet to become widespread, it is the most commonly detected NAI-resistant influenza B virus in surveillance studies. 2018 Antimicrobial agents and chemotherapy Abstract IV D197N 11 16 NAI 87 90 30201817 Characterization of Influenza B Virus Variants with Reduced Neuraminidase Inhibitor Susceptibility. Our data suggest that the influenza B virus variant with the H273Y NA substitution had a more notable reduction in fitness compared to wild-type viruses than the influenza B variant with the D197N NA substitution. 2018 Antimicrobial agents and chemotherapy Abstract IV H273Y;D197N 61;191 66;196 NA;NA 67;197 69;199 30201817 Characterization of Influenza B Virus Variants with Reduced Neuraminidase Inhibitor Susceptibility. Our results highlight the need to carefully monitor circulating viruses for the spread of influenza B viruses with the D197N NA substitution. 2018 Antimicrobial agents and chemotherapy Abstract IV D197N 119 124 125 127 30201817 Characterization of Influenza B Virus Variants with Reduced Neuraminidase Inhibitor Susceptibility. The D197N and H273Y variants were characterized in vitro by assessing NA enzyme activity and affinity, as well as replication in cell culture compared to those of NAI-sensitive wild-type viruses. 2018 Antimicrobial agents and chemotherapy Abstract IV D197N;H273Y 4;14 9;19 NA;NAI 70;163 72;166 30201817 Characterization of Influenza B Virus Variants with Reduced Neuraminidase Inhibitor Susceptibility. The data revealed that the H273Y variant had NA enzyme function similar to that of its wild type but had slightly reduced replication and transmission efficiency in vivo The D197N variant had impaired NA enzyme function, but there was no evidence of reduction in replication or transmission efficiency in ferrets. 2018 Antimicrobial agents and chemotherapy Abstract IV H273Y;D197N 27;174 32;179 NA;NA 45;201 47;203 30201817 Characterization of Influenza B Virus Variants with Reduced Neuraminidase Inhibitor Susceptibility. This study characterized two contemporary influenza B viruses with known resistance-conferring NA amino acid substitutions, D197N and H273Y, detected during routine surveillance. 2018 Antimicrobial agents and chemotherapy Abstract IV D197N;H273Y 124;134 129;139 95 97 30202644 Molecular identification of avian influenza virus subtypes H5N1 and H9N2 in birds from farms and live bird markets and in respiratory patients. Sequencing of the haemagglutination gene (HA) in nine representative H5N1 isolates revealed a multi-basic amino acid motif at the cleavage site (321-PQGEKRRKKR/GLF-333), which is characteristic of highly pathogenic AIV, in five of our isolates, while the other four isolates showed an amino acid substitution (Q322K) at this cleavage site to make it (321-P K GEKRRKKR/GLF-333). 2018 PeerJ Abstract IV Q322K 310 315 HA 42 44 30227889 Effects of mutations in the effector domain of influenza A virus NS1 protein. Analysis of WT and mutant NS1 interaction partners identified hsp70 as specifically binding to NS1 E96A/E97A. 2018 BMC research notes Abstract IV E96A;E97A 99;104 103;108 NS1;NS1 26;95 29;98 30227889 Effects of mutations in the effector domain of influenza A virus NS1 protein. RESULTS: The NS1 dimerisation mutant W187R retained the functions of binding cellular NXF1 as well as stabilising NXF1 interaction with viral segment 7 mRNAs and promoting their nuclear export. 2018 BMC research notes Abstract IV W187R 37 42 NS1 13 16 30227889 Effects of mutations in the effector domain of influenza A virus NS1 protein. The Trim25-binding mutant NS1 E96A/E97A bound NXF1 and supported NXF1 interactions with segment 7 mRNA but no longer supported mRNA nuclear export. 2018 BMC research notes Abstract IV E96A;E97A 30;35 34;39 NS1 26 29 30227889 Effects of mutations in the effector domain of influenza A virus NS1 protein. Two PI3K-binding mutants, NS1 Y89F and Y89A still bound NXF1 but no longer promoted NXF1 interactions with segment 7 mRNA or its nuclear export. 2018 BMC research notes Abstract IV Y89F;Y89A 30;39 34;43 NS1 26 29 30227889 Effects of mutations in the effector domain of influenza A virus NS1 protein. Whilst these data suggest the possibility of functional links between NS1's effects on intracellular signalling and its role in viral mRNA nuclear export, they also indicate potential pleiotropic effects of the NS1 mutations; in the case of E96A/E97A possibly via disrupted protein folding leading to chaperone recruitment. 2018 BMC research notes Abstract IV E96A;E97A 241;246 245;250 NS1;NS1 70;211 73;214 30230312 A Robust Proton Flux (pHlux) Assay for Studying the Function and Inhibition of the Influenza A M2 Proton Channel. The inhibition of M2 was measured for five different inhibitors, including Rimantadine, Amantadine, and spiro type compounds, and the drug resistance of the M2 mutant variants (swine flu, V27A, and S31N) was confirmed. 2018 Biochemistry Abstract IV V27A;S31N 188;198 192;202 M2;M2 18;157 20;159 30237955 Genetic variations of the Hemagglutinin gene of Pandemic Influenza A (H1N1) viruses in Assam, India during 2016. Sequence analysis of the HA gene of 20 positive Assam/H1N1pdm09 strains revealed 3 mutations (K180Q, S202T, S220T) at the antigenic sites along with several other reported mutations which are in close proximity to the antigenic sites and therefore might affect the viral antigenicity. 2018 3 Biotech Abstract IV K180Q;S202T;S220T 94;101;108 99;106;113 HA 25 27 30241880 High genetic stability in MDCK-SIAT1 passaged human influenza viruses. MDCK-induced amino acid (AA) mutation, such as D151G/N in the neuraminidase (NA) of influenza A/H3N2 viruses, is of concern. 2019 Journal of infection and chemotherapy Abstract IV D151G;D151N 47;47 54;54 NA;NA 77;62 79;75 30241880 High genetic stability in MDCK-SIAT1 passaged human influenza viruses. NA D151G/N changes were not seen in any of the MDCK-SIAT1 passaged A/H3N2 viruses, even in the small variants analysis conducted using deep sequencing. 2019 Journal of infection and chemotherapy Abstract IV D151G;D151N 3;3 10;10 0 2 30245911 The 2015 Outbreak of Severe Influenza in Kashmir, North India: Emergence of a New Clade of A/H1n1 Influenza Virus. No H275Y mutation was reported from A/H1N1 positives. 2018 PLoS currents Abstract IV H275Y 3 8 30245911 The 2015 Outbreak of Severe Influenza in Kashmir, North India: Emergence of a New Clade of A/H1n1 Influenza Virus. Testing for H275Y mutation was done to determine sensitivity to oseltamivir. 2018 PLoS currents Abstract IV H275Y 12 17 3024963 Mutations blocking the transport of the influenza virus hemagglutinin between the rough endoplasmic reticulum and the Golgi apparatus. It involves the replacement of aspartic acid at position 457 by asparagine thereby introducing a new glycosylation site which appears to be located in a cryptic position in the lower part of the hemagglutinin stalk. 1986 The EMBO journal Abstract IV D457N 31 74 HA 195 208 3024963 Mutations blocking the transport of the influenza virus hemagglutinin between the rough endoplasmic reticulum and the Golgi apparatus. The hemagglutinin of ts1 has an essential amino acid exchange at position 275 where serine is replaced by glycine. 1986 The EMBO journal Abstract IV S275G 74 113 HA 4 17 3025850 Mutational analysis of the signal-anchor domain of influenza virus neuraminidase. On the other hand, substitution of arginine for isoleucine at position 26 blocked the migration of the NA protein from the Golgi complex to the cell surface. 1987 Proc Natl Acad Sci U S A Abstract IV I26R 35 73 103 105 3025850 Mutational analysis of the signal-anchor domain of influenza virus neuraminidase. When the altered NA proteins were expressed in CV-1 cells, two phenotypes were observed: substitution of arginine in place of glycine at position 11 and substitution of aspartic acid for valine at position 17 did not abolish the signal, the anchor, or the transport functions. 1987 Proc Natl Acad Sci U S A Abstract IV G11R;V17D 105;169 148;208 17 19 30282714 Amino Acid Residue 217 in the Hemagglutinin Glycoprotein Is a Key Mediator of Avian Influenza H7N9 Virus Antigenicity. The analysis showed that the emergent immune escape viruses contained mutations A125T, A151T, and L217Q in the hemagglutinin (HA) glycoprotein as early as passage 5 and that these mutations persisted until passage 10. 2019 Journal of virology Abstract IV A125T;A151T;L217Q 80;87;98 85;92;103 HA;HA 126;111 128;124 30282714 Amino Acid Residue 217 in the Hemagglutinin Glycoprotein Is a Key Mediator of Avian Influenza H7N9 Virus Antigenicity. The HA gene sequences of viruses recovered after the fifth passage showed that the viruses readily acquired mutations at three different amino acid positions (A125T, A151T, and L217Q). 2019 Journal of virology Abstract IV A125T;A151T;L217Q 159;166;177 164;171;182 HA 4 6 30282714 Amino Acid Residue 217 in the Hemagglutinin Glycoprotein Is a Key Mediator of Avian Influenza H7N9 Virus Antigenicity. The results revealed that a single mutation, L217Q, in the HA of H7N9 virus led to 23- and 8-fold reductions in hemagglutination inhibition (HI) titer with ferret and chicken antisera, respectively. 2019 Journal of virology Abstract IV L217Q 45 50 HA 59 61 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. Furthermore, we observed that P212S and V178I mutation in NS1 of PR8 virus enhanced virulence and promoted the virus replication in vivo. 2018 Veterinary research Abstract IV P212S;V178I 30;40 35;45 NS1 58 61 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. Interestingly, the amino acid residue S212 was identified to have a profound effect on the primary function of NS1, since S212P substitution disabled H7N9 NS1 in suppressing the host RIG-I-dependent interferon response, as well as the ability to promote the virus replication. 2018 Veterinary research Abstract IV S212P 122 127 NS1;NS1 111;155 114;158 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. When the isoleucine was replaced by valine at 178 site (I178V mutation), NS1 of H7N9 underwent rapid degradation through proteasome pathway. 2018 Veterinary research Abstract IV I178V;I178V 56;9 61;49 NS1 73 76 30301950 Tree shrew as a new animal model to study the pathogenesis of avian influenza (H9N2) virus infection. In this study, we used the tree shrew experimental model to investigate the pathogenesis of avian influenza A (H9N2) virus infection and the effect of the E627K mutation in the PB2 gene, an adaptation to mammalian hosts. 2018 Emerging microbes & infections Abstract IV E627K 155 160 PB2 177 180 Influenza A virus H9N2 infection 98 132 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. K154E greatly enhanced in vitro activity in a range of antiviral (HCV, Zika virus, influenza virus and encephalomyocarditis virus) and gene expression assays. 2018 PLoS pathogens Abstract IV K154E 0 5 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. The most notable variant was K154E, which was found in African Congo rainforest 'Pygmy' hunter-gatherers. 2018 PLoS pathogens Abstract IV K154E 29 34 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. To further understand how genetic variation between and within species affects IFNlambda4 function, we screened a panel of all known extant coding variants of human IFNlambda4 for their antiviral potential and identify three that substantially affect activity: P70S, L79F and K154E. 2018 PLoS pathogens Abstract IV P70S;L79F;K154E 261;267;276 265;271;281 30315875 Clinical management and viral genomic diversity analysis of a child's influenza A(H1N1)pdm09 infection in the context of a severe combined immunodeficiency. METHODS: Conventional real-time RT-PCR methods were used to estimate viral load and to detect the presence of the common N1 neuraminidase (NA) H275Y substitution responsible for oseltamivir resistance. 2018 Antiviral research Abstract IV H275Y 143 148 NA;NA 139;124 141;137 30315875 Clinical management and viral genomic diversity analysis of a child's influenza A(H1N1)pdm09 infection in the context of a severe combined immunodeficiency. NGS found influenza quasispecies harboring NA-E119A substitution (10.3%). 2018 Antiviral research Abstract IV E119A 46 51 43 45 30315875 Clinical management and viral genomic diversity analysis of a child's influenza A(H1N1)pdm09 infection in the context of a severe combined immunodeficiency. RESULTS: The patient was first treated with oral oseltamivir, leading to detection of low-levels of NA-H275Y substitution. 2018 Antiviral research Abstract IV H275Y 103 108 100 102 30316915 In vitro characterization of baloxavir acid, a first-in-class cap-dependent endonuclease inhibitor of the influenza virus polymerase PA subunit. Additionally, serial passages of the viruses in the presence of BXA result in isolation of PA/I38T variants with reduced BXA susceptibility. 2018 Antiviral research Abstract IV I38T 94 98 PA 91 93 30328013 CypA Regulates AIP4-Mediated M1 Ubiquitination of Influenza A Virus. More importantly, both the mutations of M1 (K102R/K104R) and CypA inhibited the nuclear export of M1, indicating that CypA regulates the cellular localization of M1 via inhibition of AIP4-mediated M1 ubiquitination at K102 and K104, which results in the reduced replication of IAV. 2018 Virologica Sinica Abstract IV K102R;K104R 44;50 49;55 M1;M1;M1;M1 40;98;162;197 42;100;164;199 30328013 CypA Regulates AIP4-Mediated M1 Ubiquitination of Influenza A Virus. The recombinant IAV with mutant M1 (K102R/K104R) could not be rescued, suggesting that the ubiquitination of M1 at K102/K104 was essential for IAV replication. 2018 Virologica Sinica Abstract IV K102R;K104R 36;42 41;47 M1;M1 32;109 34;111 30336188 Molecular epidemiology of the hemagglutinin gene of prevalent influenza virus A/H1N1/pdm09 among patient in Iran. Phylogenetic analysis of the HA genes of the A/H1N1pdm09 viruses revealed the circulation of clade 6B1, characterized by amino acid substitutions S84N, S162N and I216T, where position 162 became glycosylated. 2019 Virus research Abstract IV S84N;S162N;I216T 146;152;162 150;157;167 HA 29 31 3033905 [Expression and mutagenesis of genes coding for protein synthesis in the influenza virus]. Double-stranded cDNA copies of the neuraminidase genes of influenza viruses A/Tokyo/3/67 (N2), A/tern/Australia/G70C/75 (N9), and B/Lee/40, and the hemagglutinin genes of A/Memphis/1/71 (H3) and B/Hong Kong/8/73 were cloned into a SV40 vector in which the late region was replaced by the influenza sequences. 1987 Voprosy virusologii Abstract IV G70C 112 116 HA;N9;NA 148;121;35 161;123;48 30349332 Antiviral resistance markers in influenza virus sequences in Mexico, 2000-2017. Only one of the resistance-associated markers (Q136K) in NA (1.5%) was present in the analyzed H3N2 sequences, while sequences of influenza B virus did not present resistance markers to NA inhibitors. 2018 Infection and drug resistance Abstract IV Q136K 47 52 NA;NA 57;186 59;188 30349332 Antiviral resistance markers in influenza virus sequences in Mexico, 2000-2017. The more frequent resistance marker in H1N1 pdm2009 NA sequences was H275Y, present in 3.6%, while S247N was present in 0.30%. 2018 Infection and drug resistance Abstract IV H275Y;S247N 69;99 74;104 52 54 30349332 Antiviral resistance markers in influenza virus sequences in Mexico, 2000-2017. Two resistance markers conferring resistance to NA inhibitors were present in seasonal H1N1 sequences, H275Y (50.0%) and N70S (33.3%). 2018 Infection and drug resistance Abstract IV H275Y;N70S 103;121 108;125 48 50 30352857 The mechanism of resistance to favipiravir in influenza. K229R also conferred favipiravir resistance to RNA polymerases of other influenza A virus strains, and its location within a highly conserved structural feature of the RdRP suggests that other RNA viruses might also acquire resistance through mutations in motif F. 2018 Proc Natl Acad Sci U S A Abstract IV K229R 0 5 30352857 The mechanism of resistance to favipiravir in influenza. This mutation has a cost to viral fitness, but fitness can be restored by a P653L mutation in the PA subunit of the polymerase. 2018 Proc Natl Acad Sci U S A Abstract IV P653L 76 81 PA 98 100 30352857 The mechanism of resistance to favipiravir in influenza. We demonstrate that a K229R mutation in motif F of the PB1 subunit of the influenza virus RNA-dependent RNA polymerase (RdRP) confers resistance to favipiravir in vitro and in cell culture. 2018 Proc Natl Acad Sci U S A Abstract IV K229R 22 27 PB1 55 58 30353004 Genome-wide characterization of the seasonal H3N2 virus in Shanghai reveals natural temperature-sensitive strains conferred by the I668V mutation in the PA subunit. A polymerase activity assay and mutational analysis demonstrated that the PA I668V mutation of the 2016-2017win viruses suppressed polymerase activity in vitro at high temperatures. 2018 Emerging microbes & infections Abstract IV I668V 77 82 PA 74 76 30353004 Genome-wide characterization of the seasonal H3N2 virus in Shanghai reveals natural temperature-sensitive strains conferred by the I668V mutation in the PA subunit. Taken together, these data suggest that the I668V mutation in the PA subunit of the 2016-2017win strains may confer temperature sensitivity and attenuate viral replication and polymerase activity; meanwhile, the 2017sum strains maintained virulence at high temperatures. 2018 Emerging microbes & infections Abstract IV I668V 44 49 PA 66 68 30355680 Plasticity of Amino Acid Residue 145 Near the Receptor Binding Site of H3 Swine Influenza A Viruses and Its Impact on Receptor Binding and Antibody Recognition. On the hemagglutinin (HA) of the H3N2 IAVs, the amino acid substitution N 145 K causes significant antigenic changes. 2019 Journal of virology Abstract IV N145K 72 79 HA;HA 22;7 24;20 30365885 Structure-Based Optimization of N-Substituted Oseltamivir Derivatives as Potent Anti-Influenza A Virus Agents with Significantly Improved Potency against Oseltamivir-Resistant N1-H274Y Variant. Besides, 21h was 5- to 86-fold more potent than OSC toward N1, N8, and N1-H274Y mutant NAs in the inhibitory assays. 2018 Journal of medicinal chemistry Abstract IV H274Y 74 79 87 90 30365885 Structure-Based Optimization of N-Substituted Oseltamivir Derivatives as Potent Anti-Influenza A Virus Agents with Significantly Improved Potency against Oseltamivir-Resistant N1-H274Y Variant. Computational studies provided a plausible rationale for the high potency of 21h against group-1 and N1-H274Y NAs. 2018 Journal of medicinal chemistry Abstract IV H274Y 104 109 110 113 30381484 Mutations in Influenza A Virus Neuraminidase and Hemagglutinin Confer Resistance against a Broadly Neutralizing Hemagglutinin Stem Antibody. Structural analyses revealed that the selected HA mutations (S123G, N460S, and N203V) are away from the F10 epitope but may indirectly impact influenza virus receptor binding, endosomal fusion, or budding. 2019 Journal of virology Abstract IV S123G;N460S;N203V 61;68;79 66;73;84 HA 47 49 30381484 Mutations in Influenza A Virus Neuraminidase and Hemagglutinin Confer Resistance against a Broadly Neutralizing Hemagglutinin Stem Antibody. The NA mutation E329K, which was previously identified to be associated with antibody escape, affects the active site of NA, highlighting the importance of the balance between HA and NA function for viral survival. 2019 Journal of virology Abstract IV E329K 16 21 HA;NA;NA;NA 176;4;121;183 178;6;123;185 3038931 Effects of mutations in three domains of the vesicular stomatitis viral glycoprotein on its lateral diffusion in the plasma membrane. Eight mutant proteins were also examined: dTM14, lacking six amino acids from the transmembrane domain; TA2, lacking an oligosaccharide in the extracellular domain; QN2, possessing an extra N-linked oligosaccharide in the extracellular domain; CS2, possessing a serine instead of a cysteine at residue 489 in the cytoplasmic domain, preventing palmitate addition to the glycoprotein; TMR-stop, lacking the entire cytoplasmic domain except an arginine at residue 483; and three chimeric proteins, G mu, G23, and GHA, containing in place of the 29 amino acid wild type cytoplasmic domain the cytoplasmic domains from the surface IgM from the spike protein of the infectious bronchitis virus or from the hemagglutinin protein of the influenza virus, respectively. 1987 The Journal of cell biology Abstract IV C489S 262 305 HA 701 714 30400276 Combination Therapy with Oseltamivir and Favipiravir Delays Mortality but Does Not Prevent Oseltamivir Resistance in Immunodeficient Mice Infected with Pandemic A(H1N1) Influenza Virus. Treatment of immunosuppressed mice with high (50 mg/kg) but not low (20 mg/kg) doses of favipiravir in combination with oseltamivir (20 mg/kg) significantly delayed mortality and reduced lung viral titers compared to treatment with a single drug regimen with oseltamivir but did not prevent the emergence of oseltamivir-resistant H275Y neuraminidase variants. 2018 Viruses Abstract IV H275Y 330 335 336 349 30405591 Identification of Amino Acid Residues Responsible for Inhibition of Host Gene Expression by Influenza A H9N2 NS1 Targeting of CPSF30. Amino acid substitutions L103F, I106M, P114S, G125D and N139D in HK/97 NS1 resulted in binding to the 30-kDa subunit of the cleavage and polyadenylation specificity factor (CPSF30) and, in consequence, inhibition of host gene expression. 2018 Frontiers in microbiology Abstract IV L103F;I106M;P114S;G125D;N139D 25;32;39;46;56 30;37;44;51;61 NS1 71 74 30428893 Analysis of influenza B virus lineages and the HA1 domain of its hemagglutinin gene in Guangzhou, southern China, during 2016. A comparison isolates in our Victoria lineage with the B/Brisbane/60/2008 strain indicated 12 mutation sites in the HA1 domain, 4 of which (I132V, N144D, C196S, and E198D) were in antigenic epitopes. 2018 Virology journal Abstract IV I132V;N144D;C196S;E198D 140;147;154;165 145;152;159;170 HA1 116 119 30429954 Structure-Property Relationship Studies of Influenza A Virus AM2-S31N Proton Channel Blockers. Majority of current circulating influenza A viruses carry the S31N mutation in their M2 genes, rendering AM2-S31N as a high profile antiviral drug target. 2018 ACS medicinal chemistry letters Abstract IV S31N;S31N 62;109 66;113 M2 85 87 30429954 Structure-Property Relationship Studies of Influenza A Virus AM2-S31N Proton Channel Blockers. We also showed for the first time that AM2-S31N channel blockers such as 10e inhibited influenza virus replication at both low and high multiply of infection (102-106 pfu/mL) and the inhibition was not cell-type dependent. 2018 ACS medicinal chemistry letters Abstract IV S31N 43 47 30429954 Structure-Property Relationship Studies of Influenza A Virus AM2-S31N Proton Channel Blockers. With our continuous interest in developing AM2-S31N channel blockers as novel antivirals targeting both oseltamivir-sensitive and -resistant influenza A viruses, we report herein the structure-property relationship studies of AM2-S31N inhibitors. 2018 ACS medicinal chemistry letters Abstract IV S31N;S31N 47;230 51;234 30439983 Influenza B viruses circulated during last 5 years in Mongolia. Interestingly, G104R was identified as a novel mutation, which might have a significant role in drug resistance of the virus. 2018 PloS one Abstract IV G104R 15 20 30462955 [Genetic characteristics of hemagglutinin and neuraminidase of avian influenza A (H7N9) virus in Guizhou province, 2014-2017]. All the strains had a stalk deletion of 5 amino acid residue "QISNT" in NA protein, and drug resistance mutation R294K occurred in strain A/Guizhou-Danzhai/18980/2017. 2018 Zhonghua liu xing bing xue za zhi Abstract IV R294K 113 118 72 74 30462955 [Genetic characteristics of hemagglutinin and neuraminidase of avian influenza A (H7N9) virus in Guizhou province, 2014-2017]. Mutations A134V, G186V and Q226L at the receptor binding sites were found in the HA. 2018 Zhonghua liu xing bing xue za zhi Abstract IV A134V;G186V;Q226L 10;17;27 15;22;32 HA 81 83 30463209 A PB1-K577E Mutation in H9N2 Influenza Virus Increases Polymerase Activity and Pathogenicity in Mice. A recombinant H9N2 virus bearing only the PB1-K577E mutation showed enhanced pathogenicity in mice, with increased virus titers in nasal turbinates compared to that in mice infected with the wild-type virus. 2018 Viruses Abstract IV K577E 46 51 PB1 42 45 30463209 A PB1-K577E Mutation in H9N2 Influenza Virus Increases Polymerase Activity and Pathogenicity in Mice. Among the detected mutations, PB1-K577E was a novel mutation that had not been previously reported to involve mammalian adaptation. 2018 Viruses Abstract IV K577E 34 39 PB1 30 33 30463209 A PB1-K577E Mutation in H9N2 Influenza Virus Increases Polymerase Activity and Pathogenicity in Mice. In addition, the PB1-K577E mutation increased virus polymerase activity in human cell culture at a lower temperature. 2018 Viruses Abstract IV K577E 21 26 PB1 17 20 30463209 A PB1-K577E Mutation in H9N2 Influenza Virus Increases Polymerase Activity and Pathogenicity in Mice. These data suggest that the PB1-K577E mutation is a novel pathogenicity determinant of H9N2 virus in mice and could be a signature for mammalian adaptation. 2018 Viruses Abstract IV K577E 32 37 PB1 28 31 30466301 Activity of enisamium, an isonicotinic acid derivative, against influenza viruses in differentiated normal human bronchial epithelial cells. RESULTS: Enisamium inhibited replication of multiple subtypes of influenza A viruses, including seasonal H1N1, 2009 pandemic H1N1, seasonal H3N2, the zoonotic H5N1 and H7N9, neuraminidase inhibitor-resistant variant carrying the H275Y NA substitution (N1 numbering), and influenza B virus at doses 23- to 64-fold lower than cytotoxic concentrations. 2018 Antiviral chemistry & chemotherapy Abstract IV H275Y 229 234 NA;NA 235;174 237;187 30509291 Conserved methionine 165 of matrix protein contributes to the nuclear import and is essential for influenza A virus replication. M165A protein was co-localized with CLUH protein in the cytoplasm and around the nucleus but transport of M165-CLUH complex through the nuclear membrane was restricted. 2018 Virology journal Abstract IV M165A 0 5 30509291 Conserved methionine 165 of matrix protein contributes to the nuclear import and is essential for influenza A virus replication. Single M165A substitution was lethal for rescuing infection virus and had a striking effect on the distribution of M1 and NP proteins. 2018 Virology journal Abstract IV M165A 7 12 M1;NP 115;122 117;124 30509291 Conserved methionine 165 of matrix protein contributes to the nuclear import and is essential for influenza A virus replication. We have observed statistically significant reduction in distribution of both M165A (p<0,05) and NP (p<0,001) proteins to the nucleus in the cells transfected with the reverse -genetic system with mutated M1. 2018 Virology journal Abstract IV M165A 77 82 M1;NP 204;96 206;98 30515728 Glycosylation and an amino acid insertion in the head of hemagglutinin independently affect the antigenic properties of H5N1 avian influenza viruses. The E131N mutation and insertion of leucine at position 134 in the HA protein of the antigenically drifted strains eliminated the reactivity of the virus with the MAbs. 2019 Science China. Life sciences Abstract IV E131N 4 9 HA 67 69 30533399 Potential Pandemic of H7N9 Avian Influenza A Virus in Human. Among the six internal viral genes, amino acid changes do not differ significantly between H9N2 and H7N9, except for V100A in PA, and K526R, D627K, and D701N in PB2. 2018 Frontiers in cellular and infection microbiology Abstract IV V100A;K526R;D627K;D701N 117;134;141;152 122;139;146;157 PA;PB2 126;161 128;164 30533399 Potential Pandemic of H7N9 Avian Influenza A Virus in Human. Among these, six amino acid sites in HA1 are receptor binding sites, and PB2-A588V was shown to promote the adaptation of AIVs to mammals. 2018 Frontiers in cellular and infection microbiology Abstract IV A588V 77 82 HA1;PB2 37;73 40;76 30548432 Consecutive influenza surveillance of neuraminidase mutations and neuraminidase inhibitor resistance in Japan. Even in Japan, no spread of NAI-resistant viruses has been observed, and A/H1N1pdm09 viruses carrying H275Y remain limited. 2019 Influenza and other respiratory viruses Abstract IV H275Y 102 107 NAI 28 31 30548432 Consecutive influenza surveillance of neuraminidase mutations and neuraminidase inhibitor resistance in Japan. Four of the five mutations in the catalytic sites of A/H1N1pdm09 consisted of H275Y, which was related to high resistance to oseltamivir and peramivir. 2019 Influenza and other respiratory viruses Abstract IV H275Y 78 83 30548432 Consecutive influenza surveillance of neuraminidase mutations and neuraminidase inhibitor resistance in Japan. Most (10/13) of the catalytic site mutations in A/H3N2 were associated with MDCK-passaged induction (D151G/N). 2019 Influenza and other respiratory viruses Abstract IV D151G;D151N 101;101 108;108 30569291 The D253N Mutation in the Polymerase Basic 2 Gene in Avian Influenza (H9N2) Virus Contributes to the Pathogenesis of the Virus in Mammalian Hosts. In this study, we investigated the functional roles of the D253N mutation in PB2 in an H9N2 virus. 2018 Virologica Sinica Abstract IV D253N 59 64 PB2 77 80 30569291 The D253N Mutation in the Polymerase Basic 2 Gene in Avian Influenza (H9N2) Virus Contributes to the Pathogenesis of the Virus in Mammalian Hosts. Our results supported that the D253N mutation in the middle domain of PB2, similar to mutations at the 627 and NLS domains, specifically contributed to the replication of avian influenza viruses in human cells. 2018 Virologica Sinica Abstract IV D253N 31 36 PB2 70 73 30569291 The D253N Mutation in the Polymerase Basic 2 Gene in Avian Influenza (H9N2) Virus Contributes to the Pathogenesis of the Virus in Mammalian Hosts. The virus with the D253N mutation showed higher polymerase activity and transiently increased viral replication in human cells. 2018 Virologica Sinica Abstract IV D253N 19 24 30574137 Susceptibility of Influenza Viruses to the Novel Cap-Dependent Endonuclease Inhibitor Baloxavir Marboxil. First, we generated a reference virus possessing an I38T substitution in the polymerase acidic subunit (PA), which is known to be associated with reduced susceptibility to baloxavir, and demonstrated the validity of our systems using this reference virus. 2018 Frontiers in microbiology Abstract IV I38T 52 56 PA;PA 104;77 106;102 30593364 A novel recombinant attenuated Newcastle disease virus expressing H9 subtype hemagglutinin protected chickens from challenge by genotype VII virulent Newcastle disease virus and H9N2 avian influenza virus. Furthermore, a prime-boost vaccination of chickens with rmNA-H9F induced higher levels of NDV- and H9- HI and secretory IgA, as well as reduced viral shedding and virus-induced gross lesions, compared with the commercial vaccine. 2019 Veterinary microbiology Abstract IV H9F 61 64 30593364 A novel recombinant attenuated Newcastle disease virus expressing H9 subtype hemagglutinin protected chickens from challenge by genotype VII virulent Newcastle disease virus and H9N2 avian influenza virus. Remarkably, non-shedding of influenza virus and higher levels of H9 subtype HI titers were observed 7 days post challenge (dpc) in rmNA-H9F vaccinated chickens, than other recombinants. 2019 Veterinary microbiology Abstract IV H9F 136 139 30593364 A novel recombinant attenuated Newcastle disease virus expressing H9 subtype hemagglutinin protected chickens from challenge by genotype VII virulent Newcastle disease virus and H9N2 avian influenza virus. rmNA-H9, rmNA-H9F, and rmNA-H9 (ECTO) stably expressed the modified HA gene for 10 egg passages and the three recombinants were found innocuous to chickens. 2019 Veterinary microbiology Abstract IV H9F 14 17 HA 68 70 30593364 A novel recombinant attenuated Newcastle disease virus expressing H9 subtype hemagglutinin protected chickens from challenge by genotype VII virulent Newcastle disease virus and H9N2 avian influenza virus. Therefore, in the present work, a cloned full-length copy of the genome of the lentogenic NDV strain rmNA-1 was selected as a backbone vector to construct three chimeric NDVs that expressed (i) the ORF encoding the HA, (ii) the ectodomain of HA fused with the transmembrane domain and cytoplasmic tail regions derived from the NDV F protein and (iii) the ectodomain of HA fused with a short GS linker and the GCN4 sequences, and designated as rmNA-H9, rmNA-H9F, and rmNA-H9 (ECTO), respectively. 2019 Veterinary microbiology Abstract IV H9F 457 460 HA;HA;HA 215;242;369 217;244;371 30593364 A novel recombinant attenuated Newcastle disease virus expressing H9 subtype hemagglutinin protected chickens from challenge by genotype VII virulent Newcastle disease virus and H9N2 avian influenza virus. Therefore, the recombinant rmNA-H9F is a promising bivalent vaccine candidate against NDV and H9 subtype AIV in chickens. 2019 Veterinary microbiology Abstract IV H9F 32 35 30602610 In Vitro and In Vivo Characterization of Novel Neuraminidase Substitutions in Influenza A(H1N1)pdm09 Virus Identified Using Laninamivir-Mediated In Vitro Selection. After the generation of single mutants possessing each identified mutation, two A(H1N1)pdm09 recombinants possessing novel NA gene substitutions (i.e., D199E and P458T) were shown to exhibit resistance to more than one NAI. 2019 Journal of virology Abstract IV D199E;P458T 152;162 157;167 NA;NAI 123;219 125;222 30602610 In Vitro and In Vivo Characterization of Novel Neuraminidase Substitutions in Influenza A(H1N1)pdm09 Virus Identified Using Laninamivir-Mediated In Vitro Selection. Of note, mutants possessing P458T-which is located outside of the catalytic or framework residue of the NA active site-exhibited highly reduced inhibition by all four approved NAIs. 2019 Journal of virology Abstract IV P458T 28 33 NA;NAI 104;176 106;180 30602610 In Vitro and In Vivo Characterization of Novel Neuraminidase Substitutions in Influenza A(H1N1)pdm09 Virus Identified Using Laninamivir-Mediated In Vitro Selection. Reverse mutations to the WT were observed in lung homogenate samples from D199E-infected mice after 3 serial passages. 2019 Journal of virology Abstract IV D199E 74 79 30602610 In Vitro and In Vivo Characterization of Novel Neuraminidase Substitutions in Influenza A(H1N1)pdm09 Virus Identified Using Laninamivir-Mediated In Vitro Selection. We found several novel substitutions in NA (D199E and P458T) in an A(H1N1)pdm09 background which conferred resistance to NAIs and which had an impact on viral fitness. 2019 Journal of virology Abstract IV D199E;P458T 44;54 49;59 NA;NAI 40;121 42;125 30619194 Influenza A Virus NS1 Protein Suppresses JNK1-Dependent Autophagosome Formation Mediated by Rab11a Recycling Endosomes. The autophagosome formation was induced by infection with NS1 mutant virus lacking the dsRNA-binding activity for inhibition of innate immune responses (R38AK41A) or the activation of PI3K-Akt signaling pathway (Y89F). 2018 Frontiers in microbiology Abstract IV Y89F 212 216 NS1 58 61 30619194 Influenza A Virus NS1 Protein Suppresses JNK1-Dependent Autophagosome Formation Mediated by Rab11a Recycling Endosomes. We also found that the amount of phosphorylated TSC2, which activates mTOR, increased in wild type-infected cells but not in Y89F mutant-infected cells. 2018 Frontiers in microbiology Abstract IV Y89F 125 129 30621708 Multiple amino acid substitutions involved in the adaption of three avian-origin H7N9 influenza viruses in mice. Further analysis of the amino acids changes revealed 10 amino acid substitutions located in PB2 (E627K), PB1 (W215R and D638G), PA (T97I), HA (H3 numbering: R220G, L226S, G279R and G493R) and NA (P3Q and R134I) proteins. 2019 Virology journal Abstract IV P3Q;E627K;W215R;D638G;T97I;R220G;L226S;G279R;G493R;R134I 196;97;110;120;132;157;164;171;181;204 199;102;115;125;136;162;169;176;186;209 HA;NA;PA;PB1;PB2 139;192;128;105;92 141;194;130;108;95 30621708 Multiple amino acid substitutions involved in the adaption of three avian-origin H7N9 influenza viruses in mice. Moreover, PB2 E627K substitution was shared by the three mouse-adapted viruses (two viruses belong to YRD lineage and one virus belongs to PRD lineage), and PA T97A substitution was shared by two mouse-adapted viruses (belong to YRD lineage). 2019 Virology journal Abstract IV E627K;T97A 14;160 19;164 PA;PB2 157;10 159;13 30621708 Multiple amino acid substitutions involved in the adaption of three avian-origin H7N9 influenza viruses in mice. PB2 E627K and PA T97A substitutions are vital in mouse adaption and should be monitored during epidemiological study of H7N9 virus. 2019 Virology journal Abstract IV E627K;T97A 4;17 9;21 PA;PB2 14;0 16;3 30633245 [Three Mutations in the Stalk Region of Hemagglutinin Affect the pH of Fusion and Pathogenicity of H5N1 Influenza Virus]. The purpose of this work is to clarify the role of three mutations in the stalk region of HA: Asp54Asn in HA1 and Val48Ile and Lys131Thr in HA2 (H3 HA numbering). 2018 Molekuliarnaia biologiia Abstract IV D54N;V48I;K131T 94;114;127 102;122;136 HA;HA;HA;HA1 90;140;148;106 92;142;150;109 30640922 Molecular characterization of influenza A(H1N1)pdm09 in Cameroon during the 2014-2016 influenza seasons. Majority of the samples had some mutations in the NA gene notably: I117M, N248D, and N369K while the amantadine-resistant M mutant, S31N, was found to be absent only in the two sequences collected in 2014. 2019 PloS one Abstract IV I117M;N248D;N369K;S31N 67;74;85;132 72;79;90;136 M;NA 122;50 123;52 30670142 Detection of influenza A(H3N2) viruses exhibiting reduced susceptibility to the novel cap-dependent endonuclease inhibitor baloxavir in Japan, December 2018. Two influenza A(H3N2) viruses carrying an I38T substitution in the polymerase acidic subunit (PA) were detected in baloxavir-treated children in December 2018. 2019 Euro surveillance Abstract IV I38T 42 46 PA;PA 94;67 96;92 30695536 [INCLUSION OF SITE-SPECIFIC MUTATIONS INTO CONSERVATIVE SEG- MENTS OF PA-GENE RESULTS IN ATTENUATION OF VIRULENT INFLUENZA VIRUS STRAIN A/WSN/33]. Introduction of F658A substitution into COOH-domain of the PA-gene in combination with introduction of ts-mutations from ca influenzavirus strains into the genome ofthe virulent strain resulted in obtaining transfectants that have phenotypic characteristics typical for live influenza vaccine candidates. 2017 Zhurnal mikrobiologii, epidemiologii i immunobiologii Abstract IV F658A 16 21 PA 59 61 30695536 [INCLUSION OF SITE-SPECIFIC MUTATIONS INTO CONSERVATIVE SEG- MENTS OF PA-GENE RESULTS IN ATTENUATION OF VIRULENT INFLUENZA VIRUS STRAIN A/WSN/33]. RESULTS: Transfectants with F658A substitution in the COOH-domain of the PA-gene were shown to acquire ts-phenotype and sharply reduce the ability to reproduce in mice lungs. 2017 Zhurnal mikrobiologii, epidemiologii i immunobiologii Abstract IV F658A 28 33 PA 73 75 30700609 The Molecular Basis for Antigenic Drift of Human A/H2N2 Influenza Viruses. Two amino acid substitutions, T128D and N139K, located in the head domain of the H2 hemagglutinin (HA) molecule, were identified as important determinants of antigenic change during A/H2N2 virus evolution. 2019 Journal of virology Abstract IV T128D;N139K 30;40 35;45 HA;HA 99;84 101;97 30733797 In silico thermodynamic stability of mammalian adaptation and virulence determinants in polymerase complex proteins of H9N2 virus. In addition, eight markers related to virulence were identified, including the combination of 627V and 391E in the PB2 gene with full-length PB1-F2 and PA-X proteins were observed in all viruses and the substitution N66S in PB1-F2 which suggest increasing virus virulence. 2018 Journal, genetic engineering & biotechnology Abstract IV N66S 216 220 PA-X;PB1F2;PB1F2;PB2 152;141;224;115 156;147;230;118 30744302 [Genetic characteristic of hemagglutinin of avian influenza A (H7N9) virus in Guizhou Province in 2017]. Mutation G186V at the receptor binding sites in the HA was found in all 14 strains, and mutation Q226L in 13 strains besides A/Guizhou-Weining/CSY01/2017. 2019 Zhonghua yu fang yi xue za zhi [Chinese journal of preventive medicine] Abstract IV G186V;Q226L 9;97 14;102 HA 52 54 30787926 Mutation S110L of H1N1 Influenza Virus Hemagglutinin: A Potent Determinant of Attenuation in the Mouse Model. Characterization of a pandemic 2009 H1N1 influenza virus isolated from a fatal case patient (F-IAV), showed the presence of three different mutations; potential determinants of its high pathogenicity that were located in the polymerase subunits (PB2 A221T and PA D529N) and the hemagglutinin (HA S110L). 2019 Frontiers in immunology Abstract IV A221T;D529N;S110L 250;263;296 255;268;301 HA;HA;PA;PB2 293;278;260;246 295;291;262;249 30787926 Mutation S110L of H1N1 Influenza Virus Hemagglutinin: A Potent Determinant of Attenuation in the Mouse Model. Here, we have evaluated the contribution of HA S110L to F-IAV pathogenicity, through introduction of this point mutation in CAL recombinant virus (HA mut). 2019 Frontiers in immunology Abstract IV S110L 47 52 HA;HA 44;147 46;149 30787926 Mutation S110L of H1N1 Influenza Virus Hemagglutinin: A Potent Determinant of Attenuation in the Mouse Model. In addition, recombinant viruses containing HA S110L alone or in combination with polymerase mutations considerably increased the LD50 in infected mice. 2019 Frontiers in immunology Abstract IV S110L 47 52 HA 44 46 30787926 Mutation S110L of H1N1 Influenza Virus Hemagglutinin: A Potent Determinant of Attenuation in the Mouse Model. Our results indicate that, mutation HA S110L constitutes a determinant of attenuation and suggest that its interaction with components of the respiratory tract mucus and lectins, that play an important role on influenza virus outcome, may constitute a physical barrier impeding the infection of the target cells, thus compromising the infection outcome. 2019 Frontiers in immunology Abstract IV S110L 39 44 HA 36 38 30787926 Mutation S110L of H1N1 Influenza Virus Hemagglutinin: A Potent Determinant of Attenuation in the Mouse Model. Recombinant viruses containing individually or in combination the polymerase mutations in the backbone of A/California/04/09 (CAL) showed that PA D529N was clearly involved in the increased pathogenicity of the F-IAV virus. 2019 Frontiers in immunology Abstract IV D529N 146 151 PA 143 145 30787926 Mutation S110L of H1N1 Influenza Virus Hemagglutinin: A Potent Determinant of Attenuation in the Mouse Model. The change HA S110L leads to a non-significant trend to reduce the replication capacity of influenza virus in tissue culture, and HA mut is better neutralized than CAL virus by monoclonal and polyclonal antibodies against HA from CAL strain. 2019 Frontiers in immunology Abstract IV S110L 14 19 HA;HA;HA 11;130;222 13;132;224 30787926 Mutation S110L of H1N1 Influenza Virus Hemagglutinin: A Potent Determinant of Attenuation in the Mouse Model. The HA S110L protein has similar pH stability, comparable mobility, and entry properties both in human and mouse cultured cells that wild type HA. 2019 Frontiers in immunology Abstract IV S110L 7 12 HA;HA 4;143 6;145 30792414 Molecular evolution of influenza B virus during 2011-2017 in Chaoyang, Beijing, suggesting the free influenza vaccine policy. Substitutions L58P, I146V were observed in HA1 region of Victoria-lineage virus in 2011-2012 and I117V, N129D were showed in 2015-2017. 2019 Scientific reports Abstract IV L58P;I146V;I117V;N129D 14;20;97;104 18;25;102;109 HA1 43 46 30792414 Molecular evolution of influenza B virus during 2011-2017 in Chaoyang, Beijing, suggesting the free influenza vaccine policy. The amino acids substitutions of HA1 region were R279K in strains of 2011-2014 and L173Q, M252V in strains of 2014-2017. 2019 Scientific reports Abstract IV R279K;L173Q;M252V 49;83;90 54;88;95 HA1 33 36 30799182 Atypical influenza A(H1N1)pdm09 strains caused an influenza virus outbreak in Saudi Arabia during the 2009-2011 pandemic season. RESULTS: Concatenated whole-genome phylogenetic analysis along with hemagglutinin (HA) signature changes, that is, Aspartic Acid (D) at position 187, P83S, S203T, and R223Q confirmed that the Saudi strains belong to the antigenic category of A/California/07/2009. 2019 Journal of infection and public health Abstract IV P83S;S203T;R223Q 150;156;167 154;161;172 HA;HA 83;68 85;81 30866072 Genetic diversity of influenza A(H3N2) viruses in Northern Cameroon during the 2014-2016 influenza seasons. Analysis of the coding regions of the NA and M genes showed that none had genetic markers of resistance to neuraminidase inhibitors but all strains possessed the S31N substitution of resistance to amantadine. 2019 Journal of medical virology Abstract IV S31N 162 166 M;NA;NA 45;38;107 46;40;120 30899824 Evolved avian influenza virus (H7N9) isolated from human cases in a middle Yangtze River city in China, from February to April 2017. The hemagglutinin segment contained Thr160Ala, Gly186Val and Gln226Leu substitutions, which are associated with increased binding affinity in humans. 2019 Heliyon Abstract IV T160A;G186V;Q226L 36;47;61 45;56;70 HA 4 17 30899824 Evolved avian influenza virus (H7N9) isolated from human cases in a middle Yangtze River city in China, from February to April 2017. The proportion of PB2 Ala588Val substitutions in viruses revealed a significantly increasing in recent years, from 0.8 % (1 of 128 cases) to 84.9 % (275 of 324 cases). 2019 Heliyon Abstract IV A588V 22 31 PB2 18 21 30909490 The PB2 Polymerase Host Adaptation Substitutions Prime Avian Indonesia Sub Clade 2.1 H5N1 Viruses for Infecting Humans. A similar mechanism is observed in the Qinghai-lineage H5N1 viruses that have caused many human cases in Egypt; here, E627K predisposes towards human infections. 2019 Viruses Abstract IV E627K 118 123 30909490 The PB2 Polymerase Host Adaptation Substitutions Prime Avian Indonesia Sub Clade 2.1 H5N1 Viruses for Infecting Humans. Testing the hypothesis that this mutation may prime avian H5N1 virus for human infection, we showed that: (1) K526R is rarely found in avian influenza viruses but was identified in H5N1 viruses 2-3 years after the virus emerged in Indonesia, coincident with the emergence of H5N1 human infections in Indonesia; (2) K526R is required for efficient replication of Indonesia H5N1 virus in mammalian cells in vitro and in vivo and reverse substitution to 526K in human isolates abolishes this ability; (3) Indonesian H5N1 virus, which contains K526R-PB2, is stable and does not further acquire E627K following replication in infected mice; and (4) virus containing K526R-PB2 shows no fitness deficit in avian species. 2019 Viruses Abstract IV K526R;K526R;K526R;E627K;K526R 110;315;540;590;661 115;320;545;595;666 PB2;PB2 546;667 549;670 Influenza A virus H5N1 infection 275 296 30909490 The PB2 Polymerase Host Adaptation Substitutions Prime Avian Indonesia Sub Clade 2.1 H5N1 Viruses for Infecting Humans. We previously showed PB2-K526R is present in 80% of Indonesian H5N1 human isolates, which lack the more common PB2-E627K substitution. 2019 Viruses Abstract IV K526R;E627K 25;115 30;120 PB2;PB2 21;111 24;114 30914078 Influenza A(H3N2) virus exhibiting reduced susceptibility to baloxavir due to a polymerase acidic subunit I38T substitution detected from a hospitalised child without prior baloxavir treatment, Japan, January 2019. An epidemiological analysis suggests possible transmission of the PA I38T mutant A(H3N2) virus among humans. 2019 Euro surveillance Abstract IV I38T 69 73 PA 66 68 30914078 Influenza A(H3N2) virus exhibiting reduced susceptibility to baloxavir due to a polymerase acidic subunit I38T substitution detected from a hospitalised child without prior baloxavir treatment, Japan, January 2019. In January 2019, two influenza A(H3N2) viruses carrying an I38T substitution in the polymerase acidic subunit (PA), which confers reduced susceptibility to baloxavir, were detected from epidemiologically unrelated hospitalised children in Japan. 2019 Euro surveillance Abstract IV I38T 59 63 PA;PA 111;84 113;109 30926385 Positive charge of Arg-201 on hemagglutinin is required for the binding of H6N1 avian influenza virus to its target through a two-step process. We found that the positive charge on R201 was critical for binding HA to the negatively charged surface of host cells because the mutant R201A of H6HA0 lost its binding capacity substantially. 2019 Virus research Abstract IV R201A 137 142 HA 67 69 30996301 Bacterial glycosyltransferase-mediated cell-surface chemoenzymatic glycan modification. Here, we identify Pasteurella multocida alpha2-3-sialyltransferase M144D mutant, Photobacterium damsela alpha2-6-sialyltransferase, and Helicobacter mustelae alpha1-2-fucosyltransferase, as efficient tools for live-cell glycan modification. 2019 Nature communications Abstract IV M144D 67 72 31008587 Hydrogen-Deuterium Exchange Supports Independent Membrane-Interfacial Fusion Peptide and Transmembrane Domains in Subunit 2 of Influenza Virus Hemagglutinin Protein, a Structured and Aqueous-Protected Connection between the Fusion Peptide and Soluble Ectodomain, and the Importance of Membrane Apposition by the Trimer-of-Hairpins Structure. Fusion is highly impaired with either mutant, which correlates with reduced membrane apposition and, for G1E, FP binding to SE rather than the target membrane. 2019 Biochemistry Abstract IV G1E 105 108 31008587 Hydrogen-Deuterium Exchange Supports Independent Membrane-Interfacial Fusion Peptide and Transmembrane Domains in Subunit 2 of Influenza Virus Hemagglutinin Protein, a Structured and Aqueous-Protected Connection between the Fusion Peptide and Soluble Ectodomain, and the Importance of Membrane Apposition by the Trimer-of-Hairpins Structure. Similar trends are observed for the G1E mutant as well as less exchange for G1E FP. 2019 Biochemistry Abstract IV G1E;G1E 36;76 39;79 31008587 Hydrogen-Deuterium Exchange Supports Independent Membrane-Interfacial Fusion Peptide and Transmembrane Domains in Subunit 2 of Influenza Virus Hemagglutinin Protein, a Structured and Aqueous-Protected Connection between the Fusion Peptide and Soluble Ectodomain, and the Importance of Membrane Apposition by the Trimer-of-Hairpins Structure. The I173E mutant exhibits greater exchange for residues 22-69 and 150-191, consistent with dissociation of SE C-terminal strands from interior N-helices. 2019 Biochemistry Abstract IV I173E 4 9 31044563 Alternative interaction sites in the influenza A virus nucleoprotein mediate viral escape from the importin-alpha7 mediated nuclear import pathway. We show that three mutations in particular occur with high frequency in the viral nucleoprotein (NP) protein (G102R, M105K and D375N) in a specific structural area upon in vivo adaptation. 2019 The FEBS journal Abstract IV G102R;M105K;D375N 110;117;127 115;122;132 NP;NP 97;82 99;95 31081750 Mutations in PB2 and HA enhanced pathogenicity of H4N6 avian influenza virus in mice. Although individual L331I or G453R substitutions in HA did not change the pathogenicity of BJ21 in mice, both mutations significantly enhanced virulence. 2020 The Journal of general virology Abstract IV L331I;G453R 20;29 25;34 HA 52 54 31081750 Mutations in PB2 and HA enhanced pathogenicity of H4N6 avian influenza virus in mice. Further studies showed that the introduction of E158K and/or E627K substitutions into PB2 significantly increased polymerase activity, which led to the enhanced replication and virulence of BJ21-MA. 2020 The Journal of general virology Abstract IV E158K;E627K 48;61 53;66 PB2 86 89 31081750 Mutations in PB2 and HA enhanced pathogenicity of H4N6 avian influenza virus in mice. Molecular analysis of BJ21-MA identified four mutations, located in proteins PB2 (E158K and E627K) and HA (L331I and G453R, H3 numbering). 2020 The Journal of general virology Abstract IV E158K;E627K;L331I;G453R 82;92;107;117 87;97;112;122 HA;PB2 103;77 105;80 31111259 PB2 and hemagglutinin mutations confer a virulent phenotype on an H1N2 avian influenza virus in mice. By evaluating the virulence of mouse-adapted H1N2 variants at different generations, we found that the PB2-D701N and HA-G228S mutations both contribute to the virulence of this virus in mammals. 2019 Archives of virology Abstract IV D701N;G228S 107;120 112;125 HA;PB2 117;103 119;106 31111259 PB2 and hemagglutinin mutations confer a virulent phenotype on an H1N2 avian influenza virus in mice. Furthermore, we found that the PB2-D701N and HA-G228S mutations both enhance the ability of the virus to replicate in vivo and in vitro and that the PB2-D701N substitution results in an expansion of viral tissue tropism. 2019 Archives of virology Abstract IV D701N;G228S;D701N 35;48;153 40;53;158 HA;PB2;PB2 45;31;149 47;34;152 31111259 PB2 and hemagglutinin mutations confer a virulent phenotype on an H1N2 avian influenza virus in mice. These results suggest that the PB2-D701N mutation and the HA-G228S mutation are the major mammalian determinants of H1N2 virus. 2019 Archives of virology Abstract IV D701N;G228S 35;61 40;66 HA;PB2 58;31 60;34 31111259 PB2 and hemagglutinin mutations confer a virulent phenotype on an H1N2 avian influenza virus in mice. We previously obtained mouse-adapted variants of H1N2 avian influenza virus that contained PB2-L134H, PB2-I647L, PB2-D701N, HA-G228S, and M1-D231N mutations. 2019 Archives of virology Abstract IV L134H;I647L;D701N;G228S;D231N 95;106;117;127;141 100;111;122;132;146 HA;M1;PB2;PB2;PB2 124;138;91;102;113 126;140;94;105;116 31150476 Pathogenicity of the H1N1 influenza virus enhanced by functional synergy between the NPV100I and NAD248N pair. To investigate the effect of these co-occurring substitution pairs, the V100I substitution in NP and the D248N substitution in NA were introduced into laboratory-adapted WSN IAVs. 2019 PloS one Abstract IV V100I;D248N 72;105 77;110 NA;NP 127;94 129;96 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. An approach to prevent L194P would therefore be beneficial. 2019 Cell host & microbe Abstract IV L194P 23 28 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. Importantly, wild-type HA antigenicity is maintained with G186V, but not L194P. 2019 Cell host & microbe Abstract IV G186V;L194P 58;73 63;78 HA 23 25 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. The L194P mutation is commonly observed in egg-based H3N2 vaccine seed strains and significantly alters HA antigenicity. 2019 Cell host & microbe Abstract IV L194P 4 9 HA 104 106 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. We show that emergence of L194P during egg passaging can be impeded by preexistence of a G186V mutation, revealing strong incompatibility between these mutations. 2019 Cell host & microbe Abstract IV L194P;G186V 26;89 31;94 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. X-ray structures illustrate that individual G186V and L194P mutations have opposing effects on the HA receptor-binding site (RBS), and when both G186V and L194P are present, the RBS is severely disrupted. 2019 Cell host & microbe Abstract IV G186V;L194P;G186V;L194P 44;54;145;155 49;59;150;160 HA 99 101 31169484 Segment 2 from influenza A(H1N1) 2009 pandemic viruses confers temperature-sensitive haemagglutinin yield on candidate vaccine virus growth in eggs that can be epistatically complemented by PB2 701D. Of these, PB2 N701D affected the temperature dependence of viral transcription and, furthermore, improved and drastically reduced the temperature sensitivity of the HA yield from the 5 : 3 CVV mimic. 2019 The Journal of general virology Abstract IV N701D 14 19 HA;PB2 165;10 167;13 31173771 Two mutations in viral protein enhance the adaptation of waterfowl-origin H3N2 virus in murine model. Furthermore, we found that PB2-D701N could enhance viral replication in vitro and in vivo and expanded viral tissue tropism. 2019 Virus research Abstract IV D701N 31 36 PB2 27 30 31173771 Two mutations in viral protein enhance the adaptation of waterfowl-origin H3N2 virus in murine model. Our data suggest that PB2-D701N and M1-M192V are the virulence markers of H3N2 avian influenza virus, and these markers can be used in the trans-species transmission surveillance for the H3N2 avian influenza virus. 2019 Virus research Abstract IV D701N;M192V 26;39 31;44 M1;PB2 36;22 38;25 31173771 Two mutations in viral protein enhance the adaptation of waterfowl-origin H3N2 virus in murine model. We found that both PB2-D701N mutation and M1-M192V mutation were implicated in the viral pathogenic phenotypic variation of H3N2 avian influenza virus in mice. 2019 Virus research Abstract IV D701N;M192V 23;45 28;50 M1;PB2 42;19 44;22 31175183 The L46P mutant confers a novel allosteric mechanism of resistance toward the influenza A virus M2 S31N proton channel blockers. In this study, serial viral passages were applied to select resistance against a newly developed isoxazole-conjugated adamantane inhibitor that targets the AM2 S31N channel. 2019 Molecular pharmacology Abstract IV S31N 160 164 31175183 The L46P mutant confers a novel allosteric mechanism of resistance toward the influenza A virus M2 S31N proton channel blockers. Intriguingly, when the L46P mutant was introduced to AM2 WT, the channel remained sensitive toward amantadine inhibition. 2019 Molecular pharmacology Abstract IV L46P 23 27 31175183 The L46P mutant confers a novel allosteric mechanism of resistance toward the influenza A virus M2 S31N proton channel blockers. It was found that the L46P mutation caused a conformational change in the N terminus of transmembrane residues 22-31 that ultimately broadened the drug-binding site of AM2 S31N inhibitor 4, which spans residues 26-34, but not of AM2 WT inhibitor amantadine, which spans residues 31-34. 2019 Molecular pharmacology Abstract IV L46P;S31N 22;172 26;176 31175183 The L46P mutant confers a novel allosteric mechanism of resistance toward the influenza A virus M2 S31N proton channel blockers. Molecular dynamics simulations showed that L46P causes a dilation of drug-binding site between residues 22 and 31, which affects the binding of AM2 S31N channel blockers, but not the AM2 WT inhibitor amantadine. 2019 Molecular pharmacology Abstract IV L46P;S31N 43;148 47;152 31175183 The L46P mutant confers a novel allosteric mechanism of resistance toward the influenza A virus M2 S31N proton channel blockers. Overall, these results demonstrate a unique allosteric resistance mechanism toward AM2 S31N channel blockers, and the L46P mutant represents the first experimentally confirmed drug-resistant AM2 mutant that is located outside of the pore where drug binds. 2019 Molecular pharmacology Abstract IV S31N;L46P 87;118 91;122 31175183 The L46P mutant confers a novel allosteric mechanism of resistance toward the influenza A virus M2 S31N proton channel blockers. SIGNIFICANCE STATEMENT: AM2 S31N is a high-profile antiviral drug target, as more than 95% of currently circulating influenza A viruses carry this mutation. 2019 Molecular pharmacology Abstract IV S31N 28 32 31175183 The L46P mutant confers a novel allosteric mechanism of resistance toward the influenza A virus M2 S31N proton channel blockers. The Food and Drug Administration-approved influenza A antiviral amantadine inhibits the wild-type (WT) AM2 channel but not the S31N mutant predominantly found in circulating strains. 2019 Molecular pharmacology Abstract IV S31N 127 131 31175183 The L46P mutant confers a novel allosteric mechanism of resistance toward the influenza A virus M2 S31N proton channel blockers. The L46P mutant is located outside of the drug-binding site. 2019 Molecular pharmacology Abstract IV L46P 4 8 31175183 The L46P mutant confers a novel allosteric mechanism of resistance toward the influenza A virus M2 S31N proton channel blockers. The MM-GBSA calculations showed stronger binding stability for 4 in complex with AM2 S31N compared with 4 in complex with AM2 S31N/L46P, and equal binding free energies of amantadine in complex with AM2 WT and AM2 L46P. 2019 Molecular pharmacology Abstract IV S31N;L46P;L46P 85;131;214 89;135;218 31175183 The L46P mutant confers a novel allosteric mechanism of resistance toward the influenza A virus M2 S31N proton channel blockers. This led to the identification of the novel drug-resistant mutation L46P located outside the drug-binding site, which suggests an allosteric resistance mechanism. 2019 Molecular pharmacology Abstract IV L46P 68 72 31175183 The L46P mutant confers a novel allosteric mechanism of resistance toward the influenza A virus M2 S31N proton channel blockers. Understanding the mechanism of drug resistance is critical in designing the next generation of AM2 S31N channel blockers. 2019 Molecular pharmacology Abstract IV S31N 99 103 31175183 The L46P mutant confers a novel allosteric mechanism of resistance toward the influenza A virus M2 S31N proton channel blockers. Using a previously developed AM2 S31N channel blocker as a chemical probe, this study was the first to identify a novel resistant mutant, L46P. 2019 Molecular pharmacology Abstract IV S31N;L46P 33;138 37;142 31176096 Design, synthesis and biological evaluation of "Multi-Site"-binding influenza virus neuraminidase inhibitors. Among the synthesized compounds, compound 15e, the most potent N1-selective inhibitor targeting 150-cavity, showed 1.5 and 1.8 times greater activity than oseltamivir carboxylate (OSC) against N1 (H5N1) and N1 (H5N1-H274Y). 2019 European journal of medicinal chemistry Abstract IV H274Y 216 221 31176096 Design, synthesis and biological evaluation of "Multi-Site"-binding influenza virus neuraminidase inhibitors. Molecular docking studies provided insights into the high potency of 15e against N1 and N1-H274Y mutant NA. 2019 European journal of medicinal chemistry Abstract IV H274Y 91 96 104 106 31200112 Adaptive amino acid substitutions enhance the virulence of an avian-origin H6N1 influenza virus in mice. The results showed that PB2 (L193H and E627K), PA (S709F) and HA (V127I) proteins had multiple amino acid substitutions. 2019 Infection, genetics and evolution Abstract IV L193H;E627K;S709F;V127I 29;39;51;66 34;44;56;71 HA;PA;PB2 62;47;24 64;49;27 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. Four residues in the N-terminal region of PA are critical in mediating the PB2 E627K acquisition. 2019 mBio Abstract IV E627K 79 84 PA;PB2 42;75 44;78 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. Furthermore, the impaired viral polymerase activity of H7N9 AIV caused by the depletion of ANP32A led to reduced virus replication in Anp32a-/- mice, abolishing the acquisition of the PB2 E627K mutation and instead driving the virus to acquire the alternative PB2 D701N mutation. 2019 mBio Abstract IV E627K;D701N 188;264 193;269 PB2;PB2 184;260 187;263 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. H7N9 AIVs that emerged in 2013 possess a prominent ability in gaining the PB2 E627K mutation in humans. 2019 mBio Abstract IV E627K 78 83 PB2 74 77 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. Here, we demonstrate that the acquisition of the H7N9 PB2 E627K mutation is driven by the low polymerase activity conferred by the viral PA protein in human cells, and four PA residues are collectively involved in this process. 2019 mBio Abstract IV E627K 58 63 PA;PA;PB2 137;173;54 139;175;57 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. Notably, the H7N9 PA protein leads to significant dependence of viral polymerase function on human ANP32A protein, and Anp32a knockout abolishes PB2 E627K acquisition in mice. 2019 mBio Abstract IV E627K 149 154 PA;PB2 18;145 20;148 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. Taken together, our findings show that the emergence of the PB2 E627K mutation of H7N9 AIV is driven by the intrinsic low polymerase activity conferred by the viral PA protein, which also involves the engagement of mammalian ANP32A.IMPORTANCE The emergence of the PB2 E627K substitution is critical in the mammalian adaptation and pathogenesis of AIV. 2019 mBio Abstract IV E627K;E627K 64;268 69;273 PA;PB2;PB2 165;60;264 167;63;267 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. The H7N9 AIVs that emerged in 2013 in China easily acquired the PB2 E627K mutation upon replication in humans. 2019 mBio Abstract IV E627K 68 73 PB2 64 67 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. The PB2 E627K mutation is known to play a prominent role in the mammalian adaptation of AIVs. 2019 mBio Abstract IV E627K 8 13 PB2 4 7 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. These findings reveal that viral PA and host ANP32A are crucial for the emergence of PB2 E627K during adaptation of H7N9 AIVs to humans. 2019 mBio Abstract IV E627K 89 94 PA;PB2 33;85 35;88 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. We show that the low polymerase activity attributed to the viral PA protein is the intrinsic driving force behind the emergence of PB2 E627K during H7N9 AIV replication in mice. 2019 mBio Abstract IV E627K 135 140 PA;PB2 65;131 67;134 31223581 Genetic and Phylogenetic Characterization of the M Gene of Influenza A Virus Isolated from Iranian Patients. Amino acid sequence analysis showed S31N substitution in all isolates rendering the virus resistant to adamantanes. 2019 Iranian journal of public health Abstract IV S31N 36 40 31228489 Effect of influenza H1N1 neuraminidase V116A and I117V mutations on NA activity and sensitivity to NA inhibitors. In contrast, V116A, I117V, E119A, and N295S substitutions resulted in significantly lower viral titers (1.2 logs) than the parental CA/04 virus in NHBE cells. 2019 Antiviral research Abstract IV V116A;I117V;E119A;N295S 13;20;27;38 18;25;32;43 31228489 Effect of influenza H1N1 neuraminidase V116A and I117V mutations on NA activity and sensitivity to NA inhibitors. The efficiencies of NAs with E119A, H275Y, and N295S mutations to catalyze all substrates were ~19.4% of the CA/04 NA. 2019 Antiviral research Abstract IV E119A;H275Y;N295S 29;36;47 34;41;52 NA;NA 115;20 117;23 31228489 Effect of influenza H1N1 neuraminidase V116A and I117V mutations on NA activity and sensitivity to NA inhibitors. Two NA mutations, V116A and I117V, are found in ~0.6% of human, avian, and swine N1 isolates. 2019 Antiviral research Abstract IV V116A;I117V 18;28 23;33 4 6 31228489 Effect of influenza H1N1 neuraminidase V116A and I117V mutations on NA activity and sensitivity to NA inhibitors. Using the A/California/04/09-like (CA/04, H1N1) background, we examined the impact of V116A and I117V NA mutations on NAI susceptibility, substrate specificity, and replicative capacity in normal human bronchial (NHBE) cells and a human respiratory epithelial cell line (Calu-3). 2019 Antiviral research Abstract IV V116A;I117V 86;96 91;101 NA;NAI 102;118 104;121 31228489 Effect of influenza H1N1 neuraminidase V116A and I117V mutations on NA activity and sensitivity to NA inhibitors. V116A conferred reduced sensitivity to oseltamivir and zanamivir (13.7-fold). 2019 Antiviral research Abstract IV V116A 0 5 31228489 Effect of influenza H1N1 neuraminidase V116A and I117V mutations on NA activity and sensitivity to NA inhibitors. We compared the impact of V116A and I117V on the functional properties of NA and compared these mutations with that of previously reported NAI-resistant mutations, E119A, H275Y, and N295S. 2019 Antiviral research Abstract IV V116A;I117V;E119A;H275Y;N295S 26;36;164;171;182 31;41;169;176;187 NA;NAI 74;139 76;142 31228489 Effect of influenza H1N1 neuraminidase V116A and I117V mutations on NA activity and sensitivity to NA inhibitors. When MUNANA, 3'SL, and 6'SL substrates were applied, we observed that V116A reduced binding ability for all substrates (13.9-fold) and I117V led to the significantly decreased affinity for MUNANA and 6'SL (4.2-fold). 2019 Antiviral research Abstract IV V116A;I117V 70;135 75;140 31233807 Passaging of an influenza A(H1N1)pdm09 virus in a difluoro sialic acid inhibitor selects for a novel, but unfit I106M neuraminidase mutant. A third group retained the I106M, but had a compensating R363K substitution, which regained almost wild type NA properties. 2019 Antiviral research Abstract IV I106M;R363K 27;57 32;62 109 111 31233807 Passaging of an influenza A(H1N1)pdm09 virus in a difluoro sialic acid inhibitor selects for a novel, but unfit I106M neuraminidase mutant. The I106M may impact NA function through steric effects on the movement of the 150 and 430-loops. 2019 Antiviral research Abstract IV I106M 4 9 21 23 31233807 Passaging of an influenza A(H1N1)pdm09 virus in a difluoro sialic acid inhibitor selects for a novel, but unfit I106M neuraminidase mutant. The I106M substitution was unstable, with progeny rapidly reverting to wild type by three different mechanisms. 2019 Antiviral research Abstract IV I106M 4 9 31233807 Passaging of an influenza A(H1N1)pdm09 virus in a difluoro sialic acid inhibitor selects for a novel, but unfit I106M neuraminidase mutant. The I106M viruses had similar replication kinetics in MDCK cells as wild type viruses, but their ability to bind to and infect CHO-K1 cells expressing high levels of cell-bound mucin was compromised. 2019 Antiviral research Abstract IV I106M 4 9 31233807 Passaging of an influenza A(H1N1)pdm09 virus in a difluoro sialic acid inhibitor selects for a novel, but unfit I106M neuraminidase mutant. These had a novel non-active site I106M substitution in the NA gene, but unexpectedly no HA changes. 2019 Antiviral research Abstract IV I106M 34 39 HA;NA 89;60 91;62 31233807 Passaging of an influenza A(H1N1)pdm09 virus in a difluoro sialic acid inhibitor selects for a novel, but unfit I106M neuraminidase mutant. We propose that the activity in the I106M mutant is insufficient to remove carbohydrates from the virion HA and NA, sterically limiting HA access to CRBC receptors, thus resulting in poor HA binding. 2019 Antiviral research Abstract IV I106M 36 41 HA;HA;HA;NA 105;136;188;112 107;138;190;114 31266524 Highly pathogenic avian influenza H7N9 viruses with reduced susceptibility to neuraminidase inhibitors showed comparable replication capacity to their sensitive counterparts. CONCLUSIONS: All 4 amino acid substitutions (R292 K, E119V, A246T or H274Y) in NA reduced the susceptibility of HPAI H7N9 to NAIs. 2019 Virology journal Abstract IV R292K;E119V;A246T;H274Y 45;53;60;69 51;58;65;74 NA;NAI 79;125 81;129 Influenza A virus H7N9 infection 112 221 31266524 Highly pathogenic avian influenza H7N9 viruses with reduced susceptibility to neuraminidase inhibitors showed comparable replication capacity to their sensitive counterparts. RESULTS: Four potential NAI resistance sites, R292 K, E119V, A246T or H274Y, were screened. 2019 Virology journal Abstract IV R292K;E119V;A246T;H274Y 46;54;61;70 52;59;66;75 NAI 24 27 31267843 Mammalian-adaptive mutation NP-Q357K in Eurasian H1N1 Swine Influenza viruses determines the virulence phenotype in mice. In addition, a single substitution, Q357K, in the NP protein of the EA H1N1 viruses alters the virulence phenotype. 2019 Emerging microbes & infections Abstract IV Q357K 36 41 NP 50 52 31267843 Mammalian-adaptive mutation NP-Q357K in Eurasian H1N1 Swine Influenza viruses determines the virulence phenotype in mice. Our study demonstrates that the substitution Q357K in the NP protein plays a key role in the virulence phenotype of EA H1N1 SIVs, and provides important information for evaluating the pandemic risk of field influenza strains. 2019 Emerging microbes & infections Abstract IV Q357K 45 50 NP 58 60 31267843 Mammalian-adaptive mutation NP-Q357K in Eurasian H1N1 Swine Influenza viruses determines the virulence phenotype in mice. The NP-Q357K substitution is readily to be occurred when avian influenza viruses circulate in pigs, and may facilitate their infection of humans and allow viruses also carrying NP-357K to circulate in humans. 2019 Emerging microbes & infections Abstract IV Q357K 7 12 NP;NP 4;177 6;179 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. By introducing a single adaptive substitution, G218E, into the hemagglutinin (HA), we generated reassortant A(H7N9)-G218E CVVs that were characterized by significantly enhanced growth in both cells and eggs. 2019 Journal of virology Abstract IV G218E;G218E 47;116 52;121 HA;HA 78;63 80;76 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. In contrast, the G218E-mediated growth improvement was attributed to relatively balanced HA and NA functions, resulted from reduced HA binding to both human- and avian-type receptors, and thus facilitated NA-mediated virus release. 2019 Journal of virology Abstract IV G218E 17 22 HA;HA;NA;NA 89;132;96;205 91;134;98;207 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. The in vitro and in vivo experiments demonstrated comparable antigenicity of the G218E CVVs with that of their wild-type (WT) counterparts, and both the WT and the G218E CVVs fully protected ferrets from parental HPAI virus challenge. 2019 Journal of virology Abstract IV G218E;G218E 81;164 86;169 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. These G218E CVVs retained the original antigenicity, as determined by a hemagglutination inhibition assay, and effectively protected ferrets from lethal challenge with the highly pathogenic parental virus. 2019 Journal of virology Abstract IV G218E 6 11 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. We generated low-pathogenic reassortant CVVs derived from the emerging A(H7N9) with improved virus replication and protein yield in both MDCK cells and eggs by introducing a single substitution, G218E, into HA, which was associated with reducing HA receptor binding and subsequently balancing HA-NA functions. 2019 Journal of virology Abstract IV G218E 195 200 HA;HA;HA;NA 207;246;293;296 209;248;295;298 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. With high yield traits and the anticipated antigenicity, the G218E CVVs should benefit preparedness against the threat of an A(H7N9) influenza pandemic. 2019 Journal of virology Abstract IV G218E 61 66 31292247 Serial Section Array Scanning Electron Microscopy Analysis of Cells from Lung Autopsy Specimens following Fatal A/H1N1 2009 Pandemic Influenza Virus Infection. A/H1N1/pdm09 harboring the D222G substitution has a receptor-binding preference for alpha-2,3-linked sialic acids expressed on human AECs and infects them in the same way as H5N1 and H7N9 avian IAVs. 2019 Journal of virology Abstract IV D222G 27 32 31292247 Serial Section Array Scanning Electron Microscopy Analysis of Cells from Lung Autopsy Specimens following Fatal A/H1N1 2009 Pandemic Influenza Virus Infection. This was because the majority of A/H1N1/pdm09 in the lung tissue harbored an aspartic acid-to-glycine substitution at position 222 (D222G) of the hemagglutinin protein. 2019 Journal of virology Abstract IV D222G;D222G 132;77 137;130 HA 146 159 31299269 A cross-reactive human monoclonal antibody targets the conserved H7 antigenic site A from fifth wave H7N9-infected humans. By generating escape mutant variants, we found that a single G151E substitution in the viral H7 antigenic site A could abort the neutralizing activity. 2019 Antiviral research Abstract IV G151E 61 66 31305236 Prevailing I292V PB2 mutation in avian influenza H9N2 virus increases viral polymerase function and attenuates IFN-beta induction in human cells. Here, we identify I292V as the prevalent mutation in PB2 of circulating avian H9N2 and pandemic H1N1 viruses. 2019 The Journal of general virology Abstract IV I292V 18 23 PB2 53 56 31309975 Treatment-Emergent Influenza Variant Viruses With Reduced Baloxavir Susceptibility: Impact on Clinical and Virologic Outcomes in Uncomplicated Influenza. BACKGROUND: Single-dose baloxavir rapidly reduces influenza virus titers and symptoms in patients with uncomplicated influenza, but viruses with reduced in vitro susceptibility due to amino acid substitutions at position 38 of polymerase acidic protein (PA/I38X) sometimes emerge. 2020 The Journal of infectious diseases Abstract IV I38X 257 261 PA;PA 254;227 256;244 Influenza 117 126 31309975 Treatment-Emergent Influenza Variant Viruses With Reduced Baloxavir Susceptibility: Impact on Clinical and Virologic Outcomes in Uncomplicated Influenza. CONCLUSIONS: The emergence of viruses with PA/I38X substitutions following baloxavir treatment was associated with transient rises in infectious virus titers, prolongation of virus detectability, initial delay in symptom alleviation, and uncommonly with symptom rebound. 2020 The Journal of infectious diseases Abstract IV I38X 46 50 PA 43 45 31309975 Treatment-Emergent Influenza Variant Viruses With Reduced Baloxavir Susceptibility: Impact on Clinical and Virologic Outcomes in Uncomplicated Influenza. Median time to sustained cessation of infectious virus detection was 192, 48, and 96 hours in the baloxavir recipients with PA/I38X-substituted viruses, without PA/I38X-substituted viruses, and placebo recipients, respectively. 2020 The Journal of infectious diseases Abstract IV I38X;I38X 127;164 131;168 PA;PA 124;161 126;163 31309975 Treatment-Emergent Influenza Variant Viruses With Reduced Baloxavir Susceptibility: Impact on Clinical and Virologic Outcomes in Uncomplicated Influenza. METHODS: We evaluated the kinetics, risk factors, and effects on clinical and virologic outcomes of emergence of PA/I38X-substituted viruses. 2020 The Journal of infectious diseases Abstract IV I38X 116 120 PA 113 115 31309975 Treatment-Emergent Influenza Variant Viruses With Reduced Baloxavir Susceptibility: Impact on Clinical and Virologic Outcomes in Uncomplicated Influenza. RESULTS: Viruses containing PA/I38X substitutions were identified 3-9 days after baloxavir treatment in 9.7% (36/370) of patients, of whom 85.3% had transient virus titer rises. 2020 The Journal of infectious diseases Abstract IV I38X 31 35 PA 28 30 31309975 Treatment-Emergent Influenza Variant Viruses With Reduced Baloxavir Susceptibility: Impact on Clinical and Virologic Outcomes in Uncomplicated Influenza. The potential transmissibility of PA/I38X-substituted viruses requires careful study. 2020 The Journal of infectious diseases Abstract IV I38X 37 41 PA 34 36 31323237 The Val430Ile neuraminidase (NA) substitution, identified in influenza B virus isolates, impacts the catalytic 116Arg residue causing reduced susceptibility to NA inhibitors. As part of a 2015-2018 clinical trial of peramivir treatment for acute influenza infections in the elderly, an influenza B/Yamagata/16/1988-like isolate harbouring a Val430Ile neuraminidase (NA) substitution was recovered from a single patient. 2019 Antiviral research Abstract IV V430I 166 175 NA;NA 191;176 193;189 IV infections 71 91 31323237 The Val430Ile neuraminidase (NA) substitution, identified in influenza B virus isolates, impacts the catalytic 116Arg residue causing reduced susceptibility to NA inhibitors. In NA inhibition assays, oseltamivir, zanamivir and peramivir IC50s of the Val430Ile isolate were 4-, 15- and 16-fold higher compared to a wild-type (WT) strain. 2019 Antiviral research Abstract IV V430I 75 84 3 5 31323237 The Val430Ile neuraminidase (NA) substitution, identified in influenza B virus isolates, impacts the catalytic 116Arg residue causing reduced susceptibility to NA inhibitors. In reverse genetics experiments, the Ile430Val reversion restored the drug susceptible phenotype. 2019 Antiviral research Abstract IV I430V 37 46 31323237 The Val430Ile neuraminidase (NA) substitution, identified in influenza B virus isolates, impacts the catalytic 116Arg residue causing reduced susceptibility to NA inhibitors. Molecular dynamics simulations suggested that Val430Ile impacts the NA binding through a mechanism involving the catalytic Arg116 residue. 2019 Antiviral research Abstract IV V430I 46 55 68 70 31323237 The Val430Ile neuraminidase (NA) substitution, identified in influenza B virus isolates, impacts the catalytic 116Arg residue causing reduced susceptibility to NA inhibitors. The Val430Ile mutant and the WT strain had comparable replication kinetics in ST6GalI-MDCK cells and the NA mutation was stable after four passages in that cell line. 2019 Antiviral research Abstract IV V430I 4 13 105 107 31329089 Biological properties of influenza A virus mutants with amino acid substitutions in the HA2 glycoprotein of the HA1/HA2 interaction region. However, the HA2 mutation V662H and double mutation T642H, V662H shifted the fusion pH maximum to lower values (ranging from 5.1 to 5.3) compared to pH from 5.4 to 5.6 for the wild-type and 64 mutant. 2019 The Journal of general virology Abstract IV V662H;T642H;V662H 26;52;59 31;57;64 HA 13 15 31329089 Biological properties of influenza A virus mutants with amino acid substitutions in the HA2 glycoprotein of the HA1/HA2 interaction region. We prepared mutants of neurotropic IAV A/WSN/33 (H1N1) with aa substitutions in HA2 gp at the site of HA1/HA2 interaction, namely T642H (HA2 numbering position 64, H1 numbering position HA407; referred to as mutant '64'), V662H ('66') (HA409); and a double mutant ('D') with two aa substitutions (T642H, V662H). 2019 The Journal of general virology Abstract IV T642H;V662H;T642H;V662H 130;222;297;304 135;227;302;309 HA;HA;HA;HA;HA;HA1 80;106;137;186;236;102 82;108;139;188;238;105 31336147 Rapid isolation of a potent human antibody against H7N9 influenza virus from an infected patient. Additionally, the 3L11 escape strains had G151R (Gly151 Arg151) and S152P (Ser152 Pro152) mutations within a conserved antigenic site A near the RBS that were not observed in field strains. 2019 Antiviral research Abstract IV G151R;S152P 42;68 47;73 31351233 Evolution of H9N2 low pathogenic avian influenza virus during passages in chickens. For example, the amino-acid substitution N337K in the haemagglutinin (HA) cleavage site region detected in the 6th passage as low frequency variant had undergone rapid selection and became predominant in the 7th passage. 2019 Infection, genetics and evolution Abstract IV N337K 41 46 HA;HA 70;54 72;68 31356626 Severe cases of seasonal influenza in Russia in 2017-2018. One strain of influenza virus A(H1N1)pdm09 was resistant to oseltamivir and had the H275Y amino acid substitution in the NA protein. 2019 PloS one Abstract IV H275Y 84 89 121 123 31356626 Severe cases of seasonal influenza in Russia in 2017-2018. This study demonstrated the importance of monitoring D222G/N polymorphism, including detection of minor viral variants with the mutations, in the hemagglutinin gene of A(H1N1)pdm09 for epidemiological surveillance. 2019 PloS one Abstract IV D222G;D222N 53;53 60;60 HA 146 159 31366399 Naturally occurring mutations in PB1 affect influenza A virus replication fidelity, virulence, and adaptability. These results suggest that the PB1-S216G substitution enhances viral epidemiological fitness by increasing the frequency of adaptive mutations in human influenza A/H1N1 viruses. 2019 Journal of biomedical science Abstract IV S216G 35 40 PB1 31 34 31382442 A Single Mutation N166D in Hemagglutinin Affects Antigenicity and Pathogenesis of H9N2 Avian Influenza Virus. Although N166D did not significantly affect viral replication in Madin-Darby canine kidney (MDCK) cells and viral shedding in the larynx and cloaca of chicken, N166D attenuated the pathogenesis of the virus in mice. 2019 Viruses Abstract IV N166D;N166D 9;160 14;165 31382442 A Single Mutation N166D in Hemagglutinin Affects Antigenicity and Pathogenesis of H9N2 Avian Influenza Virus. Considering the field strains of H9N2 with N166D mutation are frequently isolated in the countries with H9N2 vaccination, the findings that the single mutation in HA, N166D, affected both the antigenicity and pathogenesis of H9N2 highlight the significance of surveillance on such mutation that may contribute to the failure of H9N2 vaccination in the field. 2019 Viruses Abstract IV N166D;N166D 43;167 48;172 HA 163 165 31382442 A Single Mutation N166D in Hemagglutinin Affects Antigenicity and Pathogenesis of H9N2 Avian Influenza Virus. In this study, seven critical sites in HA associated with the antigenicity were identified and the effects of a HA mutation (N166D) derived from a H9N2 escape mutant (m3F2) were investigated. 2019 Viruses Abstract IV N166D 125 130 HA;HA 39;112 41;114 31382442 A Single Mutation N166D in Hemagglutinin Affects Antigenicity and Pathogenesis of H9N2 Avian Influenza Virus. Moreover, hemagglutination inhibition (HI) assay for the sera from the chickens infected with wild type H9N2 and mutant m3F2 showed that N166D mutation could result in weak antibody response in chickens. 2019 Viruses Abstract IV N166D 137 142 31400550 The evolution and characterization of influenza A(H7N9) virus under the selective pressure of peramivir. The NA-H274Y variant showed decreased replicative fitness at the early stage of infection accompanied with impaired NA function. 2019 Virology Abstract IV H274Y 7 12 NA;NA 4;116 6;118 31400550 The evolution and characterization of influenza A(H7N9) virus under the selective pressure of peramivir. Two important amino acid substitutions were identified in NA, I222T and H274Y, which caused reduced susceptibilities to oseltamivir or both oseltamivir and peramivir as confirmed by enzyme- and cell-based assays. 2019 Virology Abstract IV I222T;H274Y 62;72 67;77 58 60 31406333 The neuraminidase of A(H3N2) influenza viruses circulating since 2016 is antigenically distinct from the A/Hong Kong/4801/2014 vaccine strain. This antigenic drift was mainly caused by amino acid mutations at NA residues 245, 247 (S245N/S247T; introducing an N-linked glycosylation site at residue 245) and 468. 2019 Nature microbiology Abstract IV S245N;S247T 88;94 93;99 66 68 31407570 Diagnosis of Tamiflu-Resistant Influenza Virus in Human Nasal Fluid and Saliva Using Surface-Enhanced Raman Scattering. By combining SERS-active urchin Au nanoparticles and oseltamivir hexylthiol, an excellent receptor for the pH1N1/H275Y mutant virus, we detected the pH1N1/H275Y virus specifically and sensitively in human saliva and nasal fluid samples. 2019 ACS sensors Abstract IV H275Y;H275Y 113;155 118;160 31412173 [Change of phenotypic properties of escape mutants and readaptants of influenza virus A (H1N1)pdm09 under the influence of selected mutations in the molecule of hemagglutinin.] A correlation was found between a decrease in virulence of a low-virulent escape mutant associated with the substitution D190N in the hemagglutinin molecule and an increase in the hemagglutinating titer to inhibitors in normal mouse serum. 2019 Voprosy virusologii Abstract IV D190N 121 126 HA 134 147 31412173 [Change of phenotypic properties of escape mutants and readaptants of influenza virus A (H1N1)pdm09 under the influence of selected mutations in the molecule of hemagglutinin.] RESULTS: The amino acid substitution A198E acquired in the process of readaptation leads to changes in the antigenic specificity. 2019 Voprosy virusologii Abstract IV A198E 37 42 31413133 Development and Characterization of a Reverse-Genetics System for Influenza D Virus. In addition, we developed an IDV minigenome replication assay and identified the E697K mutation in PB1 and the L462F mutation in PB2 that directly affected the activity of the IDV ribonucleoprotein (RNP) complex, resulting in either attenuated or replication-incompetent viruses. 2019 Journal of virology Abstract IV E697K;L462F 81;111 86;116 PB1;PB2;RNP 99;129;199 102;132;202 31420169 The structure and conformational plasticity of the nonstructural protein 1 of the 1918 influenza A virus. Here, we present the solution NMR structure of the NS1-ED W187R of the 1918 influenza A virus, which caused the "Spanish flu." Structural plasticity is an essential property to understand the molecular mechanism by which NS1-ED interacts with multiple host proteins. 2019 Biochemical and biophysical research communications Abstract IV W187R 58 63 NS1;NS1 51;221 54;224 31436527 Human-to-Human Transmission of Influenza A(H3N2) Virus with Reduced Susceptibility to Baloxavir, Japan, February 2019. In 2019, influenza A(H3N2) viruses carrying an I38T substitution in the polymerase acidic gene, which confers reduced susceptibility to baloxavir, were detected in Japan in an infant without baloxavir exposure and a baloxavir-treated sibling. 2019 Emerging infectious diseases Abstract IV I38T 47 51 PA 72 89 31445105 Amino acid changes in HA and determinants of pathogenicity associated with influenza virus A H1N1pdm09 during the winter seasons 2015-2016 and 2016-2017 in Mexico. The IAVs presented the substitution S162 N, which introduces a new glycosylation site in the hemagglutinin. 2019 Virus research Abstract IV S162N 36 42 HA 93 106 31445105 Amino acid changes in HA and determinants of pathogenicity associated with influenza virus A H1N1pdm09 during the winter seasons 2015-2016 and 2016-2017 in Mexico. The new glycosylation site in HA (S162 N) is a major change that may affect the efficacy of the current vaccine. 2019 Virus research Abstract IV S162N 34 40 HA 30 32 31445105 Amino acid changes in HA and determinants of pathogenicity associated with influenza virus A H1N1pdm09 during the winter seasons 2015-2016 and 2016-2017 in Mexico. We also found the D222 G substitution, which has been associated with a higher tropism towards the lower respiratory tract, and a non-reported insertion of one Ile in NS1 (Ile113). 2019 Virus research Abstract IV D222G 18 24 NS1 167 170 31462570 Tyr82 Amino Acid Mutation in PB1 Polymerase Induces an Influenza Virus Mutator Phenotype. As a result, we isolated various novel mutators other than PB1-Y82C with higher mutation frequencies. 2019 Journal of virology Abstract IV Y82C 63 67 PB1 59 62 31462570 Tyr82 Amino Acid Mutation in PB1 Polymerase Induces an Influenza Virus Mutator Phenotype. Based on structural data of RdRp, rational targeting of key residues, and screening of fidelity variants, we isolated a novel low-fidelity mutator strain of influenza virus that harbors a Tyr82-to-Cys (Y82C) single-amino-acid substitution in the PB1 polymerase subunit. 2019 Journal of virology Abstract IV Y82C;Y82C 188;202 200;206 PB1 246 249 31462570 Tyr82 Amino Acid Mutation in PB1 Polymerase Induces an Influenza Virus Mutator Phenotype. Interestingly, although the PB1-Y82C variant replicated with wild-type PB1-like kinetics in tissue culture, the 50% lethal dose of the PB1-Y82C mutant was 10 times lower than that of wild-type PB1 in embryonated chicken eggs. 2019 Journal of virology Abstract IV Y82C;Y82C 32;139 36;143 PB1;PB1;PB1;PB1 28;71;135;193 31;74;138;196 31462570 Tyr82 Amino Acid Mutation in PB1 Polymerase Induces an Influenza Virus Mutator Phenotype. The purified PB1-Y82C polymerase indeed showed an increased frequency of misincorporation compared with the wild-type PB1 in an in vitro biochemical assay. 2019 Journal of virology Abstract IV Y82C 17 21 PB1;PB1 13;118 16;121 31462570 Tyr82 Amino Acid Mutation in PB1 Polymerase Induces an Influenza Virus Mutator Phenotype. Viruses containing the PB1-Y82C substitution showed growth kinetics and viral RNA synthesis levels similar to those of the wild-type virus in cell culture; however, they had significantly attenuated phenotypes in a chicken egg infection experiment. 2019 Journal of virology Abstract IV Y82C 27 31 PB1 23 26 31477028 A study of the relationship between human infection with avian influenza a (H5N6) and environmental avian influenza viruses in Fujian, China. The R294K or N294S substitution was not detected in the neuraminidase (NA). 2019 BMC infectious diseases Abstract IV R294K;N294S 4;13 9;18 NA;NA 71;56 73;69 31477028 A study of the relationship between human infection with avian influenza a (H5N6) and environmental avian influenza viruses in Fujian, China. The S31 N substitution in the matrix2 (M2) gene was detected but only in one strain from the environmental samples. 2019 BMC infectious diseases Abstract IV S31N 4 9 M2;M 39;30 41;36 31508993 Identification of antigenic epitopes in the haemagglutinin protein of H7 avian influenza virus. The epitope 103RESGSS107 was highly conserved among Eurasian lineage strains of H7 AIV, whereas three amino acid substitutions (E104R, E104K and E104G) in the epitope occurred in 98.44% of North-American lineage strains. 2020 Avian pathology Abstract IV E104R;E104K;E104G 128;135;145 133;140;150 31526451 Mutated influenza A virus exhibiting reduced susceptibility to baloxavir marboxil from an experimentally infected horse. A mutated virus with PA-I38T was less susceptible to BXM than viruses with PA-N675D or without mutation. 2019 The Journal of general virology Abstract IV I38T;N675D 24;78 28;83 PA;PA 21;75 23;77 31526451 Mutated influenza A virus exhibiting reduced susceptibility to baloxavir marboxil from an experimentally infected horse. A PA-I38T mutation has also been detected in viruses recovered from humans treated with BXM and is responsible for the reduction in susceptibility to BXM. 2019 The Journal of general virology Abstract IV I38T 5 9 PA 2 4 31526451 Mutated influenza A virus exhibiting reduced susceptibility to baloxavir marboxil from an experimentally infected horse. These mutations were the substitution of isoleucine with threonine at position 38 (PA-I38T) and that of asparagine with aspartic acid at position 675 in PA (PA-N675D). 2019 The Journal of general virology Abstract IV I38T;N675D;I38T;N675D 86;160;41;104 90;165;81;149 PA;PA;PA 83;153;157 85;155;159 31534039 Hepatitis C Virus Infection Is Inhibited by a Noncanonical Antiviral Signaling Pathway Targeted by NS3-NS4A. Here, we identified a Tyr-16-Phe (Y16F) change in the NS4A transmembrane domain that prevents NS3-NS4A targeting of Riplet but not MAVS. 2019 Journal of virology Abstract IV Y16F;Y16F 22;34 32;38 NS;NS;NS 54;94;98 56;96;100 31534039 Hepatitis C Virus Infection Is Inhibited by a Noncanonical Antiviral Signaling Pathway Targeted by NS3-NS4A. In addition, TBK1 inhibition or IRF3 deletion in Huh7 cells was sufficient to restore HCV Y16F replication, and the Y16F protease lacked the ability to prevent IRF3 activation or interferon induction. 2019 Journal of virology Abstract IV Y16F;Y16F 90;116 94;120 31534039 Hepatitis C Virus Infection Is Inhibited by a Noncanonical Antiviral Signaling Pathway Targeted by NS3-NS4A. Rather, we found that Huh-7.5 cells lack Riplet expression and that the addition of Riplet to these cells reduced HCV Y16F replication, whereas the addition of Riplet lacking the RING domain restored HCV Y16F replication. 2019 Journal of virology Abstract IV Y16F;Y16F 118;204 122;208 31534039 Hepatitis C Virus Infection Is Inhibited by a Noncanonical Antiviral Signaling Pathway Targeted by NS3-NS4A. Surprisingly, deletion of RIG-I in Huh7 cells did not restore Y16F viral replication. 2019 Journal of virology Abstract IV Y16F 62 66 31534039 Hepatitis C Virus Infection Is Inhibited by a Noncanonical Antiviral Signaling Pathway Targeted by NS3-NS4A. This Y16F substitution reduces HCV replication in Huh7 cells, but not in Huh-7.5 cells, known to lack RIG-I signaling. 2019 Journal of virology Abstract IV Y16F 5 9 31538643 Oseltamivir Resistance in Severe Influenza A(H1N1)pdm09 Pneumonia and Acute Respiratory Distress Syndrome: A French Multicenter Observational Cohort Study. In a multicenter cohort study including 22 oseltamivir-treated patients with influenza A(H1N1)pdm09 acute respiratory distress syndrome, prevalence of the H275Y substitution in the neuraminidase, responsible for highly reduced sensitivity to oseltamivir, was 23%. 2020 Clinical infectious diseases Abstract IV H275Y 155 160 181 194 Respiratory distress syndrome 100 135 31538643 Oseltamivir Resistance in Severe Influenza A(H1N1)pdm09 Pneumonia and Acute Respiratory Distress Syndrome: A French Multicenter Observational Cohort Study. Patients infected with the H275Y mutant virus had higher day 28 mortality than others (80% vs 12%; P = .011). 2020 Clinical infectious diseases Abstract IV H275Y 27 32 31538644 Baloxavir Marboxil in Japanese Pediatric Patients With Influenza: Safety and Clinical and Virologic Outcomes. Among patients with PA/I38T/M-substituted virus emergence, those with baseline hemagglutinin inhibition (HAI) antibody titer <40 experienced delay in time to illness alleviation (median, 85.4 vs 56.0 hours in patients with higher baseline HAI antibody titer). 2020 Clinical infectious diseases Abstract IV I38T;I38M 23;23 29;29 HA;PA 79;20 92;22 31538644 Baloxavir Marboxil in Japanese Pediatric Patients With Influenza: Safety and Clinical and Virologic Outcomes. CONCLUSIONS: A single, oral dose of baloxavir marboxil was well tolerated and rapidly reduced viral titers, but the common emergence of PA/I38T/M-substituted viruses warrants consideration of alternative dosing regimens in young children. 2020 Clinical infectious diseases Abstract IV I38T;I38M 139;139 145;145 PA 136 138 31538644 Baloxavir Marboxil in Japanese Pediatric Patients With Influenza: Safety and Clinical and Virologic Outcomes. Emergence was associated with longer infectious virus detectability (median time, 180.0 hours) and time to illness alleviation (median, 79.6 vs 42.8 hours in patients without PA/I38T/M-substituted viruses). 2020 Clinical infectious diseases Abstract IV I38T;I38M 178;178 184;184 PA 175 177 31538644 Baloxavir Marboxil in Japanese Pediatric Patients With Influenza: Safety and Clinical and Virologic Outcomes. However, viruses with amino acid substitutions in the viral polymerase acidic protein at position I38 (PA/I38T/M) emerged in 18 of 77 (23.4%) patients. 2020 Clinical infectious diseases Abstract IV I38T;I38M 106;106 112;112 PA;PA 103;60 105;77 31575766 Influenza Virus Polymerase Mutation Stabilizes a Foreign Gene Inserted into the Virus Genome by Enhancing the Transcription/Replication Efficiency of the Modified Segment. Although the inserted Venus gene was deleted during serial passages of WT-Venus-PR8, we discovered that the PB2-E712D mutation stabilizes the Venus gene. 2019 mBio Abstract IV E712D 112 117 PB2 108 111 31575766 Influenza Virus Polymerase Mutation Stabilizes a Foreign Gene Inserted into the Virus Genome by Enhancing the Transcription/Replication Efficiency of the Modified Segment. Deep sequencing analysis revealed that PB2-E712D does not cause an appreciable change in the mutation rate, suggesting that the stability of the Venus gene is not affected by polymerase fidelity. 2019 mBio Abstract IV E712D 43 48 PB2 39 42 31575766 Influenza Virus Polymerase Mutation Stabilizes a Foreign Gene Inserted into the Virus Genome by Enhancing the Transcription/Replication Efficiency of the Modified Segment. In contrast, the transcription/replication efficiency of the modified NS segment was enhanced by the PB2-E712D mutation. 2019 mBio Abstract IV E712D 105 110 NS;PB2 70;101 72;104 31581279 Influenza virus polymerase subunits co-evolve to ensure proper levels of dimerization of the heterotrimer. Strikingly the PA-E349K mutation, and also the PB2-G74R and PB1-K577G mutations present on other revertants, are located at a dimerization interface of the polymerase. 2019 PLoS pathogens Abstract IV E349K;G74R;K577G 18;51;64 23;55;69 PA;PB1;PB2 15;60;47 17;63;50 31581279 Influenza virus polymerase subunits co-evolve to ensure proper levels of dimerization of the heterotrimer. The PA-E349K mutation appeared to play a major role in correcting the initial defect in replication (cRNA -> vRNA) of the PR8xWSN-PB2 reassortant. 2019 PLoS pathogens Abstract IV E349K 7 12 PA;PB2 4;130 6;133 31585646 H5N8 avian influenza virus acquires enhanced pathogenicity after a single passage in chicken. Sequence analysis revealed a single mutation, M374 V, in nucleoprotein (NP) of the passaged virus, and this substitution was conserved after a further inoculation study. 2019 Veterinary microbiology Abstract IV M374V 46 52 NP;NP 72;57 74;70 31590265 Insights into the Acquisition of Virulence of Avian Influenza Viruses during a Single Passage in Ferrets. In most instances the virus had acquired the common virulence substitution PB2 E627K but, in one case, a previously unidentified combination of two amino acid substitutions at PB2 S489P and NP V408I, which enhanced polymerase activity, was found. 2019 Viruses Abstract IV E627K;S489P;V408I 79;180;193 84;185;198 NP;PB2;PB2 190;75;176 192;78;179 31597771 Identification of Key Amino Acids in the PB2 and M1 Proteins of H7N9 Influenza Virus That Affect Its Transmission in Guinea Pigs. We found that the neuraminidase (NA) of the nontransmissible virus A/chicken/Shanghai/S1053/2013 had low enzymatic activity that impaired the transmission of AH/1 virus, and three amino acid mutations-V292I and K627E in PB2 and D156E in M1-independently abolished the transmission of the AH/1 virus. 2019 Journal of virology Abstract IV V292I;K627E;D156E 201;211;228 206;216;233 M1;NA;NA;PB2 237;33;18;220 239;35;31;223 31600274 Adaptation of H3N2 canine influenza virus to feline cell culture. Among them, HA1-K299R, HA2-T107I, NA-L35R, and M2-W41C mutations individually increased virus growth in CRFK cells. 2019 PloS one Abstract IV W41C;K299R;T107I;L35R 50;16;27;37 54;21;32;41 HA;HA1;M2;NA 23;12;47;34 25;15;49;36 31600274 Adaptation of H3N2 canine influenza virus to feline cell culture. Both HA1-K299R and HA2-T107I mutations increased thermal resistance of the viruses. 2019 PloS one Abstract IV K299R;T107I 9;23 14;28 HA;HA1 19;5 21;8 31600274 Adaptation of H3N2 canine influenza virus to feline cell culture. In addition, HA2-T107I increased the pH requirement for membrane fusion. 2019 PloS one Abstract IV T107I 17 22 HA 13 15 31600542 Amantadine resistance markers among low pathogenic avian influenza H9N2 viruses isolated from poultry in India, during 2009-2017. Four isolates showed presence of V27A + S31 N dual mutations. 2019 Microbial pathogenesis Abstract IV V27A;S31N 33;40 37;45 31600542 Amantadine resistance markers among low pathogenic avian influenza H9N2 viruses isolated from poultry in India, during 2009-2017. Majority of the resistant viruses exhibited S31 N mutation. 2019 Microbial pathogenesis Abstract IV S31N 44 49 31600542 Amantadine resistance markers among low pathogenic avian influenza H9N2 viruses isolated from poultry in India, during 2009-2017. Matrix genes of 48H9N2 viruses isolated from India during 2009-2017 were sequenced and M2 trans-membrane region sequences were screened for mutations which are known to confer resistance to amantadine namely, L26F, V27A, A30 T/V, S31N and G34E. 2019 Microbial pathogenesis Abstract IV L26F;V27A;A30T;A30V;S31N;G34E 209;215;221;221;230;239 213;219;228;228;234;243 M2;M 87;0 89;6 31608791 Insights into species-specific regulation of ANP32A on the mammalian-restricted influenza virus polymerase activity. The PB2 N567D, T598V, A613V or F636L mutations promoted PB2 627E polymerase activity and chANP32A-X1 showed additive effects, providing further support that species-specific regulation of ANP32A might be only relevant with the PB2 E627K mutation. 2019 Emerging microbes & infections Abstract IV N567D;T598V;A613V;F636L;E627K 8;15;22;31;231 13;20;27;36;236 PB2;PB2;PB2 4;56;227 7;59;230 31635227 Antigenic Site Variation in the Hemagglutinin of Pandemic Influenza A(H1N1)pdm09 Viruses between 2009-2017 in Ukraine. Genetic changes were observed in each of the antigenic sites: Sa - S162T, K163Q, K163I; Sb - S185T, A186T, S190G, S190R; Ca1 - S203T, R205K, E235V, E235D, S236P; Ca2 - P137H, H138R, A141T, D222G, D222N; Cb - A73S, S74R, S74N. 2019 Pathogens (Basel, Switzerland) Abstract IV S162T;K163Q;K163I;S185T;A186T;S190G;S190R;S203T;R205K;E235V;E235D;S236P;P137H;H138R;A141T;D222G;D222N;A73S;S74R;S74N 67;74;81;93;100;107;114;127;134;141;148;155;168;175;182;189;196;208;214;220 72;79;86;98;105;112;119;132;139;146;153;160;173;180;187;194;201;212;218;224 31645133 Peramivir binding affinity with influenza A neuraminidase and research on its mutations using an induced-fit docking approach. Mutations on this residue greatly reduced the binding affinity of peramivir with NA, with 3 mutations R378Q, R378K and R378L (NA6) capable of deteriorating the docking performance of peramivir by over 50%. 2019 SAR and QSAR in environmental research Abstract IV R378Q;R378K;R378L 102;109;119 107;114;124 NA;NA 81;126 83;128 31666492 Genetic Characterization of a Novel Reassortant H5N6 Avian Influenza Virus Identified from a 10-Year-Old Girl. Q226L and G228S mutations were not observed, but S128P, S137A, and T160A substitutions were identified in the receptor binding sites. 2020 Japanese journal of infectious diseases Abstract IV Q226L;G228S;S128P;S137A;T160A 0;10;49;56;67 5;15;54;61;72 31666492 Genetic Characterization of a Novel Reassortant H5N6 Avian Influenza Virus Identified from a 10-Year-Old Girl. The resistance mutation D198N in the neuraminidase (NA) protein was also identified in this strain. 2020 Japanese journal of infectious diseases Abstract IV D198N 24 29 NA;NA 52;37 54;50 31669761 Discovery of M2 channel blockers targeting the drug-resistant double mutants M2-S31N/L26I and M2-S31N/V27A from the influenza A viruses. In this study, we identified four amantadine-resistant M2 mutants among avian and human influenza A H5N1 strains circulating between 2002 and 2019: the single S31N and V27A mutants, and the S31N/L26I and S31N/V27A double mutants. 2020 European journal of pharmaceutical sciences Abstract IV S31N;V27A;S31N;L26I;S31N;V27A 159;168;190;195;204;209 163;172;194;199;208;213 M2 55 57 Influenza 82 97 31669761 Discovery of M2 channel blockers targeting the drug-resistant double mutants M2-S31N/L26I and M2-S31N/V27A from the influenza A viruses. Three compounds 6, 7, and 15 were found to significantly block all three M2 mutants: M2-S31N, M2-S31N/L26I, and M2-S31N/V27A. 2020 European journal of pharmaceutical sciences Abstract IV S31N;L26I;S31N;S31N;V27A 88;102;97;115;120 92;106;101;119;124 M2;M2;M2;M2 73;85;94;112 75;87;96;114 31669761 Discovery of M2 channel blockers targeting the drug-resistant double mutants M2-S31N/L26I and M2-S31N/V27A from the influenza A viruses. Using recombinant viruses generated from reverse genetics, we further showed that these compounds also inhibited the replication of recombinant viruses harboring either the single S31N or double S31N/L26I and S31N/V27A mutants. 2020 European journal of pharmaceutical sciences Abstract IV V27A;S31N;S31N;L26I;S31N 214;180;195;200;209 218;184;199;204;213 31694942 Hemagglutinin Stability Regulates H1N1 Influenza Virus Replication and Pathogenicity in Mice by Modulating Type I Interferon Responses in Dendritic Cells. Here, we investigated the mechanisms by which a destabilizing HA mutation, Y17H (activation pH, 6.0), attenuates virus replication and pathogenicity in DBA/2 mice compared to wild-type (WT) virus (activation pH, 5.5). 2020 Journal of virology Abstract IV Y17H 75 79 HA 62 64 31694942 Hemagglutinin Stability Regulates H1N1 Influenza Virus Replication and Pathogenicity in Mice by Modulating Type I Interferon Responses in Dendritic Cells. In contrast, the HA-Y17H mutation reduced virus replication in murine airway murine nasal epithelial cell and murine tracheal epithelial cell cultures and attenuated virus replication, virus spread, the severity of infection, and cellular infiltration in the lungs of mice. 2020 Journal of virology Abstract IV Y17H 20 24 HA 17 19 31694942 Hemagglutinin Stability Regulates H1N1 Influenza Virus Replication and Pathogenicity in Mice by Modulating Type I Interferon Responses in Dendritic Cells. Normalizing virus infection and weight loss in mice by inoculating them with Y17H virus at a dose 500-fold higher than that of WT virus revealed that the destabilized mutant virus triggered the upregulation of more host genes and increased type I IFN responses and cytokine expression in DBA/2 mouse lungs. 2020 Journal of virology Abstract IV Y17H 77 81 31694942 Hemagglutinin Stability Regulates H1N1 Influenza Virus Replication and Pathogenicity in Mice by Modulating Type I Interferon Responses in Dendritic Cells. The Y17H virus had accelerated replication kinetics in MDCK, A549, and RAW 264.7 cells when inoculated at a multiplicity of infection (MOI) of 3 PFU/cell. 2020 Journal of virology Abstract IV Y17H 4 8 31694942 Hemagglutinin Stability Regulates H1N1 Influenza Virus Replication and Pathogenicity in Mice by Modulating Type I Interferon Responses in Dendritic Cells. WT and Y17H viruses had similar environmental stability at pH 7.0; thus, extracellular inactivation was unlikely to attenuate the Y17H virus. 2020 Journal of virology Abstract IV Y17H;Y17H 7;130 11;134 31703251 Evolution of H5-Type Avian Influenza A Virus Towards Mammalian Tropism in Egypt, 2014 to 2015. Interestingly, using ISM analysis, we identified a LP 7+1 virus (LP-S10739C) expressing the monobasic H5-HA of AIV A/Chicken/Egypt/S10739C/2015(H5N1) that showed high affinity towards human-type receptors. 2019 Pathogens (Basel, Switzerland) Abstract IV S10739C;S10739C 68;131 75;138 HA 105 107 31703251 Evolution of H5-Type Avian Influenza A Virus Towards Mammalian Tropism in Egypt, 2014 to 2015. Sequence comparison between the LP-S10739C and the LP-7271 H5-HA, revealed distinct amino acid changes. 2019 Pathogens (Basel, Switzerland) Abstract IV S10739C 35 42 HA 62 64 31703251 Evolution of H5-Type Avian Influenza A Virus Towards Mammalian Tropism in Egypt, 2014 to 2015. Their contribution to the increased mammalian receptor propensity of LP-S10739C demands further investigation to better deduce the molecular determinant behind the reported high morbidity of 2014 to 2015 HPAI H5N1 virus in humans in Egypt. 2019 Pathogens (Basel, Switzerland) Abstract IV S10739C 72 79 31718675 Mouse-adapted H9N2 avian influenza virus causes systemic infection in mice. Genomic sequence alignment revealed 10 amino acid mutations coded by 4 different gene segments (PB2, PA, HA, and M) in G1-MA compared with the G1 virus and 23 amino acid mutations in 5 gene segments (PB1, PA, HA, M, and NS) in ZB-MA compared to ZB virus, indicating that the mutations in the polymerase, HA, M, and NS genes play critical roles in the adaptation of H9N2 AIVs to mammals, especially, the mutations of M1-Q198H and M1-A239T were shared in G1-MA and ZB-MA viruses. 2019 Virology journal Abstract IV Q198H;A239T 419;432 424;437 HA;HA;HA;M;M;M;M1;M1;NS;NS;PA;PA;PB1;PB2 105;209;304;113;213;308;416;429;220;315;101;205;200;96 107;211;306;114;214;309;418;431;222;317;103;207;203;99 31719554 Synergistic PA and HA mutations confer mouse adaptation of a contemporary A/H3N2 influenza virus. First, the HA substitutions were shown to enhanced viral replication in vitro and, second, the PA-K615E substitution increased polymerase activity, although did not alter virus replication in vitro or in mice. 2019 Scientific reports Abstract IV K615E 98 103 HA;PA 11;95 13;97 31719554 Synergistic PA and HA mutations confer mouse adaptation of a contemporary A/H3N2 influenza virus. Seven mutations were found in the genome of MA-H3N2: PA(K615E), NP(G384R), NA(G320E) and HA(N122D, N144E, N246K, and A304T). 2019 Scientific reports Abstract IV K615E;G384R;G320E;N122D;N144E;N246K;A304T 56;67;78;92;99;106;117 61;72;83;97;104;111;122 HA;NA;NP;PA 89;75;64;53 91;77;66;55 31747596 Avian-to-Human Receptor-Binding Adaptation of Avian H7N9 Influenza Virus Hemagglutinin. Mutagenesis and structural studies reveal that a G186V substitution is sufficient for H7N9 AIVs to acquire human receptor-binding capacity, and a Q226L substitution would favor binding to both avian and human receptors only when paired with A138/V186/P221 hydrophobic residues. 2019 Cell reports Abstract IV G186V;Q226L 49;146 54;151 31749796 Enhanced Antiviral Activity of Human Surfactant Protein D by Site-Specific Engineering of the Carbohydrate Recognition Domain. Inspired by pSP-D, the lectin domain of iSP-D has 5 amino acids replaced (Asp324Asn, Asp330Asn, Val251Glu, Lys287Gln, Glu289Lys) and 3 amino acids inserted (326Gly-Ser-Ser). 2019 Frontiers in immunology Abstract IV D324N;D330N;V251E;K287Q;E289K 74;85;96;107;118 83;94;105;116;127 31773463 Source of oseltamivir resistance due to single E119D and double E119D/H274Y mutations in pdm09H1N1 influenza neuraminidase. In the present study, all-atom molecular dynamics simulations were applied to understand the oseltamivir resistance caused by the single E119D and double E119D/H274Y mutations on NA. 2020 Journal of computer-aided molecular design Abstract IV E119D;E119D;H274Y 137;154;160 142;159;165 179 181 31783761 Influenza A virus hemagglutinin mutations associated with use of neuraminidase inhibitors correlate with decreased inhibition by anti-influenza antibodies. Recombinant A/California/04/09 (H1N1)-like viruses carrying HA V152I, G155E, S162 N, S183P, and D222G mutations were generated. 2019 Virology journal Abstract IV V152I;G155E;S162N;S183P;D222G 63;70;77;85;96 68;75;83;90;101 HA 60 62 31783761 Influenza A virus hemagglutinin mutations associated with use of neuraminidase inhibitors correlate with decreased inhibition by anti-influenza antibodies. RESULTS: We found that the G155E and D222G mutations significantly increased viral titers ~ 13-fold compared to the wild-type virus. 2019 Virology journal Abstract IV G155E;D222G 27;37 32;42 31783761 Influenza A virus hemagglutinin mutations associated with use of neuraminidase inhibitors correlate with decreased inhibition by anti-influenza antibodies. The hemagglutination and microneutralization activity of goat and ferret antisera, monoclonal antibodies, and human serum samples raised against pandemic A(H1N1)pdm09 viruses was ~ 100-fold lower against mutants carrying G155E or D222G compared to the wild-type virus. 2019 Virology journal Abstract IV G155E;D222G 221;230 226;235 31790712 Influenza B viruses from different genetic backgrounds are variably impaired by neuraminidase inhibitor resistance-associated substitutions. D197N reduced inhibition by all NAIs in BR/08 but only by oseltamivir and peramivir in PH/13; R150K caused HRI by all NAIs in PH/13. 2020 Antiviral research Abstract IV D197N;R150K 0;94 5;99 NAI;NAI 32;118 36;122 31790712 Influenza B viruses from different genetic backgrounds are variably impaired by neuraminidase inhibitor resistance-associated substitutions. E105K, R150K, and D197N attenuated replication efficiency of BR/08 in vitro and in mice; only E105K had this effect in PH/13. 2020 Antiviral research Abstract IV E105K;R150K;D197N;E105K 0;7;18;94 5;12;23;99 31790712 Influenza B viruses from different genetic backgrounds are variably impaired by neuraminidase inhibitor resistance-associated substitutions. In both backgrounds, I221 L/N/T/V resulted in reduced or highly reduced inhibition (HRI) by one to three currently available NAIs. 2020 Antiviral research Abstract IV I221L;I221N;I221T;I221V 21;21;21;21 33;33;33;33 NAI 125 129 31790712 Influenza B viruses from different genetic backgrounds are variably impaired by neuraminidase inhibitor resistance-associated substitutions. Notably, the I221 L/N/T/V substitutions did not severely impair replication, particularly in PH/13. 2020 Antiviral research Abstract IV I221L;I221N;I221T;I221V 13;13;13;13 25;25;25;25 31790712 Influenza B viruses from different genetic backgrounds are variably impaired by neuraminidase inhibitor resistance-associated substitutions. To improve antiviral management and understand whether clinically identified neuraminidase (NA) inhibitor (NAI) resistance-associated markers affect influenza B viruses of the Victoria- or Yamagata-lineages differentially, we generated a panel of NAI-resistant viruses (carrying E105K, G145E, R150K, D197N, I221 L/N/T/V, H273Y, N294S, or G407S substitutions; B numbering) in B/Brisbane/60/2008 (BR/08) and B/Phuket/3073/2013 (PH/13). 2020 Antiviral research Abstract IV E105K;G145E;R150K;D197N;I221L;I221N;I221T;I221V;H273Y;N294S;G407S 279;286;293;300;307;307;307;307;321;328;338 284;291;298;305;319;319;319;319;326;333;343 NA;NAI;NAI;NA 92;107;247;77 94;110;250;90 31805964 The tyrosine 73 and serine 83 dephosphorylation of H1N1 swine influenza virus NS1 protein attenuates virus replication and induces high levels of beta interferon. Knockdown of RIG-I dramatically impaired the induction of IFN-beta and ISG56 in NS1 Y73F or S83A mutant-infected cells, indicating that RIG-I plays a role in the IFN-beta response upon rSIV NS1 Y73F and rSIV NS1 S83A infection. 2019 Virology journal Abstract IV Y73F;S83A;Y73F;S83A 84;92;194;212 88;96;198;216 NS1;NS1;NS1 80;190;208 83;193;211 31805964 The tyrosine 73 and serine 83 dephosphorylation of H1N1 swine influenza virus NS1 protein attenuates virus replication and induces high levels of beta interferon. To study the role of NS1 phosphorylation sites, we rescued NS1 mutants (Y73F and S83A) of A/swine/Shanghai/3/2014(H1N1) strain and compared their replication ability, cytokine production as well as the intracellular localization in cultured cells. 2019 Virology journal Abstract IV Y73F;S83A 72;81 76;85 NS1;NS1 21;59 24;62 31810278 Equine Mx1 Restricts Influenza A Virus Replication by Targeting at Distinct Site of its Nucleoprotein. A substantial reduction in Mx1 resistance was observed for the two mutations G34S and H52N in H3N8JL89 NP. 2019 Viruses Abstract IV H52N;G34S 86;77 90;81 NP 103 105 31839904 Complete genome sequencing of H1N1pdm09 swine influenza isolates from Nigeria reveals likely reverse zoonotic transmission at the human-animal interface in intensive piggery. A Q240R and S31N substitution among others were detected in the haemagglutinin and matrix genes, respectively, indicating potentials for mutations during interspecies co-mingling and transmission. 2019 Infection ecology & epidemiology Abstract IV Q240R;S31N 2;12 7;16 HA;M 64;83 78;89 31842256 Antiviral Activity of Benzoic Acid Derivative NC-5 Against Influenza A Virus and Its Neuraminidase Inhibition. NC-5 inhibited influenza A viruses A/FM/1/47 (H1N1), A/Beijing/32/92 (H3N2) and oseltamivir-resistant mutant A/FM/1/47-H275Y (H1N1-H275Y) in a dose-dependent manner. 2019 International journal of molecular sciences Abstract IV H275Y;H275Y 119;131 124;136 31842256 Antiviral Activity of Benzoic Acid Derivative NC-5 Against Influenza A Virus and Its Neuraminidase Inhibition. Orally administered NC-5 protected mice infected with H1N1 and H1N1-H275Y, conferring 80% and 60% survival at 100 mg/kg/d, reducing body weight loss, and alleviating virus-induced lung injury. 2019 International journal of molecular sciences Abstract IV H275Y 68 73 Lung lesions 166 191 31842256 Antiviral Activity of Benzoic Acid Derivative NC-5 Against Influenza A Virus and Its Neuraminidase Inhibition. The 50% effective concentrations (EC50) for H1N1 and H1N1-H275Y were 33.6 muM and 32.8 muM, respectively, which showed that NC-5 had a great advantage over oseltamivir in drug-resistant virus infections. 2019 International journal of molecular sciences Abstract IV H275Y 58 63 31843969 The influenza NS1 protein modulates RIG-I activation via a strain-specific direct interaction with the second CARD of RIG-I. Furthermore, we determined that the R21Q mutation does not impede the interaction between NS1 and TRIM25 or NS1RBD's ability to bind RNA. 2020 The Journal of biological chemistry Abstract IV R21Q 36 40 NS1 90 93 31843969 The influenza NS1 protein modulates RIG-I activation via a strain-specific direct interaction with the second CARD of RIG-I. Here we investigate the functional consequences of an R21Q mutation on NS1's ability to antagonize RIG-I signaling. 2020 The Journal of biological chemistry Abstract IV R21Q 54 58 NS1 71 74 31843969 The influenza NS1 protein modulates RIG-I activation via a strain-specific direct interaction with the second CARD of RIG-I. In support of this, we determined that an R21Q mutation in NS1 results in a marked deficit in NS1's ability to antagonize TRIM25-mediated ubiquitination of the RIG-I CARDs, a critical step in RIG-I activation. 2020 The Journal of biological chemistry Abstract IV R21Q 42 46 NS1;NS1 59;94 62;97 31843969 The influenza NS1 protein modulates RIG-I activation via a strain-specific direct interaction with the second CARD of RIG-I. We also identified that a single strain-specific polymorphism in the NS1RBD (R21Q) completely abrogates this interaction. 2020 The Journal of biological chemistry Abstract IV R21Q 77 81 31843969 The influenza NS1 protein modulates RIG-I activation via a strain-specific direct interaction with the second CARD of RIG-I. We also observed that WT NS1 is capable of binding directly to the tandem RIG-I CARDs, whereas the R21Q mutation in NS1 significantly inhibits this interaction. 2020 The Journal of biological chemistry Abstract IV R21Q 99 103 NS1;NS1 25;116 28;119 31843969 The influenza NS1 protein modulates RIG-I activation via a strain-specific direct interaction with the second CARD of RIG-I. We observed that an influenza virus harboring the R21Q mutation in NS1 results in significant up-regulation of RIG-I signaling. 2020 The Journal of biological chemistry Abstract IV R21Q 50 54 NS1 67 70 31852473 Continuing evolution of H6N2 influenza a virus in South African chickens and the implications for diagnosis and control. More concerning, sub-lineage I H6N2 viruses acquired three of the nine HA mutations associated with human receptor-binding preference (A13S, V187D and A193N) since 2002. 2019 BMC veterinary research Abstract IV A13S;V187D;A193N 135;141;151 139;146;156 HA 71 73 31852473 Continuing evolution of H6N2 influenza a virus in South African chickens and the implications for diagnosis and control. Most sub-lineage I viruses isolated since 2015 acquired the K702R mutation in PB2 associated with the ability to infect humans, whereas prior to 2015 most viruses in sub-lineages I and II contained the avian lysine marker. 2019 BMC veterinary research Abstract IV K702R 60 65 PB2 78 81 31854280 Agathisflavone, a Biflavonoid from Anacardium occidentale L., Inhibits Influenza Virus Neuraminidase. Sequential passages of the virus in the presence of agathisflavone revealed the emergence of mutation R249S, A250S and R253Q in the NA gene. 2020 Current topics in medicinal chemistry Abstract IV R249S;A250S;R253Q 102;109;119 107;114;124 132 134 31855133 Influenza A/H4N2 mallard infection experiments further indicate zanamivir as less prone to induce environmental resistance development than oseltamivir. Two neuraminidase substitutions emerged, H274N (ZA IC50 increased 5.5-fold) and E119G (ZA IC50 increased 110-fold) at 10 and 100 microg l-1 of ZA, respectively. 2020 The Journal of general virology Abstract IV H274N;E119G 41;80 46;85 4 17 31863839 Sporadic occurrence of H9N2 avian influenza infections in human in Anhui province, eastern China: A notable problem. None of the human-isolated H9N2 AIVs had the I368V mutation in PB1 protein, but all the poultry-isolated H9N2 viruses in 2017 carried this mutation. 2020 Microbial pathogenesis Abstract IV I368V 45 50 PB1 63 66 31864377 Changes in RNA secondary structure affect NS1 protein expression during early stage influenza virus infection. Growth curve experiments and ELISA data show that, at least in the first viral replication cycle, mutations G123A and A132G affecting RNA structure in the (82-148) NS RNA region influence NS1 protein expression. 2019 Virology journal Abstract IV G123A;A132G 108;118 113;123 NS;NS1 164;188 166;191 31880262 Neuraminidase from Influenza A and B Viruses is Susceptible to the Compound 4-(4-Phenyl-1H-1,2,3-Triazol-1-yl)-2,2,6,6-Tetramethylpiperidine-1- Oxyl. When we passaged the influenza A virus in the presence of Tritempo, a mutant virus with the G248P change in the NA was detected. 2020 Current topics in medicinal chemistry Abstract IV G248P 92 97 112 114 31894969 X-ray Crystal Structures of the Influenza M2 Proton Channel Drug-Resistant V27A Mutant Bound to a Spiro-Adamantyl Amine Inhibitor Reveal the Mechanism of Adamantane Resistance. A 300 ns molecular dynamics simulation of the M2(22-46) V27A-spiro-adamantyl amine complex predicts with accuracy the position of the ligands and waters inside the pore in the X-ray crystal structure of the M2(22-46) V27A complex. 2020 Biochemistry Abstract IV V27A;V27A 56;217 60;221 M2;M2 46;207 48;209 31894969 X-ray Crystal Structures of the Influenza M2 Proton Channel Drug-Resistant V27A Mutant Bound to a Spiro-Adamantyl Amine Inhibitor Reveal the Mechanism of Adamantane Resistance. Additionally, in the structure of the M2(21-61) V27A construct, the C-terminus of the channel is tightly packed relative to that of the M2(22-46) construct. 2020 Biochemistry Abstract IV V27A 48 52 M2;M2 38;136 40;138 31894969 X-ray Crystal Structures of the Influenza M2 Proton Channel Drug-Resistant V27A Mutant Bound to a Spiro-Adamantyl Amine Inhibitor Reveal the Mechanism of Adamantane Resistance. Compared to the M2 "wild type" (WT) with valine at position 27, we observe that the channel pore is wider at its N-terminus as a result of the V27A mutation and that this removes V27 side chain hydrophobic interactions that are important for binding of amantadine and rimantadine. 2020 Biochemistry Abstract IV V27A 143 147 M2 16 18 31894969 X-ray Crystal Structures of the Influenza M2 Proton Channel Drug-Resistant V27A Mutant Bound to a Spiro-Adamantyl Amine Inhibitor Reveal the Mechanism of Adamantane Resistance. The spiro-adamantyl amine inhibitor blocks proton conductance in the WT and V27A mutant channels by shifting its binding site in the pore depending on which residue is present at position 27. 2020 Biochemistry Abstract IV V27A 76 80 31894969 X-ray Crystal Structures of the Influenza M2 Proton Channel Drug-Resistant V27A Mutant Bound to a Spiro-Adamantyl Amine Inhibitor Reveal the Mechanism of Adamantane Resistance. The V27A mutation confers adamantane resistance on the influenza A matrix 2 (M2) proton channel and is becoming more prevalent in circulating populations of influenza A virus. 2020 Biochemistry Abstract IV V27A 4 8 M2;M 77;67 79;73 31894969 X-ray Crystal Structures of the Influenza M2 Proton Channel Drug-Resistant V27A Mutant Bound to a Spiro-Adamantyl Amine Inhibitor Reveal the Mechanism of Adamantane Resistance. We have used X-ray crystallography to determine structures of a spiro-adamantyl amine inhibitor bound to M2(22-46) V27A and also to M2(21-61) V27A in the Inwardclosed conformation. 2020 Biochemistry Abstract IV V27A;V27A 115;142 119;146 M2;M2 105;132 107;134 31906790 Contribution of Fc-dependent cell-mediated activity of a vestigial esterase-targeting antibody against H5N6 virus infection. Additionally, ADCC/ADCP deficient L234A, L235A (LALA) and CDC deficient K322A mutants were generated and displayed comparable binding affinity and neutralizing activity as wild type 9F4 (9F4-WT). 2020 Emerging microbes & infections Abstract IV L234A;L235A;K322A 34;41;72 39;46;77 31906790 Contribution of Fc-dependent cell-mediated activity of a vestigial esterase-targeting antibody against H5N6 virus infection. However, only 9F4-WT and 9F4-K322A but not 9F4-LALA were able to reduce viral pathogenesis in H5N6 challenged mice. 2020 Emerging microbes & infections Abstract IV K322A 29 34 31906790 Contribution of Fc-dependent cell-mediated activity of a vestigial esterase-targeting antibody against H5N6 virus infection. Notably, 9F4-WT, 9F4-LALA and 9F4-K322A exhibit in vivo protective efficacies against H5N6 infections in that they were able to reduce viral loads in mice. 2020 Emerging microbes & infections Abstract IV K322A 34 39 Influenza A virus H5N6 infection 86 101 31917822 The effect of mutations derived from mouse-adapted H3N2 seasonal influenza A virus to pathogenicity and host adaptation. Additionally, the PB2 F323L mutation presented delayed but elevated replication competence in the respiratory tract, whereas the S331R mutation in NA showed no considerable effects on mouse adaptation. 2020 PloS one Abstract IV F323L;S331R 22;129 27;134 NA;PB2 147;18 149;21 31917822 The effect of mutations derived from mouse-adapted H3N2 seasonal influenza A virus to pathogenicity and host adaptation. By contrast, the NP D34N mutation caused rapid and widespread infection in multiple organs without presenting virulent symptoms. 2020 PloS one Abstract IV D34N 20 24 NP 17 19 31943329 E190V substitution of H6 hemagglutinin is one of key factors for binding to sulfated sialylated glycan receptor and infection to chickens. Binding preference of mutant HAs revealed that an E190V substitution is critical for the recognition of sulfated SAalpha2,3Gal glycans. 2020 Microbiology and immunology Abstract IV E190V 50 55 31943329 E190V substitution of H6 hemagglutinin is one of key factors for binding to sulfated sialylated glycan receptor and infection to chickens. It was revealed that E190V and N192D substitutions of the HA increased the recovery of viruses derived from an H6 duck virus isolate, A/duck/Hong Kong/960/1980 (H6N2), in chickens. 2020 Microbiology and immunology Abstract IV E190V;N192D 21;31 26;36 HA 58 60 31948040 H7N9 Influenza Virus Containing a Polybasic HA Cleavage Site Requires Minimal Host Adaptation to Obtain a Highly Pathogenic Disease Phenotype in Mice. In addition to the PBC site, we identified three other mutations that are important for host-adaptation and virulence in mice: HA (A452T), PA (D347G), and PB2 (M483K). 2020 Viruses Abstract IV A452T;D347G;M483K 131;143;160 136;148;165 HA;PA;PB2 127;139;155 129;141;158 31951605 Reassortment and adaptive mutations of an emerging avian influenza virus H7N4 subtype in China. Mutations in PB2 (E627K), PB2 (K683T), PB1-F2 (N47S), HA (N283D), HA(K321E), NA(A137V), NA(K296R) and M2 (C19Y) were identified in the human isolate while no mutations were found in PB1, NP, NS1, and NS2 of the human H7N4 compared to the avian H7N4 viruses. 2020 PloS one Abstract IV E627K;K683T;N47S;N283D;K321E;A137V;K296R;C19Y 18;31;47;58;69;80;91;106 23;36;51;63;73;84;95;110 HA;HA;M2;NA;NA;NP;NS1;NS2;PB1;PB1F2;PB2;PB2 54;66;102;77;88;187;191;200;182;39;13;26 56;68;104;79;90;189;194;203;185;45;16;29 31955521 Antigenic variants of influenza B viruses isolated in Japan during the 2017-2018 and 2018-2019 influenza seasons. One B/Yamagata-lineage isolate carrying a G407S mutation in its NA showed a marked reduction in susceptibility to zanamivir, peramivir, and laninamivir. 2020 Influenza and other respiratory viruses Abstract IV G407S 42 47 64 66 32004620 Global update on the susceptibilities of human influenza viruses to neuraminidase inhibitors and the cap-dependent endonuclease inhibitor baloxavir, 2017-2018. PA gene sequence data, available from public databases (n = 13523), were screened for amino acid substitutions associated with reduced susceptibility to baloxavir (PA E23G/K/R, PA A36V, PA A37T, PA I38F/M/T/L, PA E119D, PA E199G): 11 (0.08%) viruses possessed such substitutions. 2020 Antiviral research Abstract IV E23G;E23K;E23R;A36V;A37T;I38F;I38M;I38T;I38L;E119D;E199G 167;167;167;180;189;198;198;198;198;213;223 175;175;175;184;193;208;208;208;208;218;228 PA;PA;PA;PA;PA;PA;PA 0;164;177;186;195;210;220 2;166;179;188;197;212;222 32034420 Detection of Variants With Reduced Baloxavir Marboxil Susceptibility After Treatment of Children With Influenza A During the 2018-2019 Influenza Season. During the 2018-2019 influenza seasons, we detected reduced baloxavir marboxil (baloxavir) susceptible variants with I38S or I38T amino acid substitutions on the PA subunit of influenza virus ribonucleic acid polymerase in 7 of 18 baloxavi-treated children and found that virus titer rebounded in some of these children with variants. 2020 The Journal of infectious diseases Abstract IV I38S;I38T 117;125 121;129 PA 162 164 32036809 Filamentous versus Spherical Morphology: A Case Study of the Recombinant A/WSN/33 (H1N1) Virus. Bioinformatics algorithms predicted a neutral structural effect of the Ser126Cys mutation. 2020 Microscopy and microanalysis Abstract IV S126C 71 80 32036809 Filamentous versus Spherical Morphology: A Case Study of the Recombinant A/WSN/33 (H1N1) Virus. Next-generation sequencing (NGS) suggested a rare Ser126Cys substitution in the M1 protein of rWSN, which was confirmed by the mass spectrometric analysis. 2020 Microscopy and microanalysis Abstract IV S126C 50 59 M1 80 82 32036809 Filamentous versus Spherical Morphology: A Case Study of the Recombinant A/WSN/33 (H1N1) Virus. The mrWSN_M1_126S virus generated after the introduction of the reverse Cys126Ser substitution exhibited a similar host-dependent partially filamentous phenotype. 2020 Microscopy and microanalysis Abstract IV C126S 72 81 32064779 Rapid detection of an I38T amino acid substitution in influenza polymerase acidic subunit associated with reduced susceptibility to baloxavir marboxil. In vitro studies have revealed that an I38T substitution in the polymerase acidic subunit (PA) is associated with reduced susceptibility of influenza viruses to baloxavir. 2020 Influenza and other respiratory viruses Abstract IV I38T 39 43 PA;PA 91;64 93;89 32064779 Rapid detection of an I38T amino acid substitution in influenza polymerase acidic subunit associated with reduced susceptibility to baloxavir marboxil. METHODS: Three assays were developed based on RNase H2-dependent PCR (rhPCR) and named A/H1pdm PA_I38T rhPCR, A/H3 PA_I38T rhPCR, and B PA_I38T rhPCR. 2020 Influenza and other respiratory viruses Abstract IV I38T;I38T;I38T 98;118;139 102;122;143 PA;PA;PA 95;115;136 97;117;138 32064779 Rapid detection of an I38T amino acid substitution in influenza polymerase acidic subunit associated with reduced susceptibility to baloxavir marboxil. OBJECTIVES: Development of a rapid and simple method for monitoring influenza A(H1N1)pdm09, A(H3N2), and B viruses possessing the I38T substitution in PA. 2020 Influenza and other respiratory viruses Abstract IV I38T 130 134 PA 151 153 32069052 Optimization of 4-Aminopiperidines as Inhibitors of Influenza A Viral Entry That Are Synergistic with Oseltamivir. Compound 16 displayed a significant decrease of viral titer when evaluated in the infectious assays with influenza virus H1N1 (A/Puerto Rico/8/1934) or H5N1 (A/Vietnam/1203/2004) strains and the oseltamivir-resistant strain with the most common H274Y mutation. 2020 Journal of medicinal chemistry Abstract IV H274Y 245 250 32093780 Acetylation at K108 of the NS1 protein is important for the replication and virulence of influenza virus. In vitro and mouse studies showed that the deacetylation-mimic mutation K108R in the NS1 protein attenuated the replication and virulence of WSN-NS1-108R, while the constant acetylation-mimic mutant virus WSN-NS1-108Q showed similar replication and pathogenicity as the wild-type WSN virus (WSN-wt). 2020 Veterinary research Abstract IV K108R 72 77 NS1;NS1;NS1 85;145;209 88;148;212 32093780 Acetylation at K108 of the NS1 protein is important for the replication and virulence of influenza virus. To further explore the function of the K108 acetylation modification of the NS1 protein, a deacetylation-mimic mutation (K108R) and a constant acetylation-mimic mutation (K108Q) were introduced into the NS1 protein in the background of A/WSN/1933 H1N1 (WSN), resulting in two mutant viruses (WSN-NS1-108R and WSN-NS1-108Q). 2020 Veterinary research Abstract IV K108R;K108Q 121;171 126;176 NS1;NS1;NS1;NS1 76;203;296;313 79;206;299;316 32093780 Acetylation at K108 of the NS1 protein is important for the replication and virulence of influenza virus. To further explore the potential mechanism, the type I interferon (IFN-I) antagonistic activity of the three NS1 proteins (NS1-108Q, NS1-108R, and NS1-wt) was compared in cells, which showed that the K108R mutation significantly attenuated the IFN-beta antagonistic activity of the NS1 protein compared with NS1-wt and NS1-108Q. 2020 Veterinary research Abstract IV K108R 200 205 NS1;NS1;NS1;NS1;NS1;NS1;NS1 109;123;133;147;282;308;319 112;126;136;150;285;311;322 32095441 Comparison of antigenic mutation during egg and cell passage cultivation of H3N2 influenza virus. On the other hand, mutations occurred in three amino acid sequences (H156R, G186S, S219F) in hemagglutinin up to 15 passages when cultured in eggs. 2020 Clinical and experimental vaccine research Abstract IV H156R;G186S;S219F 69;76;83 74;81;88 HA 93 106 32102741 Multiple Border-Zone Infarcts Triggered by Influenza A Virus Infection in a Patient With Cerebral Autosomal Dominant Arteriopathy Presenting With Subcortical Infarcts and Leukoencephalopathy. Gene analysis identified a heterozygous mutation c.160C>T in exon 2 of the NOTCH3 gene (p.Arg54Cys). 2020 Journal of stroke and cerebrovascular diseases Abstract IV R54C 88 98 3211187 [Changes in the amino acid sequence of hemagglutinin during sequential adaptation of human influenza virus A to replication in mice]. At the first stage of adaptation (3-rd passage) only a single mutation was detected: Asn 127----Asp. 1988 Molekuliarnaia genetika, mikrobiologiia i virusologiia Abstract IV N127D 85 99 3211187 [Changes in the amino acid sequence of hemagglutinin during sequential adaptation of human influenza virus A to replication in mice]. In the HA1 coding region of mice-adapted virus (11 passages) there are two amino acid substitutions: Thr 89----Ala and Asn 127----Asp. 1988 Molekuliarnaia genetika, mikrobiologiia i virusologiia Abstract IV T89A;N127D 101;119 114;133 HA1 7 10 32130243 Epidemic of influenza A(H1N1)pdm09 analyzed by full genome sequences and the first case of oseltamivir-resistant strain in Myanmar 2017. One case with no prior history of oseltamivir treatment possessed H275Y mutated virus in neuraminidase (NA), which confers resistance to oseltamivir and peramivir with elevated IC50 values. 2020 PloS one Abstract IV H275Y 66 71 NA;NA 104;89 106;102 32130243 Epidemic of influenza A(H1N1)pdm09 analyzed by full genome sequences and the first case of oseltamivir-resistant strain in Myanmar 2017. Phylogenetic analysis of the hemagglutinin sequence showed that the Myanmar strains belonged to the genetic subclade 6B.1, possessing mutations of S162N and S164T at potential antigenic sites. 2020 PloS one Abstract IV S162N;S164T 147;157 152;162 HA 29 42 32135195 Antigenic changes among the predominantly circulating C/Sao Paulo lineage strains of influenza C virus in Yamagata, Japan, between 2015 and 2018. Aichi99 sublineage strains exhibiting decreased reactivity with the monoclonal antibody YA3 became predominant after 2016, and these strains possessed the K190N mutation. 2020 Infection, genetics and evolution Abstract IV K190N 155 160 32135195 Antigenic changes among the predominantly circulating C/Sao Paulo lineage strains of influenza C virus in Yamagata, Japan, between 2015 and 2018. The Aichi99 sublineage strains possessing the K190N mutation were detected after 2012 in Europe, Australia, the USA, and Asia as well as Japan. 2020 Infection, genetics and evolution Abstract IV K190N 46 51 32135195 Antigenic changes among the predominantly circulating C/Sao Paulo lineage strains of influenza C virus in Yamagata, Japan, between 2015 and 2018. These observations suggest that antigenic variants with K190N mutations have circulated extensively around the world and caused outbreaks in Japan between 2016 and 2018. 2020 Infection, genetics and evolution Abstract IV K190N 56 61 32159230 Antigenic drift of hemagglutinin and neuraminidase in seasonal H1N1 influenza viruses from Saudi Arabia in 2014 to 2015. Amino acid changes at key antigenic sites, such as position S101N, S179N (antigenic site-Sa), I233T (antigenic site-Sb) in the head domain might have resulted in antigenic drift and emergence of variant viruses. 2020 Journal of medical virology Abstract IV S101N;S179N;I233T 60;67;94 65;72;99 32159230 Antigenic drift of hemagglutinin and neuraminidase in seasonal H1N1 influenza viruses from Saudi Arabia in 2014 to 2015. For NA protein, 36% isolates showed the presence of amino acid changes such as V13I (n = 29), I314M (n = 29) and 12% had I34V (n = 10). 2020 Journal of medical virology Abstract IV V13I;I314M;I34V 79;94;121 83;99;125 4 6 32159230 Antigenic drift of hemagglutinin and neuraminidase in seasonal H1N1 influenza viruses from Saudi Arabia in 2014 to 2015. However, H257Y mutation responsible for resistance to neuraminidase inhibitors was missing. 2020 Journal of medical virology Abstract IV H257Y 9 14 54 67 32161172 An R195K Mutation in the PA-X Protein Increases the Virulence and Transmission of Influenza A Virus in Mammalian Hosts. PA-X R195K was present in all human H7N9 and H1N1/2009 viruses and predominated in human H5N6 viruses. 2020 Journal of virology Abstract IV R195K 5 10 PA-X 0 4 32161172 An R195K Mutation in the PA-X Protein Increases the Virulence and Transmission of Influenza A Virus in Mammalian Hosts. Reverse genetics analyses of PA-X substitutions conserved in human influenza viruses indicated that R195K, K206R, and P210L substitutions conferred significantly increased replication and pathogenicity on H9N2 virus in mice and ferrets. 2020 Journal of virology Abstract IV R195K;K206R;P210L 100;107;118 105;112;123 PA-X 29 33 32200160 Amino acid substitutions involved in the adaptation of a novel H7N7 avian influenza virus in mice. Genomic analysis of the mouse-adapted virus revealed amino acid changes in the PB2 (E525G, M645I, and D701N), NP (I475V), HA(D103N), and NA(K142E) proteins. 2020 Research in veterinary science Abstract IV E525G;M645I;D701N;I475V;D103N;K142E 84;91;102;114;125;140 89;96;107;119;130;145 HA;NA;NP;PB2 122;137;110;79 124;139;112;82 32211197 Detection of H3N8 influenza A virus with multiple mammalian-adaptive mutations in a rescued Grey seal (Halichoerus grypus) pup. From examining the protein alignments, we found several residue changes in the seal virus that did not occur in the bird viruses, including D701N in the PB2 segment, a rare mutation, and a hallmark of mammalian adaptation of bird viruses. 2020 Virus evolution Abstract IV D701N 140 145 PB2 153 156 32215120 A multiplex real-time PCR assay for detection of oseltamivir-resistant strains of influenza virus. The resistance against this drug has probably developed through antigenic drift by a point mutation in one amino acid at position 275 (H275Y). 2014 Central European journal of biology Abstract IV H275Y 135 140 32215564 Influenza vaccine effectiveness by A(H3N2) phylogenetic sub-cluster and prior vaccination history: 2016-17 and 2017-18 epidemics in Canada. Circulating 3C.2a viruses showed considerable diversity in the hemagglutinin glycoprotein and the egg-adapted vaccine strain also bore mutations, notably T160K loss-of-glycosylation. 2020 The Journal of infectious diseases Abstract IV T160K 154 159 HA 63 76 32220685 N-benzyl 4,4-disubstituted piperidines as a potent class of influenza H1N1 virus inhibitors showing a novel mechanism of hemagglutinin fusion peptide interaction. Furthermore, the HA1-S326V mutation resulting in resistance to 2 is close to the proposed new binding pocket. 2020 European journal of medicinal chemistry Abstract IV S326V 21 26 HA1 17 20 32231159 Insertion of Basic Amino Acids in the Hemagglutinin Cleavage Site of H4N2 Avian Influenza Virus (AIV)-Reduced Virus Fitness in Chickens is Restored by Reassortment with Highly Pathogenic H5N1 AIV. Efficient cell culture replication of T327R/K carrying H4N2 viruses increased by treatment with trypsin, particularly in MDCK cells, and reassortment with HPAIV H5N1. 2020 International journal of molecular sciences Abstract IV T327K;T327R 38;38 45;45 32231159 Insertion of Basic Amino Acids in the Hemagglutinin Cleavage Site of H4N2 Avian Influenza Virus (AIV)-Reduced Virus Fitness in Chickens is Restored by Reassortment with Highly Pathogenic H5N1 AIV. Here, we investigated the virulence of this virus in chickens after expansion of the polybasic CS by substitution of T327R (322PEKRRRR/G329) or T327K (322PEKRRKR/G329) with or without reassortment with HPAIV H5N1 and H7N7. 2020 International journal of molecular sciences Abstract IV T327R;T327K 117;144 122;149 32253432 Treatment-Emergent Influenza Virus Polymerase Acidic Substitutions Independent of Those at I38 Associated With Reduced Baloxavir Susceptibility and Virus Rebound in Trials of Baloxavir Marboxil. Influenza viruses harboring treatment-emergent I38F/M/N/T substitutions in the polymerase acidic (PA) endonuclease exhibited reduced susceptibility to baloxavir and were associated with virus rebound and variable clinical response in clinical trials. 2020 The Journal of infectious diseases Abstract IV I38F;I38M;I38N;I38T 47;47;47;47 57;57;57;57 PA;PA 98;79 100;96 32253432 Treatment-Emergent Influenza Virus Polymerase Acidic Substitutions Independent of Those at I38 Associated With Reduced Baloxavir Susceptibility and Virus Rebound in Trials of Baloxavir Marboxil. US regulatory review of registrational trial data also identified treatment-emergent PA substitutions E23K in A/H1N1 viruses and E23G/K, A37T, and E199G in A/H3N2 viruses, which conferred reduced susceptibility to baloxavir, although to a lesser degree than I38F/M/N/T substitutions, and were associated with virus rebound. 2020 The Journal of infectious diseases Abstract IV E23K;E23G;E23K;A37T;E199G;I38F;I38M;I38N;I38T 102;129;129;137;147;258;258;258;258 106;135;135;141;152;268;268;268;268 PA 85 87 32256457 Identification of Chebulinic Acid and Chebulagic Acid as Novel Influenza Viral Neuraminidase Inhibitors. Moreover, oseltamivir-resistance mutation NA/H274Y of NA is susceptible to CHLA or CHLI, suggesting a different mechanism of action for CHLA and CHLI. 2020 Frontiers in microbiology Abstract IV H274Y 45 50 NA;NA 42;54 44;56 32266186 Childhood Nephrotic Syndrome Complicated by Catastrophic Multiple Arterial Thrombosis Requiring Bilateral Above-Knee Amputation. However, whole-exome sequencing revealed a thrombotic risk variant (T630I) in the PROS1 gene encoding protein S. 2020 Frontiers in pediatrics Abstract IV T630I 68 73 32272772 Influenza PB1-F2 Inhibits Avian MAVS Signaling. The D122A mutation of human 2CARD abrogates signaling by affecting MAVS engagement, and the reciprocal A120D mutation in duck 2CARD improves signaling in human cells. 2020 Viruses Abstract IV D122A;A120D 4;103 9;108 32285202 Genetic variability of avian influenza virus subtype H5N8 in Egypt in 2017 and 2018. Analysis of these viruses revealed mutations specific to Egyptian strains and not the original virus characterized in 2017 (A/duck/Egypt/F446/2017), with a novel antiviral resistance marker, V27A, indicating resistance to amantadine in the M2 protein of two strains. 2020 Archives of virology Abstract IV V27A 191 195 M2 240 242 32326238 Experimental Infection Using Mouse-Adapted Influenza B Virus in a Mouse Model. A Victoria lineage (clade 1A) IBV was serially passaged 17 times in BALB/c mice, and adaptive amino acid substitutions were found in hemagglutinin (HA) (T214I) and neuraminidase (NA) (D432N). 2020 Viruses Abstract IV T214I;D432N 153;184 158;189 HA;HA;NA;NA 148;133;179;164 150;146;181;177 32351035 Substitutions in the PB2 methionine 283 residue affect H5 subtype avian influenza virus virulence. The substitution PB2-M283I had an opposite phenotype. 2020 Transboundary and emerging diseases Abstract IV M283I 21 26 PB2 17 20 32351035 Substitutions in the PB2 methionine 283 residue affect H5 subtype avian influenza virus virulence. The substitution PB2-M283L displayed high virulence, resulting in a greater virus load in different tissues, more severe histopathological lesions and proinflammatory cytokines burst in mice. 2020 Transboundary and emerging diseases Abstract IV M283L 21 26 PB2 17 20 32351035 Substitutions in the PB2 methionine 283 residue affect H5 subtype avian influenza virus virulence. The substitution PB2-M283L enhanced the growth capacity and polymerase activity in human and mammalian cells in comparison to the rWT virus. 2020 Transboundary and emerging diseases Abstract IV M283L 21 26 PB2 17 20 32393488 Laninamivir-Interferon Lambda 1 Combination Treatment Promotes Resistance by Influenza A Virus More Rapidly than Laninamivir Alone. Moreover, the E119G NA mutation emerged together with concomitant hemagglutinin (HA) mutations (T197A and D222G), which were selected more rapidly by combination treatment with laninamivir plus IFN-lambda1 (passages 2 and 3, respectively) than by laninamivir alone (passage 10). 2020 Antimicrobial agents and chemotherapy Abstract IV E119G;T197A;D222G 14;96;106 19;101;111 HA;HA;NA 81;66;20 83;79;22 32393488 Laninamivir-Interferon Lambda 1 Combination Treatment Promotes Resistance by Influenza A Virus More Rapidly than Laninamivir Alone. Surprisingly, laninamivir used in combination with IFN-lambda1 promoted the emergence of the E119G NA mutation five passages earlier than laninamivir alone (passage 2 versus passage 7, respectively). 2020 Antimicrobial agents and chemotherapy Abstract IV E119G 93 98 99 101 32415096 mRNA display with library of even-distribution reveals cellular interactors of influenza virus NS1. We also use md-LED to identify a mutant of NS1, D92Y, results in a loss of interaction with CPSF1. 2020 Nature communications Abstract IV D92Y 48 52 NS1 43 46 32433222 Baloxavir Marboxil 2% Granules in Japanese Children With Influenza: An Open-label Phase 3 Study. Polymerase acidic protein/I38T/M-substituted viruses were detected in 5 children infected with influenza A, but none with influenza B. 2020 The Pediatric infectious disease journal Abstract IV I38T;I38M 26;26 32;32 PA 0 17 32449254 Baloxavir for the treatment of Influenza in allogeneic hematopoietic stem cell transplant recipients previously treated with oseltamivir. Of the three patients infected with wild-type influenza virus, two cleared the virus after baloxavir treatment, while the third patient developed the polymerase I38T variant linked to baloxavir resistance. 2020 Transplant infectious disease Abstract IV I38T 161 165 32449254 Baloxavir for the treatment of Influenza in allogeneic hematopoietic stem cell transplant recipients previously treated with oseltamivir. RESULTS: Two patients were infected with influenza A/H1pdm09 carrying a neuraminidase variant (H275Y) linked to oseltamivir resistance. 2020 Transplant infectious disease Abstract IV H275Y 95 100 72 85 32456831 A D200N hemagglutinin substitution contributes to antigenic changes and increased replication of avian H9N2 influenza virus. Firstly, the substitution of D200N changed the antigenicity of H9N2 AIVs. 2020 Veterinary microbiology Abstract IV D200N 29 34 32456831 A D200N hemagglutinin substitution contributes to antigenic changes and increased replication of avian H9N2 influenza virus. In summary, the D200N substitution is a newly identified antigenicity and replication determinant of H9N2 AIVs, which should be paid more attention during surveillance. 2020 Veterinary microbiology Abstract IV D200N 16 21 32456831 A D200N hemagglutinin substitution contributes to antigenic changes and increased replication of avian H9N2 influenza virus. In the present study, through analyzing the amino acid sequences of H9N2 avian influenza viruses (AIVs) isolated from China, we identified a multi-functional substitution of D200N in HA1 protein. 2020 Veterinary microbiology Abstract IV D200N 174 179 HA1 183 186 32456831 A D200N hemagglutinin substitution contributes to antigenic changes and increased replication of avian H9N2 influenza virus. Secondly, the D200N increased the HA cleavage efficiency and reduced acid and thermal stability of HA protein, which triggered viral-endosomal membrane fusion whereby promoted the release of viral genome into the host cytoplasm. 2020 Veterinary microbiology Abstract IV D200N 14 19 HA;HA 34;99 36;101 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. HA1 D222N substitution, associated with increased virulence, was identified in two A(H1N1)pdm09 viruses. 2020 Journal of medical microbiology Abstract IV D222N 4 9 HA1 0 3 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. However, without selection pressure of vaccine antibodies, NP had undergone two high-frequency mutations, namely, V186I and L466I, and a high-frequency mutation of L77I appeared in the NS gene. 2020 AMB Express Abstract IV V186I;L466I;L77I 114;124;164 119;129;168 NP;NS 59;185 61;187 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. Moreover, under the selection pressure of vaccine antibodies, 10 amino acids (67-76) of the NA protein of all quasispecies were deleted, and PB2 of the quasispecies had undergone a high-frequency R355K mutation. 2020 AMB Express Abstract IV R355K 196 201 NA;PB2 92;141 94;144 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. We found for the first time that there were three mutation hotspots in the HA genes of the quasispecies under the selection pressure of vaccine antibodies, which were K131R, A168T, and N201D. 2020 AMB Express Abstract IV K131R;A168T;N201D 167;174;185 172;179;190 HA 75 77 32483655 Genetic and antigenic characterization of influenza A/H5N1 viruses isolated from patients in Indonesia, 2008-2015. Only a few substitutions associated with human adaptation were observed, a remarkably low prevalence of the human adaptive substitution PB2-E627K, which is common during human infection with other H5N1 clades and a known virulence marker for avian influenza viruses during human infections. 2020 Virus genes Abstract IV E627K 140 145 PB2 136 139 32486222 Antibody Neutralization of an Influenza Virus that Uses Neuraminidase for Receptor Binding. Specifically, a virus with a receptor-binding G147R N1 NA and a binding-deficient HA is completely neutralized in single-cycle infections by an antibody that binds near the NA active site. 2020 Viruses Abstract IV G147R 46 51 HA;NA;NA 82;55;173 84;57;175 32490728 Cold and distant: structural features of the nucleoprotein complex of a cold-adapted influenza A virus strain. In the filament interface peptide model, it was shown that the peptide corresponding in primary structure to the wild-type NP (SGYDFEREGYS) is prone to temperature-dependent self-association, unlike the peptide corresponding to E292G substitution (SGYDFGREGYS). 2021 Journal of biomolecular structure & dynamics Abstract IV E292G 228 233 NP 123 125 32490728 Cold and distant: structural features of the nucleoprotein complex of a cold-adapted influenza A virus strain. Presence of the E292G substitution was shown by DSF to affect nucleoprotein complex melting temperature. 2021 Journal of biomolecular structure & dynamics Abstract IV E292G 16 21 NP 62 75 32490728 Cold and distant: structural features of the nucleoprotein complex of a cold-adapted influenza A virus strain. The data suggest that the mechanism behind cold adaptation with E292G is associated with a weakening of the interaction between strands of the ribonucleoprotein complex and, as a result, the appearance of inter-chain interface flexibility necessary for complex function at low temperature.Communicated by Ramaswamy H. 2021 Journal of biomolecular structure & dynamics Abstract IV E292G 64 69 32490728 Cold and distant: structural features of the nucleoprotein complex of a cold-adapted influenza A virus strain. The E292G mutation has been previously shown to provide cold adaptation. 2021 Journal of biomolecular structure & dynamics Abstract IV E292G 4 9 32490728 Cold and distant: structural features of the nucleoprotein complex of a cold-adapted influenza A virus strain. Two influenza A nucleoprotein variants (wild-type: G102R; and mutant: G102R and E292G) were studied with regard to macro-molecular interactions in oligomeric form (24-mers). 2021 Journal of biomolecular structure & dynamics Abstract IV G102R;G102R;E292G 51;70;80 56;75;85 NP 16 29 32526195 Early treatment with baloxavir marboxil in high-risk adolescent and adult outpatients with uncomplicated influenza (CAPSTONE-2): a randomised, placebo-controlled, phase 3 trial. Polymerase acidic protein variants with Ile38Thr, Ile38Met, or Ile38Asn substitutions conferring reduced baloxavir susceptibility emerged in 15 (5%) of 290 baloxavir recipients assessed for amino acid substitutions in the virus. 2020 The Lancet. Infectious diseases Abstract IV I38T;I38M;I38N 40;50;63 48;58;71 PA 0 17 32547518 Characterization of Influenza A and B Viruses Circulating in Southern China During the 2017-2018 Season. One of the mutations (K180N) was noted to likely alter the epitope and to potentially affect the viral antigenicity. 2020 Frontiers in microbiology Abstract IV K180N 22 27 32599753 Virtual Screening Identifies Chebulagic Acid as an Inhibitor of the M2(S31N) Viral Ion Channel and Influenza A Virus. Chebulagic acid selectively restores growth of M2(S31N)-expressing yeast. 2020 Molecules (Basel, Switzerland) Abstract IV S31N 50 54 M2 47 49 32599753 Virtual Screening Identifies Chebulagic Acid as an Inhibitor of the M2(S31N) Viral Ion Channel and Influenza A Virus. However, all currently circulating influenza A virus strains are now resistant to licensed M2-targeting adamantane drugs, primarily due to the widespread prevalence of an M2 variant encoding a serine to asparagine 31 mutation (S31N). 2020 Molecules (Basel, Switzerland) Abstract IV S31N;S31N 227;193 231;216 M2;M2 91;171 93;173 32599753 Virtual Screening Identifies Chebulagic Acid as an Inhibitor of the M2(S31N) Viral Ion Channel and Influenza A Virus. Molecular modeling also suggests that chebulagic acid hydrolysis fragments preferentially interact with the highly-conserved histidine residue within the pore of M2(S31N) but not adamantane-sensitive M2(S31). 2020 Molecules (Basel, Switzerland) Abstract IV S31N 165 169 M2;M2 162;200 164;202 32599753 Virtual Screening Identifies Chebulagic Acid as an Inhibitor of the M2(S31N) Viral Ion Channel and Influenza A Virus. Taken together, results implicate chebulagic acid and/or its hydrolysis fragments as new chemical leads for M2(S31N) and influenza-directed antiviral development. 2020 Molecules (Basel, Switzerland) Abstract IV S31N 111 115 M2 108 110 32599753 Virtual Screening Identifies Chebulagic Acid as an Inhibitor of the M2(S31N) Viral Ion Channel and Influenza A Virus. To identify new chemical leads that may target M2(S31N), we performed a virtual screen of molecules from two natural product libraries and identified chebulagic acid as a candidate M2(S31N) inhibitor and influenza antiviral. 2020 Molecules (Basel, Switzerland) Abstract IV S31N;S31N 50;184 54;188 M2;M2 47;181 49;183 32601336 Pre-existing immunity to influenza virus hemagglutinin stalk might drive selection for antibody-escape mutant viruses in a human challenge model. Here we show that immune pressure on the HA stalk can lead to expansion of escape mutant viruses in study participants challenged with a 2009 H1N1 pandemic influenza virus inoculum containing an A388V polymorphism in the HA stalk (45% wild type and 55% mutant). 2020 Nature medicine Abstract IV A388V 195 200 HA;HA 41;221 43;223 32601336 Pre-existing immunity to influenza virus hemagglutinin stalk might drive selection for antibody-escape mutant viruses in a human challenge model. The A388V mutation conferred resistance to some of the potent HA stalk broadly neutralizing monoclonal antibodies (bNAbs). 2020 Nature medicine Abstract IV A388V 4 9 HA 62 64 32624252 Predominance of influenza virus A(H3N2) 3C.2a1b and A(H1N1)pdm09 6B.1A5A genetic subclades in the WHO European Region, 2018-2019. All genetically characterized A(H1N1)pdm09 viruses fell in subclade 6B.1A, of which 90% carried the amino acid substitution S183P in the HA gene. 2020 Vaccine Abstract IV S183P 124 129 HA 137 139 32629810 Replication of a Dog-Origin H6N1 Influenza Virus in Cell Culture and Mice. This report verifies PB2 E627K mutation in virulence and spotlights the potential for the dog H6N1 virus to extend interspecies transmission. 2020 Viruses Abstract IV E627K 25 30 PB2 21 24 32631240 Successful treatment with baloxavir marboxil of a patient with peramivir-resistant influenza A/H3N2 with a dual E119D/R292K substitution after allogeneic hematopoietic cell transplantation: a case report. CONCLUSIONS: In a highly immunocompromised host, clinicians should take care when peramivir is used for extended periods to treat influenza virus A/H3N2 infection as this could potentially leading to a dual E119D/R292K substitution in neuraminidase protein. 2020 BMC infectious diseases Abstract IV E119D;R292K 207;213 212;218 235 248 32631240 Successful treatment with baloxavir marboxil of a patient with peramivir-resistant influenza A/H3N2 with a dual E119D/R292K substitution after allogeneic hematopoietic cell transplantation: a case report. Subsequently, sequence analysis of the nasopharyngeal specimen revealed the dual E119D/R292K neuraminidase mutant influenza A/H3N2. 2020 BMC infectious diseases Abstract IV R292K;E119D 87;81 93;86 93 106 32631240 Successful treatment with baloxavir marboxil of a patient with peramivir-resistant influenza A/H3N2 with a dual E119D/R292K substitution after allogeneic hematopoietic cell transplantation: a case report. To our knowledge, no report is available on the clinical course of a severely immunocompromised patient with a dual E119D/R292K neuraminidase mutated-influenza A/H3N2 during the administration of peramivir. 2020 BMC infectious diseases Abstract IV E119D;R292K 116;122 121;127 128 141 32631440 Characterization of neuraminidase inhibitor-resistant influenza virus isolates from immunocompromised patients in the Republic of Korea. RESULTS: Two A(H1N1)pdm09 isolates harboring an H275Y substitution in the neuraminidase sequence were detected in patients with acute hematologic cancer. 2020 Virology journal Abstract IV H275Y 48 53 74 87 Acute hematologic cancer 128 152 32636820 Enhanced Potency of a Broad H7N9-Neutralizing Antibody HNIgGA6 Through Structure-Based Design. Importantly, the S28H variant also exhibited broad H7N9-neutralizing activity. 2020 Frontiers in microbiology Abstract IV S28H 17 21 32636820 Enhanced Potency of a Broad H7N9-Neutralizing Antibody HNIgGA6 Through Structure-Based Design. When administered to BALB/c mice, mAb S28H showed enhanced potency in inhibiting the pulmonary virus titre and reducing lung lesions and resulted in better protection of the animals than did the original antibody. 2020 Frontiers in microbiology Abstract IV S28H 38 42 Lung lesions 120 132 32640124 Baloxavir Marboxil for Prophylaxis against Influenza in Household Contacts. In the baloxavir group, the viral PA substitutions I38T/M or E23K were detected in 10 (2.7%) and 5 (1.3%) participants, respectively. 2020 The New England journal of medicine Abstract IV I38T;I38M;E23K 51;51;61 57;57;65 PA 34 36 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. We report A4 antibody specifically recognizing and binding to the mutant I223R/H275Y neuraminidase and prove the applicability of A4 antibody for direct detection of antiviral multidrug-resistant viruses in various sensing platforms, including naked-eye detection, surface-enhanced Raman scattering-based immunoassay, and lateral flow system. 2020 Nature communications Abstract IV I223R;H275Y 73;79 78;84 85 98 32677963 Influenza A virus NS1 optimises virus infectivity by enhancing genome packaging in a dsRNA-binding dependent manner. Furthermore, the incorporation of NS1 and the minigenome into VLP were impaired by introducing a point mutation (R38A) in the double stranded RNA-binding domain of NS1. 2020 Virology journal Abstract IV R38A 113 117 NS1;NS1 34;164 37;167 32709116 Genetic Characterization of a Novel North American-Origin Avian Influenza A (H6N5) Virus Isolated from Bean Goose of South Korea in 2018. For comparison, K6 and K17 were found to be dissimilar for various mutations, such as A274T of PB2, S375N/T of PB1, or V105M of NP, each concerning the increased virulence of K6 in mammalian system. 2020 Viruses Abstract IV A274T;S375N;S375T;V105M 86;100;100;119 91;107;107;124 NP;PB1;PB2 128;111;95 130;114;98 32709116 Genetic Characterization of a Novel North American-Origin Avian Influenza A (H6N5) Virus Isolated from Bean Goose of South Korea in 2018. However, molecular analysis revealed the E119V mutation in the NA gene and a human host marker mutation E382D in the polymerase acidic (PA) gene, implying their susceptibility to neuraminidase inhibitors and potential infectivity in humans, respectively. 2020 Viruses Abstract IV E119V;E382D 41;104 46;109 NA;NA;PA;PA 63;179;136;117 65;192;138;134 32714761 Structural Basis of Human Helicase DDX21 in RNA Binding, Unwinding, and Antiviral Signal Activation. The mutant D339H/E340G dramatically increases RNA binding activity. 2020 Advanced science (Weinheim, Baden-Wurttemberg, Germany) Abstract IV D339H;E340G 11;17 16;22 32721992 Differential Viral-Host Immune Interactions Associated with Oseltamivir-Resistant H275Y and Wild-Type H1N1 A(pdm09) Influenza Virus Pathogenicity. The acquisition of oseltamivir resistance (OR) mutations, such as H275Y, hampers viral fitness. 2020 Viruses Abstract IV H275Y 66 71 32721992 Differential Viral-Host Immune Interactions Associated with Oseltamivir-Resistant H275Y and Wild-Type H1N1 A(pdm09) Influenza Virus Pathogenicity. The objective of this work was to compare the fitness of two strains of OR (R6 and R7) containing the H275Y mutation, and a wild-type (F) pandemic influenza A (H1N1) 2009 (pdm09) virus both in vitro and in vivo in mice and to select one OR strain for a comparison with F in ferrets. 2020 Viruses Abstract IV H275Y 102 107 32739481 Design and synthesis of pinane oxime derivatives as novel anti-influenza agents. Currently, to design non-adamantane compounds targeting the S31N mutant of M2 proton channel is a promising direction for the development of novel anti-influenza drugs. 2020 Bioorganic chemistry Abstract IV S31N 60 64 M2 75 77 32739481 Design and synthesis of pinane oxime derivatives as novel anti-influenza agents. In our previous research, a pinanamine-based antiviral M090 was discovered to target hemagglutinin instead of M2, with its structure being highly similar to reported M2-S31N inhibitors. 2020 Bioorganic chemistry Abstract IV S31N 169 173 HA;M2;M2 85;110;166 98;112;168 32739481 Design and synthesis of pinane oxime derivatives as novel anti-influenza agents. Utilizing a combination of structure-activity relationship analysis, electrophysiological assay and molecular docking, the most potent compound 11h, as a M2-S31N blocker, exhibited excellent activity with EC50 value at the low micromolar level against both H3N2 and H1N1. 2020 Bioorganic chemistry Abstract IV S31N 157 161 M2 154 156 32741181 [Epidemiological and genetic characteristics of H5 subtype avian influenza virus in Guangzhou, 2014-2019]. However, mutations of S123P, S133A and T156A occurred, which implied that these strains could tend to bind to human receptors. 2020 Zhonghua liu xing bing xue za zhi Abstract IV S123P;S133A;T156A 22;29;39 27;34;44 32750468 Functional neuraminidase inhibitor resistance motifs in avian influenza A(H5Nx) viruses. In contrast the mutations E119V, H274Y and N294S had more variable effects with NAI susceptibility being drug- and strain-specific. 2020 Antiviral research Abstract IV E119V;H274Y;N294S 26;33;43 31;38;48 NAI 80 83 32750468 Functional neuraminidase inhibitor resistance motifs in avian influenza A(H5Nx) viruses. The R292K and N294S drug resistant H5N6 viruses had single amino acid substitutions in their haemagglutinin (HA): Y98F and A189T, respectively (H3 numbering) which reduced receptor binding properties possibly balancing the reduced NA activity seen. 2020 Antiviral research Abstract IV R292K;N294S;Y98F;A189T 4;14;114;123 9;19;118;128 HA;HA;NA 109;93;231 111;107;233 32750468 Functional neuraminidase inhibitor resistance motifs in avian influenza A(H5Nx) viruses. Using the established MUNANA assay we showed that a R292K substitution in H5N6 and H5N2 viruses significantly reduced susceptibility to three licenced NAIs: oseltamivir, zanamivir and peramivir. 2020 Antiviral research Abstract IV R292K 52 57 NAI 151 155 32786258 Chemical Probes for Blocking of Influenza A M2 Wild-type and S31N Channels. In the active M2 S31N blockers 1 and 6, the phenyl and isoxazolyl head groups achieve a deeper binding position and high kon/low koff and high kon/high koff rate constants, compared to inactive 2-5, which have much lower kon and higher koff. 2020 ACS chemical biology Abstract IV S31N 17 21 M2 14 16 32786258 Chemical Probes for Blocking of Influenza A M2 Wild-type and S31N Channels. Infection of cell cultures by influenza virus containing M2 WT or M2 S31N is inhibited by 1-5 or 1-4 and 6, respectively. 2020 ACS chemical biology Abstract IV S31N 69 73 M2;M2 57;66 59;68 32786258 Chemical Probes for Blocking of Influenza A M2 Wild-type and S31N Channels. Study of 1-6 shows that, according to molecular dynamics (MD) simulations and molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) calculations, all bind in the M2 S31N channel with the adamantyl group positioned between V27 and G34 and the aryl group projecting out of the channel with the phenyl (or isoxazole in 6) embedded in the V27 cluster. 2020 ACS chemical biology Abstract IV S31N 172 176 M2 169 171 32786258 Chemical Probes for Blocking of Influenza A M2 Wild-type and S31N Channels. The binding kinetics measured using electrophysiology (EP) for M2 S31N channel are very dependent on the length between the adamantane moiety and the first ring of the aryl headgroup realized in 2 and 3 and the girth and length of the adamantane adduct realized in 4 and 5. 2020 ACS chemical biology Abstract IV S31N 66 70 M2 63 65 32786258 Chemical Probes for Blocking of Influenza A M2 Wild-type and S31N Channels. We report on using the synthetic aminoadamantane-CH2-aryl derivatives 1-6 as sensitive probes for blocking M2 S31N and influenza A virus (IAV) M2 wild-type (WT) channels as well as virus replication in cell culture. 2020 ACS chemical biology Abstract IV S31N 110 114 M2;M2 107;143 109;145 32786258 Chemical Probes for Blocking of Influenza A M2 Wild-type and S31N Channels. While 1 and 6 block infection through the M2 block mechanism in the S31N variant, 2-4 may block M2 S31N virus replication in cell culture through the lysosomotropic effect, just as chloroquine is thought to inhibit SARS-CoV-2 infection. 2020 ACS chemical biology Abstract IV S31N;S31N 68;99 72;103 M2;M2 42;96 44;98 32796071 L226Q Mutation on Influenza H7N9 Virus Hemagglutinin Increases Receptor-Binding Avidity and Leads to Biased Antigenicity Evaluation. Analysis of amino acid mutations in the HAs between H7/AH13 and H7/GD16 revealed that L226Q substitution increases the HA binding avidity to sialic acid receptors on red blood cells, leading to decreased HI titers against viruses containing HA Q226 and thus resulting in a biased antigenic evaluation based on HI assay. 2020 Journal of virology Abstract IV L226Q 86 91 HA;HA 119;241 121;243 32796071 L226Q Mutation on Influenza H7N9 Virus Hemagglutinin Increases Receptor-Binding Avidity and Leads to Biased Antigenicity Evaluation. In this study, we found that the L226Q substitution in HA of A/Guangdong/17SF003/2016 (H7/GD16) increased the viral receptor-binding avidity to red blood cells with no impact on the antigenicity of H7N9 virus. 2020 Journal of virology Abstract IV L226Q 33 38 HA 55 57 32803713 Nucleoprotein phosphorylation site (Y385) mutation confers temperature sensitivity to influenza A virus due to impaired nucleoprotein oligomerization at a lower temperature. Moreover, the replication of Y385F virus was significantly reduced in both A549 and MDCK cells grown at 33 C, when compared to that at 37 C. 2021 Science China. Life sciences Abstract IV Y385F 29 34 32803713 Nucleoprotein phosphorylation site (Y385) mutation confers temperature sensitivity to influenza A virus due to impaired nucleoprotein oligomerization at a lower temperature. Notably, the Y385F virus showed much lower replicative capacity in turbinates of mice compared with the wild type virus. 2021 Science China. Life sciences Abstract IV Y385F 13 18 32803713 Nucleoprotein phosphorylation site (Y385) mutation confers temperature sensitivity to influenza A virus due to impaired nucleoprotein oligomerization at a lower temperature. The constructive NP phosphorylation mimicked by Y385E mutation was fatal for virus replication, while the continuous Y385 dephosphorylation mimicked by Y385F mutation had little impact on virus replication in vitro. 2021 Science China. Life sciences Abstract IV Y385E;Y385F 48;152 53;157 NP 17 19 32803713 Nucleoprotein phosphorylation site (Y385) mutation confers temperature sensitivity to influenza A virus due to impaired nucleoprotein oligomerization at a lower temperature. These results indicated that the Y385F mutation led to cold sensitivity of virus. 2021 Science China. Life sciences Abstract IV Y385F 33 38 32803713 Nucleoprotein phosphorylation site (Y385) mutation confers temperature sensitivity to influenza A virus due to impaired nucleoprotein oligomerization at a lower temperature. We further found that the cold sensitivity of Y385F virus could be attributed to diminished NP oligomerization rather than any changes in intracellular localization. 2021 Science China. Life sciences Abstract IV Y385F 46 51 NP 92 94 32820654 Bilobetin, a novel small molecule inhibitor targeting influenza virus polymerase acidic (PA) endonuclease was screened from plant extracts. Dose-dependent inhibition assay showed that Epimedii folium can effectivity inhibit the PAN and PAN-I38T with IC50 of 11.23 and 26.03 muM, respectively. 2021 Natural product research Abstract IV I38T 100 104 32820654 Bilobetin, a novel small molecule inhibitor targeting influenza virus polymerase acidic (PA) endonuclease was screened from plant extracts. folium were virtually screened using the in silico method, and the compounds ginkgetin and bilobetin bind to the active pocket of PAN and PAN-I38T with a strong interaction force. 2021 Natural product research Abstract IV I38T 142 146 32820654 Bilobetin, a novel small molecule inhibitor targeting influenza virus polymerase acidic (PA) endonuclease was screened from plant extracts. In 45 kinds of plant extracts, eight can effectively inhibit the PAN and PAN-I38T mutant in the primary screening. 2021 Natural product research Abstract IV I38T 77 81 32832869 Investigation of the Drug Resistance Mechanism of M2-S31N Channel Blockers through Biomolecular Simulations and Viral Passage Experiments. Overall, this is the first systematic study of the drug resistance mechanism of M2-S31N channel blockers using multiple viruses in different cell lines. 2020 ACS pharmacology & translational science Abstract IV S31N 83 87 M2 80 82 32832869 Investigation of the Drug Resistance Mechanism of M2-S31N Channel Blockers through Biomolecular Simulations and Viral Passage Experiments. Recent efforts in drug development against influenza A virus (IAV) M2 proton channel S31N mutant resulted in conjugates of amantadine linked with aryl head heterocycles. 2020 ACS pharmacology & translational science Abstract IV S31N 85 89 M2 67 69 32832869 Investigation of the Drug Resistance Mechanism of M2-S31N Channel Blockers through Biomolecular Simulations and Viral Passage Experiments. The MD simulations show that the V27A, V27F, G34E, and R45H mutations increase the diameter and hydration state of the pore in complex with compound 3. 2020 ACS pharmacology & translational science Abstract IV V27A;V27F;G34E;R45H 33;39;45;55 37;43;49;59 32832869 Investigation of the Drug Resistance Mechanism of M2-S31N Channel Blockers through Biomolecular Simulations and Viral Passage Experiments. The Molecular Mechanics Generalized Born (MM-GBSA) calculations result in more positive binding free energies for the complexes of resistant M2 (V27A, V27F, G34E, R45H) with compound 3 compared to the stable complexes (S31N and I32N). 2020 ACS pharmacology & translational science Abstract IV V27A;V27F;G34E;R45H;S31N;I32N 145;151;157;163;219;228 149;155;161;167;223;232 M2 141 143 32832869 Investigation of the Drug Resistance Mechanism of M2-S31N Channel Blockers through Biomolecular Simulations and Viral Passage Experiments. This approach not only identified M2 mutations around the drug-binding site, including the pore-lining residues (V27A, V27F, N31S, and G34E) and an interhelical residue (I32N), but also a new allosteric mutation (R45H), in addition to L46P previously identified, located at the C-terminus of M2 that is more than 10 A away from the drug-binding site. 2020 ACS pharmacology & translational science Abstract IV V27A;N31S;V27F;G34E;I32N;R45H;L46P 113;125;119;135;170;213;235 117;129;123;139;174;217;239 M2;M2 34;292 36;294 32832869 Investigation of the Drug Resistance Mechanism of M2-S31N Channel Blockers through Biomolecular Simulations and Viral Passage Experiments. To understand the mechanism of drug resistance, we chose a representative M2-S31N inhibitor, compound 3, as a chemical probe to identify resistant mutants. 2020 ACS pharmacology & translational science Abstract IV S31N 77 81 M2 74 76 32847862 Human Monoclonal Antibody Derived from Transchromosomic Cattle Neutralizes Multiple H1 Clades of Influenza A Virus by Recognizing a Novel Conformational Epitope in the Hemagglutinin Head Domain. The E212A mutation may provide structural stability for the epitope, while the substitution G172E probably compensates for loss of fitness introduced by S207R. 2020 Journal of virology Abstract IV E212A;G172E;S207R 4;92;153 9;97;158 32847862 Human Monoclonal Antibody Derived from Transchromosomic Cattle Neutralizes Multiple H1 Clades of Influenza A Virus by Recognizing a Novel Conformational Epitope in the Hemagglutinin Head Domain. The results of our experiments supported a critical role for substitution of arginine at position 207 (S207R) in mediating resistance to 53C10, while substitutions at either G172E or E212A did not alter antibody recognition and neutralization. 2020 Journal of virology Abstract IV S207R;G172E;E212A 103;174;183 108;179;188 32853849 Profile and generation of reduced neuraminidase inhibitor susceptibility in highly pathogenic avian influenza H7N9 virus from human cases in Mainland of China, 2016-2019. In presence of NAIs, R238I, A146E, G151E and G234T substitutions were found in HA1 region of HA. 2020 Virology Abstract IV R238I;A146E;G151E;G234T 21;28;35;45 26;33;40;50 HA;HA1;NAI 93;79;15 95;82;19 32853849 Profile and generation of reduced neuraminidase inhibitor susceptibility in highly pathogenic avian influenza H7N9 virus from human cases in Mainland of China, 2016-2019. Passage with zanamivir induced an E119G substitution in NA, whereas passage with oseltamivir induced R292K and E119V substitutions that simulated that seen in oseltamivir -treated HPAI H7N9 cases, indicating that the high frequency of resistant strains in the HPAI H7N9 isolates is related to NAIs use. 2020 Virology Abstract IV E119G;R292K;E119V 34;101;111 39;106;116 NA;NAI 56;293 58;297 Influenza A virus H7N9 infection;Influenza A virus H7N9 infection 180;260 189;269 32873642 Dynamic PB2-E627K substitution of influenza H7N9 virus indicates the in vivo genetic tuning and rapid host adaptation. Notably, our findings also demonstrate the correlation between rapid host adaptation of H7N9 PB2-E627K and the fatal outcome and disease severity in humans. 2020 Proc Natl Acad Sci U S A Abstract IV E627K 97 102 PB2 93 96 32926330 Genetic and Molecular Characterization of H9N2 Avian Influenza Viruses Isolated from Live Poultry Markets in Hubei Province, Central China, 2013-2017. Molecular analysis demonstrated that six H9N2 isolates had additional potential glycosylation sites at position 218 in the hemagglutinin protein, and all isolates had I155T and Q226L mutations. 2021 Virologica Sinica Abstract IV I155T;Q226L 167;177 172;182 HA 123 136 32926330 Genetic and Molecular Characterization of H9N2 Avian Influenza Viruses Isolated from Live Poultry Markets in Hubei Province, Central China, 2013-2017. Moreover, 44 strains had A558V mutations in the PB2 protein and four had E627V mutations, along with H9N2 human infection strains A/Beijing/1/2016 and A/Beijing/1/2017. 2021 Virologica Sinica Abstract IV A558V;E627V 25;73 30;78 PB2 48 51 Influenza A virus H9N2 infection 101 121 32929001 RNA-seq accuracy and reproducibility for the mapping and quantification of influenza defective viral genomes. We further examine the features of DVGs produced by wild-type and transcription-defective (PA-K635A or PA-R638A) influenza viruses, and show an increased diversity and frequency of DVGs produced by the PA mutants compared to the wild-type virus. 2020 RNA (New York, N.Y.) Abstract IV K635A;R638A 94;106 99;111 PA;PA;PA 91;103;202 93;105;204 32962203 PA from a Recent H9N2 (G1-Like) Avian Influenza a Virus (AIV) Strain Carrying Lysine 367 Confers Altered Replication Efficiency and Pathogenicity to Contemporaneous H5N1 in Mammalian Systems. Furthermore, H5N1PA-R367K caused higher mortality in BALB/c mice. 2020 Viruses Abstract IV R367K 20 25 32962203 PA from a Recent H9N2 (G1-Like) Avian Influenza a Virus (AIV) Strain Carrying Lysine 367 Confers Altered Replication Efficiency and Pathogenicity to Contemporaneous H5N1 in Mammalian Systems. Introducing the single substitution 367K into the PA of H5N1EGY enabled the mutant virus H5N1PA-R367K to replicate more efficiently at 37C in primary human bronchial epithelial (NHBE) cells and also in A549 and Calu-3 cells at 33C and 39C. 2020 Viruses Abstract IV R367K 96 101 PA 50 52 33016861 Neddylation of M1 negatively regulates the replication of influenza A virus. However, we found that NEDD8 overexpression can still inhibit the replication of PB2 K699R mutant viruses, implying that other viral protein(s) can be neddylated. 2020 The Journal of general virology Abstract IV K699R 85 90 PB2 81 84 33016861 Neddylation of M1 negatively regulates the replication of influenza A virus. In addition, we found that the neddylation-deficient M1 mutant (M1 K187R) had a longer half-life than that of wild-type M1, indicating that the neddylation of M1 reduces stability. 2020 The Journal of general virology Abstract IV K187R 67 72 M1;M1;M1;M1 53;64;120;159 55;66;122;161 33016861 Neddylation of M1 negatively regulates the replication of influenza A virus. More importantly, we observed that overexpression of NEDD8 inhibited the replication of the wild-type WSN more effectively than that of WSN-M1 K187R. 2020 The Journal of general virology Abstract IV K187R 143 148 M1 140 142 33016861 Neddylation of M1 negatively regulates the replication of influenza A virus. The data showed that the replication of WSN-M1 K187R was more efficient than that of wild-type WSN. 2020 The Journal of general virology Abstract IV K187R 47 52 M1 44 46 33016861 Neddylation of M1 negatively regulates the replication of influenza A virus. Then we performed a viral infection assay and found that WSN-M1 K187R exhibited greater virulence in mice than wild-type WSN, suggesting that the neddylation of M1 reduced IAV replication in vivo. 2020 The Journal of general virology Abstract IV K187R 64 69 M1;M1 61;161 63;163 33016861 Neddylation of M1 negatively regulates the replication of influenza A virus. We generated an IAV M1 K187R mutant (WSN-M1 K187R) and compared the growth of wild-type and mutant viruses in Madin-Darby canine kidney (MDCK) cells. 2020 The Journal of general virology Abstract IV K187R;K187R 23;44 28;49 M1;M1 20;41 22;43 33024040 Structure-Based Modification of an Anti-neuraminidase Human Antibody Restores Protection Efficacy against the Drifted Influenza Virus. Furthermore, Z2B3-D102R can protect mice from A/Serbia/NS-601/2014 H1N1 virus (NA contains E432) infection while the wild-type Z2B3 antibody shows no protection. 2020 mBio Abstract IV D102R 18 23 NA;NS 79;55 81;57 33024040 Structure-Based Modification of an Anti-neuraminidase Human Antibody Restores Protection Efficacy against the Drifted Influenza Virus. Here, we investigate a monoclonal antibody, Z2B3, isolated from an H7N9-infected patient, that exhibited cross-reactivity to both N9 (group 2) and a broad range of seasonal and avian N1 (group 1) proteins but lost activity to the N1 with the substitution K432E. 2020 mBio Abstract IV K432E 255 260 N9 130 132 33024040 Structure-Based Modification of an Anti-neuraminidase Human Antibody Restores Protection Efficacy against the Drifted Influenza Virus. It shows cross-reactivity to both group 1 (N1) and group 2 (N9) neuraminidases (NAs) but is sensitive to N1 NA with a K432E substitution. 2020 mBio Abstract IV K432E 118 123 N9;NA;NA;NA 60;108;80;64 62;110;83;78 33024040 Structure-Based Modification of an Anti-neuraminidase Human Antibody Restores Protection Efficacy against the Drifted Influenza Virus. Structure-based modification of Z2B3 with D102R in heavy chain reversed the salt bridge and restored the binding and inhibition of N1 with E432. 2020 mBio Abstract IV D102R 42 47 33028722 PA Mutations Inherited during Viral Evolution Act Cooperatively To Increase Replication of Contemporary H5N1 Influenza Virus with an Expanded Host Range. Clade 2.2.1 avian influenza viruses (H5N1) are unique to Egypt and generally carry the human adaptation PB2-E627K substitution during their dissemination in nature. 2020 Journal of virology Abstract IV E627K 108 113 PB2 104 107 33028722 PA Mutations Inherited during Viral Evolution Act Cooperatively To Increase Replication of Contemporary H5N1 Influenza Virus with an Expanded Host Range. These mutations were in the polymerase PA subunit and acted cooperatively with the E627K mutation in the PB2 polymerase subunit to provide higher replication in contemporary clade 2.2.1.2 viruses than in ancestral clade 2.2.1 viruses. 2020 Journal of virology Abstract IV E627K 83 88 PA;PB2 39;105 41;108 33044658 Inhibitory Activity of Honeysuckle Extracts against Influenza A Virus In Vitro and In Vivo. The acids-flavonoids mixture had the strongest inhibitory effects in vitro with EC50 values of 3.8, 4.1, and > 20 mug/mL against H1N1, H3N2 and H1N1-H275Y, respectively, showing competitive antiviral activity with oseltamivir and ribavirin. 2021 Virologica Sinica Abstract IV H275Y 149 154 33044658 Inhibitory Activity of Honeysuckle Extracts against Influenza A Virus In Vitro and In Vivo. The cytopathic effect reduction assay showed that all the four extracts inhibited the replication of influenza viruses H1N1, H3N2 and the oseltamivir-resistant mutant strain H1N1-H275Y. 2021 Virologica Sinica Abstract IV H275Y 179 184 33055248 In Vitro Profiling of Laninamivir-Resistant Substitutions in N3 to N9 Avian Influenza Virus Neuraminidase Subtypes and Their Association with In Vivo Susceptibility. Both ma81K-N3R292K and ma81K-N8Q136K virus-infected mice exhibited reduced weight loss, mortality, and lung viral titers when treated with their susceptible NAIs, confirming the in vitro susceptibility of these substitutions. 2020 Journal of virology Abstract IV R292K;Q136K 13;31 18;36 NAI 157 161 33055248 In Vitro Profiling of Laninamivir-Resistant Substitutions in N3 to N9 Avian Influenza Virus Neuraminidase Subtypes and Their Association with In Vivo Susceptibility. To determine whether the in vitro susceptibility of multi-NAI-resistant AIVs is associated with in vivo susceptibility, we infected BALB/c mice with recombinant AIVs with R292K (ma81K-N3R292K) or Q136K (ma81K-N8Q136K) NA substitutions, which impart in vitro susceptibility only to LAN or OS, respectively. 2020 Journal of virology Abstract IV R292K;Q136K 171;196 176;201 NA;NAI 218;58 220;61 33063654 Detection and discrimination of influenza B Victoria lineage deletion variant viruses by real-time RT-PCR. There are currently five antigenically distinct HA proteins expressed by co-circulating influenza B viruses: B/YAM, B/VIC V1A (no deletion), B/VIC V1A-2DEL (2 aa deletion) and two antigenically distinguishable groups of B/VIC V1A-3DEL (3 aa deletion). 2020 Euro surveillance Abstract IV V1A;V1A;V1A 122;147;226 125;150;229 HA 48 50 33063654 Detection and discrimination of influenza B Victoria lineage deletion variant viruses by real-time RT-PCR. We used propagated influenza B/VIC variant viruses and clinical specimens to assess assay performance.ResultsThis rRT-PCR assay detects and distinguishes the influenza B/VIC V1A, B/VIC V1A-2DEL, and B/VIC V1A-3DEL variant viruses, with no cross-reactivity. 2020 Euro surveillance Abstract IV V1A;V1A;V1A 174;185;205 177;188;208 33075446 V292I mutation in PB2 polymerase induces increased effects of E627K on influenza H7N9 virus replication in cells. Here, we studied two new potential adaptive mutations, V292I and D740A, in the PB2 protein that were identified by a multi-factor regression model. 2021 Virus research Abstract IV V292I;D740A 55;65 60;70 PB2 79 82 33075446 V292I mutation in PB2 polymerase induces increased effects of E627K on influenza H7N9 virus replication in cells. The study shows that the prevalence of the PB2-V292I mutation is increased in H7N9 influenza viruses isolated from both humans and birds over the past 6 years. 2021 Virus research Abstract IV V292I 47 52 PB2 43 46 33099886 Comprehensive assessment of amino acid substitutions in the trimeric RNA polymerase complex of influenza A virus detected in clinical trials of baloxavir marboxil. RESULTS: PA/I38N in A(H1N1)pdm09 and PA/I38R in A(H3N2) were newly identified as treatment-emergent substitutions in the CAPSTONE-2 study. 2021 Influenza and other respiratory viruses Abstract IV I38N;I38R 12;40 16;44 PA;PA 9;37 11;39 33099886 Comprehensive assessment of amino acid substitutions in the trimeric RNA polymerase complex of influenza A virus detected in clinical trials of baloxavir marboxil. The I38N substitution conferred reduced susceptibility by 24-fold, whereas replicative capacity of the I38N-substituted virus was impaired compared with the wild-type. 2021 Influenza and other respiratory viruses Abstract IV I38N;I38N 4;103 8;107 33099886 Comprehensive assessment of amino acid substitutions in the trimeric RNA polymerase complex of influenza A virus detected in clinical trials of baloxavir marboxil. The I38R-substituted virus was not viable in cell culture. 2021 Influenza and other respiratory viruses Abstract IV I38R 4 8 33115873 Viral Subpopulation Screening Guides in Designing a High Interferon-Inducing Live Attenuated Influenza Vaccine by Targeting Rare Mutations in NS1 and PB2 Proteins. The enhanced interferon-inducing phenotypes were linked to either a deletion in NS1 (NS1Delta76-86) or a substitution in polymerase basic 2 protein (PB2-D309N). 2020 Journal of virology Abstract IV D309N 153 158 NS1;PB2;PB1F2 80;149;121 83;152;147 33115873 Viral Subpopulation Screening Guides in Designing a High Interferon-Inducing Live Attenuated Influenza Vaccine by Targeting Rare Mutations in NS1 and PB2 Proteins. The PB2-D309N substitution enhanced the early transcription of interferon mRNA, revealing a novel role for the 309D residue in suppression of interferon responses. 2020 Journal of virology Abstract IV D309N 8 13 PB2 4 7 33126184 The N-terminal residual arginine(19) of influenza A virus NS1 protein is required for its nuclear localization and RNA binding. Biological analysis of the rescued viruses indicated that the R19A mutation of NS1 did not interfere the replication of H5N1 virus during infection and attenuated the virulence of H5N1 virus in mice. 2020 Veterinary microbiology Abstract IV R19A 62 66 NS1 79 82 33142846 A Mutated PB1 Residue 319 Synergizes with the PB2 N265S Mutation of the Live Attenuated Influenza Vaccine to Convey Temperature Sensitivity. Furthermore, we show that the combined PB1 L319Q and PB2 N265S mutations confer temperature sensitivity on IAV polymerase activity in two different genetic backgrounds, PR8 and A/Cal/04/09. 2020 Viruses Abstract IV L319Q;N265S 43;57 48;62 PB1;PB2 39;53 42;56 33142846 A Mutated PB1 Residue 319 Synergizes with the PB2 N265S Mutation of the Live Attenuated Influenza Vaccine to Convey Temperature Sensitivity. Here, we describe the origin/discovery of this unique mutation and demonstrate that, when combined with the PB2 N265S mutation of LAIV, it conveys an even greater level of temperature sensitivity and attenuation on PR8 than the complete set of attenuating mutations from LAIV. 2020 Viruses Abstract IV N265S 112 117 PB2 108 111 33151742 Variability of nonpathogenic influenza virus H5N3 under immune pressure. Additionally, mutation S145P increased the temperature of HA heat inactivation, compared to wild-type, as was proved by reverse genetics. 2020 Acta virologica Abstract IV S145P 23 28 HA 58 60 33154243 Genetic sequencing of influenza A (H1N1) pdm09 isolates from South India, collected between 2011 and 2015 to detect mutations affecting virulence and resistance to oseltamivir. All the study isolates possessed H274 residue and 7 strains had N295S, the next most common mutation found in oseltamivir-resistant variants. 2020 Indian journal of medical microbiology Abstract IV N295S 64 69 33154243 Genetic sequencing of influenza A (H1N1) pdm09 isolates from South India, collected between 2011 and 2015 to detect mutations affecting virulence and resistance to oseltamivir. Conclusion: In this study, although H274Y mutation associated with oseltamivir resistance has not been noted, significant mutations have been noted in both HA and NA genes including D239N, N295S, V106I, Q136K, N248D, V267A. 2020 Indian journal of medical microbiology Abstract IV H274Y;D239N;N295S;V106I;Q136K;N248D;V267A 36;182;189;196;203;210;217 41;187;194;201;208;215;222 HA;NA 156;163 158;165 33154243 Genetic sequencing of influenza A (H1N1) pdm09 isolates from South India, collected between 2011 and 2015 to detect mutations affecting virulence and resistance to oseltamivir. Two samples collected from expired patients had D239N (D222G or D225G) mutation in HA. 2020 Indian journal of medical microbiology Abstract IV D239N;D222G;D225G 48;55;64 53;60;69 HA 83 85 33179567 Adsorptive mutation and N-linked glycosylation modulate influenza virus antigenicity and fitness. We utilize the H9N2 A/chicken/Pakistan/SKP-827/16 virus which naturally contains HA residue T180 that we have previously shown to be an adsorptive mutant relative to virus with T180A. 2020 Emerging microbes & infections Abstract IV T180A 177 182 HA 81 83 33202790 Identification of Novel Influenza Polymerase PB2 Inhibitors Using a Cascade Docking Virtual Screening Approach. Among these, four compounds (11D4, 12C5, 21A5, and 21B1) showed inhibition of a broad spectrum of influenza virus strains, including oseltamivir-resistant ones, the PR/8-R292K mutant (H1N1, recombinant oseltamivir-resistant strain), the PR/8-I38T mutant (H1N1, recombinant baloxavir-resistant strain), and the influenza B/Lee/40 virus strain. 2020 Molecules (Basel, Switzerland) Abstract IV R292K;I38T 170;242 175;246 33208942 Host ANP32A mediates the assembly of the influenza virus replicase. Host-adaptive mutations, particularly a glutamic-acid-to-lysine mutation at amino acid residue 627 (E627K) in the 627 domain of the PB2 subunit, enable avian FluPolA to overcome this restriction and efficiently replicate viral RNA in the presence of human ANP32 proteins. 2020 Nature Abstract IV E627K 100 105 PB2 132 135 33208942 Host ANP32A mediates the assembly of the influenza virus replicase. The C-terminal low-complexity acidic region of ANP32A inserts between the two juxtaposed PB2 627 domains of the asymmetric FluPolA dimer, suggesting a mechanism for how the adaptive PB2(E627K) mutation enables the replication of viral RNA in mammalian hosts. 2020 Nature Abstract IV E627K 186 191 PB2;PB2 89;182 92;185 33248127 Mechanism and Kinetics of Copper Complexes Binding to the Influenza A M2 S31N and S31N/G34E Channels. Electrophysiology and DFT studies also show that the complexes block the G34E amantadine-resistant mutant despite some crowding in the binding site by the glutamates. 2021 Biophysical journal Abstract IV G34E 73 77 33248127 Mechanism and Kinetics of Copper Complexes Binding to the Influenza A M2 S31N and S31N/G34E Channels. In voltage-clamp oocyte studies using the ubiquitous amantadine-insensitive M2 S31N variant, the current block showed fast and slow phases, in contrast to the single phase found for amantadine block of wild-type M2. 2021 Biophysical journal Abstract IV S31N 79 83 M2;M2 76;212 78;214 33268526 Mutations in PB1, NP, HA, and NA Contribute to Increased Virus Fitness of H5N2 Highly Pathogenic Avian Influenza Virus Clade 2.3.4.4 in Chickens. The reassortant virus with the HA and NA from the chicken virus, where mutations in functionally known gene regions were acquired as the virus circulated in turkeys (HA S141P and NA S416G) and later in chickens (HA M66I, L322Q), showed faster virus growth, bigger plaque size and enhanced heat persistence in vitro, and increased pathogenicity and transmissibility in chickens. 2020 Journal of virology Abstract IV S141P;S416G;M66I;L322Q 169;182;215;221 174;187;219;226 HA;HA;HA;NA;NA 31;166;212;38;179 33;168;214;40;181 33268526 Mutations in PB1, NP, HA, and NA Contribute to Increased Virus Fitness of H5N2 Highly Pathogenic Avian Influenza Virus Clade 2.3.4.4 in Chickens. Viruses with the wild bird virus backbone and either PB1, NP, or the entire polymerase complex of the chicken isolate, caused higher and earlier mortality in chickens, with three mutations (PB1 E180D, M317V, and NP I109T) identified to increase polymerase activity in chicken cells. 2020 Journal of virology Abstract IV E180D;M317V;I109T 194;201;215 199;206;220 NP;NP;PB1;PB1 58;212;53;190 60;214;56;193 33270431 Colorimetric Detection of SARS-CoV-2 and Drug-Resistant pH1N1 Using CRISPR/dCas9. Using the developed method, we successfully identified SARS-CoV-2, pH1N1, and pH1N1/H275Y viruses by the naked eye. 2020 ACS sensors Abstract IV H275Y 84 89 33276361 [The Effect of I155T, K156Q, K156E and N186K Mutations in Hemagglutinin on the Virulence and Reproduction of Influenza A/H5N1 Viruses]. Amino acid substitutions I155T, K156Q, K156E+V138A, N186K led to a decrease in thermal stability, replication activity of the mutant viruses in chicken embryos, and virulence for mice, although these effects differed between the variants. 2020 Molekuliarnaia biologiia Abstract IV I155T;K156Q;V138A;K156E;N186K 25;32;45;39;52 30;37;50;44;57 33276361 [The Effect of I155T, K156Q, K156E and N186K Mutations in Hemagglutinin on the Virulence and Reproduction of Influenza A/H5N1 Viruses]. The A138V and N186K mutations seem to be adaptive in mammalian viruses. 2020 Molekuliarnaia biologiia Abstract IV A138V;N186K 4;14 9;19 33276361 [The Effect of I155T, K156Q, K156E and N186K Mutations in Hemagglutinin on the Virulence and Reproduction of Influenza A/H5N1 Viruses]. The analysis of the frequency of these mutations in natural isolates of H5N1 influenza viruses indicated that the K156E/Q and N186K mutations have little chance to gain a foothold during evolution, in contrast to the I155T mutation, which is the most responsible for antigenic drift. 2020 Molekuliarnaia biologiia Abstract IV K156E;K156Q;N186K;I155T 114;114;126;217 121;121;131;222 33276361 [The Effect of I155T, K156Q, K156E and N186K Mutations in Hemagglutinin on the Virulence and Reproduction of Influenza A/H5N1 Viruses]. The K156Q and N186K mutations reduced viral reproduction at elevated temperature (40 C). 2020 Molekuliarnaia biologiia Abstract IV K156Q;N186K 4;14 9;19 33281788 Altering Intracellular Localization of the RNA Interference Factors by Influenza A Virus Non-structural Protein 1. We found that the single residue substitution of aspartic acid with histidine at position 101 (D101H) of IAV-PR8 NS1 was sufficient to induce the nuclear import process and to enhance the virulence of IAV-PR8 in mice. 2020 Frontiers in microbiology Abstract IV D101H;D101H 95;49 100;93 NS1 113 116 33309772 Deep sequencing of the transcriptome from murine lung infected with H5N8 subtype avian influenza virus with combined substitutions I283M and K526R in PB2 gene. Especially, PB2-I283M-K526R mutation strongly induced a sharp expression of cytokine storm-related genes, including MX1, CXCL10, and IFN-gamma, performed by qRT-PCR. 2021 Infection, genetics and evolution Abstract IV I283M;K526R 16;22 21;27 PB2 12 15 33309772 Deep sequencing of the transcriptome from murine lung infected with H5N8 subtype avian influenza virus with combined substitutions I283M and K526R in PB2 gene. Here, RNA-seq method was used to analyze the global host response of murine lungs after infecting with parental r-JY virus and JY-PB2-I283M-K526R mutant virus. 2021 Infection, genetics and evolution Abstract IV I283M;K526R 134;140 139;145 PB2 130 133 33309772 Deep sequencing of the transcriptome from murine lung infected with H5N8 subtype avian influenza virus with combined substitutions I283M and K526R in PB2 gene. Taken together, our data demonstrated that PB2-I283M-K526R of H5N8 subtype HPAIV exacerbated the innate immune response and the level of cell apoptosis, which might be a key pathogenic mechanism for the enhanced pathogenicity of mutants in mammals. 2021 Infection, genetics and evolution Abstract IV I283M;K526R 47;53 52;58 PB2 43 46 33309772 Deep sequencing of the transcriptome from murine lung infected with H5N8 subtype avian influenza virus with combined substitutions I283M and K526R in PB2 gene. We also found that PB2-I283M-K526R mutation accelerated the level of cell apoptosis by heat map analysis of apoptosis-related DEGs in lungs and apoptosis assay in vitro. 2021 Infection, genetics and evolution Abstract IV I283M;K526R 23;29 28;34 PB2 19 22 33351916 Multiple polymerase acidic (PA) I38X substitutions in influenza A(H1N1)pdm09 virus permit polymerase activity and cause reduced baloxavir inhibition. METHODS: Influenza A(H1N1)pdm09 viral polymerase complexes containing all 19 I38X AA substitutions were reconstituted in HEK293T cells in a mini-replicon assay. 2021 The Journal of antimicrobial chemotherapy Abstract IV I38X 77 81 33351916 Multiple polymerase acidic (PA) I38X substitutions in influenza A(H1N1)pdm09 virus permit polymerase activity and cause reduced baloxavir inhibition. PA I38T/M/F substitutions reduce its antiviral efficacy. 2021 The Journal of antimicrobial chemotherapy Abstract IV I38T;I38M;I38F 3;3;3 11;11;11 PA 0 2 33360319 Ser-Leu substitution at P2 position of the hemagglutinin cleavage site attenuates replication and pathogenicity of Eurasian avian-like H1N2 swine influenza viruses. In this study, we found a serine-leucine (Ser-Leu) substitution at the P2 position of the HA cleavage site (S328 L) in naturally occurring EA H1N2 virus. 2021 Veterinary microbiology Abstract IV S328L 108 114 HA 90 92 33360319 Ser-Leu substitution at P2 position of the hemagglutinin cleavage site attenuates replication and pathogenicity of Eurasian avian-like H1N2 swine influenza viruses. In vivo analyses revealed that, while all mice inoculated with r/DG2-S328 L or r/YJ28 viruses survived, the survival rates of r/DG2- and r/YJ28-L328S-inoculated animals were 20 % and 40 %, respectively. 2021 Veterinary microbiology Abstract IV L328S 144 149 33367751 Synthesis, inhibitory activity and oral dosing formulation of AV5124, the structural analogue of influenza virus endonuclease inhibitor baloxavir. Notably, AV5116 was equipotent or more potent than baloxavir acid (BXA) against WT (I38-WT) viruses and viruses with reduced BXA susceptibility carrying an I38T polymerase acidic (PA) substitution. 2021 The Journal of antimicrobial chemotherapy Abstract IV I38T 156 160 PA;PA 180;161 182;178 33385836 Discovery of highly potent and selective influenza virus neuraminidase inhibitors targeting 150-cavity. Among them, compound 5c bearing 4-(3-methoxybenzyloxy)benzyl group exhibited the most potent activity, which was lower or modestly improved activities than oseltamivir carboxylate (OSC) against N1 (H1N1), N1 (H5N1) and N1 (H5N1-H274Y). 2021 European journal of medicinal chemistry Abstract IV H274Y 228 233 33385836 Discovery of highly potent and selective influenza virus neuraminidase inhibitors targeting 150-cavity. However, 5c displayed 4.85-fold more potent activity than OSC against H5N1-H274Y NA. 2021 European journal of medicinal chemistry Abstract IV H274Y 75 80 81 83 33385836 Discovery of highly potent and selective influenza virus neuraminidase inhibitors targeting 150-cavity. Molecular docking studies provided insights into the high potency of 5c against N1 and N1-H274Y mutant NAs. 2021 European journal of medicinal chemistry Abstract IV H274Y 90 95 103 106 33408177 Phosphorylation of Influenza A Virus NS1 at Serine 205 Mediates Its Viral Polymerase-Enhancing Function. CK2 inhibition significantly reduced the replication of WT viruses and decreased NS1-DDX21 interaction, as observed for NS1 S205G. 2021 Journal of virology Abstract IV S205G 124 129 NS1;NS1 81;120 84;123 33408177 Phosphorylation of Influenza A Virus NS1 at Serine 205 Mediates Its Viral Polymerase-Enhancing Function. However, PR8 NS1 S205N showed remarkably higher attenuation than PR8 NS1 S205G in a human cell line, highlighting a potential host-independent advantage of phosphorylatable S205, while an asparagine at this position led to a potential host-specific attenuation. 2021 Journal of virology Abstract IV S205N;S205G 17;73 22;78 NS1;NS1 13;69 16;72 33408177 Phosphorylation of Influenza A Virus NS1 at Serine 205 Mediates Its Viral Polymerase-Enhancing Function. Interestingly, PR8 NS1 S205G did not show polymerase activity-enhancing functions, in contrast to the WT, which can be attributed to diminished interaction with cellular restriction factor DDX21. 2021 Journal of virology Abstract IV S205G 23 28 NS1 19 22 33408177 Phosphorylation of Influenza A Virus NS1 at Serine 205 Mediates Its Viral Polymerase-Enhancing Function. To identify NS1 functions regulated by S205 phosphorylation, we generated recombinant PR8 H1N1 NS1 mutants with S205G (nonphosphorylatable) or S205N (H1N1pdm09 signature), as well as H1N1pdm09 viruses harboring the reverse mutation NS1 N205S or N205D (phosphomimetic). 2021 Journal of virology Abstract IV S205G;S205N;N205S;N205D 112;143;236;245 117;148;241;250 NS1;NS1;NS1 12;95;232 15;98;235 33408229 Next-Generation Sequencing Analysis of the Within-Host Genetic Diversity of Influenza A(H1N1)pdm09 Viruses in the Upper and Lower Respiratory Tracts of Patients with Severe Influenza. However, the D222G/N substitution in hemagglutinin (HA) protein was the only amino acid substitution common to multiple patients. 2021 mSphere Abstract IV D222G;D222N 13;13 20;20 HA;HA 52;37 54;50 33408229 Next-Generation Sequencing Analysis of the Within-Host Genetic Diversity of Influenza A(H1N1)pdm09 Viruses in the Upper and Lower Respiratory Tracts of Patients with Severe Influenza. Therefore, it is important to investigate influenza A(H1N1)pdm09 virus populations using multiple paired samples from the upper and lower respiratory tract to avoid overlooking potentially important substitutions, especially in patients with severe disease.IMPORTANCE The D222G/N substitution in the hemagglutinin (HA) protein of influenza A(H1N1)pdm09 virus has been reported to be associated with disease severity and mortality in numerous previous studies. 2021 mSphere Abstract IV D222G;D222N 272;272 279;279 HA;HA 315;300 317;313 33418392 A bivalent live attenuated influenza virus vaccine protects against H1N2 and H3N2 viral infection in swine. The elastase dependent SD191-R342V virus possesses a mutation from arginine to valine at amino acid (aa) 342 on HA, whereas the elastase dependent SD69-K345V virus possesses a mutation from lysine to valine at aa 345 on HA. 2021 Veterinary microbiology Abstract IV R342V;K345V;K345V 29;152;190 34;157;216 HA;HA 112;220 114;222 33418392 A bivalent live attenuated influenza virus vaccine protects against H1N2 and H3N2 viral infection in swine. The hemagglutinin (HA) cleavage site from both SD191-WT and SD69-WT were engineered from a trypsin-sensitive to an elastase-sensitive motif, to generate SD191-R342V and SD69-K345V, respectively. 2021 Veterinary microbiology Abstract IV R342V;K345V 159;174 164;179 HA;HA 19;4 21;17 33421685 Generation and properties of one strain of H3N2 influenza virus with enhanced replication. For this viral strain all segments exhibit a homology close to 100 % with its parental strain A/Canine/Jiangsu/06/2010 (JS/10), except for two site mutations K156E and R201 K which occur in the receptor-binding sites of hemagglutinin (HA) and antigen binding sites of neuraminidase (NA), respectively. 2021 Veterinary microbiology Abstract IV K156E;R201K 158;168 163;174 HA;HA;NA;NA 235;220;283;268 237;233;285;281 33424035 The Effect of I155T, K156Q, K156E and N186K Mutations in Hemagglutinin on the Virulence and Reproduction of Influenza A/H5N1 Viruses. Amino acid substitutions I155T, K156Q, K156E+V138A, N186K led to a decrease in thermal stability, replication activity of the mutant viruses in chicken embryos, and virulence for mice, although these effects differed between the variants. 2020 Molecular biology Abstract IV K156E;I155T;K156Q;V138A;N186K 39;25;32;45;52 44;30;37;50;57 33424035 The Effect of I155T, K156Q, K156E and N186K Mutations in Hemagglutinin on the Virulence and Reproduction of Influenza A/H5N1 Viruses. The A138V and N186K mutations seem to be adaptive in mammalian viruses. 2020 Molecular biology Abstract IV A138V;N186K 4;14 9;19 33424035 The Effect of I155T, K156Q, K156E and N186K Mutations in Hemagglutinin on the Virulence and Reproduction of Influenza A/H5N1 Viruses. The analysis of the frequency of these mutations in natural isolates of H5N1 influenza viruses indicated that the K156E/Q and N186K mutations have little chance to gain a foothold during evolution, in contrast to the I155T mutation, which is the most responsible for antigenic drift. 2020 Molecular biology Abstract IV K156Q;K156E;N186K;I155T 114;114;126;217 121;121;131;222 33424035 The Effect of I155T, K156Q, K156E and N186K Mutations in Hemagglutinin on the Virulence and Reproduction of Influenza A/H5N1 Viruses. The K156Q and N186K mutations reduced viral reproduction at elevated temperature (40 C). 2020 Molecular biology Abstract IV K156Q;N186K 4;14 9;19 33436086 N-linked glycosylation at site 158 of the HA protein of H5N6 highly pathogenic avian influenza virus is important for viral biological properties and host immune responses. We have shown earlier that lack of glycosylation at position 158 of the hemagglutinin (HA) glycoprotein due to the T160A mutation is a key determinant of the dual receptor binding property of clade 2.3.4.4 H5NX subtypes. 2021 Veterinary research Abstract IV T160A 115 120 HA;HA 87;72 89;85 33451024 Identification of Important N-Linked Glycosylation Sites in the Hemagglutinin Protein and Their Functional Impact on DC-SIGN Mediated Avian Influenza H5N1 Infection. Furthermore, combined mutations (N27Q&N39Q) significantly waned the interaction on either H5N1-PVs or -RG infection in cis and in trans (p < 0.01). 2021 International journal of molecular sciences Abstract IV N27Q;N39Q 33;38 37;42 33451024 Identification of Important N-Linked Glycosylation Sites in the Hemagglutinin Protein and Their Functional Impact on DC-SIGN Mediated Avian Influenza H5N1 Infection. Human recombinant DC-SIGN (rDC-SIGN) coated ELISA showed that H5N1-PVs bound to DC-SIGN, however, mutation on the N27Q, N39Q, and N181Q significantly reduced this binding (p < 0.05). 2021 International journal of molecular sciences Abstract IV N27Q;N39Q;N181Q 114;120;130 118;124;135 33451024 Identification of Important N-Linked Glycosylation Sites in the Hemagglutinin Protein and Their Functional Impact on DC-SIGN Mediated Avian Influenza H5N1 Infection. Infectivity and capture assay demonstrated that N27Q and N39Q mutations significantly ameliorated DC-SIGN mediated H5N1 infection. 2021 International journal of molecular sciences Abstract IV N27Q;N39Q 48;57 52;61 Influenza A virus H5N1 infection 115 129 33480324 Can molecular dynamics explain decreased pathogenicity in mutant camphecene-resistant influenza virus? Specifically, camphecene causes a significant mutation in HA (V615L). 2021 Journal of biomolecular structure & dynamics Abstract IV V615L 62 67 HA 58 60 33515926 Mutations during the adaptation of H7N9 avian influenza virus to mice lungs enhance human-like sialic acid binding activity and virulence in mice. Sequence analysis showed that the two viruses differed by 27 amino acids distributed among six genes, containing changes in PB2 (E627K, D701N) and HA (Q226L) genes. 2021 Veterinary microbiology Abstract IV E627K;D701N;Q226L 129;136;151 134;141;156 HA;PB2 147;124 149;127 33518109 Characterization of the low-pathogenic H7N7 avian influenza virus in Shanghai, China. Mutations were found in HA (A135 T, T136S, and T160 A [H3 numbering]), M1 (N30D and T215 A), NS1 (P42S and D97 E), PB2 (R389 K), and PA (N383D) proteins; these mutations have been shown to be related to mammalian adaptation and changes in virulence of AIVs. 2021 Poultry science Abstract IV A135T;T136S;T160A;N30D;T215A;P42S;D97E;R389K;N383D 28;36;47;75;84;98;107;120;137 34;41;53;79;90;102;112;126;142 HA;M1;NS1;PA;PB2 24;71;93;133;115 26;73;96;135;118 33540229 Design, synthesis, and bioassay of 4-thiazolinone derivatives as influenza neuraminidase inhibitors. In addition, D41 showed low toxicity and greater potency than reference compounds Oseltamivir and Amantadine against N1-H275Y variant in cellular assays. 2021 European journal of medicinal chemistry Abstract IV H275Y 120 125 3354203 A mutation in the PA protein gene of cold-adapted B/Ann Arbor/1/66 influenza virus associated with reversion of temperature sensitivity and attenuated virulence. The predicted PA proteins of wt and ca B/AA/1/66 are known to differ by six amino acid substitutions including a valine to methionine substitution at residue 431. 1988 Virology Abstract IV V431M 113 161 PA 14 16 33568453 Identification and Characterization of Novel Antibody Epitopes on the N2 Neuraminidase. In addition, a natural isolate from the 2017-2018 season was found to contain the E258K mutation and was resistant to numerous antibodies tested. 2021 mSphere Abstract IV E258K 82 87 33568453 Identification and Characterization of Novel Antibody Epitopes on the N2 Neuraminidase. The mutation S331N, was identified in virus passaged in the presence of antibody; however, it had little impact on MAb activity and greatly decreased viral fitness. 2021 mSphere Abstract IV S331N 13 18 33568453 Identification and Characterization of Novel Antibody Epitopes on the N2 Neuraminidase. These viruses contained mutations K199E/T, E258K, A272D, and S331N. 2021 mSphere Abstract IV K199E;K199T;E258K;A272D;S331N 34;34;43;50;61 41;41;48;55;66 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. Moreover, the airborne transmission of a 2009 pandemic H1N1 PB1/K612R mutant virus was impaired in ferrets, resulting in reversion to wild-type PB1 K612. 2021 PLoS pathogens Abstract IV K612R 64 69 PB1;PB1 60;144 63;147 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. When tested in vivo, we found that the virulence of SUMOylation-defective PB1/K612R mutant IAVs was highly attenuated in mice. 2021 PLoS pathogens Abstract IV K612R 78 83 PB1 74 77 33577807 Development of cycling probe based real-time PCR methodology for influenza A viruses possessing the PA/I38T amino acid substitution associated with reduced baloxavir susceptibility. After baloxavir treatment, the most frequently detected substitution is Ile38Thr in polymerase acidic protein (PA/I38T), and this substitution reduces baloxavir susceptibility in influenza A viruses. 2021 Antiviral research Abstract IV I38T;I38T 72;114 80;118 PA;PA 111;84 113;101 33577807 Development of cycling probe based real-time PCR methodology for influenza A viruses possessing the PA/I38T amino acid substitution associated with reduced baloxavir susceptibility. Although human-to-human transmission of PA/I38T variant may have occurred in a closed environment, the prevalence of this variant in influenza A viruses was still limited. 2021 Antiviral research Abstract IV I38T 43 47 PA 40 42 33577807 Development of cycling probe based real-time PCR methodology for influenza A viruses possessing the PA/I38T amino acid substitution associated with reduced baloxavir susceptibility. In addition, we found PA/I38T variant in siblings who did not received baloxavir treatment during an infection caused by A (H3N2) that afflicted the entire family. 2021 Antiviral research Abstract IV I38T 25 29 PA 22 24 33577807 Development of cycling probe based real-time PCR methodology for influenza A viruses possessing the PA/I38T amino acid substitution associated with reduced baloxavir susceptibility. Our cycling probe-PCR system is thus useful for antiviral surveillance of influenza A viruses possessing PA/I38T. 2021 Antiviral research Abstract IV I38T 108 112 PA 105 107 33577807 Development of cycling probe based real-time PCR methodology for influenza A viruses possessing the PA/I38T amino acid substitution associated with reduced baloxavir susceptibility. This real-time PCR system discriminated between PA/I38T and wild type viruses well. 2021 Antiviral research Abstract IV I38T 51 55 PA 48 50 33577807 Development of cycling probe based real-time PCR methodology for influenza A viruses possessing the PA/I38T amino acid substitution associated with reduced baloxavir susceptibility. To rapidly investigate the frequency of PA/I38T in influenza A (H1N1)pdm09 and A (H3N2) viruses in clinical samples, we established a rapid real-time system to detect single nucleotide polymorphisms in PA, using cycling probe real-time PCR. 2021 Antiviral research Abstract IV I38T 43 47 PA;PA 40;202 42;204 33577807 Development of cycling probe based real-time PCR methodology for influenza A viruses possessing the PA/I38T amino acid substitution associated with reduced baloxavir susceptibility. Using our cycling probe real-time PCR system, we detected no (0/129, 0.0%) influenza A (H1N1)pdm09 viruses with PA/I38T substitutions and four A (H3N2) (4/229, 1.7%) with PA/I38T substitution prior to treatment. 2021 Antiviral research Abstract IV I38T;I38T 115;174 119;178 PA;PA 112;171 114;173 33577807 Development of cycling probe based real-time PCR methodology for influenza A viruses possessing the PA/I38T amino acid substitution associated with reduced baloxavir susceptibility. We designed two sets of probes that were labeled with either 6-carboxyfluorescein (FAM) or 6-carboxy-X-rhodamine (ROX) to identify PA/I38 (wild type strain) or PA/I38T, respectively. 2021 Antiviral research Abstract IV I38T 163 167 PA;PA 131;160 133;162 33581212 Susceptibility of widely diverse influenza a viruses to PB2 polymerase inhibitor pimodivir. A rare PB2 substitution H357N was identified in an A(H4N2) subtype poultry virus that displayed >100-fold reduced pimodivir susceptibility. 2021 Antiviral research Abstract IV H357N 24 29 PB2 7 10 33581212 Susceptibility of widely diverse influenza a viruses to PB2 polymerase inhibitor pimodivir. Human seasonal viruses with PB2 substitutions S324C, S324R, or N510K displayed a 27-317-fold reduced pimodivir susceptibility by HINT. 2021 Antiviral research Abstract IV S324C;S324R;N510K 46;53;63 51;58;68 PB2 28 31 33604005 In silico analysis and molecular characterization of Influenza A (H1N1) pdm09 virus circulating and causing major outbreaks in central India, 2009-2019. The frequency of S220T amino acid substitution was found to be high followed by S202T, K300E A273T, K180Q. 2020 Iranian journal of microbiology Abstract IV K300E;A273T;S220T;S202T;K180Q 87;93;17;80;100 92;98;22;85;105 33605468 Investigation of genetic variation: Neuraminidase gene of influenza A virus H1N1/pdm09, Shiraz, Iran (2015-2016). Based on sequencing results, 2 of the 44 sequenced isolates exhibited H275Y substitution, which presented oseltamivir resistance. 2021 Journal of medical virology Abstract IV H275Y 70 75 33647314 The active form of the influenza cap-snatching endonuclease inhibitor baloxavir marboxil is a tight binding inhibitor. Here we studied the mechanisms underlying the high potency of BXA and how the I38T mutation confers resistance to the drug. 2021 The Journal of biological chemistry Abstract IV I38T 78 82 33647314 The active form of the influenza cap-snatching endonuclease inhibitor baloxavir marboxil is a tight binding inhibitor. The apparent inhibitor constant (Kiapp) is 12 nM, while the I38T mutation increased Kiapp by ~18-fold. 2021 The Journal of biological chemistry Abstract IV I38T 60 64 33647314 The active form of the influenza cap-snatching endonuclease inhibitor baloxavir marboxil is a tight binding inhibitor. The collective data support the conclusion that BXA is a tight binding inhibitor and the I38T mutation diminishes these properties. 2021 The Journal of biological chemistry Abstract IV I38T 89 93 33673017 Structural and Thermodynamic Analysis of the Resistance Development to Pimodivir (VX-787), the Clinical Inhibitor of Cap Binding to PB2 Subunit of Influenza A Polymerase. First major mutation, F404Y, causing resistance was identified during preclinical testing, next the mutation M431I was identified in patients during the second phase of clinical trials. 2021 Molecules (Basel, Switzerland) Abstract IV F404Y;M431I 22;109 27;114 33673017 Structural and Thermodynamic Analysis of the Resistance Development to Pimodivir (VX-787), the Clinical Inhibitor of Cap Binding to PB2 Subunit of Influenza A Polymerase. Here we present four crystal structures of PB2-WT, PB2-F404Y, PB2-M431I and PB2-H357N in complex with pimodivir. 2021 Molecules (Basel, Switzerland) Abstract IV F404Y;M431I;H357N 55;66;80 60;71;85 PB2;PB2;PB2;PB2 43;51;62;76 46;54;65;79 33673017 Structural and Thermodynamic Analysis of the Resistance Development to Pimodivir (VX-787), the Clinical Inhibitor of Cap Binding to PB2 Subunit of Influenza A Polymerase. The mutation H357N was identified during testing of IAV strains at Centers for Disease Control and Prevention. 2021 Molecules (Basel, Switzerland) Abstract IV H357N 13 18 33679636 Improved in vitro Efficacy of Baloxavir Marboxil Against Influenza A Virus Infection by Combination Treatment With the MEK Inhibitor ATR-002. IAV with the PA-I38T mutation shows resistance against BXA, but is still susceptible toward ATR-002. 2021 Frontiers in microbiology Abstract IV I38T 16 20 PA 13 15 33713731 Secondary substitutions in the hemagglutinin and neuraminidase genes associated with neuraminidase inhibitor resistance are rare in the Influenza Resistance Information Study (IRIS). All cultured viruses with the known resistance substitutions H275Y or R292K showed reduced susceptibility to oseltamivir in the NA-star assay. 2021 Antiviral research Abstract IV H275Y;R292K 61;70 66;75 128 130 33713731 Secondary substitutions in the hemagglutinin and neuraminidase genes associated with neuraminidase inhibitor resistance are rare in the Influenza Resistance Information Study (IRIS). Known resistance substitutions were detected by mutation specific RT-PCR in viruses of 57 of 1803 (3.2%) oseltamivir-treated individuals, including 39 individuals infected with A/H1N1pdm09 [H275Y] virus and 18 with A/H3N2 [R292K] virus. 2021 Antiviral research Abstract IV H275Y;R292K 190;223 195;228 33713731 Secondary substitutions in the hemagglutinin and neuraminidase genes associated with neuraminidase inhibitor resistance are rare in the Influenza Resistance Information Study (IRIS). Only in two A/H1N1pdm09 [H275Y] viruses, the potentially compensatory secondary substitutions HA-D52N and NA-R152K were detected. 2021 Antiviral research Abstract IV H275Y;D52N;R152K 25;97;109 30;101;114 HA;NA 94;106 96;108 33782012 Discovery of a Novel Respiratory Syncytial Virus Replication Inhibitor. Consistent with these findings, deep sequencing of the genomes of triazole-1-resistant mutants revealed a single point mutation (A to G) at nucleotide 13546 of the RSV genome, leading to a T-to-A change at amino acid position 1684 of the L protein, which is the RSV RNA polymerase for both viral transcription and replication. 2021 Antimicrobial agents and chemotherapy Abstract IV A13546G;T1684A 128;189 156;230 33782012 Discovery of a Novel Respiratory Syncytial Virus Replication Inhibitor. The effect of triazole-1 on minigenome transcription, which was mediated by the L protein containing the T1684A mutation, was significantly reduced, suggesting that the T1684A mutation alone conferred viral resistance to triazole-1. 2021 Antimicrobial agents and chemotherapy Abstract IV T1684A;T1684A 105;169 111;175 3379640 Structure of an escape mutant of glycoprotein N2 neuraminidase of influenza virus A/Tokyo/3/67 at 3 A. The mutant virus, selected by growing the virus in the presence of a monoclonal antibody to the neuraminidase, is shown to have undergone a single amino acid change of lysine to glutamic acid at residue 368. 1988 Journal of molecular biology Abstract IV K368E 168 206 96 109 33827947 Development of a Genetically Stable Live Attenuated Influenza Vaccine Strain Using an Engineered High-Fidelity Viral Polymerase. As expected, PB1-L66V showed at least two-times-lower mutation rates and decreased misincorporation rates, compared to the wild type (WT). 2021 Journal of virology Abstract IV L66V 17 21 PB1 13 16 33827947 Development of a Genetically Stable Live Attenuated Influenza Vaccine Strain Using an Engineered High-Fidelity Viral Polymerase. Consequently, we identified a Leu66-to-Val single amino acid mutation in polymerase basic protein 1 (PB1). 2021 Journal of virology Abstract IV L66V 30 42 PB1 101 104 33827947 Development of a Genetically Stable Live Attenuated Influenza Vaccine Strain Using an Engineered High-Fidelity Viral Polymerase. In this study, we isolated a novel influenza virus strain with a Leu66-to-Val single amino acid mutation in PB1 that displayed a significantly higher fidelity than the WT. 2021 Journal of virology Abstract IV L66V 65 77 PB1 108 111 33827947 Development of a Genetically Stable Live Attenuated Influenza Vaccine Strain Using an Engineered High-Fidelity Viral Polymerase. The high-fidelity phenotype of PB1-L66V was confirmed using next-generation sequencing analysis and biochemical assays with the purified influenza viral polymerase. 2021 Journal of virology Abstract IV L66V 35 39 PB1 31 34 33827947 Development of a Genetically Stable Live Attenuated Influenza Vaccine Strain Using an Engineered High-Fidelity Viral Polymerase. The PB1-L66V mutation prevented reversion of the ts phenotype to the WT phenotype, suggesting that the high-fidelity viral polymerase could contribute to generating an LAIV with high genetic stability, which would not revert to the pathogenic virus.IMPORTANCE The LAIV currently in use is prescribed for actively immunizing individuals aged 2 to 49 years. 2021 Journal of virology Abstract IV L66V 8 12 PB1 4 7 33827947 Development of a Genetically Stable Live Attenuated Influenza Vaccine Strain Using an Engineered High-Fidelity Viral Polymerase. Therefore, we next generated an attenuated PB1-L66V virus with a temperature-sensitive (ts) phenotype based on FluMist, a live attenuated influenza vaccine (LAIV) that can restrict virus propagation by ts mutations, and examined the genetic stability of the attenuated PB1-L66V virus using serial virus passages. 2021 Journal of virology Abstract IV L66V;L66V 47;273 51;277 PB1;PB1 43;269 46;272 33840358 PB1 S524G mutation of wild bird-origin H3N8 influenza A virus enhances virulence and fitness for transmission in mammals. We further found that the PB1 S524G mutation conferred T222 virus airborne transmissibility between ferrets. 2021 Emerging microbes & infections Abstract IV S524G 30 35 PB1 26 29 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. Co-occurrence of the mutations D222G and D222N was detected in a substantial number of the studied fatal cases (41%). 2021 PloS one Abstract IV D222G;D222N 31;41 36;46 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. The D222G/N mutations in the hemagglutinin (HA) gene of A(H1N1)pdm09 are associated with severe and fatal human influenza cases. 2021 PloS one Abstract IV D222G;D222N 4;4 11;11 HA;HA 44;29 46;42 Influenza 106 121 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. The D222G/N mutations were detected at a low frequency (less than 1%) in the rest of the studied samples from fatal and nonfatal cases of influenza. 2021 PloS one Abstract IV D222N;D222G 4;4 11;11 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. The high rate of occurrence of HA D222G/N mutations in A(H1N1)pdm09 viruses, their increased ability to replicate in the LRT and their association with fatal outcomes points to the importance of monitoring the mutations in circulating A(H1N1)pdm09 viruses for the evaluation of their epidemiological significance and for the consideration of disease prevention and treatment options. 2021 PloS one Abstract IV D222G;D222N 34;34 41;41 HA 31 33 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. The presence of HA D222Y/V/A mutations was detected in a few fatal cases. 2021 PloS one Abstract IV D222Y;D222V;D222A 19;19;19 28;28;28 HA 16 18 33933515 An influenza A(H5N8) virus isolated during an outbreak at a poultry farm in Russia in 2017 has an N294S substitution in the neuraminidase and shows reduced susceptibility to oseltamivir. An NA-N293/294S substitution was not present in sequences from the GISAID database. 2021 Antiviral research Abstract IV N293S;N294S 6;6 15;15 3 5 33933515 An influenza A(H5N8) virus isolated during an outbreak at a poultry farm in Russia in 2017 has an N294S substitution in the neuraminidase and shows reduced susceptibility to oseltamivir. Fewer than 1% of analyzed viruses had amino acid substitutions associated with reduced susceptibility to baloxavir (PA-E199G, PA-E199E/G) or reduced or highly reduced inhibition by neuraminidase inhibitors (NA-R150/152K, NA-I221/222M, NA-I221/222I/M, NA-I221/222V, NA-I115/117V, NA-G145/147R, NA-R291/292R/K). 2021 Antiviral research Abstract IV E199G;E199E;E199G;R291K;R292K;R291R;R292R;G145R;G147R;I115V;I117V;I221V;I222V;I221I;I222I;I221M;I222M;I221I;I221M;R150K;R152K 119;129;129;296;296;296;296;282;282;268;268;254;254;224;238;224;238;238;238;210;210 124;136;136;307;307;307;307;291;291;277;277;263;263;233;249;233;249;249;249;219;219 NA;NA;NA;NA;NA;NA;NA;NA;PA;PA 207;221;235;251;265;279;293;181;116;126 209;223;237;253;267;281;295;194;118;128 33933515 An influenza A(H5N8) virus isolated during an outbreak at a poultry farm in Russia in 2017 has an N294S substitution in the neuraminidase and shows reduced susceptibility to oseltamivir. Only one strain bore an amino acid substitution associated with adamantane resistance (M2-S31N). 2021 Antiviral research Abstract IV S31N 90 94 M2 87 89 33933515 An influenza A(H5N8) virus isolated during an outbreak at a poultry farm in Russia in 2017 has an N294S substitution in the neuraminidase and shows reduced susceptibility to oseltamivir. The M2 protein of A(H5N8) viruses from the 2.3.4.4c clade had an M2-S31N substitution associated with reduced susceptibility to adamantanes. 2021 Antiviral research Abstract IV S31N 68 72 M2;M2 4;65 6;67 33933515 An influenza A(H5N8) virus isolated during an outbreak at a poultry farm in Russia in 2017 has an N294S substitution in the neuraminidase and shows reduced susceptibility to oseltamivir. The neuraminidase of 1 strain had an NA-N293/294S (N8/N2 numbering) substitution associated with reduced inhibition by oseltamivir and normal inhibition by zanamivir, which was confirmed phenotypically. 2021 Antiviral research Abstract IV N293S;N294S 40;40 49;49 33933515 An influenza A(H5N8) virus isolated during an outbreak at a poultry farm in Russia in 2017 has an N294S substitution in the neuraminidase and shows reduced susceptibility to oseltamivir. To the best of our knowledge, influenza A(H5N8) viruses with reduced inhibition by oseltamivir bearing an NA-N293/294S substitution have not been previously reported in epidemiological surveillance studies. 2021 Antiviral research Abstract IV N293S;N294S 109;109 118;118 106 108 33975931 Analysis of the Evolution of Pandemic Influenza A(H1N1) Virus Neuraminidase Reveals Entanglement of Different Phenotypic Characteristics. For example, the substitution K432E in the second sialic acid binding site, next to the catalytic site, was shown to affect catalytic activity, substrate specificity, and the pH optimum for maximum activity. 2021 mBio Abstract IV K432E 30 35 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. Extracellular and intracellular pH returned to baseline by 7 DPI in mice infected with HA1-Y17H and was restored later in wildtype-infected. 2021 PloS one Abstract IV Y17H 91 95 HA1 87 90 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. Here, we inoculated DBA/2J mice intranasally with A/TN/1-560/2009 (H1N1) (activation pH 5.5) or a mutant containing the destabilizing mutation HA1-Y17H (pH 6.0). 2021 PloS one Abstract IV Y17H 147 151 HA1 143 146 33985852 Changes in sialic acid binding associated with egg adaptation decrease live attenuated influenza virus replication in human nasal epithelial cell cultures. In the 2012-2013 northern hemisphere vaccine, the H3N2 HA vaccine strain contained three amino acid changes - H156Q, G186V and S219Y - which altered HA antigenic structure and thus presumably decreased vaccine efficacy. 2021 Vaccine Abstract IV H156Q;G186V;S219Y 110;117;127 115;122;132 HA;HA 55;149 57;151 34008327 The PB2 co-adaptation of H10N8 avian influenza virus increases the pathogenicity to chickens and mice. Among them, PB2-A588V significantly enhanced the activity of polymerase in avian and mammalian cells. 2021 Transboundary and emerging diseases Abstract IV A588V 16 21 PB2 12 15 34008327 The PB2 co-adaptation of H10N8 avian influenza virus increases the pathogenicity to chickens and mice. In this study, we found that the mutations of PB2-I292V, PB2-R389K, PB2-A588V, PB2-T598M/V, PB2-L648V, and PB2-T676M substitutions significantly increased after 2012. 2021 Transboundary and emerging diseases Abstract IV I292V;R389K;A588V;T598M;T598V;L648V;T676M 50;61;72;83;83;96;111 55;66;77;90;90;101;116 PB2;PB2;PB2;PB2;PB2;PB2 46;57;68;79;92;107 49;60;71;82;95;110 34008327 The PB2 co-adaptation of H10N8 avian influenza virus increases the pathogenicity to chickens and mice. Notably, animal experiments showed that PB2-A588V substitution increased the pathogenicity and transmissibility in chickens and the virulence of mice. 2021 Transboundary and emerging diseases Abstract IV A588V 44 49 PB2 40 43 34008327 The PB2 co-adaptation of H10N8 avian influenza virus increases the pathogenicity to chickens and mice. Several well-known adaptive mutations in the PB2 gene, such as E627K, D701N, and A588V, significantly enhanced the virulence of the AIVs in mammals. 2021 Transboundary and emerging diseases Abstract IV E627K;D701N;A588V 63;70;81 68;75;86 PB2 45 48 34008327 The PB2 co-adaptation of H10N8 avian influenza virus increases the pathogenicity to chickens and mice. The combined mutations of PB2-F6 (including PB2-I292V, PB2-R389K, PB2-A588V, PB2-T598M, PB2-L648V, and PB2-T676M) obtained higher adaptability of AIVs in avians and mammals than that of the single mutation of PB2-A588V, which suggested that the PB2 588 site is a key co-adaptation site and that synergies with other mutation sites can further enhance this co-adaptability. 2021 Transboundary and emerging diseases Abstract IV I292V;R389K;A588V;T598M;L648V;T676M;A588V 48;59;70;81;92;107;213 53;64;75;86;97;112;218 PB2;PB2;PB2;PB2;PB2;PB2;PB2;PB2;PB2 26;44;55;66;77;88;103;209;245 29;47;58;69;80;91;106;212;248 34020222 Development of 6E3 antibody-mediated SERS immunoassay for drug-resistant influenza virus. Furthermore, it was immobilized on Au nanoplate and nanoparticles, enabling surface-enhanced Raman scattering (SERS)-based detection of the H275Y mutant pH1N1. 2021 Biosensors & bioelectronics Abstract IV H275Y 140 145 34020222 Development of 6E3 antibody-mediated SERS immunoassay for drug-resistant influenza virus. Here we report a novel 6E3 monoclonal antibody capable of recognizing and binding to the H275Y neuraminidase (NA) mutation, which has been associated with reduced susceptibility of influenza viruses to NA inhibitors. 2021 Biosensors & bioelectronics Abstract IV H275Y 89 94 NA;NA;NA 110;202;95 112;204;108 34020222 Development of 6E3 antibody-mediated SERS immunoassay for drug-resistant influenza virus. Molecular modeling studies also suggest the high-affinity binding of this antibody to pH1N1 H275Y NA. 2021 Biosensors & bioelectronics Abstract IV H275Y 92 97 98 100 34020222 Development of 6E3 antibody-mediated SERS immunoassay for drug-resistant influenza virus. The 6E3 antibody had a KD of 72.74 muM for wild-type NA and 32.76 pM for H275Y NA, suggesting that it can identify drug-resistant pandemic H1N1 (pH1N1) influenza virus. 2021 Biosensors & bioelectronics Abstract IV H275Y 73 78 NA;NA 53;79 55;81 34033262 Evolution of the PB1 gene of human influenza A (H3N2) viruses circulating between 1968 and 2019. In contrast, the backward mutant, A113V/R586K/N619D/I709V, reduced polymerase activity in human cells. 2021 Transboundary and emerging diseases Abstract IV A113V;R586K;N619D;I709V 34;40;46;52 39;45;51;57 34033262 Evolution of the PB1 gene of human influenza A (H3N2) viruses circulating between 1968 and 2019. The PB1 I709V decreased viral replication in vitro, but this mutant only showed less effect on mice infection experiment, which suggested influenza A virus evolved in human host was not always consisted with highly replication efficiency and pathogenicity in other mammalian host. 2021 Transboundary and emerging diseases Abstract IV I709V 8 13 PB1 4 7 34033262 Evolution of the PB1 gene of human influenza A (H3N2) viruses circulating between 1968 and 2019. The PB1 V709I or PB1 V113A/K586R/D619N/V709I induced higher polymerase activity of HK/68 in human cells. 2021 Transboundary and emerging diseases Abstract IV V709I;V709I;V113A;K586R;D619N 8;39;21;27;33 13;44;26;32;38 PB1;PB1 4;17 7;20 34061017 Double mutations in the H9N2 avian influenza virus PB2 gene act cooperatively to increase viral host adaptation and replication for human infections. K526R, E627V or E627K), indicating a host adaptation advantage for these double mutations. 2021 The Journal of general virology Abstract IV K526R;E627V;E627K 0;7;16 5;12;21 34061017 Double mutations in the H9N2 avian influenza virus PB2 gene act cooperatively to increase viral host adaptation and replication for human infections. Most of the relevant human virus isolates carry the PB2-A588V mutation together with another PB2 mutation. 2021 The Journal of general virology Abstract IV A588V 56 61 PB2;PB2 52;93 55;96 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. However, sequencing revealed the mutation that conferred resistance, K229R, decreased in frequency over time within ferrets. 2021 PLoS pathogens Abstract IV K229R 69 74 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. Modelling revealed that due to a fitness advantage for the PA P653L mutant, reassortment with the wild-type virus to gain wild-type PB1 segment in vivo resulted in the loss of the PB1 resistance mutation K229R. 2021 PLoS pathogens Abstract IV P653L;K229R 62;204 67;209 PA;PB1;PB1 59;132;180 61;135;183 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. We demonstrated that this fitness advantage of PA P653L in the background of our starting virus A/England/195/2009 was due to a maladapted PA in first wave isolates from the 2009 pandemic. 2021 PLoS pathogens Abstract IV P653L 50 55 PA;PA 47;139 49;141 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. We previously described a favipiravir resistant influenza A virus generated by in vitro passage in presence of drug with two mutations: K229R in PB1, which conferred resistance at a cost to polymerase activity, and P653L in PA, which compensated for the cost of polymerase activity. 2021 PLoS pathogens Abstract IV K229R;P653L 136;215 141;220 PA;PB1 224;145 226;148 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. We show there is no fitness advantage of P653L in more recent pH1N1 influenza A viruses. 2021 PLoS pathogens Abstract IV P653L 41 46 34065033 Novel Clade 2.3.4.4b Highly Pathogenic Avian Influenza A H5N8 and H5N5 Viruses in Denmark, 2020. Genetic analyses of one of the H5N8 viruses revealed the presence of a substitution (PB2-M64T) that is highly conserved in human seasonal influenza A viruses. 2021 Viruses Abstract IV M64T 89 93 PB2 85 88 34068322 Dual R108K and G189D Mutations in the NS1 Protein of A/H1N1 Influenza Virus Counteract Host Innate Immune Responses. The 2018 virus harbored amino acid mutations (I123V and N205S) in important functional sites; however, 108R and 189G were highly conserved between A/California/07/2009 and the 2018 variant. 2021 Viruses Abstract IV I123V;N205S 46;56 51;61 34068322 Dual R108K and G189D Mutations in the NS1 Protein of A/H1N1 Influenza Virus Counteract Host Innate Immune Responses. To better understand interactions between influenza viruses and the human innate immune system, we generated and rescued seasonal 2009 H1N1 IAV mutants expressing an NS1 protein harboring a dual mutation (R108K/G189D) at these conserved residues and then analyzed its biological characteristics. 2021 Viruses Abstract IV R108K;G189D 205;211 210;216 NS1 166 169 34070388 Molecular Characterization of Seasonal Influenza A and B from Hospitalized Patients in Thailand in 2018-2019. Amino acid sequence analysis revealed 10 mutations at antigenic sites including T144A/I, T151K, Q213R, S214P, T176K, D69N, Q277R, N137K, N187K, and E78K/G. 2021 Viruses Abstract IV T144A;T144I;T151K;Q213R;S214P;T176K;D69N;Q277R;N137K;N187K;E78K;E78G 80;80;89;96;103;110;117;123;130;137;148;148 87;87;94;101;108;115;121;128;135;142;154;154 34070388 Molecular Characterization of Seasonal Influenza A and B from Hospitalized Patients in Thailand in 2018-2019. In comparison to the B/Colorado/06/2017, which is the representative of influenza B Victoria lineage vaccine strain, these substitutions include G129D, G133R, K136E, and V180R for HA protein. 2021 Viruses Abstract IV G129D;G133R;K136E;V180R 145;152;159;170 150;157;164;175 HA 180 182 34070388 Molecular Characterization of Seasonal Influenza A and B from Hospitalized Patients in Thailand in 2018-2019. Interestingly, we observed additional mutations at antigenic sites (S91R, S181T, T202I) as well as a unique mutation at a receptor binding site (S200P). 2021 Viruses Abstract IV S91R;S181T;T202I;S200P 68;74;81;145 72;79;86;150 34131512 Identification of H3N2 NA and PB1-F2 genetic variants and their association with disease symptoms during the 2014-15 influenza season. In human nasal epithelial cell cultures, a virus with the novel NAg+F2P genotype replicated less well compared with a virus with the parental genotype. 2021 Virus evolution Abstract IV F2P 68 71 34131512 Identification of H3N2 NA and PB1-F2 genetic variants and their association with disease symptoms during the 2014-15 influenza season. Retrospective analyses of clinical data showed that NAg+F2P genotype viruses were associated with increased cough and shortness of breath in infected patients. 2021 Virus evolution Abstract IV F2P 56 59 34131512 Identification of H3N2 NA and PB1-F2 genetic variants and their association with disease symptoms during the 2014-15 influenza season. The isolates were classified by HA clade and the presence of a new set of co-selected mutations in NA (a glycosylation site, NAg+) and PB1-F2 (H75P). 2021 Virus evolution Abstract IV H75P 143 147 HA;NA;PB1F2 32;99;135 34;101;141 34131512 Identification of H3N2 NA and PB1-F2 genetic variants and their association with disease symptoms during the 2014-15 influenza season. The NA and PB1-F2 mutations were present in a subset of clade 3C.2a viruses (NAg+F2P), which dominated during the subsequent influenza seasons. 2021 Virus evolution Abstract IV F2P 81 84 NA;PB1F2 4;11 6;17 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. BACKGROUND: Oseltamivir (OTV)-resistant influenza virus exhibits His-to-Tyr mutation at residue 274 (H274Y) in N1 neuraminidase (NA). 2021 PeerJ Abstract IV H274Y;H274Y 101;65 106;99 NA;NA 129;114 131;127 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. H274Y mutation significantly enhanced the interaction between residue 274 and the three interface residues in NA, thereby significantly decreasing the interaction between OTV and its surrounding loop 150 residues. 2021 PeerJ Abstract IV H274Y 0 5 110 112 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. However, the molecular mechanisms by which the H274Y mutation in NA reduces its binding affinity to OTV have not been fully elucidated. 2021 PeerJ Abstract IV H274Y 47 52 65 67 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. METHODS: In this study, we used dynamic residue interaction network (dRIN) analysis based on molecular dynamics simulation to investigate the correlation between the OTV binding site of NA and its H274Y mutation site. 2021 PeerJ Abstract IV H274Y 197 202 186 188 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. RESULTS: dRIN analysis revealed that the OTV binding site and H274Y mutation site of NA interact via the three interface residues connecting them. 2021 PeerJ Abstract IV H274Y 62 67 85 87 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. Using dRIN analysis, we succeeded in understanding the characteristic changes in residue interactions due to H274Y mutation, which can elucidate the molecular mechanism of reduction in OTV binding affinity to influenza NA. 2021 PeerJ Abstract IV H274Y 109 114 219 221 34156583 Genetic characterisation of the influenza viruses circulating in Bulgaria during the 2019-2020 winter season. The HA genes of A(H3N2) viruses analysed belonged to clades 3C.3a (21 strains) and 3C.2a (5 strains): subclades 3C.2a1b + T131K, 3C.2a1b + T135K-B and 3C.2a1b + T135K-A. 2021 Virus genes Abstract IV T131K;T135K;T135K 122;139;161 127;144;166 HA 4 6 34164347 Risk of Environmental Exposure to H7N9 Influenza Virus via Airborne and Surface Routes in a Live Poultry Market in Hebei, China. More importantly, after 5 passages in mice, the virus acquired two adaptive mutations, PB1-H115Q and B2-E627K, exhibiting increased virulence and aerosol transmissibility. 2021 Frontiers in cellular and infection microbiology Abstract IV H115Q;E627K 91;104 96;109 PB1 87 90 34194404 Host Adaptive Evolution of Avian-Origin H3N2 Canine Influenza Virus. Notably, six substitutions, including HA-G146S, M1-V15I, NS1-E227K, PA-C241Y, PB2-K251R, and PB2-G590S, have been reported to play imperative roles in facilitating the transmission and spillover of IAVs across species barriers. 2021 Frontiers in microbiology Abstract IV G146S;V15I;E227K;C241Y;K251R;G590S 41;51;61;71;82;97 46;55;66;76;87;102 HA;M1;NS1;PA;PB2;PB2 38;48;57;68;78;93 40;50;60;70;81;96 34207098 Virus Adaptation Following Experimental Infection of Chickens with a Domestic Duck Low Pathogenic Avian Influenza Isolate from the 2017 USA H7N9 Outbreak Identifies Polymorphic Mutations in Multiple Gene Segments. For comparison, NGS analysis of clinical samples obtained from duck specimen collected during the outbreak indicated three polymorphic sides in the M1 segment and a minor population of viruses carrying the D139N (21.4%) substitution in the NS1 segment. 2021 Viruses Abstract IV D139N 206 211 M1;NS1 148;240 150;243 34217753 Baloxavir-oseltamivir combination therapy inhibits the emergence of resistant substitutions in influenza A virus PA gene in a mouse model. Baloxavir marboxil (BXM) treatment-emergent polymerase acid (PA) I38X amino acid substitution (AAS) in the resistant variants of influenza viruses raise concerns regarding their emergence and spread. 2021 Antiviral research Abstract IV I38X 65 69 PA 61 63 34217753 Baloxavir-oseltamivir combination therapy inhibits the emergence of resistant substitutions in influenza A virus PA gene in a mouse model. Deep sequencing analysis revealed that 67% (n = 4/6) of the population treated with BXM single therapy (1 or 5 mg/kg) possessed the treatment-emergent PA-I38X AAS variants (I38T, I38S, and I38V). 2021 Antiviral research Abstract IV I38X;I38T;I38S;I38V 154;173;179;189 158;177;183;193 PA 151 153 34217753 Baloxavir-oseltamivir combination therapy inhibits the emergence of resistant substitutions in influenza A virus PA gene in a mouse model. Notably, BXM-OS combination therapy impeded PA-I38X AAS emergence. 2021 Antiviral research Abstract IV I38X 47 51 PA 44 46 34240696 Nanopore metagenomic sequencing of influenza virus directly from respiratory samples: diagnosis, drug resistance and nosocomial transmission, United Kingdom, 2018/19 influenza season. We identified an influenza A(H3N2) genome encoding the oseltamivir resistance S331R mutation in neuraminidase, potentially associated with an emerging distinct intra-subtype reassortant. 2021 Euro surveillance Abstract IV S331R 78 83 96 109 34242774 Genetic and antigenic diversity of H7N9 highly pathogenic avian influenza virus in China. Molecular simulations found that the mutations (V135T, S145P, and L226Q) around the HA receptor pocket increased the affinity to alpha2,3-linked sialic acid (SIA) while decreased to alpha2,6-linked SIA. 2021 Infection, genetics and evolution Abstract IV V135T;S145P;L226Q 48;55;66 53;60;71 HA 84 86 34253060 In Vivo Therapy with M2e-Specific IgG Selects for an Influenza A Virus Mutant with Delayed Matrix Protein 2 Expression. Deep sequencing analysis of viral RNA isolated at different time points after treatment revealed that the sequence variation in M2e was limited to P10H/L and/or I11T in anti-M2e MAb-treated mice. 2021 mBio Abstract IV P10H;P10L;I11T 147;147;161 153;153;165 34270849 Acetylation of the influenza A virus polymerase subunit PA in the N-terminal domain positively regulates its endonuclease activity. Notably, the substitution of the lysine residue at position 19 with glutamine, a mimic of the acetyl-lysine residue, enhanced its endonuclease activity in vitro; this point mutation also accelerated influenza A virus RNA-dependent RNA polymerase activity in the cell. 2022 The FEBS journal Abstract IV K19Q 33 77 34337007 Full Genomic Sequences of H5N1 Highly Pathogenic Avian Influenza Virus in Human Autopsy Specimens Reveal Genetic Variability and Adaptive Changes for Growth in MDCK Cell Cultures. Our study suggested that the adaptation changes for the viral fitness to survive in a new host species (MDCK cells) might involve many genes, for example, the amino acid substitution 177G or 177W adjacent to the receptor-binding residues in the HA1 globular head and the substitution M315I in PB2. 2021 BioMed research international Abstract IV M315I 284 289 HA1;PB2 245;293 248;296 34339766 Investigating the sequence variation in the influenza A matrix genes during the 2017-2018 and 2018-2019 seasons in samples from a local population in London. All samples displayed the core mutations for H1N1 M1(C154T; G174A and G238A) and for H3N2 M1(C153T; C163T and G189T); three of the H1N1pdm09 viruses also showed a small number of point mutations. 2021 Journal of virological methods Abstract IV C154T;G174A;G238A;C153T;C163T;G189T 53;60;70;93;100;110 58;65;75;98;105;115 M1;M1 50;90 52;92 34347386 Pathogenesis and genetic characteristics of a novel reassortant low pathogenic avian influenza A(H7N6) virus isolated in Cambodia in 2019. Although avian-origin A(H7Nx) LPAIVs do not contain the critical mammalian-adaptive substitution (E627K) in PB2, the lethality and morbidity of the A(H7N6) virus in BALB/c mice were similar to those of A(H7N9) viruses, suggesting potential for interspecies transmission. 2021 Transboundary and emerging diseases Abstract IV E627K 98 103 PB2 108 111 34358217 Mutation E48K in PB1 Polymerase Subunit Improves Stability of a Candidate Live Attenuated Influenza B Virus Vaccine. A third attempted mutation (K391E) in PB1 was not always stable. 2021 Vaccines Abstract IV K391E 28 33 PB1 38 41 34358217 Mutation E48K in PB1 Polymerase Subunit Improves Stability of a Candidate Live Attenuated Influenza B Virus Vaccine. In previous work, incorporation of two mutations (E580G, S660A) along with the addition of an HA epitope tag in the PB1 segment of B/Brisbane/60/2008 (B/Bris) resulted in an attenuated strain that was safe and effective as a live attenuated vaccine. 2021 Vaccines Abstract IV E580G;S660A 50;57 55;62 HA;PB1 94;116 96;119 34358217 Mutation E48K in PB1 Polymerase Subunit Improves Stability of a Candidate Live Attenuated Influenza B Virus Vaccine. Interestingly, viruses that maintained the K391E mutation were associated with the mutation E48K. 2021 Vaccines Abstract IV K391E;E48K 43;92 48;96 34358217 Mutation E48K in PB1 Polymerase Subunit Improves Stability of a Candidate Live Attenuated Influenza B Virus Vaccine. These results confirm the compensatory effect of mutation E48K to stabilize the K391E mutation, resulting in a safer, yet still protective, IBV LAIV vaccine. 2021 Vaccines Abstract IV E48K;K391E 58;80 62;85 34358217 Mutation E48K in PB1 Polymerase Subunit Improves Stability of a Candidate Live Attenuated Influenza B Virus Vaccine. To explore the contribution of the E48K mutation to stability of the K391E mutation, a vaccine candidate was generated by inserting both mutations, along with attenuating mutations E580G and S660A, in PB1 of B/Bris (B/Bris PB1att 4M). 2021 Vaccines Abstract IV E48K;K391E;E580G;S660A 35;69;181;191 39;74;186;196 PB1 201 204 34379499 Role of the Chaperone Protein 14-3-3epsilon in the Regulation of Influenza A Virus-Activated Beta Interferon. Influenza A virus expressing C terminus-truncated NS1 with a T49A mutation dramatically increases IFN-beta mRNA in infected cells and causes slower replication than that of virus without the T-to-A mutation. 2021 Journal of virology Abstract IV T49A 61 65 NS1 50 53 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. In particular, we employed a single-turnover NTP incorporation assay for the first time on IAV RdRp to show that K235R mutant RdRp possessed a 1.9-fold increase in the transcription activity of the cognate NTP and a 4.6-fold increase in fidelity compared to wild-type. 2021 Nucleic acids research Abstract IV K235R 113 118 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. Our all-atom molecular dynamics simulations further elucidated that the higher activity is attributed to the shorter distance between K235R and the triphosphate moiety of NTP compared with wild-type. 2021 Nucleic acids research Abstract IV K235R 134 139 34702977 Ancestral sequence reconstruction pinpoints adaptations that enable avian influenza virus transmission in pigs. PB1-Q621R and NP-R351K increased viral replication and transmission in piglets when introduced into the 1979-1983 ancestral virus that lacked efficient transmissibility. 2021 Nature microbiology Abstract IV Q621R;R351K 4;17 9;22 NP;PB1 14;0 16;3 35021372 Superb Specific, Ultrasensitive, and Rapid Identification of the Oseltamivir-Resistant H1N1 Virus: Naked-Eye and SERS Dual-Mode Assay Using Functional Gold Nanoparticles. By measuring the SERS signals, we could detect the pH1N1/H275Y mutant virus with a detection limit of 10 PFU. 2019 ACS applied bio materials Abstract IV H275Y 57 62 35021372 Superb Specific, Ultrasensitive, and Rapid Identification of the Oseltamivir-Resistant H1N1 Virus: Naked-Eye and SERS Dual-Mode Assay Using Functional Gold Nanoparticles. Herein, we report specific and ultrasensitive detection of oseltamivir-resistant (pH1N1/H275Y mutant) virus using functional Au nanoparticles (NPs). 2019 ACS applied bio materials Abstract IV H275Y 88 93 NP 143 146 35021372 Superb Specific, Ultrasensitive, and Rapid Identification of the Oseltamivir-Resistant H1N1 Virus: Naked-Eye and SERS Dual-Mode Assay Using Functional Gold Nanoparticles. Importantly, the pH1N1/H275Y mutant virus could be detected by using the functional Au NPs even in a mixture of mutant and wild-type viruses with a ratio of 1/100. 2019 ACS applied bio materials Abstract IV H275Y 23 28 NP 87 90 35021372 Superb Specific, Ultrasensitive, and Rapid Identification of the Oseltamivir-Resistant H1N1 Virus: Naked-Eye and SERS Dual-Mode Assay Using Functional Gold Nanoparticles. OHT is an excellent receptor for the pH1N1/H275Y mutant virus because it has a 250-fold higher binding affinity for the pH1N1/H275Y mutant virus than for the wild-type virus. 2019 ACS applied bio materials Abstract IV H275Y;H275Y 43;126 48;131 35021372 Superb Specific, Ultrasensitive, and Rapid Identification of the Oseltamivir-Resistant H1N1 Virus: Naked-Eye and SERS Dual-Mode Assay Using Functional Gold Nanoparticles. Only in the presence of the pH1N1/H275Y mutant virus, the functional Au NPs aggregate, and the color of the NPs changes from red to purple. 2019 ACS applied bio materials Abstract IV H275Y 34 39 NP;NP 72;108 75;111 35021372 Superb Specific, Ultrasensitive, and Rapid Identification of the Oseltamivir-Resistant H1N1 Virus: Naked-Eye and SERS Dual-Mode Assay Using Functional Gold Nanoparticles. The SERS signal of MGITC on Au NPs allows us to detect pH1N1/H275Y mutant viruses sensitively and quantitatively. 2019 ACS applied bio materials Abstract IV H275Y 61 66 NP 31 34 35044213 The Species-Specific 282 Residue in the PB2 Subunit of the Polymerase Regulates RNA Synthesis and Replication of Influenza A Viruses Infecting Bat and Nonbat Hosts. Introduction of E282S mutation in the human-adapted PB2 (influenza A/H1N1/WSN/1933) drastically reduces polymerase activity and replication efficiency of the virus in human, bat, and canine cells. 2022 Journal of virology Abstract IV E282S 16 21 PB2 52 55 35044215 N-Glycolylneuraminic Acid Binding of Avian and Equine H7 Influenza A Viruses. The additional mutations S128T, I130V, T189A, and K193R converted the specificity from NeuAc to NeuGc. 2022 Journal of virology Abstract IV S128T;I130V;T189A;K193R 25;32;39;50 30;37;44;55 35044215 N-Glycolylneuraminic Acid Binding of Avian and Equine H7 Influenza A Viruses. We found that the A135E mutation is key for binding alpha2,3-linked NeuGc but does not abolish NeuAc binding. 2022 Journal of virology Abstract IV A135E 18 23 35045267 Identification of a Permissive Secondary Mutation That Restores the Enzymatic Activity of Oseltamivir Resistance Mutation H275Y. Here, we identified a new helper mutation, Y276F, that can rescue the functional defects of H275Y and contribute to the evolution of drug resistance in IAV. 2022 Journal of virology Abstract IV Y276F;H275Y 43;92 48;97 35045267 Identification of a Permissive Secondary Mutation That Restores the Enzymatic Activity of Oseltamivir Resistance Mutation H275Y. In prior work, we identified a hyperactive mutation (Y276F) that increased NA activity by approximately 70%. 2022 Journal of virology Abstract IV Y276F 53 58 75 77 35045267 Identification of a Permissive Secondary Mutation That Restores the Enzymatic Activity of Oseltamivir Resistance Mutation H275Y. In this study, we measured the relative fitness, NA activity, and surface expression, as well as sensitivity to oseltamivir, for several oseltamivir resistance mutations, including H275Y in the wild-type and Y276F genetic background. 2022 Journal of virology Abstract IV H275Y;Y276F 181;208 186;213 49 51 35045267 Identification of a Permissive Secondary Mutation That Restores the Enzymatic Activity of Oseltamivir Resistance Mutation H275Y. Our results demonstrate that Y276F selectively rescues the fitness defect of H275Y by restoring its NA surface expression and enzymatic activity, elucidating the local compensatory structural impacts of Y276F on the adjacent H275Y. 2022 Journal of virology Abstract IV Y276F;H275Y;Y276F;H275Y 29;77;203;225 34;82;208;230 100 102 35045267 Identification of a Permissive Secondary Mutation That Restores the Enzymatic Activity of Oseltamivir Resistance Mutation H275Y. Previous studies have identified a panel of permissive or compensatory mutations in neuraminidase (NA) that restore the growth defect of the predominant oseltamivir resistance mutation (H275Y) in H1N1 influenza A virus. 2022 Journal of virology Abstract IV H275Y 186 191 NA;NA 99;84 101;97 35045267 Identification of a Permissive Secondary Mutation That Restores the Enzymatic Activity of Oseltamivir Resistance Mutation H275Y. The main oseltamivir resistance mutation, H275Y, occurs in the neuraminidase (NA) protein of IAV and reduces drug binding as well as NA function. 2022 Journal of virology Abstract IV H275Y 42 47 NA;NA;NA 78;133;63 80;135;76 35045267 Identification of a Permissive Secondary Mutation That Restores the Enzymatic Activity of Oseltamivir Resistance Mutation H275Y. While Y276F had not been previously identified as a permissive mutation, we hypothesized that Y276F may counteract the defects caused by H275Y by buffering its reduced NA expression and enzyme activity. 2022 Journal of virology Abstract IV Y276F;Y276F;H275Y 6;94;137 11;99;142 168 170 35067005 Genetic and biological properties of H10N3 avian influenza viruses: A potential pandemic candidate? Importantly, several key molecular markers associated with mammalian adaptation had been detected in both avian and human-isolated H10N3 influenza viruses in the HA (G228S), PB2 (I292V and A588V), PB1 (M317V and I368V), and PA (A343S, K356R and S409N) protein. 2022 Transboundary and emerging diseases Abstract IV G228S;I292V;A588V;M317V;I368V;A343S;K356R;S409N 166;179;189;202;212;228;235;245 171;184;194;207;217;233;240;250 HA;PA;PB1;PB2 162;224;197;174 164;226;200;177 35446141 Novel Epitopes of the Influenza Virus N1 Neuraminidase Targeted by Human Monoclonal Antibodies. We observed escape mutations on the head domain of the N1 protein around the enzymatic site (S364N, N369T, and R430Q) and also detected escape mutations located on the sides and bottom of the NA (N88D, N270D, and Q313K/R). 2022 Journal of virology Abstract IV S364N;N369T;R430Q;N88D;N270D;Q313K;Q313R 93;100;111;196;202;213;213 98;105;116;200;207;220;220 192 194 35467364 Interactions between Influenza A Virus Nucleoprotein and Gene Segment Untranslated Regions Facilitate Selective Modulation of Viral Gene Expression. We previously demonstrated that a single substitution in the viral nucleoprotein (NP:F346S) selectively modulates neuraminidase (NA) gene segment expression while leaving other segments largely unaffected. 2022 Journal of virology Abstract IV F346S 85 90 NA;NA;NP;NP 129;114;82;67 131;127;84;80 35467364 Interactions between Influenza A Virus Nucleoprotein and Gene Segment Untranslated Regions Facilitate Selective Modulation of Viral Gene Expression. While the NP:F346S substitution did not significantly alter the RNA binding or oligomerization activities of NP in vitro, it specifically decreased the ability of NP to promote NA segment viral RNA (vRNA) synthesis. 2022 Journal of virology Abstract IV F346S 13 18 NA;NP;NP;NP 177;10;109;163 179;12;111;165 35509388 New substitutions on NS1 protein from influenza A (H1N1) virus: Bioinformatics analyses of Indian strains isolated from 2009 to 2020. The D2E substitution evolved simultaneously with the E125D substitution that involved viral replication. 2022 Health science reports Abstract IV D2E;E125D 4;53 7;58 35509388 New substitutions on NS1 protein from influenza A (H1N1) virus: Bioinformatics analyses of Indian strains isolated from 2009 to 2020. Three paired substitutions were (i) D2E and E125D, (ii) T80A and A155T, and (iii) E55K and K131E. 2022 Health science reports Abstract IV D2E;E125D;T80A;A155T;E55K;K131E 36;44;56;65;82;91 39;49;60;70;86;96 35511288 A novel E198K substitution in the PA gene of influenza A virus with reduced susceptibility to baloxavir acid. Here, we identified a novel PA subunit substitution, PA E198K, that reduced susceptibility to BXA. 2022 Archives of virology Abstract IV E198K 56 61 PA;PA 28;53 30;55 35511288 A novel E198K substitution in the PA gene of influenza A virus with reduced susceptibility to baloxavir acid. The IC50 of BXA toward influenza A viruses containing PA E198K increased approximately 2- to 6-fold. 2022 Archives of virology Abstract IV E198K 57 62 PA 54 56 3576971 Extragenic and intragenic suppression of a transport mutation in the hemagglutinin gene of an influenza A virus as revealed by backcross and sequence determination. The amino acid replacement in position 480 from Thr to Ile, leading to the loss of a complex carbohydrate side chain, is responsible for the ts phenotype. 1987 Virology Abstract IV T480I 39 58 3727394 Primary structure of influenza virus genome regions coding for polypeptides from the major antigenic sites of H3 hemagglutinin. One of them was accompanied by a change in the coded amino acid (Asp53----Tyr) located in the antigenic site E of the HA glycoprotein. 1986 Virologie Abstract IV D53Y 65 77 HA 118 120 3753607 Studies on the mechanism of membrane fusion: site-specific mutagenesis of the hemagglutinin of influenza virus. Three mutants have been constructed that introduce single, nonconservative amino acid changes in the fusion peptide, and three fusion phenotypes were observed: substitution of glutamic acid for the glycine residue at the amino-terminus of HA2 abolished all fusion activity; substitution of glutamic acid for the glycine residue at position 4 in HA2 raised the threshold pH and decreased the efficiency of fusion; and, finally, extension of the hydrophobic stretch by replacement of the glutamic acid at position 11 with glycine yielded a mutant protein that induced fusion of erythrocytes with cells with the same efficiency and pH profile as the wild-type protein. 1986 The Journal of cell biology Abstract IV G4E;E11G 290;486 341;527 HA;HA 239;345 241;347 3811232 Crystals of antibodies complexed with influenza virus neuraminidase show isosteric binding of antibody to wild-type and variant antigens. Crystals have been grown of Fab fragments of monoclonal antibody NC41, complexed with influenza virus neuraminidase (NA) of the N9 subtype and with a variant of N9 NA having a sequence change of Asn to Asp at position 331. 1987 Virology Abstract IV N331D 195 221 N9;N9;NA;NA;NA 128;161;117;164;102 130;163;119;166;115 3811232 Crystals of antibodies complexed with influenza virus neuraminidase show isosteric binding of antibody to wild-type and variant antigens. This reduces, but does not abolish, the binding of NC41 antibody (in the case of another variant, Ser 371 to Leu, binding of NC41 antibody appears to be abolished). 1987 Virology Abstract IV S371L 98 112 3811237 Effects of site-specific mutation on structure and activity of influenza virus B/Lee/40 neuraminidase. Mutation of an apparently unpaired cysteine residue to serine at position 251 had no effect on protein transport or folding as judged by cell-surface reactivity with monoclonal antibodies, and the NA retained enzyme activity, confirming that this Cys is not essential for correct folding of the polypeptide. 1987 Virology Abstract IV C251S 35 77 197 199 3811237 Effects of site-specific mutation on structure and activity of influenza virus B/Lee/40 neuraminidase. Mutation of Trp 364 to Leu abolished detectable enzyme activity, while mutation of Thr 368 to Val reduced enzyme activity to less than 25% of wild-type levels. 1987 Virology Abstract IV W364L;T368V 12;83 26;97 6203216 Sequence of the neuraminidase gene of influenza virus A/Tokyo/3/67 and previously uncharacterized monoclonal variants. In another variant, arginine at position 253 changed to serine, a change that also occurred in field strains. 1984 Virology Abstract IV R253S 20 62 6208279 Characterization of the murine TH response to influenza virus hemagglutinin: evidence for three major specificities. Three hybridomas with specificity 1 failed to respond to the PR8 mutant RV6 (Glu115----Lys), two with specificity 2 failed to respond to PR8 mutant DV4 (Ser136----Pro), and two with specificity 3 responded to all antibody-selected PR8 mutants without exception. 1984 Journal of immunology (Baltimore, Md. Abstract IV E115K;S136P 77;153 90;166 6224879 Influenza virus site recognized by a murine helper T cell specific for H1 strains. Localization to a nine amino acid sequence in the hemagglutinin molecule. A conserved region of the hemagglutinin molecule around amino acid position 115 in the heavy chain (HA1) was implicated as being important in this recognition by the lack of stimulatory activity associated with a glutamic acid to lysine substitution at position 115 in the laboratory mutant RV6, derived from wild-type PR8. 1983 The Journal of experimental medicine Abstract IV E115K 213 265 HA1;HA 100;26 103;39 6580621 Hemagglutinin of swine influenza virus: a single amino acid change pleiotropically affects viral antigenicity and replication. Change at residue 155 from Gly to Glu is associated with change from L to H HA phenotype. 1983 Proc Natl Acad Sci U S A Abstract IV G155E 18 37 HA 76 78 7507932 Stoichiometry of recombinant cystic fibrosis transmembrane conductance regulator in epithelial cells and its functional reconstitution into cells in vitro. Furthermore, expression of the most frequent mutant allele of the cystic fibrosis (CF) gene, the delta F508 mutant in these epithelial cells, indicated that it is biosynthetically arrested at the endoplasmic reticulum and fails to traffic to the plasma membrane. 1994 The Journal of biological chemistry Abstract IV delta F508 97 107 7508997 Influenza A virus M2 ion channel protein: a structure-function analysis. A glycosylated M2 mutant protein (M2 + V, A30T) exhibited an ion channel activity with a voltage-activated, time-dependent kinetic component. 1994 Journal of virology Abstract IV A30T 42 46 M2;M2 15;34 17;36 7508997 Influenza A virus M2 ion channel protein: a structure-function analysis. The membrane currents of oocytes expressing mutant M2 ion channels were measured at both normal and low pH, and the amantadine-resistant mutant containing the change of alanine at residue 30 to threonine was found to have a significantly attenuated low pH activation response. 1994 Journal of virology Abstract IV A30T 169 203 M2 51 53 7527838 Neutralization escape mutants of type A influenza virus are readily selected by antisera from mice immunized with whole virus: a possible mechanism for antigenic drift. The HA genes of three of these were part sequenced and had a predicted single amino acid substitution (Gly-144-->Glu) in site A. 1994 The Journal of general virology Abstract IV G144E 103 116 HA 4 6 7605205 Amino acid replacements leading to temperature-sensitive defects of the NS1 protein of influenza A virus. Ts 412 has a single base substitution (G100-->A) leading to an amino acid replacement (Arg 25-->Lys) in the NS1 protein. 1995 Archives of virology Abstract IV G100A;R25K 39;87 47;99 NS1 108 111 7605205 Amino acid replacements leading to temperature-sensitive defects of the NS1 protein of influenza A virus. Ts 451 also has a single base substitution (U273-->C) leading to an amino acid replacement (Ser 83-->Pro) in the NS1 protein. 1995 Archives of virology Abstract IV S83P 92 104 NS1 113 116 7621857 Immunodominance with progenitor B cell diversity in the neutralizing antibody repertoire to influenza infection. A majority of mAb, established from individual BALB/c (H-2d) mice, select mutant viruses containing the same single amino acid substitution in the membrane distal ecto-domain, HA1 198 A-->E, whereas changes at either HA1 158 G-->E or HA1 198 A-->E are selected for by mAb from BALB.K (H-2k) donors. 1995 European journal of immunology Abstract IV A198E;G158E;A198E 180;221;238 189;230;247 HA1;HA1;HA1 176;217;234 179;220;237 7685965 Modulation of CD4+ T-cell recognition of influenza hemagglutinin by carbohydrate side chains located outside a T-cell determinant. Two distinct T-cell clones raised to the H3 subtype influenza virus A/Memphis/71 fail to proliferate in response to other H3 viruses that contain the amino acid substitution Asp63-->Asn within the heavy (HA1) chain of the hemagglutinin (HA). 1993 Virology Abstract IV D63N 174 185 HA;HA1;HA 237;204;222 239;207;235 7710364 Specific changes in the M1 protein during adaptation of influenza virus to mouse. Comparison of the M gene sequences of the mouse brain adapted variants A/NWS/33 and A/WSN/33 to their parent, A/WS/33, identified two specific amino acid substitutions in the M1 protein which correlated with virulence for mouse: Ala41-->Val and Thr139-->Ala. 1995 Archives of virology Abstract IV A41V;T139A 229;245 240;257 M;M1 18;175 19;177 7798313 The small GTP-binding protein rab6 functions in intra-Golgi transport. Over-expression of wild-type rab6 and rab6 Q72L greatly reduced transport of both markers between cis/medial (alpha-mannosidase II positive) and late (sialyl-transferase positive) Golgi compartments, without affecting transport from the endoplasmic reticulum (ER) to cis/medial-Golgi or from the trans-Golgi network (TGN) to the plasma membrane. 1994 The Journal of cell biology Abstract IV Q72L 43 47 7798313 The small GTP-binding protein rab6 functions in intra-Golgi transport. Overexpression of both rab6 Q72L and rab6 T27N altered the morphology of the Golgi apparatus as well as that of the TGN, as assessed at the immunofluorescence level with several markers. 1994 The Journal of cell biology Abstract IV Q72L;T27N 28;42 32;46 7798313 The small GTP-binding protein rab6 functions in intra-Golgi transport. We have transiently overexpressed in mouse L cells and human HeLa cells wild-type rab6, GTP (rab6 Q72L), and GDP (rab6 T27N) -bound mutants of rab6 and analyzed the intracellular transport of a soluble secreted form of alkaline phosphatase (SEAP) and of a plasma membrane protein, the hemagglutinin protein (HA) of influenza virus. 1994 The Journal of cell biology Abstract IV Q72L;T27N 98;119 102;123 HA;HA 308;285 310;298 7798313 The small GTP-binding protein rab6 functions in intra-Golgi transport. Whereas overexpression of rab6 T27N did not affect the individual steps of transport between ER and the plasma membrane, it caused an apparent delay in secretion, most likely due to the accumulation of the transport markers in late Golgi compartments. 1994 The Journal of cell biology Abstract IV T27N 31 35 7822785 Genetic evidence for difference between intracellular and extracellular peptides in influenza A matrix peptide-specific CTL recognition. During the course of extensive mutagenesis of HLA-A2.1, we examined influenza A matrix peptide (FMP)-specific CTL recognition of HMy2.C1R (C1R) cells expressing mutant HLA-A2.1 molecules, sensitized with synthetic peptide, FMP 58-66, (exogenous peptide), or infected with influenza A virus (endogenous peptide). 1995 Journal of immunology (Baltimore, Md. Abstract IV C1R;C1R 134;139 137;142 M 80 113 7822785 Genetic evidence for difference between intracellular and extracellular peptides in influenza A matrix peptide-specific CTL recognition. Pulse-chase analyses followed by endoglycosidase-H treatment show that the rate of maturation and processing of the five mutant HLA-A2 molecules in C1R cells is identical to that of wild type. 1995 Journal of immunology (Baltimore, Md. Abstract IV C1R 148 151 7822785 Genetic evidence for difference between intracellular and extracellular peptides in influenza A matrix peptide-specific CTL recognition. The remaining three mutants, Y27N, Q32K, and S132C, fail to present exogenous peptide, but present endogenous peptide to FMP-specific CTL. 1995 Journal of immunology (Baltimore, Md. Abstract IV Y27N;Q32K;S132C 29;35;45 33;39;50 7822785 Genetic evidence for difference between intracellular and extracellular peptides in influenza A matrix peptide-specific CTL recognition. Two of the five mutants, F9L and T134K, present exogenous peptide to FMP-specific CTL, but fail to present endogenous peptide to CTL. 1995 Journal of immunology (Baltimore, Md. Abstract IV F9L;T134K 25;33 28;38 7856092 Probing the structure of influenza B hemagglutinin using site-directed mutagenesis. None of the mutations affected hemagglutination activity, but mutations T196P or Q1971 eliminated binding of a monoclonal antibody. 1995 Virology Abstract IV T196P 72 77 7998391 [Changes in its hemagglutinin during the adaptation of the influenza virus to mice and their role in the acquisition of virulent properties and resistance to serum inhibitors]. In another experiment, the adapted virus (15th passage) did not differ in its antigenic, virulent, and reproductive properties from clone 7p but had only one substitution in HA Asn127-->Asp. 1994 Voprosy virusologii Abstract IV N127D 177 189 HA 174 176 7998391 [Changes in its hemagglutinin during the adaptation of the influenza virus to mice and their role in the acquisition of virulent properties and resistance to serum inhibitors]. Passages of influenza A/USSR/90/77 virus in mouse lungs produced a virulent virus (18th passage) carrying two mutations in hemagglutinin (HA) Asn127-->Asp and Tre89-->Ala. 1994 Voprosy virusologii Abstract IV N127D;T89A 142;159 154;170 HA;HA 138;123 140;136 8057456 Mutations at palmitylation sites of the influenza virus hemagglutinin affect virus formation. The change from cysteine at position 553 to serine or alanine does not significantly alter the phenotype of the virus. 1994 Journal of virology Abstract IV C553S 16 50 8071101 Mutation of the alpha 2 domain disulfide bridge of the class I molecule HLA-A*0201. Effect on maturation and peptide presentation. Mutant C164A cells infected with influenza virus were partially recognized by influenza matrix peptide-specific CTLs, while C101S cells were not lysed. 1994 Human immunology Abstract IV C164A;C101S 7;124 12;129 M 88 116 8071101 Mutation of the alpha 2 domain disulfide bridge of the class I molecule HLA-A*0201. Effect on maturation and peptide presentation. Mutation of cysteine 101 to a serine (C101S) or of cysteine 164 to alanine (C164A) decreased the rate of maturation of the heavy chain, the total amount of mature heavy chain within the cell, and the level of surface expression. 1994 Human immunology Abstract IV C101S;C164A;C101S;C164A 38;76;12;51 43;81;36;74 8113760 An estimation of the nucleotide substitution rate at defined positions in the influenza virus haemagglutinin gene. Particularly interesting amino acid changes, not previously reported, were observed in the p7 monoclonal antibody-specific mutants, in which only Gly to Ser and Gly to Asp at position 226 were detected. 1994 The Journal of general virology Abstract IV G226D 161 187 8163832 Attenuation of virulence in influenza B viral infection of volunteers. A difference in MAb reactivity, together with an aspartate for asparagine amino acid substitution at position 196 in a 432 base pair region of the viral HA gene, was observed. 1994 The Journal of infection Abstract IV N196D 49 113 HA 153 155 8183284 Both major and minor peptide-binding pockets in HLA-A2 influence the presentation of influenza virus matrix peptide to cytotoxic T lymphocytes. With the exception of Tyr substitution for Phe9, single amino acid substitutions in the peptide-binding groove had only minor effects on peptide binding. 1994 Molecular immunology Abstract IV F9Y 22 47 8288899 Affinity ranking of influenza neuraminidase mutants with monoclonal antibodies using an optical biosensor. Comparison with ELISA and slot blot assays. Applications of this biosensor technique for comparing the binding of related neuraminidases, purified from escape mutants of influenza virus NWS/G70C/75 (N9), to two antibody Fab fragments, are described. 1994 Journal of immunological methods Abstract IV G70C 146 150 N9;NA 155;78 157;92 8300410 Recognition by HLA-A2-restricted cytotoxic T lymphocytes of endogenously generated and exogenously provided synthetic peptide analogues of the influenza A virus matrix protein. The endogenously presented analogues 58-66L60A, G61A, T65A, and L66A were recognized more efficiently than the corresponding exogenously presented analogues. 1993 Human immunology Abstract IV G61A;T65A;L66A 48;54;64 52;58;68 8300410 Recognition by HLA-A2-restricted cytotoxic T lymphocytes of endogenously generated and exogenously provided synthetic peptide analogues of the influenza A virus matrix protein. This difference in recognition was most striking for peptide 58-66G61A. 1993 Human immunology Abstract IV G61A 66 70 8336120 Influenza A virus haemagglutinin polymorphism: pleiotropic antigenic variants of A/Shanghai/11/87 (H3N2) virus selected as high yield reassortants. Differences in HA phenotype were related to a Ser to Ile change at amino acid position 186. 1993 The Journal of general virology Abstract IV S186I 46 90 HA 15 17 8376958 A temperature-sensitive mutation in the acidic polymerase gene of an influenza A virus alters the regulation of viral protein synthesis. The temperature-sensitive defect of mutant ts 263 of fowl plague virus (FPV) is located in the acidic polymerase (PA) gene and is due to a single base substitution (C2036T), which leads to an amino acid replacement (Ala671 to Val) in a highly conserved region of the protein. 1993 The Journal of general virology Abstract IV C2036T;A671V 165;216 171;229 PA 114 116 8389079 Mutations in murine Mx1: effects on localization and antiviral activity. These conclusions are based on the findings showing that: (i) none of the mutants retained antiviral activity; (ii) only a mutant with a Leu to Lys substitution at residue 612 within the nuclear targeting signal retained the characteristic punctate nuclear localization of wildtype Mx1; (iii) diffuse nuclear localization was observed for mutants with substitutions of Pro for Leu at residue 619, 626, or both 619 and 626, and deletions of residues 23 to 95, 159 to 185, 369 to 409, 387 to 440, 522 to 560, or 541 to 596; and (iv) cytoplasmic localization was observed for mutants with carboxy-terminal truncations of 15, 30, or 61 amino acids, or a deletion of residues 610 to 624. 1993 Virology Abstract IV L612K;L619P 137;369 175;395 8494822 Residues in pockets B and F of HLA-B27 are critical in the presentation of an influenza A virus nucleoprotein peptide and influence the stability of peptide - MHC complexes. HLA-B27 mutant molecules with single amino acid substitutions at residues 9his-->phe, 24thr-->ser, 45glu-->thr, and 67cys-->ala in pocket B; 114his-->asn in pocket D; and 116asp-->phe in pocket F have been generated and characterized for their capacity to present an influenza A nucleoprotein peptide (NP 383-391) for cytotoxic T lymphocyte recognition. 1993 International immunology Abstract IV T24S;E45T;C67A;H114N 86;99;116;141 97;110;127;153 NP;NP 302;279 304;292 8503186 An influenza virus temperature-sensitive mutant defective in the nuclear-cytoplasmic transport of the negative-sense viral RNAs. Nucleotide sequencing of the M segment revealed a predicted single amino acid change of phenylalanine to serine at amino acid position 79 in the M1 protein. 1993 Virology Abstract IV F79S 88 137 M;M1 29;145 30;147 8534806 Activation of the M2 ion channel of influenza virus: a role for the transmembrane domain histidine residue. Oocytes expressing the M2-H37E mutant protein also had a voltage-activated Cl- conductance that was observed only for oocytes that expressed a mass of protein exceeding a large threshold value. 1995 Biophysical journal Abstract IV H37E 26 30 M2 23 25 8534806 Activation of the M2 ion channel of influenza virus: a role for the transmembrane domain histidine residue. Oocytes expressing the M2-H37E protein also had a voltage-independent conductance with a current-voltage relationship similar to that of the wild-type M2 channel. 1995 Biophysical journal Abstract IV H37E 26 30 M2;M2 23;151 25;153 8534806 Activation of the M2 ion channel of influenza virus: a role for the transmembrane domain histidine residue. Oocytes expressing the M2-H37G protein had a voltage-independent conductance with current-voltage relationship similar to that of the wild-type M2 channel. 1995 Biophysical journal Abstract IV H37G 26 30 M2;M2 23;144 25;146 8534806 Activation of the M2 ion channel of influenza virus: a role for the transmembrane domain histidine residue. Oocytes expressing the M2-H37K and M2-H37R mutant proteins could not be studied because the oocytes did not survive more than a few hours in culture. 1995 Biophysical journal Abstract IV H37K;H37R 26;38 30;42 M2;M2 23;35 25;37 8534806 Activation of the M2 ion channel of influenza virus: a role for the transmembrane domain histidine residue. The conductance of the M2-H37E protein was reversibly inhibited by amantadine and was also only very slightly modulated by changes in pHout over the range pH 5.4 to pH 8.2. 1995 Biophysical journal Abstract IV H37E 26 30 M2 23 25 8534806 Activation of the M2 ion channel of influenza virus: a role for the transmembrane domain histidine residue. The conductance of the M2-H37G protein was reversibly inhibited by the M2 ion channel blocker amantadine and was only very slightly modulated by changes in pHout over the range pH 5.4 to pH 8.2. 1995 Biophysical journal Abstract IV H37G 26 30 M2;M2 23;71 25;73 8534806 Activation of the M2 ion channel of influenza virus: a role for the transmembrane domain histidine residue. The specific activity of the M2-H37G protein was 1.36 +/- 0.37 microA/ng and the specific activity of the M2-H37E protein was 30 +/- 3 microA/ng at pH 6.2. 1995 Biophysical journal Abstract IV H37G;H37E 32;109 36;113 M2;M2 29;106 31;108 8551626 The cytoplasmic tail of influenza A virus neuraminidase (NA) affects NA incorporation into virions, virion morphology, and virulence in mice but is not essential for virus replication. A NOTAIL virus containing an additional mutation (Ser-12 to Pro) in the transmembrane domain incorporated three times more NA molecules into virions than did the NOTAIL parent but approximately half of the amount incorporated by the wild-type virus. 1996 Journal of virology Abstract IV S12P 50 63 123 125 8553549 Generation and characterization of an influenza virus neuraminidase variant with decreased sensitivity to the neuraminidase-specific inhibitor 4-guanidino-Neu5Ac2en. A variant of the influenza virus NWS/G70C has been generated which has decreased sensitivity in vitro to the neuraminidase-specific inhibitor, 4-guanidino-Neu5Ac2en. 1995 Virology Abstract IV G70C 37 41 109 122 8553549 Generation and characterization of an influenza virus neuraminidase variant with decreased sensitivity to the neuraminidase-specific inhibitor 4-guanidino-Neu5Ac2en. Sequence analysis of this virus revealed a mutation at a previously conserved site in the enzyme active site of the neuraminidase, Glu 119 to Gly. 1995 Virology Abstract IV E119G 131 145 116 129 8577282 Identification of the sites for suppressor mutations on the hemagglutinin molecule to temperature-sensitive phenotype of the influenza virus. These were caused by a change at amino acid residue 157 from tyrosine to histidine in the HA protein. 1995 Microbiology and immunology Abstract IV Y157H 52 82 HA 90 92 8607283 The persistent variant of influenza C virus carries one characteristic point mutation in RNA segment 1. Nucleotide 28 mutated from T to C which leads to a change of amino acid 3 from Leu to Phe. 1995 Virus research Abstract IV L3F 72 89 8609159 Different biosynthetic transport routes to the plasma membrane in BHK and CHO cells. In addition, we also have studied the transport of a hemagglutinin mutant (Cys543Tyr) which is basolateral in MDCK cells. 1996 The Journal of cell biology Abstract IV C543Y 75 84 HA 53 66 8611525 On the dynamics and conformation of the HA2 domain of the influenza virus hemagglutinin. Extensive intramolecular cysteine-cysteine cross-linking was observed not only for F63C and I66C but also for H64C. 1996 Biochemistry Abstract IV H64C;F63C;I66C 110;83;92 114;87;96 8611525 On the dynamics and conformation of the HA2 domain of the influenza virus hemagglutinin. Four consecutive single-cysteine mutants, F63C, H64C, Q65C, and I66C, were generated using site-directed mutagenesis. 1996 Biochemistry Abstract IV H64C;Q65C;F63C;I66C 48;54;42;64 52;58;46;68 8627706 Characterization of mutants of influenza A virus selected with the neuraminidase inhibitor 4-guanidino-Neu5Ac2en. Sequence analysis established that a substitution had occurred in the NA (Arg-249 to Lys) and in the HA2 subunit of the hemagglutinin (Gly-75 to Glu), in the vicinity of the proposed second sialic acid binding site. 1996 Journal of virology Abstract IV R249K;G75E 74;135 88;148 HA;HA;NA 101;120;70 103;133;72 8787876 Generation and characterization of variants of NWS/G70C influenza virus after in vitro passage in 4-amino-Neu5Ac2en and 4-guanidino-Neu5Ac2en. NWS/G70C virus (H1N9) was cultured in each drug by limiting-dilution passaging. 1996 Antimicrobial agents and chemotherapy Abstract IV G70C 4 8 8799206 Neurovirulence of influenza A virus. In the M gene, two specific amino acid substitutions in the M1 protein have been observed, Ala41-->Val and Thr139-->Ala, which correlate with increased virulence for mouse. 1996 Journal of neurovirology Abstract IV A41V;T139A 91;107 102;119 M;M1 7;60 8;62 8879138 Mutations in the hemagglutinin and matrix genes of a virulent influenza virus variant, A/FM/1/47-MA, control different stages in pathogenesis. Sequence analysis indicated that the unmapped mutation in the control of FM-MA virulence is either the K482-->R substitution in the PB2 protein or the D538-->G substitution in the PB1 protein. 1996 Virus research Abstract IV K482R;D538G 103;151 111;159 PB1;PB2 180;132 183;135 8918554 Mutation in the influenza virus neuraminidase gene resulting in decreased sensitivity to the neuraminidase inhibitor 4-guanidino-Neu5Ac2en leads to instability of the enzyme. We previously isolated a variant of the influenza virus NWS/G70C, with a decreased sensitivity to the neuraminidase-specific inhibitor 4-guanidino-Neu5Ac2en in vitro, which has a mutation in one of the conserved residues of the neuraminidase Glu 119 to Gly. 1996 Virology Abstract IV G70C;E119G 60;242 64;256 NA;NA 102;228 115;241 8941323 Characterization of a hemagglutinin-specific inhibitor of influenza A virus. The resistant virus isolated contained a phenylalanine to serine change at amino acid 110 of the HA2 subunit. 1996 Virology Abstract IV F110S 41 89 HA 97 99 8995671 The CD4-independent tropism of human immunodeficiency virus type 2 involves several regions of the envelope protein and correlates with a reduced activation threshold for envelope-mediated fusion. Mutations located immediately upstream of a proposed coiled coil domain in the transmembrane protein (A526T or I528M) and flanking the base of the V4 loop (L378F and K403R) are crucial for the CD4-independent phenotype. 1997 Journal of virology Abstract IV A526T;I528M;L378F;K403R 102;111;156;166 107;116;161;171 8995671 The CD4-independent tropism of human immunodeficiency virus type 2 involves several regions of the envelope protein and correlates with a reduced activation threshold for envelope-mediated fusion. Of several mutations conferring a positive charge in V1, V2, and V3, only the change in V3 (Q310K) helped to enhance the CD4-independent phenotype but could not mediate it on its own. 1997 Journal of virology Abstract IV Q310K 92 97 9049394 Role of GTPase activity of murine Mx1 protein in nuclear localization and anti-influenza virus activity. Mutant S50I, which had no GTP-binding or GTPase activities, formed linear structures in nuclei and lacked anti-viral activity, while C71S appeared diffuse in nuclei as minute dots without granules, but retained the inhibitory activity against influenza virus growth. 1995 The Journal of general virology Abstract IV C71S;S50I 133;7 137;11 9049394 Role of GTPase activity of murine Mx1 protein in nuclear localization and anti-influenza virus activity. Wild-type Mx1 and two mutant Mx1 proteins, each carrying a single mutation either in the GTP-binding motif (S50I) or in the self-assembly motif (C71S), were expressed in MDCK cells. 1995 The Journal of general virology Abstract IV C71S;S50I 145;108 149;112 9060610 Dominant-negative mutants of human MxA protein: domains in the carboxy-terminal moiety are important for oligomerization and antiviral activity. Mutant T103A with threonine at position 103 replaced by alanine had lost both GTPase and antiviral activities. 1997 Journal of virology Abstract IV T103A;T103A 7;18 12;63 9060610 Dominant-negative mutants of human MxA protein: domains in the carboxy-terminal moiety are important for oligomerization and antiviral activity. T103A exhibited a dominant-interfering effect on the antiviral activity of wild-type MxA rendering MxA-expressing cells susceptible to infection with influenza A virus, Thogoto virus, and vesicular stomatitis virus. 1997 Journal of virology Abstract IV T103A 0 5 9060610 Dominant-negative mutants of human MxA protein: domains in the carboxy-terminal moiety are important for oligomerization and antiviral activity. To determine which sequences are critical for the dominant-negative effect of T103A, we expressed truncated forms of T103A together with wild-type protein. 1997 Journal of virology Abstract IV T103A;T103A 78;117 83;122 9060611 Preferential selection of receptor-binding variants of influenza virus hemagglutinin by the neutralizing antibody repertoire of transgenic mice expressing a human immunoglobulin mu minigene. The residue changes in variant virus V-21.2 (HA1 135 G-->R, 225 G-->D) abrogated neutralization by each of the MAbs; nevertheless V-21.2 was recognized by its own selecting MAb in enzyme-linked immunosorbent assay and therefore qualified as an adsorptive mutant rather than an antigenic variant. 1997 Journal of virology Abstract IV G135R;G225D 49;60 58;69 HA1 45 48 9060710 Differences in sialic acid-galactose linkages in the chicken egg amnion and allantois influence human influenza virus receptor specificity and variant selection. This change in receptor specificity was accompanied by the appearance of variants in the population with Leu-to-Gln mutations at position 226 in their HA. 1997 Journal of virology Abstract IV L226Q 105 141 HA 151 153 9094607 Catalytic and framework mutations in the neuraminidase active site of influenza viruses that are resistant to 4-guanidino-Neu5Ac2en. The resistance of the mutant stems from replacement of one of three invariant arginines (Arg 292-->Lys) that are conserved among all viral and bacterial NAs and participate in the conformational change of sialic acid moiety necessary for substrate catalysis. 1997 Journal of virology Abstract IV R292K 89 102 153 156 9123857 Hemagglutinin specificity and neuraminidase coding capacity of neuraminidase-deficient influenza viruses. The HA-coding segments of parental H1N9 and mutant NWSc-Mvi predict a change of Pro to His at residue 227 (H3 numbering), close to the receptor-binding site of H3 HA, compared to the HA of an H1N2 reassortant that contains the NWS/33 HA gene. 1997 Virology Abstract IV P227H 80 105 HA;HA;HA;HA 4;163;183;234 6;165;185;236 9144179 The active oligomeric state of the minimalistic influenza virus M2 ion channel is a tetramer. This was done by studying the currents of oocytes that expressed mixtures of the wild-type M2 protein (epitope tagged) and the mutant protein M2-V27S, which is resistant to the inhibitor amantadine. 1997 Proc Natl Acad Sci U S A Abstract IV V27S 145 149 M2;M2 91;142 93;144 9144226 A nontoxic mutant of cholera toxin elicits Th2-type responses for enhanced mucosal immunity. Both S61F and native CT enhanced the induction of ovalbumin-specific CD4(+) T cells in lung and splenic tissues, and these T cells produced a Th2-type cytokine pattern of interleukin 4 (IL-4), IL-5, IL-6, and IL-10 as determined by analysis of secreted proteins and by quantitation of cytokine-specific mRNA. 1997 Proc Natl Acad Sci U S A Abstract IV S61F 5 9 9144226 A nontoxic mutant of cholera toxin elicits Th2-type responses for enhanced mucosal immunity. Further, high protein-specific IgA antibody responses were observed in nasal and vaginal washes, saliva, and fecal extracts as well as increased numbers of IgG and IgA antibody forming cells in cervical lymph nodes and lung tissues of mice intranasally immunized with these proteins and S61F or native CT, but not with recombinant CT-B or protein alone. 1997 Proc Natl Acad Sci U S A Abstract IV S61F 287 291 9144226 A nontoxic mutant of cholera toxin elicits Th2-type responses for enhanced mucosal immunity. Mice immunized with these proteins plus S61F showed high serum titers of protein-specific IgG and IgA antibodies that were comparable to those induced by native CT. 1997 Proc Natl Acad Sci U S A Abstract IV S61F 40 44 9144226 A nontoxic mutant of cholera toxin elicits Th2-type responses for enhanced mucosal immunity. Mice were intranasally immunized with ovalbumin, tetanus toxoid, or influenza virus either alone or together with mutant CT S61F, native CT, or recombinant CT-B. 1997 Proc Natl Acad Sci U S A Abstract IV S61F 124 128 9144226 A nontoxic mutant of cholera toxin elicits Th2-type responses for enhanced mucosal immunity. The mutant CT was made by substitution of serine with phenylalanine at position 61 of the A subunit (S61F), which resulted in loss of ADP ribosyltransferase activity and toxicity. 1997 Proc Natl Acad Sci U S A Abstract IV S61F;S61F 101;42 105;82 9144226 A nontoxic mutant of cholera toxin elicits Th2-type responses for enhanced mucosal immunity. These results have shown that mutant CT S61F is an effective mucosal adjuvant when administrated intranasally and induces mucosal and systemic antibody responses which are mediated by CD4(+) Th2-type cells. 1997 Proc Natl Acad Sci U S A Abstract IV S61F 40 44 9150402 The membrane topology of the fusion peptide region of influenza hemagglutinin determined by spin-labeling EPR. Through site-directed mutagenesis, eight cysteine (Cys) mutants in the fusion peptide region of HA2 (A5C, I6C, A7C, G8C, I10C, N12C, G13C, W14C) were generated and modified with a nitroxide spin label. 1997 Journal of molecular biology Abstract IV I6C;N12C;W14C;A5C;A7C;G8C;I10C;G13C 106;127;139;101;111;116;121;133 109;131;143;104;114;119;125;137 HA 96 98 9157085 Functional significance of varied quantitative and qualitative expression of HLA-A2.1 antigens in determining the susceptibility of cells to cytotoxic T lymphocytes. This difference results in an amino acid substitution from tyrosine to cysteine at position 99 of HLA-A2.1 heavy chains. 1996 Human immunology Abstract IV Y99C 59 94 9299618 A single sequence change destabilizes the influenza virus neuraminidase tetramer. A single change (E119G) in the influenza A virus N9 neuraminidase (NA) results in resistance of the enzyme to the NA inhibitor 4-Guanidino-Neu5Ac2en (4-GuDANA). 1997 Virology Abstract IV E119G 17 22 N9;NA;NA;NA 49;67;114;52 51;69;116;65 9299618 A single sequence change destabilizes the influenza virus neuraminidase tetramer. It is suggested that the E119G alteration in the 4-GuDANA-resistant NA leads to the abrogation of this interaction and thus to the instability of the NA tetramers. 1997 Virology Abstract IV E119G 25 30 NA;NA 68;150 70;152 9299618 A single sequence change destabilizes the influenza virus neuraminidase tetramer. These small crystals were of sufficient quality to yield X-ray crystallographic data which confirmed the E119G change and demonstrated the presence of electron density representing either a strong structural-water molecule or an anionic species in place of the glutamate carboxylate. 1997 Virology Abstract IV E119G 105 110 9334200 Tyrosine-dependent basolateral sorting signals are distinct from tyrosine-dependent internalization signals. Converting cysteine 543 to tyrosine in the influenza virus hemagglutinin (HA) introduces both a basolateral sorting signal and an internalization signal into the HA cytoplasmic domain. 1997 The Journal of biological chemistry Abstract IV C543Y 11 35 HA;HA;HA 74;162;59 76;164;72 9334200 Tyrosine-dependent basolateral sorting signals are distinct from tyrosine-dependent internalization signals. For HA C543Y, the same sequence positions were important for both basolateral sorting and internalization, but the two functions responded differently to individual amino acid replacements, indicating that they were distinct. 1997 The Journal of biological chemistry Abstract IV C543Y 7 12 HA 4 6 9334200 Tyrosine-dependent basolateral sorting signals are distinct from tyrosine-dependent internalization signals. To test this hypothesis, second-site mutations were introduced into HA C543Y or HA+8 to determine if the internalization and basolateral sorting functions can be separated. 1997 The Journal of biological chemistry Abstract IV C543Y 71 76 HA;HA 68;80 70;82 9499107 Mutations in a conserved residue in the influenza virus neuraminidase active site decreases sensitivity to Neu5Ac2en-derived inhibitors. NWS/G70C variants generated in vitro, with decreased sensitivity to 6-carboxamide, contained hemagglutinin (HA) and/or NA mutations. 1998 Journal of virology Abstract IV G70C 4 8 HA;HA;NA 108;93;119 110;106;121 9559786 Generation and characterization of a mutant of influenza A virus selected with the neuraminidase inhibitor BCX-140. One is a change in HA1 of Ala-133 to Thr, a residue close to the binding site, while the other change was Arg-132 of HA1 to Gln, which in HA1 of serotype H3 is a sialic acid contact (Asn-137). 1998 Antimicrobial agents and chemotherapy Abstract IV A133T 26 40 HA1;HA1;HA1 19;117;138 22;120;141 9601502 Postreassortment changes in influenza A virus hemagglutinin restoring HA-NA functional match. One substitution, N248D in HA1, is the same in two independently selected nonaggregating variants. 1998 Virology Abstract IV N248D 18 23 HA1 27 30 9655825 Drug design against a shifting target: a structural basis for resistance to inhibitors in a variant of influenza virus neuraminidase. CONCLUSIONS: The Arg292-->Lys variant of influenza neuraminidase affects the binding of substrate by modification of the interaction with the substrate carboxylate. 1998 Structure (London, England Abstract IV R292K 17 29 51 64 9655825 Drug design against a shifting target: a structural basis for resistance to inhibitors in a variant of influenza virus neuraminidase. Inhibitors that have replacements for the glycerol at position 6 are further affected in the Arg292-->Lys variant because of structural changes in the binding site that apparently raise the energy barrier for the conformational change in the enzyme required to accommodate such inhibitors. 1998 Structure (London, England Abstract IV R292K 93 105 9655825 Drug design against a shifting target: a structural basis for resistance to inhibitors in a variant of influenza virus neuraminidase. RESULTS: The neuraminidase variant Arg292-->Lys is modified in one of three arginine residues that encircle the carboxylate group of the substrate. 1998 Structure (London, England Abstract IV R292K 35 47 13 26 9656997 The interaction of neuraminidase and hemagglutinin mutations in influenza virus in resistance to 4-guanidino-Neu5Ac2en. This variant has been found to also harbor a hemagglutinin (HA) mutation in the receptor binding site, Ser 186 to Phe. 1998 Virology Abstract IV S186F 103 117 HA;HA 60;45 62;58 9656997 The interaction of neuraminidase and hemagglutinin mutations in influenza virus in resistance to 4-guanidino-Neu5Ac2en. We have previously described a 4-guanidino-Neu5Ac2en (zanamivir)-resistant neuraminidase (NA) variant G70C4-G, with an active site mutation Glu 119 to Gly. 1998 Virology Abstract IV E119G 140 154 NA;NA 90;75 92;88 9683567 Substrate, inhibitor, or antibody stabilizes the Glu 119 Gly mutant influenza virus neuraminidase. This variant, which has a mutation in the active site, Glu 119 Gly (E119G), has the same specific activity as the wild-type neuraminidase (NA), but is inherently unstable, as measured by loss of both enzyme activity and NC10 monoclonal antibody reactivity. 1998 Virology Abstract IV E119G;E119G 68;55 73;66 NA;NA 139;124 141;137 9692956 Critical interactions in binding antibody NC41 to influenza N9 neuraminidase: amino acid contacts on the antibody heavy chain. Asp97 forms a salt link with NA critical contact Lys434; of the four mutants, D97K shows the largest reduction in binding to NA. 1998 Biochemistry Abstract IV D97K 78 82 NA;NA 29;125 31;127 9692956 Critical interactions in binding antibody NC41 to influenza N9 neuraminidase: amino acid contacts on the antibody heavy chain. Association constants (Ka) for wild-type and mutant scFvs are as follows: wild type, 2 x 10(7) M-1; Asn31-->Gln, 2 x 10(7) M-1; Glu96-->Asp, 1 x 10(7) M-1; Asp97-->Lys, 6 x 10(6) M-1; and Asn98-->Gln, 8 x 10(6) M-1. 1998 Biochemistry Abstract IV N31Q;E96D;D97K;N98Q 100;128;156;188 111;139;167;199 9692956 Critical interactions in binding antibody NC41 to influenza N9 neuraminidase: amino acid contacts on the antibody heavy chain. Mutant N98Q also shows reduced binding, most likely through the loss of interaction with NA residue Thr401. 1998 Biochemistry Abstract IV N98Q 7 11 89 91 9692956 Critical interactions in binding antibody NC41 to influenza N9 neuraminidase: amino acid contacts on the antibody heavy chain. NC41 residue Glu96 interacts with NA critical contact Ser368, yet E96D showed only a 2-fold reduction in binding to NA, apparently because the H bond can still form. 1998 Biochemistry Abstract IV E96D 66 70 NA;NA 34;116 36;118 9692956 Critical interactions in binding antibody NC41 to influenza N9 neuraminidase: amino acid contacts on the antibody heavy chain. Substitution N31Q had no effect on Ka. 1998 Biochemistry Abstract IV N31Q 13 17 9696865 The role of influenza A virus hemagglutinin residues 226 and 228 in receptor specificity and host range restriction. Our results showed that the Ser-to-Gly mutation at position 228, in addition to the Leu-to-Gln mutation at position 226 of the HA of the H3 subtype, is critical for human virus HA to support virus replication in duck intestine. 1998 Journal of virology Abstract IV S228G;L226Q 28;84 63;119 HA;HA 127;177 129;179 9754551 Efficient induction of cytotoxic CD8+ T cells against exogenous proteins: establishment and characterization of a T cell line specific for the membrane protein ActA of Listeria monocytogenes. To overcome the potential problem of presentation of the immunodominant epitope LL091-99 by H-2Kd, a variant LLO92A was established in which Tyr 92 was replaced by Ala. 1998 European journal of immunology Abstract IV Y92A 141 167 9780244 Evidence for zanamivir resistance in an immunocompromised child infected with influenza B virus. A hemagglutinin mutation (198 Thr-->Ile) reduced the virus affinity for receptors found on susceptible human cells. 1998 The Journal of infectious diseases Abstract IV T198I 26 39 HA 2 15 9780244 Evidence for zanamivir resistance in an immunocompromised child infected with influenza B virus. A mutation in the neuraminidase active site (152 Arg-->Lys) led to a 1000-fold reduction in the enzyme sensitivity to zanamivir. 1998 The Journal of infectious diseases Abstract IV R152K 45 58 18 31 9796066 Mucosal immunoadjuvant activity of recombinant Escherichia coli heat-labile enterotoxin and its B subunit: induction of systemic IgG and secretory IgA responses in mice by intranasal immunization with influenza virus surface antigen. However, supplementation of the antigen with E112K or rLTB resulted in a substantial stimulation of the serum IgG level and in induction of a strong S-IgA response in the nasal cavity. 1998 Vaccine Abstract IV E112K 45 50 9796066 Mucosal immunoadjuvant activity of recombinant Escherichia coli heat-labile enterotoxin and its B subunit: induction of systemic IgG and secretory IgA responses in mice by intranasal immunization with influenza virus surface antigen. Mice were immunized intranasally (i.n.) with influenza virus subunit antigen, consisting mostly of the isolated surface glycoprotein hemagglutinin (HA), supplemented with either recombinant LTB (rLTB), a nontoxic LT mutant (E112K, with a Glu112-->Lys substitution in the A subunit), or LT holotoxin, and the induction of systemic IgG and local S-IgA responses was evaluated by direct enzyme-linked immunosorbent assay (ELISA). 1998 Vaccine Abstract IV E112K;E112K 224;238 229;250 HA;HA 148;133 150;146 9796066 Mucosal immunoadjuvant activity of recombinant Escherichia coli heat-labile enterotoxin and its B subunit: induction of systemic IgG and secretory IgA responses in mice by intranasal immunization with influenza virus surface antigen. The adjuvant activity of E112K or rLTB under these conditions was essentially the same as that of the LT holotoxin. 1998 Vaccine Abstract IV E112K 25 30 9811753 The vaccinia virus 14-kilodalton (A27L) fusion protein forms a triple coiled-coil structure and interacts with the 21-kilodalton (A17L) virus membrane protein through a C-terminal alpha-helix. Binding assays with purified proteins expressed in Escherichia coli and cytoplasmic extracts from cells infected with a virus that does not produce the 14-kDa protein during infection (VVindA27L) show that the 21-kDa protein (encoded by the A17L gene) is the specific viral binding partner and identify the putative Leu zipper, the predicted third alpha-helix on the C terminus of the 14-kDa protein, as the region involved in protein binding. 1998 Journal of virology Abstract IV A17L 241 245 9811753 The vaccinia virus 14-kilodalton (A27L) fusion protein forms a triple coiled-coil structure and interacts with the 21-kilodalton (A17L) virus membrane protein through a C-terminal alpha-helix. The vaccinia virus 14-kDa protein (encoded by the A27L gene) plays an important role in the biology of the virus, acting in virus-to-cell and cell-to-cell fusions. 1998 Journal of virology Abstract IV A27L 50 54 9835519 Characterization of human influenza virus variants selected in vitro in the presence of the neuraminidase inhibitor GS 4071. After eight passages, variants containing two amino acid substitutions in the hemagglutinin (A28T in HA1 and R124M in HA2) but no changes in the neuraminidase were isolated. 1998 Antimicrobial agents and chemotherapy Abstract IV A28T;R124M 93;109 97;114 HA;HA1;HA;NA 118;101;78;145 120;104;91;158 9835519 Characterization of human influenza virus variants selected in vitro in the presence of the neuraminidase inhibitor GS 4071. These results suggest that although the R292K neuraminidase mutation confers high-level resistance to GS 4071 in vitro, its effect on viral virulence is likely to render this mutation of limited clinical significance. 1998 Antimicrobial agents and chemotherapy Abstract IV R292K 40 45 46 59 9874196 Site-directed mutagenesis of catalytic residues of influenza virus neuraminidase as an aid to drug design. Based on the pH profile of neuraminidase activity of the D149E mutant protein, we conclude that Asp149 is not a proton donor, but is involved in stabilizing the transition state. 1998 European journal of biochemistry Abstract IV D149E 57 62 27 40 17055070 H5N1 Oseltamivir-resistance detection by real-time PCR using two high sensitivity labeled TaqMan probes. Eighteen percent of the children (N = 9/50) had neuraminidase mutations at Arg292Lys (N = 6/9) or Glu119Val (N = 2/9) or Asn294Ser (N = 1/9). 2007 Journal of virological methods Introduction IV R292K;E119V;N294S 76;100;124 85;109;133 49 62 17055070 H5N1 Oseltamivir-resistance detection by real-time PCR using two high sensitivity labeled TaqMan probes. It has recently been reported that Oseltamivir-resistant influenza A (H5N1) viruses with the H274Y mutation have been isolated from three patients. 2007 Journal of virological methods Introduction IV H274Y 93 98 17055070 H5N1 Oseltamivir-resistance detection by real-time PCR using two high sensitivity labeled TaqMan probes. The assay enables to identify the H274Y mutation from samples originated directly from infected tissue and plasma. 2007 Journal of virological methods Introduction IV H274Y 34 39 17055070 H5N1 Oseltamivir-resistance detection by real-time PCR using two high sensitivity labeled TaqMan probes. Volunteers experimentally infected with influenza A/Texas/36/91 (H1N1) virus and treated with oseltamivir have shown an H274Y substitution at the neuraminidase active site. 2007 Journal of virological methods Introduction IV H274Y 120 125 146 159 17922571 A single mutation in the PB1-F2 of H5N1 (HK/97) and 1918 influenza A viruses contributes to increased virulence. An alignment of the aa sequences of isolates from the Hong Kong 1997 H5N1 outbreak revealed that a mutation, N66S, was associated with high pathogenicity phenotype in mice. 2007 PLoS pathogens Introduction IV N66S 109 113 17922571 A single mutation in the PB1-F2 of H5N1 (HK/97) and 1918 influenza A viruses contributes to increased virulence. Using a recombinant A/WSN/33 virus with the PB1 segment of A/HK/156/97, we observed increased morbidity and mortality of mice infected with a virus that contained the N66S mutation. 2007 PLoS pathogens Introduction IV N66S 167 171 PB1 44 47 18248089 Interaction of polymerase subunit PB2 and NP with importin alpha1 is a determinant of host range of influenza A virus. Interestingly, the authors of this study hypothesized that PB2 mutation D701N which is also a host range determinant as pointed out above, may affect the binding of importin alpha5 to PB2. 2008 PLoS pathogens Introduction IV D701N 72 77 PB2;PB2 59;184 62;187 18248089 Interaction of polymerase subunit PB2 and NP with importin alpha1 is a determinant of host range of influenza A virus. PB2 mutation D701N has also been implicated in the adaptation of H5N1 viruses to mammalian hosts but other mutations may be involved, too, notably PB2 mutation E627K. 2008 PLoS pathogens Introduction IV D701N;E627K 13;160 18;165 PB2;PB2 0;147 3;150 18248089 Interaction of polymerase subunit PB2 and NP with importin alpha1 is a determinant of host range of influenza A virus. Thus, in a comparative study of the avian strain SC35 (H7N7) and its mouse-adapted variant SC35M we showed that adaptation to mice was the result of seven mutations in the polymerase proteins, six of which (L13P and S678N in PB1, D701N and S714R in PB2, K615N in PA, and N319K in NP) were responsible for enhanced polymerase activity in mammalian cells. 2008 PLoS pathogens Introduction IV L13P;S678N;D701N;S714R;K615N;N319K 207;216;230;240;254;271 211;221;235;245;259;276 NP;PA;PB1;PB2 280;263;225;249 282;265;228;252 18248089 Interaction of polymerase subunit PB2 and NP with importin alpha1 is a determinant of host range of influenza A virus. We show that adaptative mutations D701N and N319K improve binding of PB2 and NP, respectively, to importin alpha1 in mammalian, but not in avian cells. 2008 PLoS pathogens Introduction IV D701N;N319K 34;44 39;49 NP;PB2 77;69 79;72 18601954 Treatment of influenza A (H1N1) virus infections in mice and ferrets with cyanovirin-N. In this case the HA gene of A/New Caledonia/20/99 was genetically altered to contain an Asp225Gly mutation in the HA1 subunit. 2008 Antiviral research Introduction IV D225G 88 97 HA;HA1 17;114 19;117 18601954 Treatment of influenza A (H1N1) virus infections in mice and ferrets with cyanovirin-N. The Asp225Gly substitution is a mutation that effects the receptor binding site for the HA1 that appears to aid in virus adaptation to a new host as previously reported in the context of the 1918 pandemic influenza virus. 2008 Antiviral research Introduction IV D225G 4 13 HA1 88 91 18601954 Treatment of influenza A (H1N1) virus infections in mice and ferrets with cyanovirin-N. The HA gene of the mouse adapted recombinant virus was sequenced and found to contain no additional mutations other than the introduced Asp225Gly. 2008 Antiviral research Introduction IV D225G 136 145 HA 4 6 18601954 Treatment of influenza A (H1N1) virus infections in mice and ferrets with cyanovirin-N. We reported a 94A mutation and an Asp225Gly mutation that arose during adaptation of influenza A/New Caledonia/20/99 (H1N1) virus to mice (Smee et al., 2008). 2008 Antiviral research Introduction IV D225G 34 43 18769709 Host determinant residue lysine 627 lies on the surface of a discrete, folded domain of influenza virus polymerase PB2 subunit. Subsequently it was shown that the substitution D701N significantly affects the interaction of PB2 with importin alpha1 in mammalian but not avian cells. 2008 PLoS pathogens Introduction IV D701N 48 53 PB2 95 98 18769709 Host determinant residue lysine 627 lies on the surface of a discrete, folded domain of influenza virus polymerase PB2 subunit. The high resolution crystal structure of this domain from a human influenza A strain and of the K627E variant, shows that it has a novel fold with Lys/Glu627 exposed to the solvent. 2008 PLoS pathogens Introduction IV K627E 96 101 Influenza 60 75 19014974 Aurintricarboxylic acid inhibits influenza virus neuraminidase. We also found that ATA is equally effective in inhibiting the wild-type NA and the oseltamivir-resistant NA with a H274Y mutation (NAH274Y). 2009 Antiviral research Introduction IV H274Y 115 120 NA;NA;NA 72;105;131 74;107;133 19119420 Transmission of influenza virus in a mammalian host is increased by PB2 amino acids 627K or 627E/701N. A mechanism has recently been proposed to explain the contribution of D701N to improved growth of a mouse adapted avian-like H7N7 virus, SC35M, in mammalian cell culture: D701N appears to enhance the binding of PB2 to importin alpha1 and correspondingly increase PB2 levels in the nucleus in mammalian, but not avian, cells. 2009 PLoS pathogens Introduction IV D701N;D701N 70;171 75;176 PB2;PB2 211;263 214;266 19119420 Transmission of influenza virus in a mammalian host is increased by PB2 amino acids 627K or 627E/701N. A single passage in mice has been reported to be sufficient for an E627K variant to dominate the resultant H5N1 virus population. 2009 PLoS pathogens Introduction IV E627K 67 72 19119420 Transmission of influenza virus in a mammalian host is increased by PB2 amino acids 627K or 627E/701N. Furthermore, the mutation K627E decreases the transmission efficiency of both rPan99 and rVN1203 viruses. 2009 PLoS pathogens Introduction IV K627E 26 31 19119420 Transmission of influenza virus in a mammalian host is increased by PB2 amino acids 627K or 627E/701N. Our second hypothesis did prove correct in that combination of glutamic acid at 627 with an aspartic acid to asparagine change at position 701 rescues the phenotype of the 627E viruses: rPan99 virus with 627E+701N transmits with similar efficiency to the parental rPan99 virus, while the rVN1203 627E 701N virus transmits with higher efficiency than the wild-type strain. 2009 PLoS pathogens Introduction IV D701N 92 142 19119420 Transmission of influenza virus in a mammalian host is increased by PB2 amino acids 627K or 627E/701N. Similarly to E627K, a change of PB2 amino acid 701 from aspartic acid to asparagine has been implicated in expanding the host range of avian (or avian-like) H5N1 and H7N7 subtype viruses to include mice and humans. 2009 PLoS pathogens Introduction IV E627K;D701N 13;47 18;83 PB2 32 35 19119420 Transmission of influenza virus in a mammalian host is increased by PB2 amino acids 627K or 627E/701N. This finding has also been confirmed in the context of infected cell cultures: the growth of A/Viet Nam/1204/04 virus (VN1204; H5N1) in mammalian cell lines is improved at 33 C, but not 37 C or 41 C, by the single amino acid change, PB2 E627K. 2009 PLoS pathogens Introduction IV E627K 237 242 PB2 233 236 19249874 Recognition of mannosylated ligands and influenza A virus by human surfactant protein D: contributions of an extended site and residue 343. Our experiments demonstrate greatly enhanced anti-viral activity of R343V associated with utilization of a modified carbohydrate binding site for alpha1-2 linked mannoses, which are commonly displayed at the termini of asparagine-linked viral glycans. 2009 Biochemistry Introduction IV R343V 68 73 19249874 Recognition of mannosylated ligands and influenza A virus by human surfactant protein D: contributions of an extended site and residue 343. The ligand binding surfaces of the serum conglutinin and CL-43 diverge from SP-D at several locations, but are most notably characterized by insertions near the ligand binding site and by the substitution of valine or isoleucine for arginine at position 343. 2009 Biochemistry Introduction IV R343I 218 257 19331731 Oseltamivir-resistant influenza virus A (H1N1), Europe, 2007-08 season. In late January 2008, we reported an unexpected high level and unexpected spread of oseltamivir-resistant influenza viruses A (H1N1) (ORVs) in Europe caused by a H275Y (H274Y in N2 numbering) amino acid substitution in the neuraminidase (NA) of these viruses. 2009 Emerging infectious diseases Introduction IV H275Y;H274Y 162;169 167;174 NA;NA 238;223 240;236 19394063 The origin and global emergence of adamantane resistant A/H3N2 influenza viruses. In particular, it has been proposed that the increased global frequency of the S31N mutation in the M2 protein resulted from a chance hitchhiking event involving linkage to advantageous mutations in other segments following a major 4 + 4 reassortment event, including mutations in HA1 at positions 193 and 225 near the receptor-binding site. 2009 Virology Introduction IV S31N 79 83 HA1;M2 281;100 284;102 19394063 The origin and global emergence of adamantane resistant A/H3N2 influenza viruses. In particular, to understand the global emergence of the S31N adamantane resistance mutation within the context of antigenic evolution, we conducted a phylogenetic analysis of influenza virus sequence data for the HA, M1/2, and NA segments that was obtained through ten years of sampling in both subtropical and temperate regions. 2009 Virology Introduction IV S31N 57 61 HA;M1;NA 214;218;228 216;220;230 19394063 The origin and global emergence of adamantane resistant A/H3N2 influenza viruses. In the vast majority of cases, the basis for resistance is a single Ser to Asn amino acid replacement (S31N) in the matrix M2 ion channel, which interferes with the drug's ability to block M2 ion channel activity and viral replication. 2009 Virology Introduction IV S31N 103 107 M2;M2;M 123;189;116 125;191;122 19394063 The origin and global emergence of adamantane resistant A/H3N2 influenza viruses. Recently, the S31N mutation was detected in 100% of influenza viruses sampled from multiple Asian countries, although sample sizes were relatively small. 2009 Virology Introduction IV S31N 14 18 19394063 The origin and global emergence of adamantane resistant A/H3N2 influenza viruses. This reassortment event, which most likely occurred in early 2005, generated a new global lineage of adamantane resistant A/H3N2 viruses, termed the 'N-lineage', characterized by an antigenically A/Wisconsin/67/2005-like HA and an M2 protein bearing the S31N replacement. 2009 Virology Introduction IV S31N 254 258 HA;M2 221;231 223;233 19857993 Evaluation of a rapid molecular algorithm for detection of pandemic influenza A (H1N1) 2009 virus and screening for a key oseltamivir resistance (H275Y) substitution in neuraminidase. A single nucleotide mutation (cytosine to thymine) at position 823 of the pandemic neuraminidase gene can result in a histidine to tyrosine substitution at position 275. 2010 Journal of clinical virology Introduction IV H275Y 118 168 83 96 19857993 Evaluation of a rapid molecular algorithm for detection of pandemic influenza A (H1N1) 2009 virus and screening for a key oseltamivir resistance (H275Y) substitution in neuraminidase. We have developed and evaluated the performance of a novel RT-PCR assay targeting both the hemagglutinin and neuraminidase genes of the pandemic influenza A/H1N1 virus and a discrimination assay for detection of the H275Y oseltamivir resistance mutation in neuraminidase. 2010 Journal of clinical virology Introduction IV H275Y 216 221 HA;NA;NA 91;109;257 104;122;270 19893749 Inhibition of neuraminidase inhibitor-resistant influenza virus by DAS181, a novel sialidase fusion protein. However, because of the ease of transmission and significant pathogenicity in high risk patients, it is now concluded that the current oseltamivir-resistant H274Y mutant likely possesses the same degree of virulence as the wild-type strain. 2009 PloS one Introduction IV H274Y 157 162 19893749 Inhibition of neuraminidase inhibitor-resistant influenza virus by DAS181, a novel sialidase fusion protein. Interestingly, this H274Y mutation was once believed to confer reduced viral fitness. 2009 PloS one Introduction IV H274Y 20 25 19893749 Inhibition of neuraminidase inhibitor-resistant influenza virus by DAS181, a novel sialidase fusion protein. The frequency of isolates with the H274Y mutation has increased with each flu season, including in countries that do not regularly prescribe oseltamivir. 2009 PloS one Introduction IV H274Y 35 40 19893749 Inhibition of neuraminidase inhibitor-resistant influenza virus by DAS181, a novel sialidase fusion protein. While neuraminidase inhibitor (NAI)-resistance has been observed to occur via different molecular mechanisms, the dominating change conferring oseltamivir-resistance in the current seasonal IFV is a mutation in the neuraminidase (NA) gene, H274Y. 2009 PloS one Introduction IV H274Y 240 245 NA;NAI;NA;NA 230;31;6;215 232;34;19;228 19905033 Design and pharmacological characterization of inhibitors of amantadine-resistant mutants of the M2 ion channel of influenza A virus. Although the S31N mutation was observed in more then 90% of influenza A cases in certain years, other amantadine insensitive phenotypes like L26F and V27A were isolated from influenza A patients with the emerging frequencies of 8-67%. 2009 Biochemistry Introduction IV S31N;L26F;V27A 13;141;150 17;145;154 19905033 Design and pharmacological characterization of inhibitors of amantadine-resistant mutants of the M2 ion channel of influenza A virus. Naturally occurring point mutations of the pore lining residues located outside of the H37xxxW41 motif, such as L26F, V27A, A30T, S31N and G34E result in the formation of amantadine-insensitive influenza A virus phenotypes. 2009 Biochemistry Introduction IV L26F;V27A;A30T;S31N;G34E 112;118;124;130;139 116;122;128;134;143 19905033 Design and pharmacological characterization of inhibitors of amantadine-resistant mutants of the M2 ion channel of influenza A virus. The current study shows that a novel compound, spiran amine 8, is a potent inhibitor of the L26F and V27A amantadine resistant mutants of the A/M2 protein. 2009 Biochemistry Introduction IV L26F;V27A 92;101 96;105 M2 144 146 19905033 Design and pharmacological characterization of inhibitors of amantadine-resistant mutants of the M2 ion channel of influenza A virus. Thus there is a great need for novel anti-influenza drugs that target the most common amantadine resistant phenotypes, S31N, V27A and L26F. 2009 Biochemistry Introduction IV S31N;V27A;L26F 119;125;134 123;129;138 19905033 Design and pharmacological characterization of inhibitors of amantadine-resistant mutants of the M2 ion channel of influenza A virus. We found a simple amino derivative of BL-1743, spiro[5.5]undecan-3-amine (spiran amine 8, Table 1) to be effective not only for inhibition of the wt A/M2 channel, but also for inhibition of two widely occurring amantadine resistant mutants, L26F and V27A. 2009 Biochemistry Introduction IV L26F;V27A 241;250 245;254 M2 151 153 19934602 A Serine12Stop mutation in PB1-F2 of the 2009 pandemic (H1N1) influenza A: a possible reason for its enhanced transmission and pathogenicity to humans. The N66S mutation contributed to the high pathogenicity of the 1918 pandemic A/Brevig Mission/18 virus, and its replacement (S66N) attenuated this virus in mice. 2009 Journal of veterinary science Introduction IV N66S;S66N 4;125 8;129 19946717 Readaptation of a low-virulence influenza H9 escape mutant in mice: the role of changes in hemagglutinin as revealed by site-specific mutagenesis. The assay of mouse mortality revealed that the extent of the decrease in virulence in the reverse-genetic H9N1 single-gene reassortant carrying the escape mutation T198N (designated as rg-PR8-HA-m8C4) was of the same magnitude as the decrease observed for the original escape mutant m8C4 (Table 1). 2010 Archives of virology Introduction IV T198N 164 169 HA 192 194 19946717 Readaptation of a low-virulence influenza H9 escape mutant in mice: the role of changes in hemagglutinin as revealed by site-specific mutagenesis. The decrease in the affinity to 2'-6' sialyl substrates produced by the mutation T198N did not induce a decrease in virus accumulation in NT, although it did correlate with a lower virus accumulation in mouse lungs (Table 2). 2010 Archives of virology Introduction IV T198N 81 86 19946717 Readaptation of a low-virulence influenza H9 escape mutant in mice: the role of changes in hemagglutinin as revealed by site-specific mutagenesis. The loss of virulence associated with the mutation T198N and the restoration of virulence associated with the mutation N198D as measured in log10(EID50/MLD50) were on the order of 3 log10. 2010 Archives of virology Introduction IV T198N;N198D 51;119 56;124 19946717 Readaptation of a low-virulence influenza H9 escape mutant in mice: the role of changes in hemagglutinin as revealed by site-specific mutagenesis. The low-virulence mutants had an amino acid change in the HA, T198N, leading to the acquisition of a potential glycosylation site, whereas the readaptation was associated with the loss of the glycosylation site as a result of N198S or N198D reverse amino acid changes. 2010 Archives of virology Introduction IV T198N;N198S;N198D 62;226;235 67;231;240 HA 58 60 19946717 Readaptation of a low-virulence influenza H9 escape mutant in mice: the role of changes in hemagglutinin as revealed by site-specific mutagenesis. The point mutations encoding substitutions in the HA of a low-virulence escape mutant (T198N) or in a readapted variant (N198D) were inserted by using a Quickchange site-directed mutagenesis kit (Stratagene), and the H9N1 reassortant viruses were generated by DNA transfection of 293T cells. 2010 Archives of virology Introduction IV T198N;N198D 87;121 92;126 HA 50 52 19958488 Prediction of avian influenza A binding preference to human receptor using conformational analysis of receptor bound to hemagglutinin. A Kan-1 derived strain with further HA mutations L129V and A134V is considered a quasi-species which exhibited higher selectivity toward human cell type receptor. 2009 BMC genomics Introduction IV L129V;A134V 49;59 54;64 HA 36 38 19958488 Prediction of avian influenza A binding preference to human receptor using conformational analysis of receptor bound to hemagglutinin. A Sing-97 descendent that infected a human in 2004, A/Thailand/1(KAN-1)/2004 (abbreviated as Kan-1), has a single mutation in the HA binding pocket (S129L). 2009 BMC genomics Introduction IV S129L 149 154 HA 130 132 19958488 Prediction of avian influenza A binding preference to human receptor using conformational analysis of receptor bound to hemagglutinin. The H5 HA X-ray structure from A/Duck/Singapore/3/97 (abbreviated as Sing-97) shows preferential binding to Siaalpha(2,3)Gal receptor, owing to Q222L and G224S mutations. 2009 BMC genomics Introduction IV Q222L;G224S 144;154 149;159 HA 7 9 19995550 X-ray structures of NS1 effector domain mutants. Here, we report the crystal structures of the W187Y and W187A mutant NS1A-EDs (residue 79-205) from influenza A/Udorn/72(A/Udorn) virus strain. 2010 Archives of biochemistry and biophysics Introduction IV W187Y;W187A 46;56 51;61 NS 69 71 19995550 X-ray structures of NS1 effector domain mutants. The W187Y mutant shows almost wild type binding affinity toward CPSF30, and could serve as a drug target for the development of new antiviral drugs against influenza A virus. 2010 Archives of biochemistry and biophysics Introduction IV W187Y 4 9 20237225 Mutations in the NS1 C-terminal tail do not enhance replication or virulence of the 2009 pandemic H1N1 influenza A virus. 1, lower box: W220R, T225A and S228T). 2010 The Journal of general virology Introduction IV W220R;T225A;S228T 14;21;31 19;26;36 20237225 Mutations in the NS1 C-terminal tail do not enhance replication or virulence of the 2009 pandemic H1N1 influenza A virus. 2(d and e) both the rCal/09 STOPmut and E217K viruses grew with similar kinetics to WT during multicycle growth analyses in both human and swine cell-types (input m.o.i. 2010 The Journal of general virology Introduction IV E217K 40 45 20237225 Mutations in the NS1 C-terminal tail do not enhance replication or virulence of the 2009 pandemic H1N1 influenza A virus. All viruses reached similar titres in the trachea and lungs; however, the rCal/09 E217K virus grew to titres approximately 10-fold lower than both WT and STOPmut viruses in nasal turbinates (Table 1, lower panel). 2010 The Journal of general virology Introduction IV E217K 82 87 20237225 Mutations in the NS1 C-terminal tail do not enhance replication or virulence of the 2009 pandemic H1N1 influenza A virus. Although human influenza A virus NS1 proteins do not generally have a consensus Crk/CrkL-binding motif, we sought to assess the impact of the E217K aa substitution as it has already arisen naturally in a human 2009 H1N1 virus isolate (A/Wisconsin/629-D00022/09), and Crk/CrkL binding is a feature of both highly pathogenic avian influenza A viruses and the devastating 1918 pandemic virus. 2010 The Journal of general virology Introduction IV E217K 142 147 NS1 33 36 20237225 Mutations in the NS1 C-terminal tail do not enhance replication or virulence of the 2009 pandemic H1N1 influenza A virus. Analysis of precipitated proteins by Western blot revealed that endogenous CrkL was only co-precipitated with the Cal/09-NS1 E217K mutant, and not with WT Cal/09 NS1. 2010 The Journal of general virology Introduction IV E217K 125 130 NS1;NS1 121;162 124;165 20237225 Mutations in the NS1 C-terminal tail do not enhance replication or virulence of the 2009 pandemic H1N1 influenza A virus. As described previously (, a plasmid-based reverse genetics system was used to generate recombinant mutant Cal/09 viruses expressing NS1 with either a C-terminal extension of 11 aa, or an E217K aa substitution. 2010 The Journal of general virology Introduction IV E217K 188 193 NS1 133 136 20237225 Mutations in the NS1 C-terminal tail do not enhance replication or virulence of the 2009 pandemic H1N1 influenza A virus. Finally, we studied replication of the rCal/09 WT, rCal/09 STOPmut and rCal/09 E217K viruses in a ferret model. 2010 The Journal of general virology Introduction IV E217K 79 84 20237225 Mutations in the NS1 C-terminal tail do not enhance replication or virulence of the 2009 pandemic H1N1 influenza A virus. Given that human seasonal influenza A virus NS1 proteins are generally 230 aa in length, and many have lysine at position 217 [albeit commonly without Crk/CrkL binding due to substitution of threonine for proline at 215. 2010 The Journal of general virology Introduction IV P215T 191 219 20237225 Mutations in the NS1 C-terminal tail do not enhance replication or virulence of the 2009 pandemic H1N1 influenza A virus. Glutathione S-transferase (GST) fused to either WT Cal/09 NS1 or Cal/09 NS1-E217K was expressed in human embryonic kidney (293T) cells, and protein lysates were subjected to GST pull-down assays. 2010 The Journal of general virology Introduction IV E217K 76 81 NS1;NS1 58;72 61;75 20237225 Mutations in the NS1 C-terminal tail do not enhance replication or virulence of the 2009 pandemic H1N1 influenza A virus. However, the rCal/09 STOPmut virus seemed to be cleared marginally faster than both the WT and E217K viruses, as evidenced by viral titres on day 7 (Table 1, upper panel). 2010 The Journal of general virology Introduction IV E217K 95 100 20237225 Mutations in the NS1 C-terminal tail do not enhance replication or virulence of the 2009 pandemic H1N1 influenza A virus. However, we confirmed that the single E217K aa change was able to confer CrkL-binding activity to the Cal/09 NS1 protein. 2010 The Journal of general virology Introduction IV E217K 38 43 NS1 109 112 20237225 Mutations in the NS1 C-terminal tail do not enhance replication or virulence of the 2009 pandemic H1N1 influenza A virus. Interestingly, the rCal/09 E217K virus displayed a small-plaque phenotype. 2010 The Journal of general virology Introduction IV E217K 27 32 20237225 Mutations in the NS1 C-terminal tail do not enhance replication or virulence of the 2009 pandemic H1N1 influenza A virus. Overall, our data indicate that neither the C-terminal extension of NS1 nor the E217K substitution (both resulting from single nucleotide changes) has a major effect on replication, virulence or transmissibility of the novel 2009 H1N1 virus. 2010 The Journal of general virology Introduction IV E217K 80 85 NS1 68 71 20237225 Mutations in the NS1 C-terminal tail do not enhance replication or virulence of the 2009 pandemic H1N1 influenza A virus. To test whether the increased length of NS1 or its ability to bind Crk/CrkL would affect in vivo replication and/or pathogenicity of the 2009 H1N1 virus, we initially compared the rCal/09 WT, rCal/09 STOPmut and rCal/09 E217K viruses in the highly susceptible DBA/2J mouse model. 2010 The Journal of general virology Introduction IV E217K 220 225 NS1 40 43 20303563 Substitution of lysine at 627 position in PB2 protein does not change virulence of the 2009 pandemic H1N1 virus in mice. The E627K substitution was observed to enhance virulence and viral replication in mice and other mammals. 2010 Virology Introduction IV E627K 4 9 20303563 Substitution of lysine at 627 position in PB2 protein does not change virulence of the 2009 pandemic H1N1 virus in mice. To investigate the potential pathogenic effect of PB2 E627K substitution in the pandemic (H1N1) 2009 virus, we reconstructed a recombinant virus with a single residue substitution at PB2 627 position from A/California/04/2009 strain and tested its pathogenicity in mice and its growth properties in MDCK cells under different temperatures. 2010 Virology Introduction IV E627K 54 59 PB2;PB2 50;183 53;186 20303563 Substitution of lysine at 627 position in PB2 protein does not change virulence of the 2009 pandemic H1N1 virus in mice. Whether the substitution of E627K in PB2 gene of the pandemic (H1N1) 2009 virus may occur after prevailing in human for a period of time, and whether such change may alter the virulence of current pandemic H1N1 virus is still unknown. 2010 Virology Introduction IV E627K 28 33 PB2 37 40 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. Despite a high degree of conservation of these residues, the NA substitutions identified in NA inhibitor-resistant influenza viruses isolated both in vitro and clinically tend to be NA subtype-specific: E119A/G/D/V, R292K, and N294S in the N2 and N9 subtypes and H274Y and N294S in the N1 subtype. 2010 PLoS pathogens Introduction IV E119A;E119G;E119D;E119V;R292K;N294S;H274Y;N294S 203;203;203;203;216;227;263;273 214;214;214;214;221;232;268;278 N9;NA;NA;NA 247;61;92;182 249;63;94;184 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. In contrast, neither the H274Y nor the N294S NA mutation compromised the lethality or virulence of clade 1 A/Vietnam/1203/04 (H5N1) virus in mice. 2010 PLoS pathogens Introduction IV H274Y;N294S 25;39 30;44 45 47 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. In ferrets, an oseltamivir-resistant H5N1 virus carrying an H274Y NA mutation replicated approximately 10 times less efficiently in the upper respiratory tract than the wild-type virus. 2010 PLoS pathogens Introduction IV H274Y 60 65 66 68 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. Infection of ferrets with the recombinant H5N1 viruses caused mild disease of various duration, although NA inhibitor-resistant variants with the E119A and N294S mutations were more virulent than the wild-type virus. 2010 PLoS pathogens Introduction IV E119A;N294S 146;156 151;161 105 107 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. *1 relative to reference A/New York/20/2009(H1N1) which additionally differs from A/California/07/2009(H1N1) by the HA mutations P100S, S220T, I338V; *2 low reactor against A/California/07/2009(H1N1)-derived antisera; *3 normal reactor against A/California/07/2009(H1N1)-derived antisera. 2010 PLoS currents Introduction IV P100S;S220T;I338V 129;136;143 134;141;148 HA 116 118 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. All of these variants co-occur with the globally dominant strain (variant (ii) in Table 1) characterized by the 5 substitutions HA-S220T, NA-V106I, NA-N248D, NP-V100I and NS1-I123V. 2010 PLoS currents Introduction IV S220T;V106I;N248D;V100I;I123V 131;141;151;161;175 136;146;156;166;180 HA;NA;NA;NP;NS1 128;138;148;158;171 130;140;150;160;174 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. Analysis of their co-occurrences identifies 9 clusters, 5 of which include HA-E391K (Table 1). 2010 PLoS currents Introduction IV E391K 78 83 HA 75 77 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. As 4 of the 5 cases with HA-E391K and HA-V47A were closely temporally related (within ~2 weeks), the co-occurrence could derive from the same transmission chain/cluster as also indicated by their grouping in the phylogenetic analysis. 2010 PLoS currents Introduction IV E391K;V47A 29;42 34;46 HA;HA 26;39 28;41 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. As also identified by the authors of another HA crystal structure published while this analysis was in preparation, the HA-E391K mutation alters this very same region. 2010 PLoS currents Introduction IV E391K 124 129 HA;HA 45;121 47;123 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. At the same time, there have been three other cases with both HA-E391K and HA-V47A but showing only mild symptoms. 2010 PLoS currents Introduction IV E391K;V47A 65;78 70;82 HA;HA 62;75 64;77 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. Besides HA-E391K, the sample additionally had the mutation HA-N142D which was previously recognized as antibody escape mutant in the context of H5-type viruses (N142D corresponds to N129D in H3 numbering in Table 2 of reference). 2010 PLoS currents Introduction IV E391K;N142D;N142D;N129D 11;62;161;182 16;67;166;187 HA;HA 8;59 10;61 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. Clinical information for samples with E391K. 2010 PLoS currents Introduction IV E391K 38 43 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. Consequently, if the common variations between dominant and vaccine strain do not alter antigenicity, the only additional mutation shared among the low reacting samples was HA-E391K. 2010 PLoS currents Introduction IV E391K 176 181 HA 173 175 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. Emergence of the HA-E391K mutation. 2010 PLoS currents Introduction IV E391K 20 25 HA 17 19 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. For 5 samples of 2009(H1N1) with HA-E391K, reaction towards the vaccine based on strain A/California/07/2009(H1N1) was tested through hemagglutination inhibition assays by the regional WHO collaborating centre in Melbourne. 2010 PLoS currents Introduction IV E391K 36 41 HA 33 35 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. For the severe cases, no additional known mutation, such as HA-D239G (D222G or D225G in alternative numberings ), was found that could directly explain severity. 2010 PLoS currents Introduction IV D239G;D222G;D225G 63;70;79 68;75;84 HA 60 62 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. HA-E391K has been found in samples from 20 countries so far. 2010 PLoS currents Introduction IV E391K 3 8 HA 0 2 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. HA-E391K in the oligomer interface of the crystal structure. 2010 PLoS currents Introduction IV E391K 3 8 HA 0 2 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. Hence, it is not clear if the vaccine failure in these cases was due to HA-E391K, HA-N142D or patient-specific factors. 2010 PLoS currents Introduction IV E391K;N142D 75;85 80;90 HA;HA 72;82 74;84 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. However, it should be noted that 3 of the 5 samples with HA-E391K (one with both HA-E391K and HA-V47A) still showed normal A/California/07/2009(H1N1)-like antigenicity. 2010 PLoS currents Introduction IV E391K;E391K;V47A 60;84;97 65;89;101 HA;HA;HA 57;81;94 59;83;96 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. In both of the severe cases with HA-E391K, we also find a HA-V47A mutation which is structurally located in vicinity (13 Angstrom) of the E391K mutation (Figure 4) and, hence, could contribute to any effects in the region as discussed above. 2010 PLoS currents Introduction IV E391K;V47A;E391K 36;61;138 41;65;143 HA;HA 33;58 35;60 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. In their studies with mouse-adapted H1N1 influenza virus variant A/FM/1/47, the W47G substitution causes a decrease in optimum pH of membrane fusion which led to an increase in necrosis of the bronchiolar epithelium, peribronchiolar lymphocytes, and airway obstruction. 2010 PLoS currents Introduction IV W47G 80 84 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. Initially, the HA-E391K mutation came to our attention as it occurred in a special case where a patient had been vaccinated but still contracted 2009(H1N1) as evidenced by sequencing. 2010 PLoS currents Introduction IV E391K 18 23 HA 15 17 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. Interestingly, a recent second vaccine failure case showed the same co-occurrence of HA-E391K and HA-N142D. 2010 PLoS currents Introduction IV E391K;N142D 89;102 94;107 HA;HA 86;99 88;101 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. Looking at the temporal detail of the variants including HA-E391K, the percentage of co-occurrences with PA-V14I, PA-K716Q and PB1-K736G has changed from September 2009 to December 2009 (56.3%, 68.0%, 57.4% and 34.8% respectively). 2010 PLoS currents Introduction IV E391K;V14I;K716Q;K736G;E391K;V14I;K716Q;K736G 61;109;118;132;60;108;117;131 66;113;123;137;65;112;122;136 HA;PA;PA;PB1 57;105;114;127 59;107;116;130 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. New substitutions that are globally found in more than 20% of the sequences with collection date December 2009 in the NCBI Influenza Virus Resource include HA-D114N, HA-E391K, PA-V14I, PA-K716Q, PB1-K736G, PB1-R563K and PB2-K340N. 2010 PLoS currents Introduction IV D114N;E391K;V14I;K716Q;K736G;R563K;K340N 159;169;179;188;199;210;224 164;174;183;193;204;215;229 HA;HA;PA;PA;PB1;PB1;PB2 156;166;176;185;195;206;220 158;168;178;187;198;209;223 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. Other sequence clusters that include a second co-occurring mutation among all closely related strains in the respective subtree are found for HA-E391K with HA-D114N (see discussion of global appearance of these coupled mutations above) as well as HA-E391K with V47A which would be indicative of founder effects for these cases. 2010 PLoS currents Introduction IV E391K;D114N;E391K;V47A 145;159;250;261 150;164;255;265 HA;HA;HA 142;156;247 144;158;249 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. Overall, these examples are interesting but not sufficient to significantly link the HA-E391K mutation (with or without HA-V47A) to increased severity or lower vaccine efficacy as this may depend on many other patient-specific factors and the fact that these cases had the mutation could readily be explained by the fact that strains with HA-E391K are currently the most common flavor among all locally available samples. 2010 PLoS currents Introduction IV E391K;V47A;E391K 88;123;342 93;127;347 HA;HA;HA 85;120;339 87;122;341 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. PB2-K340N is also of interest as it frequently co-occurred with the potentially virulent HA-D239G mutation but this may also be the reason for its increased occurrence due to a sampling bias towards sequencing more severe cases. 2010 PLoS currents Introduction IV K340N;D239G 4;92 9;97 HA;PB2 89;0 91;3 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. Phylogenetic analysis of the Singaporean sequences including their closest non-Singaporean international matches shows that sequences with HA-E391K have appeared multiple times in different contexts (Figure 2). 2010 PLoS currents Introduction IV E391K 142 147 HA 139 141 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. The age distribution among patients with HA-E391K continues to follow the general pattern of 2009(H1N1) by strongly affecting the younger age groups. 2010 PLoS currents Introduction IV E391K 44 49 HA 41 43 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. The clinical phenotype for 35 Singaporean samples that had the HA-E391K mutation was available for analysis (Table 2). 2010 PLoS currents Introduction IV E391K 66 71 HA 63 65 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. The co-occurrence of HA-E391K with HA-D114N, PB1-R563K and PA-V14I was found in December 2009 in one strain from Spain. 2010 PLoS currents Introduction IV E391K;D114N;R563K;V14I 24;38;49;62 29;43;54;66 HA;HA;PA;PB1 21;35;59;45 23;37;61;48 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. The co-occurrences of HA-E391K with PB2-K340N was found only recently in 2 viral strains in December 2009 (one in Poland and the other in Greece). 2010 PLoS currents Introduction IV E391K;K340N 25;40 30;45 HA;PB2 22;36 24;39 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. The HA-E391K co-occurrences with HA-D114N and PB1-R563K on the other hand increased from September 2009 to December 2009 (6.3%, 26.7%, 39.3% to 47.8% respectively). 2010 PLoS currents Introduction IV E391K;D114N;R563K 7;36;50 12;41;55 HA;HA;PB1 4;33;46 6;35;49 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. The mutation HA-E391K was first identified in New York in July 2009 and appeared shortly after also in Singaporean samples but only grew rapidly in appearance recently (Figure 1). 2010 PLoS currents Introduction IV E391K 16 21 HA 13 15 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. The relative dominance of HA-E391K containing strains in Singapore compared to their average global occurrence in December 2009 (Figure 1) may have originated from founder effects. 2010 PLoS currents Introduction IV E391K 29 34 HA 26 28 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. Ultimately, only experimental or detailed clinical data will be able to establish if HA-E391K has the potential to alter the biology of the virus-host interactions and antigenicity or if its increasing occurrence is due to founder effects. 2010 PLoS currents Introduction IV E391K 88 93 HA 85 87 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. Variants with HA-E391K but without the 6 other substitutions were also found in Germany, Nicaragua, Taiwan and the USA. 2010 PLoS currents Introduction IV E391K 17 22 HA 14 16 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. While in some cases, the best match is another Singaporean sequence without HA-E391K, in others it is a non-Singaporean sequence already with HA-E391K which could indicate import from or exchange with other global outbreak clusters including HA-E391K. 2010 PLoS currents Introduction IV E391K;E391K;E391K 79;145;245 84;150;250 HA;HA;HA 76;142;242 78;144;244 20655872 Drug sensitivity, drug-resistant mutations, and structures of three conductance domains of viral porins. The drugs, amantadine and rimantadine, were effective against influenza A until recently when the influenza A strains became dominated by an S31N mutation displaying drug resistance. 2011 Biochimica et biophysica acta Introduction IV S31N 141 145 20661429 Oseltamivir-resistant pandemic A/H1N1 virus is as virulent as its wild-type counterpart in mice and ferrets. Early reports demonstrated that pH1N1 strains were resistant to the adamantanes due to a S31N mutation in the M2 gene but remained susceptible to neuraminidase inhibitors (NAIs) such as oseltamivir and zanamivir. 2010 PLoS pathogens Introduction IV S31N 89 93 M2;NAI;NA 110;172;146 112;176;159 20661429 Oseltamivir-resistant pandemic A/H1N1 virus is as virulent as its wild-type counterpart in mice and ferrets. Indeed, during the 2008-09 influenza season, almost all characterized influenza A/Brisbane/59/2007-like (H1N1) strains from North America and Europe were resistant to oseltamivir due to a H274Y (N2 numbering) mutation in the neuraminidase (NA) gene. 2010 PLoS pathogens Introduction IV H274Y 188 193 NA;NA 240;225 242;238 20661429 Oseltamivir-resistant pandemic A/H1N1 virus is as virulent as its wild-type counterpart in mice and ferrets. We recently reported the emergence of such an oseltamivir-resistant H274Y mutant in a familial cluster of pH1N1 infections. 2010 PLoS pathogens Introduction IV H274Y 68 73 Influenza A virus H1N1 infection 106 122 20686654 Oseltamivir-resistant pandemic H1N1/2009 influenza virus possesses lower transmissibility and fitness in ferrets. During the H1N1/2009 influenza pandemic, to date, almost all tested viruses have remained susceptible to oseltamivir and zanamivir, but oseltamivir-resistant variants with H275Y NA mutation have been isolated from individuals receiving prophylaxis and from immunocompromised patients under drug selection pressure. 2010 PLoS pathogens Introduction IV H275Y 172 177 178 180 20686654 Oseltamivir-resistant pandemic H1N1/2009 influenza virus possesses lower transmissibility and fitness in ferrets. The A/DM/528/09 virus, carrying the H275Y NA mutation, was isolated from a patient on oseltamivir prophylaxis, and its ancestor is likely to have been A/DM/524/09 virus. 2010 PLoS pathogens Introduction IV H275Y 36 41 42 44 20686654 Oseltamivir-resistant pandemic H1N1/2009 influenza virus possesses lower transmissibility and fitness in ferrets. The situation changed dramatically during the 2007-2008 season, when seasonal H1N1 influenza viruses with the common oseltamivir-resistance NA H275Y mutation (275 in N1 numbering, 274 in N2 numbering) became widespread in first the northern and then the southern hemispheres. 2010 PLoS pathogens Introduction IV H275Y 143 148 140 142 20686654 Oseltamivir-resistant pandemic H1N1/2009 influenza virus possesses lower transmissibility and fitness in ferrets. These studies differed in the influenza A subtypes studied (H1N1, H3N2, or H5N1), the NA mutations involved (H275Y, R292K, E119V or I222V), the animal model used (ferret or guinea pig), and the transmission routes studied (direct contact and respiratory droplets); in these studies, the transmissibility of most of the NA inhibitor-resistant influenza viruses was to some extent less efficient. 2010 PLoS pathogens Introduction IV H275Y;R292K;E119V;I222V 109;116;123;132 114;121;128;137 NA;NA 86;319 88;321 20689744 The PB2-E627K mutation attenuates viruses containing the 2009 H1N1 influenza pandemic polymerase. Independent examples of selection of the PB2-D701N mutation have also been observed, for example, in the nonpandemic avian origin European swine H1N1 viruses as well as in some HPAI H5N1 viruses. 2010 mBio Introduction IV D701N 45 50 PB2 41 44 20689744 The PB2-E627K mutation attenuates viruses containing the 2009 H1N1 influenza pandemic polymerase. Residue 701, residing in a region of PB2 implicated in nuclear localization, has similarly been identified as a host-adaptive locus, with the D701N mutation increasing both replication in mice and transmission in guinea pigs. 2010 mBio Introduction IV D701N 142 147 PB2 37 40 20689744 The PB2-E627K mutation attenuates viruses containing the 2009 H1N1 influenza pandemic polymerase. There has been concern that the 2009 pandemic H1N1 virus could acquire human-adaptive changes at these residues, and two viral isolates with the PB2-E627K mutation have been reported. 2010 mBio Introduction IV E627K 149 154 PB2 145 148 20833142 Solution NMR structure of the V27A drug resistant mutant of influenza A M2 channel. Another common drug resistant mutant is V27A, which sometimes coexists with S31N mutation. 2010 Biochemical and biophysical research communications Introduction IV V27A;S31N 40;76 44;80 20833142 Solution NMR structure of the V27A drug resistant mutant of influenza A M2 channel. Distinct feature of the V27A channel pore also provides an explanation for its faster rate of proton conduction. 2010 Biochemical and biophysical research communications Introduction IV V27A 24 28 20833142 Solution NMR structure of the V27A drug resistant mutant of influenza A M2 channel. Furthermore, owing to the higher quality NMR data acquired for the C-terminal region of V27A18-60 (as compared to that of WT), the mutant structure shows more clearly the structured region that connects the channel domain to the C-terminal AP helices. 2010 Biochemical and biophysical research communications Introduction IV V27A 88 92 20833142 Solution NMR structure of the V27A drug resistant mutant of influenza A M2 channel. It has been suggested that the mechanism of V27A resistance may be different than that of S31N. 2010 Biochemical and biophysical research communications Introduction IV V27A;S31N 44;90 48;94 20833142 Solution NMR structure of the V27A drug resistant mutant of influenza A M2 channel. Recent studies indicate that the resistance is rising and now exceeds 90%, with S31N being the most frequent substitution. 2010 Biochemical and biophysical research communications Introduction IV S31N 80 84 20833142 Solution NMR structure of the V27A drug resistant mutant of influenza A M2 channel. The similarities and differences in the structure and dynamic properties between the wildtype (WT), V27A, and S31N variants allowed an in-depth analysis of possible modes of drug resistance. 2010 Biochemical and biophysical research communications Introduction IV V27A;S31N 100;110 104;114 20833142 Solution NMR structure of the V27A drug resistant mutant of influenza A M2 channel. Therefore, in order to fully understand the resistance, it is of high importance to obtain structural data on the V27A mutant. 2010 Biochemical and biophysical research communications Introduction IV V27A 114 118 20836794 Oseltamivir-resistant influenza A 2009 H1N1 virus in immunocompromised patients. 5 Oseltamivir resistance of 2009 H1N1 virus has been sporadically reported worldwide and linked primarily to de novo development of the H275Y mutation with exposure to oseltamivir therapy or chemoprophylaxis. 2010 Influenza and other respiratory viruses Introduction IV H275Y 137 142 20836794 Oseltamivir-resistant influenza A 2009 H1N1 virus in immunocompromised patients. The H275Y mutation in the neuraminidase (NA) gene confers oseltamivir resistance in seasonal H1N1 and 2009 H1N1 viruses. 2010 Influenza and other respiratory viruses Introduction IV H275Y 4 9 NA;NA 41;26 43;39 20836794 Oseltamivir-resistant influenza A 2009 H1N1 virus in immunocompromised patients. We screened 191 2009 H1N1-positive samples and describe four cases occurring in immunocompromised patients in Utah, one of whom was infected with H275Y mutant virus in the absence of prior oseltamivir exposure. 2010 Influenza and other respiratory viruses Introduction IV H275Y 146 151 20920297 Characterization of an H3N2 triple reassortant influenza virus with a mutation at the receptor binding domain (D190A) that occurred upon virus transmission from turkeys to pigs. In H1 subtypes, Glu190Asp and Gly225Glu mutations appear critical for adaptation of avian viruses to humans. 2010 Virology journal Introduction IV E190D;G225E 16;30 25;39 20920297 Characterization of an H3N2 triple reassortant influenza virus with a mutation at the receptor binding domain (D190A) that occurred upon virus transmission from turkeys to pigs. In H2 and H3 subtypes, Gln226Leu and Gly228Ser mutations accounted for shifting from avian to human receptor binding specificity. 2010 Virology journal Introduction IV Q226L;G228S 23;37 32;46 20920297 Characterization of an H3N2 triple reassortant influenza virus with a mutation at the receptor binding domain (D190A) that occurred upon virus transmission from turkeys to pigs. In this study, we characterized an H3N2 triple reassortant (TR) influenza virus with a mutation at the RBD (Asp190Ala) that occurred upon virus transmission from turkeys to pigs in an experimental infection study. 2010 Virology journal Introduction IV D190A 108 117 21048522 Oseltamivir-resistant influenza A and B viruses pre- and postantiviral therapy in children and young adults with cancer. E119V and N294S mutations occur in the framework region of the NA. 2011 The Pediatric infectious disease journal Introduction IV E119V;N294S 0;10 5;15 63 65 21048522 Oseltamivir-resistant influenza A and B viruses pre- and postantiviral therapy in children and young adults with cancer. In influenza viruses of the N2 subtype, a glutamic acid to valine substitution in residue 119 (E119V, N2 numbering here and through the text) confers resistance to oseltamivir but not to zanamivir; an arginine to lysine substitution at position 292 (R292K) confers resistance to both NAIs. 2011 The Pediatric infectious disease journal Introduction IV E119V;R292K;E119V;R292K 95;250;42;201 100;255;93;248 NAI 284 288 21048522 Oseltamivir-resistant influenza A and B viruses pre- and postantiviral therapy in children and young adults with cancer. Most H1N1 viruses circulating since the 2007-2008 influenza season have a histidine to tyrosine substitution at residue 274 (H274Y), which is also associated with resistance to oseltamivir but not zanamivir. 2011 The Pediatric infectious disease journal Introduction IV H274Y;H274Y 125;74 130;123 21048522 Oseltamivir-resistant influenza A and B viruses pre- and postantiviral therapy in children and young adults with cancer. Other mutations such as an asparagine to serine substitution at position 294 (N294S), have been reported in both N2- and N1-containing viruses; these mutations are associated with a greater loss of in vitro susceptibility to oseltamivir in N2 than in N1 viruses but strains possessing these mutations retain susceptibility to zanamivir. 2011 The Pediatric infectious disease journal Introduction IV N294S;N294S 78;27 83;76 21048522 Oseltamivir-resistant influenza A and B viruses pre- and postantiviral therapy in children and young adults with cancer. Resistance to the second class of anti-influenza drugs, adamantanes, results in most cases from a single serine to asparagine amino acid replacement (S31N) in the matrix M2 protein, which can interfere with the drug's ability to block M2 ion channel activity and viral replication. 2011 The Pediatric infectious disease journal Introduction IV S31N 150 154 M2;M2;M 170;235;163 172;237;169 21172786 Pandemic H1N1 2009 influenza virus with the H275Y oseltamivir resistance neuraminidase mutation shows a small compromise in enzyme activity and viral fitness. In contrast, seasonal H1N1 influenza viruses from the 2007-08 season onwards were predominantly resistant to oseltamivir with resistance conferred by the H275Y mutation in the viral NA. 2011 The Journal of antimicrobial chemotherapy Introduction IV H275Y 154 159 182 184 21172786 Pandemic H1N1 2009 influenza virus with the H275Y oseltamivir resistance neuraminidase mutation shows a small compromise in enzyme activity and viral fitness. It is likely that certain other sequence variations, such as the D344N (N1 numbering) change found within the NA gene of oseltamivir-resistant viruses from the 2007-08 season, counteract the decrease in enzyme function that H275Y confers. 2011 The Journal of antimicrobial chemotherapy Introduction IV D344N;H275Y 65;224 70;229 110 112 21172786 Pandemic H1N1 2009 influenza virus with the H275Y oseltamivir resistance neuraminidase mutation shows a small compromise in enzyme activity and viral fitness. Pandemic influenza A/H1N1 2009 virus (pH1N1) crossed into humans carrying a well-characterized amantadine-resistance mutation, S31N, within the M2 ion channel protein, rendering the adamantane class of antiviral drug ineffective against the virus. 2011 The Journal of antimicrobial chemotherapy Introduction IV S31N 127 131 M2 144 146 21172786 Pandemic H1N1 2009 influenza virus with the H275Y oseltamivir resistance neuraminidase mutation shows a small compromise in enzyme activity and viral fitness. This study aimed to assess in vitro the effect of the H275Y mutation in the NA of a prototypic pH1N1 2009 isolate. 2011 The Journal of antimicrobial chemotherapy Introduction IV H275Y 54 59 76 78 21172786 Pandemic H1N1 2009 influenza virus with the H275Y oseltamivir resistance neuraminidase mutation shows a small compromise in enzyme activity and viral fitness. This suggested that it may tolerate mutations such as H275Y that would concomitantly decrease NA activity and confer oseltamivir resistance. 2011 The Journal of antimicrobial chemotherapy Introduction IV H275Y 54 59 94 96 21172786 Pandemic H1N1 2009 influenza virus with the H275Y oseltamivir resistance neuraminidase mutation shows a small compromise in enzyme activity and viral fitness. Traditionally, the H275Y mutation was associated with compromised viral fitness amongst H1N1 isolates. 2011 The Journal of antimicrobial chemotherapy Introduction IV H275Y 19 24 21226922 Influenza A virus NS1 gene mutations F103L and M106I increase replication and virulence. Further analysis of A/HK/1/68 (H3N2) mouse adapted mutations of the HKMA variant demonstrate that all mutated genome segments enhanced disease severity including the NS1 V23A mutation that increased virulence by 100.8 fold. 2011 Virology journal Introduction IV V23A 170 174 NS1 166 169 21226922 Influenza A virus NS1 gene mutations F103L and M106I increase replication and virulence. Here we show that the F103L and M106I NS1 gene mutations are adaptive and control IAV replication and virulence. 2011 Virology journal Introduction IV F103L;M106I 22;32 27;37 NS1 38 41 21226922 Influenza A virus NS1 gene mutations F103L and M106I increase replication and virulence. Here, we extend the experimental mouse model to identify two adaptive mutations in the NS1 gene, F103L and M106I that have previously been observed in fatal human infections with A/HK/156/97 (H5N1). 2011 Virology journal Introduction IV F103L;M106I 97;107 102;112 NS1 87 90 21226922 Influenza A virus NS1 gene mutations F103L and M106I increase replication and virulence. In contrast, other studies have identified F103L and M106I mutations in this H5N1 NS1 gene that result in a loss of the ability to bind the cleavage and polyadenylation specificity factor and inhibit IFN induction when transferred into A/Udorn/1/1972 (H3N2) virus. 2011 Virology journal Introduction IV F103L;M106I 43;53 48;58 NS1 82 85 21226922 Influenza A virus NS1 gene mutations F103L and M106I increase replication and virulence. Key mutations in the PB2 gene increased pathogenicity and viral transmission such as E627K and D701N and mutation sites in H3 HA1 and HA2 subunits, G218W and T156N respectively, have been shown to affect both growth and virulence in the mouse. 2011 Virology journal Introduction IV E627K;D701N;G218W;T156N 85;95;148;158 90;100;153;163 HA;HA1;PB2 134;126;21 136;129;24 21226922 Influenza A virus NS1 gene mutations F103L and M106I increase replication and virulence. With respect to the role of the NS1 protein in virulence, previous studies have identified single mutations in the NS1 gene (S42P, D92E and V149A) as well as multiple mutations in the PDZ ligand domain that increased viral pathogenicity. 2011 Virology journal Introduction IV S42P;D92E;V149A 125;131;140 129;135;145 NS1;NS1 32;115 35;118 21349290 Development of a real-time RT-PCR assay for detection of resistance to oseltamivir in influenza A pandemic (H1N1) 2009 virus using single nucleotide polymorphism probes. Currently, the gold standard method for detection of the C823T nucleotide polymorphism that leads to the H275Y amino acid change is dideoxy Sanger sequencing of the NA gene. 2011 Journal of virological methods Introduction IV C823T;H275Y 57;105 62;110 165 167 21349290 Development of a real-time RT-PCR assay for detection of resistance to oseltamivir in influenza A pandemic (H1N1) 2009 virus using single nucleotide polymorphism probes. Phylogenetic studies have revealed that the oseltamivir-resistant seasonal IFVA (H1N1) strain evolved from a susceptible strain (clade 2B) which circulated in the 2007-2008 season by acquiring the H275Y change in the NA gene. 2011 Journal of virological methods Introduction IV H275Y 197 202 217 219 21349290 Development of a real-time RT-PCR assay for detection of resistance to oseltamivir in influenza A pandemic (H1N1) 2009 virus using single nucleotide polymorphism probes. Real-time reverse-transcriptase (RT)-PCR assays using single nucleotide polymorphism (SNP) probes for allelic discrimination have been described for the detection of H275Y mutation in seasonal H1N1 viruses and pandemic (H1N1) 2009 viruses. 2011 Journal of virological methods Introduction IV H275Y 166 171 21349290 Development of a real-time RT-PCR assay for detection of resistance to oseltamivir in influenza A pandemic (H1N1) 2009 virus using single nucleotide polymorphism probes. Resistance to oseltamivir has been reported to result from point mutations in several regions of the NA protein of the virus (e.g., D79G, S247G or S247N, and H275Y). 2011 Journal of virological methods Introduction IV D79G;S247G;S247N;H275Y 132;138;147;158 136;143;152;163 101 103 21349290 Development of a real-time RT-PCR assay for detection of resistance to oseltamivir in influenza A pandemic (H1N1) 2009 virus using single nucleotide polymorphism probes. This study describes the validation of a high throughput, sensitive and specific RT-PCR for detection of the C823T nucleotide polymorphism leading to the H275Y amino acid change in the NA protein of pandemic (H1N1) 2009 virus. 2011 Journal of virological methods Introduction IV C823T;H275Y 109;154 114;159 185 187 21407805 A single base-pair change in 2009 H1N1 hemagglutinin increases human receptor affinity and leads to efficient airborne viral transmission in ferrets. Finally, we constructed a CA04/09 virus harboring the Ile219 Lys HA mutation using reverse genetics and showed that this mutant virus transmits efficiently via respiratory droplets in ferrets. 2011 PloS one Introduction IV I219K 54 64 HA 65 67 21407805 A single base-pair change in 2009 H1N1 hemagglutinin increases human receptor affinity and leads to efficient airborne viral transmission in ferrets. We demonstrate that a single Ile219 Lys mutation in the RBS of 2009 H1N1 HA (CA04/09mut1) substantially increases its human receptor affinity in comparison with that of CA04/09 HA. 2011 PloS one Introduction IV I219K 29 39 HA;HA 73;177 75;179 21455300 Assessing the in vitro fitness of an oseltamivir-resistant seasonal A/H1N1 influenza strain using a mathematical model. During the 2007-2008 influenza season, however, the A/Brisbane/59/2007-like (H1N1) H275Y mutant emerged and rapidly disseminated worldwide in the apparent absence of antiviral pressure. 2011 PloS one Introduction IV H275Y 83 88 21455300 Assessing the in vitro fitness of an oseltamivir-resistant seasonal A/H1N1 influenza strain using a mathematical model. For these reasons, strains carrying the H275Y mutation were not thought to be a great concern for public health. 2011 PloS one Introduction IV H275Y 40 45 21455300 Assessing the in vitro fitness of an oseltamivir-resistant seasonal A/H1N1 influenza strain using a mathematical model. However, the results also indicate that this longer latent infection period for cells infected by the H275Y mutant is compensated for by a shorter infecting time required for that cell, once releasing virions, to successfully infect other cells. 2011 PloS one Introduction IV H275Y 102 107 21455300 Assessing the in vitro fitness of an oseltamivir-resistant seasonal A/H1N1 influenza strain using a mathematical model. It has been shown, however, that two other mutations in the NA gene (V234M and R222Q) can provide a compensatory effect by increasing NA surface expression, and that these two substitutions indeed occurred in the evolution of the H1N1 seasonal strain between 1999 and 2007. 2011 PloS one Introduction IV V234M;R222Q 69;79 74;84 NA;NA 60;134 62;136 21455300 Assessing the in vitro fitness of an oseltamivir-resistant seasonal A/H1N1 influenza strain using a mathematical model. Our previous study assessed the in vitro replicative capacity and fitness of pairs of WT influenza virus strains and their H275Y mutant counterparts by use of viral yield assays and by qualitatively comparing plaque sizes. 2011 PloS one Introduction IV H275Y 123 128 21455300 Assessing the in vitro fitness of an oseltamivir-resistant seasonal A/H1N1 influenza strain using a mathematical model. Recent work suggests that the origin of both the fitness reduction conferred by the H275Y mutation and the unique fitness of the A/Brisbane/59/2007 mutant strain is found in the virus NA activity and surface expression. 2011 PloS one Introduction IV H275Y 84 89 184 186 21455300 Assessing the in vitro fitness of an oseltamivir-resistant seasonal A/H1N1 influenza strain using a mathematical model. Recently, our group performed a study on the replicative capacities of the A/Brisbane/59/2007 H275Y mutant strain where we showed that its fitness, based on in vitro and animal studies, was similar to that of its wild-type (WT), oseltamivir-susceptible, counterpart. 2011 PloS one Introduction IV H275Y 94 99 21455300 Assessing the in vitro fitness of an oseltamivir-resistant seasonal A/H1N1 influenza strain using a mathematical model. Specifically, the reduction of NA activity conferred by the H275Y mutation has been associated with a reduced expression of surface neuraminidase, possibly due to defects in the folding of the molecule or its transport through the cellular membrane. 2011 PloS one Introduction IV H275Y 60 65 NA;NA 31;132 33;145 21455300 Assessing the in vitro fitness of an oseltamivir-resistant seasonal A/H1N1 influenza strain using a mathematical model. The eventual dominance of the H275Y mutant may be due to a better balance between the hemagglutinin (HA) and NA activity. 2011 PloS one Introduction IV H275Y 30 35 HA;HA;NA 101;86;109 103;99;111 21455300 Assessing the in vitro fitness of an oseltamivir-resistant seasonal A/H1N1 influenza strain using a mathematical model. The H275Y mutation in the neuraminidase (NA) gene (H274Y in N2 numbering), first described in 2000, is the most frequent mutation associated with oseltamivir-resistance in the N1 subtype, but it had long been thought to critically reduce viral fitness. 2011 PloS one Introduction IV H275Y;H274Y 4;51 9;56 NA;NA 41;26 43;39 21455300 Assessing the in vitro fitness of an oseltamivir-resistant seasonal A/H1N1 influenza strain using a mathematical model. The kinetics parameters extracted through our method suggest that the H275Y mutant has weaker NA activity compared to its WT counterpart : confirmed by NA activity assays : which manifests itself as a longer phase of latent infection before viral release : confirmed by single-cycle viral yield experiments. 2011 PloS one Introduction IV H275Y 70 75 NA;NA 94;152 96;154 21455300 Assessing the in vitro fitness of an oseltamivir-resistant seasonal A/H1N1 influenza strain using a mathematical model. The neuraminidase of contemporary (A/Brisbane/59/2007-like) strains susceptible to oseltamivir have shown a higher affinity for the substrate in NA activity assays than older H1N1 seasonal strains (e.g., A/New Caledonia/20/99 and A/Solomon Islands/3/06); contemporary oseltamivir-resistant strains (with the H275Y substitution) have shown a decrease in that affinity, but remain above the level of older strains. 2011 PloS one Introduction IV H275Y 308 313 NA;NA 145;4 147;17 21455300 Assessing the in vitro fitness of an oseltamivir-resistant seasonal A/H1N1 influenza strain using a mathematical model. These observations, and those of others, correlate with the clinical situation encountered in the 2008-2009 season where almost 100% of the A/H1N1 viruses isolated in North America and Europe were resistant to oseltamivir due to the H275Y mutation. 2011 PloS one Introduction IV H275Y 233 238 21455300 Assessing the in vitro fitness of an oseltamivir-resistant seasonal A/H1N1 influenza strain using a mathematical model. Thus, it seems that these pre-existing mutations led to an over-expression of NA and provided a favorable environment for the appearance of the H275Y mutation. 2011 PloS one Introduction IV H275Y 144 149 78 80 21466220 Exploring the size limit of templates for inhibitors of the M2 ion channel of influenza A virus. Also, at 100 muM, 8 inhibited the A/M2 V27A channel activity by 10.6%, quite similar to Amt (10.8%). 2011 Journal of medicinal chemistry Introduction IV V27A 39 43 M2 36 38 21466220 Exploring the size limit of templates for inhibitors of the M2 ion channel of influenza A virus. Amongst all the new compounds tested, 8 was the only one able to inhibit A/M2 S31N channel with an IC50 of 252 muM, slightly higher than that of Amt (IC50 = 200 muM). 2011 Journal of medicinal chemistry Introduction IV S31N 78 82 M2 75 77 21466220 Exploring the size limit of templates for inhibitors of the M2 ion channel of influenza A virus. Amt-resistant mutants are frequently detected among the two currently circulating subtypes of influenza A virus, A/H3N2 and A/H1N1, with the S31N mutation being observed in more than 90% of influenza A isolates in certain years. 2011 Journal of medicinal chemistry Introduction IV S31N 141 145 21466220 Exploring the size limit of templates for inhibitors of the M2 ion channel of influenza A virus. Interestingly, 24 (at a concentration of 100 muM) inhibited the A/M2 V27A channel activity by 17.7%, which is superior to Amt (10.8%), although much less than 3 (53.4%). 2011 Journal of medicinal chemistry Introduction IV V27A 69 73 M2 66 68 21466220 Exploring the size limit of templates for inhibitors of the M2 ion channel of influenza A virus. Naturally arising single amino acid substitutions associated with Amt resistance, such as L26F, V27A, A30T, S31N and G34E, are all located outside of the H37xxxW41 motif. 2011 Journal of medicinal chemistry Introduction IV L26F;V27A;A30T;S31N;G34E 90;96;102;108;117 94;100;106;112;121 21466220 Exploring the size limit of templates for inhibitors of the M2 ion channel of influenza A virus. Taking into account that the bisnoradamantane derivative 8 showed an interesting activity against wt and S31N A/M2 channels, compounds 14, 15, 16, 18 and 19 were synthesized. 2011 Journal of medicinal chemistry Introduction IV S31N 105 109 M2 112 114 21466220 Exploring the size limit of templates for inhibitors of the M2 ion channel of influenza A virus. We have identified a promising compound, 8, that is capable of inhibiting the M2-S31N mutant ion channel. 2011 Journal of medicinal chemistry Introduction IV S31N 81 85 M2 78 80 21504394 Oseltamivir-resistant influenza viruses get by with a little help from permissive mutations. However, H1N1 viruses possessing the oseltamivir-resistant H274Y mutation appeared during the 2007-2008 IAV season and these viruses became the dominant seasonal H1N1 strain by the 2008-2009 season. 2011 Expert review of anti-infective therapy Introduction IV H274Y 59 64 21504394 Oseltamivir-resistant influenza viruses get by with a little help from permissive mutations. NA residue 274 is located near the enzymatic site of NA and the H274Y substitution causes a structural change in NA that reduces oseltamivir-binding affinity. 2011 Expert review of anti-infective therapy Introduction IV H274Y 64 69 NA;NA;NA 0;53;113 2;55;115 21504394 Oseltamivir-resistant influenza viruses get by with a little help from permissive mutations. NAI-resistant viruses possessing a histidine to tyrosine substitution at NA residue 274 (H274Y, N2 numbering) were isolated from humans in a clinical trial designed to test the efficacy of oseltamivir. 2011 Expert review of anti-infective therapy Introduction IV H274Y 89 94 NA;NAI 73;0 75;3 21504394 Oseltamivir-resistant influenza viruses get by with a little help from permissive mutations. These viruses did not have the same replication defect seen earlier with older H1N1 viruses possessing H274Y. 2011 Expert review of anti-infective therapy Introduction IV H274Y 103 108 21504394 Oseltamivir-resistant influenza viruses get by with a little help from permissive mutations. Through an elegant combination of computational and experimental approaches, it was discovered that H274Y decreases surface expression of NA in older H1N1 strains, but permissive mutations present in newer H1N1 strains negate this effect. 2011 Expert review of anti-infective therapy Introduction IV H274Y 100 105 138 140 21504394 Oseltamivir-resistant influenza viruses get by with a little help from permissive mutations. unequivocally answered these questions by identifying permissive mutations that arose over the last several years, which allowed H1N1 viruses to tolerate the H274Y mutation. 2011 Expert review of anti-infective therapy Introduction IV H274Y 158 163 21504394 Oseltamivir-resistant influenza viruses get by with a little help from permissive mutations. Using H1N1 strains from the 1930s and 1990s, it was found that viruses possessing H274Y replicate poorly, so it was concluded that viruses possessing this particular mutation would probably not persist in the human population. 2011 Expert review of anti-infective therapy Introduction IV H274Y 82 87 21504394 Oseltamivir-resistant influenza viruses get by with a little help from permissive mutations. What changed? Why could these newer H1N1 viruses tolerate the H274Y mutation? Bloom et al. 2011 Expert review of anti-infective therapy Introduction IV H274Y 62 67 21555520 Biophysical analysis of influenza A virus RNA promoter at physiological temperatures. We also evaluated the impact of two different mutations in the 3'-sequence on the promoter duplex: (i) a 3'-G3U mutation that inactivates IAV promoter function in reporter gene assays and (ii) a compensatory mutation, C8A that restores wild-type levels of gene expression. 2011 The Journal of biological chemistry Introduction IV C8A 218 221 21744829 Molecular dynamics simulation directed rational design of inhibitors targeting drug-resistant mutants of influenza A virus M2. Although a variety of mutations can lead to amantadine-resistance in vitro, only three mutants, S31N, V27A and L26F, are generally observed in transmissible viruses that infect pigs, birds and humans. 2011 Journal of the American Chemical Society Introduction IV S31N;V27A;L26F 96;102;111 100;106;115 21744829 Molecular dynamics simulation directed rational design of inhibitors targeting drug-resistant mutants of influenza A virus M2. Although S31N is the substitution found in current resistant strains, in other years V27A has predominated. 2011 Journal of the American Chemical Society Introduction IV S31N;V27A 9;85 13;89 21744829 Molecular dynamics simulation directed rational design of inhibitors targeting drug-resistant mutants of influenza A virus M2. Here we use a combination of molecular dynamics (MD) and classical medicinal chemistry approaches to design very potent inhibitors of V27A and L26F. 2011 Journal of the American Chemical Society Introduction IV V27A;L26F 134;143 138;147 21744829 Molecular dynamics simulation directed rational design of inhibitors targeting drug-resistant mutants of influenza A virus M2. Instead V27A was identified to be the major mutation emerging from drug selection pressure. 2011 Journal of the American Chemical Society Introduction IV V27A 8 12 21744829 Molecular dynamics simulation directed rational design of inhibitors targeting drug-resistant mutants of influenza A virus M2. L26F, S31N, and V27A are relatively unique in terms of retaining near-native proton flux and pH activation curves, which appear to be parameters finely tuned to respond to the properties of a given virus' hemagglutinin protein while minimizing toxicity for the parent cell until viral production is complete. 2011 Journal of the American Chemical Society Introduction IV L26F;S31N;V27A 0;6;16 4;10;20 HA 205 218 21744829 Molecular dynamics simulation directed rational design of inhibitors targeting drug-resistant mutants of influenza A virus M2. MD was used to explore the mechanism of binding of amantadine to WT and of the designed inhibitor to V27A, thereby informing the mechanism and potency of the designed compounds. 2011 Journal of the American Chemical Society Introduction IV V27A 101 105 21744829 Molecular dynamics simulation directed rational design of inhibitors targeting drug-resistant mutants of influenza A virus M2. Recent studies showed that the current predominance of S31N is not the result of drug selection pressure, because S31N was prevalent before the introduction of amantadine, and has become widespread in regions where amantadine was never used. 2011 Journal of the American Chemical Society Introduction IV S31N;S31N 55;114 59;118 21744829 Molecular dynamics simulation directed rational design of inhibitors targeting drug-resistant mutants of influenza A virus M2. These sites appear to be retained in the L26F and V27A mutants, and formed the basis for the design of inhibitors that target these variants while maintaining affinity for WT. 2011 Journal of the American Chemical Society Introduction IV L26F;V27A 41;50 45;54 21744829 Molecular dynamics simulation directed rational design of inhibitors targeting drug-resistant mutants of influenza A virus M2. While the L26F and S31N mutation cause a 10 to 20-decrease in the IC50s for amantadine inhibition, the corresponding V27A mutation renders the channel entirely resistant to both amantadine and rimantadine. 2011 Journal of the American Chemical Society Introduction IV L26F;S31N;V27A 10;19;117 14;23;121 21819109 Exploring organosilane amines as potent inhibitors and structural probes of influenza a virus M2 proton channel. 4,4-Dimethyl silacyclohexane amines 10 and 14 showed a high potency against the WT A/M2 and only minimal inhibition against A/M2-V27A mutant (Table 2), which was expected, as A/M2-V27A prefers binding molecules with extended conformations. 2011 Journal of the American Chemical Society Introduction IV V27A;V27A 129;180 133;184 M2;M2;M2 85;126;177 87;128;179 21819109 Exploring organosilane amines as potent inhibitors and structural probes of influenza a virus M2 proton channel. A/M2 is more conserved than other drug targets of influenza A virus with only three predominant drug resistant mutations S31N, V27A and L26F observed in widely circulating viruses, all of which are located in the transmembrane domain drug binding site. 2011 Journal of the American Chemical Society Introduction IV S31N;V27A;L26F 121;127;136 125;131;140 M2 2 4 21819109 Exploring organosilane amines as potent inhibitors and structural probes of influenza a virus M2 proton channel. Noteworthy was an increase in antiviral potency of silaspirane amine inhibitors against A/M2-V27A compared to their carbon analogs. 2011 Journal of the American Chemical Society Introduction IV V27A 93 97 M2 90 92 21819109 Exploring organosilane amines as potent inhibitors and structural probes of influenza a virus M2 proton channel. Similarly, a 3.3 fold potency increase against the V27A mutant was seen when the quaternary carbon in 8 was switched to silicon to give 5. 2011 Journal of the American Chemical Society Introduction IV V27A 51 55 21819109 Exploring organosilane amines as potent inhibitors and structural probes of influenza a virus M2 proton channel. The dramatic antiviral potency increase against V27A by switching to silicon might be due to the larger size and higher lipophilicity of silicon compared with carbon, thus providing better hydrophobic contact between the drug and the channel. 2011 Journal of the American Chemical Society Introduction IV V27A 48 52 21819109 Exploring organosilane amines as potent inhibitors and structural probes of influenza a virus M2 proton channel. The IC50 of 6 against A/M2-V27A was 31.1 muM, which is more than 2.7 fold more potent than the previously identified weak A/M2-V27A inhibitor 7. 2011 Journal of the American Chemical Society Introduction IV V27A;V27A 27;127 31;131 M2;M2 24;124 26;126 21819109 Exploring organosilane amines as potent inhibitors and structural probes of influenza a virus M2 proton channel. The silaspirane amines were as potent as their carbon counterparts against WT, and were more potent in targeting drug resistant V27A, which highlights their promise for further optimization. 2011 Journal of the American Chemical Society Introduction IV V27A 128 132 21819109 Exploring organosilane amines as potent inhibitors and structural probes of influenza a virus M2 proton channel. The size expansion effect of carbon to silicon switch might contribute to the antiviral potency increase of organosilane against A/M2-V27A, as the expanded organosilane amines is able to fill in the extra space created by the bulky valine 27 to smaller alanine mutation (Table 1). 2011 Journal of the American Chemical Society Introduction IV V27A 134 138 M2 131 133 21819109 Exploring organosilane amines as potent inhibitors and structural probes of influenza a virus M2 proton channel. The synthesized inhibitors were tested in a two-electrode voltage clamp assay using Xenopus laevis frog oocytes microinjectected with RNA expressing either the WT A/M2 or A/M2-V27A mutant protein. 2011 Journal of the American Chemical Society Introduction IV V27A 176 180 M2;M2 165;173 167;175 21821881 Conservation of a crystallographic interface suggests a role for beta-sheet augmentation in influenza virus NS1 multifunctionality. In this paper, we report a third X-ray crystallographic structure of the PR8 NS1 ED containing the W187A mutation. 2011 Acta crystallographica. Section F, Structural biology and crystallization communications Introduction IV W187A 99 104 NS1 77 80 21821881 Conservation of a crystallographic interface suggests a role for beta-sheet augmentation in influenza virus NS1 multifunctionality. The introduction of a W187A mutation into the ED induces a monomeric phenotype (Hale, Barclay et al., 2008; Kerry et al., 2011; Xia & Robertus, 2010) and, intriguingly, two crystal structures of the PR8 NS1 ED containing this mutation also exhibit this strand-strand interface. 2011 Acta crystallographica. Section F, Structural biology and crystallization communications Introduction IV W187A 22 27 NS1 203 206 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. A dose-dependent direct binding glycan array analysis of virus carrying the D222G HA mutation showed observable changes in binding to glycans terminated by both alpha2-6 and alpha2-3-linked sialic acids. 2011 PloS one Introduction IV D222G 76 81 HA 82 84 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. A potential virulence marker associated with 2009 H1N1 viruses was first identified among patients in Norway, with a change from aspartic acid to glycine at position 222 (D222G) in HA1 present in 18% of clinical specimens from patients with severe disease but in 0% of those from mild cases. 2011 PloS one Introduction IV D222G;D222G 171;129 176;169 HA1 181 184 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. However, other groups have not observed substantial differences between wild-type and D222G viruses in mouse or ferret models, indicating the need for further investigation into the role of D222G in virulence of 2009 H1N1 pandemic viruses. 2011 PloS one Introduction IV D222G;D222G 86;190 91;195 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. In the present study, a 2009 H1N1 virus A/California/04/09 (CA/04) was mutated to generate the HA D222G mutation in order to study the role of D222G in pathogenesis and transmission in both ferret and mouse models. 2011 PloS one Introduction IV D222G;D222G 98;143 103;148 HA 95 97 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. Recent studies have reported that the D222G mutation confers enhanced binding to alpha2-3 linked sialic acids, suggesting a greater ability to bind to lung cells in the lower respiratory tract in humans and cause an exacerbation of disease. 2011 PloS one Introduction IV D222G 38 43 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. Several studies in in vitro and in vivo models have examined the role of D222G in 2009 H1N1 virus virulence with varying outcomes. 2011 PloS one Introduction IV D222G 73 78 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. The majority of studies have reported that presence of D222G is sufficient to enhance virus replication and lethality in mouse models, with this effect ranging from modest to pronounced. 2011 PloS one Introduction IV D222G 55 60 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. These retrospective analyses have found that cases bearing the D222G mutation were more likely to be associated with severe pneumonia, admission to intensive care facilities, and death. 2011 PloS one Introduction IV D222G 63 68 Pneumonia 124 133 21980293 Multidrug resistant 2009 A/H1N1 influenza clinical isolate with a neuraminidase I223R mutation retains its virulence and transmissibility in ferrets. A compensatory role was assigned to the NA amino acid changes V234M, R222Q and D344N. 2011 PLoS pathogens Introduction IV V234M;R222Q;D344N 62;69;79 67;74;84 40 42 21980293 Multidrug resistant 2009 A/H1N1 influenza clinical isolate with a neuraminidase I223R mutation retains its virulence and transmissibility in ferrets. An isoleucine to arginine substitution at position 223 in NA (I223R, N1 numbering) was detected in the patient after antiviral therapy with OS had failed due to the emergence of the H275Y mutation and therapy was switched to ZA. 2011 PLoS pathogens Introduction IV I223R;H275Y;I223R 62;182;3 67;187;54 58 60 21980293 Multidrug resistant 2009 A/H1N1 influenza clinical isolate with a neuraminidase I223R mutation retains its virulence and transmissibility in ferrets. In addition, recombinant NL/602/09 with a single I223R amino acid substitution transmitted as well as its recombinant parental virus, suggesting that no additional mutations are needed to compensate for the presence of this I223R mutation in the 2009 pandemic A/H1N1 virus backbone. 2011 PLoS pathogens Introduction IV I223R;I223R 49;224 54;229 21980293 Multidrug resistant 2009 A/H1N1 influenza clinical isolate with a neuraminidase I223R mutation retains its virulence and transmissibility in ferrets. In another case, an I223R/H275Y double mutant virus was isolated that showed high resistance to the NAIs. 2011 PLoS pathogens Introduction IV H275Y;I223R 26;20 31;25 NAI 100 104 21980293 Multidrug resistant 2009 A/H1N1 influenza clinical isolate with a neuraminidase I223R mutation retains its virulence and transmissibility in ferrets. Nevertheless, 565 cases of patients infected with an (H275Y, N1 numbering) oseltamivir (OS) resistant virus have been reported to the World Health Organization. 2011 PLoS pathogens Introduction IV H275Y 54 59 21980293 Multidrug resistant 2009 A/H1N1 influenza clinical isolate with a neuraminidase I223R mutation retains its virulence and transmissibility in ferrets. Overall, these data indicate that pandemic viruses with the NA H275Y substitution were comparable to their oseltamivir susceptible counterparts in pathogenicity and transmissibility in animal models. 2011 PLoS pathogens Introduction IV H275Y 63 68 60 62 21980293 Multidrug resistant 2009 A/H1N1 influenza clinical isolate with a neuraminidase I223R mutation retains its virulence and transmissibility in ferrets. Recently, several research groups have studied the fitness of H275Y mutant pandemic influenza A/H1N1 viruses using both in vitro and in vivo experiments. 2011 PLoS pathogens Introduction IV H275Y 62 67 21980293 Multidrug resistant 2009 A/H1N1 influenza clinical isolate with a neuraminidase I223R mutation retains its virulence and transmissibility in ferrets. Remarkably, earlier studies on H275Y mutant H1N1 viruses had characterized these viruses as attenuated and not of clinical importance. 2011 PLoS pathogens Introduction IV H275Y 31 36 21980293 Multidrug resistant 2009 A/H1N1 influenza clinical isolate with a neuraminidase I223R mutation retains its virulence and transmissibility in ferrets. Successful clearance of a H275Y mutant virus from a patient treated with ZA was reported previously. 2011 PLoS pathogens Introduction IV H275Y 26 31 21980293 Multidrug resistant 2009 A/H1N1 influenza clinical isolate with a neuraminidase I223R mutation retains its virulence and transmissibility in ferrets. The H275Y mutant viruses are cross-resistant to peramivir (PER), but remain susceptible to zanamivir (ZA). 2011 PLoS pathogens Introduction IV H275Y 4 9 21980293 Multidrug resistant 2009 A/H1N1 influenza clinical isolate with a neuraminidase I223R mutation retains its virulence and transmissibility in ferrets. These substitutions may have restored the initial loss of NA activity due to the NAI resistance mutation and facilitated the appearance of the H275Y change in the epidemic influenza A/H1N1 viruses that circulated before the 2009 outbreak of the new pandemic virus. 2011 PLoS pathogens Introduction IV H275Y 143 148 NA;NAI 58;81 60;84 21980293 Multidrug resistant 2009 A/H1N1 influenza clinical isolate with a neuraminidase I223R mutation retains its virulence and transmissibility in ferrets. This I223R containing isolate, in which the H275Y mutation had disappeared, showed reduced susceptibility to OS (45-fold), PER (7-fold) and ZA (10-fold). 2011 PLoS pathogens Introduction IV I223R;H275Y 5;44 10;49 21980293 Multidrug resistant 2009 A/H1N1 influenza clinical isolate with a neuraminidase I223R mutation retains its virulence and transmissibility in ferrets. This resistance phenotype was also caused by a H275Y mutation. 2011 PLoS pathogens Introduction IV H275Y 47 52 21980293 Multidrug resistant 2009 A/H1N1 influenza clinical isolate with a neuraminidase I223R mutation retains its virulence and transmissibility in ferrets. We here show that this 2009 pandemic influenza A/H1N1 clinical isolate, harboring a neuraminidase I223R substitution retains its virulence and transmissibility, but is less pathogenic than a virus prototype without this mutation. 2011 PLoS pathogens Introduction IV I223R 98 103 84 97 22022458 Minor changes in the hemagglutinin of influenza A(H1N1)2009 virus alter its antigenic properties. During the year 2010 viruses with double mutations N125D and E374K have been found with increased frequency in the southern hemisphere. 2011 PloS one Introduction IV N125D;E374K 51;61 56;66 22022458 Minor changes in the hemagglutinin of influenza A(H1N1)2009 virus alter its antigenic properties. Especially, double mutations N125D and N156K (2009 virus isolate) or N125D and E374K (2010 virus isolates) were associated with declined antibody recognition in vaccinated individuals. 2011 PloS one Introduction IV N125D;N156K;N125D;E374K 29;39;69;79 34;44;74;84 22022458 Minor changes in the hemagglutinin of influenza A(H1N1)2009 virus alter its antigenic properties. Here we report that several amino acid changes, namely N125D, N156K, S162R, and E374K, are associated with reduced recognition by sera collected from patients having experienced natural A(H1N1)2009 infection or having received vaccination as analyzed by the hemagglutination inhibition (HI) test. 2011 PloS one Introduction IV N125D;N156K;S162R;E374K 55;62;69;80 60;67;74;85 22022458 Minor changes in the hemagglutinin of influenza A(H1N1)2009 virus alter its antigenic properties. However, antigenic analysis with ferret anti-sera showed no remarkable differences in antibody titers against the N125D virus as compared to the A/California/07/2009 vaccine virus. 2011 PloS one Introduction IV N125D 114 119 22022458 Minor changes in the hemagglutinin of influenza A(H1N1)2009 virus alter its antigenic properties. Other mutations, such as D127E, S183P and D222G have been shown to be associated with a more virulent phenotype in humans or mice. 2011 PloS one Introduction IV D127E;S183P;D222G 25;32;42 30;37;47 22022458 Minor changes in the hemagglutinin of influenza A(H1N1)2009 virus alter its antigenic properties. Recent reports on the evolution of influenza A(H1N1)2009 describe mutations S183P (amino acid numbering throughout the text starts from the mature HA0 without signal peptide) and I191L in HA that enhance viral replication in cell culture and in embryonated hens' eggs. 2011 PloS one Introduction IV S183P;I191L 76;179 81;184 HA 188 190 22022458 Minor changes in the hemagglutinin of influenza A(H1N1)2009 virus alter its antigenic properties. Recently, a new frequently observed mutation, E374K has been found. 2011 PloS one Introduction IV E374K 46 51 22022458 Minor changes in the hemagglutinin of influenza A(H1N1)2009 virus alter its antigenic properties. The D127E and S183P mutations have lead to antigenic changes and impaired recognition by ferret antisera raised against the A/California/07/2009 virus. 2011 PloS one Introduction IV D127E;S183P 4;14 9;19 22022458 Minor changes in the hemagglutinin of influenza A(H1N1)2009 virus alter its antigenic properties. The N125D mutation is located in the Sa epitope of A(H1N1)2009 HA and in an avian influenza strain (A/Mallard/Pennsylvania/10218/84(H5N2)) the corresponding amino acid was reported to cause antigenic drift as an immune escape mutant. 2011 PloS one Introduction IV N125D 4 9 HA 63 65 22022458 Minor changes in the hemagglutinin of influenza A(H1N1)2009 virus alter its antigenic properties. These viruses typically had N125D substitution in their HA molecule. 2011 PloS one Introduction IV N125D 28 33 HA 56 58 22111074 First Fatal Oseltamivir-Resistant 2009 Pandemic Influenza A (H1N1) Case in an Adult in Korea. However, increasing use of oseltamivir has led to the emergence of the oseltamivir-resistant H1N1 2009 virus, which harbors an H274/275Y or I223V neuraminidase mutation. 2011 Chonnam medical journal Introduction IV I223V 140 145 146 159 22138712 The 2008-2009 H1N1 influenza virus exhibits reduced susceptibility to antibody inhibition: Implications for the prevalence of oseltamivir resistant variant viruses. However, the emergence of a H275Y resistant H1N1 variant in patients without pre-exposure to oseltamivir was identified in Norway in 2007. 2012 Antiviral research Introduction IV H275Y 28 33 22138712 The 2008-2009 H1N1 influenza virus exhibits reduced susceptibility to antibody inhibition: Implications for the prevalence of oseltamivir resistant variant viruses. It was also shown that resistant mutants obtained through selection in culture or isolated from patients treated with neuraminidase inhibitors are subtype specific, with E119V and R292K NA mutations occurring mainly in H3N2 subtype viruses exposed to either oseltamivir or zanamivir, and the H275Y mutation in the NA protein found almost exclusively among H1N1 subtype viruses in response to oseltamivir treatment. 2012 Antiviral research Introduction IV E119V;R292K;H275Y 170;180;292 175;185;297 NA;NA;NA 186;314;118 188;316;131 22138712 The 2008-2009 H1N1 influenza virus exhibits reduced susceptibility to antibody inhibition: Implications for the prevalence of oseltamivir resistant variant viruses. Prior to 2007, only a very small number of H275Y mutant oseltamivir resistant viruses were recognized, mainly clinical isolates following oseltamivir treatment. 2012 Antiviral research Introduction IV H275Y 43 48 22138712 The 2008-2009 H1N1 influenza virus exhibits reduced susceptibility to antibody inhibition: Implications for the prevalence of oseltamivir resistant variant viruses. The H275Y variant was found to replicate and transmit similarly to wild type virus in cells and in a competitive mixture model, respectively. 2012 Antiviral research Introduction IV H275Y 4 9 22138712 The 2008-2009 H1N1 influenza virus exhibits reduced susceptibility to antibody inhibition: Implications for the prevalence of oseltamivir resistant variant viruses. The mechanism for the emergence and prevalence of this H275Y variant is not fully understood. 2012 Antiviral research Introduction IV H275Y 55 60 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. In addition, Bloom and colleagues recently described two other secondary NA mutations at codons 222 and 234 that may have counteracted the compromising impact of the H275Y mutation. 2011 PLoS pathogens Introduction IV H275Y 166 171 73 75 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. In an attempt to provide a molecular explanation for this observation, previous authors suggested that secondary NA mutations such as D344N that emerged in H1N1 variants isolated after the 2006-07 season were associated with higher NA activity and affinity and could have facilitated the emergence of the H275Y mutation. 2011 PLoS pathogens Introduction IV D344N;H275Y 134;305 139;310 NA;NA 113;232 115;234 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. In that study, the V234M and R222Q mutations were shown to restore the viral fitness of an A/New Caledonia/20/99 H1N1 variant containing the H275Y mutation. 2011 PLoS pathogens Introduction IV V234M;R222Q;H275Y 19;29;141 24;34;146 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. Recent reports by our group and others have confirmed the differential impact of the H275Y mutation on viral fitness and enzymatic properties in the context of old and recent influenza H1N1 isolates. 2011 PLoS pathogens Introduction IV H275Y 85 90 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. The H275Y (H274Y in N2 numbering) NA mutation conferring resistance to oseltamivir and peramivir has been detected with increasing frequency in seasonal A/H1N1 viruses since 2007 to the extent that almost all characterized A/Brisbane/59/2007-like (Bris07) (H1N1) influenza strains that circulated worldwide during the 2008-09 season were H275Y variants. 2011 PLoS pathogens Introduction IV H275Y;H274Y;H275Y 4;11;338 9;16;343 34 36 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. The rapid dissemination of the H275Y Bris07 variants in the absence of antiviral pressure suggests that the H275Y NA mutation may not compromise viral fitness and transmissibility in this recent H1N1 viral background. 2011 PLoS pathogens Introduction IV H275Y;H275Y 31;108 36;113 114 116 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. This contrasts with previous studies that analyzed the role of the H275Y mutation using older (A/Texas/36/91 and A/New Caledonia/99/01) drug-selected H1N1 variants. 2011 PLoS pathogens Introduction IV H275Y 67 72 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. To further investigate which secondary NA mutations may have facilitated the introduction of the H275Y mutation in contemporarily seasonal H1N1 viruses and allowed their dissemination, we developed a reverse genetics system using a clinical Bris07 (H1N1) isolate as genetic background and evaluated the impact of the H275Y oseltamivir resistance mutation as well as several potential compensatory NA mutations on enzyme activity, viral fitness and transmissibility. 2011 PLoS pathogens Introduction IV H275Y;H275Y 97;317 102;322 NA;NA 39;397 41;399 22194944 Adaption of seasonal H1N1 influenza virus in mice. Previous studies have shown that mouse-adapted A/FM/1/47(H1N1) (FM-MA) from 12 sequential mouse-lung passages has a high ability to replicate and virulence, which is associated with the mutations of Gly-to-Try at residue 47 of the HA2 subunit and Thr-to-Ala at residue 139 of the matrix protein. 2011 PloS one Introduction IV T139A 247 272 HA;M 231;280 233;286 22230322 Highly pathogenic avian influenza virus H5N1 controls type I IFN induction in chicken macrophage HD-11 cells: a polygenic trait that involves NS1 and the polymerase complex. A recent study, for instance, reported that the highly pathogenic (HP) AIV A/goose/Guangdong/1/96 (H5N1) antagonized the induction of type I IFN in chicken embryo fibroblasts, whereas a recombinant virus carrying a valine instead of the alanine at position 149 of NS1 lost this function and became avirulent. 2012 Virology journal Introduction IV A149V 215 260 NS1 264 267 22235288 Acute respiratory distress syndrome induced by a swine 2009 H1N1 variant in mice. In the present study, we used a virulent variant 2009 H1N1 virus, which was isolated from a pig and possessed a virulence-associated HA-D222G mutation, to establish an ARDS mouse model. 2012 PloS one Introduction IV D222G 136 141 HA 133 135 Acute respiratory distress syndrome 168 172 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. If the flexibility of the loop regions impacts on the RNA binding groove and mediates RNA binding and protein self-association, differences should be observed between NP and R361A. 2012 PloS one Introduction IV R361A 174 179 NP 167 169 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. In contrast, a limited access for RNA binding was seen in R361A, caused by a reduced loop flexibility via a salt bridge between E80 (loop 1) and R208 (loop 2) and hydrophobic interactions between loops 1 and 2 observed in the dynamic simulations. 2012 PloS one Introduction IV R361A 58 63 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. In particular salt bridges between adjacent monomers were essential for the stability of the trimer; the single point mutation located in the swapping loop, R416A, disrupted the trimer by breaking a salt bridge with E339 of the adjacent monomer and R416A exclusively formed monomers. 2012 PloS one Introduction IV R416A;R416A 157;249 162;254 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. The flexibility of the wt protein was compared to the fluctuations of a mutant R361A selected for its location in the RNA binding groove. 2012 PloS one Introduction IV R361A 79 84 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. The replacement of the two consecutive glutamates or R204A and R208A by two alanines aimed at avoiding the formation of the salt bridge between loops 1 and 2 and at recovering access for RNA binding. 2012 PloS one Introduction IV R204A;R208A 53;63 58;68 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. The simulations highlighted the flexibility of three defined regions in NP monomer that were perturbed either by oligomerization via trimer formation or by the R361A mutation. 2012 PloS one Introduction IV R361A 160 165 NP 72 74 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. To test this hypothesis, we expressed wt NP, wt-E80A-E81A and wt-R204A-R208A on the one hand and the R361A and the triple mutants R361A-E80A-E81A, R361A-R204A-R208A on the other hand. 2012 PloS one Introduction IV E80A;E81A;E80A;R204A;R208A;R361A;R361A;E81A;R361A;R204A;R208A 136;53;48;65;71;101;130;141;147;153;159 140;57;52;70;76;106;135;145;152;158;164 NP 41 43 22363521 Frequency of D222G and Q223R hemagglutinin mutants of pandemic (H1N1) 2009 influenza virus in Japan between 2009 and 2010. In addition to the D222G substitution, we focused on two other substitutions {aspartic acid187glutamic acid (D187E) and glutamine223argine (Q223R)}, known to be critical for receptor binding, which cause a shift from alpha2,6 to alpha2,3 sialic acid receptor specificity. 2012 PloS one Introduction IV D222G;D187E;Q223R;D187E 19;109;140;78 24;114;145;107 22363521 Frequency of D222G and Q223R hemagglutinin mutants of pandemic (H1N1) 2009 influenza virus in Japan between 2009 and 2010. Since the first appearance of H1N1pdm, one particular amino acid substitution {aspartic acid to glycine at position 222 (D222G)} within the hemagglutinin (HA) molecule has appeared sporadically. 2012 PloS one Introduction IV D222G;D222G 121;79 126;119 HA;HA 155;140 157;153 22363521 Frequency of D222G and Q223R hemagglutinin mutants of pandemic (H1N1) 2009 influenza virus in Japan between 2009 and 2010. The D222G substitution is known to cause a shift from alpha2,6-sialic acid receptor specificity to mixed alpha2,3/alpha2,6-sialic acid receptor specificity. 2012 PloS one Introduction IV D222G 4 9 22438920 Mutations in polymerase genes enhanced the virulence of 2009 pandemic H1N1 influenza virus in mice. A mutation close to the cap-binding region of PB2, T271A, may also enhance viral polymerase activity in mammalian cells. 2012 PloS one Introduction IV T271A 51 56 PB2 46 49 22438920 Mutations in polymerase genes enhanced the virulence of 2009 pandemic H1N1 influenza virus in mice. However, point mutations of known molecular markers, such as PB2 E627K / D701N/ E677G, PB1-F2 N66S, and PA T97I, produced no significant change in pathogenicity when incorporated in pH1N1 individually. 2012 PloS one Introduction IV E627K;D701N;E677G;N66S;T97I 65;73;80;94;107 70;78;85;98;111 PA;PB1F2;PB2 104;87;61 106;93;64 22438920 Mutations in polymerase genes enhanced the virulence of 2009 pandemic H1N1 influenza virus in mice. In this study we fully characterized the variants containing substitution PA-A36T or PB2-H357N in vitro and in vivo. 2012 PloS one Introduction IV A36T;H357N 77;89 81;94 PA;PB2 74;85 76;88 22438920 Mutations in polymerase genes enhanced the virulence of 2009 pandemic H1N1 influenza virus in mice. PB2-590/591 (SR) polymorphism were found to help pH1N1 overcome host restriction by enhancing viral replication and PB2-E158G was a determinant mutation in the adaptation of avian PB2 genes of pH1N1 in mammals. 2012 PloS one Introduction IV E158G 120 125 PB2;PB2;PB2 0;116;180 3;119;183 22438920 Mutations in polymerase genes enhanced the virulence of 2009 pandemic H1N1 influenza virus in mice. Synergistic effect of mutations in PA (F35L) and HA (D222G and K163E) was recently reported in a mouse-adaptive pH1N1 virus. 2012 PloS one Introduction IV F35L;D222G;K163E 39;53;63 43;58;68 HA;PA 49;35 51;37 22438920 Mutations in polymerase genes enhanced the virulence of 2009 pandemic H1N1 influenza virus in mice. The D222G substitution in pH1N1 HA, occurring either naturally or as a mouse-adaptation, was associated with severe or fatal disease in mice by altering cell tropism. 2012 PloS one Introduction IV D222G 4 9 HA 32 34 22438920 Mutations in polymerase genes enhanced the virulence of 2009 pandemic H1N1 influenza virus in mice. The mutants with single polymerase mutation of PA-A36T or PB2-H357N were found in mouse-adapted descendants of SC. 2012 PloS one Introduction IV A36T;H357N 50;62 54;67 PA;PB2 47;58 49;61 22564359 Effect of receptor specificity of A/Hong Kong/1/68 (H3N2) influenza virus variants on replication and transmission in pigs. 21 , 22 Roberts and colleagues used a pair of recombinant influenza viruses with L226Q/S228G substitutions in the A/Victoria/3/75 (H3N2) backbone to examine their transmissibility in ferrets. 2013 Influenza and other respiratory viruses Introduction IV L226Q;S228G 83;89 88;94 22564359 Effect of receptor specificity of A/Hong Kong/1/68 (H3N2) influenza virus variants on replication and transmission in pigs. 24 Therefore, we aimed to determine whether L226Q/S228G mutations in the HA of A/Hong Kong/1/68 (H3N2) would affect (i) replication potential in porcine respiratory explants, (ii) replication potential and organ tropism in pigs, and (iii) pig-to-pig transmission. 2013 Influenza and other respiratory viruses Introduction IV L226Q;S228G 45;51 50;56 HA 74 76 22809692 Both influenza hemagglutinin and polymerase acidic genes are important for delayed pandemic 2009 H1N1 virus clearance in the ferret model. We previously showed that the 2009 A(H1N1) pandemic influenza virus (A(H1N1)pdm09) could be further adapted to normal human bronchial epithelial (NHBE) cells through the acquisition of two mutations (hemagglutinin K154Q and polymerase acidic protein L295P). 2012 Virology Introduction IV K154Q;L295P 214;250 219;255 HA;PA 200;224 213;241 22809862 Treatment of oseltamivir-resistant influenza A (H1N1) virus infections in mice with antiviral agents. A fatal case of oseltamivir-resistant H1N1 H275Y virus infection was recently reported from Korea, underscoring the virulence potential of the resistant virus. 2012 Antiviral research Introduction IV H275Y 43 48 22809862 Treatment of oseltamivir-resistant influenza A (H1N1) virus infections in mice with antiviral agents. A pandemic virus resistant to oseltamivir, A/Hong Kong/2369/2009 (H1N1) H275Y (hereafter referred to as A/HK-275Y), was acquired by us and subsequently adapted for lethality in mice. 2012 Antiviral research Introduction IV H275Y 72 77 22809862 Treatment of oseltamivir-resistant influenza A (H1N1) virus infections in mice with antiviral agents. Another virus strain serially passaged in mice, influenza A/Hawaii/21/2007 (H1N1) H275Y, was found to only be partially lethal to the animals, and no further work was done with that virus. 2012 Antiviral research Introduction IV H275Y 82 87 22809862 Treatment of oseltamivir-resistant influenza A (H1N1) virus infections in mice with antiviral agents. In the present article the viruses are all referred to as H275Y. 2012 Antiviral research Introduction IV H275Y 58 63 22809862 Treatment of oseltamivir-resistant influenza A (H1N1) virus infections in mice with antiviral agents. In the present studies we demonstrate the efficacy of several influenza virus inhibitors over a range of doses in mice lethally infected with the A/MS-H275Y and the A/HK-H275Y viruses. 2012 Antiviral research Introduction IV H275Y;H275Y 151;170 156;175 22809862 Treatment of oseltamivir-resistant influenza A (H1N1) virus infections in mice with antiviral agents. Infections of mice with these novel mouse adapted strains, particularly A/MS-H275Y, will be useful as models for studying treatment regimens that may combat oseltamivir-resistant virus infections. 2012 Antiviral research Introduction IV H275Y 77 82 22809862 Treatment of oseltamivir-resistant influenza A (H1N1) virus infections in mice with antiviral agents. Our efforts began prior to the emergence of the 2009 pandemic and before the published work of with the genetically engineered influenza A/WSN/33 (H1N1) H275Y virus. 2012 Antiviral research Introduction IV H275Y 153 158 22809862 Treatment of oseltamivir-resistant influenza A (H1N1) virus infections in mice with antiviral agents. reported a mouse-adapted influenza A/WSN/33 (H1N1) H275Y (referred to as H274Y in the publication) infection model in mice. 2012 Antiviral research Introduction IV H275Y;H274Y 51;73 56;78 22809862 Treatment of oseltamivir-resistant influenza A (H1N1) virus infections in mice with antiviral agents. The effectiveness of treatment of oseltamivir-resistant H1N1 H275Y virus infections has been shown to be reduced in pediatric clinical settings. 2012 Antiviral research Introduction IV H275Y 61 66 22809862 Treatment of oseltamivir-resistant influenza A (H1N1) virus infections in mice with antiviral agents. The H275Y virus that was used for the studies of was created by genetic engineering. 2012 Antiviral research Introduction IV H275Y 4 9 22809862 Treatment of oseltamivir-resistant influenza A (H1N1) virus infections in mice with antiviral agents. The influenza A/California/04/2009 (H1N1) virus that was mouse adapted had the following mutations compared to wild-type virus: 1 in PB2 (E158G), 3 in HA (G155E, S183P, and D222G), and 1 in NP (D101G) genes. 2012 Antiviral research Introduction IV E158G;G155E;S183P;D222G;D101G 138;155;162;173;194 143;160;167;178;199 HA;NP;PB2 151;190;133 153;192;136 22809862 Treatment of oseltamivir-resistant influenza A (H1N1) virus infections in mice with antiviral agents. The predominant mutation conferring resistance to oseltamivir was in the viral neuraminidase at position 275 where histidine was replaced by tyrosine (H275Y). 2012 Antiviral research Introduction IV H275Y;H275Y 151;105 156;149 79 92 22809862 Treatment of oseltamivir-resistant influenza A (H1N1) virus infections in mice with antiviral agents. Thus, all earlier H1N1 viruses with an H275Y mutation were referred to as H274Y. 2012 Antiviral research Introduction IV H275Y;H274Y 39;74 44;79 22809862 Treatment of oseltamivir-resistant influenza A (H1N1) virus infections in mice with antiviral agents. We determined that a mouse-adapted influenza A/Mississippi/03/2001 (H1N1) H275Y (hereafter referred to as A/MS-H275Y) was consistently lethal to BALB/c mice in repeated experiments. 2012 Antiviral research Introduction IV H275Y;H275Y 74;111 79;116 22809862 Treatment of oseltamivir-resistant influenza A (H1N1) virus infections in mice with antiviral agents. Yen and colleagues engineered an influenza A/Vietnam/1203/2004 (H5N1) virus with an H275Y mutation that conferred oseltamivir resistance and yet retained lethality in mice. 2012 Antiviral research Introduction IV H275Y 84 89 22958470 Molecular and phylogenetic analysis of matrix gene of avian influenza viruses isolated from wild birds and live bird markets in the USA. 23 The most commonly observed mutation is at position 31 leading to change from serine to asparagine (S31N). 2013 Influenza and other respiratory viruses Introduction IV S31N 103 107 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. Both I223R and H275Y changes are near the active site of A/H1N1 pandemic NA. 2012 PLoS pathogens Introduction IV I223R;H275Y 5;15 10;20 73 75 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. Both in vitro studies and in animal models, viruses with I223R and the combination of I223R with H275Y were found not to be compromised in their replication capacity or transmissibility. 2012 PLoS pathogens Introduction IV I223R;I223R;H275Y 57;86;97 62;91;102 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. Here we address the role of the I223R in NAI resistance alone and in combination with H275Y. 2012 PLoS pathogens Introduction IV I223R;H275Y 32;86 37;91 NAI 41 44 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. In contrast to earlier observations on H275Y mutants, this change did not compromise viral replication or transmissibility in the background of the 2007-2008 H1N1 virus. 2012 PLoS pathogens Introduction IV H275Y 39 44 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. In contrast to the frequently observed H275Y change, which causes selective resistance to oseltamivir, the I223R mutation conferred a resistance phenotype against both oseltamivir and zanamivir. 2012 PLoS pathogens Introduction IV H275Y;I223R 39;107 44;112 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. Resistance to oseltamivir was caused by a previously identified, and frequently observed, histidine to tyrosine change in the NA at position 275 (H275Y). 2012 PLoS pathogens Introduction IV H275Y 146 151 126 128 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. Soon after the identification of this first clinical case, the I223R change was found as a single change or in combination with H275Y, in a number of other cases. 2012 PLoS pathogens Introduction IV I223R;H275Y 63;128 68;133 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. The I223R/H275Y double mutant proved to have high levels of resistance to oseltamivir. 2012 PLoS pathogens Introduction IV I223R;H275Y 4;10 9;15 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. The structural basis of resistance conferred by the H275Y has been described previously. 2012 PLoS pathogens Introduction IV H275Y 52 57 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. Together with this structure we present the structures of the I223R mutant neuraminidase in complex with oseltamivir and zanamivir to investigate the resistance mechanism of the I223R mutant neuraminidase. 2012 PLoS pathogens Introduction IV I223R;I223R 62;178 67;183 NA;NA 75;191 88;204 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. We identified a novel isoleucine to arginine change at position 223 (I223R) in the NA of a virus isolated from an immune suppressed child on prolonged oseltamivir and zanamivir therapy. 2012 PLoS pathogens Introduction IV I223R;I223R 69;22 74;67 83 85 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. This study examined the contribution of importin alpha isofoms for NP localization to the nucleus and viral multiplication via the unconventional NLS and found that Qip1 is responsible for S9A virus multiplication independent of nuclear localization. 2013 PloS one Introduction IV S9A 189 192 NP 67 69 23383318 Inhibitors of the influenza A virus M2 proton channel discovered using a high-throughput yeast growth restoration assay. These are single amino acid substitutions in the channel - V27A, L26F or S31N. 2013 PloS one Introduction IV V27A;L26F;S31N 59;65;73 63;69;77 23397331 Influenza virus A(H1N1)pdm09 hemagglutinin polymorphism and associated disease in southern Germany during the 2010/11 influenza season. Of note, another mutation involving the same residue (D222E) was also observed but could not be associated with more severe cases. 2013 Archives of virology Introduction IV D222E 54 59 23397331 Influenza virus A(H1N1)pdm09 hemagglutinin polymorphism and associated disease in southern Germany during the 2010/11 influenza season. The D222G mutation in the receptor-binding domain of the HA gene has been linked to severe cases. 2013 Archives of virology Introduction IV D222G 4 9 HA 57 59 23437033 Quantitative description of glycan-receptor binding of influenza A virus H7 hemagglutinin. Finally we introduced the Gln226 Leu and Gly228 Ser double mutation in the RBS of FC and CC HAs since the Leu-226/Ser-228 combination in the RBS is a hallmark of all the human-adapted H3N2 HAs (belong to the same group 2 clade as H7) and characterize the effect of these mutations on quantitative glycan receptor-binding affinity of these HAs. 2013 PloS one Introduction IV Q226L;G228S 26;41 36;51 23437033 Quantitative description of glycan-receptor binding of influenza A virus H7 hemagglutinin. In fact a single amino acid mutation Gln226 Leu in H2 HA completely shifts its receptor binding preference from avian to human receptors and confers airborne viral transmission in ferrets. 2013 PloS one Introduction IV Q226L 37 47 HA 54 56 23437217 Parallel screening of wild-type and drug-resistant targets for anti-resistance neuraminidase inhibitors. Because the I223R/H275Y dual mutation affects the activities of current drugs including zanamivir, oseltamivir, and peramivir, discovering new inhibitors is critical to treatment of the MDR strain. 2013 PloS one Introduction IV I223R;H275Y 12;18 17;23 23437217 Parallel screening of wild-type and drug-resistant targets for anti-resistance neuraminidase inhibitors. However, some drug-resistant strains have been reported, including an oseltamivir carboxylate-resistant strain (H275Y in N1 numbering; a tyrosine for histidine substitution at position 275 in NA), a zanamivir-resistant strain (I223R; an arginine for isoleucine substitution at position 223 in NA), and a multiple drug-resistant (MDR) strain with both I223R and H275Y mutations. 2013 PloS one Introduction IV H275Y;I223R;I223R;H275Y;H275Y;I223R 112;227;351;361;137;237 117;232;356;366;188;289 NA;NA 192;293 194;295 23437217 Parallel screening of wild-type and drug-resistant targets for anti-resistance neuraminidase inhibitors. We analyzed the subsite containing the dual H275Y/I223R mutation using site-moiety maps. 2013 PloS one Introduction IV H275Y;I223R 44;50 49;55 23437766 Discovery of novel dual inhibitors of the wild-type and the most prevalent drug-resistant mutant, S31N, of the M2 proton channel from influenza A virus. 2-Chloro analogue 49 also showed much lower S31N activity than 44, which may be attributed to the fact that chlorine is a weaker hydrogen acceptor than a hydroxyl group. 2013 Journal of medicinal chemistry Introduction IV S31N 44 48 23437766 Discovery of novel dual inhibitors of the wild-type and the most prevalent drug-resistant mutant, S31N, of the M2 proton channel from influenza A virus. A secondary amine is preferred over an imine analogue for S31N activity (42% and 21% inhibition for compounds 20 and 26, respectively). 2013 Journal of medicinal chemistry Introduction IV S31N 58 62 23437766 Discovery of novel dual inhibitors of the wild-type and the most prevalent drug-resistant mutant, S31N, of the M2 proton channel from influenza A virus. Again, a variety of substituents were tolerated when the target was WT, but only the simple primary amine found in amantadine gave significant activity against S31N. 2013 Journal of medicinal chemistry Introduction IV S31N 160 164 23437766 Discovery of novel dual inhibitors of the wild-type and the most prevalent drug-resistant mutant, S31N, of the M2 proton channel from influenza A virus. Although the unsubstituted derivative 5 was inactive toward S31N (1% inhibition), it did show significant inhibition against the WT (77% inhibition) at 100 muM drug concentration. 2013 Journal of medicinal chemistry Introduction IV S31N 60 64 23437766 Discovery of novel dual inhibitors of the wild-type and the most prevalent drug-resistant mutant, S31N, of the M2 proton channel from influenza A virus. Amantadine (1) is, however, more active than rimantadine (2) against S31N (199.9 muM vs >2 mM) (Figure 2A). 2013 Journal of medicinal chemistry Introduction IV S31N 69 73 23437766 Discovery of novel dual inhibitors of the wild-type and the most prevalent drug-resistant mutant, S31N, of the M2 proton channel from influenza A virus. As a result, there is an urgent need to develop second-generation novel M2 inhibitors targeting the most prevalent S31N mutant. 2013 Journal of medicinal chemistry Introduction IV S31N 115 119 M2 72 74 23437766 Discovery of novel dual inhibitors of the wild-type and the most prevalent drug-resistant mutant, S31N, of the M2 proton channel from influenza A virus. As was the case for 4-methyl ether 21 (Table 2), 2-methyl ether 30 also decreased rather than enhanced the S31N inhibitory activity. 2013 Journal of medicinal chemistry Introduction IV S31N 107 111 23437766 Discovery of novel dual inhibitors of the wild-type and the most prevalent drug-resistant mutant, S31N, of the M2 proton channel from influenza A virus. At the same time of writing this article, a pinanamine bearing an imidazole derivative was reported to show weak inhibitory activity against the S31N M2 channel. 2013 Journal of medicinal chemistry Introduction IV S31N 145 149 M2 150 152 23437766 Discovery of novel dual inhibitors of the wild-type and the most prevalent drug-resistant mutant, S31N, of the M2 proton channel from influenza A virus. Attention was turned to effects of 3-substituents in the context of the 4-hydroxy 20, which had significant activity against S31N and WT (Table 5). 2013 Journal of medicinal chemistry Introduction IV S31N 125 129 23437766 Discovery of novel dual inhibitors of the wild-type and the most prevalent drug-resistant mutant, S31N, of the M2 proton channel from influenza A virus. Compound 44 had an EC50 of 3.2 muM against S31N and was 7-fold more potent than amantadine (1) (EC50 = 22.5 muM) (Figure 4A). 2013 Journal of medicinal chemistry Introduction IV S31N 43 47 23437766 Discovery of novel dual inhibitors of the wild-type and the most prevalent drug-resistant mutant, S31N, of the M2 proton channel from influenza A virus. Compound 44 was approximately 6-fold more potent against S31N than amantadine (1) (IC50 = 199.9 muM), and only 2-fold less potent than amantadine (1) for WT (IC50 = 16 muM) in the TEVC assay. 2013 Journal of medicinal chemistry Introduction IV S31N 57 61 23437766 Discovery of novel dual inhibitors of the wild-type and the most prevalent drug-resistant mutant, S31N, of the M2 proton channel from influenza A virus. For example, installation of 2-hydroxy to 4-fluoro analogue 19 markedly improved S31N inhibitory activity from 8% to 37% inhibition (compound 46). 2013 Journal of medicinal chemistry Introduction IV S31N 81 85 23437766 Discovery of novel dual inhibitors of the wild-type and the most prevalent drug-resistant mutant, S31N, of the M2 proton channel from influenza A virus. However, methylation of 2-hydroxy in 44 and 45 (compounds 47 and 48, respectively) dramatically reduced both S31N and WT activities, which might be due to the steric hindrance at this position. 2013 Journal of medicinal chemistry Introduction IV S31N 109 113 23437766 Discovery of novel dual inhibitors of the wild-type and the most prevalent drug-resistant mutant, S31N, of the M2 proton channel from influenza A virus. However, none showed significantly better activity vs S31N than had already been seen for amantadine. 2013 Journal of medicinal chemistry Introduction IV S31N 54 58 23437766 Discovery of novel dual inhibitors of the wild-type and the most prevalent drug-resistant mutant, S31N, of the M2 proton channel from influenza A virus. However, the closely related benzamide 9 and benzylamine 10 lost considerable potency against both S31N and WT. 2013 Journal of medicinal chemistry Introduction IV S31N 99 103 23437766 Discovery of novel dual inhibitors of the wild-type and the most prevalent drug-resistant mutant, S31N, of the M2 proton channel from influenza A virus. However, they showed no activity against S31N (0% inhibition for both) in our electrophysiological TEVC assay. 2013 Journal of medicinal chemistry Introduction IV S31N 41 45 23437766 Discovery of novel dual inhibitors of the wild-type and the most prevalent drug-resistant mutant, S31N, of the M2 proton channel from influenza A virus. In establishing an assay for S31N, we found it important to verify that the assay identified true M2 inhibitors, as we found both vesicle proton flux assays and viral inhibition assays are complicated by the fact that many amantadine-like compounds are proton carriers. 2013 Journal of medicinal chemistry Introduction IV S31N 29 33 M2 98 100 23437766 Discovery of novel dual inhibitors of the wild-type and the most prevalent drug-resistant mutant, S31N, of the M2 proton channel from influenza A virus. Interestingly, 4-cyclohexanol 24, a saturated version of 20, dramatically dropped S31N activity from 42% to 19% inhibition, which demonstrated that the aromaticity is crucial for S31N activity. 2013 Journal of medicinal chemistry Introduction IV S31N;S31N 82;179 86;183 23437766 Discovery of novel dual inhibitors of the wild-type and the most prevalent drug-resistant mutant, S31N, of the M2 proton channel from influenza A virus. Interestingly, a Boc derivative of the aniline of 6 improved S31N activity to 20% inhibition (compound 7), and acetylation of 6 further boosted S31N activity to 32% inhibition (compound 8), which is similar to the activity of 1 (35% inhibition). 2013 Journal of medicinal chemistry Introduction IV S31N;S31N 61;144 65;148 23437766 Discovery of novel dual inhibitors of the wild-type and the most prevalent drug-resistant mutant, S31N, of the M2 proton channel from influenza A virus. Introduction of a 4-amino substituent (compound 6) increased S31N activity from 1% to 10% inhibition but decreased activity against WT from 77% to 31% inhibition. 2013 Journal of medicinal chemistry Introduction IV S31N 61 65 23437766 Discovery of novel dual inhibitors of the wild-type and the most prevalent drug-resistant mutant, S31N, of the M2 proton channel from influenza A virus. Introduction of a pyrazole 11 or imidazole 12 gave compounds with some activity against S31N (26% and 25% inhibition, respectively) but still less potent than unsubstituted amantadine (1). 2013 Journal of medicinal chemistry Introduction IV S31N 88 92 23437766 Discovery of novel dual inhibitors of the wild-type and the most prevalent drug-resistant mutant, S31N, of the M2 proton channel from influenza A virus. Methyl ketone 23 and methyl ether 21 showed similar S31N activity (31% inhibition). 2013 Journal of medicinal chemistry Introduction IV S31N 52 56 23437766 Discovery of novel dual inhibitors of the wild-type and the most prevalent drug-resistant mutant, S31N, of the M2 proton channel from influenza A virus. Methylation of the 4-hydroxyl group of 20 reduced S31N inhibitory activity from 42% to 31% inhibition (compound 21), which indicated the importance of the 4-hydroxy group. 2013 Journal of medicinal chemistry Introduction IV S31N 50 54 23437766 Discovery of novel dual inhibitors of the wild-type and the most prevalent drug-resistant mutant, S31N, of the M2 proton channel from influenza A virus. Methylation of the 4-hydroxyl group of 35 (compound 40) maintained both WT and S31N activity and displayed slightly decreased activity than the more constrained 41. 2013 Journal of medicinal chemistry Introduction IV S31N 79 83 23437766 Discovery of novel dual inhibitors of the wild-type and the most prevalent drug-resistant mutant, S31N, of the M2 proton channel from influenza A virus. Moreover, NMR studies showed that S31N was more dynamic and possibly also more hydrated in the pore than the corresponding WT protein. 2013 Journal of medicinal chemistry Introduction IV S31N 34 38 23437766 Discovery of novel dual inhibitors of the wild-type and the most prevalent drug-resistant mutant, S31N, of the M2 proton channel from influenza A virus. One carbon homologated derivative of 20 (compound 22) markedly decreased S31N inhibitory activity from 42% to 17% inhibition. 2013 Journal of medicinal chemistry Introduction IV S31N 73 77 23437766 Discovery of novel dual inhibitors of the wild-type and the most prevalent drug-resistant mutant, S31N, of the M2 proton channel from influenza A virus. Other substituents at the 4-position such as sulfone 15, sulfoxide 16, nitro 17, cyano 18, and fluorine 19 showed some improvement in S31N activity compared to that of the parent compound 5 but did not reach the same activity as that of amantadine (1). 2013 Journal of medicinal chemistry Introduction IV S31N 134 138 23437766 Discovery of novel dual inhibitors of the wild-type and the most prevalent drug-resistant mutant, S31N, of the M2 proton channel from influenza A virus. Our journey to discover S31N inhibitors started with modification of amantadine (1) whose potency against S31N drops approximately 12-fold from 16 muM against WT to 200 muM in a TEVC (two electrode voltage clamp) electrophysiological assay. 2013 Journal of medicinal chemistry Introduction IV S31N;S31N 24;106 28;110 23437766 Discovery of novel dual inhibitors of the wild-type and the most prevalent drug-resistant mutant, S31N, of the M2 proton channel from influenza A virus. Pleasingly, the 2,4-dihydroxy substituted analogue, 44, markedly enhanced S31N inhibitory activity (67% inhibition at 100 muM, IC50 = 35.2 muM). 2013 Journal of medicinal chemistry Introduction IV S31N 74 78 23437766 Discovery of novel dual inhibitors of the wild-type and the most prevalent drug-resistant mutant, S31N, of the M2 proton channel from influenza A virus. Replacement of aniline of 6 with its bioisomer, 4-pyridine 14, slightly increased S31N and WT activity. 2013 Journal of medicinal chemistry Introduction IV S31N 82 86 23437766 Discovery of novel dual inhibitors of the wild-type and the most prevalent drug-resistant mutant, S31N, of the M2 proton channel from influenza A virus. Since amantadine (1) is more potent against S31N (35% inhibition) than rimantadine (2) (13% inhibition) and pinanamine (0% inhibition) in a TEVC assay, we envisioned that installation of an aromatic group to the amine group of amantadine (5-49) might improve activity against S31N as well as WT. 2013 Journal of medicinal chemistry Introduction IV S31N;S31N 44;276 48;280 23437766 Discovery of novel dual inhibitors of the wild-type and the most prevalent drug-resistant mutant, S31N, of the M2 proton channel from influenza A virus. Since the reported nonamantadine-based aryl-containing M2 inhibitors (Table 1) showed essentially no inhibition against S31N, we started to explore amantadine-based derivatives with an aromatic group appended to the primary amine group, which led to the discovery of a new series of substituted N-benzyl amantadines as promising M2 inhibitors against S31N as well as WT. 2013 Journal of medicinal chemistry Introduction IV S31N;S31N 120;351 124;355 M2;M2 55;329 57;331 23437766 Discovery of novel dual inhibitors of the wild-type and the most prevalent drug-resistant mutant, S31N, of the M2 proton channel from influenza A virus. The 4-phenolic derivative, 4-(adamantan-1-ylaminomethyl)-phenol (20) was the first compound that showed slightly higher inhibitory activity against S31N (IC50 = 166 muM) than amantadine (1) (IC50 = 199.9 muM). 2013 Journal of medicinal chemistry Introduction IV S31N 148 152 23437766 Discovery of novel dual inhibitors of the wild-type and the most prevalent drug-resistant mutant, S31N, of the M2 proton channel from influenza A virus. The mutation S31N disrupts the size and polarity of the pore in precisely the region that accommodates the adamantane group of amantadine, explaining the decrease in potency of amantadine from 16 muM against WT to 200 muM in a TEVC electrophysiological assay. 2013 Journal of medicinal chemistry Introduction IV S31N 13 17 23437766 Discovery of novel dual inhibitors of the wild-type and the most prevalent drug-resistant mutant, S31N, of the M2 proton channel from influenza A virus. The secondary amine linker also showed better S31N activity than either a tertiary amine or an ether linkage (31%, 20%, and 13% inhibition for compounds 21, 27, and 28, respectively). 2013 Journal of medicinal chemistry Introduction IV S31N 46 50 23437766 Discovery of novel dual inhibitors of the wild-type and the most prevalent drug-resistant mutant, S31N, of the M2 proton channel from influenza A virus. These compounds showed excellent activity for WT, and some were highly active against V27A and L26F. 2013 Journal of medicinal chemistry Introduction IV V27A;L26F 86;95 90;99 23437766 Discovery of novel dual inhibitors of the wild-type and the most prevalent drug-resistant mutant, S31N, of the M2 proton channel from influenza A virus. This led to the discovery of benzyl-substituted amantadine derivatives as dual WT and S31N inhibitors, which is described in the present article. 2013 Journal of medicinal chemistry Introduction IV S31N 86 90 23437766 Discovery of novel dual inhibitors of the wild-type and the most prevalent drug-resistant mutant, S31N, of the M2 proton channel from influenza A virus. Two phenol regioisomers of 20, 3-hydroxy 34, and 2-hydroxy 29 displayed much lower S31N inhibitory activity (6% and 18% inhibition, respectively) but improved WT inhibitory activity (88% and 81% inhibition, respectively). 2013 Journal of medicinal chemistry Introduction IV S31N 83 87 23437766 Discovery of novel dual inhibitors of the wild-type and the most prevalent drug-resistant mutant, S31N, of the M2 proton channel from influenza A virus. V27A, L26F, and S31N have consistently comprised more than 99% of transmissible M2 mutants, among which S31N is now predominant in 98-100% of the transmissible amantadine-resistant H1N1, H5N1, and H3N2 strains isolated from humans, birds, and swine in the past decade. 2013 Journal of medicinal chemistry Introduction IV V27A;L26F;S31N;S31N 0;6;16;104 4;10;20;108 M2 80 82 23437766 Discovery of novel dual inhibitors of the wild-type and the most prevalent drug-resistant mutant, S31N, of the M2 proton channel from influenza A virus. We also found that 4-hydroxy cannot be replaced with two cyclic bioisomers, 42 and 43, which displayed much weaker activity against S31N (10% and 12% inhibition, respectively). 2013 Journal of medicinal chemistry Introduction IV S31N 132 136 23437766 Discovery of novel dual inhibitors of the wild-type and the most prevalent drug-resistant mutant, S31N, of the M2 proton channel from influenza A virus. We also found that methylation of the 4-hydroxy 45 maintained the potency for both WT and S31N with IC50 values of 79 muM and 41.3 muM, respectively. 2013 Journal of medicinal chemistry Introduction IV S31N 90 94 23437766 Discovery of novel dual inhibitors of the wild-type and the most prevalent drug-resistant mutant, S31N, of the M2 proton channel from influenza A virus. We also found that the 4-hydroxy of 20 could not be replaced by its bioisomer, 3-furan 25, as this modification led to a marked loss of S31N inhibitory activity from 42% to 8%, respectively. 2013 Journal of medicinal chemistry Introduction IV S31N 136 140 23437766 Discovery of novel dual inhibitors of the wild-type and the most prevalent drug-resistant mutant, S31N, of the M2 proton channel from influenza A virus. We envisioned that the S31N inhibitory activity could be restored if we captured additional interactions within the channel. 2013 Journal of medicinal chemistry Introduction IV S31N 23 27 23437766 Discovery of novel dual inhibitors of the wild-type and the most prevalent drug-resistant mutant, S31N, of the M2 proton channel from influenza A virus. We report here the first examples of compounds with specificity for both S31N and WT. 2013 Journal of medicinal chemistry Introduction IV S31N 73 77 23437766 Discovery of novel dual inhibitors of the wild-type and the most prevalent drug-resistant mutant, S31N, of the M2 proton channel from influenza A virus. We therefore focused on phenyl substituents with a hydrogen-bonding donor/acceptor at 4-position (Table 2) and were gratified to observe that the S31N inhibitory activity did increase gradually for 4-substituted series. 2013 Journal of medicinal chemistry Introduction IV S31N 146 150 23437766 Discovery of novel dual inhibitors of the wild-type and the most prevalent drug-resistant mutant, S31N, of the M2 proton channel from influenza A virus. We turned our attention to the strategy of introducing additional groups (warhead groups) to the amine, in order to enhance affinity for S31N as well as WT by introducing direct/water mediated hydrogen binding/electrostatic interactions with backbone or the groups lining the pore of the M2 channel (Figure 3, approach II). 2013 Journal of medicinal chemistry Introduction IV S31N 137 141 M2 288 290 23437766 Discovery of novel dual inhibitors of the wild-type and the most prevalent drug-resistant mutant, S31N, of the M2 proton channel from influenza A virus. While we succeeded in inhibiting V27A and L26F, none of these compounds inhibited S31N. 2013 Journal of medicinal chemistry Introduction IV V27A;L26F;S31N 33;42;82 37;46;86 23451169 Simultaneous detection of oseltamivir- and amantadine-resistant influenza by oligonucleotide microarray visualization. Furthermore, more than 99% of amantadine resistance generally resulted from mutations V27A and S31N in M2. 2013 PloS one Introduction IV V27A;S31N 86;95 90;99 M2 103 105 23451169 Simultaneous detection of oseltamivir- and amantadine-resistant influenza by oligonucleotide microarray visualization. Most N1 subtypes that are resistant to oseltamivir have been associated with the NA H275Y mutation, while N2 subtypes have been associated with the NA E119V mutation. 2013 PloS one Introduction IV H275Y;E119V 84;151 89;156 NA;NA 81;148 83;150 23451169 Simultaneous detection of oseltamivir- and amantadine-resistant influenza by oligonucleotide microarray visualization. The objective of this study was to design a cost-effective oligonucleotide microarray visualization method to simultaneously detect NA H275Y, NA E119V, M2 V27A, and M2 S31N mutations of influenza A (H3N2), seasonal influenza A (H1N1), and 2009 influenza A (H1N1). 2013 PloS one Introduction IV H275Y;E119V;V27A;S31N 135;145;155;168 140;150;159;172 M2;M2;NA;NA 152;165;132;142 154;167;134;144 23555270 Monomeric nucleoprotein of influenza A virus. By mutagenesis we generated the S165D mutant to mimic this phosphorylation. 2013 PLoS pathogens Introduction IV S165D 32 37 23555270 Monomeric nucleoprotein of influenza A virus. For some mutants like R416A and E339A the equilibrium is shifted to the monomeric form whereas for the Y148A mutant the equilibrium is shifted to the trimeric form. 2013 PLoS pathogens Introduction IV R416A;E339A;Y148A 22;32;103 27;37;108 23555270 Monomeric nucleoprotein of influenza A virus. Here we show the structure of the monomeric R416A mutant and describe the RNA binding characteristics of monomeric wild type NP. 2013 PLoS pathogens Introduction IV R416A 44 49 NP 125 127 23555270 Monomeric nucleoprotein of influenza A virus. S165D was monomeric with the same biophysical characteristics as the R416A mutant but showed high cooperativity for RNA binding at concentrations above the Kd. 2013 PLoS pathogens Introduction IV S165D;R416A 0;69 5;74 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. In September 2011, a cluster of 29 cases infected with oseltamivir-resistant influenza A(H1N1)pdm09 viruses was reported in Australia.18, 19 These oseltamivir-resistant H275Y viruses were in circulation between May, 2011, and August, 2011, a period corresponding to the peak of the SH 2011 influenza season.20 Majority of the patients from whom they were recovered had no known oseltamivir exposure. 2013 Influenza and other respiratory viruses Introduction IV H275Y 169 174 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. Resistance to NAIs among influenza viruses circulating worldwide was previously low (<1%),7, 8 but during the 2007-2008 season, a dramatic emergence of oseltamivir-resistant seasonal influenza A(H1N1) viruses with the H275Y mutation in the NA occurred.9, 10, 11, 12, 13 By the 2008-2009 season, many countries were reporting up to 100% oseltamivir resistance among seasonal influenza A(H1N1) viruses.14, 15 In contrast, oseltamivir resistance among the pandemic A(H1N1)pdm09 viruses circulating in 2009-2010 was <1% in the United States, with majority of oseltamivir-resistant viruses recovered from patients with a history of oseltamivir exposure, many of whom were severely immunocompromised.16 In the subsequent 2010-2011 season, the United States reported approximately 1 0% oseltamivir resistance among the A(H1N1)pdm09 viruses,17 with evidence suggesting a low level of community transmission of these H275Y variants. 2013 Influenza and other respiratory viruses Introduction IV H275Y;H275Y 218;908 223;913 NA;NAI 240;14 242;18 23626667 Quantitative characterization of glycan-receptor binding of H9N2 influenza A virus hemagglutinin. Although the H9N2 virus is yet to adapt to a human host, reassorted viruses carrying HA and NA from a H9N2 virus isolated from a wild terrestrial bird (A/Guinea Fowl/Hong Kong/WF10/99 or WF10) and other genes from human-adapted H3N2 or 2009 pandemic H1N1 have been able to transmit via respiratory droplet in ferrets by acquiring as few as two amino acid changes in the HA, Thr-189 Ala in the RBS and Gly-192 Arg in the HA2 subunit. 2013 PloS one Introduction IV T189A;G192R 374;401 385;412 HA;HA;HA;NA 85;370;420;92 87;372;422;94 23638404 Virtual screening for oseltamivir-resistant a (H5N1) influenza neuraminidase from traditional Chinese medicine database: a combined molecular docking with molecular dynamics approach. In particular H274Y, the principal mutation isolated in association with oseltamivir treatment that is specific to the N1 group (Yen et al.) and that has recently been shown to be present in substantial numbers of H5N1 viruses isolated from humans (Uyeki). 2013 SpringerPlus Introduction IV H274Y 14 19 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. Additionally, the PB2-D701N virus reduced secretion of the antiviral IFN-lambda cytokines and showed enhanced replication in primary human alveolar epithelial cells relative to the wild type H1N1pdm virus. 2013 PloS one Introduction IV D701N 22 27 PB2 18 21 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. However, this contradiction was nicely explained by two studies showing that a unique substitution (PB2-Q591R) in the avian-lineage PB2 of the H1N1pdm virus compensated for the PB2-627E commonly found in human H1N1pdm viruses. 2013 PloS one Introduction IV Q591R 104 109 PB2;PB2;PB2 100;132;177 103;135;180 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. Several groups have shown that introduction of the PB2-E627K substitution into H1N1pdm viruses had little effect on the pathogenesis and/or transmission of H1N1pdm viruses in mice and ferrets. 2013 PloS one Introduction IV E627K 55 60 PB2 51 54 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. The results show that although the wild type H1N1pdm virus contained the PB2-591R polymorphism, the PB2-D701N substitution increased the viral polymerase activity in human cell lines, conferred more efficient virus replication in a restrictive mouse epithelial cell line, increased virulence in the BALB/c mouse model, and increased virus transmission in the ferret transmission model. 2013 PloS one Introduction IV D701N 104 109 PB2;PB2 73;100 76;103 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. Therefore, to evaluate the potential role that PB2-D701N may play in the adaptation of H1N1pdm viruses to humans, we conducted a comprehensive study to determine the influence that PB2-D701N has on viral replication and transmissibility. 2013 PloS one Introduction IV D701N;D701N 51;185 56;190 PB2;PB2 47;181 50;184 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. We hypothesized that since the PB2-D701N substitution has been observed in some zoonotic avian H5N1 viruses and some avian-lineage swine influenza viruses, it may provide an advantage to H1N1pdm viruses as their avian-lineage PB2 gene segment evolves in the human population. 2013 PloS one Introduction IV D701N 35 40 PB2;PB2 31;226 34;229 23860768 Resistance to neuraminidase inhibitors conferred by an R292K mutation in a human influenza virus H7N9 isolate can be masked by a mixed R/K viral population. Neuraminidase (NA) inhibitors have been used as the front-line therapeutic option because the novel H7N9 viruses contain the S31N mutation in the M2 protein conferring resistance to the M2 ion channel blockers. 2013 mBio Introduction IV S31N 125 129 M2;M2;NA;NA 146;186;15;0 148;188;17;13 23860768 Resistance to neuraminidase inhibitors conferred by an R292K mutation in a human influenza virus H7N9 isolate can be masked by a mixed R/K viral population. Recently, the emergence of the R292K mutation in 2 of 14 patients infected with the novel H7N9 influenza virus was reported to be associated with poor clinical outcome. 2013 mBio Introduction IV R292K 31 36 23860768 Resistance to neuraminidase inhibitors conferred by an R292K mutation in a human influenza virus H7N9 isolate can be masked by a mixed R/K viral population. The A/Shanghai/1/2013 isolate has been reported to possess an R292K NA mutation (N2 numbering; R294K for N9 numbering), which is R289K for the novel H7N9 viruses due to the five-amino-acid deletion in the NA stalk region. 2013 mBio Introduction IV R292K;R294K;R289K 62;95;129 67;100;134 N9;NA;NA 105;68;205 107;70;207 23894575 Analysis of adaptation mutants in the hemagglutinin of the influenza A(H1N1)pdm09 virus. An example of one such mutation that has been studied fairly thoroughly is the D222G mutation which has been shown to alter receptor specificity and tropism. 2013 PloS one Introduction IV D222G 79 84 23894575 Analysis of adaptation mutants in the hemagglutinin of the influenza A(H1N1)pdm09 virus. D222G has also been shown to be associated with increased virulence, though other groups have not seen this association . 2013 PloS one Introduction IV D222G 0 5 23894575 Analysis of adaptation mutants in the hemagglutinin of the influenza A(H1N1)pdm09 virus. In contrast, for many mutations that have arisen, including S143G, S185T, A134T, D222E, P297S and E374K, there exists little data reported other than epidemiology, phylogeny, and some limited antigenicity studies. 2013 PloS one Introduction IV S143G;S185T;A134T;D222E;P297S;E374K 60;67;74;81;88;98 65;72;79;86;93;103 23902660 Frequency of D222G haemagglutinin mutant of pandemic (H1N1) pdm09 influenza virus in Tunisia between 2009 and 2011. In addition to the D222G substitution, we focused on another substitution {glutamic acid 374 to lysine acid (E374K)}, mutation located at the stalk of HA2 in the cavity where the fusion domain of mature HA molecules might have an impact on the antigenicity or neutralization activity of influenza A(H1N1)pdm09. 2013 Diagnostic pathology Introduction IV D222G;E374K 19;109 24;114 HA;HA 151;203 153;205 23902660 Frequency of D222G haemagglutinin mutant of pandemic (H1N1) pdm09 influenza virus in Tunisia between 2009 and 2011. In an attempt to understand the relevance of HA D222G substitution among influenza A(H1N1)pdm09 causing infections in Tunisia, HA gene sequences from respiratory specimens of severe and non-severe cases were examined. 2013 Diagnostic pathology Introduction IV D222G 48 53 HA;HA 45;127 47;129 23902660 Frequency of D222G haemagglutinin mutant of pandemic (H1N1) pdm09 influenza virus in Tunisia between 2009 and 2011. Since the first appearance of influenza A(H1N1)pdm09, one particular amino acid substitution {aspartic acid to glycine at position 222 (D222G)} (225 in H3 numbering) within the hemagglutinin (HA) molecule has appeared sporadically in 20 countries, including Norway, Mexico, Ukraine and the USA. 2013 Diagnostic pathology Introduction IV D222G;D222G 136;93 141;134 HA;HA 192;177 194;190 23902660 Frequency of D222G haemagglutinin mutant of pandemic (H1N1) pdm09 influenza virus in Tunisia between 2009 and 2011. The D222G substitution is known to cause a shift from alpha2,6-SA receptor specificity to mixed alpha2,3/alpha2,6-sialic acid receptor specificity. 2013 Diagnostic pathology Introduction IV D222G 4 9 23951116 Resistance mutation R292K is induced in influenza A(H6N2) virus by exposure of infected mallards to low levels of oseltamivir. In N1 virus compensatory mutations in NA and concomitant mutations at the receptor binding site in HA related to H274Y have been described. 2013 PloS one Introduction IV H274Y 113 118 HA;NA 99;38 101;40 23951116 Resistance mutation R292K is induced in influenza A(H6N2) virus by exposure of infected mallards to low levels of oseltamivir. In N2 virus with the R292K mutation no compensatory mutations in NA have been defined, however secondary balancing mutations in the HA are described; in a patient (R228S) and in vitro (N199S and G143E). 2013 PloS one Introduction IV R292K;R228S;N199S;G143E 21;164;185;195 26;169;190;200 HA;NA 132;65 134;67 23951116 Resistance mutation R292K is induced in influenza A(H6N2) virus by exposure of infected mallards to low levels of oseltamivir. The most common resistance mutations are H274Y (N2 numbering, this numbering is used throughout the paper) in the N1, and R292K or E119V in the N2 group. 2013 PloS one Introduction IV H274Y;R292K;E119V 41;122;131 46;127;136 24074585 Mutation from arginine to lysine at the position 189 of hemagglutinin contributes to the antigenic drift in H3N2 swine influenza viruses. In addition, this study was conducted to determine if the R189K mutation contributes to the cross-reaction to sera against human seasonal viruses. 2013 Virology Introduction IV R189K 58 63 24074585 Mutation from arginine to lysine at the position 189 of hemagglutinin contributes to the antigenic drift in H3N2 swine influenza viruses. In this study, four reassortants with 189R or 189K were generated by reverse genetics, and serological assays were conducted for these reassortants to determine if the R189K mutation drives the antigenic drift of these H3N2 SIVs. 2013 Virology Introduction IV R189K 168 173 24139991 Asp44 stabilizes the Trp41 gate of the M2 proton channel of influenza A virus. Finally, we used solution NMR and MD simulations to examine the relative stability of the Cclosed versus Copen state of the channel for wild-type (WT) (Asp44) versus D44N variant of the Udorn protein. 2013 Structure (London, England Introduction IV D44N 166 170 24139991 Asp44 stabilizes the Trp41 gate of the M2 proton channel of influenza A virus. Here, we performed an in-depth electrophysiological examination of the conductance properties of M2 from the A/Udorn/72 and A/FPV/Weybridge/27 strains of the virus, which contain Asp44, with the channel from A/FPV/Rostock/34, which has the D44N mutation. 2013 Structure (London, England Introduction IV D44N 240 244 M2 97 99 24139991 Asp44 stabilizes the Trp41 gate of the M2 proton channel of influenza A virus. The enhanced conductance of M2 in Rostock has been correlated with a mutation of Asp44 to Asn. 2013 Structure (London, England Introduction IV D44N 81 93 M2 28 30 24162312 Adaptation of novel H7N9 influenza A virus to human receptors. H7N9 viruses isolated from human possess for instance the E627K substitution in the PB2 RNA polymerase subunit, which has been shown to facilitate RNA replication in mammalian cells and transmission between ferrets. 2013 Scientific reports Introduction IV E627K 58 63 PB2 84 87 24165891 Characterization of two distinct neuraminidases from avian-origin human-infecting H7N9 influenza viruses. Amino acid sequence alignment of A/Anhui/1/2013 N9 and A/Shanghai/1/2013 N9 with the previously characterized A/Tern/Australia/G70C/1975(H11N9) N9 illustrates that H7N9 N9 is missing five amino acids in the stem region (Figure 1). 2013 Cell research Introduction IV G70C 127 131 N9;N9;N9;N9 48;73;144;169 50;75;146;171 24165891 Characterization of two distinct neuraminidases from avian-origin human-infecting H7N9 influenza viruses. Furthermore, viruses carrying R294K exhibit compromised growth and fitness in vitro and were found to revert back to wild-type NA (R294) following multiple cycles of replication. 2013 Cell research Introduction IV R294K 30 35 127 129 24165891 Characterization of two distinct neuraminidases from avian-origin human-infecting H7N9 influenza viruses. However, naturally-occurring N9 carrying the R294K substitution has never been found in nature before. 2013 Cell research Introduction IV R294K 45 50 N9 29 31 24165891 Characterization of two distinct neuraminidases from avian-origin human-infecting H7N9 influenza viruses. Moreover, there are 23 amino acid polymorphisms between the A/Anhui/1/2013 N9 and A/Tern/Australia/G70C/1975 N9 head regions. 2013 Cell research Introduction IV G70C 99 103 N9;N9 75;109 77;111 24165891 Characterization of two distinct neuraminidases from avian-origin human-infecting H7N9 influenza viruses. Our findings demonstrate that the H7N9 R294K substitution not only confers multidrug resistance, but also decreases NA activity and impairs virus replication. 2013 Cell research Introduction IV R294K 39 44 116 118 24165891 Characterization of two distinct neuraminidases from avian-origin human-infecting H7N9 influenza viruses. The R294K substitution has later been reported in 3 other H7N9 patients that were treated with oseltamivir. 2013 Cell research Introduction IV R294K 4 9 24165891 Characterization of two distinct neuraminidases from avian-origin human-infecting H7N9 influenza viruses. This explains why H7N9 carrying R294K (A/Shanghai/1/2013 virus as its prototype) failed to be the dominant virus in this outbreak. 2013 Cell research Introduction IV R294K 32 37 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. Comparisons between WT and D325A+R343V SP-D NCRDs allow the linking of viral neutralization to molecular properties underlying HA/SP-D binding, thereby promoting a greater understanding of the recognition of IAV by innate host defense molecules. 2013 Biochemistry Introduction IV D325A;R343V 27;33 32;38 HA 127 129 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. For example, we have reported that unlike WT, D325A+R343V inhibits seasonal and poorly glycosylated pandemic strains of IAV and protects against influenza infection when administered intra-tracheally to mice . 2013 Biochemistry Introduction IV D325A;R343V 46;52 51;57 IV infections 145 164 24237039 3-Azatetracyclo[5.2.1.1(5,8).0(1,5)]undecane derivatives: from wild-type inhibitors of the M2 ion channel of influenza A virus to derivatives with potent activity against the V27A mutant. Alkylation of 14a to 15a reduced the inhibitory potency both for the wt and the V27A mutant. 2013 Journal of medicinal chemistry Introduction IV V27A 80 84 24237039 3-Azatetracyclo[5.2.1.1(5,8).0(1,5)]undecane derivatives: from wild-type inhibitors of the M2 ion channel of influenza A virus to derivatives with potent activity against the V27A mutant. Also, since recent MD calculations suggested that larger, more hydrophobic molecules may fill the pore of the V27A mutant better, we designed two novel, larger analogs of the dual inhibitor 16a. 2013 Journal of medicinal chemistry Introduction IV V27A 110 114 24237039 3-Azatetracyclo[5.2.1.1(5,8).0(1,5)]undecane derivatives: from wild-type inhibitors of the M2 ion channel of influenza A virus to derivatives with potent activity against the V27A mutant. As expected, in going from 14a and 16a to the smaller analogs 14b and 16b, an important reduction of the activity against the V27A mutant was observed, although both compounds kept the inhibitory activity against the wt. 2013 Journal of medicinal chemistry Introduction IV V27A 126 130 24237039 3-Azatetracyclo[5.2.1.1(5,8).0(1,5)]undecane derivatives: from wild-type inhibitors of the M2 ion channel of influenza A virus to derivatives with potent activity against the V27A mutant. Based on these promising results, we reasoned that the synthesis of pyrrolidine analogs of the already active bisnoradamantane 7, featuring an unprecedented 3-azatetracyclo[5.2.1.15,8.01,5]undecane ring, may lead to compounds with higher activity against the wt and the V27A mutant of A/M2. 2013 Journal of medicinal chemistry Introduction IV V27A 270 274 M2 287 289 24237039 3-Azatetracyclo[5.2.1.1(5,8).0(1,5)]undecane derivatives: from wild-type inhibitors of the M2 ion channel of influenza A virus to derivatives with potent activity against the V27A mutant. In agreement with the previous trend observed in going from 8 and 9 to 10 and 11, pyrrolidines 14a and 16a were potent inhibitors of the wt channel (IC50 of 9.7 and 6.1 muM, respectively) and, very interestingly, were better inhibitors of the V27A mutant channel than 7, with the guanidine 16a showing an IC50 of 11.4 muM. 2013 Journal of medicinal chemistry Introduction IV V27A 243 247 24237039 3-Azatetracyclo[5.2.1.1(5,8).0(1,5)]undecane derivatives: from wild-type inhibitors of the M2 ion channel of influenza A virus to derivatives with potent activity against the V27A mutant. In agreement with the TEV assays (see above), all the compounds were not active against the amantadine-resistant A/PR/8/34 strain that carries the M2-S31N mutation. 2013 Journal of medicinal chemistry Introduction IV S31N 150 154 M2 147 149 24237039 3-Azatetracyclo[5.2.1.1(5,8).0(1,5)]undecane derivatives: from wild-type inhibitors of the M2 ion channel of influenza A virus to derivatives with potent activity against the V27A mutant. In going from the dimethyl derivatives 14a and 16a to their corresponding diethyl derivatives, 14c and 16c, the activity against both the wt and the V27A mutant channels diminished, probably because the freely rotating ethyl chains of 14c and 16c make destabilizing contacts with the backbone of the protein. 2013 Journal of medicinal chemistry Introduction IV V27A 149 153 24237039 3-Azatetracyclo[5.2.1.1(5,8).0(1,5)]undecane derivatives: from wild-type inhibitors of the M2 ion channel of influenza A virus to derivatives with potent activity against the V27A mutant. In our basic CPE reduction assays with influenza virus, performed in MDCK cell cultures, three virus strains were used: the A/PR/8/34 strain, an A/H1N1 virus with two amantadine-resistance mutations (S31N and V27T) in the A/M2 protein; the A/HK/7/87 strain, which has a wt A/M2 protein, and the B/HK/5/72 strain. 2013 Journal of medicinal chemistry Introduction IV S31N;V27T 200;209 204;213 M2;M2 224;275 226;277 24237039 3-Azatetracyclo[5.2.1.1(5,8).0(1,5)]undecane derivatives: from wild-type inhibitors of the M2 ion channel of influenza A virus to derivatives with potent activity against the V27A mutant. In the conformationally more rigid amine 14d and guanidine 16d the low micromolar inhibitory activity against the wt channel was restored and, pleasingly, good inhibition of the V27A mutant channel was observed, with 16d showing an IC50 of 0.29 muM. 2013 Journal of medicinal chemistry Introduction IV V27A 178 182 24237039 3-Azatetracyclo[5.2.1.1(5,8).0(1,5)]undecane derivatives: from wild-type inhibitors of the M2 ion channel of influenza A virus to derivatives with potent activity against the V27A mutant. Interestingly, 11 (at a concentration of 100 muM) inhibited the A/M2 V27A channel activity by 17.7%, which is superior to Amt (10.8%), yet much less than 1-3. 2013 Journal of medicinal chemistry Introduction IV V27A 69 73 M2 66 68 24237039 3-Azatetracyclo[5.2.1.1(5,8).0(1,5)]undecane derivatives: from wild-type inhibitors of the M2 ion channel of influenza A virus to derivatives with potent activity against the V27A mutant. L26F, V27A, and S31N) have been observed in transmissible viruses, with the S31N mutation being the most frequently occurring Amt-resistance mutation. 2013 Journal of medicinal chemistry Introduction IV L26F;V27A;S31N;S31N 0;6;16;76 4;10;20;80 24237039 3-Azatetracyclo[5.2.1.1(5,8).0(1,5)]undecane derivatives: from wild-type inhibitors of the M2 ion channel of influenza A virus to derivatives with potent activity against the V27A mutant. Moreover, while the primary amines 8 and 9 did not show any activity against the V27A mutant form of A/M2, both pyrrolidine derivatives showed a marginal activity against this mutant (Table 1). 2013 Journal of medicinal chemistry Introduction IV V27A 81 85 M2 103 105 24237039 3-Azatetracyclo[5.2.1.1(5,8).0(1,5)]undecane derivatives: from wild-type inhibitors of the M2 ion channel of influenza A virus to derivatives with potent activity against the V27A mutant. Most recently, this group also discovered new compounds, such as 4 and 5, that inhibit the most prevalent drug-resistant A/M2 mutant, S31N (Chart 1). 2013 Journal of medicinal chemistry Introduction IV S31N 134 138 M2 123 125 24237039 3-Azatetracyclo[5.2.1.1(5,8).0(1,5)]undecane derivatives: from wild-type inhibitors of the M2 ion channel of influenza A virus to derivatives with potent activity against the V27A mutant. Recent experimental and computational studies have shown that the mutation of Val27 to a residue with a smaller side chain such as alanine (A/M2-V27A mutant) destroyed the hydrophobic gate formed by this residue and increased the pore radius by ~2 A at the N-terminal end. 2013 Journal of medicinal chemistry Introduction IV V27A 145 149 M2 142 144 24237039 3-Azatetracyclo[5.2.1.1(5,8).0(1,5)]undecane derivatives: from wild-type inhibitors of the M2 ion channel of influenza A virus to derivatives with potent activity against the V27A mutant. Several pyrrolidine derivatives were found to inhibit the wt channel as well as the M2-V27A mutant ion channel. 2013 Journal of medicinal chemistry Introduction IV V27A 87 91 M2 84 86 24237039 3-Azatetracyclo[5.2.1.1(5,8).0(1,5)]undecane derivatives: from wild-type inhibitors of the M2 ion channel of influenza A virus to derivatives with potent activity against the V27A mutant. Spiroadamantane 3 inhibits the L26F and V27A A/M2 mutants with good efficacy in electrophysiological and virus plaque reduction assays. 2013 Journal of medicinal chemistry Introduction IV L26F;V27A 31;40 35;44 M2 47 49 24237039 3-Azatetracyclo[5.2.1.1(5,8).0(1,5)]undecane derivatives: from wild-type inhibitors of the M2 ion channel of influenza A virus to derivatives with potent activity against the V27A mutant. The amine 14a and guanidine 16a displayed higher inhibitory activity against the M2-V27A mutant channel than their corresponding smaller analogs, 14b and 16b (see below). 2013 Journal of medicinal chemistry Introduction IV V27A 84 88 M2 81 83 24237039 3-Azatetracyclo[5.2.1.1(5,8).0(1,5)]undecane derivatives: from wild-type inhibitors of the M2 ion channel of influenza A virus to derivatives with potent activity against the V27A mutant. The best compound, guanidine 16d, has a low micromolar activity against the wt channel (IC50 = 3.4 muM) and submicromolar activity against the M2-V27A mutant (IC50 = 0.29 muM). 2013 Journal of medicinal chemistry Introduction IV V27A 146 150 M2 143 145 24237039 3-Azatetracyclo[5.2.1.1(5,8).0(1,5)]undecane derivatives: from wild-type inhibitors of the M2 ion channel of influenza A virus to derivatives with potent activity against the V27A mutant. They displayed similar IC50 values for wt A/M2 as Amt, but, unfortunately, were inactive against the Amt-resistant S31N or V27A mutant forms of A/M2. 2013 Journal of medicinal chemistry Introduction IV S31N;V27A 115;123 119;127 M2;M2 44;146 46;148 24312396 Conformational polymorphism of m7GTP in crystal structure of the PB2 middle domain from human influenza A virus. Here we report PB2 middle domain structure (318-483) belonging to subtype H1N1 human influenza with m7GTP (Figure 1), which has two mutations (P453H, I471T) to increase solubility of this domain. 2013 PloS one Introduction IV P453H;I471T 143;150 148;155 PB2 15 18 Influenza 79 94 24312396 Conformational polymorphism of m7GTP in crystal structure of the PB2 middle domain from human influenza A virus. Our structure is the first deposited structure of a PB2 domain containing the pathogenicity determinant lysine 627 in the Protein Data Bank (2008 Apr 21) and we also revealed the RNA binding ability of this domain which is strengthened by the E627K mutation. 2013 PloS one Introduction IV E627K 243 248 PB2 52 55 24312396 Conformational polymorphism of m7GTP in crystal structure of the PB2 middle domain from human influenza A virus. The crystal structures of the large C-terminal domain of PB2, including this E627K mutation, which enables human infection, were reported by us and other. 2013 PloS one Introduction IV E627K 77 82 PB2 57 60 24391498 A single amino acid in the stalk region of the H1N1pdm influenza virus HA protein affects viral fusion, stability and infectivity. Recent surveillance data has revealed the emergence of a prominent mutation, E47K (HA2 numbering) in the HA2 stalk region of H1N1pdm isolates. 2014 PLoS pathogens Introduction IV E47K 77 81 HA;HA 83;105 85;107 24391498 A single amino acid in the stalk region of the H1N1pdm influenza virus HA protein affects viral fusion, stability and infectivity. The vaccine yield was improved by the E119K and G186D (H1 numbering) changes in the HA1 head region of the HA. 2014 PLoS pathogens Introduction IV E119K;G186D 38;48 43;53 HA;HA1 107;84 109;87 24503069 The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus. In this study, we examined the effects of the Phe95 Tyr mutation at the levels of both recombinant protein and virus. 2014 Virology Introduction IV F95Y 46 55 24503069 The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus. Our data demonstrate that the mutation Phe95 Tyr restores all three hydrogen bonds made by Tyr-98 in influenza A/H3 HA and has the potential to enhance receptor binding. 2014 Virology Introduction IV F95Y 39 48 HA 116 118 24503069 The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus. Since this glycosylation site is located on the 190-helix that forms the upper edge of the receptor-binding site, we tested the mutation Phe95 Tyr on influenza B virus HA with a glycosylation at HA1 194 (wild type) or without (Asn194 Asp). 2014 Virology Introduction IV F95Y;N194D 137;227 146;237 HA;HA1 168;195 170;198 24524021 Generation and Characterization of Recombinant Influenza A(H1N1) Viruses Resistant to Neuraminidase Inhibitors. Other NA mutations (N2 numbering: E119G, H274Y, R292K, and N295S) that have been reported to confer resistance to NAIs were each introduced into recombinant A/Vietnam/1203/04(H5N1) influenza virus. 2013 Osong public health and research perspectives Introduction IV E119G;H274Y;R292K;N295S 34;41;48;59 39;46;53;64 NA;NAI 6;114 8;118 24524021 Generation and Characterization of Recombinant Influenza A(H1N1) Viruses Resistant to Neuraminidase Inhibitors. Particularly, most isolated seasonal influenza A(H1N1) viruses during the 2008-2009 season were found to encode the H275Y substitution in the NA gene, conferring resistance to oseltamivir. 2013 Osong public health and research perspectives Introduction IV H275Y 116 121 142 144 24524021 Generation and Characterization of Recombinant Influenza A(H1N1) Viruses Resistant to Neuraminidase Inhibitors. The dominant change conferring oseltamivir resistance in the current seasonal influenza viruses is a mutation in the NA gene, H275Y (N1 numbering). 2013 Osong public health and research perspectives Introduction IV H275Y 126 131 117 119 24524021 Generation and Characterization of Recombinant Influenza A(H1N1) Viruses Resistant to Neuraminidase Inhibitors. The frequency of isolates with the H275Y mutation has increased with each flu season, including in countries where oseltamivir is not prescribed regularly. 2013 Osong public health and research perspectives Introduction IV H275Y 35 40 24563658 Synergistic combinations of favipiravir and oseltamivir against wild-type pandemic and oseltamivir-resistant influenza A virus infections in mice. In addition, these inhibitors were also tested in a newly developed oseltamivir-resistant (H275Y, N1 numbering) virus infection model in mice. 2013 Future virology Introduction IV H275Y 91 96 24569063 An investigational antiviral drug, DAS181, effectively inhibits replication of zoonotic influenza A virus subtype H7N9 and protects mice from lethality. In 4 influenza A(H7N9)-infected patients, emergence of virus variants with Arg292Lys (R292K) substitution in the NA (N2 numbering) was detected during antiviral treatment, at least one of which was a fatal case. 2014 The Journal of infectious diseases Introduction IV R292K;R292K 75;86 84;91 113 115 24569063 An investigational antiviral drug, DAS181, effectively inhibits replication of zoonotic influenza A virus subtype H7N9 and protects mice from lethality. R292K was shown to be associated with decreased susceptibility to oseltamivir and other NAIs. 2014 The Journal of infectious diseases Introduction IV R292K 0 5 NAI 88 92 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. Epidemiological investigations revealed that this OR virus had spread in the near absence of oseltamivir treatment, prompting concern that these A(H1N1)pdm09 viruses may have obtained the capability to acquire the NA H275Y mutation without compromising viral fitness, much as seasonal A(H1N1) viruses had done previously. 2014 PLoS pathogens Introduction IV H275Y 217 222 214 216 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. Experiments with early A(H1N1)pdm09 viruses (from 2009) demonstrated that introduction of the H275Y mutation decreased total NA activity, largely by decreasing NA expression levels. 2014 PLoS pathogens Introduction IV H275Y 94 99 NA;NA 125;160 127;162 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. However in 2008, OR (H275Y) seasonal A(H1N1) viruses emerged and spread globally within 12 months, in the absence of oseltamivir selection pressure, clearly demonstrating that the fitness of H275Y seasonal A(H1N1) viruses was no longer compromised by the resistance mutation. 2014 PLoS pathogens Introduction IV H275Y;H275Y 21;191 26;196 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. Previously, we used a computational analysis to predict that two NA mutations present in a large number of A(H1N1)pdm09 viruses sampled during 2010-2011 (V241I and N369K) and a third NA mutation which, although absent from the majority of A(H1N1)pdm09 viruses, was present in viruses from the HNE2011 cluster (N386S), could potentially offset the deleterious effect of H275Y upon the A(H1N1)pdm09 NA. 2014 PLoS pathogens Introduction IV V241I;N369K;N386S;H275Y 154;164;310;369 159;169;315;374 NA;NA;NA 65;183;397 67;185;399 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. Since 2009, virological surveillance has reported that the proportion of OR A(H1N1)pdm09 viruses encoding the NA H275Y mutation has remained around 1% globally, and for the first two years following its emergence only limited sporadic transmissions of H275Y A(H1N1)pdm09 viruses were reported between individuals in closed or near-contact settings. 2014 PLoS pathogens Introduction IV H275Y;H275Y 113;252 118;257 110 112 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. Since its emergence, there has been a concern that the same NA H275Y mutation may also become fixed within circulating A(H1N1)pdm09 viruses. 2014 PLoS pathogens Introduction IV H275Y 63 68 60 62 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. Subsequent analysis of more recent A(H1N1)pdm09 NA sequences submitted to GISAID and GenBank since mid 2012 revealed that V241I and N369K are now present in virtually all (>99%) of globally circulating A(H1N1)pdm09 viruses, whereas the N386S NA mutation has not been maintained in contemporary A(H1N1)pdm09 viruses (Figure S1). 2014 PLoS pathogens Introduction IV V241I;N369K;N386S 122;132;236 127;137;241 NA;NA 48;242 50;244 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. Subsequent investigations revealed the presence of several "permissive" mutations (R222Q, V234M, and possibly D354G) in the NA of 2008-2009 seasonal A(H1N1) viruses that enabled the acquisition of H275Y without compromising viral fitness. 2014 PLoS pathogens Introduction IV R222Q;V234M;D354G;H275Y 83;90;110;197 88;95;115;202 124 126 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. The most common oseltamivir resistance (OR) mutation detected in A/H1N1 viruses is the NA H275Y mutation. 2014 PLoS pathogens Introduction IV H275Y 90 95 87 89 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. Therefore enhancing the total NA activity of viruses containing H275Y is likely to be a key factor required for the efficient replication and transmission of OR A(H1N1)pdm09 viruses. 2014 PLoS pathogens Introduction IV H275Y 64 69 30 32 24751348 PCR for detection of oseltamivir resistance mutation in influenza A(H7N9) virus. Studies have shown that the NA R292K mutation can cause a high level of resistance to oseltamivir in influenza A(H7N9) virus . 2014 Emerging infectious diseases Introduction IV R292K 31 36 28 30 24751348 PCR for detection of oseltamivir resistance mutation in influenza A(H7N9) virus. We reported emergence of an influenza virus with a mutation in the neuraminidase (NA) gene (R292K) and its association with severe clinical outcome in infected persons. 2014 Emerging infectious diseases Introduction IV R292K 92 97 NA;NA 82;67 84;80 24795482 A novel I221L substitution in neuraminidase confers high-level resistance to oseltamivir in influenza B viruses. In 2007-2008, seasonal influenza A viruses bearing an H275Y substitution in neuraminidase (NA) conferring resistance to oseltamivir emerged in patients who were not receiving oseltamivir treatment. 2014 The Journal of infectious diseases Introduction IV H275Y 54 59 NA;NA 91;76 93;89 24795482 A novel I221L substitution in neuraminidase confers high-level resistance to oseltamivir in influenza B viruses. Influenza B viruses carrying NA-I221T and, more recently, the I221V substitution were recovered from untreated patients. 2014 The Journal of infectious diseases Introduction IV I221T;I221V 32;62 37;67 29 31 24795482 A novel I221L substitution in neuraminidase confers high-level resistance to oseltamivir in influenza B viruses. The most frequent substitutions responsible for oseltamivir resistance in vivo correspond to H275Y, E119V/I, and D197N/E/Y for N1, N2, and influenza B virus neuraminidases, respectively. 2014 The Journal of infectious diseases Introduction IV H275Y;E119V;E119I;D197N;D197E;D197Y 93;100;100;113;113;113 98;107;107;122;122;122 157 171 24795482 A novel I221L substitution in neuraminidase confers high-level resistance to oseltamivir in influenza B viruses. We are the first to report influenza B viruses, isolated from an immunocompromised patient after prolonged oseltamivir treatment, with good fitness carrying a novel I221L substitution (B numbering) in NA that confers high-level resistance to oseltamivir. 2014 The Journal of infectious diseases Introduction IV I221L 165 170 201 203 24889237 Enhanced human receptor binding by H5 haemagglutinins. An H5 virus in which the Gln226Leu substitution has occurred has not been isolated from either birds or from humans. 2014 Virology Introduction IV Q226L 25 34 24889237 Enhanced human receptor binding by H5 haemagglutinins. Based on these results, the human and avian receptor binding modes of H5 HAs bearing the Ser227Asn/Gln196Arg, Asn186Lys, and Delta133/Ile155Thr substitutions were determined by X-ray crystallography. 2014 Virology Introduction IV Q196R;I155T;S227N;N186K;S227Q;S227R 99;134;89;110;89;89 108;143;98;119;98;98 24889237 Enhanced human receptor binding by H5 haemagglutinins. The clade 2.2 H5 double mutant Delta133/Ile155Thr HA also had increased affinity for human receptor but had little changed affinity for avian receptor. 2014 Virology Introduction IV I155T 40 49 HA 50 52 24889237 Enhanced human receptor binding by H5 haemagglutinins. The receptor binding specificity and transmissibility changes described in all these H5 transmission studies involved the substitution Gln226Leu in HA (in H3 HA numbering here and subsequently), a substitution previously correlated experimentally with the avian to human receptor binding change. 2014 Virology Introduction IV Q226L 135 144 HA;HA 148;158 150;160 24889237 Enhanced human receptor binding by H5 haemagglutinins. The results indicate that two substitutions in H5 clade 1 HA Asn186Lys and Ser227Asn significantly decreased affinity for avian receptor and that the former mutation, which introduces a positive charge, enhanced human receptor binding. 2014 Virology Introduction IV N186K;S227N 61;75 70;84 HA 58 60 24928037 The R35 residue of the influenza A virus NS1 protein has minimal effects on nuclear localization but alters virus replication through disrupting protein dimerization. Recombinant viruses with the R35A mutation were only rescued when spontaneous, novel second site mutations at position D39 arose. 2014 Virology Introduction IV R35A 29 33 24928037 The R35 residue of the influenza A virus NS1 protein has minimal effects on nuclear localization but alters virus replication through disrupting protein dimerization. Viruses encoding the R37A, R38A and K41A mutations were recovered and had minimal effects on virus replication and NS1 nuclear localization. 2014 Virology Introduction IV R37A;R38A;K41A 21;27;36 25;31;40 NS1 115 118 24928037 The R35 residue of the influenza A virus NS1 protein has minimal effects on nuclear localization but alters virus replication through disrupting protein dimerization. We demonstrate that second site mutation at position D39 are able to correct for a loss in dimerization caused by the R35A mutation, thereby restoring virus replication. 2014 Virology Introduction IV R35A 118 122 24941437 Easily accessible polycyclic amines that inhibit the wild-type and amantadine-resistant mutants of the M2 channel of influenza A virus. Again, several of these novel compounds displayed similar IC50 values for wt A/M2 as Amt, and, interestingly, we found three guanidine derivatives that displayed low micromolar to submicromolar IC50 values against the V27A mutant channel. 2014 Journal of medicinal chemistry Introduction IV V27A 218 222 M2 79 81 24941437 Easily accessible polycyclic amines that inhibit the wild-type and amantadine-resistant mutants of the M2 channel of influenza A virus. Altogether, guanidine 14 emerged as the more promising compound, being more potent than Amt against the wt M2 channel and endowed with fair activity against the V27A mutant channel. 2014 Journal of medicinal chemistry Introduction IV V27A 161 165 M2 107 109 24941437 Easily accessible polycyclic amines that inhibit the wild-type and amantadine-resistant mutants of the M2 channel of influenza A virus. Amt inhibited wt A/M2 channel with an IC50 of 16.0 muM while being inactive against the V27A mutant channel. 2014 Journal of medicinal chemistry Introduction IV V27A 88 92 M2 19 21 24941437 Easily accessible polycyclic amines that inhibit the wild-type and amantadine-resistant mutants of the M2 channel of influenza A virus. Compared to compound 18, the lower, more compact size of Amt should likely enhance the exchange rate between the two ligand orientations, eventually leading to an easier release from the pore that could account for the reduction in inhibitory potency against the V27A channel (Table 1). 2014 Journal of medicinal chemistry Introduction IV V27A 263 267 24941437 Easily accessible polycyclic amines that inhibit the wild-type and amantadine-resistant mutants of the M2 channel of influenza A virus. During the past years, our group has synthesized several polycyclic Amt analogues containing different scaffolds, including ring-contracted, ring-rearranged, and 2,2-dialkyl derivatives of Amt.- Several of them displayed similar IC50 values for wt A/M2 as Amt but, unfortunately, were inactive against the Amt-resistant S31N or V27A mutant forms of A/M2. 2014 Journal of medicinal chemistry Introduction IV S31N;V27A 320;328 324;332 M2;M2 250;351 252;353 24941437 Easily accessible polycyclic amines that inhibit the wild-type and amantadine-resistant mutants of the M2 channel of influenza A virus. Finally, amine 18 and guanidine 19 also proved to be active against the wt channel, with similar IC50 values as Amt (18.5 and 10.7 muM, respectively) while being endowed with submicromolar IC50 against the V27A mutant (0.7 and 0.5 muM, respectively). 2014 Journal of medicinal chemistry Introduction IV V27A 206 210 24941437 Easily accessible polycyclic amines that inhibit the wild-type and amantadine-resistant mutants of the M2 channel of influenza A virus. Furthermore, we have identified two compounds, 18 and 19, that are capable of inhibiting the M2-V27A mutant ion channel with submicromolar IC50 values. 2014 Journal of medicinal chemistry Introduction IV V27A 96 100 M2 93 95 24941437 Easily accessible polycyclic amines that inhibit the wild-type and amantadine-resistant mutants of the M2 channel of influenza A virus. However, only a few of these mutations (i.e., L26F, V27A, and S31N) have been observed in transmissible viruses, with the S31N mutation being the most frequently occurring Amt-resistance mutation. 2014 Journal of medicinal chemistry Introduction IV L26F;V27A;S31N;S31N 46;52;62;122 50;56;66;126 24941437 Easily accessible polycyclic amines that inhibit the wild-type and amantadine-resistant mutants of the M2 channel of influenza A virus. In addition, both compounds are able to inhibit the M2 wt channel with an IC50 value similar to that of Amt, and both are also low micromolar inhibitors of the M2-L26F mutant channel. 2014 Journal of medicinal chemistry Introduction IV L26F 163 167 M2;M2 52;160 54;162 24941437 Easily accessible polycyclic amines that inhibit the wild-type and amantadine-resistant mutants of the M2 channel of influenza A virus. In two replicas of the V27A-18 complex, the inhibitor adopts the down orientation, but in the third replica it turns over at the beginning of the trajectory and the inhibitor adopts the opposite (up) orientation (the distance of the amine nitrogen to the His37 plane and the tilt angle are, on average, 14.9 A and 145.3 ; Figure 1 and Supporting Information Figure S3). 2014 Journal of medicinal chemistry Introduction IV V27A 23 27 24941437 Easily accessible polycyclic amines that inhibit the wild-type and amantadine-resistant mutants of the M2 channel of influenza A virus. It was noted that the structure of the S31N variant closely resembled previous structures of the wt M2 channel, showing most similarity to the Amt-bound channel structure solved by solid-state NMR. 2014 Journal of medicinal chemistry Introduction IV S31N 39 43 M2 100 102 24941437 Easily accessible polycyclic amines that inhibit the wild-type and amantadine-resistant mutants of the M2 channel of influenza A virus. Moreover, both compounds were low micromolar inhibitors of the L26F mutant (8.6 and 7.5 muM, respectively). 2014 Journal of medicinal chemistry Introduction IV L26F 63 67 24941437 Easily accessible polycyclic amines that inhibit the wild-type and amantadine-resistant mutants of the M2 channel of influenza A virus. Previously, we have seen that, in related polycyclic compounds, on going from secondary to tertiary amines, the inhibitory effect on either wt or V27A mutant M2 channels diminished. 2014 Journal of medicinal chemistry Introduction IV V27A 146 150 M2 158 160 24941437 Easily accessible polycyclic amines that inhibit the wild-type and amantadine-resistant mutants of the M2 channel of influenza A virus. Regarding the activity against the V27A M2 mutant channel, three trends were found, i.e., guanidine performed better than its corresponding amine (e.g., 7 vs 6 or 13 vs 11), the fully saturated compounds were more potent than their corresponding unsaturated analogues (e.g., 7 vs 5 or 14 vs 13), and the cyclobutane/cyclobutene analogues were more potent than the cyclopropane derivatives (e.g., 12 vs 6 or 14 vs 7). 2014 Journal of medicinal chemistry Introduction IV V27A 35 39 M2 40 42 24941437 Easily accessible polycyclic amines that inhibit the wild-type and amantadine-resistant mutants of the M2 channel of influenza A virus. Remarkably, Amt was found in the up orientation in the three replicas run for the V27A channel (Supporting Information Figure S4), and even in one case Amt was released to the solvent after few nanoseconds. 2014 Journal of medicinal chemistry Introduction IV V27A 82 86 24941437 Easily accessible polycyclic amines that inhibit the wild-type and amantadine-resistant mutants of the M2 channel of influenza A virus. reported that spiro compound 1 is able of inhibiting the L26F and V27A M2 mutants with good efficacy in electrophysiological and plaque reduction assays.- More recently, our group has reported the first non-adamantane inhibitor of the V27A mutant, the polycyclic pyrrolidine 2 (Chart 1). 2014 Journal of medicinal chemistry Introduction IV L26F;V27A;V27A 57;66;235 61;70;239 M2 71 73 24941437 Easily accessible polycyclic amines that inhibit the wild-type and amantadine-resistant mutants of the M2 channel of influenza A virus. Taking into account that recent experimental and computational studies have shown that the M2-V27A mutant channel has a larger cavity than the wt M2 channel,- we also synthesized larger compounds derived from 4 and 6. 2014 Journal of medicinal chemistry Introduction IV V27A 94 98 M2;M2 91;146 93;148 24941437 Easily accessible polycyclic amines that inhibit the wild-type and amantadine-resistant mutants of the M2 channel of influenza A virus. The lack of inhibitory potency of compound 18 against the S31N variant can be realized from the comparison of the inhibitor bound to the wt M2 channel and the solid-state NMR-derived structural data available for the complex of the S31N channel bound to the 5-thienyl isoxazole derivative containing a 1-(1-adamantylamino)-methylene group in position 3 (PDB entry 2LY0). 2014 Journal of medicinal chemistry Introduction IV S31N;S31N 58;232 62;236 M2 140 142 24941437 Easily accessible polycyclic amines that inhibit the wild-type and amantadine-resistant mutants of the M2 channel of influenza A virus. The root-mean-square deviation (RMSD) of the protein backbone for the transmembrane helices between the wt channel and its V27A variant amounts to 1.4 A, which compare with the typical range of RMSD values obtained for the ligand-bound forms of the two channels (between 1.2 and 1.7 A; Supporting Information Table S1). 2014 Journal of medicinal chemistry Introduction IV V27A 123 127 24941437 Easily accessible polycyclic amines that inhibit the wild-type and amantadine-resistant mutants of the M2 channel of influenza A virus. This effect may explain, at least in part, the antiviral activity of these compounds, although they were devoid of activity against the S31N M2 mutant channel. 2014 Journal of medicinal chemistry Introduction IV S31N 136 140 M2 141 143 24941437 Easily accessible polycyclic amines that inhibit the wild-type and amantadine-resistant mutants of the M2 channel of influenza A virus. This structural rearrangement likely contributes to the displacement of the amine nitrogen of compound 18 in the V27A channel, which is pushed away from the His37 plane by 1.6 A (from 6.1 A in the wt channel to 7.7 A in the V27A variant for the inhibitor in the down orientation) and might facilitate the exchange between down and up arrangements of the inhibitor. 2014 Journal of medicinal chemistry Introduction IV V27A;V27A 113;224 117;228 24941437 Easily accessible polycyclic amines that inhibit the wild-type and amantadine-resistant mutants of the M2 channel of influenza A virus. This suggests that the gross structural features of the channel are not drastically altered by the Val27 Ala mutation, in agreement with previous studies. 2014 Journal of medicinal chemistry Introduction IV V27A 99 110 24941437 Easily accessible polycyclic amines that inhibit the wild-type and amantadine-resistant mutants of the M2 channel of influenza A virus. Three other compounds, i.e., 8, 11, and 18, showed strong activity against the A/PR/8/34 strain, an A/H1N1 virus with two mutations (S31N and V27T) in the M2 protein. 2014 Journal of medicinal chemistry Introduction IV S31N;V27T 133;142 137;146 M2 155 157 24941437 Easily accessible polycyclic amines that inhibit the wild-type and amantadine-resistant mutants of the M2 channel of influenza A virus. To explore the molecular basis of the exchange between down and up orientations found in the V27A channel, additional MD simulations were run for the apo forms of both wt and V27A channels. 2014 Journal of medicinal chemistry Introduction IV V27A;V27A 93;175 97;179 24941437 Easily accessible polycyclic amines that inhibit the wild-type and amantadine-resistant mutants of the M2 channel of influenza A virus. To gain insight into the inhibitory data of the more compact pyrrolidine derivatives, the interaction of 18 with the wt M2 channel and its V27A variant was examined by means of molecular dynamics (MD) simulations and compared with the trends found for the binding of Amt. 2014 Journal of medicinal chemistry Introduction IV V27A 139 143 M2 120 122 25043638 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2012-2013. Amino acid substitutions D344N and R222Q in the NA of former seasonal A(H1N1) compensated for the detrimental effect of the HRI H275Y substitution on virus fitness, allowing the virus to spread efficiently. 2014 Antiviral research Introduction IV D344N;R222Q;H275Y 25;35;128 30;40;133 48 50 25043638 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2012-2013. The most extreme example was in 2007/2008, when the former seasonal A(H1N1) virus acquired the NA H275Y substitution and spread globally in approximately 12 months. 2014 Antiviral research Introduction IV H275Y 98 103 95 97 25066276 Development and clinical testing of a simple, low-density gel element array for influenza identification, subtyping, and H275Y detection. The objectives of this study were therefore to develop a simplified gel element microarray test for influenza A and B virus detection, influenza A sub typing, and H275Y variant detection in both seasonal and pandemic influenza A/H1N1 subtypes, with an emphasis on minimizing overall microarray test complexity for diagnostic ease-of-use and eventual translation into a sample-to-answer, fully automated system. 2014 Journal of virological methods Introduction IV H275Y 163 168 25078692 A single amino acid substitution in the novel H7N9 influenza A virus NS1 protein increases CPSF30 binding and virulence. A single I106M substitution in novel H7N9 NS1 enhances CPSF30 binding and inhibition of host gene expression. 2014 Journal of virology Introduction IV I106M 9 14 NS1 42 45 25078692 A single amino acid substitution in the novel H7N9 influenza A virus NS1 protein increases CPSF30 binding and virulence. An H7N9-based virus expressing NS1-I106M shows enhanced replication and virulence in vivo. 2014 Journal of virology Introduction IV I106M 35 40 NS1 31 34 25078692 A single amino acid substitution in the novel H7N9 influenza A virus NS1 protein increases CPSF30 binding and virulence. Characterization of an H7N9-based virus expressing NS1-I106M in vitro. 2014 Journal of virology Introduction IV I106M 55 60 NS1 51 54 25078692 A single amino acid substitution in the novel H7N9 influenza A virus NS1 protein increases CPSF30 binding and virulence. Even in the highly virulent rSh/1 (6+2) background, the NS1-I106M mutation led to a modest ~2.5-fold increase in MLD50, and mice infected with the NS1-I106M virus exhibited greater overall mortality. 2014 Journal of virology Introduction IV I106M;I106M 60;151 65;156 NS1;NS1 56;147 59;150 25078692 A single amino acid substitution in the novel H7N9 influenza A virus NS1 protein increases CPSF30 binding and virulence. However, FLAG-CPSF30 bound efficiently (and equally) to NS1-I106M and NS1-DM, suggesting that the H7N9 NS1-CPSF30 interaction is indeed weak but can be strengthened by the single I106M substitution. 2014 Journal of virology Introduction IV I106M;I106M 60;179 65;184 NS1;NS1;NS1 56;70;103 59;73;106 25078692 A single amino acid substitution in the novel H7N9 influenza A virus NS1 protein increases CPSF30 binding and virulence. In agreement with our pulldown studies, NS1-L103F was also unable to inhibit Renilla luciferase activity, while both NS1-I106M and NS1-DM proteins efficiently limited activity. 2014 Journal of virology Introduction IV L103F;I106M 44;121 49;126 NS1;NS1;NS1 40;117;131 43;120;134 25078692 A single amino acid substitution in the novel H7N9 influenza A virus NS1 protein increases CPSF30 binding and virulence. Notably, both WT and NS1-I106M virus infection led to the same low-level (~3- to 5-fold) induction of the reporter. 2014 Journal of virology Introduction IV I106M 25 30 NS1 21 24 25078692 A single amino acid substitution in the novel H7N9 influenza A virus NS1 protein increases CPSF30 binding and virulence. Notably, qRT-PCR analysis of lung homogenates from independently infected mice suggested a trend for the NS1-I106M virus to induce less IFN-beta mRNA than the WT virus; however, this difference was not statistically significant. 2014 Journal of virology Introduction IV I106M 109 114 NS1 105 108 25078692 A single amino acid substitution in the novel H7N9 influenza A virus NS1 protein increases CPSF30 binding and virulence. Only a small amount of FLAG-CPSF30 could be precipitated by NS1-WT or NS1-L103F. 2014 Journal of virology Introduction IV L103F 74 79 NS1;NS1 60;70 63;73 25078692 A single amino acid substitution in the novel H7N9 influenza A virus NS1 protein increases CPSF30 binding and virulence. Surprisingly, multicycle replication experiments revealed that the recombinant WT and NS1-I106M viruses grew with kinetics identical to each other in primary differentiated human tracheobronchial epithelial (HTBE) cells (Clonetics, Lonza, Walkersville, MD, USA). 2014 Journal of virology Introduction IV I106M 90 95 NS1 86 89 25078692 A single amino acid substitution in the novel H7N9 influenza A virus NS1 protein increases CPSF30 binding and virulence. The I106M substitution also did not have an impact on the coprecipitation of Riplet with NS1, although there was a possible enhancement of this interaction when NS1 constructs contained the L103F substitution. 2014 Journal of virology Introduction IV I106M;L103F 4;190 9;195 NS1;NS1 89;161 92;164 25078692 A single amino acid substitution in the novel H7N9 influenza A virus NS1 protein increases CPSF30 binding and virulence. The I106M substitution specifically enhanced CPSF30 binding, as no differences were observed between NS1-WT and any of the NS1 mutants with regard to interaction with RIG-I or TRIM25. 2014 Journal of virology Introduction IV I106M 4 9 NS1;NS1 101;123 104;126 25078692 A single amino acid substitution in the novel H7N9 influenza A virus NS1 protein increases CPSF30 binding and virulence. The NS1-I106M virus replicated to titers >5-fold higher than those of the WT by day 2 (P = 0.0056), while titers at day 4 were similar. 2014 Journal of virology Introduction IV I106M 8 13 NS1 4 7 25078692 A single amino acid substitution in the novel H7N9 influenza A virus NS1 protein increases CPSF30 binding and virulence. The two viruses [rSh/1 (6+2) WT and rSh/1 (6+2) NS1-I106M, where "r" indicates recombinant] were plaque purified, and stocks were grown and titrated in MDCK cells. 2014 Journal of virology Introduction IV I106M 52 57 NS1 48 51 25078692 A single amino acid substitution in the novel H7N9 influenza A virus NS1 protein increases CPSF30 binding and virulence. These results indicate that the single I106M substitution in H7N9 NS1 restores both CPSF30 binding and the inhibition of cellular gene expression. 2014 Journal of virology Introduction IV I106M 39 44 NS1 66 69 25078692 A single amino acid substitution in the novel H7N9 influenza A virus NS1 protein increases CPSF30 binding and virulence. To test whether increased affinity of H7N9 NS1 toward CPSF30 would affect viral replication and pathogenicity in vivo, we determined 50% mouse lethal dose (MLD50) values for the WT and NS1-I106M viruses in 6- to 8-week-old C57BL/6 mice (Jackson Laboratory, ME). 2014 Journal of virology Introduction IV I106M 189 194 NS1;NS1 43;185 46;188 25078692 A single amino acid substitution in the novel H7N9 influenza A virus NS1 protein increases CPSF30 binding and virulence. Using an H7N9 reverse genetics system, we generated recombinant WT and NS1-I106M viruses containing the 6 "internal" gene segments of Sh/1 and the HA and NA gene segments from A/Puerto Rico/8/1934 (PR8; H1N1). 2014 Journal of virology Introduction IV I106M 75 80 HA;NA;NS1 147;154;71 149;156;74 25078692 A single amino acid substitution in the novel H7N9 influenza A virus NS1 protein increases CPSF30 binding and virulence. We identify the single I106M natural polymorphism found in non-H7N9 strains as a potential gain-of-function mechanism by which the H7N9 NS1 could acquire CPSF30 binding and provide evidence that this substitution promotes virus replication and virulence in vivo. 2014 Journal of virology Introduction IV I106M 23 28 NS1 136 139 25078692 A single amino acid substitution in the novel H7N9 influenza A virus NS1 protein increases CPSF30 binding and virulence. We speculate that the virulence-enhancing impact of H7N9 NS1-I106M may be even more pronounced in the context of non-PR8 glycoproteins, where the respective WT virus would have a much higher MLD50. 2014 Journal of virology Introduction IV I106M 61 66 NS1 57 60 25078692 A single amino acid substitution in the novel H7N9 influenza A virus NS1 protein increases CPSF30 binding and virulence. We tested the coprecipitation of FLAG-tagged CPSF30 with bacterially expressed 6His-tagged wild-type (WT) Sh/2 NS1, as well as with L103F, I106M, or L103F/I106M double-mutant (DM) variants that we predicted might have a different CPSF30-binding profile. 2014 Journal of virology Introduction IV L103F;I106M;L103F;I106M 132;139;149;155 137;144;154;160 NS1 111 114 25119465 Functional balance between the hemagglutinin and neuraminidase of influenza A(H1N1)pdm09 HA D222 variants. In mouse models, conflicting results have been reported, with some suggesting that D222G H1N1pdm viruses acquire an enhanced pathogenicity while others fail to display evidence of such an effect. 2014 PloS one Introduction IV D222G 83 88 25119465 Functional balance between the hemagglutinin and neuraminidase of influenza A(H1N1)pdm09 HA D222 variants. Preliminary epidemiological studies from Norway reported a higher frequency of the D222G mutation in hemagglutinin (HA, H1 numbering) of influenza viruses cultured from severe cases compared with mild cases. 2014 PloS one Introduction IV D222G 83 88 HA;HA 116;101 118;114 25119465 Functional balance between the hemagglutinin and neuraminidase of influenza A(H1N1)pdm09 HA D222 variants. Previous studies have indicated that the D222G substitution influenced the receptor binding specificity of the 1918 pandemic influenza A(H1N1) virus. 2014 PloS one Introduction IV D222G 41 46 25119465 Functional balance between the hemagglutinin and neuraminidase of influenza A(H1N1)pdm09 HA D222 variants. The D222G mutation in HA has only been detected sporadically and did not form a distinct phylogenetic cluster associated with a sustained chain of transmission. 2014 PloS one Introduction IV D222G 4 9 HA 22 24 25124927 Characterization of drug-resistant influenza A(H7N9) variants isolated from an oseltamivir-treated patient in Taiwan. Both NA changes, R292K and E119V, were previously associated with oseltamivir resistance in patients infected with seasonal influenza A(H3N2). 2015 The Journal of infectious diseases Introduction IV R292K;E119V 17;27 22;32 5 7 25124927 Characterization of drug-resistant influenza A(H7N9) variants isolated from an oseltamivir-treated patient in Taiwan. For example, replication of influenza A(H3N2) containing NA-R292K was impaired when tested in ferrets. 2015 The Journal of infectious diseases Introduction IV R292K 60 65 57 59 25124927 Characterization of drug-resistant influenza A(H7N9) variants isolated from an oseltamivir-treated patient in Taiwan. Furthermore, a mixture of 119Glu/Val (119E/V) was detected in influenza A(H7N9) collected from a patient following oseltamivir treatment; the patient died of acute respiratory distress syndrome. 2015 The Journal of infectious diseases Introduction IV E119V 26 36 Acute respiratory distress syndrome 158 193 25124927 Characterization of drug-resistant influenza A(H7N9) variants isolated from an oseltamivir-treated patient in Taiwan. However, oseltamivir-resistant viruses can overcome reduction in fitness; seasonal influenza A(H1N1) carrying NA-H275Y spread globally during the 2008-2009 influenza seasons. 2015 The Journal of infectious diseases Introduction IV H275Y 113 118 110 112 25124927 Characterization of drug-resistant influenza A(H7N9) variants isolated from an oseltamivir-treated patient in Taiwan. In addition to NA-R292K, pyrosequencing identified changes at conserved residues NA-E119V, NA-I222K, or NA-I222R in the E1 isolate. 2015 The Journal of infectious diseases Introduction IV R292K;E119V;I222K;I222R 18;84;94;107 23;89;99;112 NA;NA;NA;NA 15;81;91;104 17;83;93;106 25124927 Characterization of drug-resistant influenza A(H7N9) variants isolated from an oseltamivir-treated patient in Taiwan. It was reported that A/Shanghai/1/2013 (Shanghai/1), collected from the patient soon after initiation of oseltamivir treatment, contained the NA substitution Arg292Lys (R292K in N2 amino acid numbering; R289K in 2013 H7N9 numbering). 2015 The Journal of infectious diseases Introduction IV R292K;R292K;R289K 158;169;203 167;174;208 142 144 25124927 Characterization of drug-resistant influenza A(H7N9) variants isolated from an oseltamivir-treated patient in Taiwan. Recombinant influenza A(H7N9) with or without NA-R292K displayed comparable virulence in mice and transmissibility in guinea pigs. 2015 The Journal of infectious diseases Introduction IV R292K 49 54 46 48 25124927 Characterization of drug-resistant influenza A(H7N9) variants isolated from an oseltamivir-treated patient in Taiwan. The Shanghai/1 NA-R292K virus was shown to replicate efficiently in cell culture. 2015 The Journal of infectious diseases Introduction IV R292K 18 23 15 17 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. Our results identify a single V43I mutation in PB1 protein that affects viral genetic diversity and provides the first experimental evidence of the role of genetic diversity in IAV pathogenicity. 2014 Nature communications Introduction IV V43I 30 34 PB1 47 50 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. PB1-V43I mutation is identified to increase polymerase fidelity in recombinant Wuhan95 virus as well as in a highly pathogenic H5N1 virus (A/Vietnam/1203/04; VN04). 2014 Nature communications Introduction IV V43I 4 8 PB1 0 3 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. The recombinant VN04 virus with the PB1-V43I mutation replicates to comparable titres as the wild-type counterpart in vitro or in the mouse lungs, but has reduced population diversity at day 3 post-inoculation. 2014 Nature communications Introduction IV V43I 40 44 PB1 36 39 25191344 Prevalence of Oseltamivir-Resistant 2009 H1N1 Influenza Virus among Patients with Pandemic 2009 H1N1 Influenza infection in NRITLD, Tehran, Iran. Oseltamivir-resistant infection with the 2009 pandemic influenza A (H1N1) virus that is conferred by the H275Y substitution in the neuraminidase (NA) has so far been described in 298 patients by the WHO. 2011 Tanaffos Introduction IV H275Y 105 110 NA;NA 146;131 148;144 25328558 Influenza A H1N1pdm 2009 Virus in Paraguay: Nucleotide Point Mutations in Hemagglutinin and Neuraminidase Genes are not Associated with Drug Resistance. In Argentina, a study carried out in 2009 isolated six oseltamivir-resistant strains containing the NA H275Y mutation, from 262 cases with mild to severe forms of the disease; none of the mutations in HA or NA were related to fatal cases. 2014 The open virology journal Introduction IV H275Y 103 108 HA;NA;NA 201;100;207 203;102;209 25328558 Influenza A H1N1pdm 2009 Virus in Paraguay: Nucleotide Point Mutations in Hemagglutinin and Neuraminidase Genes are not Associated with Drug Resistance. In the HA protein, we did not find the S101N mutation, which is thought to be an adaptation to the human host, or D239E/G, which has been associated with severe clinical outcomes and exacerbate forms of respiratory disease, or N387H, localized at a glycosylation site that could potentially affect the antigenic properties of influenza viruses. 2014 The open virology journal Introduction IV S101N;D239E;D239G;N387H 39;114;114;227 44;121;121;232 HA 7 9 25328558 Influenza A H1N1pdm 2009 Virus in Paraguay: Nucleotide Point Mutations in Hemagglutinin and Neuraminidase Genes are not Associated with Drug Resistance. The amino acid S220 is localized within the HA antigenic site designated Ca (site C, subsite a) as well as at the receptor binding domain (RBD); thus, S220T could affect the transmissibility and infectivity of H1N1 in humans. 2014 The open virology journal Introduction IV S220T 151 156 HA 44 46 25328558 Influenza A H1N1pdm 2009 Virus in Paraguay: Nucleotide Point Mutations in Hemagglutinin and Neuraminidase Genes are not Associated with Drug Resistance. The NA protein of the Paraguayan viruses showed two amino acid substitutions, V106I (100%) and N248D (100%). 2014 The open virology journal Introduction IV V106I;N248D 78;95 83;100 4 6 25328558 Influenza A H1N1pdm 2009 Virus in Paraguay: Nucleotide Point Mutations in Hemagglutinin and Neuraminidase Genes are not Associated with Drug Resistance. The substitution E391K found in this study has been previously identified as part of a highly conserved epitope in the 1918 H1N1 virus, with a possible role in membrane fusion. 2014 The open virology journal Introduction IV E391K 17 22 25328558 Influenza A H1N1pdm 2009 Virus in Paraguay: Nucleotide Point Mutations in Hemagglutinin and Neuraminidase Genes are not Associated with Drug Resistance. Two amino acid substitutions, S220T (100%), and E391K (30.8%), were observed in the HA protein of the Paraguayan viruses (Table 2). 2014 The open virology journal Introduction IV S220T;E391K 30;48 35;53 HA 84 86 25328558 Influenza A H1N1pdm 2009 Virus in Paraguay: Nucleotide Point Mutations in Hemagglutinin and Neuraminidase Genes are not Associated with Drug Resistance. V106I was reported in H1N1 cases of the 20th century (in 1918 [pandemic] and 1977), whereas N248D was also reported in 1977. 2014 The open virology journal Introduction IV V106I;N248D 0;92 5;97 25328558 Influenza A H1N1pdm 2009 Virus in Paraguay: Nucleotide Point Mutations in Hemagglutinin and Neuraminidase Genes are not Associated with Drug Resistance. We did not find the NA D199N mutation associated with an increase in oseltamivir resistance published in both seasonal and H5N1 virus strains, or the I223R mutation associated with resistance to oseltamivir, zanamivir and peramivir, or H275Y, located at the DTD and related to oseltamivir resistance especially in immunocompromised or severely ill people. 2014 The open virology journal Introduction IV D199N;I223R;H275Y 23;150;236 28;155;241 20 22 25409547 The K526R substitution in viral protein PB2 enhances the effects of E627K on influenza virus replication. A T271A substitution in PB2 was also described to enhance replication of 2009 H1N1 and H5N1 viruses in mammalian cells in vitro. 2014 Nature communications Introduction IV T271A 2 7 PB2 24 27 25409547 The K526R substitution in viral protein PB2 enhances the effects of E627K on influenza virus replication. Genetic and structural analyses found that the HA of H7N9 contains a Q226L substitution, which may confer a certain level of ability for binding to human type sialic acid receptors. 2014 Nature communications Introduction IV Q226L 69 74 HA 47 49 25409547 The K526R substitution in viral protein PB2 enhances the effects of E627K on influenza virus replication. However, the Q226L mutation has been found in avian H9N2 viruses, which have been prevalent in poultry for several years, with only a limited number of human infections having been identified since 1997 (ref.). 2014 Nature communications Introduction IV Q226L 13 18 25409547 The K526R substitution in viral protein PB2 enhances the effects of E627K on influenza virus replication. PB2 D701N and Q591K substitutions were also found to support H5N1 virus replication in mammalian hosts. 2014 Nature communications Introduction IV D701N;Q591K 4;14 9;19 PB2 0 3 25409547 The K526R substitution in viral protein PB2 enhances the effects of E627K on influenza virus replication. The E627K substitution enhances H5N1 virus replication in the upper respiratory tract, where the temperature, at 33 C, is slightly lower than the core body temperature. 2014 Nature communications Introduction IV E627K 4 9 25409547 The K526R substitution in viral protein PB2 enhances the effects of E627K on influenza virus replication. The most well-characterized adaptation marker is PB2 E627K, which was found in a significant proportion of H5N1 human infections and also in one case of H7N7 infection. 2014 Nature communications Introduction IV E627K 53 58 PB2 49 52 Influenza A virus H5N1 infection;Influenza A virus H7N7 infection 107;153 128;167 25409547 The K526R substitution in viral protein PB2 enhances the effects of E627K on influenza virus replication. Various PB2 adaptation markers are identified among the H7N9 human isolates, and a K526R substitution associated with other previously defined adaptive markers is detected in some human isolates. 2014 Nature communications Introduction IV K526R 83 88 PB2 8 11 25409547 The K526R substitution in viral protein PB2 enhances the effects of E627K on influenza virus replication. While about 50% of H5N1 human isolates contain known PB2 adaptation markers, mainly E627K with some D701N and a few instances of 591K, as described above, the other half of human infections are not associated with known adaptation markers. 2014 Nature communications Introduction IV E627K;D701N 84;100 89;105 PB2 53 56 25470189 Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel. Among these three drug resistant mutants, S31N is the predominant mutant and persists in more than 95% of currently circulating influenza viruses. 2014 Journal of the American Chemical Society Introduction IV S31N 42 46 25470189 Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel. As an illustration, the H5N1 strains isolated from Vietnam, Thailand, and Cambodia have the characteristic S31N mutation, which confers amantadine resistance. 2014 Journal of the American Chemical Society Introduction IV S31N 107 111 25470189 Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel. Corroborating observations in cell cultures, large-scale sequencing of transmissible viruses from 1918 to 2008 have identified only three major amantadine-resistant M2 mutants, S31N, V27A, and L26F. 2014 Journal of the American Chemical Society Introduction IV S31N;V27A;L26F 177;183;193 181;187;197 M2 165 167 25470189 Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel. Herein, we describe the extension of these studies to design dual inhibitors targeting both WT and the S31N mutant. 2014 Journal of the American Chemical Society Introduction IV S31N 103 107 25470189 Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel. Herein, we focus on M2 as a drug target and report the design of a novel class of M2 channel blockers that are active against both the WT and the S31N mutant. 2014 Journal of the American Chemical Society Introduction IV S31N 146 150 M2;M2 20;82 22;84 25470189 Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel. However, mutations surrounding the drug binding site, such as S31N, V27A, A30T, and L26F, lead to escape of drug inhibition. 2014 Journal of the American Chemical Society Introduction IV S31N;V27A;A30T;L26F 62;68;74;84 66;72;78;88 25470189 Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel. Nevertheless, progress has been made in designing inhibitors targeting the drug-resistant mutants of M2 guided by MD simulations- and NMR structures M2.- The designed small molecule channel blockers inhibit V27A, L26F, and S31N M2 with potencies greater than that of amantadine in both electrophysiological assays and antiviral plaque reduction assays. 2014 Journal of the American Chemical Society Introduction IV V27A;L26F;S31N 207;213;223 211;217;227 M2;M2;M2 101;149;228 103;151;230 25470189 Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel. These inhibitors not only represent excellent leads for further development, but also help stabilize the otherwise dynamic M2 protein, leading to the determination of the first high resolution solution NMR structure of the A/M2-S31N mutant. 2014 Journal of the American Chemical Society Introduction IV S31N 228 232 M2;M2 123;225 125;227 25589893 Identification of novel compounds against an R294K substitution of influenza A (H7N9) virus using ensemble based drug virtual screening. Orientation and stabilization of various inhibitors in NA protein depend major on two or three Arginine residues in 150 loop, R292K mutation succeeded to unbalance stability and orientation of these inhibitors leading to drug resistance. 2015 International journal of medical sciences Introduction IV R292K 126 131 55 57 25589893 Identification of novel compounds against an R294K substitution of influenza A (H7N9) virus using ensemble based drug virtual screening. Single amino acid change known as the "H275Y" mutation in 2009 H1N1 flu virus and "R292K" mutation in influenza A virus is conferred by drug resistance. 2015 International journal of medical sciences Introduction IV H275Y;R292K 38;82 44;88 25589893 Identification of novel compounds against an R294K substitution of influenza A (H7N9) virus using ensemble based drug virtual screening. The most remarkable mutation is in S31N position that maintains the function of M2 channel in the present of adamantine drugs. 2015 International journal of medical sciences Introduction IV S31N 35 39 M2 80 82 25589893 Identification of novel compounds against an R294K substitution of influenza A (H7N9) virus using ensemble based drug virtual screening. Unexpectedly, all novel influenza A H7N9 viruses possess the mutation S31N in M2 protein channel and N9 serotype (designated as A/Shanghai/1/2013) encoded for R294K mutation. 2015 International journal of medical sciences Introduction IV S31N;R294K 70;159 74;164 M2;N9 78;101 80;103 25659818 Assessment of transmission, pathogenesis and adaptation of H2 subtype influenza viruses in ferrets. During a respiratory droplet transmission experiment in ferrets there was an apparent selection of a virus variant with a receptor binding site (Gln226Leu) mutation in the HA, which rendered the virus transmissible. 2015 Virology Introduction IV Q226L 145 154 HA 172 174 25659818 Assessment of transmission, pathogenesis and adaptation of H2 subtype influenza viruses in ferrets. Previous studies of 1957 H2N2 HA suggested that both a hydrophobic switch from Gln to Leu at 226 and a slight elongation (~0.5 A) of the receptor-binding site (RBS) were critical for avian H2 HA to acquire human receptor specificity. 2015 Virology Introduction IV Q226L 79 96 HA;HA 30;192 32;194 25713566 PB2 segment promotes high-pathogenicity of H5N1 avian influenza viruses in mice. The PB1-F2 Asn66Ser variant also reduced the production of host IFN alpha/beta (Conenello et al.,). 2015 Frontiers in microbiology Introduction IV N66S 11 19 PB1F2 4 10 25721488 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2013-2014. Additional NA substitutions (R222Q, V234M, D344N and D354G) compensated for the detrimental effect of the H275Y substitution on virus fitness, allowing the virus to spread efficiently. 2015 Antiviral research Introduction IV R222Q;V234M;D344N;D354G;H275Y 29;36;43;53;106 34;41;48;58;111 11 13 25721488 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2013-2014. Animal models have shown that A(H1N1)pdm09 H275Y viruses with additional NA amino acid substitutions, V241I and N369K, have increased replication and transmission fitness. 2015 Antiviral research Introduction IV H275Y;V241I;N369K 43;102;112 48;107;117 73 75 25721488 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2013-2014. Despite >99% of circulating viruses being sensitive to all four NAIs during the 2012-2013 period, localised community circulation of influenza viruses with RI or HRI has occurred in recent years, most notably with A(H1N1)pdm09 viruses containing the H275Y NA substitution. 2015 Antiviral research Introduction IV H275Y 250 255 NA;NAI 256;64 258;68 25721488 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2013-2014. Experience from 2007-2008, when the former seasonal A(H1N1) virus acquired oseltamivir resistance due to an H275Y neuraminidase (NA) amino acid substitution and spread globally within 12 months, has demonstrated that surveillance for NAI-resistant viruses is essential both to guide seasonal clinical management and inform pandemic preparedness strategies. 2015 Antiviral research Introduction IV H275Y 108 113 NA;NAI;NA 129;234;114 131;237;127 25721488 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2013-2014. Importantly, >97% of the N1 sequences from circulating A(H1N1)pdm09 viruses in 2012-2013 contained the two NA substitutions V241I and N369 K that improve viral fitness of the variant virus. 2015 Antiviral research Introduction IV V241I;N369K 124;134 129;140 107 109 25721488 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2013-2014. The former seasonal A(H1N1) H275Y virus exhibited highly reduced inhibition (HRI) by oseltamivir and peramivir in vitro and was shown to be clinically resistant to oseltamivir. 2015 Antiviral research Introduction IV H275Y 28 33 25742269 Oseltamivir-resistant influenza A(H1N1)pdm2009 strains found in Brazil are endowed with permissive mutations, which compensate the loss of fitness imposed by antiviral resistance. Nevertheless, the H275Y change may emerge in a NA endowed with permissive mutations, which compensates for the decrease in viral fitness imposed by OST resistance. 2015 Memorias do Instituto Oswaldo Cruz Introduction IV H275Y 18 23 47 49 25742269 Oseltamivir-resistant influenza A(H1N1)pdm2009 strains found in Brazil are endowed with permissive mutations, which compensate the loss of fitness imposed by antiviral resistance. Remarkably, community transmission of OST-resistant influenza A(H1N1)pdm09 has drawn special attention because mutation H275Y in the neuraminidase (NA) may decrease viral fitness . 2015 Memorias do Instituto Oswaldo Cruz Introduction IV H275Y 120 125 NA;NA 148;133 150;146 25766295 Structure and receptor binding of the hemagglutinin from a human H6N1 influenza virus. For example, for avian H5N1 virus, Glu190Asp and Gly225Asp mutations abolished receptor binding, while Gln226Leu and Gly228Ser mutations produced partial recognition of alpha2-6 linked receptors, but alpha2-3 binding was not lost. 2015 Cell host & microbe Introduction IV E190D;G225D;Q226L;G228S 35;49;103;117 44;58;112;126 25766295 Structure and receptor binding of the hemagglutinin from a human H6N1 influenza virus. For H1 subtypes, Glu190Asp and Gly225Asp substitutions are critical for attaining specificity for human receptors, as in the 1918 and 2009 pandemic H1N1 strains. 2015 Cell host & microbe Introduction IV E190D;G225D 17;31 26;40 25766295 Structure and receptor binding of the hemagglutinin from a human H6N1 influenza virus. In contrast, for the 1957 H2N2 and 1968 H3N2 pandemic viruses, Gln226Leu and Gly228Ser substitutions were responsible for the switch between avian-type and human-type receptor specificity. 2015 Cell host & microbe Introduction IV Q226L;G228S 63;77 72;86 25768797 Adamantane-resistant influenza a viruses in the world (1902-2013): frequency and distribution of M2 gene mutations. constructed recombinant H1N1 influenza A viruses with the commonly observed L26F, V27A, A30T, S31N, G34E, and V27A/S31N mutations in the M2 gene by using reverse genetics, and showed all of these mutations are able to cause amantadine resistance. 2015 PloS one Introduction IV L26F;V27A;A30T;S31N;G34E;V27A;S31N 76;82;88;94;100;110;115 80;86;92;98;104;114;119 M2 137 139 25768797 Adamantane-resistant influenza a viruses in the world (1902-2013): frequency and distribution of M2 gene mutations. In particular, the S31N substitution renders the virus highly resistant to adamantanes, and the incidence of clinical isolates bearing this mutation has jumped from a small percentage to approximately 97% in recent years. 2015 PloS one Introduction IV S31N 19 23 25768797 Adamantane-resistant influenza a viruses in the world (1902-2013): frequency and distribution of M2 gene mutations. So far, the known mutations that confer resistance against adamantanes are L26F, V27A, A30T, A30V, S31N, G34E and L38F in the M2 transmembrane region. 2015 PloS one Introduction IV L26F;V27A;A30T;A30V;S31N;G34E;L38F 75;81;87;93;99;105;114 79;85;91;97;103;109;118 M2 126 128 25861376 Molecular docking of potential inhibitors for influenza H7N9. Furthermore, the authors proposed that the drug resistance caused by mutation of R294K in H7N9 was more serious than that caused by mutation of H274Y in H7N1. 2015 Computational and mathematical methods in medicine Introduction IV R294K;H274Y 81;144 86;149 25861376 Molecular docking of potential inhibitors for influenza H7N9. Previously, it was observed that the Asp701Asn mutation in PB2 and the Ser31Asn mutation in hemagglutinin increased the adaptability to mammals, and the Ser31Asn mutation of M2 contributed at least partly to the resistance of antivirus drugs including amantadine and rimantadine. 2015 Computational and mathematical methods in medicine Introduction IV D701N;S31N;S31N 37;71;153 46;79;161 HA;M2;PB2 92;174;59 105;176;62 25861376 Molecular docking of potential inhibitors for influenza H7N9. solved the structures for neuraminidases of A/Anhui/1/2013 (N9, R294) and A/Shanghai/1/2013 (N9, K294), which showed that the mutation of R294K could induce conformation changes and generate oseltamivir resistance through interfering with the binding of oseltamivir carboxylate. 2015 Computational and mathematical methods in medicine Introduction IV R294K 138 143 N9;N9;NA 60;93;26 62;95;40 25966032 Virological characterization of influenza H1N1pdm09 in Vietnam, 2010-2013. Amino acid substitution in NP (D101G), PA L295P), and PB2 (E158E/A) was associated with virulence or enhanced transcription and replication activity. 2015 Influenza and other respiratory viruses Introduction IV D101G;L295P;E158E;E158A 31;42;59;59 36;47;66;66 NP;PA;PB2 27;39;54 29;41;57 25966032 Virological characterization of influenza H1N1pdm09 in Vietnam, 2010-2013. For example, the amino acid substitution at position D222G/E/N (H1 numbering) in the HA molecule was associated with increased viremia, severe pneumonia, and deaths; a substitution (I219K) in the glycan receptor-binding site of HA quantitatively increased its human receptor-binding affinity; and substitutions D131E, S186, and A198E contribute to virulence in mice. 2015 Influenza and other respiratory viruses Introduction IV D222G;D222E;D222N;I219K;D131E;A198E 53;53;53;182;311;328 62;62;62;187;316;333 HA;HA 85;228 87;230 Pneumonia 143 152 25966032 Virological characterization of influenza H1N1pdm09 in Vietnam, 2010-2013. In addition, substitutions I117V, I223R, and H275Y on the NA protein conferred reduced susceptibility to oseltamivir. 2015 Influenza and other respiratory viruses Introduction IV I117V;I223R;H275Y 27;34;45 32;39;50 58 60 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. An isoleucine-to-valine mutation at residue 223 (I223V) of the NA protein also reduced susceptibility to oseltamivir (6-fold), peramivir (3-fold), and zanamivir (2-fold). 2015 PloS one Introduction IV I223V;I223V 49;3 54;47 63 65 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. Another study of the I223R mutant observed a 6-12 hour delay of initial viral replication with MDCK-2,6 (SIAT-1) cells. 2015 PloS one Introduction IV I223R 21 26 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. Comparative studies and competition trials have demonstrated that the H275Y mutation is accompanied by only a minor reduction in fitness, and evidence of community transmission has recently been observed. 2015 PloS one Introduction IV H275Y 70 75 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. Experimental measurements of IC50 values revealed that the H275Y mutation reduces susceptibility to both oseltamivir (980-fold for A/Quebec/144147/09) and peramivir (660-fold). 2015 PloS one Introduction IV H275Y 59 64 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. Fitness studies of mutations at residue 223 have produced varied results, from reduced viral titers and plaques sizes for the I223R mutant to improved replication for both I223R and I223V. 2015 PloS one Introduction IV I223R;I223R;I223V 126;172;182 131;177;187 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. However in recent years some resistance has been reported, and subsequent analysis revealed the presence of the H275Y mutation in a large number of these cases. 2015 PloS one Introduction IV H275Y 112 117 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. In this report, we apply a mathematical model introduced in previous work, to analyze a set of experiments with the H1N1pdm09 wild-type strain and its I223V single-mutant counterpart. 2015 PloS one Introduction IV I223V 151 156 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. Initial studies showed that the H1N1pdm09 strain did not bear the H275Y mutation and was susceptible to NA inhibitors. 2015 PloS one Introduction IV H275Y 66 71 104 106 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. The I223V and isoleucine-to-arginine (I223R) mutations have been detected in patients treated with oseltamivir, suggesting the possible emergence of a viable resistant strain through an I223 mutation. 2015 PloS one Introduction IV I223V;I223R 4;38 9;43 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. The resistance in the seasonal strain, due to a histidine-to-tyrosine mutation at position 275 of the neuraminidase (NA) protein (H275Y) and subsequent permissive mutations, raised concern about similar mutations occurring within the pandemic strain. 2015 PloS one Introduction IV H275Y;H275Y 130;48 135;94 NA;NA 117;102 119;115 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. This analysis revealed that the primary effects of the H275Y substitution were an increase of the initial eclipse period and a decrease of the viral burst size, with little decrease to overall fitness. 2015 PloS one Introduction IV H275Y 55 60 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. We also compare these extracted parameters to those recovered from our previous work to assess the fitness of both the H275Y and I223V single-mutants, relative to the H1N1pdm09 influenza strain and to one another. 2015 PloS one Introduction IV H275Y;I223V 119;129 124;134 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. We evaluate the impact of this I223V mutation on the fitness of the H1N1pdm09 influenza strain by analyzing the viral load curves and extracting the key biological parameters characterizing the replicative fitness. 2015 PloS one Introduction IV I223V 31 36 25999284 Egg-adaptive mutations in H3N2v vaccine virus enhance egg-based production without loss of antigenicity or immunogenicity. Of these four, the combinationG1861V + N2461K (the subscript indicates HA1) produced the greatest HA yields. 2015 Vaccine Introduction IV N2461K 39 45 HA;HA1 98;71 100;74 25999284 Egg-adaptive mutations in H3N2v vaccine virus enhance egg-based production without loss of antigenicity or immunogenicity. The G186V substitution in the receptor-binding domain of H3 HA1 is reported to be egg-adaptive and improve virus yield, as are amino acid changes at positions 183, 194-196, and 226. 2015 Vaccine Introduction IV G186V 4 9 HA1 60 63 26038410 Adaptive mutation in influenza A virus non-structural gene is linked to host switching and induces a novel protein by alternative splicing. Among 11 individual adaptive NS1 mutations, the nonsynonymous nucleotide substitution A374G inducing the D125G(GAT GGT) mutation caused the greatest increase in viral replication and virulence in the mouse in vivo, which were associated with increased RNA polymerase activity, interferon antagonism, and protein synthesis in mouse cells in vitro. 2012 Emerging microbes & infections Introduction IV A374G;D125G 86;105 91;110 NS1 29 32 26038410 Adaptive mutation in influenza A virus non-structural gene is linked to host switching and induces a novel protein by alternative splicing. For instance, 226I and 227K NS1 mutations are convergent with the 1918 H1N1 Spanish flu, and the F103L and M106I NS1 mutations, that have been shown to be adaptive, have been previously selected in the highly pathogenic avian H5N1 and its precursor from low pathogenic H9N2 lineages. 2012 Emerging microbes & infections Introduction IV F103L;M106I 97;107 102;112 NS1;NS1 28;113 31;116 26038410 Adaptive mutation in influenza A virus non-structural gene is linked to host switching and induces a novel protein by alternative splicing. In this study, we show the first reported case of IAV adaptation to a new host by the selection of a mutation, NS1 D125G(GAT GGT), which introduced a new splice site into the NS gene, hence producing the novel NS3 protein by alternative splicing. 2012 Emerging microbes & infections Introduction IV D125G 115 120 NS;NS;NS1 175;210;111 177;212;114 26038410 Adaptive mutation in influenza A virus non-structural gene is linked to host switching and induces a novel protein by alternative splicing. This mutated codon was adjacent to the independently selected NS1 coding mutation, M124I (nucleotide A372G). 2012 Emerging microbes & infections Introduction IV M124I;A372G 83;101 88;106 NS1 62 65 26038484 Human H7N9 avian influenza virus infection: a review and pandemic risk assessment. An N31S mutation in the nH7N9 M2 protein confers resistance to amantadine and rimantadine. 2013 Emerging microbes & infections Introduction IV N31S 3 7 M2 30 32 26038484 Human H7N9 avian influenza virus infection: a review and pandemic risk assessment. Because influenza infection of ostrich and emu can lead to the selection of PB2-E267K and PB2-D701N mutants and because ratite-origin influenza isolates of low pathogenicity can easily be converted to a highly pathogenic avian influenza virus in chickens, meticulous care must be taken to prevent the spread of nH7N9 to ostrich and other members of the Ratitae family. 2013 Emerging microbes & infections Introduction IV E267K;D701N 80;94 85;99 PB2;PB2 76;90 79;93 IV infections 8 27 26038484 Human H7N9 avian influenza virus infection: a review and pandemic risk assessment. Influenza infection of ostrich and emu can lead to the selection of PB2-E627K and PB2-D701N mutants, and ratite-origin isolates of low pathogenicity can easily be converted to highly pathogenic avian influenza viruses in chickens. 2013 Emerging microbes & infections Introduction IV E627K;D701N 72;86 77;91 PB2;PB2 68;82 71;85 IV infections 0 19 26038484 Human H7N9 avian influenza virus infection: a review and pandemic risk assessment. nH7N9 isolated from humans contains features related to human adaptation, such as a Q226L mutation in the HA cleavage site and E627K and D701N mutations in the PB2 protein, that facilitate nH7N9 binding to and replication in the human upper respiratory tract. 2013 Emerging microbes & infections Introduction IV Q226L;E627K;D701N 84;127;137 89;132;142 HA;PB2 106;160 108;163 26038484 Human H7N9 avian influenza virus infection: a review and pandemic risk assessment. nH7N9 viruses isolated from humans contain features related to human adaptation, such as a Q226L mutation in the HA and E627K and D701N mutations in the PB2 protein. 2013 Emerging microbes & infections Introduction IV Q226L;E627K;D701N 91;120;130 96;125;135 HA;PB2 113;153 115;156 26038484 Human H7N9 avian influenza virus infection: a review and pandemic risk assessment. Serial passage of H9N2 viruses into quails and chickens can lead to the production of mutants with short NA stalks that can infect mice without prior adaptation and result in the selection of PB2-E627K mutants. 2013 Emerging microbes & infections Introduction IV E627K 196 201 NA;PB2 105;192 107;195 26038484 Human H7N9 avian influenza virus infection: a review and pandemic risk assessment. The acquisition of the PB2-E627K mutation has been reported in a HPH5N1 virus at Qinghai Lake in 2005. 2013 Emerging microbes & infections Introduction IV E627K 27 32 PB2 23 26 26038484 Human H7N9 avian influenza virus infection: a review and pandemic risk assessment. The control of a human nH7N9 outbreak may prevent further adaptation of nH7N9 in humans because PB2-E267K and PB2-D701N mutants can be selected during replication in humans. 2013 Emerging microbes & infections Introduction IV E267K;D701N 100;114 105;119 PB2;PB2 96;110 99;113 26038484 Human H7N9 avian influenza virus infection: a review and pandemic risk assessment. The only reported fatal case of a low pathogenic H7N7 avian influenza virus was with a virus containing a PB2-E627K mutation, which is absent in those patients presenting with mild conjunctivitis. 2013 Emerging microbes & infections Introduction IV E627K 110 115 PB2 106 109 26038484 Human H7N9 avian influenza virus infection: a review and pandemic risk assessment. The PB2-D701N mutation allows the avian influenza virus to cross the host species barrier and to infect mammalian cells. 2013 Emerging microbes & infections Introduction IV D701N 8 13 PB2 4 7 26038484 Human H7N9 avian influenza virus infection: a review and pandemic risk assessment. The PB2-E627K mutation also allowed efficient replication of the avian influenza virus at both 33 C and 37 C. 2013 Emerging microbes & infections Introduction IV E627K 8 13 PB2 4 7 26038484 Human H7N9 avian influenza virus infection: a review and pandemic risk assessment. The PB2-E627K mutation increased the viral polymerase activity, replication efficiency and pathogenicity of this avian influenza virus in the mammalian host. 2013 Emerging microbes & infections Introduction IV E627K 8 13 PB2 4 7 26038484 Human H7N9 avian influenza virus infection: a review and pandemic risk assessment. The Q226L mutation in HA facilitated the adhesion of nH7N9 to the human upper respiratory tract, a property that enhanced the ability of this avian influenza virus to transmit via aerosols. 2013 Emerging microbes & infections Introduction IV Q226L 4 9 HA 22 24 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. In the present study, we obtained an R292K mutant virus derived from an H7N9 (Anhui1 lineage)-infected patient in whom we observed a sustained high viral load despite continued NAI treatment. 2014 Emerging microbes & infections Introduction IV R292K 37 42 NAI 177 180 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. The initial sequence analysis of Shanghai1 revealed that its neuraminidase (NA) protein has an R292K (N2 numbering) mutation, which has been reported to confer resistance to NA inhibitors (NAIs). 2014 Emerging microbes & infections Introduction IV R292K 95 100 NA;NA;NAI;NA 76;174;189;61 78;176;193;74 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. Therefore, further comprehensive analysis of the R292K mutant virus from this clinically dominant Anhui1 subclade is necessary to further understand the resistance spectrum, viral fitness and pathogenesis and to explore possible therapeutic options for the control of this clinically challenging variant. 2014 Emerging microbes & infections Introduction IV R292K 49 54 26056814 Molecular Characterisation of the Haemagglutinin Glycan-Binding Specificity of Egg-Adapted Vaccine Strains of the Pandemic 2009 H1N1 Swine Influenza A Virus. We, and others identified mutation sites in the HA molecule that significantly facilitated viral rescue and amplification in eggs namely, K123N, D225G and Q226R. 2015 Molecules (Basel, Switzerland) Introduction IV K123N;D225G;Q226R 138;145;155 143;150;160 HA 48 50 26391278 Dual E627K and D701N mutations in the PB2 protein of A(H7N9) influenza virus increased its virulence in mammalian models. As residues at positions 627 and 701 of the polymerase basic protein 2 (PB2) are considered critical for the mammalian adaptation of avian influenza viruses, several studies have independently shown that single E627K (glutamic acid to lysine) or D701N (aspartic acid to asparagine) mutations could increase polymerase activity and viral replication in mammalian cells and the pathogenicity of H7N9 viruses in the BALB/c mouse model. 2015 Scientific reports Introduction IV E627K;D701N 211;246 216;251 PB2 72 75 26391278 Dual E627K and D701N mutations in the PB2 protein of A(H7N9) influenza virus increased its virulence in mammalian models. Our findings show that both the E627K and D701N mutations occurred in ferrets that had direct contact with infected animals within a few days post-exposure. 2015 Scientific reports Introduction IV E627K;D701N 32;42 37;47 26391278 Dual E627K and D701N mutations in the PB2 protein of A(H7N9) influenza virus increased its virulence in mammalian models. Yet it is still unknown whether spontaneous emergence of dual D701N and E627K mutations can occur readily in infected mammals and whether these will synergistically enhance the virulence of H7N9 viruses. 2015 Scientific reports Introduction IV D701N;E627K 62;72 67;77 26422258 Oseltamivir Resistance in Influenza A(H6N2) Caused by an R292K Substitution in Neuraminidase Is Not Maintained in Mallards without Drug Pressure. In addition to the R292K substitution, also the D113N and D141N substitutions of unknown significance were observed in NA. 2015 PloS one Introduction IV R292K;D113N;D141N 19;48;58 24;53;63 119 121 26422258 Oseltamivir Resistance in Influenza A(H6N2) Caused by an R292K Substitution in Neuraminidase Is Not Maintained in Mallards without Drug Pressure. In addition we aimed to determine a possible fitness modulating effect by the D113N or D141N substitutions. 2015 PloS one Introduction IV D113N;D141N 78;87 83;92 26422258 Oseltamivir Resistance in Influenza A(H6N2) Caused by an R292K Substitution in Neuraminidase Is Not Maintained in Mallards without Drug Pressure. In an H10N8 virus though, despite classed as group N1 neuraminidase, NAI treatment selected for the R292K substitution. 2015 PloS one Introduction IV R292K 100 105 NAI;NA 69;54 72;67 26422258 Oseltamivir Resistance in Influenza A(H6N2) Caused by an R292K Substitution in Neuraminidase Is Not Maintained in Mallards without Drug Pressure. In the present study we tested if the resistant H6N2/R292K virus could maintain the resistance in Mallards without drug exposure. 2015 PloS one Introduction IV R292K 53 58 26422258 Oseltamivir Resistance in Influenza A(H6N2) Caused by an R292K Substitution in Neuraminidase Is Not Maintained in Mallards without Drug Pressure. NAI resistance substitutions in poultry adapted avian IAVs, detected in treated humans, are also subtype-specific, with R292K or E119V most usual in H7N9 viruses and H274Y in H5N1 viruses. 2015 PloS one Introduction IV R292K;E119V;H274Y 120;129;166 125;134;171 NAI 0 3 26422258 Oseltamivir Resistance in Influenza A(H6N2) Caused by an R292K Substitution in Neuraminidase Is Not Maintained in Mallards without Drug Pressure. The H274Y NA substitution was induced in a Mallard H1N1 virus by oseltamivir exposure, and was retained when drug exposure was removed. 2015 PloS one Introduction IV H274Y 4 9 10 12 26422258 Oseltamivir Resistance in Influenza A(H6N2) Caused by an R292K Substitution in Neuraminidase Is Not Maintained in Mallards without Drug Pressure. The NA amino acid substitutions that generate resistance to NAIs are subtype-specific, as the two phylogenetic NA groups N1 (including N1, N4, N5, N8) and N2 (including N2, N3, N6, N7, N9) differ in structure and substrate binding; in N1 viruses the H274Y (N2 numbering) substitution is most common, while in N2 viruses R292K or E119V are most common. 2015 PloS one Introduction IV H274Y;R292K;E119V 250;320;329 255;325;334 N9;NA;NA;NAI 185;4;111;60 187;6;113;64 26422258 Oseltamivir Resistance in Influenza A(H6N2) Caused by an R292K Substitution in Neuraminidase Is Not Maintained in Mallards without Drug Pressure. The resistant H6N2/R292K virus infected and transmitted equal to wild type virus in Mallards and the resistance was retained through drug free chicken egg propagation, indicating a retained viral fitness. 2015 PloS one Introduction IV R292K 19 24 26422258 Oseltamivir Resistance in Influenza A(H6N2) Caused by an R292K Substitution in Neuraminidase Is Not Maintained in Mallards without Drug Pressure. When Mallards were infected with H6N2 virus and exposed to oseltamivir the virus became resistant by the R292K substitution. 2015 PloS one Introduction IV R292K 105 110 26738596 Species difference in ANP32A underlies influenza A virus polymerase host restriction. Acquisition of host-adapting mutations, such as PB2 E627K, enables polymerase activity to be supported by the shorter ANP32 proteins typical of mammalian hosts. 2016 Nature Introduction IV E627K 52 57 PB2 48 51 26738596 Species difference in ANP32A underlies influenza A virus polymerase host restriction. Each RH clone was screened for the ability to support activity of a H5N1 avian influenza virus polymerase (A/turkey/England/50-92/91 virus (50-92)) compared with its human-adapted isoform bearing PB2 E627K. 2016 Nature Introduction IV E627K 200 205 PB2 196 199 26738596 Species difference in ANP32A underlies influenza A virus polymerase host restriction. In mammalian cells, the low activity of reconstituted avian virus polymerase can be significantly increased by a single amino acid substitution (E627K) in PB2 . 2016 Nature Introduction IV E627K 145 150 PB2 155 158 26754751 Coupling high-throughput genetics with phylogenetic information reveals an epistatic interaction on the influenza A virus M segment. These analyses led us to identify and experimentally validate the epistatic interaction between A209T and Q214H, in which A209T was able to compensate the deleterious effect of Q214H. 2016 BMC genomics Introduction IV A209T;Q214H;A209T;Q214H 96;106;122;177 101;111;127;182 26782141 PB2-588 V promotes the mammalian adaptation of H10N8, H7N9 and H9N2 avian influenza viruses. Another well-known substitution D701N in PB2 is primarily found in a duck H5N1 virus that was highly pathogenic to mice. 2016 Scientific reports Introduction IV D701N 32 37 PB2 41 44 26782141 PB2-588 V promotes the mammalian adaptation of H10N8, H7N9 and H9N2 avian influenza viruses. In addition, the mutation S714R coupled with 701 N in PB2 increases the polymerase activity of the avian H5N1 influenza virus in human cells and enhances virulence in mice. 2016 Scientific reports Introduction IV S714R 26 31 PB2 54 57 26782141 PB2-588 V promotes the mammalian adaptation of H10N8, H7N9 and H9N2 avian influenza viruses. One well-characterized mutation in PB2 is the glutamate change to lysine at position 627 (E627K) that results in efficient virus replication in mammalian cells and enhanced virulence in mammals. 2016 Scientific reports Introduction IV E627K;E627K 90;46 95;88 PB2 35 38 26782141 PB2-588 V promotes the mammalian adaptation of H10N8, H7N9 and H9N2 avian influenza viruses. The single substitution A588V in PB2 enhanced polymerase activity, virus replication, and virulence of avian influenza H10N8, H7N9, and H9N2 virus isolates. 2016 Scientific reports Introduction IV A588V 24 29 PB2 33 36 26845764 Genomic Signatures for Avian H7N9 Viruses Adapting to Humans. It was reported that a single Q226L mutation (H3 numbering) on the influenza A hemagglutinin (HA) enabled the H7N9 viruses to have a mixed alpha-2,3/alpha-2,6 receptor preference, which increased binding to mammalian-like receptors in the human upper airway. 2016 PloS one Introduction IV Q226L 30 35 HA;HA 94;79 96;92 26845764 Genomic Signatures for Avian H7N9 Viruses Adapting to Humans. Moreover, the replication-promoting PB2 E627K mutation dominated the H7N9 patient isolates. 2016 PloS one Introduction IV E627K 40 45 PB2 36 39 26845764 Genomic Signatures for Avian H7N9 Viruses Adapting to Humans. Other PB2 mutations including Q591K, and D701N were also investigated for their enhancing polymerase activity in human 293T cells. 2016 PloS one Introduction IV Q591K;D701N 30;41 35;46 PB2 6 9 26845764 Genomic Signatures for Avian H7N9 Viruses Adapting to Humans. Three genetic substitutions, PB2 E627K, D701N, and Q591R, have been reported to affect host cell tropism. 2016 PloS one Introduction IV E627K;D701N;Q591R 33;40;51 38;45;56 PB2 29 32 26847414 Amino acid changes in PB2 and HA affect the growth of a recombinant influenza virus expressing a fluorescent reporter protein. MA-Venus-PR8 differs from WT-Venus-PR8 by two amino acid changes: one in the viral polymerase subunit PB2 (PB2-E712D) and the other in the hemagglutinin (HA) surface glycoprotein (HA-T380A; H1 HA numbering). 2016 Scientific reports Introduction IV E712D;T380A 111;183 116;188 HA;HA;HA;HA;PB2;PB2 154;180;193;139;102;107 156;182;195;152;105;110 27097026 Novel Polymerase Gene Mutations for Human Adaptation in Clinical Isolates of Avian H5N1 Influenza Viruses. However, a recent study showed that PB2-K526R, particularly in combination with PB2-627K, enhanced replication of certain influenza virus subtypes. 2016 PLoS pathogens Introduction IV K526R 40 45 PB2;PB2 36;80 39;83 27097026 Novel Polymerase Gene Mutations for Human Adaptation in Clinical Isolates of Avian H5N1 Influenza Viruses. Moreover, the PB2-D701N, PB2-Q591K, PB2-K526R, PB2-G590S/Q591R and PB2-I147T/K399T/A588T mutations increase influenza virus replication in mammalian hosts. 2016 PLoS pathogens Introduction IV D701N;Q591K;K526R;G590S;Q591R;I147T;K399T;A588T 18;29;40;51;57;71;77;83 23;34;45;56;62;76;82;88 PB2;PB2;PB2;PB2;PB2 14;25;36;47;67 17;28;39;50;70 27097026 Novel Polymerase Gene Mutations for Human Adaptation in Clinical Isolates of Avian H5N1 Influenza Viruses. The most well-known human adaptation polymerase mutation is the PB2-E627K substitution, which is present in most seasonal human viruses, except for the 2009 pandemic H1N1 virus, and is also in some H5N1 and H7N9 human isolates and one H7N7 human isolate. 2016 PLoS pathogens Introduction IV E627K 68 73 PB2 64 67 27097026 Novel Polymerase Gene Mutations for Human Adaptation in Clinical Isolates of Avian H5N1 Influenza Viruses. The PB2-E627K mutation correlates with the high virulence of H5N1 virus in mice and allows the virus to replicate efficiently in the mouse upper respiratory tract, where the temperature is slightly lower than the core body temperature. 2016 PLoS pathogens Introduction IV E627K 8 13 PB2 4 7 27097026 Novel Polymerase Gene Mutations for Human Adaptation in Clinical Isolates of Avian H5N1 Influenza Viruses. The polymerase activity of AI viruses with a single PB2-E627K mutation or a reassortment PB2 from human viruses with PB2-627K was still lower than that of seasonal human influenza viruses, supporting the above concern. 2016 PLoS pathogens Introduction IV E627K 56 61 PB2;PB2;PB2 52;89;117 55;92;120 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. While most of the mutations completely abolished antibody binding, a CR6261 escape mutation (His111Leu in HA2) and an S6-B01 escape mutation (Ile384Thr) only partially reduced binding, suggesting an alternative escape mechanism. 2016 PLoS pathogens Introduction IV H111L;I384T 93;142 102;151 HA 106 108 27413002 Pulmonary changes in Norwegian fatal cases of pandemic influenza H1N1 (2009) infection: a morphologic and molecular genetic study. Our results show a possible association between obesity, pre-existing illness, the viral mutation HA D222G and mortality in fatal Norwegian cases. 2016 Influenza and other respiratory viruses Introduction IV D222G 101 106 HA 98 100 27535054 NS1 Protein Mutation I64T Affects Interferon Responses and Virulence of Circulating H3N2 Human Influenza A Viruses. Moreover, a virus containing the I64T mutation resulted in an attenuated phenotype in mice. 2016 Journal of virology Introduction IV I64T 33 37 27535054 NS1 Protein Mutation I64T Affects Interferon Responses and Virulence of Circulating H3N2 Human Influenza A Viruses. Moreover, I64T substitution in NS1 affected virus growth, the ability to inhibit induction of type I IFN in vitro and in vivo, the sensitivity of the virus to the antiviral effect of type I IFN, and virus pathogenesis in mice. 2016 Journal of virology Introduction IV I64T 10 14 NS1 31 34 27535054 NS1 Protein Mutation I64T Affects Interferon Responses and Virulence of Circulating H3N2 Human Influenza A Viruses. The effect of the mutations found (E26K, I64T, and R224K) on the ability of the NS1 protein to inhibit the type I IFN responses and host gene expression was analyzed. 2016 Journal of virology Introduction IV E26K;I64T;R224K 35;41;51 39;45;56 NS1 80 83 27572837 The hemifusion structure induced by influenza virus haemagglutinin is determined by physical properties of the target membranes. All analyzed G1S VLP fusion intermediates showed lipidic junctions. 2016 Nature microbiology Introduction IV G1S 13 16 27572837 The hemifusion structure induced by influenza virus haemagglutinin is determined by physical properties of the target membranes. Distributional properties of WT (HD size and energy) in the presence of M1 was dependent on cholesterol and the differences between WT with and without M1 was much greater than for G1S. 2016 Nature microbiology Introduction IV G1S 181 184 M1;M1 72;152 74;154 27572837 The hemifusion structure induced by influenza virus haemagglutinin is determined by physical properties of the target membranes. For G1S VLP-liposome mixtures, binding and fusion intermediates were observed, but not complete fusion, as expected from this mutation's phenotype in cell-cell fusion. 2016 Nature microbiology Introduction IV G1S 4 7 27572837 The hemifusion structure induced by influenza virus haemagglutinin is determined by physical properties of the target membranes. G1S HA supports lipid mixing but not fusion pore opening or content mixing, conditions necessary for observable hemifusion. 2016 Nature microbiology Introduction IV G1S 0 3 HA 4 6 27572837 The hemifusion structure induced by influenza virus haemagglutinin is determined by physical properties of the target membranes. Instead, WT VLP-liposome fusion products demonstrated the same lipidic junctions and HD as found in G1S VLP. 2016 Nature microbiology Introduction IV G1S 100 103 27572837 The hemifusion structure induced by influenza virus haemagglutinin is determined by physical properties of the target membranes. Interestingly, differences between WT and G1S were revealed when the presence and absence of M1 layer was taken into consideration. 2016 Nature microbiology Introduction IV G1S 42 45 M1 93 95 27572837 The hemifusion structure induced by influenza virus haemagglutinin is determined by physical properties of the target membranes. Observed HD structure was independent of the cholesterol concentration or the absence of PE in the G1S VLP. 2016 Nature microbiology Introduction IV G1S 99 102 27572837 The hemifusion structure induced by influenza virus haemagglutinin is determined by physical properties of the target membranes. Ruptures were even more apparent in liposomes showing multiple lipidic junctions on the surface of filamentous G1S VLP. 2016 Nature microbiology Introduction IV G1S 111 114 27572837 The hemifusion structure induced by influenza virus haemagglutinin is determined by physical properties of the target membranes. Since negative spontaneous curvature, conferred by lipids such as cholesterol and PE, is known to play a role in membrane fusion we analyzed G1S VLP fusion intermediates with liposomes containing different lipid compositions: (i) 95 mol % PC and 5 mol % gangliosides and (ii) 42 mol % PC, 13 mol % PE, 40 mol % cholesterol and 5 mol % gangliosides, in addition to the liposome composition described above (66 mol % PC, 13 mol % PE, 16 mol % cholesterol and 5 mol % gangliosides). 2016 Nature microbiology Introduction IV G1S 141 144 27572837 The hemifusion structure induced by influenza virus haemagglutinin is determined by physical properties of the target membranes. The combined average of the HD diameters and lipidic junction chords formed by G1S VLP was ~ 20 nm. 2016 Nature microbiology Introduction IV G1S 79 82 27572837 The hemifusion structure induced by influenza virus haemagglutinin is determined by physical properties of the target membranes. The variation in the small and large HD fractions as a function of cholesterol and the fraction differences between WT and G1S with and without M1 suggest that compensatory mechanisms may exist for handling differences in the endosomal cholesterol concentration and/or negative spontaneous curvature depending on the infected host cell. 2016 Nature microbiology Introduction IV G1S 123 126 M1 144 146 27572837 The hemifusion structure induced by influenza virus haemagglutinin is determined by physical properties of the target membranes. To elucidate the effect of G1S mutation we analyzed WT VLP-liposome mixtures at low pH. 2016 Nature microbiology Introduction IV G1S 27 30 27572837 The hemifusion structure induced by influenza virus haemagglutinin is determined by physical properties of the target membranes. To study WT and G1S hemagglutinin-induced membrane fusion intermediates, we used influenza VLP that are composed of both HA and neuraminidase (NA) glycoproteins, matrix 1 (M1) layer and an ion channel M2. 2016 Nature microbiology Introduction IV G1S 16 19 HA;HA;M1;M2;M;NA;NA 121;20;172;201;162;143;128 123;33;174;203;168;145;141 27587808 H9N2 Influenza A Virus Isolated from a Greater White-Fronted Wild Goose (Anser albifrons) in Alaska Has a Mutation in the PB2 Gene, Which Is Associated with Pathogenicity in Human Pandemic 2009 H1N1. demonstrated that the introduction of a point mutation (Q591K) increased polymerase activity and allowed the virus to replicate in human cells. 2016 Genome announcements Introduction IV Q591K 56 61 27587808 H9N2 Influenza A Virus Isolated from a Greater White-Fronted Wild Goose (Anser albifrons) in Alaska Has a Mutation in the PB2 Gene, Which Is Associated with Pathogenicity in Human Pandemic 2009 H1N1. This virus contained the G590S mutation in the polymerase basic (PB) 2 gene, which is associated with infections in humans. 2016 Genome announcements Introduction IV G590S 25 30 27657178 Discovery of Potent Antivirals against Amantadine-Resistant Influenza A Viruses by Targeting the M2-S31N Proton Channel. Among these, S31N is the most prevalent mutant and is persist in the majority of current circulating influenza A viruses, including the pandemic A/California/07/2009 (H1N1) strain and the recently emerged A/Switzerland/9715293/2013 (H3N2) strain in North America. 2016 ACS infectious diseases Introduction IV S31N 13 17 27657178 Discovery of Potent Antivirals against Amantadine-Resistant Influenza A Viruses by Targeting the M2-S31N Proton Channel. Genetic sequencing revealed that more than 95% of current circulating influenza A viruses carry this mutation, rendering M2-S31N a high-profile drug target. 2016 ACS infectious diseases Introduction IV S31N 124 128 M2 121 123 27657178 Discovery of Potent Antivirals against Amantadine-Resistant Influenza A Viruses by Targeting the M2-S31N Proton Channel. In this study, in order to provide additional structure diverse lead compounds for in vivo animal studies, we examined the structure-activity relationships of M2-S31N inhibitors by diversifying the aromatic head groups and the hydrophobic substitutions (Figure 1D). 2016 ACS infectious diseases Introduction IV S31N 162 166 M2 159 161 27657178 Discovery of Potent Antivirals against Amantadine-Resistant Influenza A Viruses by Targeting the M2-S31N Proton Channel. It has been found that the adamantane template and the ammonium linker are essential for M2-S31N inhibition. 2016 ACS infectious diseases Introduction IV S31N 92 96 M2 89 91 27657178 Discovery of Potent Antivirals against Amantadine-Resistant Influenza A Viruses by Targeting the M2-S31N Proton Channel. It is important to stress that although a large number of M2 mutants were selected from cell culture, animals, and human patients upon drug treatment, only a limited number of M2 mutants evolved the fitness of transmission among humans, namely V27A, S31N, and L26F. 2016 ACS infectious diseases Introduction IV V27A;S31N;L26F 244;250;260 248;254;264 M2;M2 58;176 60;178 27657178 Discovery of Potent Antivirals against Amantadine-Resistant Influenza A Viruses by Targeting the M2-S31N Proton Channel. Propelled by mechanistic studies of the proton conductance and drug inhibition mechanisms by X-ray crystallography, NMR, and molecular dynamics simulations, recent years have witnessed steady progress toward designing inhibitors targeting M2-S31N, which was previously considered undruggable despite decades of traditional medicinal chemistry efforts. 2016 ACS infectious diseases Introduction IV S31N 242 246 M2 239 241 27657178 Discovery of Potent Antivirals against Amantadine-Resistant Influenza A Viruses by Targeting the M2-S31N Proton Channel. Substituting adamantane with other hydrophobic cage structures leads to a decrease of M2-S31N channel inhibition. 2016 ACS infectious diseases Introduction IV S31N 89 93 M2 86 88 27657178 Discovery of Potent Antivirals against Amantadine-Resistant Influenza A Viruses by Targeting the M2-S31N Proton Channel. The M2-S31N proton channel is such a drug target that meets this criterion. 2016 ACS infectious diseases Introduction IV S31N 7 11 M2 4 6 27657178 Discovery of Potent Antivirals against Amantadine-Resistant Influenza A Viruses by Targeting the M2-S31N Proton Channel. The pharmacophore of M2-S31N channel blockers consists of a hydrophobic template such as adamantane, a positively charged ammonium linker, and an aromatic head group with a hydrophobic substitution (Figure 1). 2016 ACS infectious diseases Introduction IV S31N 24 28 M2 21 23 27658193 Sensitive Detection and Simultaneous Discrimination of Influenza A and B Viruses in Nasopharyngeal Swabs in a Single Assay Using Next-Generation Sequencing-Based Diagnostics. Current methods that evaluate antiviral resistance require two independent tests for the S31N substitutions conferring amantadine-resistance and the H274Y substitution conferring oseltamivir-resistance. 2016 PloS one Introduction IV S31N;H274Y 89;149 93;154 27714496 Community- and hospital-acquired infections with oseltamivir- and peramivir-resistant influenza A(H1N1)pdm09 viruses during the 2015-2016 season in Japan. A survey of the influenza sequences in the public database (Influenza Sequence Database, http://www.ncbi.nlm.nih.gov/genomes/FLU/FLU.html) revealed that the N386 K mutation is not unique to H275Y viruses. 2017 Virus genes Introduction IV N386K;H275Y 157;190 163;195 27714496 Community- and hospital-acquired infections with oseltamivir- and peramivir-resistant influenza A(H1N1)pdm09 viruses during the 2015-2016 season in Japan. Another Japanese group demonstrated that oseltamivir was less effective for children but it was effective for adult infected with seasonal H275Y A(H1N1) virus. 2017 Virus genes Introduction IV H275Y 139 144 27714496 Community- and hospital-acquired infections with oseltamivir- and peramivir-resistant influenza A(H1N1)pdm09 viruses during the 2015-2016 season in Japan. Community-acquired oseltamivir- and peramivir-resistant viruses with the H275Y mutation have been recently identified in several countries. 2017 Virus genes Introduction IV H275Y 73 78 27714496 Community- and hospital-acquired infections with oseltamivir- and peramivir-resistant influenza A(H1N1)pdm09 viruses during the 2015-2016 season in Japan. demonstrated in a small number of pediatric patients that oseltamivir and peramivir retain the clinical effectiveness against the H275Y mutant virus. 2017 Virus genes Introduction IV H275Y 130 135 27714496 Community- and hospital-acquired infections with oseltamivir- and peramivir-resistant influenza A(H1N1)pdm09 viruses during the 2015-2016 season in Japan. Five of A(H1N1)pdm09 isolates (5/282, 1.8 %) were found to possess the H275Y mutation. 2017 Virus genes Introduction IV H275Y 71 76 27714496 Community- and hospital-acquired infections with oseltamivir- and peramivir-resistant influenza A(H1N1)pdm09 viruses during the 2015-2016 season in Japan. Further studies are warranted to better assess clinical effectiveness of oseltamivir and peramivir against the H275Y A(H1N1)pdm09 variant. 2017 Virus genes Introduction IV H275Y 111 116 27714496 Community- and hospital-acquired infections with oseltamivir- and peramivir-resistant influenza A(H1N1)pdm09 viruses during the 2015-2016 season in Japan. have recently suggested using structural modeling that the N386 K substitution which was detected in this study slightly impairs the stabilizing effect of the V241I and N369 K mutations. 2017 Virus genes Introduction IV N386K;V241I;N369K 59;159;169 65;164;175 27714496 Community- and hospital-acquired infections with oseltamivir- and peramivir-resistant influenza A(H1N1)pdm09 viruses during the 2015-2016 season in Japan. However, we could not obtain a sample from the roommate to confirm whether the H275Y mutation had emerged in the patient or was transmitted from the roommate (hospital-acquired). 2017 Virus genes Introduction IV H275Y 79 84 27714496 Community- and hospital-acquired infections with oseltamivir- and peramivir-resistant influenza A(H1N1)pdm09 viruses during the 2015-2016 season in Japan. In contrast, we have previously shown that children less than 6 years of age infected with the seasonal H275Y A(H1N1) virus had delayed fever resolution compared with those infected with the sensitive virus. 2017 Virus genes Introduction IV H275Y 104 109 27714496 Community- and hospital-acquired infections with oseltamivir- and peramivir-resistant influenza A(H1N1)pdm09 viruses during the 2015-2016 season in Japan. LLC, MO, USA) was performed to assess the susceptibility of the five H275Y A(H1N1)pdm09 viruses to four NAIs. 2017 Virus genes Introduction IV H275Y 69 74 NAI 104 108 27714496 Community- and hospital-acquired infections with oseltamivir- and peramivir-resistant influenza A(H1N1)pdm09 viruses during the 2015-2016 season in Japan. One case of infection with H275Y mutant virus was detected in a hospitalized patient, while the other four were from patients presenting at community clinics. 2017 Virus genes Introduction IV H275Y 27 32 27714496 Community- and hospital-acquired infections with oseltamivir- and peramivir-resistant influenza A(H1N1)pdm09 viruses during the 2015-2016 season in Japan. The assay can simultaneously detect the presence of the H275Y mutation in A(H1N1)pdm09 viruses. 2017 Virus genes Introduction IV H275Y 56 61 27714496 Community- and hospital-acquired infections with oseltamivir- and peramivir-resistant influenza A(H1N1)pdm09 viruses during the 2015-2016 season in Japan. The duration of fever among the five cases was 1-3 days, in range with the data reported on patients infected with the H275Y mutant virus during the 2013-2014 season in Hokkaido, Japan. 2017 Virus genes Introduction IV H275Y 119 124 27714496 Community- and hospital-acquired infections with oseltamivir- and peramivir-resistant influenza A(H1N1)pdm09 viruses during the 2015-2016 season in Japan. The five H275Y isolates belonged to clade 6B.1 in both the HA and NA phylogenies forming two geographically segregated subclusters along with oseltamivir-susceptible isolates from the same season. 2017 Virus genes Introduction IV H275Y 9 14 HA;NA 59;66 61;68 27714496 Community- and hospital-acquired infections with oseltamivir- and peramivir-resistant influenza A(H1N1)pdm09 viruses during the 2015-2016 season in Japan. The H275Y mutant viruses showed highly reduced susceptibility indicated by a 300-fold increase in the IC50 values for oseltamivir and peramivir compared to the susceptible reference virus and thus assessed as resistant (Table 1). 2017 Virus genes Introduction IV H275Y 4 9 27714496 Community- and hospital-acquired infections with oseltamivir- and peramivir-resistant influenza A(H1N1)pdm09 viruses during the 2015-2016 season in Japan. The influenza sample obtained on January 25 was found to possess the H275Y mutation by real-time PCR. 2017 Virus genes Introduction IV H275Y 69 74 27714496 Community- and hospital-acquired infections with oseltamivir- and peramivir-resistant influenza A(H1N1)pdm09 viruses during the 2015-2016 season in Japan. The most frequent resistant-conferring mutation among the influenza A(H1N1)pdm09 is the H275Y. 2017 Virus genes Introduction IV H275Y 88 93 27714496 Community- and hospital-acquired infections with oseltamivir- and peramivir-resistant influenza A(H1N1)pdm09 viruses during the 2015-2016 season in Japan. The Niigata subcluster was defined by a D269 N amino acid substitution in the HA protein and the Nagasaki subcluster had a D35G mutation. 2017 Virus genes Introduction IV D269N;D35G 40;123 46;127 HA 78 80 27714496 Community- and hospital-acquired infections with oseltamivir- and peramivir-resistant influenza A(H1N1)pdm09 viruses during the 2015-2016 season in Japan. The resistant viruses in this study commonly possessed the V241I, N369 K, and N386 K substitutions in the NA that have been previously reported among A(H1N1)pdm09. 2017 Virus genes Introduction IV V241I;N369K;N386K 59;66;78 64;72;84 106 108 27714496 Community- and hospital-acquired infections with oseltamivir- and peramivir-resistant influenza A(H1N1)pdm09 viruses during the 2015-2016 season in Japan. These results suggested that the H275Y viruses possess lower affinity to the substrate which may attenuate their transmission fitness as in the case of the resistant viruses reported with low frequency in the community in 2009. 2017 Virus genes Introduction IV H275Y 33 38 27714496 Community- and hospital-acquired infections with oseltamivir- and peramivir-resistant influenza A(H1N1)pdm09 viruses during the 2015-2016 season in Japan. This suggests that the Niigata and Nagasaki H275Y viruses have evolved independently rather than being sourced from a single outbreak of resistant viruses. 2017 Virus genes Introduction IV H275Y 44 49 27714496 Community- and hospital-acquired infections with oseltamivir- and peramivir-resistant influenza A(H1N1)pdm09 viruses during the 2015-2016 season in Japan. Two of the substitutions, V241I and N369 K, were reported to confer robust viral fitness on the H275Y mutant viruses. 2017 Virus genes Introduction IV V241I;N369K;H275Y 26;36;96 31;42;101 27714496 Community- and hospital-acquired infections with oseltamivir- and peramivir-resistant influenza A(H1N1)pdm09 viruses during the 2015-2016 season in Japan. Viruses from Niigata, but not from Nagasaki, uniquely possessed a V453A substitution in the NA protein. 2017 Virus genes Introduction IV V453A 66 71 92 94 27714496 Community- and hospital-acquired infections with oseltamivir- and peramivir-resistant influenza A(H1N1)pdm09 viruses during the 2015-2016 season in Japan. We found that this mutation has been also reported among recent A(H1N1)pdm09 viruses (including H275 and H275Y strains) at increasing frequencies: 5.7 % (42/734) in 2013, 61.2 % (281/459) in 2014, 100 % (350/350) in 2015 (as of Aug 12, 2016). 2017 Virus genes Introduction IV H275Y 105 110 27714496 Community- and hospital-acquired infections with oseltamivir- and peramivir-resistant influenza A(H1N1)pdm09 viruses during the 2015-2016 season in Japan. We next determined the hemagglutinin (HA) and NA gene sequences of the five H275Y isolates in addition to eight wild-type (H275) strains. 2017 Virus genes Introduction IV H275Y 76 81 HA;HA;NA 38;23;46 40;36;48 27733236 Risk of resistant avian influenza A virus in wild waterfowl as a result of environmental release of oseltamivir. However, since 2010/2011, an increasing number of community cases with OC-resistant A(H1N1)/pdm09 viruses have been reported without previous oseltamivir exposure; in nearly all instances the resistance has been conferred by the H274Y substitution in NA. 2016 Infection ecology & epidemiology Introduction IV H274Y 229 234 251 253 27733236 Risk of resistant avian influenza A virus in wild waterfowl as a result of environmental release of oseltamivir. In IAVs containing N1 NA proteins the most common resistance-related change seen in vivo is the framework substitution H274Y (N2 numbering, used hereafter), whereas in N2-containing viruses the framework E119V and active-site R292K substitutions are most commonly described. 2016 Infection ecology & epidemiology Introduction IV H274Y;E119V;R292K 119;204;226 124;209;231 22 24 27733236 Risk of resistant avian influenza A virus in wild waterfowl as a result of environmental release of oseltamivir. This feature was primarily described in the seasonal A(H1N1) virus 2007-2009 when the circulating strain was OC resistant due to an H274Y substitution in NA, without selective drug exposure. 2016 Infection ecology & epidemiology Introduction IV H274Y 132 137 154 156 27849220 Surveillance of antiviral resistance markers in Argentina: detection of E119V neuraminidase mutation in a post-treatment immunocompromised patient. A(H3N2) viruses showing oseltamivir resistance due to the E119V NA mutation have previously been detected in immunocompromised paediatric patients undergoing oseltamivir treatment. 2016 Memorias do Instituto Oswaldo Cruz Introduction IV E119V 58 63 64 66 27849220 Surveillance of antiviral resistance markers in Argentina: detection of E119V neuraminidase mutation in a post-treatment immunocompromised patient. In some cases, the E119V oseltamivir-resistant variants were selected within a few days of oseltamivir treatment, whereas in other cases, many weeks of cumulative treatment were undertaken before the E119V variant was detected . 2016 Memorias do Instituto Oswaldo Cruz Introduction IV E119V;E119V 19;200 24;205 27849220 Surveillance of antiviral resistance markers in Argentina: detection of E119V neuraminidase mutation in a post-treatment immunocompromised patient. In this report, we describe the emergence of the E119V substitution in the NA protein of an influenza A(H3N2) isolate detected in a clinical specimen collected from an immunocompromised patient after oseltamivir treatment in Argentina during 2014 epidemic season. 2016 Memorias do Instituto Oswaldo Cruz Introduction IV E119V 49 54 75 77 27933797 Nuclear Magnetic Resonance and Molecular Dynamics Simulation of the Interaction between Recognition Protein H7 of the Novel Influenza Virus H7N9 and Glycan Cell Surface Receptors. As an example, the H1N1 virus responsible for the 1918 "Spanish flu" pandemic (SC18, "South Carolina 1918") propagated as efficiently between ferrets by aerosol as it did between humans, but a single mutation (D225G) and a double mutation (D225G/D190E) of amino acids in the H1 receptor binding site (RBS) yielded two artificial viruses, NY18 and AV18, respectively, the former being transmitted inefficiently and the latter unable to do so, while its lethality and replication activity were preserved. 2016 Biochemistry Introduction IV D225G;D225G;D190E 210;240;246 215;245;251 27933797 Nuclear Magnetic Resonance and Molecular Dynamics Simulation of the Interaction between Recognition Protein H7 of the Novel Influenza Virus H7N9 and Glycan Cell Surface Receptors. At the molecular level, the H1 (SC18) specificity switch was explained by observing that the D225G mutation on H1 removed crucial hydrogen bonds between the RBS and the LSTc nonreducing end, while the additional mutation (D190E) further reduced the extent of contact between its reducing end and the surface of helix 190. 2016 Biochemistry Introduction IV D225G;D190E 93;222 98;227 27933797 Nuclear Magnetic Resonance and Molecular Dynamics Simulation of the Interaction between Recognition Protein H7 of the Novel Influenza Virus H7N9 and Glycan Cell Surface Receptors. In addition, H7 from H7N9 virus, by analogy with H2 and H3, includes the Q226L mutation in some variants (A/Anhui/1/13), contributing to its affinity for human receptors. 2016 Biochemistry Introduction IV Q226L 73 78 27933797 Nuclear Magnetic Resonance and Molecular Dynamics Simulation of the Interaction between Recognition Protein H7 of the Novel Influenza Virus H7N9 and Glycan Cell Surface Receptors. The observed H7s differ by two amino acids, Q226L and G186V, with the human H7 having an affinity comparable to those of both human and avian receptors. 2016 Biochemistry Introduction IV Q226L;G186V 44;54 49;59 27933797 Nuclear Magnetic Resonance and Molecular Dynamics Simulation of the Interaction between Recognition Protein H7 of the Novel Influenza Virus H7N9 and Glycan Cell Surface Receptors. The same approach was then applied to predict the effect of a single G228S mutation on H7 affinity and binding epitopes toward LSTa and LSTc, a structural biology problem that has been considered only partially in the characterization of this new HA subtype. 2016 Biochemistry Introduction IV G228S 69 74 HA 247 249 27933797 Nuclear Magnetic Resonance and Molecular Dynamics Simulation of the Interaction between Recognition Protein H7 of the Novel Influenza Virus H7N9 and Glycan Cell Surface Receptors. These subtype HAs, through the Q226L and G228S mutations, changed their preference from avian to human receptors. 2016 Biochemistry Introduction IV Q226L;G228S 31;41 36;46 28087313 An M2-V27A channel blocker demonstrates potent in vitro and in vivo antiviral activities against amantadine-sensitive and -resistant influenza A viruses. Although a few compounds were reported to inhibit the M2-V27A mutant channel, there has been no report on their antiviral activity against the M2-V27A-containing influenza A virus. 2017 Antiviral research Introduction IV V27A;V27A 57;146 61;150 M2;M2 54;143 56;145 28087313 An M2-V27A channel blocker demonstrates potent in vitro and in vivo antiviral activities against amantadine-sensitive and -resistant influenza A viruses. Among this limited number of mutants, V27A was shown to be the predominant mutation under drug selection pressure. 2017 Antiviral research Introduction IV V27A 38 42 28087313 An M2-V27A channel blocker demonstrates potent in vitro and in vivo antiviral activities against amantadine-sensitive and -resistant influenza A viruses. Compound 3 was found to have potent channel blockage against V27A mutant in electrophysiological assays, with an IC50 of 0.3 +- 0.1 muM. 2017 Antiviral research Introduction IV V27A 61 65 28087313 An M2-V27A channel blocker demonstrates potent in vitro and in vivo antiviral activities against amantadine-sensitive and -resistant influenza A viruses. Genetic studies have shown that the predominant M2 mutants circulating among humans are S31N, V27A, and L26F. 2017 Antiviral research Introduction IV S31N;V27A;L26F 88;94;104 92;98;108 M2 48 50 28087313 An M2-V27A channel blocker demonstrates potent in vitro and in vivo antiviral activities against amantadine-sensitive and -resistant influenza A viruses. Given the promising channel blockage efficacy of compound 3 in inhibiting both the M2-WT and the M2-V27A mutant, we took a step further to evaluate the in vitro and in vivo antiviral efficacy of compound 3. 2017 Antiviral research Introduction IV V27A 100 104 M2;M2 83;97 85;99 28087313 An M2-V27A channel blocker demonstrates potent in vitro and in vivo antiviral activities against amantadine-sensitive and -resistant influenza A viruses. Guided by molecular dynamics simulations, we previously generated a homology model of the V27A mutant. 2017 Antiviral research Introduction IV V27A 90 94 28087313 An M2-V27A channel blocker demonstrates potent in vitro and in vivo antiviral activities against amantadine-sensitive and -resistant influenza A viruses. In fact, the 2008-2009 seasonal influenza viruses with the H275Y NA mutation were completely resistant to the only orally bioavailable drug, oseltamivir. 2017 Antiviral research Introduction IV H275Y 59 64 65 67 28087313 An M2-V27A channel blocker demonstrates potent in vitro and in vivo antiviral activities against amantadine-sensitive and -resistant influenza A viruses. In the case of the M2-V27A mutant channel, compound 3 shifted up toward the N-terminus, and there are two layers of water between the ammonium from compound 3 and the H37. 2017 Antiviral research Introduction IV V27A 22 26 M2 19 21 28087313 An M2-V27A channel blocker demonstrates potent in vitro and in vivo antiviral activities against amantadine-sensitive and -resistant influenza A viruses. On the basis of this observation, we designed a 3D-shaped spiroadamantane amine molecule (3) that has improved shape complementarity to the V27A mutant compared to amantadine. 2017 Antiviral research Introduction IV V27A 140 144 28087313 An M2-V27A channel blocker demonstrates potent in vitro and in vivo antiviral activities against amantadine-sensitive and -resistant influenza A viruses. Specifically, the antiviral activity of compound 3 against M2-WT and the M2-V27A-containing influenza A viruses was tested in plaque assays. 2017 Antiviral research Introduction IV V27A 76 80 M2;M2 59;73 61;75 28087313 An M2-V27A channel blocker demonstrates potent in vitro and in vivo antiviral activities against amantadine-sensitive and -resistant influenza A viruses. This prediction was later confirmed by the NMR investigation of M2-V27A as well as molecular dynamics simulations from another group. 2017 Antiviral research Introduction IV V27A 67 71 M2 64 66 28087313 An M2-V27A channel blocker demonstrates potent in vitro and in vivo antiviral activities against amantadine-sensitive and -resistant influenza A viruses. We therefore are interested in designing the second generation of M2 channel blockers by targeting the V27A mutant. 2017 Antiviral research Introduction IV V27A 103 107 M2 66 68 28128091 Development of oseltamivir and zanamivir resistance in influenza A(H1N1)pdm09 virus, Denmark, 2014. Among these, two well characterised mutations are the H275Y mutation which results in viruses with highly reduced inhibition by oseltamivir and the I223R mutation which results in reduced inhibition by both oseltamivir and zanamivir. 2017 Euro surveillance Introduction IV H275Y;I223R 54;148 59;153 28166830 The T160A hemagglutinin substitution affects not only receptor binding property but also transmissibility of H5N1 clade 2.3.4 avian influenza virus in guinea pigs. An experiment was conducted in guinea pigs to further investigate whether the T160A substitution of HA affected the replication of the H5N1 virus. 2017 Veterinary research Introduction IV T160A 78 83 HA 100 102 28166830 The T160A hemagglutinin substitution affects not only receptor binding property but also transmissibility of H5N1 clade 2.3.4 avian influenza virus in guinea pigs. As shown in Table 1, six consistent amino acid substitutions all located in the HA1 subunit including K90R, T160A, K222Q, S227R, N244H and A266T were identified (Additional file 1). 2017 Veterinary research Introduction IV K90R;T160A;K222Q;S227R;N244H;A266T 102;108;115;122;129;139 106;113;120;127;134;144 HA1 80 83 28166830 The T160A hemagglutinin substitution affects not only receptor binding property but also transmissibility of H5N1 clade 2.3.4 avian influenza virus in guinea pigs. For instance, the E190D (H3 numbering throughout the paper) and G225D/E mutations in HA of the H1N1/1918 pandemic viruses, as well as the Q226L and G228S substitutions in HA of the H2N2/1957 and H3N2/1968 pandemic viruses, correlated with the conversion of binding preference to SA receptors from alpha-2,3 to alpha-2,6 type. 2017 Veterinary research Introduction IV E190D;G225D;G225E;Q226L;G228S 18;64;64;138;148 23;71;71;143;153 HA;HA 85;171 87;173 28166830 The T160A hemagglutinin substitution affects not only receptor binding property but also transmissibility of H5N1 clade 2.3.4 avian influenza virus in guinea pigs. However, only the T160A mutant acquired affinity to alpha-2,6 receptors yet retained affinity to alpha-2,3 receptors, partially coincident with our previous publication indicating that this T160A-induced deglycosylation at site 158N contributed to the recognition of the human-type receptors as evidenced by hemagglutinin assay still with substantial agglutination to the alpha-2,3 sialidase pretreated goose red blood cells. 2017 Veterinary research Introduction IV T160A;T160A 18;190 23;195 HA 308 321 28166830 The T160A hemagglutinin substitution affects not only receptor binding property but also transmissibility of H5N1 clade 2.3.4 avian influenza virus in guinea pigs. In particular, we noticed that the T to A mutation at site 160 simultaneously resulted in the loss of the glycosylation site at position 158N of the HA protein. 2017 Veterinary research Introduction IV T160A 35 62 HA 149 151 28166830 The T160A hemagglutinin substitution affects not only receptor binding property but also transmissibility of H5N1 clade 2.3.4 avian influenza virus in guinea pigs. The single amino acid substitutions K90R, K222Q, S227R, N244H and A266T in HA did not obviously affect the viral binding specificity to alpha-2,3 receptors at all, as compared with HD/05 virus. 2017 Veterinary research Introduction IV K90R;K222Q;S227R;N244H;A266T 36;42;49;56;66 40;47;54;61;71 HA 75 77 28182419 Expeditious Lead Optimization of Isoxazole-Containing Influenza A Virus M2-S31N Inhibitors Using the Suzuki-Miyaura Cross-Coupling Reaction. Briefly, at the initial stage of drug design, there was no AM2-S31N structure available so molecular dynamics simulations were applied to generate homology models of AM2-S31N. 2017 Journal of medicinal chemistry Introduction IV S31N;S31N 63;170 67;174 28182419 Expeditious Lead Optimization of Isoxazole-Containing Influenza A Virus M2-S31N Inhibitors Using the Suzuki-Miyaura Cross-Coupling Reaction. In light of these promising results, we are interested in continuously developing AM2-S31N inhibitors and providing lead compounds for in vivo mouse studies. 2017 Journal of medicinal chemistry Introduction IV S31N 86 90 28182419 Expeditious Lead Optimization of Isoxazole-Containing Influenza A Virus M2-S31N Inhibitors Using the Suzuki-Miyaura Cross-Coupling Reaction. In terms of the biological activity, the designed AM2-S31N inhibitors were found to have potent antiviral activity against multidrug-resistant influenza A viruses. 2017 Journal of medicinal chemistry Introduction IV S31N 54 58 28182419 Expeditious Lead Optimization of Isoxazole-Containing Influenza A Virus M2-S31N Inhibitors Using the Suzuki-Miyaura Cross-Coupling Reaction. Initial structure-activity relationship (SAR) studies of the AM2-S31N inhibitors revealed that potent channel blockers contain the following structural features: a hydrophobic template such as adamantane or hydroxyl adamantane, an ammonium linker, and an aryl head group with a hydrophobic substitution (Figure 1A). 2017 Journal of medicinal chemistry Introduction IV S31N 65 69 28182419 Expeditious Lead Optimization of Isoxazole-Containing Influenza A Virus M2-S31N Inhibitors Using the Suzuki-Miyaura Cross-Coupling Reaction. Instead the AM2-S31N mutant is a natural mutation that happens to maintain nearly identical channel function as the wild-type AM2 (AM2-WT) but is resistant to amantadine. 2017 Journal of medicinal chemistry Introduction IV S31N 16 20 28182419 Expeditious Lead Optimization of Isoxazole-Containing Influenza A Virus M2-S31N Inhibitors Using the Suzuki-Miyaura Cross-Coupling Reaction. More importantly, the AM2-S31N inhibitors have a higher genetic barrier to drug resistance than amantadine, and resistant mutants that emerge under AM2-S31N inhibitors drug selection pressure in cell culture are rare mutations. 2017 Journal of medicinal chemistry Introduction IV S31N;S31N 26;152 30;156 28182419 Expeditious Lead Optimization of Isoxazole-Containing Influenza A Virus M2-S31N Inhibitors Using the Suzuki-Miyaura Cross-Coupling Reaction. Our goal is to design potent channel blockers of the AM2-S31N mutant and develop them as the next-generation of influenza antivirals. 2017 Journal of medicinal chemistry Introduction IV S31N 57 61 28182419 Expeditious Lead Optimization of Isoxazole-Containing Influenza A Virus M2-S31N Inhibitors Using the Suzuki-Miyaura Cross-Coupling Reaction. Propelled by mechanistic studies of AM2-S31N drug inhibition and proton conductance using X-ray crystallography, NMR, and molecular dynamics simulations, we were able to design inhibitors that target the AM2-S31N mutant, which was previously deemed undruggable as no progress had been made for decades. 2017 Journal of medicinal chemistry Introduction IV S31N;S31N 40;208 44;212 28182419 Expeditious Lead Optimization of Isoxazole-Containing Influenza A Virus M2-S31N Inhibitors Using the Suzuki-Miyaura Cross-Coupling Reaction. The AM2-S31N mutant is one of the most conserved viral proteins among currently circulating influenza A viruses, and more than 95% of the viruses carry this mutation. 2017 Journal of medicinal chemistry Introduction IV S31N 8 12 28182419 Expeditious Lead Optimization of Isoxazole-Containing Influenza A Virus M2-S31N Inhibitors Using the Suzuki-Miyaura Cross-Coupling Reaction. Thus small-molecule antiviral drugs that target the conserved viral proteins such as the AM2-S31N are highly desired. 2017 Journal of medicinal chemistry Introduction IV S31N 93 97 28182419 Expeditious Lead Optimization of Isoxazole-Containing Influenza A Virus M2-S31N Inhibitors Using the Suzuki-Miyaura Cross-Coupling Reaction. We have designed inhibitors that intend to target either the Openout-Closedin or the Closedout-Openin conformation of AM2-S31N, and so far we were only able to successfully target the Openout-Closedin conformation. 2017 Journal of medicinal chemistry Introduction IV S31N 122 126 28182419 Expeditious Lead Optimization of Isoxazole-Containing Influenza A Virus M2-S31N Inhibitors Using the Suzuki-Miyaura Cross-Coupling Reaction. With one of the AM2-S31N inhibitor M2WJ332 in hand, we were able to solve the solution NMR structure of AM2-S31N (PDB: 2LY0), and the structure indeed showed that the drug M2WJ332 bound to AM2-S31N channel when it was in the Openout-Closedin conformation. 2017 Journal of medicinal chemistry Introduction IV S31N;S31N;S31N 20;108;193 24;112;197 28323816 An NS-segment exonic splicing enhancer regulates influenza A virus replication in mammalian cells. Acquired NS G540A substitution altered the ratio of NEP/NS1 mRNA in virus infections and enhanced H7N9 virus replication in mammalian cells and mice. 2017 Nature communications Introduction IV G540A 12 17 NEP;NS;NS1 52;9;56 55;11;59 28323816 An NS-segment exonic splicing enhancer regulates influenza A virus replication in mammalian cells. Notably, the NS G540A genotype emerged in early 2000, becoming the dominant genotype among H9N2 viruses from 2012 onwards. 2017 Nature communications Introduction IV G540A 16 21 NS 13 15 28323816 An NS-segment exonic splicing enhancer regulates influenza A virus replication in mammalian cells. The here performed analysis of the 2013 H7N9 virus genome revealed a distinct E172K substitution in the NS1 protein, corresponding to nucleotide G540A. 2017 Nature communications Introduction IV E172K;G540A 78;145 83;150 NS1 104 107 28323816 An NS-segment exonic splicing enhancer regulates influenza A virus replication in mammalian cells. We identified the G540A substitution as being located in an uncharacterized NEP ESE motif that is recognized and bound by the splicing regulator SF2. 2017 Nature communications Introduction IV G540A 18 23 NEP 76 79 28402848 The 150-Loop Restricts the Host Specificity of Human H10N8 Influenza Virus. Further mutation at Thr160 or a double mutation at Asn158 (N158D, loss of glycosylation) and Gln224 (N224K), switched preference to human receptors, albeit with low affinity. 2017 Cell reports Introduction IV N158D;N224K 59;101 64;106 28402848 The 150-Loop Restricts the Host Specificity of Human H10N8 Influenza Virus. Indeed, for avian H5N1, E190D and G225D mutations abolished receptor binding, while Q226L and G228S mutations enabled only partial recognition of alpha2-6 linked receptors without loss of alpha2-3 binding. 2017 Cell reports Introduction IV E190D;G225D;Q226L;G228S 24;34;84;94 29;39;89;99 28402848 The 150-Loop Restricts the Host Specificity of Human H10N8 Influenza Virus. Previous studies on pandemic influenza strains have shown that two different pairs of substitutions of four key RBS residues were all that were required to switch HA receptor specificity (E190D and G225D for 1918 and 2009 H1N1 and Q226L and G228S for 1957 H2N2 and 1968 H3N2). 2017 Cell reports Introduction IV E190D;G225D;Q226L;G228S 188;198;231;241 193;203;236;246 HA 163 165 28418242 Slow but Steady Wins the Race: Dissimilarities among New Dual Inhibitors of the Wild-Type and the V27A Mutant M2 Channels of Influenza A Virus. Although in this analysis the second most prevalent mutant, V27A, was only observed in about 1% of the sequences, other reports have pointed out that the V27A mutant occurred in 10-77% of influenza virus isolates, depending on the viral strain and season. 2017 Journal of medicinal chemistry Introduction IV V27A;V27A 60;154 64;158 28418242 Slow but Steady Wins the Race: Dissimilarities among New Dual Inhibitors of the Wild-Type and the V27A Mutant M2 Channels of Influenza A Virus. Although several mutations appear to be viable in vitro, a recent analysis of 31,251 M2 protein sequences revealed that the most frequent Amt-resistant mutations in the circulating strains occur at position 31 (S31N) (~ 95%), followed by position 27 (V27A), while other mutations (L26F, A30T, G34E and L38F) were rare. 2017 Journal of medicinal chemistry Introduction IV S31N;V27A;L26F;A30T;G34E;L38F 211;251;281;287;293;302 215;255;285;291;297;306 M2 85 87 28418242 Slow but Steady Wins the Race: Dissimilarities among New Dual Inhibitors of the Wild-Type and the V27A Mutant M2 Channels of Influenza A Virus. Several findings add functional relevance to the V27A mutation: (i) among the most prevalent mutations, V27A is the only one proven to originate from drug selection pressure; (ii) while the S31N and L26F mutants are sensitive, to some extent, to Amt, this drug is completely ineffective against the V27A mutant M2 channel; (iii) recent studies have noticed an increased frequency of the Amt-resistant V27A/S31N double mutant; and, (iv) finally, a virus harboring this V27A/S31N double mutant form of M2 displayed significantly higher mortality compared to wild-type (wt) virus in a mouse model. 2017 Journal of medicinal chemistry Introduction IV V27A;V27A;S31N;L26F;V27A;V27A;S31N;S31N;V27A 49;104;190;199;299;401;406;473;468 53;108;194;203;303;405;410;477;472 M2;M2 311;500 313;502 28418242 Slow but Steady Wins the Race: Dissimilarities among New Dual Inhibitors of the Wild-Type and the V27A Mutant M2 Channels of Influenza A Virus. Specifically, the comparison of 2 and 3 would shed light on which position of the adamantane scaffold is more suitable for designing potent V27A inhibitors (Chart 1). 2017 Journal of medicinal chemistry Introduction IV V27A 140 144 28418242 Slow but Steady Wins the Race: Dissimilarities among New Dual Inhibitors of the Wild-Type and the V27A Mutant M2 Channels of Influenza A Virus. Taking into account that the synthesis of 1 involves six steps from 2-adamantanone and that potent inhibition of the wt and V27A mutant channels was also achieved with secondary amines, we wondered whether the synthetically more accessible analogs of 1, such as the piperidine derivatives 2 and 3 described herein, would have similar channel blockage and antiviral activity as compound 1. 2017 Journal of medicinal chemistry Introduction IV V27A 124 128 28418242 Slow but Steady Wins the Race: Dissimilarities among New Dual Inhibitors of the Wild-Type and the V27A Mutant M2 Channels of Influenza A Virus. used a computationally-driven design for the synthesis and pharmacological evaluation of the spiroadamante 1, a triple inhibitor of the wt, V27A and L26F mutant channels, that features a primary amine. 2017 Journal of medicinal chemistry Introduction IV V27A;L26F 140;149 144;153 28418242 Slow but Steady Wins the Race: Dissimilarities among New Dual Inhibitors of the Wild-Type and the V27A Mutant M2 Channels of Influenza A Virus. While numerous compounds targeting the wt channel have been synthesized, few dual inhibitors of the wt and either the V27A, or the S31N mutants, were only recently identified. 2017 Journal of medicinal chemistry Introduction IV V27A;S31N 118;131 122;135 28421062 Identification of Rare PB2-D701N Mutation from a Patient with Severe Influenza: Contribution of the PB2-D701N Mutation to the Pathogenicity of Human Influenza. A search in the NCBI Influenza Virus Resource database2 indicated that NA-L415M change has a prevalence >1% in human influenza A(H1N1)pdm09 virus NA proteins, whereas PB2-D701N and HA-K403R had a prevalence between 0.05 and 0.10%. 2017 Frontiers in microbiology Introduction IV L415M;D701N;K403R 74;171;184 79;176;189 HA;NA;NA;PB2 181;71;146;167 183;73;148;170 28421062 Identification of Rare PB2-D701N Mutation from a Patient with Severe Influenza: Contribution of the PB2-D701N Mutation to the Pathogenicity of Human Influenza. A(H1N1)pdm09 virus has an avian-lineage PB2 gene that lacks the E627K and D701N substitutions that permit transmission and cooperate in pathogenesis of avian-origin influenza viruses in humans or other mammals. 2017 Frontiers in microbiology Introduction IV E627K;D701N 64;74 69;79 PB2 40 43 28421062 Identification of Rare PB2-D701N Mutation from a Patient with Severe Influenza: Contribution of the PB2-D701N Mutation to the Pathogenicity of Human Influenza. All 13 influenza samples bore PB2-701D, indicating that PB2-701N influenza viruses were not commonly circulating in the area, and remarkably the only case here described containing PB2 D701N mutation was associated with admission to ICU. 2017 Frontiers in microbiology Introduction IV D701N 185 190 PB2;PB2;PB2 30;56;181 33;59;184 28421062 Identification of Rare PB2-D701N Mutation from a Patient with Severe Influenza: Contribution of the PB2-D701N Mutation to the Pathogenicity of Human Influenza. Many of these are located in the polymerase PB2 subunit, with E627K and D701N as the most prevalent mutations, which are rarely present in human circulating viruses. 2017 Frontiers in microbiology Introduction IV E627K;D701N 62;72 67;77 PB2 44 47 28421062 Identification of Rare PB2-D701N Mutation from a Patient with Severe Influenza: Contribution of the PB2-D701N Mutation to the Pathogenicity of Human Influenza. Mutations PA T97Y and T552S are also involved in an increased viral replication and pathogenicity of avian viruses in mice. 2017 Frontiers in microbiology Introduction IV T97Y;T552S 13;22 17;27 PA 10 12 28421062 Identification of Rare PB2-D701N Mutation from a Patient with Severe Influenza: Contribution of the PB2-D701N Mutation to the Pathogenicity of Human Influenza. PB1 has a role in pathogenicity and polymerase activity and two mutations in PB1, PB1-L473V and L598P, compensated for the absence of PB2-627K within an attenuated reassortant virus containing the H5N1 polymerase in a WSN background, both in cell culture and in the mouse model. 2017 Frontiers in microbiology Introduction IV L473V;L598P 86;96 91;101 PB1;PB1;PB1;PB2 0;77;82;134 3;80;85;137 28421062 Identification of Rare PB2-D701N Mutation from a Patient with Severe Influenza: Contribution of the PB2-D701N Mutation to the Pathogenicity of Human Influenza. Sequence analysis of the other three human isolates containing PB2-D701N mutation indicated that their HA protein was the human protein present among circulating A(H1N1)pdm09-linage viruses (Table 1, upper). 2017 Frontiers in microbiology Introduction IV D701N 67 72 HA;PB2 103;63 105;66 28421062 Identification of Rare PB2-D701N Mutation from a Patient with Severe Influenza: Contribution of the PB2-D701N Mutation to the Pathogenicity of Human Influenza. Seven of them bore PB2-D701N change (eight, including the viral isolate here described, prevalence 0.105%), and corresponded to human A(H1N1)pdm09-linage isolates obtained from the start of the 2009 pandemic until March 2016. 2017 Frontiers in microbiology Introduction IV D701N 23 28 PB2 19 22 28421062 Identification of Rare PB2-D701N Mutation from a Patient with Severe Influenza: Contribution of the PB2-D701N Mutation to the Pathogenicity of Human Influenza. Several mutations in PA have been linked to enhanced virulence, including G631S in an H5N1 avian virus, or N409S in the novel avian-origin H7N9 virus that may confer higher replication in mammals. 2017 Frontiers in microbiology Introduction IV G631S;N409S 74;107 79;112 PA 21 23 28421062 Identification of Rare PB2-D701N Mutation from a Patient with Severe Influenza: Contribution of the PB2-D701N Mutation to the Pathogenicity of Human Influenza. The comparison showed three amino acid changes; PB2-D701N, HA-K403R and NA-L415M. 2017 Frontiers in microbiology Introduction IV D701N;K403R;L415M 52;62;75 57;67;80 HA;NA;PB2 59;72;48 61;74;51 28421062 Identification of Rare PB2-D701N Mutation from a Patient with Severe Influenza: Contribution of the PB2-D701N Mutation to the Pathogenicity of Human Influenza. The K403R HA change is not described as a pathogenicity determinant of those reported for A(H1N1)pdm09 or H5N1 viruses. 2017 Frontiers in microbiology Introduction IV K403R 4 9 HA 10 12 28421062 Identification of Rare PB2-D701N Mutation from a Patient with Severe Influenza: Contribution of the PB2-D701N Mutation to the Pathogenicity of Human Influenza. The minimal set of mutations required for airborne transmission of a H5N1 virus among ferrets included, in addition of the PB2-E627K change, mutation PB1-H99Y, both mutations together had a synergistic effect, increasing viral polymerase activity and virus replication in mammalian cells. 2017 Frontiers in microbiology Introduction IV E627K;H99Y 127;154 132;158 PB1;PB2 150;123 153;126 28421062 Identification of Rare PB2-D701N Mutation from a Patient with Severe Influenza: Contribution of the PB2-D701N Mutation to the Pathogenicity of Human Influenza. The PB2-D701N change was present in 100% of the A/Aragon/270/2014 viral sequence reads, but change HA-K403R was present in 85% of total reads. 2017 Frontiers in microbiology Introduction IV D701N;K403R 8;102 13;107 HA;PB2 99;4 101;7 28421062 Identification of Rare PB2-D701N Mutation from a Patient with Severe Influenza: Contribution of the PB2-D701N Mutation to the Pathogenicity of Human Influenza. This data suggests that the previously described PB2-D701N change might be in this patient, the main viral contributor to severe outcome of the infection. 2017 Frontiers in microbiology Introduction IV D701N 53 58 PB2 49 52 28421062 Identification of Rare PB2-D701N Mutation from a Patient with Severe Influenza: Contribution of the PB2-D701N Mutation to the Pathogenicity of Human Influenza. This virus nonetheless had a compensatory PB2-Q591R substitution that rendered PB2-E627K unnecessary for effective replication. 2017 Frontiers in microbiology Introduction IV Q591R;E627K 46;83 51;88 PB2;PB2 42;79 45;82 28421062 Identification of Rare PB2-D701N Mutation from a Patient with Severe Influenza: Contribution of the PB2-D701N Mutation to the Pathogenicity of Human Influenza. We found a virus bearing the PB2-D701N mutation (A/Aragon/270/2014) in the clinical sample of one patient who met the above mentioned requirements. 2017 Frontiers in microbiology Introduction IV D701N 33 38 PB2 29 32 28433777 Design and expeditious synthesis of organosilanes as potent antivirals targeting multidrug-resistant influenza A viruses. Encouraged by this progress, in this study we report the design and expeditious synthesis of organosilane-based AM2-S31N inhibitors. 2017 European journal of medicinal chemistry Introduction IV S31N 116 120 28433777 Design and expeditious synthesis of organosilanes as potent antivirals targeting multidrug-resistant influenza A viruses. In light of advantages of exploring organosilanes as bioactive molecules, we are interested in designing organosilanes as AM2-S31N inhibitors. 2017 European journal of medicinal chemistry Introduction IV S31N 126 130 28433777 Design and expeditious synthesis of organosilanes as potent antivirals targeting multidrug-resistant influenza A viruses. In pursuing the next generation of influenza antivirals, we chose the AM2-S31N mutant as the drug target. 2017 European journal of medicinal chemistry Introduction IV S31N 74 78 28433777 Design and expeditious synthesis of organosilanes as potent antivirals targeting multidrug-resistant influenza A viruses. More than 95% of currently circulating influenza A viruses carry the S31N mutant in their M2 genes, which renders them resistant to adamantanes. 2017 European journal of medicinal chemistry Introduction IV S31N 69 73 M2 90 92 28433777 Design and expeditious synthesis of organosilanes as potent antivirals targeting multidrug-resistant influenza A viruses. Propelled by structural and mechanistic understandings of AM2 proton conductance and drug inhibition, we successfully designed the first-in-class AM2-S31N inhibitors with both potent channel blockage and antiviral activity. 2017 European journal of medicinal chemistry Introduction IV S31N 150 154 28433777 Design and expeditious synthesis of organosilanes as potent antivirals targeting multidrug-resistant influenza A viruses. Resistance to the only orally available drug, oseltamivir, continues to rise, and the 2008-2009 seasonal H1N1 strain was completely resistant to oseltamivir due to a H275Y mutation. 2017 European journal of medicinal chemistry Introduction IV H275Y 166 171 28433777 Design and expeditious synthesis of organosilanes as potent antivirals targeting multidrug-resistant influenza A viruses. The pharmacophore of AM2-S31N inhibitors consists of a hydrophobic scaffold such as adamantane, a positively charged ammonium linker, and an aromatic head group with a hydrophobic substitution. 2017 European journal of medicinal chemistry Introduction IV S31N 25 29 28433777 Design and expeditious synthesis of organosilanes as potent antivirals targeting multidrug-resistant influenza A viruses. The prevalence of this mutation thus makes AM2-S31N a desired target for drug design. 2017 European journal of medicinal chemistry Introduction IV S31N 47 51 28433777 Design and expeditious synthesis of organosilanes as potent antivirals targeting multidrug-resistant influenza A viruses. Three criteria were taken into consideration when designing AM2-S31N inhibitors: (1) the designed organosilanes should meet the pharmacophore requirements of AM2-S31N inhibitors. 2017 European journal of medicinal chemistry Introduction IV S31N;S31N 64;162 68;166 28465552 A reassortant H9N2 influenza virus containing 2009 pandemic H1N1 internal-protein genes acquired enhanced pig-to-pig transmission after serial passages in swine. A significant proportion of poultry H9N2 field isolates contains a leucine instead of glutamine residue at position 226 in the hemagglutinin (HA) receptor-binding site (RBS) (HA-Q226L, H3 numbering used throughout). 2017 Scientific reports Introduction IV Q226L;Q226L 178;67 183;119 HA;HA;HA 142;175;127 144;177;140 28465552 A reassortant H9N2 influenza virus containing 2009 pandemic H1N1 internal-protein genes acquired enhanced pig-to-pig transmission after serial passages in swine. The predominant mutation in the passaged reassortant virus was an aspartic acid to glycine at position 225 in the HA RBS. 2017 Scientific reports Introduction IV D225G 66 106 HA 114 116 28498306 A Conserved Residue, Tyrosine (Y) 84, in H5N1 Influenza A Virus NS1 Regulates IFN Signaling Responses to Enhance Viral Infection. A tyrosine (Y) to phenylalanine (F) substitution at the strictly conserved residue 89 (Y89F) in the H1N1 NS1 putative SH2-binding domain prevented binding of NS1 to p85beta, thus abrogating NS1-mediated AKT phosphorylation. 2017 Viruses Introduction IV Y89F 87 91 NS1;NS1;NS1 105;158;190 108;161;193 28498306 A Conserved Residue, Tyrosine (Y) 84, in H5N1 Influenza A Virus NS1 Regulates IFN Signaling Responses to Enhance Viral Infection. Additionally, this Y89F in the NS1 of IAV PR8 reduced virulence in infected mice. 2017 Viruses Introduction IV Y89F 19 23 NS1 31 34 28744280 Amino Acid Substitution K470R in the Nucleoprotein Increases the Virulence of H5N1 Influenza A Virus in Mammals. All recombinant viruses containing M1 mutants (Y132A/F/D) were unable to be rescued. 2017 Frontiers in microbiology Introduction IV Y132A;Y132F;Y132D 47;47;47 56;56;56 M1 35 37 28744280 Amino Acid Substitution K470R in the Nucleoprotein Increases the Virulence of H5N1 Influenza A Virus in Mammals. For the K91R and K198R mutations that did not support viral growth, we studied the cellular distribution in mammalian cells. 2017 Frontiers in microbiology Introduction IV K91R;K198R 8;17 12;22 28744280 Amino Acid Substitution K470R in the Nucleoprotein Increases the Virulence of H5N1 Influenza A Virus in Mammals. PA mutations P103H and S659L reduced viral replication in mammalian cells and attenuated pathogenicity in mice. 2017 Frontiers in microbiology Introduction IV P103H;S659L 13;23 18;28 PA 0 2 28744280 Amino Acid Substitution K470R in the Nucleoprotein Increases the Virulence of H5N1 Influenza A Virus in Mammals. Using reverse genetics, we successfully rescued K227R, K229R, and K470R mutant viruses and analyze the virulence of the recombinant viruses in vitro and in vivo. 2017 Frontiers in microbiology Introduction IV K227R;K229R;K470R 48;55;66 53;60;71 28754164 Data-driven interdisciplinary mathematical modelling quantitatively unveils competition dynamics of co-circulating influenza strains. According to Yang et al., A/H1N1 H275Y variants were seldom isolated in Taiwan until September 2008 when they were found emerging in 14.3% of A/H1N1 isolates. 2017 Journal of translational medicine Introduction IV H275Y 33 38 28754164 Data-driven interdisciplinary mathematical modelling quantitatively unveils competition dynamics of co-circulating influenza strains. As A/H1N1 subtype progressively prevailed, the proportion of A/H1N1 H275Y strains ultimately reached 100% by the end of year 2008. 2017 Journal of translational medicine Introduction IV H275Y 68 73 28754164 Data-driven interdisciplinary mathematical modelling quantitatively unveils competition dynamics of co-circulating influenza strains. Given the ever worldwide dissemination of drug-resistant seasonal A/H1N1 H275Y variants during the 2007-2009 influenza seasons, the detection of drug-resistant A/H1N1pdm09 variants was of growing concern. 2017 Journal of translational medicine Introduction IV H275Y 73 78 28754164 Data-driven interdisciplinary mathematical modelling quantitatively unveils competition dynamics of co-circulating influenza strains. On the other hand, nevertheless, the transmission dynamics of drug-resistant seasonal A/H1N1 H275Y variants was still mysterious at the human population level. 2017 Journal of translational medicine Introduction IV H275Y 93 98 28754164 Data-driven interdisciplinary mathematical modelling quantitatively unveils competition dynamics of co-circulating influenza strains. The vast majority of A/H1N1 H275Y strains belonged to clade 2B-2, which dominated the 2008-2009 influenza season in Taiwan. 2017 Journal of translational medicine Introduction IV H275Y 28 33 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. In 2007-2008, the unprecedented rise of seasonal A(H1N1) viruses carrying the NA amino acid substitution (AAS) H275Y was detected in Europe; these oseltamivir-resistant viruses rapidly spread globally. 2017 Antiviral research Introduction IV H275Y 111 116 78 80 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. In subsequent seasons, A(H1N1)pdm09 viruses containing H275Y NA AAS have been detected in patients with and without exposure to oseltamivir treatment, with large clusters reported in Australia and Japan. 2017 Antiviral research Introduction IV H275Y 55 60 61 63 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. The global spread of A(H1N1)pdm09 viruses carrying NA H275Y AAS remains the prime concern for public health because of evidence supporting their transmissibility in communities and dual resistance to oseltamivir and peramivir. 2017 Antiviral research Introduction IV H275Y 54 59 51 53 28814518 A Single-Amino-Acid Substitution at Position 225 in Hemagglutinin Alters the Transmissibility of Eurasian Avian-Like H1N1 Swine Influenza Virus in Guinea Pigs. reported that a 2-amino-acid change, D190E and D225G, in the viral hemagglutinin (HA) protein abolishes the transmission of 1918/H1N1 influenza virus in ferrets. 2017 Journal of virology Introduction IV D190E;D225G 37;47 42;52 HA;HA 82;67 84;80 28814518 A Single-Amino-Acid Substitution at Position 225 in Hemagglutinin Alters the Transmissibility of Eurasian Avian-Like H1N1 Swine Influenza Virus in Guinea Pigs. The amino acids at positions 222 and 226 of HA are critical for the 2009/H1N1 virus to bind to human-type receptors and transmit among mammals, and PB2 271A facilitates the mutation of R to Q at position 226 of the HA of 2009/H1N1 viruses. 2017 Journal of virology Introduction IV R226Q 185 207 HA;HA;PB2 44;215;148 46;217;151 28814737 Susceptibility of influenza A(H1N1)/pdm2009, seasonal A(H3N2) and B viruses to Oseltamivir in Guangdong, China between 2009 and 2014. From 2007 to 2008, oseltamivir-resistant strains that possessed H275Y mutations in their NA proteins began to emerge within seasonal H1N1 viruses. 2017 Scientific reports Introduction IV H275Y 64 69 89 91 28814737 Susceptibility of influenza A(H1N1)/pdm2009, seasonal A(H3N2) and B viruses to Oseltamivir in Guangdong, China between 2009 and 2014. WHO received the first report regarding an oseltamivir-resistant H1N1pdm2009 isolate in July 2009, and the H275Y mutation within NA was detected in the drug-resistant virus. 2017 Scientific reports Introduction IV H275Y 107 112 129 131 28815216 Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity. A second mutation, PB1 D27N, was recovered in a screen for PB1 mutants in A/WSN/33 (H1N1) that maintained RNA synthesis during ribavirin treatment. 2017 mSphere Introduction IV D27N 23 27 PB1;PB1 19;59 22;62 28815216 Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity. Additionally, we characterize the previously identified PB1 V43I and PB1 D27N mutants in the A/Puerto Rico/8/1934 (PR8 [H1N1]) genetic background. 2017 mSphere Introduction IV V43I;D27N 60;73 64;77 PB1;PB1 56;69 59;72 28815216 Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity. The PB1 V43I mutation was identified as a minority variant upon serial passage of A/Wuhan/35/95 (H3N2) in low concentrations of ribavirin and appears to have altered fidelity in that genetic background. 2017 mSphere Introduction IV V43I 8 12 PB1 4 7 28815216 Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity. We did, however, identify three mutations:PB1 T123A, PB1 M645I, and PA T97I:that were enriched in replicate drug-selected populations. 2017 mSphere Introduction IV T123A;M645I;T97I 46;57;71 51;62;75 PA;PB1;PB1 68;42;53 70;45;56 28837667 Influenza NS1 directly modulates Hedgehog signaling during infection. Incorporation of the A122V mutation into a mouse-adapted influenza virus increased expression of some Hh targets and cytokines, accelerated lethality, and increased host morbidity relative to the parental virus. 2017 PLoS pathogens Introduction IV A122V 21 26 28837667 Influenza NS1 directly modulates Hedgehog signaling during infection. These effects of NS1 are at least in part due to direct cell autonomous effects of NS1 since transfection of NS1 alone into human lung cell lines altered expression of BMP2, the mammalian homologue of Drosophila dpp, in an A122V-dependent fashion. 2017 PLoS pathogens Introduction IV A122V 223 228 NS1;NS1;NS1 17;83;109 20;86;112 28837667 Influenza NS1 directly modulates Hedgehog signaling during infection. We identified a novel point mutation in a surface residue of NS1 (A122V), however, that does abrogate this signaling function. 2017 PLoS pathogens Introduction IV A122V 66 71 NS1 61 64 28860593 Prerequisites for the acquisition of mammalian pathogenicity by influenza A virus with a prototypic avian PB2 gene. Amino acid position 627 on PB2 is located in the C-terminal RNA-binding domain, and the E627K mutation is known to increase both RNA binding and polymerase activity, increasing viral replication efficiency at 33 C, the approximate temperature of the human upper respiratory tract. 2017 Scientific reports Introduction IV E627K 88 93 PB2 27 30 28860593 Prerequisites for the acquisition of mammalian pathogenicity by influenza A virus with a prototypic avian PB2 gene. Diverse mutations in the polymerase subunits that determine the mammalian pathogenicity of AIV have been reported, and E627K in PB2 is considered a key mutation. 2017 Scientific reports Introduction IV E627K 119 124 PB2 128 131 28860593 Prerequisites for the acquisition of mammalian pathogenicity by influenza A virus with a prototypic avian PB2 gene. Furthermore, the E627K mutation may increase the mammalian pathogenicity of AIV by promoting a stronger interaction with mammalian importin-alpha isoforms and enhancing the NP-PB2 interaction in mammalian cells. 2017 Scientific reports Introduction IV E627K 17 22 NP;PB2 173;176 175;179 28860593 Prerequisites for the acquisition of mammalian pathogenicity by influenza A virus with a prototypic avian PB2 gene. Here, we identified key mutations (I66M, I109V, and I133V, collectively referred to as "MVV") that increase replication efficiency in both avian and mammalian hosts and are predicted to increase the structural integrity of the trimeric polymerase. 2017 Scientific reports Introduction IV I66M;I109V;I133V 35;41;52 39;46;57 28860626 Topological N-glycosylation and site-specific N-glycan sulfation of influenza proteins in the highly expressed H1N1 candidate vaccines. In past years, several candidate reassortant vaccines such as NIBRG-121xp and NYMC-X181A derived from A/California/07/2009 pandemic influenza viruses have been developed through serial egg passages of viruses derived from either conventional recombination techniques used by Dr. 2017 Scientific reports Introduction IV X181A 83 88 28860626 Topological N-glycosylation and site-specific N-glycan sulfation of influenza proteins in the highly expressed H1N1 candidate vaccines. In previous studies, we quantitatively analyzed the candidate vaccines of NIBRG-121xp and NYMC-X179A both derived from the influenza virus strain A/California/7/2009 by different manufacturers, and evaluated the antigenic stability of the HA and NA proteins. 2017 Scientific reports Introduction IV X179A 95 100 HA;NA 239;246 241;248 28951584 Identification of neuraminidase inhibitors against dual H274Y/I222R mutant strains. discovered a series of diazenylaryl sulfonic acids as NA inhibitors, which inhibited N1 NA with drug-resistant mutations, including H274Y, N294S, Y155H, Q136L, I427Q and I427M. 2017 Scientific reports Introduction IV H274Y;N294S;Y155H;Q136L;I427Q;I427M 132;139;146;153;160;170 137;144;151;158;165;175 NA;NA 54;88 56;90 28951584 Identification of neuraminidase inhibitors against dual H274Y/I222R mutant strains. However, the physiochemical properties of the 150-cavity were not characterized, nor an analysis based on a dual H274Y/I222R mutation of an influenza virus. 2017 Scientific reports Introduction IV H274Y;I222R 113;119 118;124 28951584 Identification of neuraminidase inhibitors against dual H274Y/I222R mutant strains. The H274Y/I222R mutation have shown an increased resistance to zanamivir, oseltamivir, and peramivir. 2017 Scientific reports Introduction IV H274Y;I222R 4;10 9;15 28951584 Identification of neuraminidase inhibitors against dual H274Y/I222R mutant strains. These strains include an oseltamivir carboxylate-resistant strain, where a tyrosine replaces histidine at position 274 in NA, and a zanamivir-resistant strain, where an arginine replaces isoleucine at position 222. 2017 Scientific reports Introduction IV Y274H;R222I 75;169 118;213 122 124 28951584 Identification of neuraminidase inhibitors against dual H274Y/I222R mutant strains. To solve these issues, our study established a site-moiety map to elucidate properties of the binding site and discover new inhibitors for dual H274Y/I222R mutant NA. 2017 Scientific reports Introduction IV H274Y;I222R 144;150 149;155 163 165 29100932 Evolution of equine influenza viruses (H3N8) during a Brazilian outbreak, 2015. The strains of the Florida sublineage had amino acid mutations in the hemagglutinin 1 (HA1) subunit and this lineage diverged into Florida Clade 1 (FC1), with the substitutions A78V and S159N, and Florida Clade 2 (FC2), represented by A/equine/South Africa/4/2003 and A/equine/Richmond/1/07, respectively. 2018 Brazilian journal of microbiology Introduction IV A78V;S159N 177;186 181;191 HA1;HA 87;70 90;83 29145498 Antigenicity of the 2015-2016 seasonal H1N1 human influenza virus HA and NA proteins. A number of virus clusters have emerged within clade 6B and two of these have been designated as subclades: viruses in subclade 6B.1 are defined by head amino acid substitutions S101N, S179N (in antigenic site Sa) and I233T, while those in subclade 6B.2 are defined by head amino acid substitutions V169T (in antigenic site Sa) and V190I. 2017 PloS one Introduction IV S101N;S179N;I233T;V169T;V190I 178;185;218;299;332 183;190;223;304;337 29145498 Antigenicity of the 2015-2016 seasonal H1N1 human influenza virus HA and NA proteins. For well over a year, viruses in clade 6, and carrying amino acid substitutions of D114N, S202T (in antigenic site Sb), and S220T (in antigenic site Ca1) in the head domain, and E391K and S468N in the stalk domain compared with A/Cal/07/09, have predominated worldwide, with a number of subclades emerging. 2017 PloS one Introduction IV D114N;S202T;S220T;E391K;S468N 83;90;124;178;188 88;95;129;183;193 29145498 Antigenicity of the 2015-2016 seasonal H1N1 human influenza virus HA and NA proteins. Interestingly, even after 7 years without an update to the vaccine strain and the emergence of several genetic subgroups, recently circulating H1N1 viruses (the majority of which fall into subclade 6B.1, defined by amino acid substitutions S101N, S179N, and I233T, have still been considered antigenically similar to the A/California/07/2009 (A/Cal/07/09), an early isolate of the pandemic. 2017 PloS one Introduction IV S101N;S179N;I233T 240;247;258 245;252;263 29145498 Antigenicity of the 2015-2016 seasonal H1N1 human influenza virus HA and NA proteins. Most of the viruses characterized since September 2014 carry HA genes in subclade 6B, which is characterized by additional amino acid substitutions of K180Q (in antigenic site Sa), A273T and K300E in the head domain and E516K in the stalk domain compared with A/Cal/07/09. 2017 PloS one Introduction IV K180Q;A273T;K300E;E516K 151;181;191;220 156;186;196;225 HA 61 63 29209052 Maintaining pH-dependent conformational flexibility of M1 is critical for efficient influenza A virus replication. Both M(NLS-88R) and M(NLS-88E) are M1 mutants in the WSN background that differ in a single mutation at M1 position 88 (G88R vs G88E). 2017 Emerging microbes & infections Introduction IV G88R;G88E 120;128 124;132 M;M;M1;M1 5;20;35;104 6;21;37;106 29209052 Maintaining pH-dependent conformational flexibility of M1 is critical for efficient influenza A virus replication. G88R but not G88E was originally acquired by the virus as a spontaneous compensatory mutation after NLS disruption. 2017 Emerging microbes & infections Introduction IV G88R;G88E 0;13 4;17 29209052 Maintaining pH-dependent conformational flexibility of M1 is critical for efficient influenza A virus replication. However, the G88E mutation causes M1 to be trapped in a face-to-face orientation regardless of pH that consequently resulted in inefficient virus growth and genetic instability. 2017 Emerging microbes & infections Introduction IV G88E 13 17 M1 34 36 29299528 Human Clade 2.3.4.4 A/H5N6 Influenza Virus Lacks Mammalian Adaptation Markers and Does Not Transmit via the Airborne Route between Ferrets. While our study suggests that the public health risk posed by this A/H5N6 virus is low, the A/H5N6 GZ/14 showed a high polymerase activity mediated by the E627K substitution in PB2, replicated to higher titers in the respiratory tracts of ferrets and was more pathogenic than a clade 2.3.4.4 A/H5N8 virus. 2018 mSphere Introduction IV E627K 155 160 PB2 177 180 29299533 Cooperating H3N2 Influenza Virus Variants Are Not Detectable in Primary Clinical Samples. More sensitive characterization of clinical samples that give rise to D151G upon lab passage can determine whether this mutation reaches high frequencies in cell culture because it is amplified from low- to modest-frequency standing diversity or whether it arises spontaneously in the lab. 2018 mSphere Introduction IV D151G 70 75 29299533 Cooperating H3N2 Influenza Virus Variants Are Not Detectable in Primary Clinical Samples. The D151G mutation did not exceed the frequency of library preparation and sequencing errors in any of these samples. 2018 mSphere Introduction IV D151G 4 9 29299533 Cooperating H3N2 Influenza Virus Variants Are Not Detectable in Primary Clinical Samples. The D151G mutation is frequently observed when influenza virus is passaged through cell culture, but it remains unclear whether the G151 variant exists within natural human infections or is primarily a cell culture artifact. 2018 mSphere Introduction IV D151G 4 9 29299533 Cooperating H3N2 Influenza Virus Variants Are Not Detectable in Primary Clinical Samples. We sought to determine whether the D151G mutation is present in viral populations isolated from natural human infections. 2018 mSphere Introduction IV D151G 35 40 29308074 Neuraminidase Gene Variations in Influenza A(H1N1)pdm09 Virus among Patients Admitted to Refferal Pulmonary Hospital, Tehran, Iran in 2009-2013. In addition, we performed a study on the prevalence of oseltamivir resistance and H275Y mutations in pandemic H1N1 strains during 2009-2010 season, using real-time probe-based polymerase chain reaction (PCR) method. 2017 Tanaffos Introduction IV H275Y 82 87 29308074 Neuraminidase Gene Variations in Influenza A(H1N1)pdm09 Virus among Patients Admitted to Refferal Pulmonary Hospital, Tehran, Iran in 2009-2013. On the other hand, resistance mutations (H275Y, E119V/G, and I22V) have been reported in in vivo and in vitro models. 2017 Tanaffos Introduction IV H275Y;E119V;E119G;I22V 41;48;48;61 46;55;55;65 29324781 Neuraminidase inhibitor susceptibility and neuraminidase enzyme kinetics of human influenza A and B viruses circulating in Thailand in 2010-2015. A recent study demonstrated that an influenza A(H1N1)pdm09 variant containing double NA substitution at residues I427T/Q313R outside the NA active site had decreased NAI susceptibility, with altered NA properties and viral fitness. 2018 PloS one Introduction IV I427T;Q313R 113;119 118;124 NA;NA;NA;NAI 85;137;199;166 87;139;201;169 29324781 Neuraminidase inhibitor susceptibility and neuraminidase enzyme kinetics of human influenza A and B viruses circulating in Thailand in 2010-2015. Antiviral surveillance studies identified novel NA substitutions (S331R in influenza A(H3N2) viruses; D342S and A395E in influenza B viruses) that were associated with reduced inhibition by oseltamivir and peramivir (as indicated by higher IC50 values for these compounds). 2018 PloS one Introduction IV S331R;D342S;A395E 66;102;112 71;107;117 48 50 29324781 Neuraminidase inhibitor susceptibility and neuraminidase enzyme kinetics of human influenza A and B viruses circulating in Thailand in 2010-2015. Here, we applied reverse genetics and generated recombinant influenza A and B viruses possessing either wild-type (WT) NA or an NA with a single I222V, S331G, or S331R substitution [in influenza A(H3N2) viruses] or a single S342S, A395T, A395V, or A395S substitution [in influenza B viruses].We then used these recombinant viruses to study the properties (activity, enzyme kinetic, thermostability) of their NAs, their susceptibility to NAIs, their replication kinetics, and the genetic stability of the NA substitutions during passages in MDCK cells. 2018 PloS one Introduction IV I222V;S331G;S331R;S342S;A395T;A395V;A395S 145;152;162;224;231;238;248 150;157;167;229;236;243;253 NA;NA;NA;NAI;NA 119;128;504;437;408 121;130;506;441;411 29324781 Neuraminidase inhibitor susceptibility and neuraminidase enzyme kinetics of human influenza A and B viruses circulating in Thailand in 2010-2015. I222T/V NA substitutions were reported to cause reduced susceptibility of A(H5N1) viruses to NAIs, with 60- to 105-fold higher IC50s to oseltamivir when compared to the wild-type NAs. 2018 PloS one Introduction IV I222T;I222V 0;0 7;7 NA;NAI;NA 8;93;179 10;97;182 29355500 Influenza Hemifusion Phenotype Depends on Membrane Context: Differences in Cell-Cell and Virus-Cell Fusion. 5c), while the hemifusion ratio remains constant because in this model the stoichiometry required for hemifusion does not differ between G1S and wild-type HA. 2018 Journal of molecular biology Introduction IV G1S 137 140 HA 155 157 29355500 Influenza Hemifusion Phenotype Depends on Membrane Context: Differences in Cell-Cell and Virus-Cell Fusion. Although G1S-expressing virus created fusion pores as efficiently as wild-type virus, productive infection was somewhat reduced, as detailed below, suggesting a relative defect in downstream steps such as fusion pore expansion and maintenance necessary for genome release. 2018 Journal of molecular biology Introduction IV G1S 9 12 29355500 Influenza Hemifusion Phenotype Depends on Membrane Context: Differences in Cell-Cell and Virus-Cell Fusion. Although prior reports have shown that G1S-expressing virus is infectious, and thus capable of membrane fusion, and indeed takes 7-8 rounds of serial passage to show reversion, the high efficiency of virus-liposome fusion was unexpected and suggests substantial differences between fusion of HA-transfected cells and fusion of infectious virus. 2018 Journal of molecular biology Introduction IV G1S 39 42 HA 292 294 29355500 Influenza Hemifusion Phenotype Depends on Membrane Context: Differences in Cell-Cell and Virus-Cell Fusion. As the surface density decreased, G1S showed a more rapid drop-off in fusion efficiency. 2018 Journal of molecular biology Introduction IV G1S 34 37 29355500 Influenza Hemifusion Phenotype Depends on Membrane Context: Differences in Cell-Cell and Virus-Cell Fusion. At a high HA surface density, the G1S mutation resulted in identical fusion efficiency to wild-type but a slight slowing of fusion rates. 2018 Journal of molecular biology Introduction IV G1S 34 37 HA 10 12 29355500 Influenza Hemifusion Phenotype Depends on Membrane Context: Differences in Cell-Cell and Virus-Cell Fusion. Because G1S fusion peptide mutants have been previously reported to revert to wild-type after 7-8 rounds of serial passage, we performed RT-PCR and amplicon deep sequencing to rule out the possibility that the productive infection events detected in plaque assays could be caused by revertant virus. 2018 Journal of molecular biology Introduction IV G1S 8 11 29355500 Influenza Hemifusion Phenotype Depends on Membrane Context: Differences in Cell-Cell and Virus-Cell Fusion. Because of the differences in fusion behavior observed between virus expressing G1S hemagglutinin and transfected cells, we tested infectivity of the G1S virus via plaque assays. 2018 Journal of molecular biology Introduction IV G1S;G1S 80;150 83;153 HA 84 97 29355500 Influenza Hemifusion Phenotype Depends on Membrane Context: Differences in Cell-Cell and Virus-Cell Fusion. Cell-cell fusion mediated by HA-expressing cells is used here to reproduce the classic model system in which the G1S hemifusion phenotype was identified and to probe its mechanistic basis; however, the cell surface presents a complex mixture of interacting biomolecules, and a synthetic system such as proteoliposome-bilayer fusion would provide a more chemically defined platform to probe the effects of the G1S mutation. 2018 Journal of molecular biology Introduction IV G1S;G1S 113;409 116;412 HA 29 31 29355500 Influenza Hemifusion Phenotype Depends on Membrane Context: Differences in Cell-Cell and Virus-Cell Fusion. Cells transfected with G1S hemagglutinin (HA) undergo lipid mixing but not contents mixing with target cells in a pH-dependent fashion, while cells expressing wild-type HA readily undergo both. 2018 Journal of molecular biology Introduction IV G1S 23 26 HA;HA;HA 42;169;27 44;171;40 29355500 Influenza Hemifusion Phenotype Depends on Membrane Context: Differences in Cell-Cell and Virus-Cell Fusion. G1S-expressing virus produced purely in 293T cells, produced and amplified in 293T/MDCK cell co-culture, and expressing the G1S mutant on either the WSN (H1N1) HA or the X-31 (H3N2) HA background all yielded equivalent results. 2018 Journal of molecular biology Introduction IV G1S 124 127 HA;HA 160;182 162;184 29355500 Influenza Hemifusion Phenotype Depends on Membrane Context: Differences in Cell-Cell and Virus-Cell Fusion. In agreement with previous reports, HA-transfected cells bearing the G1S mutation displayed a hemifusion phenotype. 2018 Journal of molecular biology Introduction IV G1S 69 72 HA 36 38 29355500 Influenza Hemifusion Phenotype Depends on Membrane Context: Differences in Cell-Cell and Virus-Cell Fusion. In cell transfectants, lipid mixing also occurs at a lower rate (this work; ) and some contents leakage has been reported in addition to fusion (see Supplement), so an increased stoichiometry of fusion pore opening is not the only alteration in fusion rates or mechanism resulting from the G1S mutation. 2018 Journal of molecular biology Introduction IV G1S 290 293 29355500 Influenza Hemifusion Phenotype Depends on Membrane Context: Differences in Cell-Cell and Virus-Cell Fusion. In general, most identified defects would readily explain a relative decrease in fusion efficiency rather than a change in gross fusion phenotype: G1S fusion peptides take on a slightly less kinked conformation via NMR or induce slightly less lipid tail protrusion or membrane curvature in simulations. 2018 Journal of molecular biology Introduction IV G1S 147 150 29355500 Influenza Hemifusion Phenotype Depends on Membrane Context: Differences in Cell-Cell and Virus-Cell Fusion. In such a model, the effect of the G1S mutation is that each hemagglutinin trimer contributes a smaller free energy towards the activation free energy for fusion DeltaG . 2018 Journal of molecular biology Introduction IV G1S 35 38 HA 61 74 29355500 Influenza Hemifusion Phenotype Depends on Membrane Context: Differences in Cell-Cell and Virus-Cell Fusion. Influenza virus expressing G1S HA did not show reversion that would account for the infectious titers recovered, and in all cases any potential reversion was less than the assay error for wild-type virus produced in the same manner. 2018 Journal of molecular biology Introduction IV G1S 27 30 HA 31 33 29355500 Influenza Hemifusion Phenotype Depends on Membrane Context: Differences in Cell-Cell and Virus-Cell Fusion. Lipid and contents mixing efficiencies were statistically indistinguishable between the wild-type and G1S WSN (H1N1) virus. 2018 Journal of molecular biology Introduction IV G1S 102 105 29355500 Influenza Hemifusion Phenotype Depends on Membrane Context: Differences in Cell-Cell and Virus-Cell Fusion. Lipid mixing rates were not statistically different between wild-type and G1S virus (p>0.15), while contents mixing rates were approximately 2-fold slower for G1S-expressing virus. 2018 Journal of molecular biology Introduction IV G1S;G1S 74;159 77;162 29355500 Influenza Hemifusion Phenotype Depends on Membrane Context: Differences in Cell-Cell and Virus-Cell Fusion. Our data suggest that the G1S hemifusion phenotype depends on factors present in the virus but not in transfected cells. 2018 Journal of molecular biology Introduction IV G1S 26 29 29355500 Influenza Hemifusion Phenotype Depends on Membrane Context: Differences in Cell-Cell and Virus-Cell Fusion. Our results unify, extend, and explain disparate previous reports of the G1S hemagglutinin mutant, its phenotype, and the mechanism by which this can occur. 2018 Journal of molecular biology Introduction IV G1S 73 76 HA 77 90 29355500 Influenza Hemifusion Phenotype Depends on Membrane Context: Differences in Cell-Cell and Virus-Cell Fusion. Sanger sequencing of the HA and NA segments showed no other mutations in the G1S virus. 2018 Journal of molecular biology Introduction IV G1S 77 80 HA;NA 25;32 27;34 29355500 Influenza Hemifusion Phenotype Depends on Membrane Context: Differences in Cell-Cell and Virus-Cell Fusion. Similar to the original reports on these mutants, the G1S mutant supports lipid mixing two- to three-fold less well in cell-transfectants than wild-type HA, and there are a small number of contents-mixing events detected (20% of those observed in wild-type transfectants). 2018 Journal of molecular biology Introduction IV G1S 54 57 HA 153 155 29355500 Influenza Hemifusion Phenotype Depends on Membrane Context: Differences in Cell-Cell and Virus-Cell Fusion. Surprisingly, we found that infectious G1S virus was able to form fusion pores at a comparable efficiency to wild-type virus, whereas cells expressing G1S hemagglutinin displayed the previously characterized hemifusion phenotype. 2018 Journal of molecular biology Introduction IV G1S;G1S 39;151 42;154 HA 155 168 29355500 Influenza Hemifusion Phenotype Depends on Membrane Context: Differences in Cell-Cell and Virus-Cell Fusion. The fusion-to-hemifusion ratio was not statistically different at 68% and 64% for wild-type and G1S virus respectively (T-test p>0.46), whereas the corresponding ratio for HA-expressing cells were 51% and 17% (T-test p<10-5). 2018 Journal of molecular biology Introduction IV G1S 96 99 HA 172 174 29355500 Influenza Hemifusion Phenotype Depends on Membrane Context: Differences in Cell-Cell and Virus-Cell Fusion. The G1S fusion peptide mutant provides a special opportunity for mechanistic insight into fusion because it has been reported to induce hemifusion but not full fusion. 2018 Journal of molecular biology Introduction IV G1S 4 7 29355500 Influenza Hemifusion Phenotype Depends on Membrane Context: Differences in Cell-Cell and Virus-Cell Fusion. The G1S mutant has therefore been extensively studied via structural and biophysical approaches, but none of the potential differences identified thus far have been able to mechanistically explain why it would support hemifusion yet not fusion. 2018 Journal of molecular biology Introduction IV G1S 4 7 29355500 Influenza Hemifusion Phenotype Depends on Membrane Context: Differences in Cell-Cell and Virus-Cell Fusion. The manner in which the G1S fusion phenotype depends on membrane context led us to hypothesize that the G1S mutation might indeed cause a quantitative defect in fusion rather than a qualitative blockade of fusion pore formation. 2018 Journal of molecular biology Introduction IV G1S;G1S 24;104 27;107 29355500 Influenza Hemifusion Phenotype Depends on Membrane Context: Differences in Cell-Cell and Virus-Cell Fusion. The quantitative model we employ does not specify the molecular mechanism by which the G1S mutation reduces the contribution of each HA trimer to the activation free-energy barrier for fusion. 2018 Journal of molecular biology Introduction IV G1S 87 90 HA 133 135 29355500 Influenza Hemifusion Phenotype Depends on Membrane Context: Differences in Cell-Cell and Virus-Cell Fusion. The ratio of G1S:wild-type fusion thus decreases as a function of HA surface density. 2018 Journal of molecular biology Introduction IV G1S 13 16 HA 66 68 29355500 Influenza Hemifusion Phenotype Depends on Membrane Context: Differences in Cell-Cell and Virus-Cell Fusion. The specific and robust conclusion we reach, however, is that if fusion pore formation by G1S hemagglutinin requires a higher protein stoichiometry than wild-type hemagglutinin, then differences in HA surface density would be sufficient to convert a mild slowing of fusion at high density to a hemifusion phenotype at low density. 2018 Journal of molecular biology Introduction IV G1S 90 93 HA;HA;HA 198;94;163 200;107;176 29355500 Influenza Hemifusion Phenotype Depends on Membrane Context: Differences in Cell-Cell and Virus-Cell Fusion. These results are sufficient to establish that the fusion behavior observed in virus-liposome assays indeed results from G1S hemagglutinin and not any rare revertant population. 2018 Journal of molecular biology Introduction IV G1S 121 124 HA 125 138 29355500 Influenza Hemifusion Phenotype Depends on Membrane Context: Differences in Cell-Cell and Virus-Cell Fusion. This hemifusion phenotype:an approximately threefold lower contents mixing:lipid mixing ratio for G1S-expressing cells than for wild-type HA-expressing cells--is in good agreement with previous reports. 2018 Journal of molecular biology Introduction IV G1S 98 101 HA 138 140 29355500 Influenza Hemifusion Phenotype Depends on Membrane Context: Differences in Cell-Cell and Virus-Cell Fusion. This model is sufficient to explain the observed fusion behavior of G1S hemagglutinin in both cells and virus. 2018 Journal of molecular biology Introduction IV G1S 68 71 HA 72 85 29355500 Influenza Hemifusion Phenotype Depends on Membrane Context: Differences in Cell-Cell and Virus-Cell Fusion. This model thus provides a consistent explanation for the observed context-dependent G1S hemifusion phenotype. 2018 Journal of molecular biology Introduction IV G1S 85 88 29355500 Influenza Hemifusion Phenotype Depends on Membrane Context: Differences in Cell-Cell and Virus-Cell Fusion. To better understand the fusion activity of the G1S hemagglutinin mutant, we have performed membrane fusion assays on both hemagglutinin-expressing cells and infectious virus expressing either wild-type or G1S hemagglutinin. 2018 Journal of molecular biology Introduction IV G1S;G1S 48;206 51;209 HA;HA;HA 52;123;210 65;136;223 29355500 Influenza Hemifusion Phenotype Depends on Membrane Context: Differences in Cell-Cell and Virus-Cell Fusion. Viral titers per mL of culture supernatant were reduced an average of 30-fold (range 10 to 85-fold) for the G1S mutant compared to wild-type; however, this is not surprising because prior reports have suggested that the efficiency of virion production is somewhat reduced for the G1S mutant. 2018 Journal of molecular biology Introduction IV G1S;G1S 108;280 111;283 29355500 Influenza Hemifusion Phenotype Depends on Membrane Context: Differences in Cell-Cell and Virus-Cell Fusion. When infectious influenza virions were generated with and without the G1S mutation, both supported full fusion with liposomes to an equal extent. 2018 Journal of molecular biology Introduction IV G1S 70 73 29355500 Influenza Hemifusion Phenotype Depends on Membrane Context: Differences in Cell-Cell and Virus-Cell Fusion. While a change in HA surface density provides a simple explanation that is sufficient, in combination with a change in fusion stoichiometry for the G1S fusion peptide, to account for the observed hemifusion phenotype, we do not claim that this is the only mechanism that could explain this phenotype. 2018 Journal of molecular biology Introduction IV G1S 148 151 HA 18 20 29489903 Design and synthesis of constrained bicyclic molecules as candidate inhibitors of influenza A neuraminidase. It is now well known that the 3-pentyl ether side chain of oseltamivir is a major cause for resistance: neuraminidases must undergo a significant rearrangement to form a pocket for oseltamivir binding and this movement can be affected by mutations, such as H274Y. 2018 PloS one Introduction IV H274Y 257 262 104 118 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. AM2-S31N inhibitors structurally related to compounds 1 and 2 have been shown to inhibit multiple strains of AM2-S31N influenza A viruses, including both oseltamivir-sensitive and -resistant strains, with a high selectivity index. 2018 Antiviral research Introduction IV S31N;S31N 4;113 8;117 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. Amantadine resistance in transmissible viruses can be caused by conservative (V27A) or nonconservative (L26F and S31N) mutations in the AM2 channel. 2018 Antiviral research Introduction IV V27A;L26F;S31N 78;104;113 82;108;117 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. As representative examples of our rationally designed AM2-S31N inhibitors, compounds 1 and 2 were chosen for the drug resistant mechanistic studies due to their high antiviral potency and selectivity index. 2018 Antiviral research Introduction IV S31N 58 62 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. Given these circumstances, there are concerns that viruses might evolve resistance against AM2-S31N inhibitors under similar drug selection pressure. 2018 Antiviral research Introduction IV S31N 95 99 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. Higher level of resistance was obtained only after exceeding drug selection pressure using compound 2 (100-fold of EC50), and a triple mutant S31N/L26I/A30T was identified to account for the higher level of resistance. 2018 Antiviral research Introduction IV A30T;S31N;L26I 152;142;147 156;146;151 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. However, among transmissible viruses, AM2-S31N channel is the most prominent. 2018 Antiviral research Introduction IV S31N 42 46 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. However, the AM2-S31N/L26I/A30T triple mutant channel had significantly reduced specific proton conductance than the AM2-S31N proton channel. 2018 Antiviral research Introduction IV A30T;S31N;L26I;S31N 27;17;22;121 31;21;26;125 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. In summary, the results presented in this study appear to suggest that AM2-S31N inhibitors have a higher genetic barrier to drug resistance than amantadine at least in cell culture, motivating further drug discovery efforts to target the AM2-S31N channel. 2018 Antiviral research Introduction IV S31N;S31N 75;242 79;246 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. In the case of the AM2-S31N mutation, the mechanism for resistance is due to a bulkier, polar asparagine which destabilizes amantadine binding through steric interference as well as by reducing the hydrophobic interaction with the adamantane cage. 2018 Antiviral research Introduction IV S31N 23 27 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. Since AM2-S31N inhibitors demonstrate promising antiviral activity, we set out to investigate the evolutionary course by which susceptible influenza A strains become resistant. 2018 Antiviral research Introduction IV S31N 10 14 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. Structure-guided design of AM2-S31N inhibitors has led to a series of biologically active small molecule antivirals such as the isoxazole-substituted amantadine analogs 1 and 2. 2018 Antiviral research Introduction IV S31N 31 35 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. The majority of H1N1 strains currently in circulation are resistant to amantadine and rimantadine because of the S31N mutation in the AM2 channel. 2018 Antiviral research Introduction IV S31N 113 117 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. The mutant virus harboring the AM2-S31N/L26I/A30T triple mutant also had attenuated replication fitness and was not able to compete against AM2-S31N containing virus. 2018 Antiviral research Introduction IV A30T;L26I;S31N;S31N 45;40;35;144 49;44;39;148 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. To address this question, we investigated the drug-resistance mechanism of two representative AM2-S31N inhibitors 1 and 2 using a combination of electrophysiology and virology techniques. 2018 Antiviral research Introduction IV S31N 98 102 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. We chose the AM2-S31N-containing 2009 pandemic-like influenza virus A/California/07/2009 (H1N1) as a model virus and performed serial viral passage experiments to select resistant mutants under the increasing drug selection pressure of compounds 1 and 2. 2018 Antiviral research Introduction IV S31N 17 21 29522492 Challenge for One Health: Co-Circulation of Zoonotic H5N1 and H9N2 Avian Influenza Viruses in Egypt. However, a recent study has found one clade 2.2.1.1 virus (A/turkey/Egypt/7/2007) with a mutation at position N295S, which can be resistant to oseltamivir. 2018 Viruses Introduction IV N295S 110 115 29522492 Challenge for One Health: Co-Circulation of Zoonotic H5N1 and H9N2 Avian Influenza Viruses in Egypt. However, antigenic drift of H9N2 isolated from quails has been found as a result of mutations in the antigenic sites A (N166D) and B (D153N and N201A), suggesting that the virus can be a new escape mutant variant cluster with an adaptive evolution in quails. 2018 Viruses Introduction IV N166D;D153N;N201A 120;134;144 125;139;149 29522492 Challenge for One Health: Co-Circulation of Zoonotic H5N1 and H9N2 Avian Influenza Viruses in Egypt. Most Egyptian H5N1 viruses possess two other mutations that may facilitate their transmissibility and replication in mammals: (1) the deletion in the 130 loop (129Delta) with a concurrent loss of glycosylation mutation (T156A) in the HA and (2) E627K mutation in the PB2 protein. 2018 Viruses Introduction IV T156A;E627K 220;245 225;250 HA;PB2 234;267 236;270 29522492 Challenge for One Health: Co-Circulation of Zoonotic H5N1 and H9N2 Avian Influenza Viruses in Egypt. Other mutations (D94N, T156A, K189R and P235S) in the HA protein have also been shown to enhance binding affinity to the human-type receptor. 2018 Viruses Introduction IV D94N;T156A;K189R;P235S 17;23;30;40 21;28;35;45 HA 54 56 29522492 Challenge for One Health: Co-Circulation of Zoonotic H5N1 and H9N2 Avian Influenza Viruses in Egypt. Some clade 2.2.1.2 viruses in 2014 possessed mutations R140K in antigenic site A and A86V in antigenic site E of the HA gene, indicating further antigenic drift. 2018 Viruses Introduction IV R140K;A86V 55;85 60;89 HA 117 119 29522492 Challenge for One Health: Co-Circulation of Zoonotic H5N1 and H9N2 Avian Influenza Viruses in Egypt. The clade 2.2.1 viruses that emerged between 2007 and 2008 had already acquired amino acid mutations (Q192H and the double 129Delta/I151T mutations), enabling human-type receptor binding during their transmission among the birds. 2018 Viruses Introduction IV Q192H;I151T 102;132 107;137 29587786 Effects of the S42 residue of the H1N1 swine influenza virus NS1 protein on interferon responses and virus replication. In this study, we constructed and rescued the NS1 mutant (S42P, D92E, and S42P/D92E) of the A/swine/Shanghai/3/2014(H1N1) strain and explored the effect of the mutant site on the cellular localization and the production of cytokines. 2018 Virology journal Introduction IV S42P;D92E;D92E;S42P 58;64;79;74 62;68;83;78 NS1 46 49 29587786 Effects of the S42 residue of the H1N1 swine influenza virus NS1 protein on interferon responses and virus replication. Our data indicate that the mutations at these two positions have minimal effects on NS1 nuclear localization; however, the mutant virus with S42P of NS1 reduced growth properties in the cell culture, couldn't antagonize the host cell interferon production and increased p-IRF3 levels. 2018 Virology journal Introduction IV S42P 141 145 NS1;NS1 84;149 87;152 29587786 Effects of the S42 residue of the H1N1 swine influenza virus NS1 protein on interferon responses and virus replication. The glutamic acid (E) at position 92 of NS1 in the H5N1 influenza virus was shown to be critical in conferring virulence and resistance to antiviral cytokines in pigs. 2018 Virology journal Introduction IV E92E 3 37 NS1 40 43 29587792 Major contribution of the RNA-binding domain of NS1 in the pathogenicity and replication potential of an avian H7N1 influenza virus in chickens. Our results showed that the double substitution in the RBD dramatically reduced the pathogenicity and replication potential of the virus, while the A149V substitution in the ED had only a modest effect. 2018 Virology journal Introduction IV A149V 148 153 29587792 Major contribution of the RNA-binding domain of NS1 in the pathogenicity and replication potential of an avian H7N1 influenza virus in chickens. To this end, we rescued a virus harbouring a well-characterized double-substitutions in its RBD (R38A-K41A) that is known to invalidate the function of the RBD, along with a virus harbouring substitution A149V in NS1's ED that was previously shown to abrogate the inhibitory activity of NS1 towards type I-IFN production in avian cells. 2018 Virology journal Introduction IV K41A;R38A;A149V 102;97;204 106;101;209 NS1;NS1 213;287 216;290 29593694 Amino Acid Substitutions HA A150V, PA A343T, and PB2 E627K Increase the Virulence of H5N6 Influenza Virus in Mice. For example, polymerase acidic (PA) R443 K, PA-K356R, polymerase basic 2 protein (PB2) E627K, PB2 D701N, and polymerase basic protein 1 (PB1) D622G) are all associated with replication and host tropism. 2018 Frontiers in microbiology Introduction IV R443K;K356R;E627K;D701N;D622G 36;47;87;98;142 42;52;92;103;147 PA;PA;PB1;PB2;PB2;PA;PB1F2 32;44;137;82;94;13;54 34;46;140;85;97;30;80 29593694 Amino Acid Substitutions HA A150V, PA A343T, and PB2 E627K Increase the Virulence of H5N6 Influenza Virus in Mice. Recently, we reported that a mouse-adapted (MA) H5N6 influenza virus A/duck/Zhejiang/6D2/2013 (6D2) carried several amino acid substitutions, including HA A150V, PA A343T, and PB2 E627K in the process of mouse lung-to-lung passage. 2018 Frontiers in microbiology Introduction IV A150V;A343T;E627K 155;165;180 160;170;185 HA;PA;PB2 152;162;176 154;164;179 29593694 Amino Acid Substitutions HA A150V, PA A343T, and PB2 E627K Increase the Virulence of H5N6 Influenza Virus in Mice. Receptor binding preference is a crucial component in adaption, pathogenicity, and transmission (citation updated and moved to backward), with only a few substitutions, for instance, HA D190E, D225G, Q192H, and K193R, influenza virus can change receptor specificity, from avian type to human type. 2018 Frontiers in microbiology Introduction IV D190E;D225G;Q192H;K193R 186;193;200;211 191;198;205;216 HA 183 185 29643248 A Single Amino Acid in the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses. Hence, identifying a common denominator for the enhanced pathogenicity of IBVs, such as the E627K PB2 mutation of avian IAVs, may be of great importance because such defined IBV pathogenic determinants might be useful for the interpretation of IBV virulence and host range. 2018 Journal of virology Introduction IV E627K 92 97 PB2 98 101 29643248 A Single Amino Acid in the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses. The PB2 E627K mutation of avian IAVs has been suggested to be associated with pathogenicity in mice. 2018 Journal of virology Introduction IV E627K 8 13 PB2 4 7 29688498 Dynamic Variation and Reversion in the Signature Amino Acids of H7N9 Virus During Human Infection. Notably, the oseltamivir-resistant NA R292K mutation increased during antiviral treatment in a fatal case of H7N9 infection, and the PB2 E627K mutation was also identified with increasing frequency during infection in a fatal human case of avian H7N7 influenza virus. 2018 The Journal of infectious diseases Introduction IV R292K;E627K 38;137 43;142 NA;PB2 35;133 37;136 29691337 Identification of the I38T PA Substitution as a Resistance Marker for Next-Generation Influenza Virus Endonuclease Inhibitors. A random mutagenesis approach in the PR/8 or A/California/04/2009 (H1N1)pdm09 (CA/04) background identified PA-T20A, -I79L, -F105S, and -E119D mutants that increased the EC50 up to 11-fold. 2018 mBio Introduction IV T20A;I79L;F105S;E119D 111;118;125;137 115;122;130;142 PA 108 110 29691337 Identification of the I38T PA Substitution as a Resistance Marker for Next-Generation Influenza Virus Endonuclease Inhibitors. Acquisition of I38T affected the ability of RO-7 to inhibit virus yield (titers were lowered only by <=1 log10 TCID50/ml) and increased plaque reduction EC50s to 538 and 867 nM in CA/04 and PR/8, respectively. 2018 mBio Introduction IV I38T 15 19 29691337 Identification of the I38T PA Substitution as a Resistance Marker for Next-Generation Influenza Virus Endonuclease Inhibitors. Additionally, 2 PAN changes were identified in nonviable replicate passages (viral RNA could be recovered, but virus titers were below detection limits), including E23K in CA/04 and E31K in PR/8 (data not shown). 2018 mBio Introduction IV E23K;E31K 164;182 168;186 29691337 Identification of the I38T PA Substitution as a Resistance Marker for Next-Generation Influenza Virus Endonuclease Inhibitors. Additionally, recent data from a phase 2 clinical trial with an endonuclease inhibitor (S-033188/baloxavir marboxil), structurally similar to RO-7, reported the detection of I38T/F PAN substitutions in four S-033188-treated patients (I38T, n = 2; I38F, n = 2) of 300 total patients from which virus genotypes could be obtained. 2018 mBio Introduction IV I38F;I38T;I38T;I38F 174;174;234;247 180;180;238;251 29691337 Identification of the I38T PA Substitution as a Resistance Marker for Next-Generation Influenza Virus Endonuclease Inhibitors. After serial passage of the two viruses in the presence of RO-7, the I38T substitution was identified within the PA endonuclease domains of both. 2018 mBio Introduction IV I38T 69 73 PA 113 115 29691337 Identification of the I38T PA Substitution as a Resistance Marker for Next-Generation Influenza Virus Endonuclease Inhibitors. E31K is associated with increased replication of egg-passaged viruses, while the impact of E23K is unknown. 2018 mBio Introduction IV E31K;E23K 0;91 4;95 29691337 Identification of the I38T PA Substitution as a Resistance Marker for Next-Generation Influenza Virus Endonuclease Inhibitors. Excluding I38T, we found 3 and 7 amino acid changes in CA/04 and PR/8 viruses, respectively (see Table S3 in the supplemental material). 2018 mBio Introduction IV I38T 10 14 29691337 Identification of the I38T PA Substitution as a Resistance Marker for Next-Generation Influenza Virus Endonuclease Inhibitors. However, E23K was identified in one influenza A virus-infected patient in a phase 2 clinical trial of a similar compound (S-033188/baloxavir marboxil), suggesting that it may play a role in endonuclease inhibitor resistance (T. 2018 mBio Introduction IV E23K 9 13 IAV infections 36 62 29691337 Identification of the I38T PA Substitution as a Resistance Marker for Next-Generation Influenza Virus Endonuclease Inhibitors. However, in replicate assays that showed reduced viral replication capacity upon passage (CA/04 at P15 and PR/8 at P4) (data not shown), viruses were isolated that contained the I38T substitution in conjunction with an E23K or E31K PA substitution. 2018 mBio Introduction IV I38T;E23K;E31K 178;219;227 182;223;231 PA 232 234 29691337 Identification of the I38T PA Substitution as a Resistance Marker for Next-Generation Influenza Virus Endonuclease Inhibitors. I38T substitution in PR/8 reactions increased polymerase activity by 43%. 2018 mBio Introduction IV I38T 0 4 29691337 Identification of the I38T PA Substitution as a Resistance Marker for Next-Generation Influenza Virus Endonuclease Inhibitors. Identification of the I38T PA substitution as a resistance marker for next-generation influenza virus endonuclease inhibitors. 2018 mBio Introduction IV I38T 22 26 PA 27 29 29691337 Identification of the I38T PA Substitution as a Resistance Marker for Next-Generation Influenza Virus Endonuclease Inhibitors. In addition, we previously reported that the resistance-associated PAN substitution E119D emerges in response to the first-generation endonuclease inhibitor L-742,001, and we therefore also determined the complex structure with this mutation at 2 A (Table S2. 2018 mBio Introduction IV E119D 84 89 29691337 Identification of the I38T PA Substitution as a Resistance Marker for Next-Generation Influenza Virus Endonuclease Inhibitors. In the case of the E119D substitution, the holoenzyme only has one bound metal ion at the two-metal active site, but the second metal ion is restored to the active site by the coordinating groups provided by RO-7, as seen in the E119D-L-742,001 complex. 2018 mBio Introduction IV E119D;E119D 19;229 24;234 29691337 Identification of the I38T PA Substitution as a Resistance Marker for Next-Generation Influenza Virus Endonuclease Inhibitors. Moreover, the I38T substitution was stably maintained in both viruses after 5 additional passages without drug pressure (EC50 range, 564 to 860 nM). 2018 mBio Introduction IV I38T 14 18 29691337 Identification of the I38T PA Substitution as a Resistance Marker for Next-Generation Influenza Virus Endonuclease Inhibitors. Our ITC data clearly show that I38T disrupts the binding of RO-7, and the structural analyses reveal that this occurs by a reduction in the size of a central hydrophobic interface. 2018 mBio Introduction IV I38T 31 35 29691337 Identification of the I38T PA Substitution as a Resistance Marker for Next-Generation Influenza Virus Endonuclease Inhibitors. Recombinant A(H1N1) viruses containing only the I38T substitution demonstrated that it alone can impart RO-7 resistance. 2018 mBio Introduction IV I38T 48 52 29691337 Identification of the I38T PA Substitution as a Resistance Marker for Next-Generation Influenza Virus Endonuclease Inhibitors. rg-CA/04-I38T and rg-PR/8-I38T viruses displayed significantly elevated EC50s (227 and 322 nM), confirming I38T as a mediator of RO-7 resistance (Table 1). 2018 mBio Introduction IV I38T;I38T;I38T 9;26;107 13;30;111 29691337 Identification of the I38T PA Substitution as a Resistance Marker for Next-Generation Influenza Virus Endonuclease Inhibitors. S3A in the supplemental material), there is only one minor difference apart from I38T: the loop residues Tyr24/Gly25/Glu26 move by ~0.8 A toward RO-7 in the I38T complex. 2018 mBio Introduction IV I38T;I38T 81;157 85;161 29691337 Identification of the I38T PA Substitution as a Resistance Marker for Next-Generation Influenza Virus Endonuclease Inhibitors. Sequence analysis of the PAN domains after P0, P1, P3, P5, P10, P16, and S5 passages revealed the selection of an I38T substitution at P10 in CA/04 and at P5 in PR/8. 2018 mBio Introduction IV I38T 114 118 29691337 Identification of the I38T PA Substitution as a Resistance Marker for Next-Generation Influenza Virus Endonuclease Inhibitors. Sequence encoding a loop-deleted version (residues 51 to 72 replaced with a GGS linker) of the PAN WT or the point mutation (I38T or E119D) from CA/04 was synthesized and inserted in pET-28a(+) expression plasmid (Genescript, Piscataway, NJ), expressed in BL21(DE3) cells, and purified by affinity chromatography and gel filtration (Protein Production Facility, SJCRH). 2018 mBio Introduction IV I38T;E119D 125;133 129;138 29691337 Identification of the I38T PA Substitution as a Resistance Marker for Next-Generation Influenza Virus Endonuclease Inhibitors. Serial passage of A/Puerto Rico/8/1934 (H1N1) (PR/8) in the presence of L-742,001 yielded the PA-T20A mutant that increased the 50% effective concentration (EC50) >2-fold. 2018 mBio Introduction IV T20A 97 101 PA 94 96 29691337 Identification of the I38T PA Substitution as a Resistance Marker for Next-Generation Influenza Virus Endonuclease Inhibitors. The 8-plasmid reverse-genetics system was used with WT- or PA-I38T-expressing pHW2000 plasmids to rescue viruses. 2018 mBio Introduction IV I38T 62 66 PA 59 61 29691337 Identification of the I38T PA Substitution as a Resistance Marker for Next-Generation Influenza Virus Endonuclease Inhibitors. The E23K PAN substitution was identified in one additional S-033188-treated patient (Shishido et al., Fifth Annual ISIRV Antiviral Group Conference). 2018 mBio Introduction IV E23K 4 8 29691337 Identification of the I38T PA Substitution as a Resistance Marker for Next-Generation Influenza Virus Endonuclease Inhibitors. The I38T PA substitution was inserted into the plasmid using gene-specific primers and the QuikChange site-directed mutagenesis kit (Agilent, Santa Clara, CA). 2018 mBio Introduction IV I38T 4 8 PA 9 11 29691337 Identification of the I38T PA Substitution as a Resistance Marker for Next-Generation Influenza Virus Endonuclease Inhibitors. The I38T substitution had variable effects on virus fitness in the minireplicon assay. 2018 mBio Introduction IV I38T 4 8 29691337 Identification of the I38T PA Substitution as a Resistance Marker for Next-Generation Influenza Virus Endonuclease Inhibitors. The implications of the I38T substitution on RO-7-like compound development are significant. 2018 mBio Introduction IV I38T 24 28 29691337 Identification of the I38T PA Substitution as a Resistance Marker for Next-Generation Influenza Virus Endonuclease Inhibitors. The introduction of I38T into recombinant influenza B virus (Yamagata lineage) increased resistance to endonuclease inhibitor S-033188/baloxavir marboxil by >5-fold (Shishido et al., Fifth Annual ISIRV Antiviral Group Conference). 2018 mBio Introduction IV I38T 20 24 29691337 Identification of the I38T PA Substitution as a Resistance Marker for Next-Generation Influenza Virus Endonuclease Inhibitors. The threonine substitution should be less effective in mediating this interaction, and this is supported by our unsuccessful efforts thus far to crystallize I38T with a bound nucleotide. 2018 mBio Introduction IV I38T 157 161 29691337 Identification of the I38T PA Substitution as a Resistance Marker for Next-Generation Influenza Virus Endonuclease Inhibitors. Therefore, we analyzed the effect of I38T with CA/04 and found that this substitution decreased polymerase activity by 48%. 2018 mBio Introduction IV I38T 37 41 29691337 Identification of the I38T PA Substitution as a Resistance Marker for Next-Generation Influenza Virus Endonuclease Inhibitors. Thermodynamic parameters for the interaction of RO-7 with purified WT or I38T mutant PAN were measured using a MicroCal auto-iTC 200 (Malvern Instruments, Malvern, United Kingdom). 2018 mBio Introduction IV I38T 73 77 29691337 Identification of the I38T PA Substitution as a Resistance Marker for Next-Generation Influenza Virus Endonuclease Inhibitors. Titrations were performed by first injecting 0.5 microl of 100 microM WT or 350 microM I38T mutant protein into a solution of 10 or 30 microM RO-7 followed by additional 3- or 2-microl injections. 2018 mBio Introduction IV I38T 87 91 29691337 Identification of the I38T PA Substitution as a Resistance Marker for Next-Generation Influenza Virus Endonuclease Inhibitors. To confirm that the I38T substitution conferred the RO-7 resistance phenotype, we conducted minireplicon polymerase assays in the presence of plasmids expressing either the WT (Ile38) or mutant (Thr38) residue in PAN. 2018 mBio Introduction IV I38T 20 24 29691337 Identification of the I38T PA Substitution as a Resistance Marker for Next-Generation Influenza Virus Endonuclease Inhibitors. To determine whether the I38T mutation has any structural effect in the absence of bound RO-7, we determined the 2.2-A crystal structure of holo-I38T PAN. 2018 mBio Introduction IV I38T;I38T 25;145 29;149 29691337 Identification of the I38T PA Substitution as a Resistance Marker for Next-Generation Influenza Virus Endonuclease Inhibitors. To gain structural insights into the I38T-mediated RO-7 resistance and the associated reduction in binding, we determined the crystal structures of WT and mutant PAN in the presence of RO-7 at 2.09 and 2.3 A, respectively (Table S1). 2018 mBio Introduction IV I38T 37 41 29691337 Identification of the I38T PA Substitution as a Resistance Marker for Next-Generation Influenza Virus Endonuclease Inhibitors. Viruses with only the I38T substitution maintained high levels of replication throughout the passage scheme. 2018 mBio Introduction IV I38T 22 26 29691337 Identification of the I38T PA Substitution as a Resistance Marker for Next-Generation Influenza Virus Endonuclease Inhibitors. We hypothesized that RO-7 resistance profiles may be due to the I38T substitution lowering the affinity of PAN for the compound, and this was confirmed using isothermal titration calorimetry (ITC). 2018 mBio Introduction IV I38T 64 68 29691337 Identification of the I38T PA Substitution as a Resistance Marker for Next-Generation Influenza Virus Endonuclease Inhibitors. We suggest that the OH group of Thr38 may contribute a hydrogen bond to help stabilize the bound mRNA, which would explain why I38T is the preferred RO-7 resistance substitution that we observed at this position. 2018 mBio Introduction IV I38T 127 131 29691337 Identification of the I38T PA Substitution as a Resistance Marker for Next-Generation Influenza Virus Endonuclease Inhibitors. When the two complexes are compared (see聽Fig.聽S3A聽in the supplemental material), there is only one minor difference apart from I38T: the loop residues Tyr24/Gly25/Glu26 move by ~0.8聽脜 toward RO-7 in the I38T complex. 2018 mBio Introduction IV I38T 203 207 29743603 Unexpected infection outcomes of China-origin H7N9 low pathogenicity avian influenza virus in turkeys. Genetic polymorphisms in this H7N9 LPAIV include Q235L (complete gene numbering) in the haemagglutinin (HA) gene of many human isolates which reflects mammalian adaptation. 2018 Scientific reports Introduction IV Q235L 49 54 HA;HA 104;88 106;102 29743603 Unexpected infection outcomes of China-origin H7N9 low pathogenicity avian influenza virus in turkeys. The E627K (PB2 gene) polymorphism has been reported in in many human isolates with continuing evolution evident at the full-genome level in both human and poultry isolates. 2018 Scientific reports Introduction IV E627K 4 9 PB2 11 14 29750015 Symmetric dimeric adamantanes for exploring the structure of two viroporins: influenza virus M2 and hepatitis C virus p7. S31N is the predominant amantadine-resistant M2 form that represents a huge challenge to drug discovery. 2018 Drug design, development and therapy Introduction IV S31N 0 4 M2 45 47 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. Moreover, we observed that the NS1 R38A/K41A virus could not survive in IFN-competent cells and mice for long periods of time because of the robust innate immune response. 2018 Frontiers in cellular and infection microbiology Introduction IV R38A;K41A 35;40 39;44 NS1 31 34 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. Recombinant A/WSN/33 (WSN) and A/Puerto Rico/8/1934 (PR8) IAVs, expressing the mutant NS1 R38A/K41A protein, induce high levels of IFN-alpha/beta and are attenuated in mice (Donelan et al.,; Gack et al.,; Ramos et al.,). 2018 Frontiers in cellular and infection microbiology Introduction IV R38A;K41A 90;95 94;99 NS1 86 89 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. The package efficiency of the NS1 R38A/K41A virus in RIG-I-knockout 293T cells was much higher than that in 293T cells. 2018 Frontiers in cellular and infection microbiology Introduction IV R38A;K41A 34;39 38;43 NS1 30 33 29783694 Adaptive Mutations in Influenza A/California/07/2009 Enhance Polymerase Activity and Infectious Virion Production. The PB2 E627K substitution adapts these viruses for efficient replication in mammalian cells and animal models. 2018 Viruses Introduction IV E627K 8 13 PB2 4 7 29933553 Kinetic, Thermodynamic, and Structural Analysis of Drug Resistance Mutations in Neuraminidase from the 2009 Pandemic Influenza Virus. Compared to the H275Y single mutant, the double mutants underwent minor additional structural changes in protein-inhibitor contacts or waters that have an effect on increased resistance. 2018 Viruses Introduction IV H275Y 16 21 29933553 Kinetic, Thermodynamic, and Structural Analysis of Drug Resistance Mutations in Neuraminidase from the 2009 Pandemic Influenza Virus. Evolution of the H275Y mutation in seasonal H1N1 was enabled by the secondary "permissive" mutations R222Q and V234M, which both individually and together increased viral fitness and transmissibility. 2018 Viruses Introduction IV H275Y;R222Q;V234M 17;101;111 22;106;116 29933553 Kinetic, Thermodynamic, and Structural Analysis of Drug Resistance Mutations in Neuraminidase from the 2009 Pandemic Influenza Virus. However, as early as the 2007-2008 winter season, oseltamivir-resistant A(H1N1) viruses bearing a H275Y mutation in NA (N1 numbering) were reported in Europe at an unexpectedly high level (0% to 68%, by country) despite low antiviral drug use, and became widespread. 2018 Viruses Introduction IV H275Y 98 103 116 118 29933553 Kinetic, Thermodynamic, and Structural Analysis of Drug Resistance Mutations in Neuraminidase from the 2009 Pandemic Influenza Virus. In addition, a loss of the hydrogen bond between R152 and oseltamivir in the H275Y mutant may contribute to the decrease in susceptibility to this inhibitor. 2018 Viruses Introduction IV H275Y 77 82 29933553 Kinetic, Thermodynamic, and Structural Analysis of Drug Resistance Mutations in Neuraminidase from the 2009 Pandemic Influenza Virus. In agreement with previous work by others, we found that the I223V or S247N amino acid substitution alone confers only a mild decrease in oseltamivir affinity to NA2009, as suggested by our kinetic and isothermal titration calorimetry (ITC) analyses. 2018 Viruses Introduction IV I223V;S247N 61;70 66;75 162 164 29933553 Kinetic, Thermodynamic, and Structural Analysis of Drug Resistance Mutations in Neuraminidase from the 2009 Pandemic Influenza Virus. In contrast, the major NA2009 mutation, H275Y, causes a significant reduction in the enzyme's ability to bind oseltamivir, as shown by detailed thermodynamic analyses and kinetic assays. 2018 Viruses Introduction IV H275Y 40 45 23 25 29933553 Kinetic, Thermodynamic, and Structural Analysis of Drug Resistance Mutations in Neuraminidase from the 2009 Pandemic Influenza Virus. In vitro experiments by Pizzorno and coworkers suggested that addition of the I223V substitution to a H275Y recombinant mutant restored the slightly decreased replicative capacity caused by the H275Y mutation. 2018 Viruses Introduction IV I223V;H275Y;H275Y 78;102;194 83;107;199 29933553 Kinetic, Thermodynamic, and Structural Analysis of Drug Resistance Mutations in Neuraminidase from the 2009 Pandemic Influenza Virus. Its combination with the I223V or S247N mutation leads to substantial impairment of oseltamivir's inhibition potency. 2018 Viruses Introduction IV I223V;S247N 25;34 30;39 29933553 Kinetic, Thermodynamic, and Structural Analysis of Drug Resistance Mutations in Neuraminidase from the 2009 Pandemic Influenza Virus. More recently, I223V and S247N substitutions have been observed in 2009 pandemic H1N1 viruses. 2018 Viruses Introduction IV I223V;S247N 15;25 20;30 29933553 Kinetic, Thermodynamic, and Structural Analysis of Drug Resistance Mutations in Neuraminidase from the 2009 Pandemic Influenza Virus. On the other hand, computer-simulated competition experiments showed a higher relative fitness for the H275Y single mutant over the I223V mutant in the presence of oseltamivir. 2018 Viruses Introduction IV H275Y;I223V 103;132 108;137 29933553 Kinetic, Thermodynamic, and Structural Analysis of Drug Resistance Mutations in Neuraminidase from the 2009 Pandemic Influenza Virus. Our structural analyses explain this effect by a shift in position of E277, which interacts directly with oseltamivir, caused by the H275Y substitution. 2018 Viruses Introduction IV H275Y 133 138 29933553 Kinetic, Thermodynamic, and Structural Analysis of Drug Resistance Mutations in Neuraminidase from the 2009 Pandemic Influenza Virus. The decrease in sensitivity to oseltamivir conferred by these single mutations alone is moderate, but when combined with the H275Y mutation, the double mutants have a greatly enhanced oseltamivir-resistant phenotype (1733-fold for H275Y/I223V and 7000-fold for H275Y/S247N compared to the recombinant wt virus). 2018 Viruses Introduction IV H275Y;I223V;H275Y;S247N;H275Y 125;237;231;267;261 130;242;236;272;266 29933553 Kinetic, Thermodynamic, and Structural Analysis of Drug Resistance Mutations in Neuraminidase from the 2009 Pandemic Influenza Virus. The mutation of His to Tyr at position 275 conferred a 750-fold reduction in susceptibility to oseltamivir and a 260-fold reduction in susceptibility to peramivir, based on a fluorometric inhibition assay (strain A/WSN/1933 (H1N1)). 2018 Viruses Introduction IV H275Y 16 42 29933553 Kinetic, Thermodynamic, and Structural Analysis of Drug Resistance Mutations in Neuraminidase from the 2009 Pandemic Influenza Virus. The structural basis of resistance conferred by the H275Y mutation has been described previously on the background of H5N1 avian influenza NA. 2018 Viruses Introduction IV H275Y 52 57 139 141 29933553 Kinetic, Thermodynamic, and Structural Analysis of Drug Resistance Mutations in Neuraminidase from the 2009 Pandemic Influenza Virus. We performed kinetic, thermodynamic, and X-ray analyses to evaluate the influence of H275Y, I223V, and S247N mutations on the sensitivity of NA from 2009 pandemic influenza (NA2009) to oseltamivir. 2018 Viruses Introduction IV H275Y;I223V;S247N 85;92;103 90;97;108 NA;NA 141;174 143;176 29933553 Kinetic, Thermodynamic, and Structural Analysis of Drug Resistance Mutations in Neuraminidase from the 2009 Pandemic Influenza Virus. While the H275Y and S247N mutations are selected only in the N1 subtype, multiple substitutions at I223 are not type- or subtype-specific and confer oseltamivir resistance on N1, N2, and B NAs. 2018 Viruses Introduction IV H275Y;S247N 10;20 15;25 189 192 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. To understand better the molecular mechanisms involved, we determined the co-crystal structures of wild-type and I38T endonuclease domains from influenza A and B viruses with bound BXA. 2018 Scientific reports Introduction IV I38T 113 117 29999583 A 627K variant in the PB2 protein of H9 subtype influenza virus in wild birds. H10N8 and H7N9, which may be fatal in human, reassortment among the hemagglutinin (HA), neuraminidase (NA), and internal genes of H9N2 have been observed, along with the E627K mutation in the polymerase PB2 protein.4, 5, 6, 7 H9N2 is widespread in nature and is sporadically detected in many poultry and even human beings.8, 9 After the isolation of the first strain in 1994, H9N2 AIVs have rapidly differentiated such that more than 102 genotypic variants have now been recognized based on the nomenclature system.10 In this study, we describe the detection and genetic characteristics of H9N2 viruses in wild birds in Anhui province in 2014-2015. 2018 Influenza and other respiratory viruses Introduction IV E627K 170 175 HA;HA;NA;NA;PB2 83;68;103;88;203 85;81;105;101;206 29999583 A 627K variant in the PB2 protein of H9 subtype influenza virus in wild birds. We successfully acquired eight H9N2 viruses, two of which harbored the E627K mutation in their PB2 protein. 2018 Influenza and other respiratory viruses Introduction IV E627K 71 76 PB2 95 98 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. It was found that immunocompromised ferrets inoculated with A/H3N2 viruses had prolonged presence of viral RNA in the upper and lower respiratory tract and that the treatment of these ferrets with Oseltamivir resulted in the rapid emergence of the resistance substitution R292K in NA. 2018 PloS one Introduction IV R292K 272 277 281 283 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. Treatment of these ferrets with Oseltamivir led to the rapid emergence of viruses with the H275Y NAI resistance substitution in NA. 2018 PloS one Introduction IV H275Y 91 96 NA;NAI 128;97 130;100 30050898 Structurally Diverse Polyketides From the Mangrove-Derived Fungus Diaporthe sp. SCSIO 41011 With Their Anti-influenza A Virus Activities. All the compounds were examined for anti-IAV activities against three influenza A virus subtypes, including A/Puerto Rico/8/34 H274Y (H1N1), A/FM-1/1/47 (H1N1), and A/Aichi/2/68 (H3N2). 2018 Frontiers in chemistry Introduction IV H274Y 127 132 30111290 Development of a quadruple qRT-PCR assay for simultaneous identification of highly and low pathogenic H7N9 avian influenza viruses and characterization against oseltamivir resistance. Furthermore, H7N9 viruses with the NA R292K mutation were frequently reported in the infected patients, and were usually accompanied by prolonged virus shedding and adverse clinical outcomes. 2018 BMC infectious diseases Introduction IV R292K 38 43 35 37 30111290 Development of a quadruple qRT-PCR assay for simultaneous identification of highly and low pathogenic H7N9 avian influenza viruses and characterization against oseltamivir resistance. However, studies have shown that the NA R292K (N2 numbering) mutation in H3N2 and H7N9 viruses, H274Y (N2 numbering) mutation in the seasonal H1N1, H1N1pdm09 and H5N1 viruses, emerged during the treatments or through spontaneous changes, resulted in a high level of resistance to oseltamivir and other NAIs. 2018 BMC infectious diseases Introduction IV R292K;H274Y 40;96 45;101 NA;NAI 37;302 39;306 30111290 Development of a quadruple qRT-PCR assay for simultaneous identification of highly and low pathogenic H7N9 avian influenza viruses and characterization against oseltamivir resistance. Neuraminidase inhibitors (NAIs) have been used as front-line therapeutic options since the novel H7N9 viruses contain the S31N mutation in the M2 protein, which confers resistance to the M2 ion channel blockers such as amantadine. 2018 BMC infectious diseases Introduction IV S31N 122 126 M2;M2;NAI;NA 143;187;26;0 145;189;30;13 30141905 The Stabilities of the Soluble Ectodomain and Fusion Peptide Hairpins of the Influenza Virus Hemagglutinin Subunit II Protein Are Positively Correlated with Membrane Fusion. Some data are consistent with shallower membrane insertion of G1E vs.WT FP. 2018 Biochemistry Introduction IV G1E 62 65 30141905 The Stabilities of the Soluble Ectodomain and Fusion Peptide Hairpins of the Influenza Virus Hemagglutinin Subunit II Protein Are Positively Correlated with Membrane Fusion. The FP is the most-conserved region of the HA sequence and is important in all steps of membrane fusion, as evidenced by both the G1E mutant (HA2 numbering), which results in no HA-cell/RBC fusion, and the G1S mutant which results in hemifusion without pore expansion. 2018 Biochemistry Introduction IV G1E;G1S 130;206 133;209 HA;HA;HA 43;142;178 45;144;180 30141905 The Stabilities of the Soluble Ectodomain and Fusion Peptide Hairpins of the Influenza Virus Hemagglutinin Subunit II Protein Are Positively Correlated with Membrane Fusion. The N-terminal G1E mutant is in the FP, whereas the I173E mutant is in the SE. 2018 Biochemistry Introduction IV G1E;I173E 15;52 18;57 30141905 The Stabilities of the Soluble Ectodomain and Fusion Peptide Hairpins of the Influenza Virus Hemagglutinin Subunit II Protein Are Positively Correlated with Membrane Fusion. The present study describes structural, biophysical, and functional studies for the G1E and I173E mutants of FHA2 and HA2, with comparison to their WT counterparts. 2018 Biochemistry Introduction IV G1E;I173E 84;92 87;97 HA 118 120 30141905 The Stabilities of the Soluble Ectodomain and Fusion Peptide Hairpins of the Influenza Virus Hemagglutinin Subunit II Protein Are Positively Correlated with Membrane Fusion. To our knowledge, there aren't yet biophysical data for the I173E mutant. 2018 Biochemistry Introduction IV I173E 60 65 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. Although some H5N1 human isolates contain known PB2 adaptation mutations, most are PB2-E627K and some are PB2-D701N as described above. 2018 Scientific reports Introduction IV E627K;D701N 87;110 92;115 PB2;PB2;PB2 48;83;106 51;86;109 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. Other mutations in PB2, PB1 and PA also influence the host range of influenza viruses; e.g., PB2-D701N, PB2-K526R, PB2-Q591K, PB2-E192K and -K702R, PB2-I147T/K399T/A588T, PB2-E158G, PB1-L13P/S678N, PB1-N105S, PB1-D175N/K198R and PA-K356R. 2018 Scientific reports Introduction IV D701N;K526R;Q591K;E192K;K702R;I147T;K399T;A588T;E158G;S678N;L13P;N105S;D175N;K198R;K356R 97;108;119;130;141;152;158;164;175;191;186;202;213;219;232 102;113;124;135;146;157;163;169;180;196;190;207;218;224;237 PA;PA;PB1;PB1;PB1;PB1;PB2;PB2;PB2;PB2;PB2;PB2;PB2 32;229;24;182;198;209;19;93;104;115;126;148;171 34;231;27;185;201;212;22;96;107;118;129;151;174 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. The best known human adaptation polymerase mutation is the PB2-E627K substitution, which has been identified in several human H5N1 and H7N9 isolates and in one human H7N7 isolate. 2018 Scientific reports Introduction IV E627K 63 68 PB2 59 62 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. The PB2-E627K mutation is correlated with increased H5N1 replication and virulence in mammals and also allows the virus to replicate efficiently in the human upper respiratory tract, where the temperature is slightly lower than in the lower respiratory tract. 2018 Scientific reports Introduction IV E627K 8 13 PB2 4 7 30186261 Acquisition of Innate Inhibitor Resistance and Mammalian Pathogenicity During Egg Adaptation by the H9N2 Avian Influenza Virus. According to the mutation profiles, 01310-CE20 might have evolved a more effective balance of HA-NA activities through the generation of a new N-glycosite (T133N) in HA and a shortened stalk length in NA. 2018 Frontiers in microbiology Introduction IV T133N 156 161 HA;HA;NA;NA 94;166;97;201 96;168;99;203 30186261 Acquisition of Innate Inhibitor Resistance and Mammalian Pathogenicity During Egg Adaptation by the H9N2 Avian Influenza Virus. In addition, 01310-CE20 has been shown to acquire multiple mutations in coding genes, specifically three in HA (T133N, V216G, and E439D, H3 numbering) and two in NA (18 amino acid deletion (55-72) and E54D). 2018 Frontiers in microbiology Introduction IV T133N;V216G;E439D;E54D 112;119;130;201 117;124;135;205 HA;NA 108;162 110;164 30201817 Characterization of Influenza B Virus Variants with Reduced Neuraminidase Inhibitor Susceptibility. Interestingly, 22 out of the 27 viruses with the D197N substitution reported in the literature were from the B/Yamagata lineage. 2018 Antimicrobial agents and chemotherapy Introduction IV D197N 49 54 30201817 Characterization of Influenza B Virus Variants with Reduced Neuraminidase Inhibitor Susceptibility. Our aim was to characterize two "naturally" occurring influenza B variant viruses containing either the H273Y or D197N NA substitution which had been detected during routine surveillance in patients not being treated with NAIs, compared to closely matched wild-type viruses by assessing their enzyme function, in vitro replication, and in vivo replication and transmission. 2018 Antimicrobial agents and chemotherapy Introduction IV H273Y;D197N 104;113 109;118 NA;NAI 119;222 121;226 30201817 Characterization of Influenza B Virus Variants with Reduced Neuraminidase Inhibitor Susceptibility. The effect of H273Y NA substitutions in influenza B viruses has been previously studied using reverse genetics (rg) in the B/Yamanashi/166/98 virus background. 2018 Antimicrobial agents and chemotherapy Introduction IV H273Y 14 19 20 22 30201817 Characterization of Influenza B Virus Variants with Reduced Neuraminidase Inhibitor Susceptibility. The fitness of influenza B viruses with either the H273Y or D197N NA substitution is of particular interest, as a number of viruses with either substitution have been recently found in patients in community settings who, unlike hospitalized or immunocompromised patients, do not typically receive NAI treatment. 2018 Antimicrobial agents and chemotherapy Introduction IV H273Y;D197N 51;60 56;65 NA;NAI 66;297 68;300 30201817 Characterization of Influenza B Virus Variants with Reduced Neuraminidase Inhibitor Susceptibility. The H273Y NA substitution in influenza B viruses occurs at the equivalent residue to that of the H275Y NA substitution in influenza A(H1N1) viruses, which was present in the oseltamivir-resistant influenza A(H1N1) viruses that spread globally in 2008/2009. 2018 Antimicrobial agents and chemotherapy Introduction IV H273Y;H275Y 4;97 9;102 NA;NA 10;103 12;105 30201817 Characterization of Influenza B Virus Variants with Reduced Neuraminidase Inhibitor Susceptibility. There have also been examples of suspected transmission of influenza B viruses with the H273Y NA substitution. 2018 Antimicrobial agents and chemotherapy Introduction IV H273Y 88 93 94 96 30201817 Characterization of Influenza B Virus Variants with Reduced Neuraminidase Inhibitor Susceptibility. To date, few studies have reported the effect of the H273Y or the D197N NA substitution on contemporary viruses, which is important because it has been shown that the fitness consequences of resistance-conferring mutations can vary due to the genetic background of the NA. 2018 Antimicrobial agents and chemotherapy Introduction IV H273Y;D197N 53;66 58;71 NA;NA 72;269 74;271 30201817 Characterization of Influenza B Virus Variants with Reduced Neuraminidase Inhibitor Susceptibility. Two reports have identified household transmission of influenza B viruses with the D197N NA substitution, and more recently, a global surveillance report identified a cluster of six influenza B viruses with the D197N NA substitution in Japan in early 2014, further suggesting potential community transmission of the variant virus. 2018 Antimicrobial agents and chemotherapy Introduction IV D197N;D197N 83;211 88;216 NA;NA 89;217 91;219 30227889 Effects of mutations in the effector domain of influenza A virus NS1 protein. Accordingly, we examined cellular interaction partners of WT NS1 and the mutants, including a complete deletion of the effector domain (NS1-N81), an RNA-binding domain mutant (R38A/K41A) and a gain-of-function mutant that restores CPSF30-binding activity (F103S/M106I), of which only the latter supported mRNA nuclear export (Table 1). 2018 BMC research notes Introduction IV R38A;K41A;F103S;M106I 176;181;256;262 180;185;261;267 NS1;NS1 61;136 64;139 30227889 Effects of mutations in the effector domain of influenza A virus NS1 protein. All viruses generally gave cytoplasmic NS1 signal above the uninfected cell background, although staining of cells infected with NS1-Y89 and NS1-E96A/E97A mutants was noticeably fainter than the WT and W187R viruses. 2018 BMC research notes Introduction IV E96A;E97A;W187R 145;150;202 149;154;207 NS1;NS1;NS1 39;129;141 42;132;144 30227889 Effects of mutations in the effector domain of influenza A virus NS1 protein. Blotting for NS1 confirmed successful infection, although the NS1-E96A/E97A polypeptide again accumulated to lower levels than the other NS1s. 2018 BMC research notes Introduction IV E96A;E97A 66;71 70;75 NS1;NS1;NS1 13;62;137 16;65;141 30227889 Effects of mutations in the effector domain of influenza A virus NS1 protein. Here, we tested whether mutations identified as affecting NS1 interactions with the p85ss subunit of PI3K (Y89A and Y89F), Trim25 (E96A/E97A) and NS1 effector domain-mediated oligomerisation (W187R) also affected NS1's ability to promote nuclear export of segment 7 viral mRNAs. 2018 BMC research notes Introduction IV Y89A;Y89F;E96A;E97A;W187R 107;116;131;136;192 111;120;135;140;197 NS1;NS1;NS1 58;146;213 61;149;216 30227889 Effects of mutations in the effector domain of influenza A virus NS1 protein. However, addition of NS1-E96A/E97A, NS1-Y89A or NS1-Y89F did not produce this shift, with a clear majority of cells displaying nuclear segment 7 mRNA, similarly to samples with no NS1-GFP. 2018 BMC research notes Introduction IV E96A;E97A;Y89A;Y89F 25;30;40;52 29;34;44;56 NS1;NS1;NS1;NS1 21;36;48;180 24;39;51;183 30227889 Effects of mutations in the effector domain of influenza A virus NS1 protein. However, in the bound fraction, hsp70 was detected only in the NS1-E96A/E97A sample (lane 17), confirming the specific interaction with hsp70 for NS1 E96A/E97A. 2018 BMC research notes Introduction IV E96A;E97A;E96A;E97A 67;72;150;155 71;76;154;159 NS1;NS1 63;146 66;149 30227889 Effects of mutations in the effector domain of influenza A virus NS1 protein. However, in the presence of PI3K-binding mutants NS1-Y89A and NS1-Y89F or the Trim25-binding mutant NS1-E96A/E97A, segment 7 mRNA was clearly still retained in the nucleus. 2018 BMC research notes Introduction IV Y89A;Y89F;E96A;E97A 53;66;104;109 57;70;108;113 NS1;NS1;NS1 49;62;100 52;65;103 30227889 Effects of mutations in the effector domain of influenza A virus NS1 protein. However, one clear difference was observed; a distinct novel polypeptide in the E96A/E97A preparation (lane 8) that was absent from other samples. 2018 BMC research notes Introduction IV E96A;E97A 80;85 84;89 30227889 Effects of mutations in the effector domain of influenza A virus NS1 protein. In cells infected with NS1-Y89A, NS1-Y89F and NS1-E96A/E97A, segment 7 mRNA was predominantly nuclear. 2018 BMC research notes Introduction IV Y89F;Y89A;E96A;E97A 37;27;50;55 41;31;54;59 NS1;NS1;NS1 23;33;46 26;36;49 30227889 Effects of mutations in the effector domain of influenza A virus NS1 protein. In contrast, the dimerization mutant NS1-W187R caused segment 7 mRNA to localise to the cytoplasm. 2018 BMC research notes Introduction IV W187R 41 46 NS1 37 40 30227889 Effects of mutations in the effector domain of influenza A virus NS1 protein. In contrast, viral mRNAs were not detected in GFP-NXF1 pulldowns from cells infected with either NS1-Y89A or NS1-Y89F viruses (lanes 11 and 12). 2018 BMC research notes Introduction IV Y89A;Y89F 101;113 105;117 NS1;NS1 97;109 100;112 30227889 Effects of mutations in the effector domain of influenza A virus NS1 protein. No viral mRNA signal was detected in the mock sample while segment 7 mRNA was cytoplasmic in WT and W187R virus-infected cells. 2018 BMC research notes Introduction IV W187R 100 105 30227889 Effects of mutations in the effector domain of influenza A virus NS1 protein. NS1 expression was confirmed by detection of GFP signal as well as by western blot, although the E96A/E97A mutant accumulated to lower levels than the other NS1s. 2018 BMC research notes Introduction IV E96A;E97A 97;102 101;106 NS1;NS1 0;157 3;161 30227889 Effects of mutations in the effector domain of influenza A virus NS1 protein. Since the E96A/E97A mutation blocked successful nuclear export of segment 7 mRNA, this finding indicated that, like the interaction between NS1 and NXF1, the interaction between NXF1 and segment 7 is necessary, but not sufficient for the successful nuclear export of segment 7 mRNA. 2018 BMC research notes Introduction IV E96A;E97A 10;15 14;19 NS1 140 143 30227889 Effects of mutations in the effector domain of influenza A virus NS1 protein. The behaviour of the NS1 E96A/E97A mutant:unable to mediate nuclear export of segment 7 mRNA despite binding to NXF1 and promoting its interaction with the mRNA:suggested the involvement of another essential factor in the hypothesised ternary export complex. 2018 BMC research notes Introduction IV E96A;E97A 25;30 29;34 NS1 21 24 30227889 Effects of mutations in the effector domain of influenza A virus NS1 protein. The NS1-W187R and -E96A/E97A mutants also supported NXF1 interactions with the viral mRNAs (lane 13, 14). 2018 BMC research notes Introduction IV W187R;E96A;E97A 8;19;24 13;23;28 NS1 4 7 30227889 Effects of mutations in the effector domain of influenza A virus NS1 protein. Thus, in both minireplicon and viral settings, the NS1 dimerization mutant W187R supported normal segment 7 mRNA nuclear export, but the PI3K-binding and Trim25-binding mutants showed loss-of-function. 2018 BMC research notes Introduction IV W187R 75 80 NS1 51 54 30227889 Effects of mutations in the effector domain of influenza A virus NS1 protein. To confirm the interaction between NS1-E96A/E97A and hsp70, repeat GFP-trap pulldowns were analysed by western blotting for hsp70 as well as for the GFP-tagged "bait" proteins. 2018 BMC research notes Introduction IV E96A;E97A 39;44 43;48 NS1 35 38 30227889 Effects of mutations in the effector domain of influenza A virus NS1 protein. When WT NS1 or NS1-W187R were added, a statistically significant shift of segment 7 mRNA localisation was confirmed, with ~ 75% of cells showing mRNA in the cytoplasm. 2018 BMC research notes Introduction IV W187R 19 24 NS1;NS1 8;15 11;18 30227889 Effects of mutations in the effector domain of influenza A virus NS1 protein. WT NS1-GFP and most mutant proteins localised largely to the cytoplasm, but the W187R mutant was found both in nucleus and cytoplasm. 2018 BMC research notes Introduction IV W187R 80 85 NS1 3 6 30245911 The 2015 Outbreak of Severe Influenza in Kashmir, North India: Emergence of a New Clade of A/H1n1 Influenza Virus. Two scientists from the Massachusetts Institute of Technology, USA in an in silico analysis of retrieved sequences of 2014 from Genbank reported that the higher virulence of the A/H1N1pdm09 in 2015 was attributable to K166Q, D225N and T200A mutations in the HA region of the amino acid sequences in the receptor binding site of A/H1N1pdm09. 2018 PLoS currents Introduction IV K166Q;D225N;T200A 218;225;235 223;230;240 HA 258 260 30282714 Amino Acid Residue 217 in the Hemagglutinin Glycoprotein Is a Key Mediator of Avian Influenza H7N9 Virus Antigenicity. In addition to human receptor binding characteristics, human H7N9 isolates often possess several other markers of mammalian adaptation, such as E627K and D701N in the PB2 protein. 2019 Journal of virology Introduction IV E627K;D701N 144;154 149;159 PB2 167 170 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. For example, amino acid substitution G45R on the NS1 protein of A/Puerto Rico/8/1934 (H1N1) enhanced viral replication and increased virulence by inducing an earlier and robust proinflammatory cytokine response, while T49E mutation impairs its binding to TRIM25 and complex formation with RIG-I, thereby switching off its interferon antagonistic activity. 2018 Veterinary research Introduction IV G45R;T49E 37;218 41;222 NS1 49 52 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. I64T, D189N and V194I mutations in NS1 protein of circulating H3N2 human influenza virus weakened NS1-mediated general inhibition of host protein synthesis by decreasing its interaction with cleavage and polyadenylation specificity factor 30 (CPSF30), leading to attenuated virulence and increased innate immune responses after the viral infection. 2018 Veterinary research Introduction IV I64T;D189N;V194I 0;6;16 4;11;21 NS1;NS1 35;98 38;101 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. In addition, the amino acid S42 of H5N1 influenza virus NS1 protein has an effect on resisting the host cell antiviral immune response via preventing the activation of the NF-kappaB and the IRF-3 pathways both mediated by the double-stranded RNA, and a single S42P mutation in NS1 protein could completely attenuate the virulence of A/Duck/Guangxi/27/03 (H5N1) virus in mice. 2018 Veterinary research Introduction IV S42P 260 264 NS1;NS1 56;277 59;280 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. It has also been found that the human A/Hong Kong/156/1997 (H5N1) influenza virus NS1 F103L and M106I mutations could both increase IFN antagonism and virulence via increasing cytoplasmic NS1 expression as well as increased binding with host factors such as RIG-I. 2018 Veterinary research Introduction IV F103L;M106I 86;96 91;101 NS1;NS1 82;188 85;191 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. Moreover, a distinct E172K substitution in the H7N9 NS1 protein could enhance virus replication in mammalian cells and mice through affecting SF2-ESE interaction that regulates splicing of NEP/NS1 mRNA. 2018 Veterinary research Introduction IV E172K 21 26 NEP;NS1;NS1 189;52;193 192;55;196 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. S212P mutation significantly impaired the antagonistic action of NS1 toward host innate immune response, and I178V mutation greatly decreased the stability of NS1 protein, resulting in NS1 degradation through proteasome pathway. 2018 Veterinary research Introduction IV S212P;I178V 0;109 5;114 NS1;NS1;NS1 65;159;185 68;162;188 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. Moreover, a common natural variant of HsIFNlambda4 (P70S), which has reduced signalling capacity, is also linked with improved HCV clearance. 2018 PLoS pathogens Introduction IV P70S 52 56 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. Whether other human IFNlambda4 variants exist in addition to P70S, which affect antiviral activity, has not been explored fully. 2018 PLoS pathogens Introduction IV P70S 61 65 30353004 Genome-wide characterization of the seasonal H3N2 virus in Shanghai reveals natural temperature-sensitive strains conferred by the I668V mutation in the PA subunit. The results presented here suggest that the mutation in PA I668V may confer temperature sensitivity and attenuate the polymerase activity of the influenza virus, changing the seasonality and adaptation of the virus. 2018 Emerging microbes & infections Introduction IV I668V 59 64 PA 56 58 30400276 Combination Therapy with Oseltamivir and Favipiravir Delays Mortality but Does Not Prevent Oseltamivir Resistance in Immunodeficient Mice Infected with Pandemic A(H1N1) Influenza Virus. Oseltamivir-resistant viruses of the H1N1 subtype carry most commonly a histidine-to-tyrosine substitution at residue 275 (H275Y) (N1 numbering) in the neuraminidase (NA) protein and this substitution confers cross-resistance to peramivir but not to zanamivir. 2018 Viruses Introduction IV H275Y;H275Y 123;72 128;121 NA;NA 167;152 169;165 30439983 Influenza B viruses circulated during last 5 years in Mongolia. As a consequence of the monitoring system, one case with H273Y (resistant to oseltamivir and peramivir) mutation in neuraminidase of the influenza B virus was detected, which occurred naturally. 2018 PloS one Introduction IV H273Y 57 62 116 129 30466301 Activity of enisamium, an isonicotinic acid derivative, against influenza viruses in differentiated normal human bronchial epithelial cells. Although the detection rate of NA inhibitor resistance was initially low (~1% of A(H1N1)pdm09 viruses are resistant to oseltamivir), reports of increases in the prevalence of A(H1N1)pdm09 influenza viruses with the H275Y NA substitution (from >1.0 to 2.5%) in Japan in 20135, and isolation of community-transmitted, oseltamivir-resistant viruses suggest that this substitution is not deleterious to the fitness of the virus. 2018 Antiviral chemistry & chemotherapy Introduction IV H275Y 215 220 NA;NA 31;221 33;223 30466301 Activity of enisamium, an isonicotinic acid derivative, against influenza viruses in differentiated normal human bronchial epithelial cells. Between 2007 and 2009, the high prevalence (~97%) of oseltamivir-resistant seasonal influenza A(H1N1) viruses carrying the H275Y NA substitution (N1 numbering) was reported globally. 2018 Antiviral chemistry & chemotherapy Introduction IV H275Y 123 128 129 131 30509291 Conserved methionine 165 of matrix protein contributes to the nuclear import and is essential for influenza A virus replication. Crucially, we showed that alanine substitution of methionine 165 was lethal for virus replication and affected the distribution of viral and cellular proteins. 2018 Virology journal Introduction IV M165A 26 64 30548432 Consecutive influenza surveillance of neuraminidase mutations and neuraminidase inhibitor resistance in Japan. These NAIs exert their antiviral function by binding to the enzymatic catalytic sites of influenza surface protein NA.1 In the 2007-2008, oseltamivir-resistant seasonal A/H1N1 viruses carrying NA amino acid (AA) mutation H275Y rapidly spread throughout the world.2 We reported a prolonged duration of fever after administrating oseltamivir in patients infected with oseltamivir-resistant A/H1N1 viruses during the 2008-2009 season in Japan, which demonstrated the association between clinical effectiveness and the acquisition of resistance to anti-influenza drugs.3, 4 In the subsequent seasons, oseltamivir-resistant A/H1N1pdm09 viruses carrying H275Y were reported,5 causing a concern for worldwide spread. 2019 Influenza and other respiratory viruses Introduction IV H275Y;H275Y 221;648 226;653 NA;NA;NAI 115;193;6 117;195;10 30574137 Susceptibility of Influenza Viruses to the Novel Cap-Dependent Endonuclease Inhibitor Baloxavir Marboxil. Furthermore, PA I38T and I38F substitutions emerged as a result of exposure to baloxavir marboxil in four (3.6%) of 112 A(H1N1)pdm09 viruses for which PA sequences were available in a Phase II clinical trial. 2018 Frontiers in microbiology Introduction IV I38T;I38F 16;25 20;29 PA;PA 13;151 15;153 30574137 Susceptibility of Influenza Viruses to the Novel Cap-Dependent Endonuclease Inhibitor Baloxavir Marboxil. In a pediatric study, PA I38T and I38M substitutions emerged in 18(23.4%) of 77 A(H3N2) viruses. 2018 Frontiers in microbiology Introduction IV I38T;I38M 25;34 29;38 PA 22 24 30574137 Susceptibility of Influenza Viruses to the Novel Cap-Dependent Endonuclease Inhibitor Baloxavir Marboxil. In a Phase III clinical trial, PA I38T and I38M substitutions were detected after exposure to this drug in 9.7% of 370 A(H3N2) viruses. 2018 Frontiers in microbiology Introduction IV I38T;I38M 34;43 38;47 PA 31 33 30574137 Susceptibility of Influenza Viruses to the Novel Cap-Dependent Endonuclease Inhibitor Baloxavir Marboxil. In vitro studies have revealed that an I38T substitution in the polymerase acidic subunit (PA) is associated with reduced susceptibility of influenza A(H1N1), A(H3N2), and B viruses to baloxavir. 2018 Frontiers in microbiology Introduction IV I38T 39 43 PA;PA 91;64 93;89 30574137 Susceptibility of Influenza Viruses to the Novel Cap-Dependent Endonuclease Inhibitor Baloxavir Marboxil. Patients infected with the PA I38T or I38F mutant viruses exhibited prolonged virus shedding and the median time to alleviation of symptoms was longer in baloxavir recipients with I38T or I38M substitutions than in those without substitutions. 2018 Frontiers in microbiology Introduction IV I38T;I38F;I38T;I38M 30;38;180;188 34;42;184;192 PA 27 29 30574137 Susceptibility of Influenza Viruses to the Novel Cap-Dependent Endonuclease Inhibitor Baloxavir Marboxil. We validated our systems by generating a reference influenza A virus possessing the PA I38T substitution. 2018 Frontiers in microbiology Introduction IV I38T 87 91 PA 84 86 30670142 Detection of influenza A(H3N2) viruses exhibiting reduced susceptibility to the novel cap-dependent endonuclease inhibitor baloxavir in Japan, December 2018. Antiviral susceptibilities of the PA I38T mutant viruses. 2019 Euro surveillance Introduction IV I38T 37 41 PA 34 36 30670142 Detection of influenza A(H3N2) viruses exhibiting reduced susceptibility to the novel cap-dependent endonuclease inhibitor baloxavir in Japan, December 2018. Both the PA I38T mutant viruses and the wild-type viruses showed normal inhibition with all four NA inhibitors, whereas the PA I38T mutant viruses exhibited 76- and 120-fold higher IC50 values to baloxavir compared with the mean value of wild-type viruses. 2019 Euro surveillance Introduction IV I38T;I38T 12;127 16;131 NA;PA;PA 97;9;124 99;11;126 30670142 Detection of influenza A(H3N2) viruses exhibiting reduced susceptibility to the novel cap-dependent endonuclease inhibitor baloxavir in Japan, December 2018. Detection of PA I38T mutant influenza A(H3N2) viruses. 2019 Euro surveillance Introduction IV I38T 16 20 PA 13 15 30670142 Detection of influenza A(H3N2) viruses exhibiting reduced susceptibility to the novel cap-dependent endonuclease inhibitor baloxavir in Japan, December 2018. In Phase II and III clinical trials, I38T, I38F and I38M substitutions in the polymerase acidic subunit (PA) were detected in A(H1N1)pdm09 and A(H3N2) influenza viruses. 2019 Euro surveillance Introduction IV I38T;I38F;I38M 37;43;52 41;47;56 PA;PA 105;78 107;103 30670142 Detection of influenza A(H3N2) viruses exhibiting reduced susceptibility to the novel cap-dependent endonuclease inhibitor baloxavir in Japan, December 2018. Sequencing analysis detected the PA I38T substitution in A/YOKOHAMA/133/2018 and A/YOKOHAMA/135/2018, but not in A/YOKOHAMA/134/2018 or A/YOKOHAMA/136/2018. 2019 Euro surveillance Introduction IV I38T 36 40 PA 33 35 30670142 Detection of influenza A(H3N2) viruses exhibiting reduced susceptibility to the novel cap-dependent endonuclease inhibitor baloxavir in Japan, December 2018. These results demonstrate that PA I38T mutant viruses were isolated from children 3 days after baloxavir administration. 2019 Euro surveillance Introduction IV I38T 34 38 PA 31 33 30670142 Detection of influenza A(H3N2) viruses exhibiting reduced susceptibility to the novel cap-dependent endonuclease inhibitor baloxavir in Japan, December 2018. These results indicate that the PA I38T mutant viruses had reduced susceptibility to baloxavir, but remained susceptible to NA inhibitors. 2019 Euro surveillance Introduction IV I38T 35 39 NA;PA 124;32 126;34 30670142 Detection of influenza A(H3N2) viruses exhibiting reduced susceptibility to the novel cap-dependent endonuclease inhibitor baloxavir in Japan, December 2018. We compared the susceptibilities of the PA I38T mutant viruses and the wild-type virus to baloxavir and four NA inhibitors approved in Japan: oseltamivir, peramivir, zanamivir and laninamivir (Table 2). 2019 Euro surveillance Introduction IV I38T 43 47 NA;PA 109;40 111;42 30733797 In silico thermodynamic stability of mammalian adaptation and virulence determinants in polymerase complex proteins of H9N2 virus. It was reported that PA mutations in the Amino acids T157A and T162A weaken the proteolysis Function of PA but some PA mutation enhances the polymerase replication activity at higher temperatures to that influence the virus adaptations. 2018 Journal, genetic engineering & biotechnology Introduction IV T157A;T162A 53;63 58;68 PA;PA;PA 21;104;116 23;106;118 30733797 In silico thermodynamic stability of mammalian adaptation and virulence determinants in polymerase complex proteins of H9N2 virus. The N66S and L82S mutations in the PB1-F2 protein are important for increasing viral pathogenicity and mammalian adaptation respectively. 2018 Journal, genetic engineering & biotechnology Introduction IV N66S;L82S 4;13 8;17 PB1F2 35 41 30909490 The PB2 Polymerase Host Adaptation Substitutions Prime Avian Indonesia Sub Clade 2.1 H5N1 Viruses for Infecting Humans. Among the known PB2 adaptive substitutions, E627K, and to a lesser extent D701N, are the most common and well characterized in H5N1 human isolates. 2019 Viruses Introduction IV E627K;D701N 44;74 49;79 PB2 16 19 30909490 The PB2 Polymerase Host Adaptation Substitutions Prime Avian Indonesia Sub Clade 2.1 H5N1 Viruses for Infecting Humans. Analysis of sequences revealed that H5N1 virus containing K526R PB2 emerged 2-3 years after the introduction of H5N1 virus into Indonesia, coincident with the emergence of human infections. 2019 Viruses Introduction IV K526R 58 63 PB2 64 67 30909490 The PB2 Polymerase Host Adaptation Substitutions Prime Avian Indonesia Sub Clade 2.1 H5N1 Viruses for Infecting Humans. Because K526R PB2, but not E627K, is predominantly found in H5N1 human isolates from Indonesia, this study examined if K526R PB2 is a predisposing factor for virus infection of humans. 2019 Viruses Introduction IV K526R;E627K;K526R 8;27;119 13;32;124 PB2;PB2 14;125 17;128 30909490 The PB2 Polymerase Host Adaptation Substitutions Prime Avian Indonesia Sub Clade 2.1 H5N1 Viruses for Infecting Humans. It has been suggested that the E627K substitution allows virus to evade host restriction of replicative activity of avian PB2 polymerases, but a detailed mechanism remains unclear. 2019 Viruses Introduction IV E627K 31 36 PB2 122 125 30909490 The PB2 Polymerase Host Adaptation Substitutions Prime Avian Indonesia Sub Clade 2.1 H5N1 Viruses for Infecting Humans. K526R is a recently identified adaptation marker that supports influenza virus replication in mammalian hosts; first observed in seasonal H3N2 viruses in the early 1970s, it is now present in all currently circulating H3N2 viruses. 2019 Viruses Introduction IV K526R 0 5 30909490 The PB2 Polymerase Host Adaptation Substitutions Prime Avian Indonesia Sub Clade 2.1 H5N1 Viruses for Infecting Humans. K526R substitution in PB2 appears to serve as a pre-existing adaptation in avian H5N1 virus from Indonesia and likely plays a role in enabling this variant to cross the species barrier and infect humans. 2019 Viruses Introduction IV K526R 0 5 PB2 22 25 30909490 The PB2 Polymerase Host Adaptation Substitutions Prime Avian Indonesia Sub Clade 2.1 H5N1 Viruses for Infecting Humans. Notably, E627K is rarely found in human H5N1 cases from Indonesia, where a K526R substitution is observed in 80% of human isolates. 2019 Viruses Introduction IV E627K;K526R 9;75 14;80 30909490 The PB2 Polymerase Host Adaptation Substitutions Prime Avian Indonesia Sub Clade 2.1 H5N1 Viruses for Infecting Humans. Recent studies also suggest that PB2 E627K and K526R substitutions may be involved in regulation of virus replication through interaction with viral NEP during virus infection of cells. 2019 Viruses Introduction IV E627K;K526R 37;47 42;52 NEP;PB2 149;33 152;36 30909490 The PB2 Polymerase Host Adaptation Substitutions Prime Avian Indonesia Sub Clade 2.1 H5N1 Viruses for Infecting Humans. Since PB2-E627K is rarely found among H5N1 human isolates from Indonesia, it seems possible that, for the genetic constellation of Indonesian H5N1 viruses, optimal function of the polymerase complex for virus replication is independent of E627K, and instead requires K526R adaptive substitution. 2019 Viruses Introduction IV E627K;E627K;K526R 10;239;267 15;244;272 PB2 6 9 30909490 The PB2 Polymerase Host Adaptation Substitutions Prime Avian Indonesia Sub Clade 2.1 H5N1 Viruses for Infecting Humans. We found that virus carrying K526R PB2 replicates better than virus without this substitution in mammalian cells and mice, but showed no apparent deficit in growth in avian cells. 2019 Viruses Introduction IV K526R 29 34 PB2 35 38 30914078 Influenza A(H3N2) virus exhibiting reduced susceptibility to baloxavir due to a polymerase acidic subunit I38T substitution detected from a hospitalised child without prior baloxavir treatment, Japan, January 2019. Antiviral susceptibilities of the polymerase acidic subunit protein I38T mutant viruses. 2019 Euro surveillance Introduction IV I38T 68 72 PA 34 59 30914078 Influenza A(H3N2) virus exhibiting reduced susceptibility to baloxavir due to a polymerase acidic subunit I38T substitution detected from a hospitalised child without prior baloxavir treatment, Japan, January 2019. Both PA I38T mutant viruses showed normal inhibition with all four NA inhibitors, but exhibited 49- and 68-fold higher IC50 values to baloxavir compared with the median IC50 value of A(H3N2) viruses isolated in the 2018/19 influenza season in Japan. 2019 Euro surveillance Introduction IV I38T 8 12 NA;PA 67;5 69;7 30914078 Influenza A(H3N2) virus exhibiting reduced susceptibility to baloxavir due to a polymerase acidic subunit I38T substitution detected from a hospitalised child without prior baloxavir treatment, Japan, January 2019. Deep sequencing analysis of the isolates using MiSeq (Illumina, San Diego, California, United States) revealed that A/YOKOHAMA/87/2019 and A/YOKOHAMA/88/2019 possessed the PA I38T substitution. 2019 Euro surveillance Introduction IV I38T 175 179 PA 172 174 30914078 Influenza A(H3N2) virus exhibiting reduced susceptibility to baloxavir due to a polymerase acidic subunit I38T substitution detected from a hospitalised child without prior baloxavir treatment, Japan, January 2019. Detection of polymerase acidic subunit I38T mutant influenza A(H3N2) viruses from hospitalised children. 2019 Euro surveillance Introduction IV I38T 39 43 PA 13 38 30914078 Influenza A(H3N2) virus exhibiting reduced susceptibility to baloxavir due to a polymerase acidic subunit I38T substitution detected from a hospitalised child without prior baloxavir treatment, Japan, January 2019. The I38T substitution was not detected in the Influenza Research Database (www.fludb.org) including 17,227 PA sequences from A(H3N2) viruses until December 2018 or during surveillance studies of baloxavir susceptibility of influenza viruses in Japan (2017/18 influenza season) and the United States prior to the introduction of baloxavir (2016/17 and 2017/18 seasons). 2019 Euro surveillance Introduction IV I38T 4 8 PA 107 109 30914078 Influenza A(H3N2) virus exhibiting reduced susceptibility to baloxavir due to a polymerase acidic subunit I38T substitution detected from a hospitalised child without prior baloxavir treatment, Japan, January 2019. The patient infected with A/YOKOHAMA/87/2019 had been treated with baloxavir, indicating the possible emergence of the PA I38T mutant virus under the selective pressure of this drug. 2019 Euro surveillance Introduction IV I38T 122 126 PA 119 121 30914078 Influenza A(H3N2) virus exhibiting reduced susceptibility to baloxavir due to a polymerase acidic subunit I38T substitution detected from a hospitalised child without prior baloxavir treatment, Japan, January 2019. Therefore, previous studies concluded that the PA I38T substitution was a baloxavir treatment-emergent substitution. 2019 Euro surveillance Introduction IV I38T 50 54 PA 47 49 30914078 Influenza A(H3N2) virus exhibiting reduced susceptibility to baloxavir due to a polymerase acidic subunit I38T substitution detected from a hospitalised child without prior baloxavir treatment, Japan, January 2019. These PA I38T mutant viruses possessed different PA sequences and therefore originated from different sources of infection. 2019 Euro surveillance Introduction IV I38T 9 13 PA;PA 6;49 8;51 30914078 Influenza A(H3N2) virus exhibiting reduced susceptibility to baloxavir due to a polymerase acidic subunit I38T substitution detected from a hospitalised child without prior baloxavir treatment, Japan, January 2019. These results indicate that the PA I38T mutant viruses had reduced susceptibility to baloxavir, but remained susceptible to NA inhibitors. 2019 Euro surveillance Introduction IV I38T 35 39 NA;PA 124;32 126;34 30914078 Influenza A(H3N2) virus exhibiting reduced susceptibility to baloxavir due to a polymerase acidic subunit I38T substitution detected from a hospitalised child without prior baloxavir treatment, Japan, January 2019. These viruses possessed an I38T substitution in the polymerase acidic subunit (PA), which confers reduced susceptibility to baloxavir. 2019 Euro surveillance Introduction IV I38T 27 31 PA;PA 79;52 81;77 30914078 Influenza A(H3N2) virus exhibiting reduced susceptibility to baloxavir due to a polymerase acidic subunit I38T substitution detected from a hospitalised child without prior baloxavir treatment, Japan, January 2019. Usage of baloxavir increased in this influenza season in Japan and an influenza outbreak occurred in the preschool attended by the 5 year-old before this patient's symptom onset, suggesting a possible acquisition of the PA I38T mutant virus by human-to-human transmission. 2019 Euro surveillance Introduction IV I38T 223 227 PA 220 222 30914078 Influenza A(H3N2) virus exhibiting reduced susceptibility to baloxavir due to a polymerase acidic subunit I38T substitution detected from a hospitalised child without prior baloxavir treatment, Japan, January 2019. We determined the susceptibilities of the PA I38T mutant viruses to baloxavir and four neuraminidase (NA) inhibitors approved in Japan: oseltamivir, laninamivir, peramivir and zanamivir (Table 2). 2019 Euro surveillance Introduction IV I38T 45 49 NA;NA;PA 102;87;42 104;100;44 30996301 Bacterial glycosyltransferase-mediated cell-surface chemoenzymatic glycan modification. Moreover, Pm2,3ST-M144D and Pd2,6ST are tolerant to large substituents introduced to the C-5 position of the cytidine-5'-monophosphate-N-acetylneuraminic acid (CMP-NeuAc) donor. 2019 Nature communications Introduction IV M144D 18 23 30996301 Bacterial glycosyltransferase-mediated cell-surface chemoenzymatic glycan modification. We report that Pasteurella multocida alpha2-3-ST M144D mutant (Pm2,3ST-M144D), Photobacterium damsela alpha2-6-ST (Pd2,6ST), and H. 2019 Nature communications Introduction IV M144D;M144D 49;71 54;76 31008587 Hydrogen-Deuterium Exchange Supports Independent Membrane-Interfacial Fusion Peptide and Transmembrane Domains in Subunit 2 of Influenza Virus Hemagglutinin Protein, a Structured and Aqueous-Protected Connection between the Fusion Peptide and Soluble Ectodomain, and the Importance of Membrane Apposition by the Trimer-of-Hairpins Structure. HA-cell/RBC fusion is also eliminated by the G1E mutation at the N-terminus of the FP. 2019 Biochemistry Introduction IV G1E 45 48 HA 0 2 31008587 Hydrogen-Deuterium Exchange Supports Independent Membrane-Interfacial Fusion Peptide and Transmembrane Domains in Subunit 2 of Influenza Virus Hemagglutinin Protein, a Structured and Aqueous-Protected Connection between the Fusion Peptide and Soluble Ectodomain, and the Importance of Membrane Apposition by the Trimer-of-Hairpins Structure. Other new features of the present study are inclusion of TM and endodomain, analysis of FP peptides, and comparison between functional WT and fusion-impaired G1E and I173E mutants. 2019 Biochemistry Introduction IV G1E;I173E 158;166 161;171 31008587 Hydrogen-Deuterium Exchange Supports Independent Membrane-Interfacial Fusion Peptide and Transmembrane Domains in Subunit 2 of Influenza Virus Hemagglutinin Protein, a Structured and Aqueous-Protected Connection between the Fusion Peptide and Soluble Ectodomain, and the Importance of Membrane Apposition by the Trimer-of-Hairpins Structure. Our study also examines the hypothesis that highly-impaired fusion for the I173E and G1E mutants is due to dissociation of C-terminal strands of the SE, with consequent destabilization of the N-terminal bundle of the SE. 2019 Biochemistry Introduction IV G1E;I173E 85;75 88;80 31008587 Hydrogen-Deuterium Exchange Supports Independent Membrane-Interfacial Fusion Peptide and Transmembrane Domains in Subunit 2 of Influenza Virus Hemagglutinin Protein, a Structured and Aqueous-Protected Connection between the Fusion Peptide and Soluble Ectodomain, and the Importance of Membrane Apposition by the Trimer-of-Hairpins Structure. The destabilizing effect of the I173E mutation may be related to loss of I173 sidechain contacts with the N-terminal bundle. 2019 Biochemistry Introduction IV I173E 32 37 31008587 Hydrogen-Deuterium Exchange Supports Independent Membrane-Interfacial Fusion Peptide and Transmembrane Domains in Subunit 2 of Influenza Virus Hemagglutinin Protein, a Structured and Aqueous-Protected Connection between the Fusion Peptide and Soluble Ectodomain, and the Importance of Membrane Apposition by the Trimer-of-Hairpins Structure. There are striking similarities to HA-cell/RBC fusion, including low pH requirement and greatly reduced fusion for the G1E and I173E mutants that are respectively in the HA2 FP's and SE strands. 2019 Biochemistry Introduction IV G1E;I173E 119;127 122;132 HA;HA 35;170 37;172 31008587 Hydrogen-Deuterium Exchange Supports Independent Membrane-Interfacial Fusion Peptide and Transmembrane Domains in Subunit 2 of Influenza Virus Hemagglutinin Protein, a Structured and Aqueous-Protected Connection between the Fusion Peptide and Soluble Ectodomain, and the Importance of Membrane Apposition by the Trimer-of-Hairpins Structure. This hypothesis is based on: (1) moderately reduced helicity of I173E vs. 2019 Biochemistry Introduction IV I173E 64 69 31008587 Hydrogen-Deuterium Exchange Supports Independent Membrane-Interfacial Fusion Peptide and Transmembrane Domains in Subunit 2 of Influenza Virus Hemagglutinin Protein, a Structured and Aqueous-Protected Connection between the Fusion Peptide and Soluble Ectodomain, and the Importance of Membrane Apposition by the Trimer-of-Hairpins Structure. This is just a hypothesis as there aren't yet structural data for G1E. 2019 Biochemistry Introduction IV G1E 66 69 31008587 Hydrogen-Deuterium Exchange Supports Independent Membrane-Interfacial Fusion Peptide and Transmembrane Domains in Subunit 2 of Influenza Virus Hemagglutinin Protein, a Structured and Aqueous-Protected Connection between the Fusion Peptide and Soluble Ectodomain, and the Importance of Membrane Apposition by the Trimer-of-Hairpins Structure. We hypothesize that G1E destabilizes the FP structure, and that destabilized FP's compete with the N-helix bundle of the SE for binding with the C-terminal strands. 2019 Biochemistry Introduction IV G1E 20 23 31008587 Hydrogen-Deuterium Exchange Supports Independent Membrane-Interfacial Fusion Peptide and Transmembrane Domains in Subunit 2 of Influenza Virus Hemagglutinin Protein, a Structured and Aqueous-Protected Connection between the Fusion Peptide and Soluble Ectodomain, and the Importance of Membrane Apposition by the Trimer-of-Hairpins Structure. WT or G1E; and (2) large and comparable reductions in Tm (up to 40 C) for I173E and G1E vs. 2019 Biochemistry Introduction IV G1E;G1E;I173E 6;85;75 9;88;80 31150476 Pathogenicity of the H1N1 influenza virus enhanced by functional synergy between the NPV100I and NAD248N pair. For example, the HA2 E47K substitution in hemagglutinin (HA) of the 2009 pH1N1 IAV reduces the pH threshold for membrane fusion, conferring the virus with thermal stability and infectivity, which partially explains its rapid spread and adaptation to humans. 2019 PloS one Introduction IV E47K 21 25 HA;HA;HA 17;57;42 19;59;55 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. Based on sequence database analysis and virus rescue experiments, this study revealed that the two most common egg-adaptive mutations on H3N2 HA, namely G186V and L194P, are incompatible. 2019 Cell host & microbe Introduction IV G186V;L194P 153;163 158;168 HA 142 144 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. Consistent with previous studies, we also showed that G186V has minimal antigenic effect, whereas L194P strongly impacts antigenicity. 2019 Cell host & microbe Introduction IV G186V;L194P 54;98 59;103 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. However, other egg-adaptive HA mutations on human H3N2 viruses, such as H183L, G186V, A196T, S219F, V226A, and V226I, minimally impact antigenicity. 2019 Cell host & microbe Introduction IV H183L;G186V;A196T;S219F;V226A;V226I 72;79;86;93;100;111 77;84;91;98;105;116 HA 28 30 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. In other words, the HA G186V/L194P double mutant was not viable despite each of the single mutants being viable. 2019 Cell host & microbe Introduction IV G186V;L194P 23;29 28;34 HA 20 22 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. Passaging the G186V mutant in eggs could prevent the emergence of the L194P mutation and vice versa. 2019 Cell host & microbe Introduction IV G186V;L194P 14;70 19;75 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. Several egg-adaptive mutations on the HA of human H3N2 viruses, such as H156Q, L194P, and T160K (loss of glycosylation), have been shown to affect antigenicity. 2019 Cell host & microbe Introduction IV H156Q;L194P;T160K 72;79;90 77;84;95 HA 38 40 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. Structural analysis illustrated that mutations G186V and L194P had opposing structural effects. 2019 Cell host & microbe Introduction IV G186V;L194P 47;57 52;62 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. The relative height of the HA RBS is increased by G186V but decreased by L194P. 2019 Cell host & microbe Introduction IV G186V;L194P 50;73 55;78 HA 27 29 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. This structural variation between G186V and L194P then leads to differences in the receptor-binding modes. 2019 Cell host & microbe Introduction IV G186V;L194P 34;44 39;49 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. When mutations G186V and L194P are both present, the HA RBS is disrupted, explaining the incompatibility of G186V and L194P. 2019 Cell host & microbe Introduction IV G186V;L194P;G186V;L194P 15;25;108;118 20;30;113;123 HA 53 55 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. Different mutations in PB2 have been identified to contribute to the adaptation of influenza viruses to mammalian hosts; these mutations include E627K, D701N, T271A, Q591R/K, and E158G. 2019 mBio Introduction IV E627K;D701N;T271A;Q591R;Q591K;E158G 145;152;159;166;166;179 150;157;164;173;173;184 PB2 23 26 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. However, not all AIVs acquire the PB2 E627K mutation upon infection of humans, such as many H5N1 viruses. 2019 mBio Introduction IV E627K 38 43 PB2 34 37 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. In particular, most H7N9 human isolates acquire the PB2 E627K substitution. 2019 mBio Introduction IV E627K 56 61 PB2 52 55 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. Remarkably, the PB2 of H7N9 viruses easily acquires the PB2 E627K or D701N adaptive mutation during replication in mammalian hosts. 2019 mBio Introduction IV E627K;D701N 60;69 65;74 PB2;PB2 16;56 19;59 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. The key role of the PB2 E627K substitution in the mammalian adaptation of AIVs has been well documented, having been shown to enhance polymerase activity, virus replication, pathogenicity, and transmission of AIVs in humans and other mammals. 2019 mBio Introduction IV E627K 24 29 PB2 20 23 IAV infections 209 213 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. The prominent ability of H7N9 AIVs to acquire the PB2 E627K substitution upon infection of humans provides us with an excellent opportunity to decipher the underlying mechanism by which AIVs rapidly acquire the PB2 E627K substitution during their adaptation to mammalian hosts, including humans. 2019 mBio Introduction IV E627K;E627K 54;215 59;220 PB2;PB2 50;211 53;214 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. We found that the low polymerase activity attributed to the H7N9 viral PA protein is the intrinsic force driving the emergence of the PB2 E627K mutation during the replication of H7N9 AIVs in mammals, a process that also involves interplay with host factors, such as ANP32A. 2019 mBio Introduction IV E627K 138 143 PA;PB2 71;134 73;137 31266524 Highly pathogenic avian influenza H7N9 viruses with reduced susceptibility to neuraminidase inhibitors showed comparable replication capacity to their sensitive counterparts. The research demonstrated that R292K and H274Y conferred a high increase in oseltamivir IC50, and E119D conferred the highest IC50 to zanamivir reported. 2019 Virology journal Introduction IV R292K;H274Y;E119D 31;41;98 36;46;103 31267843 Mammalian-adaptive mutation NP-Q357K in Eurasian H1N1 Swine Influenza viruses determines the virulence phenotype in mice. Of these, the E627K and/or D701N mutations in the PB2 protein are critical in the mammalian adaptation of avian influenza viruses. 2019 Emerging microbes & infections Introduction IV E627K;D701N 14;27 19;32 PB2 50 53 31267843 Mammalian-adaptive mutation NP-Q357K in Eurasian H1N1 Swine Influenza viruses determines the virulence phenotype in mice. Various mutations in the polymerase complex are also associated with increased virulence, including PB2-E158G, A271T, PB1-R198K, PB1-F2-N66S, PA-I127V, and so on. 2019 Emerging microbes & infections Introduction IV E158G;A271T;R198K;N66S;I127V 104;111;122;136;145 109;116;127;140;150 PA;PB1;PB1F2;PB2 142;118;129;100 144;121;135;103 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. Based on the genetic similarity between the HAs of the A(H7N9) and NL12, we introduced the G218E substitution into the HAs of rgSH2 and rgGD17 to promote viral growth. 2019 Journal of virology Introduction IV G218E 91 96 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. Furthermore, we compared the immunogenicity of the G218E variants with that of the wild-type (WT) counterparts and investigated the mechanisms underlying G218E-associated high growth of A(H7N9) CVV in this study. 2019 Journal of virology Introduction IV G218E;G218E 51;154 56;159 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. Indeed, G218E substitution significantly improved rgSH2 and rgGD17 replication in both eggs and mammalian cells, which is consistent with the recently reported G218E high-growth phenotype in another A(H7N9) CVV, A/Anhui/1/2013. 2019 Journal of virology Introduction IV G218E;G218E 8;160 13;165 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. To date, several groups have reported the results of selecting egg-adapted A(H7N9) CVVs by serial passage in the egg allantoic cavity and identified a few amino acid substitutions associated with egg adaptation in hemagglutinin (HA), including G218E, N158D, N132D, G198E, and G205E in H3 numbering. 2019 Journal of virology Introduction IV G218E;N158D;N132D;G198E;G205E 244;251;258;265;276 249;256;263;270;281 HA;HA 229;214 231;227 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. We had laid the ground work for generating adaptive H7 CVV by characterization of a cell-adapted strain from a H7N3 CVV, A/mallard/Netherlands/12/2000 (NL12), where we selected the cell-adaptive NL12 in Madin-Darby canine kidney (MDCK) cells and attributed the adaptive phenotype to a single amino acid substitution, G218E (H3 numbering), in HA. 2019 Journal of virology Introduction IV G218E 317 322 HA 342 344 31292247 Serial Section Array Scanning Electron Microscopy Analysis of Cells from Lung Autopsy Specimens following Fatal A/H1N1 2009 Pandemic Influenza Virus Infection. Since the first appearance of A/H1N1/pdm09, an amino acid substitution from aspartic acid to glycine at position 222 (D222G) in the HA protein has been identified sporadically. 2019 Journal of virology Introduction IV D222G;D222G 118;76 123;116 HA 132 134 31292247 Serial Section Array Scanning Electron Microscopy Analysis of Cells from Lung Autopsy Specimens following Fatal A/H1N1 2009 Pandemic Influenza Virus Infection. The D222G substitution alters the receptor-binding preference of HA so that it binds to alpha-2,3-linked sialic acids, which are expressed abundantly on human AECs; therefore, this virus has the potential to cause viral pneumonia. 2019 Journal of virology Introduction IV D222G 4 9 HA 65 67 31292247 Serial Section Array Scanning Electron Microscopy Analysis of Cells from Lung Autopsy Specimens following Fatal A/H1N1 2009 Pandemic Influenza Virus Infection. The results of next-generation sequencing revealed that a majority of the viruses detected in the lung carried the D222G substitution in HA. 2019 Journal of virology Introduction IV D222G 115 120 HA 137 139 31292247 Serial Section Array Scanning Electron Microscopy Analysis of Cells from Lung Autopsy Specimens following Fatal A/H1N1 2009 Pandemic Influenza Virus Infection. We used TEM and SEM to examine the distribution of influenza virus particles and matrix 1 (M1) protein-associated intranuclear dense tubules within these cell types in specimens of autopsied lung in which A/H1N1/pdm09 harboring the D222G substitution (A/H1N1/pdm09-D222G) had proliferated. 2019 Journal of virology Introduction IV D222G;D222G 232;265 237;270 M1;M 91;81 93;87 31305236 Prevailing I292V PB2 mutation in avian influenza H9N2 virus increases viral polymerase function and attenuates IFN-beta induction in human cells. Here, we identified I292V mutation in PB2 as a dominant genotype in avian H9N2 (since 2010), and in emergent H7N9 and H10N8 viruses; human isolates of such viruses frequently contain the I292V PB2 genotype. 2019 The Journal of general virology Introduction IV I292V;I292V 20;187 25;192 PB2;PB2 38;193 41;196 31305236 Prevailing I292V PB2 mutation in avian influenza H9N2 virus increases viral polymerase function and attenuates IFN-beta induction in human cells. The PB2-I292V in H9N2 virus confers increased replication and more severe pathogenicity to mice through enhancing viral polymerase and strong attenuation of IFN-beta induction. 2019 The Journal of general virology Introduction IV I292V 8 13 PB2 4 7 31305236 Prevailing I292V PB2 mutation in avian influenza H9N2 virus increases viral polymerase function and attenuates IFN-beta induction in human cells. Therefore, PB2-I292V is a newly identified mammalian adaptive determinant of avian H9N2 influenza viruses. 2019 The Journal of general virology Introduction IV I292V 15 20 PB2 11 14 31305236 Prevailing I292V PB2 mutation in avian influenza H9N2 virus increases viral polymerase function and attenuates IFN-beta induction in human cells. To overcome this restriction, the avian PB2 gene needs to acquire certain mutational changes to improve its activity in mammalian cells, as exemplified in PB2-E627K, -D701N, -T271A, -K526R and -A588V. 2019 The Journal of general virology Introduction IV E627K;D701N;T271A;K526R;A588V 159;167;175;183;194 164;172;180;188;199 PB2;PB2 40;155 43;158 31329089 Biological properties of influenza A virus mutants with amino acid substitutions in the HA2 glycoprotein of the HA1/HA2 interaction region. By reverse genetics were prepared three viruses with mutations in HA2 gp: T642H (HA2 numbering as from the N terminus of HA2 gp after HA0 cleavage. 2019 The Journal of general virology Introduction IV T642H 74 79 HA;HA;HA 66;81;121 68;83;123 31329089 Biological properties of influenza A virus mutants with amino acid substitutions in the HA2 glycoprotein of the HA1/HA2 interaction region. H1 numbering position HA407), V662H (numbering as for HA2. 2019 The Journal of general virology Introduction IV V662H 30 35 HA;HA 22;54 24;56 31329089 Biological properties of influenza A virus mutants with amino acid substitutions in the HA2 glycoprotein of the HA1/HA2 interaction region. H1 numbering position HA409) and a double mutant with both amino acid substitutions in HA2 (T642H and V662H). 2019 The Journal of general virology Introduction IV T642H;V662H 92;102 97;107 HA;HA 22;87 24;89 31420169 The structure and conformational plasticity of the nonstructural protein 1 of the 1918 influenza A virus. Here we present the solution NMR structure of the 1918 NS1-ED W187R. 2019 Biochemical and biophysical research communications Introduction IV W187R 62 67 NS1 55 58 31420169 The structure and conformational plasticity of the nonstructural protein 1 of the 1918 influenza A virus. We find that the 1918 NS1-ED W187R exists as a monomer in solution. 2019 Biochemical and biophysical research communications Introduction IV W187R 29 34 NS1 22 25 31436527 Human-to-Human Transmission of Influenza A(H3N2) Virus with Reduced Susceptibility to Baloxavir, Japan, February 2019. In January 2019, we detected a mutant influenza A(H3N2) virus carrying the PA I38T substitution from a hospitalized 5-year-old child who was not treated with baloxavir. 2019 Emerging infectious diseases Introduction IV I38T 78 82 PA 75 77 31436527 Human-to-Human Transmission of Influenza A(H3N2) Virus with Reduced Susceptibility to Baloxavir, Japan, February 2019. In phase 2 and 3 clinical trials of baloxavir, treatment-emergent amino acid substitutions--I38T or I38F for influenza A(H1N1)pdm09 (pH1N1) virus and I38T or I38M for influenza A(H3N2) virus in the polymerase acidic (PA) protein--were detected. 2019 Emerging infectious diseases Introduction IV I38T;I38F;I38T;I38M 92;100;150;158 96;104;154;162 PA;PA 217;198 219;215 31538644 Baloxavir Marboxil in Japanese Pediatric Patients With Influenza: Safety and Clinical and Virologic Outcomes. Highly oseltamivir-resistant seasonal A(H1N1) viruses, due to an H275Y substitution in the viral neuraminidase, circulated worldwide in 2008-2009, and community-level transmission of oseltamivir-resistant A(H1N1)pdm09 virus has been reported. 2020 Clinical infectious diseases Introduction IV H275Y 65 70 97 110 31538644 Baloxavir Marboxil in Japanese Pediatric Patients With Influenza: Safety and Clinical and Virologic Outcomes. However, baloxavir treatment-emergent viruses with reduced susceptibility due to amino acid substitution of isoleucine at position 38 of PA (PA/I38X) were detected in 2.2-9.7% of baloxavir-treated patients in association with prolongation of infectious virus detectability, transient rises in viral titers, and initial delay in illness alleviation. 2020 Clinical infectious diseases Introduction IV I38X 144 148 PA;PA 137;141 139;143 31538644 Baloxavir Marboxil in Japanese Pediatric Patients With Influenza: Safety and Clinical and Virologic Outcomes. The present study is the first to assess the safety, pharmacokinetics, and clinical and virologic outcomes of baloxavir treatment including the effects of PA/I38X-substituted virus emergence in children aged 1-11 years with influenza virus infection. 2020 Clinical infectious diseases Introduction IV I38X 158 162 PA 155 157 IV infections 224 249 31575766 Influenza Virus Polymerase Mutation Stabilizes a Foreign Gene Inserted into the Virus Genome by Enhancing the Transcription/Replication Efficiency of the Modified Segment. In this study, we explored the mechanisms of Venus gene stabilization by comparing events upon infection with WT-Venus-PR8 and Venus-PR8 possessing the PB2-E712D mutation (Venus-PR8-PB2-E712D). 2019 mBio Introduction IV E712D;E712D 156;186 161;191 PB2;PB2 152;182 155;185 31575766 Influenza Virus Polymerase Mutation Stabilizes a Foreign Gene Inserted into the Virus Genome by Enhancing the Transcription/Replication Efficiency of the Modified Segment. We found that a V-to-A mutation at position 25 of the polymerase subunit PB2 and a R-to-K mutation at position 443 of the polymerase subunit PA contributed to the stable maintenance of the Venus gene. 2019 mBio Introduction IV V25A 16 46 PA;PB2 141;73 143;76 31575766 Influenza Virus Polymerase Mutation Stabilizes a Foreign Gene Inserted into the Virus Genome by Enhancing the Transcription/Replication Efficiency of the Modified Segment. We found that an E-to-D mutation at position 712 of the polymerase subunit PB2 (PB2-E712D) stabilized the inserted Venus gene. 2019 mBio Introduction IV E712D 84 89 PB2;PB2 75;80 78;83 31590265 Insights into the Acquisition of Virulence of Avian Influenza Viruses during a Single Passage in Ferrets. Increased nuclear entry of the PB2 protein via enhanced binding interactions between PB2 proteins and different isoforms of the mammalian importin-alpha protein, have been identified as the molecular mechanisms which enable PB2 proteins incorporating AA changes such as E627K and D701N to adapt to mammalian hosts. 2019 Viruses Introduction IV E627K;D701N 270;280 275;285 PB2;PB2;PB2 31;85;224 34;88;227 31590265 Insights into the Acquisition of Virulence of Avian Influenza Viruses during a Single Passage in Ferrets. Mutations have been identified that appear to be necessary for avian influenza viruses to efficiently replicate in mammalian hosts, and it is now well documented that changes in the viral polymerase subunit PB2 (a key one being the E627K substitution) are necessary for this. 2019 Viruses Introduction IV E627K 232 237 PB2 207 210 31590265 Insights into the Acquisition of Virulence of Avian Influenza Viruses during a Single Passage in Ferrets. Other amino acid (AA) changes such as PB2 D701N (detected less commonly in human isolates of H5N1 and H7N7), and the PB2 G590S, Q591R combination detected in A/H1N1pdm09 viruses, similarly facilitate the adaptation of influenza viruses of non-human origin to humans. 2019 Viruses Introduction IV D701N;G590S;Q591R 42;121;128 47;126;133 PB2;PB2 38;117 41;120 31597771 Identification of Key Amino Acids in the PB2 and M1 Proteins of H7N9 Influenza Virus That Affect Its Transmission in Guinea Pigs. reported that two amino acid mutations, D190E and D225G, abolished the ability of the 1918/H1N1 virus to transmit via respiratory droplets between ferrets. 2019 Journal of virology Introduction IV D190E;D225G 40;50 45;55 31597771 Identification of Key Amino Acids in the PB2 and M1 Proteins of H7N9 Influenza Virus That Affect Its Transmission in Guinea Pigs. The amino acid mutation A271T in PB2 eliminated the transmission of 2009/H1N1 pandemic virus in guinea pigs, and the amino acids 627K and 701N in PB2 increased the transmission of H3N2 virus and H5N1 virus in guinea pigs and the transmission of H7N9 virus and H9N2 virus in ferrets. 2019 Journal of virology Introduction IV A271T 24 29 PB2;PB2 33;146 36;149 31608791 Insights into species-specific regulation of ANP32A on the mammalian-restricted influenza virus polymerase activity. During virus infection, incoming avian vRNPs (PB2 627E) are directly impaired by RIG-I leading to virus inhibition, which is impeded by the PB2 E627K mutation. 2019 Emerging microbes & infections Introduction IV E627K 144 149 PB2;PB2 46;140 49;143 31608791 Insights into species-specific regulation of ANP32A on the mammalian-restricted influenza virus polymerase activity. The human ANP32A (huANP32A) directly plays an important role in the acquisition of the PB2 E627K substitution during adaptation of H7N9 AIVs to humans. 2019 Emerging microbes & infections Introduction IV E627K 91 96 PB2 87 90 31608791 Insights into species-specific regulation of ANP32A on the mammalian-restricted influenza virus polymerase activity. The molecular mechanism of the PB2 E627K mutation in the upregulation of mammalian-restricted polymerase function has been explored for decades. 2019 Emerging microbes & infections Introduction IV E627K 35 40 PB2 31 34 31608791 Insights into species-specific regulation of ANP32A on the mammalian-restricted influenza virus polymerase activity. The PB2 E627K mutation enhanced vRNP stability in mammalian cells, but the enhanced stability may be a result of the greater amount of vRNPs produced by the higher activity of the mammalian-adapted polymerase PB2 E627K than the avian-signature polymerase PB2 627E. 2019 Emerging microbes & infections Introduction IV E627K;E627K 8;213 13;218 PB2;PB2;PB2 4;209;255 7;212;258 31608791 Insights into species-specific regulation of ANP32A on the mammalian-restricted influenza virus polymerase activity. The PB2 E627K substitutions were rapidly selected upon infection of humans with H5N1 or H7N9 viruses as well as other subtypes of AIV, which have been associated with enhanced polymerase activity, high virus replication and pathogenicity in humans. 2019 Emerging microbes & infections Introduction IV E627K 8 13 PB2 4 7 31635227 Antigenic Site Variation in the Hemagglutinin of Pandemic Influenza A(H1N1)pdm09 Viruses between 2009-2017 in Ukraine. Characteristic substitutions for the group 6B.1 include point mutations S84N, S162N (+CHO) and I216T in HA1. 2019 Pathogens (Basel, Switzerland) Introduction IV S84N;S162N;I216T 72;78;95 76;83;100 HA1 104 107 31635227 Antigenic Site Variation in the Hemagglutinin of Pandemic Influenza A(H1N1)pdm09 Viruses between 2009-2017 in Ukraine. The S162N mutation confers a potential gain of glycosylation at residues 162-164 that may mask K163Q and other epitopes relevant for neutralizing the antibody binding. 2019 Pathogens (Basel, Switzerland) Introduction IV S162N;K163Q 4;95 9;100 31669761 Discovery of M2 channel blockers targeting the drug-resistant double mutants M2-S31N/L26I and M2-S31N/V27A from the influenza A viruses. Alarmingly, in recombinant H1N1, the double mutant M2-S31N/V27A led to the highest mortality rate in vivo compared to WT or any of the single amantadine-resistant mutants, and the M2-S31N/V27A double mutant showed similar replication rates in cell culture as the WT. 2020 European journal of pharmaceutical sciences Introduction IV V27A;S31N;V27A;S31N 59;54;188;183 63;58;192;187 M2;M2 51;180 53;182 31669761 Discovery of M2 channel blockers targeting the drug-resistant double mutants M2-S31N/L26I and M2-S31N/V27A from the influenza A viruses. Altogether, the prevalence of the M2 double mutants, especially M2-S31N/L26I and M2-S31N/V27A, among H5N1 viruses offer an opportunity for therapeutic intervention. 2020 European journal of pharmaceutical sciences Introduction IV L26I;S31N;V27A;S31N 72;67;89;84 76;71;93;88 M2;M2;M2 34;64;81 36;66;83 31669761 Discovery of M2 channel blockers targeting the drug-resistant double mutants M2-S31N/L26I and M2-S31N/V27A from the influenza A viruses. As of date, no antiviral has been developed to target these amantadine-resistant double M2 mutants (S31N/L26I and S31N/V27A). 2020 European journal of pharmaceutical sciences Introduction IV L26I;S31N;V27A;S31N 105;100;119;114 109;104;123;118 M2 88 90 31669761 Discovery of M2 channel blockers targeting the drug-resistant double mutants M2-S31N/L26I and M2-S31N/V27A from the influenza A viruses. As such, in this work, we aimed to identify potent channel blockers against M2-S31N/L26I and M2-S31N/V27A double mutants. 2020 European journal of pharmaceutical sciences Introduction IV L26I;S31N;V27A;S31N 84;79;101;96 88;83;105;100 M2;M2 76;93 78;95 31669761 Discovery of M2 channel blockers targeting the drug-resistant double mutants M2-S31N/L26I and M2-S31N/V27A from the influenza A viruses. However, no M2 channel blockers have been developed against drug-resistant double mutants such as the M2-S31N/L26I and the M2-S31N/V27A, which are the predominant mutations found in H5N1 viruses. 2020 European journal of pharmaceutical sciences Introduction IV S31N;L26I;V27A;S31N 105;110;131;126 109;114;135;130 M2;M2;M2 12;102;123 14;104;125 31669761 Discovery of M2 channel blockers targeting the drug-resistant double mutants M2-S31N/L26I and M2-S31N/V27A from the influenza A viruses. In clinically isolated strains of influenza viruses, three major amantadine-resistant mutations in the M2 channels have been identified: L26F, V27A, and S31N. 2020 European journal of pharmaceutical sciences Introduction IV L26F;V27A;S31N 137;143;153 141;147;157 M2 103 105 31669761 Discovery of M2 channel blockers targeting the drug-resistant double mutants M2-S31N/L26I and M2-S31N/V27A from the influenza A viruses. In the case of human and avian origin H5N1 isolated between 1996 to 2005 in Vietnam, Cambodia, Malaysia and Thailand, more than 90% contain the double mutant M2-S31N/L26I channel. 2020 European journal of pharmaceutical sciences Introduction IV L26I;S31N 166;161 170;165 M2 158 160 31669761 Discovery of M2 channel blockers targeting the drug-resistant double mutants M2-S31N/L26I and M2-S31N/V27A from the influenza A viruses. Influenza strains with double M2 mutations have been identified in seasonally circulating strains as well, with the most commonly identified double mutant is the S31N/V27A. 2020 European journal of pharmaceutical sciences Introduction IV V27A;S31N 167;162 171;166 M2 30 32 31669761 Discovery of M2 channel blockers targeting the drug-resistant double mutants M2-S31N/L26I and M2-S31N/V27A from the influenza A viruses. M2-S31N/V27A has been identified in H1, H3, H5, and H7 strains from human, avian and swine reservoirs. 2020 European journal of pharmaceutical sciences Introduction IV V27A;S31N 8;3 12;7 M2 0 2 31669761 Discovery of M2 channel blockers targeting the drug-resistant double mutants M2-S31N/L26I and M2-S31N/V27A from the influenza A viruses. Several advancements in the structural characterization of M2 helped the development of not only mono-specific V27A and S31N inhibitors, but also dual inhibitors that target either both WT and V27A or both WT and S31N channels simultaneously. 2020 European journal of pharmaceutical sciences Introduction IV V27A;S31N;V27A;S31N 111;120;193;213 115;124;197;217 M2 59 61 31669761 Discovery of M2 channel blockers targeting the drug-resistant double mutants M2-S31N/L26I and M2-S31N/V27A from the influenza A viruses. Specifically, the M2-S31N/V27A mutation was observed in an immunocompetent child infected with the 2009 pandemic H1N1 without the treatment of adamantane. 2020 European journal of pharmaceutical sciences Introduction IV V27A;S31N 26;21 30;25 M2 18 20 31669761 Discovery of M2 channel blockers targeting the drug-resistant double mutants M2-S31N/L26I and M2-S31N/V27A from the influenza A viruses. This effort led to the discovery of three compounds 6, 7, and 15 that significantly block all three M2 mutants: M2-S31N, M2-S31N/L26I, and M2-S31N/V27A. 2020 European journal of pharmaceutical sciences Introduction IV S31N;L26I;S31N;V27A;S31N 115;129;124;147;142 119;133;128;151;146 M2;M2;M2;M2 100;112;121;139 102;114;123;141 31718675 Mouse-adapted H9N2 avian influenza virus causes systemic infection in mice. Additionally, PA-T97I, PA-E349K and HA-I204M have also been detected in mice-adapted strains previously. 2019 Virology journal Introduction IV T97I;E349K;I204M 17;26;39 21;31;44 HA;PA;PA 36;14;23 38;16;25 31718675 Mouse-adapted H9N2 avian influenza virus causes systemic infection in mice. Except for M1-239 T, there were 9 additional substitutions in ZB-MA strain also presented more frequently in human H9N2, pH1N1 or human H3N2 influenza viruses, including PA-S489C, NA-V377I, M1-S157A, M1-H158Q, M1-Q222H, M2-H10L, M2-E16G, M2-I27V, and M2-V32I. 2019 Virology journal Introduction IV S489C;V377I;S157A;H158Q;Q222H;H10L;E16G;I27V;V32I 173;183;193;203;213;223;232;241;254 178;188;198;208;218;227;236;245;258 M1;M1;M1;M1;M2;M2;M2;M2;NA;PA 11;190;200;210;220;229;238;251;180;170 13;192;202;212;222;231;240;253;182;172 31718675 Mouse-adapted H9N2 avian influenza virus causes systemic infection in mice. In the G1-MA virus, HA-I204M and HA-N206 T occur in the receptor binding site and PB2-S509R is located in the overlapping regions of the NP and PB1 binding domains; M1-Q198H and M1-A239T reside in the RNP binding region. 2019 Virology journal Introduction IV I204M;N206T;S509R;Q198H;A239T 23;36;86;168;181 28;42;91;173;186 HA;HA;M1;M1;NP;PB1;PB2;RNP 20;33;165;178;137;144;82;201 22;35;167;180;139;147;85;204 31718675 Mouse-adapted H9N2 avian influenza virus causes systemic infection in mice. In the ZB-MA virus, the M1-E29V, M1-Q198H, M1-I219V, M1-Q222H, and M1-A239T mutations reside in the RNP binding region, M1-S157A and M1-H158Q mutations reside in RNA binding region; the M2-I27V, M2-V32I, and M2-H37R mutations occur in the ion channel. 2019 Virology journal Introduction IV E29V;Q198H;I219V;Q222H;A239T;S157A;H158Q;I27V;V32I;H37R 27;36;46;56;70;123;136;189;198;211 31;41;51;61;75;128;141;193;202;215 M1;M1;M1;M1;M1;M1;M1;M2;M2;M2;RNP 24;33;43;53;67;120;133;186;195;208;100 26;35;45;55;69;122;135;188;197;210;103 31718675 Mouse-adapted H9N2 avian influenza virus causes systemic infection in mice. M1-Q198H and M1-A239T were found in both G1-MA and ZB-MA viruses and 97% of human H3N2 influenza viruses possessed M1-239 T. 2019 Virology journal Introduction IV Q198H;A239T 3;16 8;21 M1;M1;M1 0;13;115 2;15;117 31719554 Synergistic PA and HA mutations confer mouse adaptation of a contemporary A/H3N2 influenza virus. Herein, we report on a novel combination of substitutions in HA (N122D, N144E, N246K and A304T) and PA (K615E) proteins responsible for the adaptation and increased pathogenicity of a contemporary A/H3N2 seasonal virus in mice. 2019 Scientific reports Introduction IV N122D;N144E;N246K;A304T;K615E 65;72;79;89;104 70;77;84;94;109 HA;PA 61;100 63;102 31719554 Synergistic PA and HA mutations confer mouse adaptation of a contemporary A/H3N2 influenza virus. The majority of the mammalian adaptive substitutions occur in the PB2 protein; E627K and D710N are two well-characterized substitutions in PB2 protein, which are critical for mammalian adaptation in multiple subtypes of avian influenza viruses. 2019 Scientific reports Introduction IV E627K;D710N 79;89 84;94 PB2;PB2 66;139 69;142 31805964 The tyrosine 73 and serine 83 dephosphorylation of H1N1 swine influenza virus NS1 protein attenuates virus replication and induces high levels of beta interferon. The presence of an alanine (A) residue at position 149 of the GS/GD/1/96(H5N1) NS1 protein antagonizes the induction of IFN protein levels in chicken embryo fibroblasts (CEFs). 2019 Virology journal Introduction IV A149A 18 55 NS1 79 82 31805964 The tyrosine 73 and serine 83 dephosphorylation of H1N1 swine influenza virus NS1 protein attenuates virus replication and induces high levels of beta interferon. The specific exchange of E for D at position 92 of the A/HK/156/97 (H5N1) NS1 gene results in an order of magnitude increase in the quantum yield of IFN. 2019 Virology journal Introduction IV D92E 25 47 NS1 74 77 31805964 The tyrosine 73 and serine 83 dephosphorylation of H1N1 swine influenza virus NS1 protein attenuates virus replication and induces high levels of beta interferon. Upon generating recombinant influenza A/swine/Shanghai/3/2014(H1N1) viruses that encode mutant NS1 proteins (Y73F and S83A), we found that dephosphorylation at positions 73 and 83 of the NS1 protein attenuated virus replication and diminished the capability of NS1 to antagonize IFN-beta expression. 2019 Virology journal Introduction IV Y73F;S83A 109;118 113;122 NS1;NS1;NS1 95;187;261 98;190;264 31842256 Antiviral Activity of Benzoic Acid Derivative NC-5 Against Influenza A Virus and Its Neuraminidase Inhibition. We tested its antiviral activity against A/FM/1/47 (H1N1), A/Beijing/32/92 (H3N2) and A/FM/1/47-H275Y (H1N1-H275Y) in vitro and against H1N1 and H1N1-H275Y in vivo. 2019 International journal of molecular sciences Introduction IV H275Y;H275Y;H275Y 96;108;150 101;113;155 31894969 X-ray Crystal Structures of the Influenza M2 Proton Channel Drug-Resistant V27A Mutant Bound to a Spiro-Adamantyl Amine Inhibitor Reveal the Mechanism of Adamantane Resistance. Here we present X-ray crystal structures of the drug-resistant V27A mutant of M2 bound to a spiro-adamantyl amine inhibitor, using both M2(22-46) and M2(21-61) constructs for crystallization trials. 2020 Biochemistry Introduction IV V27A 63 67 M2;M2;M2 78;136;150 80;138;152 31894969 X-ray Crystal Structures of the Influenza M2 Proton Channel Drug-Resistant V27A Mutant Bound to a Spiro-Adamantyl Amine Inhibitor Reveal the Mechanism of Adamantane Resistance. In the structure of M2(21-61) V27A bound to spiro-adamantyl amine, we observe tight packing at the channel's C-terminus, particularly at residue Arg45. 2020 Biochemistry Introduction IV V27A 30 34 M2 20 22 31894969 X-ray Crystal Structures of the Influenza M2 Proton Channel Drug-Resistant V27A Mutant Bound to a Spiro-Adamantyl Amine Inhibitor Reveal the Mechanism of Adamantane Resistance. In this study, we focus on understanding the mechanism of action of spiro-adamantyl amine in inhibiting the M2 V27A mutant by solving high-resolution X-ray crystal structures. 2020 Biochemistry Introduction IV V27A 111 115 M2 108 110 31894969 X-ray Crystal Structures of the Influenza M2 Proton Channel Drug-Resistant V27A Mutant Bound to a Spiro-Adamantyl Amine Inhibitor Reveal the Mechanism of Adamantane Resistance. It was found that when Val27 is mutated to Ala, the diameter of the channel pore at the drug binding site increases and the hydrophobic interactions that stabilize the binding of adamantanes to the WT channel are removed. 2020 Biochemistry Introduction IV V27A 23 46 31894969 X-ray Crystal Structures of the Influenza M2 Proton Channel Drug-Resistant V27A Mutant Bound to a Spiro-Adamantyl Amine Inhibitor Reveal the Mechanism of Adamantane Resistance. Overall, the V27A mutation is becoming more prevalent in circulating populations of influenza, so there has been interest in designing drugs to target it. 2020 Biochemistry Introduction IV V27A 13 17 31894969 X-ray Crystal Structures of the Influenza M2 Proton Channel Drug-Resistant V27A Mutant Bound to a Spiro-Adamantyl Amine Inhibitor Reveal the Mechanism of Adamantane Resistance. Spiro-adamantyl amine was developed by molecular dynamics simulation-directed design and was able to inhibit the conductance of protons in both the V27A mutant and the WT channel in two electrode voltage clamp (TEVC) assays using Xenopus oocytes, with an IC50 of 0.3 muM against the V27A channel and an IC50 of 18.7 muM against the WT channel (compare to IC50 = 15.7 muM for amantadine against the WT channel). 2020 Biochemistry Introduction IV V27A;V27A 148;283 152;287 31894969 X-ray Crystal Structures of the Influenza M2 Proton Channel Drug-Resistant V27A Mutant Bound to a Spiro-Adamantyl Amine Inhibitor Reveal the Mechanism of Adamantane Resistance. Spiro-adamantyl amine was further shown to have both in vitro and in vivo antiviral activity against influenza A M2 V27A mutant virus. 2020 Biochemistry Introduction IV V27A 116 120 M2 113 115 31894969 X-ray Crystal Structures of the Influenza M2 Proton Channel Drug-Resistant V27A Mutant Bound to a Spiro-Adamantyl Amine Inhibitor Reveal the Mechanism of Adamantane Resistance. The percent of influenza viruses containing the V27A mutation varies widely depending on the viral strain and season, with some studies reporting incidence as high as 7-10%. 2020 Biochemistry Introduction IV V27A 48 52 31894969 X-ray Crystal Structures of the Influenza M2 Proton Channel Drug-Resistant V27A Mutant Bound to a Spiro-Adamantyl Amine Inhibitor Reveal the Mechanism of Adamantane Resistance. The two most prevalent drug-resistant mutants are S31N and V27A. 2020 Biochemistry Introduction IV S31N;V27A 50;59 54;63 31894969 X-ray Crystal Structures of the Influenza M2 Proton Channel Drug-Resistant V27A Mutant Bound to a Spiro-Adamantyl Amine Inhibitor Reveal the Mechanism of Adamantane Resistance. While the S31N mutation was present in populations of influenza before the introduction of the adamantane drugs, V27A has become enriched by selection pressure., Double mutants containing both S31N and V27A mutations have been observed. 2020 Biochemistry Introduction IV S31N;V27A;S31N;V27A 10;113;193;202 14;117;197;206 31906790 Contribution of Fc-dependent cell-mediated activity of a vestigial esterase-targeting antibody against H5N6 virus infection. Comparisons between 9F4-WT, an ADCC and ADCP deficient mutant 9F4-LALA and a CDC deficient 9F4-K322A against a mouse IgG2a isotype control revealed that the ADCP and/or ADCC but not the CDC pathways contributes significantly to the protective role of 9F4. 2020 Emerging microbes & infections Introduction IV K322A 95 100 31906790 Contribution of Fc-dependent cell-mediated activity of a vestigial esterase-targeting antibody against H5N6 virus infection. Substitutions of two leucine (L) residues to alanine (A) at position 234 and 235 (e.g. 2020 Emerging microbes & infections Introduction IV A234A 44 73 31917822 The effect of mutations derived from mouse-adapted H3N2 seasonal influenza A virus to pathogenicity and host adaptation. Additionally, the function of the NP D34N mutation is not yet known but might be related to interactions with PB2. 2020 PloS one Introduction IV D34N 37 41 NP;PB2 34;110 36;113 31917822 The effect of mutations derived from mouse-adapted H3N2 seasonal influenza A virus to pathogenicity and host adaptation. Furthermore, the E627K and D701N substitutions in the PB2 gene have been commonly detected in mouse-adapted IAVs and related to enhanced virulence in mice. 2020 PloS one Introduction IV E627K;D701N 17;27 22;32 PB2 54 57 31917822 The effect of mutations derived from mouse-adapted H3N2 seasonal influenza A virus to pathogenicity and host adaptation. The NP N319K mutation enhances interactions with importin alpha1, which increases nuclear import of ribonucleoprotein (RNP). 2020 PloS one Introduction IV N319K 7 12 NP;RNP 4;119 6;122 31951605 Reassortment and adaptive mutations of an emerging avian influenza virus H7N4 subtype in China. By comparing the virus with the avian viruses isolated on the same farm, we identified seventeen probable human-adaptive mutations, most of which were uncharacterized except the E627K and K683T mutations in PB2. 2020 PloS one Introduction IV E627K;K683T 178;188 183;193 PB2 207 210 32064779 Rapid detection of an I38T amino acid substitution in influenza polymerase acidic subunit associated with reduced susceptibility to baloxavir marboxil. In Japan, two approaches have been developed to monitor the emergence of baloxavir-resistant influenza viruses since the 2017/2018 influenza season: the focus reduction assay, which assesses baloxavir susceptibility, and sequence analysis by next-generation sequencing (NGS), which detects amino acid substitutions at amino acid residue 38 in PA.5 Using NGS, in December 2018, we detected the PA I38T substitution in two clinical strains isolated from two patients 3 days after baloxavir administration.6 As of January 2019, PA I38T substitution was found in 11 cases infected with influenza A(H3N2) viruses, including one patient untreated with baloxavir.7 Although monitoring by NGS in Japan works well, this method requires skill and is labor-intensive, and the results can take 3 days to acquire. 2020 Influenza and other respiratory viruses Introduction IV I38T;I38T 396;528 400;532 PA;PA;PA 343;393;525 345;395;527 32064779 Rapid detection of an I38T amino acid substitution in influenza polymerase acidic subunit associated with reduced susceptibility to baloxavir marboxil. Moreover, in a phase III clinical trial, PA I38T and I38M substitutions were detected after exposure to the drug in 9.7% of 370 influenza A(H3N2) viruses.4 Patients infected with mutant influenza viruses carrying PA I38T or I38F exhibited prolonged viral shedding, and the median time to alleviation of symptoms was longer in baloxavir recipients infected with viruses with PA I38T or I38M substitutions than in those without substitutions.3, 4 In a pediatric study, PA I38T and I38M substitutions emerged in 18 (23.4%) of 77 influenza A(H3N2) viruses.3 . 2020 Influenza and other respiratory viruses Introduction IV I38T;I38M;I38T;I38F;I38T;I38M;I38T;I38M 44;53;216;224;377;385;470;479 48;57;220;228;381;389;474;483 PA;PA;PA;PA 41;213;374;467 43;215;376;469 32064779 Rapid detection of an I38T amino acid substitution in influenza polymerase acidic subunit associated with reduced susceptibility to baloxavir marboxil. Moreover, in a phase III clinical trial, PA I38T and I38M substitutions were detected after exposure to the drug in 9.7% of 370 influenza A(H3N2) viruses.4 Patients infected with mutant influenza viruses carrying PA I38T or I38F exhibited prolonged viral shedding, and the median time to alleviation of symptoms was longer in baloxavir recipients infected with viruses with PA I38T or I38M substitutions than in those without substitutions.3, 4 In a pediatric study, PA I38T and I38M substitutions emerged in 18 (23.4%) of 77 influenza A(H3N2) viruses.3. 2020 Influenza and other respiratory viruses Introduction IV I38T;I38M;I38T;I38F;I38T;I38M;I38T;I38M 44;53;216;224;377;385;470;479 48;57;220;228;381;389;474;483 32064779 Rapid detection of an I38T amino acid substitution in influenza polymerase acidic subunit associated with reduced susceptibility to baloxavir marboxil. RNase H2-dependent PCR (rhPCR) was recently established to enable the performance of PCR using blocked primers containing a single ribonucleotide residue that are activated by cleavage with a thermophilic archaeal RNase H2 enzyme from Pyrococcus abyssi.8 rhPCR was found to be more sensitive than standard allele-specific PCR when applied to the detection of single-nucleotide polymorphisms (SNPs).8 In this study, for the rapid and simple monitoring of influenza viruses possessing the I38T substitution in PA in a laboratory, three rhPCR-based assays were developed for influenza A(H1N1)pdm09, A(H3N2), and B viruses, referred to as A/H1pdm PA_I38T rhPCR, A/H3 PA_I38T rhPCR, and B PA_I38T rhPCR, respectively. 2020 Influenza and other respiratory viruses Introduction IV I38T;I38T;I38T;I38T 487;646;666;687 491;650;670;691 PA;PA;PA;PA 508;643;663;684 510;645;665;686 32064779 Rapid detection of an I38T amino acid substitution in influenza polymerase acidic subunit associated with reduced susceptibility to baloxavir marboxil. The hydrolyzed active form of baloxavir marboxil (baloxavir acid; S-033447) inhibits the cap-dependent endonuclease of influenza A and B viruses.1 In vitro studies have revealed that an I38T substitution in the polymerase acidic subunit (PA) is associated with reduced susceptibility of influenza A(H1N1)pdm09, A(H3N2), and B viruses to baloxavir.2, 3 Furthermore, in a phase II clinical trial,3 PA I38T and I38F substitutions emerged following exposure to baloxavir marboxil in four (3.6%) of 112 influenza A(H1N1)pdm09 viruses for which PA sequences were available. 2020 Influenza and other respiratory viruses Introduction IV I38T;I38T;I38F 186;399;408 190;403;412 PA;PA;PA;PA 238;396;539;211 240;398;541;236 32093780 Acetylation at K108 of the NS1 protein is important for the replication and virulence of influenza virus. IFN-beta antagonist assays indicated that the K108R mutation attenuated IFN antagonistic ability compared with the NS1-wt or NS1-108Q (constant acetylation-mimic) proteins. 2020 Veterinary research Introduction IV K108R 46 51 NS1;NS1 115;125 118;128 32093780 Acetylation at K108 of the NS1 protein is important for the replication and virulence of influenza virus. The residue 187W in the ED domain is important for the dimerization of the NS1 protein, and the W187R substitution impaired NS1 dimerization and attenuated the virus in vivo. 2020 Veterinary research Introduction IV W187R 96 101 NS1;NS1 75;124 78;127 32093780 Acetylation at K108 of the NS1 protein is important for the replication and virulence of influenza virus. The results showed that the deacetylation-mimic mutation K108R in the NS1 protein attenuated the replication and virulence of the virus in vitro and in vivo. 2020 Veterinary research Introduction IV K108R 57 62 NS1 70 73 32095441 Comparison of antigenic mutation during egg and cell passage cultivation of H3N2 influenza virus. At that time, the CVV for A/Victoria/361/2011 (H3N2) was subjected to amino acid mutations in three position of HA protein by egg adaptations, which were all areas corresponding to the antigenic site as H156Q, G186V, and S219Y. 2020 Clinical and experimental vaccine research Introduction IV H156Q;G186V;S219Y 203;210;221 208;215;226 HA 112 114 32095441 Comparison of antigenic mutation during egg and cell passage cultivation of H3N2 influenza virus. Especially in the case of G186V, it is known to be a mutation that is characteristically found in the egg adaption of the influenza virus. 2020 Clinical and experimental vaccine research Introduction IV G186V 26 31 32095441 Comparison of antigenic mutation during egg and cell passage cultivation of H3N2 influenza virus. In the case of clade 3C.2a virus recommended as a vaccine strain, a glycosylation site was added according to the K160T amino acid mutation. 2020 Clinical and experimental vaccine research Introduction IV K160T 114 119 32159230 Antigenic drift of hemagglutinin and neuraminidase in seasonal H1N1 influenza viruses from Saudi Arabia in 2014 to 2015. Furthermore, a high number of the strains possessed the amino acid changes D97N (aspartic acid to asparagine), S185T (serine to threonine), K163Q (lysine to glutamine), A256T (alanine to threonine), and K283E (lysine to glutamic acid). 2020 Journal of medical virology Introduction IV D97N;S185T;K163Q;A256T;K283E 75;111;140;169;203 79;116;145;174;208 32272772 Influenza PB1-F2 Inhibits Avian MAVS Signaling. The RIG-I-MAVS interacting surfaces are not conserved between humans and ducks, but structure is conserved such that tandem T175K/T176E mutations on duck RIG-I permit interaction with human MAVS in HEK293T cells. 2020 Viruses Introduction IV T175K;T176E 124;130 129;135 32415096 mRNA display with library of even-distribution reveals cellular interactors of influenza virus NS1. In addition, we explore the use of md-LED to examine the differential cellular binders of wild-type NS1 and a point mutant, D92Y, which had been previously shown to weaken NS1's known function in disrupting the interferon response. 2020 Nature communications Introduction IV D92Y 124 128 NS1;NS1 100;172 103;175 32415096 mRNA display with library of even-distribution reveals cellular interactors of influenza virus NS1. We find that the D92Y mutant failed to engage CPSF1, likely resulting in an increased host response. 2020 Nature communications Introduction IV D92Y 17 21 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. Regarding the H5N2 subtype avian influenza virus, HA generated a Q234L mutation after many generations in the lungs of mice, which helped to the virus obtain the ability to infect mammals (Petrova and Russell). 2020 AMB Express Introduction IV Q234L 65 70 HA 50 52 32486222 Antibody Neutralization of an Influenza Virus that Uses Neuraminidase for Receptor Binding. Here, we utilize the G147R NA in conjunction with a binding-deficient HA to develop a sensitive neutralization assay for anti-NA antibodies. 2020 Viruses Introduction IV G147R 21 26 HA;NA;NA 70;27;126 72;29;128 32486222 Antibody Neutralization of an Influenza Virus that Uses Neuraminidase for Receptor Binding. Importantly, the D151G/N mutations appear to only arise in cell culture, and have not been found in actual human infections. 2020 Viruses Introduction IV D151G;D151N 17;17 24;24 32486222 Antibody Neutralization of an Influenza Virus that Uses Neuraminidase for Receptor Binding. Importantly, viruses with the G147R N1 NA can grow efficiently in cell culture even if the receptor-binding activity of HA is completely ablated by engineered mutations. 2020 Viruses Introduction IV G147R 30 35 HA;NA 120;39 122;41 32486222 Antibody Neutralization of an Influenza Virus that Uses Neuraminidase for Receptor Binding. It was soon discovered that the mutations D151G/N allow N2 NA to bind sialic-acid receptors, but ablate NA catalytic receptor-cleaving activity. 2020 Viruses Introduction IV D151G;D151N 42;42 49;49 NA;NA 59;104 61;106 32486222 Antibody Neutralization of an Influenza Virus that Uses Neuraminidase for Receptor Binding. It was subsequently shown that because D151G/N NA lacks enzymatic activity, viruses carrying these mutations can only grow in mixed "cooperating" populations with viruses encoding NA that retains receptor-cleaving activity. 2020 Viruses Introduction IV D151G;D151N 39;39 46;46 NA;NA 47;180 49;182 32486222 Antibody Neutralization of an Influenza Virus that Uses Neuraminidase for Receptor Binding. Shortly after the identification of D151G/N in N2 NA, it was discovered that the G147R mutation enables N1 NA to bind to cellular receptors while maintaining its receptor-cleaving function. 2020 Viruses Introduction IV D151G;D151N;G147R 36;36;81 43;43;86 NA;NA 50;107 52;109 32486222 Antibody Neutralization of an Influenza Virus that Uses Neuraminidase for Receptor Binding. Unlike D151G/N mutations that only arise in N2 NA in tissue culture, the G147R mutation has been identified at low frequency in several naturally occurring H1N1 and H5N1 isolates. 2020 Viruses Introduction IV D151G;D151N;G147R 7;7;73 14;14;78 47 49 32599753 Virtual Screening Identifies Chebulagic Acid as an Inhibitor of the M2(S31N) Viral Ion Channel and Influenza A Virus. Based on these observations, we hypothesized that screening of natural product-derived chemical libraries may identify new M2(S31N) inhibitors and influenza antivirals. 2020 Molecules (Basel, Switzerland) Introduction IV S31N 126 130 M2 123 125 32599753 Virtual Screening Identifies Chebulagic Acid as an Inhibitor of the M2(S31N) Viral Ion Channel and Influenza A Virus. However, while several adamantane- and non-adamantane-based inhibitors of M2(S31N) have been recently described, none are currently licensed for use in humans. 2020 Molecules (Basel, Switzerland) Introduction IV S31N 77 81 M2 74 76 32599753 Virtual Screening Identifies Chebulagic Acid as an Inhibitor of the M2(S31N) Viral Ion Channel and Influenza A Virus. More than 95% of adamantane-resistant influenza A virus strains contain a serine to asparagine mutation at position 31 in M2 (S31N); this mutation distorts interactions of adamantanes with M2 pore-lining residues without affecting M2 ion channel activity or viral fitness. 2020 Molecules (Basel, Switzerland) Introduction IV S31N;S31N 126;74 130;118 M2;M2;M2 122;189;231 124;191;233 32599753 Virtual Screening Identifies Chebulagic Acid as an Inhibitor of the M2(S31N) Viral Ion Channel and Influenza A Virus. Therefore, the discovery of additional inhibitors of M2(S31N), including those representing distinct and, as of yet, unconsidered chemical scaffolds, is warranted as part of ongoing efforts to restore this therapeutic gap. 2020 Molecules (Basel, Switzerland) Introduction IV S31N 56 60 M2 53 55 32599753 Virtual Screening Identifies Chebulagic Acid as an Inhibitor of the M2(S31N) Viral Ion Channel and Influenza A Virus. We report here the results of this screen and discovery of chebulagic acid as an inhibitor of influenza replication, which also acts on M2(S31N). 2020 Molecules (Basel, Switzerland) Introduction IV S31N 139 143 M2 136 138 32601336 Pre-existing immunity to influenza virus hemagglutinin stalk might drive selection for antibody-escape mutant viruses in a human challenge model. This study examined selection of an HA stalk antibody-escape mutant virus in human influenza challenge participants inoculated with a well-characterized IAV stock that contained a mixed population of viruses with a nonsynonymous single-nucleotide polymorphism (SNP) in the HA stalk (A388V). 2020 Nature medicine Introduction IV A388V 283 288 HA;HA 36;273 38;275 Influenza 77 92 32629810 Replication of a Dog-Origin H6N1 Influenza Virus in Cell Culture and Mice. Mutations on these RNP component proteins could change the viral polymerase activity and virulence, such as PA P190S and PA Q400P in H7N3, PA T97I in H6N1, PB1 T296R in H1N1, PB2 E627K in H7N9 and PB2 Q591K in H9N2. 2020 Viruses Introduction IV P190S;Q400P;T97I;T296R;E627K;Q591K 111;124;142;160;179;201 116;129;146;165;184;206 PA;PA;PA;PB1;PB2;PB2;RNP 108;121;139;156;175;197;19 110;123;141;159;178;200;22 32629810 Replication of a Dog-Origin H6N1 Influenza Virus in Cell Culture and Mice. The dog H6N1 virus was found to have infectivity in mammals, especially when it possessed the PB2 E627K mutation. 2020 Viruses Introduction IV E627K 98 103 PB2 94 97 32631240 Successful treatment with baloxavir marboxil of a patient with peramivir-resistant influenza A/H3N2 with a dual E119D/R292K substitution after allogeneic hematopoietic cell transplantation: a case report. Here, we demonstrate that baloxavir marboxil (hereafter referred to as baloxavir), a new selective inhibitor of influenza cap-dependent endonuclease, was effective in a highly immunocompromised patient with peramivir-resistant dual E119D/R292K NA mutated-influenza A/H3N2 after allo-HCT. 2020 BMC infectious diseases Introduction IV E119D;R292K 232;238 237;243 244 246 32631440 Characterization of neuraminidase inhibitor-resistant influenza virus isolates from immunocompromised patients in the Republic of Korea. However, since most recently detected type A influenza viruses harbor the resistance variation S31N in the matrix gene, the M2 proton-channel blockers amantadine and rimantadine are no longer clinically applied. 2020 Virology journal Introduction IV S31N 95 99 M2;M 124;107 126;113 32631440 Characterization of neuraminidase inhibitor-resistant influenza virus isolates from immunocompromised patients in the Republic of Korea. The typical drug-resistance substitutions in NA include H275Y, E119D/G, and Q136R for A(H1N1)pdm09; E119V, D151G/V/D, R224K, E276D, R292K, and N294S for A (H3N2); and G104E, E117A/D, H134Y, and R150K for B virus, although additional single and combination mutations may also result in NAI drug resistance (World Health Organization (WHO)). 2020 Virology journal Introduction IV H275Y;E119D;E119G;Q136R;E119V;D151G;D151V;D151D;R224K;E276D;R292K;N294S;G104E;E117A;E117D;H134Y;R150K 56;63;63;76;100;107;107;107;118;125;132;143;167;174;174;183;194 61;70;70;81;105;116;116;116;123;130;137;148;172;181;181;188;199 NA;NAI 45;285 47;288 32636820 Enhanced Potency of a Broad H7N9-Neutralizing Antibody HNIgGA6 Through Structure-Based Design. H7N9 has also acquired some other mammalian-adapted genetic changes, including T271A, K526R, A588V, E627K, or D701N in the viral PB2, which facilitated viral replication and increased viral-induced disease severity in mammals. 2020 Frontiers in microbiology Introduction IV T271A;K526R;A588V;E627K;D701N 79;86;93;100;110 84;91;98;105;115 PB2 129 132 32636820 Enhanced Potency of a Broad H7N9-Neutralizing Antibody HNIgGA6 Through Structure-Based Design. More importantly, the S28H variant also exhibited enhanced potency in inhibiting the pulmonary virus titre and reducing lung lesions and resulted in better protection of the animals when administered to BALB/c mice. 2020 Frontiers in microbiology Introduction IV S28H 22 26 Lung lesions 120 132 32636820 Enhanced Potency of a Broad H7N9-Neutralizing Antibody HNIgGA6 Through Structure-Based Design. Neuraminidase inhibitor (NAI) resistance (R292K substitution in NA) was detected in both NA inhibitor-treated patients and a few nonhuman-derived HP-H7N9 strains. 2020 Frontiers in microbiology Introduction IV R292K 42 47 NA;NA;NAI;NA 64;89;25;0 66;91;28;13 32636820 Enhanced Potency of a Broad H7N9-Neutralizing Antibody HNIgGA6 Through Structure-Based Design. When the serine was substituted by histidine at position 28 on the light-chain complementarity-determining region 1 (LCDR1), the S28H variant presented ~10-fold higher neutralizing activity and retained the neutralizing breadth of the parent HNIgGA6. 2020 Frontiers in microbiology Introduction IV S28H;S28H 129;9 133;59 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. According to the experimental and simulation results, the binding affinity of A4 for oseltamivir- and zanamivir-resistant mutant I223R/H275Y NA is approximately 600 times stronger than its binding affinity for oseltamivir- and zanamivir-susceptible wild-type (wt) NA. 2020 Nature communications Introduction IV I223R;H275Y 129;135 134;140 NA;NA 141;264 143;266 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. Here we develop a monoclonal antibody, A4, specific to I223R/H275Y NA. 2020 Nature communications Introduction IV I223R;H275Y 55;61 60;66 67 69 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. In 2010, an isoleucine-to-arginine change at position 223 (I223R, N1 numbering) in the neuraminidase (NA) of A H1N1 virus isolated from an immunosuppressed child on prolonged oseltamivir and zanamivir therapy was reported. 2020 Nature communications Introduction IV I223R;I223R 59;12 64;57 NA;NA 102;87 104;100 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. In animal models and in vitro studies, I223R/H275Y double-mutant virus has shown high levels of resistance to oseltamivir and zanamivir, and the combination of I223R with H275Y does not compromise the replication capacity or transmissibility of the virus. 2020 Nature communications Introduction IV I223R;H275Y;I223R;H275Y 39;45;160;171 44;50;165;176 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. In clinical cases, the I223R change has been found mostly in combination with H275Y. 2020 Nature communications Introduction IV I223R;H275Y 23;78 28;83 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. In contrast to the frequently observed H275Y (N1 numbering) change, which causes selective resistance to oseltamivir, the I223R mutation confers a phenotype resistant to both oseltamivir and zanamivir. 2020 Nature communications Introduction IV H275Y;I223R 39;122 44;127 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. Only in the presence of I223R/H275Y pH1N1, color of A4-Au NPs changes from red to purple. 2020 Nature communications Introduction IV I223R;H275Y 24;30 29;35 NP 58 61 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. Second, we apply A4 antibody to the surface-enhanced Raman scattering (SERS)-based immunoassay for I223R/H275Y viruses. 2020 Nature communications Introduction IV I223R;H275Y 99;105 104;110 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. The combination of A4 antibody with SERS improves the detection limit of I223R/H275Y virus to 1.5 plaque-forming units (PFU). 2020 Nature communications Introduction IV I223R;H275Y 73;79 78;84 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. The developed LFA system can identify I223R/H275Y pH1N1 even in the mixture with wt pH1N1. 2020 Nature communications Introduction IV I223R;H275Y 38;44 43;49 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. Third, A4-based lateral flow immunoassay (LFA) system is developed for the rapid diagnosis of I223R/H275Y pH1N1. 2020 Nature communications Introduction IV I223R;H275Y 94;100 99;105 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. This difference in the binding affinity of the A4 antibody for I223R/H275Y NA and wt NA allows to develop several detection methods for antiviral multidrug-resistant influenza viruses. 2020 Nature communications Introduction IV I223R;H275Y 63;69 68;74 NA;NA 75;85 77;87 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. This double mutation (I223R/H275Y) in the NA of the 2009 pandemic H1N1 influenza virus has been reported as an antiviral multidrug-resistant virus for both zanamivir and oseltamivir. 2020 Nature communications Introduction IV I223R;H275Y 22;28 27;33 42 44 32721992 Differential Viral-Host Immune Interactions Associated with Oseltamivir-Resistant H275Y and Wild-Type H1N1 A(pdm09) Influenza Virus Pathogenicity. Among such NA substitutions, a histidine-to-tyrosine substitution at position 275 (H275Y) is one of the best-characterized and most commonly found oseltamivir-resistant (OR) mutations. 2020 Viruses Introduction IV H275Y;H275Y 83;31 88;81 11 13 32721992 Differential Viral-Host Immune Interactions Associated with Oseltamivir-Resistant H275Y and Wild-Type H1N1 A(pdm09) Influenza Virus Pathogenicity. Despite the fact that the frequency of OR in pdm09 viruses has remained low (<2%), there are indicators which suggest that pdm09 could permanently acquire the NA H275Y mutation, as happened with its predecessor, the seasonal H1N1. 2020 Viruses Introduction IV H275Y 162 167 159 161 32721992 Differential Viral-Host Immune Interactions Associated with Oseltamivir-Resistant H275Y and Wild-Type H1N1 A(pdm09) Influenza Virus Pathogenicity. However, seasonal H1N1 with the H275Y mutation emerged and expanded globally without oseltamivir selection. 2020 Viruses Introduction IV H275Y 32 37 32721992 Differential Viral-Host Immune Interactions Associated with Oseltamivir-Resistant H275Y and Wild-Type H1N1 A(pdm09) Influenza Virus Pathogenicity. Regardless, community clusters of OR pdm09 viruses containing the H275Y mutation have been reported. 2020 Viruses Introduction IV H275Y 66 71 32721992 Differential Viral-Host Immune Interactions Associated with Oseltamivir-Resistant H275Y and Wild-Type H1N1 A(pdm09) Influenza Virus Pathogenicity. Several investigations have revealed the presence of diverse "permissive" mutations (R222Q, V234M, and possibly D354G) in seasonal and pdm09 viruses that allowed the addition of H275Y without compromising viral fitness. 2020 Viruses Introduction IV R222Q;V234M;D354G;H275Y 85;92;112;178 90;97;117;183 32721992 Differential Viral-Host Immune Interactions Associated with Oseltamivir-Resistant H275Y and Wild-Type H1N1 A(pdm09) Influenza Virus Pathogenicity. The pdm09 matrix protein (MP) gene came from the Eurasian swine lineage, which contains the S31N mutation conferring resistance to adamantine antiviral therapeutics. 2020 Viruses Introduction IV S31N 92 96 M 10 16 32746754 A single N342D substitution in Influenza B Virus NA protein determines viral pathogenicity in mice. A D701N mutation in the PB2 protein led to effective viral replication and enhanced the pathogenicity of both AIVs and swine influenza virus in mammals. 2020 Emerging microbes & infections Introduction IV D701N 2 7 PB2 24 27 IAV infections 110 114 32746754 A single N342D substitution in Influenza B Virus NA protein determines viral pathogenicity in mice. A substitution from E to K at position 627 in the PB2 protein significantly increased the pathogenicity of avian influenza viruses (AIVs) in mice. 2020 Emerging microbes & infections Introduction IV E627K 20 42 PB2 50 53 32750468 Functional neuraminidase inhibitor resistance motifs in avian influenza A(H5Nx) viruses. In this study we introduced four NAI resistance-associated mutations (E119V, H274Y, R292K, N294S) into three recent H5Nx viruses containing different avian NA subtypes: N2, N6 and N8. 2020 Antiviral research Introduction IV E119V;H274Y;R292K;N294S 70;77;84;91 75;82;89;96 NA;NAI 156;33 158;36 32750468 Functional neuraminidase inhibitor resistance motifs in avian influenza A(H5Nx) viruses. There are known motifs that confer reduced susceptibility to the NAI drugs: E119V, H274Y, R292K and N294S (amino acid numbering refers to the N2 subtype), amongst others but the level of reduced susceptibility and which drug they affect are not universal amongst the influenza A virus NAs or even NA subtype. 2020 Antiviral research Introduction IV E119V;H274Y;R292K;N294S 76;83;90;100 81;88;95;105 NA;NAI;NA 297;65;285 299;68;288 32750468 Functional neuraminidase inhibitor resistance motifs in avian influenza A(H5Nx) viruses. This analysis revealed that 0.8% of H5N1 AIV sequences (N = 1716) contained a resistance motif (defined as E119A, H274Y, or N294S). 2020 Antiviral research Introduction IV E119A;H274Y;N294S 107;114;124 112;119;129 32786258 Chemical Probes for Blocking of Influenza A M2 Wild-type and S31N Channels. Additionally the previously reported IC50 for 6 in TEVC with M2 S31N is 16 muM, similar to the Kd found here, 7.5 muM. 2020 ACS chemical biology Introduction IV S31N 64 68 M2 61 63 32786258 Chemical Probes for Blocking of Influenza A M2 Wild-type and S31N Channels. Also, 3-5, which inhibit A/WSN/33 replication in cell culture at dosages similar to 1, do not effectively block proton currents through M2 S31N expressed in oocytes (Table 3). 2020 ACS chemical biology Introduction IV S31N 139 143 M2 136 138 32786258 Chemical Probes for Blocking of Influenza A M2 Wild-type and S31N Channels. Although kon is still 6-7 orders of magnitude lower than expected for unhindered diffusion-limited binding, the association rate constant is much higher than that observed for 1 in S31N, or for 2-5 in WT (Table 2). 2020 ACS chemical biology Introduction IV S31N 181 185 32786258 Chemical Probes for Blocking of Influenza A M2 Wild-type and S31N Channels. As a contrasting case, we tested 6, a known blocker of M2 S31N. 2020 ACS chemical biology Introduction IV S31N 58 62 M2 55 57 32786258 Chemical Probes for Blocking of Influenza A M2 Wild-type and S31N Channels. As found previously, 6 shows significant blocking of the S31N channel, with almost complete blocking of inward current and low percent washout. 2020 ACS chemical biology Introduction IV S31N 57 61 32786258 Chemical Probes for Blocking of Influenza A M2 Wild-type and S31N Channels. Compounds 1-4 have low micromolar or submicromolar potency, similar to amantadine or rimantadine, inhibiting the amantadine-sensitive A/WSN/33 M2 N31S (M2 WT) replication at concentations 0.09 - 1.13 muM (WT, Table 1), while 5 has a mediocre antiviral activity (8.10 muM). 2020 ACS chemical biology Introduction IV N31S 146 150 M2;M2 143;152 145;154 32786258 Chemical Probes for Blocking of Influenza A M2 Wild-type and S31N Channels. Compounds 2-4 have moderately high anti-viral efficacies (8 - 21 muM) against A/WSN/33 in MDCK cell culture (Table 1) in the face of inefficient M2 S31N block, it is clear that 2-4 can also block influenza virus by another mechanism. 2020 ACS chemical biology Introduction IV S31N 148 152 M2 145 147 32786258 Chemical Probes for Blocking of Influenza A M2 Wild-type and S31N Channels. DeGrado and Hong showed that for complexes of M2TM S31N with 6 or analogues in DPC micelles (using solution NMR combined with MD simulations), and in DMPC lipid bilayers (using solid state NMR), the adamantane moiety of the drug is bound in the pore between N31 and G34 while the aryl tail projects through the Val27 side chains. 2020 ACS chemical biology Introduction IV S31N 51 55 32786258 Chemical Probes for Blocking of Influenza A M2 Wild-type and S31N Channels. DeGrado and Wang also discovered, using solution NMR in micelles and MD simulations, that a dual channel-type inhibitor, similar to compound 1 but consisting of a 2-bromo-thiophenyl group connected with amantadine through a methylene, is oriented with the aryl head group outward in the M2TM S31N and inward in the M2TM WT pore. 2020 ACS chemical biology Introduction IV S31N 292 296 32786258 Chemical Probes for Blocking of Influenza A M2 Wild-type and S31N Channels. DeGrado and Wang discovered potent compounds acting against M2 S31N in both EP and antiviral assays. 2020 ACS chemical biology Introduction IV S31N 63 67 M2 60 62 32786258 Chemical Probes for Blocking of Influenza A M2 Wild-type and S31N Channels. EC50 values for the A/WSN/33 (M2 N31) and A/WSN/33 M2 N31S constructs represented in Table 1 can be compared and contrasted with Kd values in the last columns of Tables 2 and 3, respectively. 2020 ACS chemical biology Introduction IV N31S 54 58 M2;M2 30;51 32;53 32786258 Chemical Probes for Blocking of Influenza A M2 Wild-type and S31N Channels. For one set of seven compounds that block M2 S31N efficiently, it was previously observed that six of the compounds have kon values range from 29 to 227 M-1s-1 and koff values range from 0.3-1.5 x 103 s-1, i.e., these compounds have fast on/slow off or slow on/slow off, with the kinetics of binding being very dependent on the adamantane scaffold but also on the aryl head group. 2020 ACS chemical biology Introduction IV S31N 45 49 M2 42 44 32786258 Chemical Probes for Blocking of Influenza A M2 Wild-type and S31N Channels. Here, we used the comparable but distinctive ligands 1-6 (Scheme 1) that expand on the structural motifs in 1 and 6, as a set of useful chemical probes for exploring the molecular features affecting the energetics, orientational trajectory, kinetics of blocking of M2 WT and S31N channels, as well as alternative mechanisms of inhibition such as potential lysosomotropic behavior. 2020 ACS chemical biology Introduction IV S31N 275 279 M2 265 267 32786258 Chemical Probes for Blocking of Influenza A M2 Wild-type and S31N Channels. In conclusion, here we describe the effect of ligand's structure on binding kinetics for M2 WT and S31N channels using the synthetic aminoadamantane-CH2-aryl derivatives 1-6 as chemical probes. 2020 ACS chemical biology Introduction IV S31N 99 103 M2 89 91 32786258 Chemical Probes for Blocking of Influenza A M2 Wild-type and S31N Channels. In constrast, 2 being over 30-fold more potent in blocking M2 WT current than 1, and moderately effective in vitro against the M2 S31N bearing influenza virus strain A/WSN/33, it is strikingly impotent against M2 S31N in the EP assay of molecular function, indicating that the simple isopropyl linker eliminates potency in this M2 S31N environment (Table 3). 2020 ACS chemical biology Introduction IV S31N;S31N;S31N 130;213;331 134;217;335 M2;M2;M2;M2 59;127;210;328 61;129;212;330 32786258 Chemical Probes for Blocking of Influenza A M2 Wild-type and S31N Channels. In the M2 S31N channel (Table 3), the percent inward current blockage by compounds 2-5 is significantly reduced (compared to WT, Table 2), and also very dependent on the linker between adamantane and the aryl head group, with compound 2 showing no measurable block. 2020 ACS chemical biology Introduction IV S31N 10 14 M2 7 9 32786258 Chemical Probes for Blocking of Influenza A M2 Wild-type and S31N Channels. In this outward binding configuration, an elongation of the ligand by only one isopropyl in rimantadine 2, by a phenyl group in 3, and the expanded diamondoid substructures instead of adamantyl in 4 and 5, respectively, seems to cause an incomplete entry, according to the kinetics observed with TEVC (Tables 2, 3) which showed, as previously described, slow entrance (reduced kon constants) and fast escape rates (increased koff) for 2-5 in S31N (Table 3) or 6 in M2 WT, compared to 1-5 in WT (Table 2) and 1 or 6 with M2 S31N (Table 3). 2020 ACS chemical biology Introduction IV S31N;S31N 442;523 446;527 M2;M2 465;520 467;522 32786258 Chemical Probes for Blocking of Influenza A M2 Wild-type and S31N Channels. Indeed, perhaps the most intriguing result in this SAR on binding kinetics is the remarkably high kon (2280 M-1s-1) for 6 in the S31N, ca. 2020 ACS chemical biology Introduction IV S31N 129 133 32786258 Chemical Probes for Blocking of Influenza A M2 Wild-type and S31N Channels. Note that for 6, an inhibitor of M2 S31N but not M2 WT, the aryl head group consists of the polar isoxazole ring linked with a hydrophobic thiophenyl ring, while in 1, which blocks both M2 isoforms, it consists of the apolar 4-methoxy group attached to a 2-hydroxyl-phenyl ring. 2020 ACS chemical biology Introduction IV S31N 36 40 M2;M2;M2 33;49;186 35;51;188 32786258 Chemical Probes for Blocking of Influenza A M2 Wild-type and S31N Channels. Noteworthy, only the binding kinetics for M2 S31N channel are very dependent on the length between the adamantane moiety and the first ring of the aryl head group realized in 2 and 3, and the girth and length of the adamantane adduct realized in 4 and 5. 2020 ACS chemical biology Introduction IV S31N 45 49 M2 42 44 32786258 Chemical Probes for Blocking of Influenza A M2 Wild-type and S31N Channels. Scheme 1 shows the dual channel-type inhibitor 1 with a 2-hydroxy-4-methoxy-phenyl group, one of the simpler aryl head groups in structure, which blocks both M2 WT and M2 S31N channels, and 6 with a 3-(2-thiophenyl)-isoxazolyl group, which only blocks the M2 S31N channel. 2020 ACS chemical biology Introduction IV S31N;S31N 171;259 175;263 M2;M2;M2 158;168;256 160;170;258 32786258 Chemical Probes for Blocking of Influenza A M2 Wild-type and S31N Channels. The converged MD simulation trajectories of the M2 S31N complexes in DMPC bilayers (Figure S4), show that the ligands bind as a whole, more outwardly in the channel, compared to the M2 WT pore, in the region between V27 and G34 with the aryl adduct facing outward and projecting through the V27 cluster (Figures 1B and 1D, S1B) (see PDB ID 2LY0). 2020 ACS chemical biology Introduction IV S31N 51 55 M2;M2 48;182 50;184 32786258 Chemical Probes for Blocking of Influenza A M2 Wild-type and S31N Channels. The difference of magnitude between the anti-viral potency and the channel inhibition constant, which is more significant for M2 S31N virus growth inhibition is not understood, but may suggest additional mechanisms of anti-viral activity, plausibly a lysosomotropic effect, as observed previously by Scholtissek, Busath and Kolocouris, and Naesens and Vazquez for amantadine variants with lipophilic adducts inhibiting virus at concentrations higher than c.a. 2020 ACS chemical biology Introduction IV S31N 129 133 M2 126 128 32786258 Chemical Probes for Blocking of Influenza A M2 Wild-type and S31N Channels. The kon of 1 for M2 S31N is 124 M-1s-1 and koff is 2.6 x 10-3 s-1. 2020 ACS chemical biology Introduction IV S31N 20 24 M2 17 19 32786258 Chemical Probes for Blocking of Influenza A M2 Wild-type and S31N Channels. The M2 S31N mutant, which is currently the main epidemic strain, is a naturally occurring amantadine- and rimantadine-resistant mutation that otherwise maintains channel function nearly identical to the M2 WT, refering to the strain A/Udorn/72 commonly used in electrophysiology (EP) studies. 2020 ACS chemical biology Introduction IV S31N 7 11 M2;M2 4;203 6;205 32786258 Chemical Probes for Blocking of Influenza A M2 Wild-type and S31N Channels. The moderate potency of 1 and high potency of 6 against the amantadine-resistant virus M2 S31N found here is consistent with previous results by Wang and DeGrado. 2020 ACS chemical biology Introduction IV S31N 90 94 M2 87 89 32786258 Chemical Probes for Blocking of Influenza A M2 Wild-type and S31N Channels. The percent-washout and the slow koff are similar to those of compounds 3 and 4 (Figures S6-S8), but the kon is very high and complete (99.2%) blocking is attained, such that 6 has high potency in blocking M2 S31N, as well as in blocking cell infection for the M2 S31N virus. 2020 ACS chemical biology Introduction IV S31N;S31N 209;264 213;268 M2;M2 206;261 208;263 32786258 Chemical Probes for Blocking of Influenza A M2 Wild-type and S31N Channels. The second generation amantadine-based drugs can block M2 S31N with association/dissociation rate constants (koff/kon) that are slow off/fast on or slow off/slow on leading to favorable Kd = koff/kon values and antiviral potency.,17. 2020 ACS chemical biology Introduction IV S31N 58 62 M2 55 57 32786258 Chemical Probes for Blocking of Influenza A M2 Wild-type and S31N Channels. The vast majority of resistant viruses (95%) bear the S31N substitution in M2. 2020 ACS chemical biology Introduction IV S31N 54 58 M2 75 77 32786258 Chemical Probes for Blocking of Influenza A M2 Wild-type and S31N Channels. This outward orientation in the M2 S31N channel is opposite from the inward orientation of amantadine in the M2 WT channel. 2020 ACS chemical biology Introduction IV S31N 35 39 M2;M2 32;109 34;111 32786258 Chemical Probes for Blocking of Influenza A M2 Wild-type and S31N Channels. We applied the cytopathic effect (CPE) inhibition assay to compare the antiviral activity of 1-6 against the A/WSN/33 virus (with naturally occurring M2 N31) and the A/WSN/33 M2 N31S virus, which was generated by reverse genetics from A/WSN/33. 2020 ACS chemical biology Introduction IV N31S 178 182 M2;M2 150;175 152;177 32786258 Chemical Probes for Blocking of Influenza A M2 Wild-type and S31N Channels. We found that molecules 1-5 strongly block the M2 WT channel-mediated proton current (Tables 2 and S1) whereas 6 has almost no potency, and that 1 and 6 produce high 10-min %-block of M2 S31N. 2020 ACS chemical biology Introduction IV S31N 187 191 M2;M2 47;184 49;186 32873642 Dynamic PB2-E627K substitution of influenza H7N9 virus indicates the in vivo genetic tuning and rapid host adaptation. Evolution modes for key mammal-adaptive mutations, including PB2-E627K, were found to differ between LPM- and patient-derived samples, indicating the dynamics of the "genetic tuning" of the H7N9 virus in adapting to the mammalian host. 2020 Proc Natl Acad Sci U S A Introduction IV E627K 65 70 PB2 61 64 32873642 Dynamic PB2-E627K substitution of influenza H7N9 virus indicates the in vivo genetic tuning and rapid host adaptation. However, studies on the longitudinal dynamics of the PB2-E627K substitution of the avian-origin virus in infected patients and its influence on disease severity are lacking. 2020 Proc Natl Acad Sci U S A Introduction IV E627K 57 62 PB2 53 56 32873642 Dynamic PB2-E627K substitution of influenza H7N9 virus indicates the in vivo genetic tuning and rapid host adaptation. However, the adaptive dynamics of PB2-E627K in H7N9 infected patients and the surrounding poultry/environment under the vision of one health has not yet been investigated. 2020 Proc Natl Acad Sci U S A Introduction IV E627K 38 43 PB2 34 37 32873642 Dynamic PB2-E627K substitution of influenza H7N9 virus indicates the in vivo genetic tuning and rapid host adaptation. Mammal infection models have shown dynamic substitution of E627K occurring during acute infection with avian-origin influenza viruses (e.g., H5N1, H10N8) with the avian signature 627E. 2020 Proc Natl Acad Sci U S A Introduction IV E627K 59 64 32873642 Dynamic PB2-E627K substitution of influenza H7N9 virus indicates the in vivo genetic tuning and rapid host adaptation. The single amino acid substitution at position 627 from Glu to Lys (E627K) in PB2 of avian-origin influenza virus was first revealed to be responsible for more efficient replication of the virus in mammalian cells. 2020 Proc Natl Acad Sci U S A Introduction IV E627K;E627K 68;47 73;66 PB2 78 81 32873642 Dynamic PB2-E627K substitution of influenza H7N9 virus indicates the in vivo genetic tuning and rapid host adaptation. While the AIVs usually contain Glu (E) at position 627 of polymerase basic protein 2 (PB2), mutation to Lys (K) is a well-recognized mammalian adaptation substitution at this position. 2020 Proc Natl Acad Sci U S A Introduction IV E627E 30 55 PB2 86 89 33024040 Structure-Based Modification of an Anti-neuraminidase Human Antibody Restores Protection Efficacy against the Drifted Influenza Virus. Structure-based modification of Z2B3 (with substitution of D102R) reestablished the salt bridge in reverse and dramatically restored the binding and inhibition to the N1 with E432 and regained protection against the influenza strain containing E432 in the NA protein. 2020 mBio Introduction IV D102R 59 64 256 258 33024040 Structure-Based Modification of an Anti-neuraminidase Human Antibody Restores Protection Efficacy against the Drifted Influenza Virus. The loss of activity of Z2B3 on seasonal N1 from viruses isolated after 2013 was localized to an antigenic drift mutation, K432E, at a site previously conserved in seasonal H1N1 viruses. 2020 mBio Introduction IV K432E 123 128 33024040 Structure-Based Modification of an Anti-neuraminidase Human Antibody Restores Protection Efficacy against the Drifted Influenza Virus. We also showed that Z2B3 binds into the conserved active site of NA, that its D102 in heavy chain forms a salt bridge with K432 of NA, and that this accounts for the sensitivity of the antibody to the recent K432E substitution in N1. 2020 mBio Introduction IV K432E 208 213 NA;NA 65;131 67;133 33028722 PA Mutations Inherited during Viral Evolution Act Cooperatively To Increase Replication of Contemporary H5N1 Influenza Virus with an Expanded Host Range. In addition, we recently reported that the H9N2 virus in the Middle East (G1-A/B subclade), centered in Egypt, commonly carries the PB2-E627V, -E543D, -A655V, and -K526R mutations, which all contributed to more fit replication in human cells and mice. 2020 Journal of virology Introduction IV E627V;E543D;A655V;K526R 136;144;152;164 141;149;157;169 PB2 132 135 33028722 PA Mutations Inherited during Viral Evolution Act Cooperatively To Increase Replication of Contemporary H5N1 Influenza Virus with an Expanded Host Range. Other mammal adaptation mutations include PB2-D701N, -K526R, -Q591K, -E192K, -K702R, and -E627V. 2020 Journal of virology Introduction IV D701N;K526R;Q591K;E192K;K702R;E627V 46;54;62;70;78;90 51;59;67;75;83;95 PB2 42 45 33028722 PA Mutations Inherited during Viral Evolution Act Cooperatively To Increase Replication of Contemporary H5N1 Influenza Virus with an Expanded Host Range. The Egyptian H5N1 clade 2.2.1 strains in poultry species generally carry the PB2-E627K mutation. 2020 Journal of virology Introduction IV E627K 81 86 PB2 77 80 33028722 PA Mutations Inherited during Viral Evolution Act Cooperatively To Increase Replication of Contemporary H5N1 Influenza Virus with an Expanded Host Range. The PB2-E627K mutation has been found in several H5N1 and H7N9 viruses that have infected humans. 2020 Journal of virology Introduction IV E627K 8 13 PB2 4 7 33028722 PA Mutations Inherited during Viral Evolution Act Cooperatively To Increase Replication of Contemporary H5N1 Influenza Virus with an Expanded Host Range. The PB2-E627K substitution is the most common influenza virus human adaptation mutation and is present in most seasonal human influenza viruses except the 2009 pandemic H1N1 virus. 2020 Journal of virology Introduction IV E627K 8 13 PB2 4 7 33028722 PA Mutations Inherited during Viral Evolution Act Cooperatively To Increase Replication of Contemporary H5N1 Influenza Virus with an Expanded Host Range. These results contrasted those for viruses isolated in Asia, where representative human adaptation mutations (e.g., PB2-E627K and -K526R) were found frequently in viruses from AI virus-infected patients but not in field AI strains, with a few exceptions. 2020 Journal of virology Introduction IV E627K;K526R 120;131 125;136 PB2 116 119 33063654 Detection and discrimination of influenza B Victoria lineage deletion variant viruses by real-time RT-PCR. Sequencing analysis confirmed that these viruses have a deletion of 6 nucleotides (nt) in the haemagglutinin (HA) gene resulting in a 2 amino acid (aa) deletion at positions 162 and 163 (corresponding to nt positions 529-534). 2020 Euro surveillance Introduction IV del 162 152 177 HA;HA 110;94 112;108 33063654 Detection and discrimination of influenza B Victoria lineage deletion variant viruses by real-time RT-PCR. The V1A-3DEL viruses have since been detected in Asia, Africa, Europe and America. 2020 Euro surveillance Introduction IV V1A 4 7 33063654 Detection and discrimination of influenza B Victoria lineage deletion variant viruses by real-time RT-PCR. There are currently five genetically distinct HA genes that yield five antigenically distinct influenza B viruses that are co-circulating: B/YAM, B/VIC V1A, B/VIC V1A-2DEL and two groups of B/VIC V1A-3DEL (Figure). 2020 Euro surveillance Introduction IV V1A;V1A;V1A 152;163;196 155;166;199 HA 46 48 33063654 Detection and discrimination of influenza B Victoria lineage deletion variant viruses by real-time RT-PCR. This B Victoria lineage 2 aa deletion virus (V1A-2DEL; K162N163 deletion) has since spread and been detected worldwide. 2020 Euro surveillance Introduction IV V1A 45 48 33063654 Detection and discrimination of influenza B Victoria lineage deletion variant viruses by real-time RT-PCR. Two B/VIC lineage variants with a deletion of 3 aa (V1A-3DEL) at aa positions 162-164 (K162N163D164. 2020 Euro surveillance Introduction IV V1A 52 55 33099886 Comprehensive assessment of amino acid substitutions in the trimeric RNA polymerase complex of influenza A virus detected in clinical trials of baloxavir marboxil. 22 K229R in the PB1 subunit of influenza A viruses confers resistance to the viral RNA polymerase inhibitor favipiravir, and the fitness cost caused by this mutation can be compensated by a P653L substitution in PA that restores the fitness while maintaining favipiravir resistance. 2021 Influenza and other respiratory viruses Introduction IV K229R;P653L 4;191 9;196 PA;PB1 213;17 215;20 33099886 Comprehensive assessment of amino acid substitutions in the trimeric RNA polymerase complex of influenza A virus detected in clinical trials of baloxavir marboxil. A(H1N1)pdm09 and A(H3N2) viruses harboring PA/I38T substitution were detected in some few subjects without prior BXM treatment, suggesting the possibility of human-to-human transmission of the variant viruses. 2021 Influenza and other respiratory viruses Introduction IV I38T 47 51 33099886 Comprehensive assessment of amino acid substitutions in the trimeric RNA polymerase complex of influenza A virus detected in clinical trials of baloxavir marboxil. In addition to the I38 substitutions, E23K/G, A37T, and E199G substitutions were identified in the PA subunit that affect BXA susceptibility by less than 10-fold. 2021 Influenza and other respiratory viruses Introduction IV E23K;E23G;A37T;E199G 39;39;47;57 45;45;51;62 33099886 Comprehensive assessment of amino acid substitutions in the trimeric RNA polymerase complex of influenza A virus detected in clinical trials of baloxavir marboxil. Influenza surveillance studies conducted in Japan during the 2018-19 influenza season confirmed treatment-emergence of PA/I38T and PA/I38M variants in A(H3N2)-infected subjects. 2021 Influenza and other respiratory viruses Introduction IV I38T;I38M 123;135 127;139 33208942 Host ANP32A mediates the assembly of the influenza virus replicase. PB2 V614 is equivalent to K591 in the swine origin 2009 H1N1 pandemic influenza A virus, which retained E627 in its avian PB2 but used a Q591K adaptation to increase polymerase activity (Extended Data. 2020 Nature Introduction IV Q591K 137 142 PB2;PB2 0;122 3;125 33208942 Host ANP32A mediates the assembly of the influenza virus replicase. Such a role for the FluPol-ANP32A complex in viral genome replication is consistent with previous observations; in particular, ANP32A and the adaptive PB2 E627K mutation have been specifically linked to viral genome replication rather than transcription providing strong support for a role of the FluPol-ANP32A complex in the former process. 2020 Nature Introduction IV E627K 155 160 PB2 151 154 33270431 Colorimetric Detection of SARS-CoV-2 and Drug-Resistant pH1N1 Using CRISPR/dCas9. For the colorimetric detection of SARS-CoV-2, pH1N1, and pH1N1/H275Y, viral lysates and biotin-protospacer adjacent motif (PAM)-presenting oligonucleotide (PAMmer) were added to dCas9/gRNA-attached well plates, followed by the horseradish peroxidase (HRP)/3,3',5,5'-tetramethylbenzidine (TMB) reaction. 2020 ACS sensors Introduction IV H275Y 63 68 33270431 Colorimetric Detection of SARS-CoV-2 and Drug-Resistant pH1N1 Using CRISPR/dCas9. Herein, we report a CRISPR/dCas9 system-based viral diagnostic method and successful detection of SARS-CoV-2, pH1N1, and pH1N1/H275Y mutant viruses. 2020 ACS sensors Introduction IV H275Y 127 132 33270431 Colorimetric Detection of SARS-CoV-2 and Drug-Resistant pH1N1 Using CRISPR/dCas9. Using this method, SARS-CoV-2, pH1N1, and pH1N1/H275Y viruses were successfully detected with the naked eye. 2020 ACS sensors Introduction IV H275Y 48 53 33424035 The Effect of I155T, K156Q, K156E and N186K Mutations in Hemagglutinin on the Virulence and Reproduction of Influenza A/H5N1 Viruses. For elucidating the effects of the I155T, K156Q, K156E+V138A and N186K substitutions in HA on phenotypic traits by reverse genetics techniques, we have obtained VNH5N1-PR8/CDC-RG (H5N1) vaccine strain mutants characterized by substitutions in HA. 2020 Molecular biology Introduction IV I155T;K156Q;K156E;V138A;N186K 35;42;49;55;65 40;47;54;60;70 HA;HA 88;243 90;245 33436086 N-linked glycosylation at site 158 of the HA protein of H5N6 highly pathogenic avian influenza virus is important for viral biological properties and host immune responses. Compared to the surface Hemagglutinin (HA) glycoprotein of the precursor H5N1 HPAIV from clade 2.3.4, the vast majority of H5N6 HPAIV and human H5N6 viruses bear a T160A (H3 numbering) mutation in the HA protein, resulting in deletion of the N-linked glycosylation site at position 158. 2021 Veterinary research Introduction IV T160A 164 169 HA;HA;HA 39;201;24 41;203;37 33436086 N-linked glycosylation at site 158 of the HA protein of H5N6 highly pathogenic avian influenza virus is important for viral biological properties and host immune responses. In addition to these H5 viruses, T160A that leads to the loss of glycosylation in the receptor-binding region of HA has been found in human H7N9 viruses. 2021 Veterinary research Introduction IV T160A 33 38 HA 113 115 33436086 N-linked glycosylation at site 158 of the HA protein of H5N6 highly pathogenic avian influenza virus is important for viral biological properties and host immune responses. Our recent study showed that lack of glycosylation at position 158 of the HA protein due to the T160A mutation affects the dual receptor binding of clade 2.3.4.4 H5NX subtype viruses. 2021 Veterinary research Introduction IV T160A 96 101 HA 74 76 33568453 Identification and Characterization of Novel Antibody Epitopes on the N2 Neuraminidase. The mutations E119V, R292K, and N294S have been shown to confer oseltamivir resistance in N2 containing viruses. 2021 mSphere Introduction IV E119V;R292K;N294S 14;21;32 19;26;37 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. Furthermore, the replication and respiratory droplet transmission of the PB1 K612R mutant of a 2009 pandemic H1N1 virus in ferrets was reduced compared with the wild-type virus, which created a stress condition that drove the R612K reversion mutation in inoculated and exposed ferrets. 2021 PLoS pathogens Introduction IV K612R;R612K 77;226 82;231 PB1 73 76 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. Importantly, a SUMOylation-deficient PB1 K612R mutation significantly attenuated the virulence of H1N1, H5N1 and H7N9 viruses in mice. 2021 PLoS pathogens Introduction IV K612R 41 46 PB1 37 40 33647314 The active form of the influenza cap-snatching endonuclease inhibitor baloxavir marboxil is a tight binding inhibitor. In a recent trial, I38T/M/F substitutions appeared in 9.7% of patients receiving BXM. 2021 The Journal of biological chemistry Introduction IV I38T;I38M;I38F 19;19;19 27;27;27 33647314 The active form of the influenza cap-snatching endonuclease inhibitor baloxavir marboxil is a tight binding inhibitor. Mutant viruses are associated with up to 50-fold increases in EC50 values with I38T showing the most significant effect. 2021 The Journal of biological chemistry Introduction IV I38T 79 83 33647314 The active form of the influenza cap-snatching endonuclease inhibitor baloxavir marboxil is a tight binding inhibitor. The biochemical data demonstrate that BXA can be classified as a tight binding inhibitor and that the I38T mutation diminishes these properties. 2021 The Journal of biological chemistry Introduction IV I38T 102 106 33647314 The active form of the influenza cap-snatching endonuclease inhibitor baloxavir marboxil is a tight binding inhibitor. The I38T mutation reduces van der Waals interactions between the hydrophobic area of BXA and its binding pocket. 2021 The Journal of biological chemistry Introduction IV I38T 4 8 33673017 Structural and Thermodynamic Analysis of the Resistance Development to Pimodivir (VX-787), the Clinical Inhibitor of Cap Binding to PB2 Subunit of Influenza A Polymerase. According to the yet unpublished data, this strain is naturally resistant to pimodivir and mutation H357N conferred approximately 100-fold increase in EC50. 2021 Molecules (Basel, Switzerland) Introduction IV H357N 100 105 33673017 Structural and Thermodynamic Analysis of the Resistance Development to Pimodivir (VX-787), the Clinical Inhibitor of Cap Binding to PB2 Subunit of Influenza A Polymerase. Almost every mutated variant occurred only once, but the M431I mutation was found in four volunteer-samples. 2021 Molecules (Basel, Switzerland) Introduction IV M431I 57 62 33673017 Structural and Thermodynamic Analysis of the Resistance Development to Pimodivir (VX-787), the Clinical Inhibitor of Cap Binding to PB2 Subunit of Influenza A Polymerase. In addition to these, Centers for Disease Control and Prevention detected resistant polymorphic mutation PB2-H357N in A/turkey/Minnesota/833/80 (H4N2) while testing nonseasonal influenza viruses from their collection. 2021 Molecules (Basel, Switzerland) Introduction IV H357N 109 114 PB2 105 108 33673017 Structural and Thermodynamic Analysis of the Resistance Development to Pimodivir (VX-787), the Clinical Inhibitor of Cap Binding to PB2 Subunit of Influenza A Polymerase. In preclinical studies, six mutated variants resistant to pimodivir were found-Q306H, S324I, S324N, S324R, F404Y and N541T. 2021 Molecules (Basel, Switzerland) Introduction IV Q306H;S324I;S324N;S324R;F404Y;N541T 79;86;93;100;107;117 84;91;98;105;112;122 33673017 Structural and Thermodynamic Analysis of the Resistance Development to Pimodivir (VX-787), the Clinical Inhibitor of Cap Binding to PB2 Subunit of Influenza A Polymerase. Mutation F404Y did not severely disrupt the viral growth and retained near the wild-type polymerase activity. 2021 Molecules (Basel, Switzerland) Introduction IV F404Y 9 14 33673017 Structural and Thermodynamic Analysis of the Resistance Development to Pimodivir (VX-787), the Clinical Inhibitor of Cap Binding to PB2 Subunit of Influenza A Polymerase. Mutation H357N increased polymerase activity and showed enhanced pathogenic phenotype. 2021 Molecules (Basel, Switzerland) Introduction IV H357N 9 14 33673017 Structural and Thermodynamic Analysis of the Resistance Development to Pimodivir (VX-787), the Clinical Inhibitor of Cap Binding to PB2 Subunit of Influenza A Polymerase. Mutations F404Y and M431I were selected under drug pressure of pimodivir during clinical studies, and mutation H357N was identified as rare polymorphic. 2021 Molecules (Basel, Switzerland) Introduction IV F404Y;M431I;H357N 10;20;111 15;25;116 33673017 Structural and Thermodynamic Analysis of the Resistance Development to Pimodivir (VX-787), the Clinical Inhibitor of Cap Binding to PB2 Subunit of Influenza A Polymerase. The examination of M431I substitution revealed a 12.5-fold reduction in replication compared to the wild-type virus. 2021 Molecules (Basel, Switzerland) Introduction IV M431I 19 24 33673017 Structural and Thermodynamic Analysis of the Resistance Development to Pimodivir (VX-787), the Clinical Inhibitor of Cap Binding to PB2 Subunit of Influenza A Polymerase. The most frequently present variant was PB2-F404Y, though all of the mutant variants found within preclinical studies are rare in nature. 2021 Molecules (Basel, Switzerland) Introduction IV F404Y 44 49 PB2 40 43 33673017 Structural and Thermodynamic Analysis of the Resistance Development to Pimodivir (VX-787), the Clinical Inhibitor of Cap Binding to PB2 Subunit of Influenza A Polymerase. We have crystallized proteins of PB2 wild-type (PB2-WT) and selected mutated forms PB2-H357N, PB2-F404Y and PB2-M431I in complex with pimodivir and obtained four high resolution structures. 2021 Molecules (Basel, Switzerland) Introduction IV H357N;F404Y;M431I 87;98;112 92;103;117 PB2;PB2;PB2;PB2;PB2 33;48;83;94;108 36;51;86;97;111 33679636 Improved in vitro Efficacy of Baloxavir Marboxil Against Influenza A Virus Infection by Combination Treatment With the MEK Inhibitor ATR-002. The PA-I38T substitution strongly reduced PA susceptibility to BXA. 2021 Frontiers in microbiology Introduction IV I38T 7 11 PA;PA 4;42 6;44 33782012 Discovery of a Novel Respiratory Syncytial Virus Replication Inhibitor. This compound targets L polymerase, as shown by the identification of a single point mutation in the L polymerase (Y1631H) in a YM-53403-resistant virus. 2021 Antimicrobial agents and chemotherapy Introduction IV Y1631H 115 121 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. Co-circulation of viruses with both D222G and D222N mutations was observed in 41% of cases with the mutations (with the frequency of each mutation being more than 1%, and ranging from 3.7 to 93.9% in individual samples). 2021 PloS one Introduction IV D222G;D222N 36;46 41;51 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. D222G/N mutations affect receptor specificity and lead to higher affinity to alpha-2,3-type sialic acid receptors, which are predominant in the lower respiratory tract. 2021 PloS one Introduction IV D222G;D222N 0;0 7;7 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. D222G/N mutations occur at the HA receptor binding site and affect receptor specificity due to altering virus affinity to alpha-2,6-type and alpha-2,3-type sialic acid receptors. 2021 PloS one Introduction IV D222G;D222N 0;0 7;7 HA 31 33 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. During the four epidemic seasons in Russia from 2015-2019, D222G/N mutations were observed in up to 32-57% of fatal cases, and the HA 222D/G polymorphism in A(H1N1)pdm09 was observed in 30-60% of fatal and severe influenza cases in other studies in Russia, Germany and Italy. 2021 PloS one Introduction IV D222G;D222N 59;59 66;66 HA 131 133 Influenza 206 222 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. It was shown that viruses with D222G/N mutations may not be detected in the upper respiratory tract in cases of severe and fatal influenza but may appear and be selected for in the lower respiratory tract. 2021 PloS one Introduction IV D222G;D222N 31;31 38;38 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. The D222G mutation has been identified in the 1918 H1N1 flu, the so-called Spanish flu. 2021 PloS one Introduction IV D222G 4 9 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. The D222G mutation was identified in the pre-pandemic H1N1 flu that was circulating until 2009. 2021 PloS one Introduction IV D222G 4 9 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. The D222G/N mutation that so quickly appeared in the virus may have been one of the first determinants of the virulence in the HA gene in the A(H1N1)pdm09. 2021 PloS one Introduction IV D222N;D222G 4;4 11;11 HA 127 129 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. The goal of this study was to investigate the presence of D222G/N mutations and other polymorphic variants in A(H1N1)pdm09 viruses by using a targeted NGS approach with a focus on the study of fatal influenza cases in Russia in the epidemic season 2018-2019. 2021 PloS one Introduction IV D222G;D222N 58;58 65;65 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. The low occurrence of mutations in circulation and less severe cases of influenza may be explained by reduced tropism of the D222G/N variants of the virus to cells in the upper respiratory tract. 2021 PloS one Introduction IV D222G;D222N 125;125 132;132 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. Variants of the virus with D222G/N mutations may already exist in the general pool of circulating viruses, or may appear during the process of virus replication in an infected organism. 2021 PloS one Introduction IV D222G;D222N 27;27 34;34 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. We observed the D222G/N mutations (proportion of virus variants with the mutations ranged from 1 to 98% in samples) only in fatal cases, with the proportion of cases with mutations being close to 60% and predominant detection of the mutations in the lower respiratory tract. 2021 PloS one Introduction IV D222G;D222N 16;16 23;23 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. A pH1N1 variant containing the mutation HA1-Y17H in the stalk region was shown to be activated at pH 6.0. 2021 PloS one Introduction IV Y17H 44 48 HA1 40 43 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. As it was unknown how IAV infection may alter extracellular and intracellular pH, in this study we aimed to determine the kinetics of respiratory pH and host responses in pH1N1-infected mice using wildtype virus (HA activation pH 5.5) and a destabilized variant (HA1-Y17H, pH 6.0) to understand virus-host interactions related to respiratory acidification. 2021 PloS one Introduction IV Y17H 267 271 HA;HA1 213;263 215;266 IAV infections 22 35 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. Although the P653L fully compensated for the cost to polymerase activity and virus replication in vitro, it is unknown whether the resistant virus would replicate in vivo or transmit whilst maintaining resistance. 2021 PLoS pathogens Introduction IV P653L 13 18 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. Interestingly, K229 is a conserved residue in the F-motif of the polymerase and favipiravir resistant chikungunya virus containing the corresponding mutation to K229R in influenza, has been shown to reproduce less efficiently in mosquitos which led to slower transmission. 2021 PLoS pathogens Introduction IV K229R 161 166 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. K229R has not been found in any natural pH1N1(2009) isolates, which is unsurprising as favipiravir has not been widely used to treat influenza cases. 2021 PLoS pathogens Introduction IV K229R 0 5 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. K229R provided resistance to favipiravir at a cost to polymerase activity which was compensated by P653L. 2021 PLoS pathogens Introduction IV K229R;P653L 0;99 5;104 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. The P653L mutation has also not been found in any natural pH1N1(2009) isolates, which may suggest that it does not confer a fitness advantage in vivo. 2021 PLoS pathogens Introduction IV P653L 4 9 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. We showed that two mutations, K229R in PB1 and P653L in PA, were needed to evolve resistance. 2021 PLoS pathogens Introduction IV K229R;P653L 30;47 35;52 PA;PB1 56;39 58;42 34068322 Dual R108K and G189D Mutations in the NS1 Protein of A/H1N1 Influenza Virus Counteract Host Innate Immune Responses. Here, we sequenced a seasonal 2009 H1N1 influenza virus isolated in 2018 and confirmed the presence of mutations I123V and N205S in important functional sites. 2021 Viruses Introduction IV I123V;N205S 113;123 118;128 34068322 Dual R108K and G189D Mutations in the NS1 Protein of A/H1N1 Influenza Virus Counteract Host Innate Immune Responses. However, the NS1 protein of the 2009 pandemic H1N1 IAV (pH1N1) virus lost the ability to bind CPSF30, so it cannot block expression of host genes, although studies show that this ability can be restored by introducing amino acid changes R108K, E125D, and G189D. 2021 Viruses Introduction IV R108K;E125D;G189D 237;244;255 242;249;260 NS1 13 16 34068322 Dual R108K and G189D Mutations in the NS1 Protein of A/H1N1 Influenza Virus Counteract Host Innate Immune Responses. Since 2009, multiple amino acid sense mutations in the NS1 protein of pandemic H1N1 influenza virus have been reported, including the I123V and N205S mutations. 2021 Viruses Introduction IV I123V;N205S 134;144 139;149 NS1 55 58 34068322 Dual R108K and G189D Mutations in the NS1 Protein of A/H1N1 Influenza Virus Counteract Host Innate Immune Responses. To increase our understanding of the antagonistic mechanisms underlying interactions between influenza virus and host innate immunity, we used a reverse genetics approach to introduce a double mutation (R108K/G189D) into the NS1 protein of the seasonal 2009 H1N1 IAV, rescued the mutant virus, and analyzed its biological characteristics. 2021 Viruses Introduction IV R108K;G189D 203;209 208;214 NS1 225 228 34068322 Dual R108K and G189D Mutations in the NS1 Protein of A/H1N1 Influenza Virus Counteract Host Innate Immune Responses. We found that the mutated NS1 protein harboring R108K/G189D exhibited systematic and selective inhibition of cytokine responses beyond the complexity of host-influenza NS1 protein interactions. 2021 Viruses Introduction IV R108K;G189D 48;54 53;59 NS1;NS1 26;168 29;171 34131512 Identification of H3N2 NA and PB1-F2 genetic variants and their association with disease symptoms during the 2014-15 influenza season. We found that viruses encoding amino acid (AA) changes in the NA (to introduce a glycosylation site near the sialidase pocket) and PB1-F2 (mutation H75P) were associated with altered proteins correlated with a higher incidence of coughing and shortness of breath. 2021 Virus evolution Introduction IV H75P 148 152 NA;PB1F2 62;131 64;137 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. As E276 is located at the OTV binding site, a conformational change due to H274Y mutation disrupts favorable interactions between OTV and the binding site residues in NA, resulting in reduced binding affinity of OTV to NA and thus conferring drug resistance to influenza virus. 2021 PeerJ Introduction IV H274Y 75 80 NA;NA 167;219 169;221 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. For example, used MD simulations to show that the H274Y mutation in NA causes the bulkier side chain of tyrosine to rotate the carboxylate group in E276 by 115 , thereby reducing hydrophobicity and pocket size; because of changes in the binding site, the pentyloxy side chain of OTV rotates by 125 , decreasing the binding free energy by approximately 5 kcal mol-1. 2021 PeerJ Introduction IV H274Y 50 55 68 70 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. Here, we successfully clarified the correlation between the OTV binding site of N1 NA and its H274Y mutation site that confers drug resistance in influenza virus. 2021 PeerJ Introduction IV H274Y 94 99 83 85 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. In this study, we investigated the changes in residue-residue and residue-ligand interactions associated with the H274Y mutation in the complex of OTV bound to influenza virus NA using dRIN analysis. 2021 PeerJ Introduction IV H274Y 114 119 176 178 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. It is unclear whether the decrease in the binding affinity of OTV to NA is influenced by a correlation between the binding site and its H274Y mutation site. 2021 PeerJ Introduction IV H274Y 136 141 69 71 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. Overall, the mechanism by which drug resistance conferring H274Y mutation in NA of influenza virus affects the dynamic behavior of residue interactions remains unclear. 2021 PeerJ Introduction IV H274Y 59 64 77 79 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. Recently,used RIN analysis to obtain a molecular perspective of drug resistance in influenza viruses with H274Y mutation in NA; however, they only examined the changes in residue interactions with the mutation based on static RINs constructed from representative average structures obtained via MD simulations (). 2021 PeerJ Introduction IV H274Y 106 111 124 126 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. The crystal structure of the complex formed by OTV and H274Y mutant NA exhibits a subtle conformational change, compared to that formed by OTV and WT NA, wherein the carboxylate side chain of the E276 adjacent to residue 274 is shifted to the OTV binding site. 2021 PeerJ Introduction IV H274Y 55 60 NA;NA 68;150 70;152 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. These OTV-resistant strains are characterized by a His-to-Tyr mutation at NA residue 274 (H274Y), located near but not in the OTV binding site of NA. 2021 PeerJ Introduction IV H274Y 90 95 NA;NA 74;146 76;148 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. This study provides novel theoretical insights into the molecular mechanism underlying OTV resistance in influenza virus caused by H274Y mutation in NA. 2021 PeerJ Introduction IV H274Y 131 136 149 151 34164347 Risk of Environmental Exposure to H7N9 Influenza Virus via Airborne and Surface Routes in a Live Poultry Market in Hebei, China. reported that mutations in PB2 (E627K), NA (R294K) and PA (V100A) were significantly correlated with increased mortality, while other mutations in HA (N276D) and PB2 (N559T) were distinctly correlated with mild cases. 2021 Frontiers in cellular and infection microbiology Introduction IV E627K;R294K;V100A;N276D;N559T 32;44;59;151;167 37;49;64;156;172 HA;NA;PA;PB2;PB2 147;40;55;27;162 149;42;57;30;165 34253060 In Vivo Therapy with M2e-Specific IgG Selects for an Influenza A Virus Mutant with Delayed Matrix Protein 2 Expression. Although only the M2e sequence was thoroughly investigated in this study, 6 synonymous and 2 nonsynonymous mutations (A127T and V228L) were also detected in M1. 2021 mBio Introduction IV A127T;V228L 118;128 123;133 M1 157 159 34253060 In Vivo Therapy with M2e-Specific IgG Selects for an Influenza A Virus Mutant with Delayed Matrix Protein 2 Expression. In one instance, resistance was acquired by a glutamic acid to glycine residue mutation at position 8 in M2e (and M1), which resulted in loss of anti-M2e IgG binding. 2021 mBio Introduction IV E8G 46 101 M1 114 116 34358217 Mutation E48K in PB1 Polymerase Subunit Improves Stability of a Candidate Live Attenuated Influenza B Virus Vaccine. Although the PB2 K267S mutation could not be rescued and the PB1 K391E mutation was unstable, the remaining mutations in PB1 (E580G, S660A, HA tag) were stably maintained for at least 20 passages in Madin-Darby canine kidney (MDCK) cells or 15 passages in specific pathogen-free (SPF) eggs. 2021 Vaccines Introduction IV K267S;K391E;E580G;S660A 17;65;126;133 22;70;131;138 HA;PB1;PB1;PB2 140;61;121;13 142;64;124;16 34358217 Mutation E48K in PB1 Polymerase Subunit Improves Stability of a Candidate Live Attenuated Influenza B Virus Vaccine. During stability tests, it was noted that the B/Bris PB1att that was serially passaged in MDCK cells retained the K391E mutation but showed an additional mutation in PB1, E48K. 2021 Vaccines Introduction IV K391E;E48K 114;171 119;175 PB1 166 169 34358217 Mutation E48K in PB1 Polymerase Subunit Improves Stability of a Candidate Live Attenuated Influenza B Virus Vaccine. Following a similar approach, we previously generated a novel IBV att strain by introducing analogous mutations in the PB1 (K391E, E580G, and S660A with C-terminus HA tag) and PB2 (K267S) genes of the B/Brisbane/60/2008 (B/Bris) strain from the B/Vic lineage. 2021 Vaccines Introduction IV K391E;E580G;S660A;K267S 124;131;142;181 129;136;147;186 HA;PB1;PB2 164;119;176 166;122;179 34358217 Mutation E48K in PB1 Polymerase Subunit Improves Stability of a Candidate Live Attenuated Influenza B Virus Vaccine. In contrast, a strain containing the PB1 K391E (but not the E48K mutation, B/Bris PB1 3M) in the B/Bris PB1att background quickly acquired the E48K mutation after serial passage in eggs, further highlighting its importance as a compensatory mutation. 2021 Vaccines Introduction IV K391E;E48K;E48K 41;60;143 46;64;147 PB1;PB1 37;82 40;85 34358217 Mutation E48K in PB1 Polymerase Subunit Improves Stability of a Candidate Live Attenuated Influenza B Virus Vaccine. Previous work in our laboratory demonstrated that incorporation of three specific mutations (K391E, D581G, A661T) in addition to an HA epitope tag (HA tag) at the C-terminus of the PB1 protein segment and a single mutation (N265S) into the PB2 protein segment of IAVs results in a temperature sensitive (ts) phenotype in vitro, attenuates (att) IAVs in vivo, and provides effective protection against aggressive virus challenge in a variety of mammalian and avian animal models. 2021 Vaccines Introduction IV K391E;D581G;A661T;N265S 93;100;107;224 98;105;112;229 HA;HA;PB1;PB2 132;148;181;240 134;150;184;243 34358217 Mutation E48K in PB1 Polymerase Subunit Improves Stability of a Candidate Live Attenuated Influenza B Virus Vaccine. To test this effect, we generated a new strain (B/Bris PB1att 4M) by incorporating E48K and K391E along with E580G and S660A mutations into the PB1 segment. 2021 Vaccines Introduction IV E48K;K391E;E580G;S660A 83;92;109;119 87;97;114;124 PB1 144 147 34358217 Mutation E48K in PB1 Polymerase Subunit Improves Stability of a Candidate Live Attenuated Influenza B Virus Vaccine. We hypothesized that E48K serves as a compensatory mutation to stabilize the K391E mutation while maintaining the attenuated phenotype. 2021 Vaccines Introduction IV E48K;K391E 21;77 25;82 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. A recent study also reported an IAV RdRp with R229K point mutation in PB1, which exhibited elevated fidelity and resistance to favipiravir. 2021 Nucleic acids research Introduction IV R229K 46 51 PB1 70 73 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. For example, we previously discovered the high fidelity V43I mutation in PB1 subunits of IAV RdRp with a slower rate for incorporating GTP analogs. 2021 Nucleic acids research Introduction IV V43I 56 60 PB1 73 76 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. Intriguingly, we found that the higher fidelity of the K235R mutant is mainly contributed by the significantly higher activity for the cognate NTP but reduced activity for the noncognate NTP. 2021 Nucleic acids research Introduction IV K235R 55 60 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. K235R mutant drastically increased the incorporation rate (kpol) while only slightly altered the dissociation constant Kd,app for the cognate NTP. 2021 Nucleic acids research Introduction IV K235R 0 5 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. Previously published researches have demonstrated that the K65R, K159R and K155A mutations significantly reduced the polymerase activity. 2021 Nucleic acids research Introduction IV K65R;K159R;K155A 59;65;75 63;70;80 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. Similarly, R174 in Poliovirus (PV) RdRp and R158 in Hepatitis C virus (HCV) RdRp structurally corresponds to R239 in IAV RdRp, and their mutations such as R174K and R158A also significantly reduced polymerase activity. 2021 Nucleic acids research Introduction IV R174K;R158A 155;165 160;170 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. Surprisingly, we discovered for the first time that a polymerase with the K235R mutation could exert both increased efficiency for cognate NTP incorporation and enhanced fidelity of transcription. 2021 Nucleic acids research Introduction IV K235R 74 79 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. The K235R mutant RdRp serves as a solid foundation for the rational design of live attenuated vaccines by manipulating transcriptional fidelity via structure-based strategies. 2021 Nucleic acids research Introduction IV K235R 4 9 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. We also conducted all-atom molecular dynamics (MD) simulations to provide an atomic explanation for the higher incorporation rate of K235R mutant RdRp being due to a shorter distance to the triphosphate moiety. 2021 Nucleic acids research Introduction IV K235R 133 138 17055070 H5N1 Oseltamivir-resistance detection by real-time PCR using two high sensitivity labeled TaqMan probes. MGB TaqMan probes were chosen from the region covering the drug resistant area (H274Y) and designed to be specific for both wild type and mutant. 2007 Journal of virological methods Method IV H274Y 80 85 17055070 H5N1 Oseltamivir-resistance detection by real-time PCR using two high sensitivity labeled TaqMan probes. Oligonucleotides designed for H274Y mutagenesis. 2007 Journal of virological methods Method IV H274Y 30 35 17055070 H5N1 Oseltamivir-resistance detection by real-time PCR using two high sensitivity labeled TaqMan probes. The series of H274Y mutations were sequenced and used as controls. 2007 Journal of virological methods Method IV H274Y 14 19 17922571 A single mutation in the PB1-F2 of H5N1 (HK/97) and 1918 influenza A viruses contributes to increased virulence. To generate pPolI vectors encoding the N66S PB1-F2 mutants, the pPolI vectors encoding the A/HK/483/97 PB1 or A/Brevig Mission/18 PB1 were subjected to site-directed mutagenesis using the Stratagene Quick-Change mutagenesis kit (Stratagene, http://www.stratagene.com/). 2007 PLoS pathogens Method IV N66S 39 43 PB1;PB1;PB1F2 103;130;44 106;133;50 18325270 Mutations in influenza A virus (H5N1) and possible limited spread, Turkey, 2006. All chicken and human isolates from the second epidemic had a unique mutation (I42T) in the M2 region. 2008 Emerging infectious diseases Method IV I42T 79 83 M2 92 94 18325270 Mutations in influenza A virus (H5N1) and possible limited spread, Turkey, 2006. DQ323672) and contained a unique mutation (S133A) near receptor binding residue GVSSAC at positions 134 through 139. 2008 Emerging infectious diseases Method IV S133A 43 48 18325270 Mutations in influenza A virus (H5N1) and possible limited spread, Turkey, 2006. Enhanced pathogenic potential of all avian and human influenza virus isolates from the second outbreak was shown by mutation E627K in the PB2 region. 2008 Emerging infectious diseases Method IV E627K 125 130 PB2 138 141 18325270 Mutations in influenza A virus (H5N1) and possible limited spread, Turkey, 2006. In addition, unique amino acid changes found only in human isolates were Q447L in FK and Q447L, R46K, and N556K in MAK. 2008 Emerging infectious diseases Method IV Q447L;Q447L;R46K;N556K 73;89;96;106 78;94;100;111 18325270 Mutations in influenza A virus (H5N1) and possible limited spread, Turkey, 2006. MAK contained mutations D158N and S227N in the HA region. 2008 Emerging infectious diseases Method IV D158N;S227N 24;34 29;39 HA 47 49 18325270 Mutations in influenza A virus (H5N1) and possible limited spread, Turkey, 2006. These 2 mutations are important because D158N results in a potential glycosylation site and S227N enhances affinity for human receptors. 2008 Emerging infectious diseases Method IV D158N;S227N 40;92 45;97 18601954 Treatment of influenza A (H1N1) virus infections in mice and ferrets with cyanovirin-N. The Asp225Gly mutation was introduced in the HA gene encoding the HA1 subunit by PCR based site-directed mutagenesis. 2008 Antiviral research Method IV D225G 4 13 HA;HA1 45;66 47;69 18601954 Treatment of influenza A (H1N1) virus infections in mice and ferrets with cyanovirin-N. The recombinant virus was designated influenza A/WSN/33 HAnc-Asp225Gly (H1N1). 2008 Antiviral research Method IV D225G;H225G;A225G;N225G;C225G 61;61;61;61;61 70;70;70;70;70 18601954 Treatment of influenza A (H1N1) virus infections in mice and ferrets with cyanovirin-N. They were infected intranasally (i.n.) with approximately 1 x 103 cell culture infectious doses (CCID50) of influenza A/WSN/33 HAnc-Asp225Gly (H1N1) virus per mouse in a 50-mul inoculum volume. 2008 Antiviral research Method IV D225G;H225G;A225G;N225G;C225G 132;132;132;132;132 141;141;141;141;141 18769709 Host determinant residue lysine 627 lies on the surface of a discrete, folded domain of influenza virus polymerase PB2 subunit. For the very high resolution native 627-domain and K627E structures individual atomic anisotropic B-factors were refined. 2008 PLoS pathogens Method IV K627E 51 56 18769709 Host determinant residue lysine 627 lies on the surface of a discrete, folded domain of influenza virus polymerase PB2 subunit. The mutation K627E in the 538-693 protein was made by PCR mutagenesis. 2008 PLoS pathogens Method IV K627E 13 18 18769709 Host determinant residue lysine 627 lies on the surface of a discrete, folded domain of influenza virus polymerase PB2 subunit. The structure of the K627E mutant was obtained by refinement. 2008 PLoS pathogens Method IV K627E 21 26 19008377 The human H5N1 influenza A virus polymerase complex is active in vitro over a broad range of temperatures, in contrast to the WSN complex, and this property can be attributed to the PB2 subunit. The E627K mutation was introduced by site-directed mutagenesis (Quick-Change mutagenesis kit, Stratagene). 2008 The Journal of general virology Method IV E627K 4 9 19014974 Aurintricarboxylic acid inhibits influenza virus neuraminidase. Although the His is not exactly located at 274 in the NAWT(WSN) or NAWT(H5N1), the His to Phe point mutation was referred to as H274Y in this study because "H274Y" has been utilized in the literature to designate this specific amino acid change responsible for Tamiflu resistance. 2009 Antiviral research Method IV H274Y;H274Y 157;128 162;133 19014974 Aurintricarboxylic acid inhibits influenza virus neuraminidase. Recombinant baculoviruses, i.e., Bac-NAWT(WSN), Bac-NAH274Y(WSN), Bac-NAWT(H5N1), Bac-NAH274Y(H5N1), were generated to express the wild-type and H274Y mutants of NA originating from influenza A/WSN/33 (H1N1) and NIBRG-14 (H5N1). 2009 Antiviral research Method IV H274Y 145 150 NA;NA;NA 52;86;162 54;88;164 19014974 Aurintricarboxylic acid inhibits influenza virus neuraminidase. VN H274Y-F (5'-AAT TAT GCC TAT GAG GAA TGC TCC TGT TAT-3'). 2009 Antiviral research Method IV H274Y 3 8 19014974 Aurintricarboxylic acid inhibits influenza virus neuraminidase. VN H274Y-R (5'-CTC ATA GGC ATA ATT AGG ATC CAA TTC-3'). 2009 Antiviral research Method IV H274Y 3 8 19014974 Aurintricarboxylic acid inhibits influenza virus neuraminidase. WSN H274Y-F (5'-AAT TCT TAC TAC GAG GAA TGT TCC TGT TAC-3'). 2009 Antiviral research Method IV H274Y 4 9 19014974 Aurintricarboxylic acid inhibits influenza virus neuraminidase. WSN H274Y-R (5'-CTC GTA GTA AGA ATT AGG TGC ATT CAA CTC-3'). 2009 Antiviral research Method IV H274Y 4 9 19249874 Recognition of mannosylated ligands and influenza A virus by human surfactant protein D: contributions of an extended site and residue 343. Data were collected at beamline X8C at the National Synchrotron Light Source, Brookhaven National Lab, and processed using DENZO and SCALEPACK. 2009 Biochemistry Method IV X8C 32 35 19249874 Recognition of mannosylated ligands and influenza A virus by human surfactant protein D: contributions of an extended site and residue 343. In particular, we performed site directed substitutions for arginine 343 within the CRD, as defined by numbering of the full length protein: valine (R343V), alanine (R343A), and lysine (R343K). 2009 Biochemistry Method IV R343V;R343A;R343K 149;166;186 154;171;191 19249874 Recognition of mannosylated ligands and influenza A virus by human surfactant protein D: contributions of an extended site and residue 343. R343V crystals belong to the same space group with a similar unit cell as the wild type protein. 2009 Biochemistry Method IV R343V 0 5 19331731 Oseltamivir-resistant influenza virus A (H1N1), Europe, 2007-08 season. Genetic analysis of virus isolates or clinical specimens was performed by using cycle-sequencing or pyrosequencing the NA gene, targeting the H275Y amino acid substitution in the N1 NA. 2009 Emerging infectious diseases Method IV H275Y 142 147 NA;NA 119;182 121;184 19394063 The origin and global emergence of adamantane resistant A/H3N2 influenza viruses. Independent introductions of the S31N replacement were inferred from clade positions on the M1/2 phylogeny and the location and dates of sampling. 2009 Virology Method IV S31N 33 37 M1 92 94 19394063 The origin and global emergence of adamantane resistant A/H3N2 influenza viruses. The occurrence of resistance to adamantane antiviral drugs was identified through a visual screening for the S31N amino acid replacement in the M2 protein using the Se-Al program. 2009 Virology Method IV S31N 109 113 M2 144 146 19394063 The origin and global emergence of adamantane resistant A/H3N2 influenza viruses. To study the emergence of adamantane resistance in a broader global context, an additional 20 A/H3N2 influenza virus isolates exhibiting the S31N adamantane resistance mutation (and for which HA1 sequences were also available) were identified, and M1/2 and HA1 sequence data was downloaded from GenBank (Bao et al. 2009 Virology Method IV S31N 141 145 HA1;HA1;M1 192;257;248 195;260;250 19436701 Avian Influenza virus glycoproteins restrict virus replication and spread through human airway epithelium at temperatures of the proximal airways. Mutant viruses were generated in either the A/Victoria/3/75 (H3N2) or A/PR/8/34 (H1N1) genetic background as follows: 1) Vic 627PB2; A/Victoria/3/75 containing a lysine to glutamic acid amino acid substitution at position 627; 2) Vic-226-228HA; A/Victoria/3/75 containing two amino acid substitutions in the HA gene (L226Q, S228G) that confer an avian-like receptor binding preference; 3) Vic+Chick N1; A/Victoria/3/75 in which segment 6 containing the endogenous N2 NA gene was exchanged for the N1 NA gene from avian isolate A/Chick/Italy/1347/99; 4) Vic-226-228HA+Chick N1; A/Victoria/3/75 containing both L226Q and S228G mutations and the avian N1; 5) PR8+Vic HA/NA; A/PR/8/34 in which the endogenous H1 and N1 were replaced with the H3 and N2 from A/Victoria/3/75 and 6) PR8+Chick HA/NA (RD3); A/PR/8/34 in which the endogenous H1 and N1 were replaced with the H7 and N1 from A/Chick/Italy/1347/99. 2009 PLoS pathogens Method IV L226Q;S228G;L226Q;S228G;K627E 317;324;609;619;162 322;329;614;624;225 HA;HA;HA;NA;NA;NA;NA 308;664;786;467;500;667;789 310;666;788;469;502;669;791 19454348 Influenza A virus NS1 targets the ubiquitin ligase TRIM25 to evade recognition by the host viral RNA sensor RIG-I. The A/Puerto Rico/8/1934 mutant virus with NS1 E96A/E97A mutations was rescued as described previously. 2009 Cell host & microbe Method IV E96A;E97A 47;52 51;56 NS1 43 46 19454348 Influenza A virus NS1 targets the ubiquitin ligase TRIM25 to evade recognition by the host viral RNA sensor RIG-I. The E9697A-rev primer contained two point mutations (A313C and A316C) which resulted in the substitutions Glu96Ala and Glu97Ala. 2009 Cell host & microbe Method IV E9697A;A313C;A316C;E96A;E97A 4;53;63;106;119 10;58;68;114;127 19454348 Influenza A virus NS1 targets the ubiquitin ligase TRIM25 to evade recognition by the host viral RNA sensor RIG-I. The parental A/Puerto Rico/8/1934 virus, the mutant viruses encoding NS1 R38A/K41A and NS1 E96A/E97A, A/Texas/36/1991 (H1N1), A/New Caledonia/20/1999 (H1N1), A/Wyoming/3/2003 (H3N2), A/Panama/2007/1999 (H3N2), and NDV-GFP were propagated in 8-day old, specific pathogen-free embryonated eggs (Charles River Laboratories, North Franklin, CT). 2009 Cell host & microbe Method IV K41A;R38A;E96A;E97A 78;73;91;96 82;77;95;100 NS1;NS1 69;87 72;90 19454348 Influenza A virus NS1 targets the ubiquitin ligase TRIM25 to evade recognition by the host viral RNA sensor RIG-I. The rescue plasmid pDZ-PR8 (NS1 E96A/E97A) was cloned by PCR mutagenesis of the A/Puerto Rico/8/1934 NS segment with the primer pair (respective to cRNA): 3' NC-Ambi G (5'-GATCGCTCTTCTGGGAGCGAAAGCAGG-3') and E9697A-rev (5'-CGCGTTACCTAACTGACATGACTCTTGCGGCAATGTCAAGGGACTGGTC-3'). 2009 Cell host & microbe Method IV E9697A;E96A;E97A 208;32;37 214;36;41 NS;NS1 101;28 103;31 19454348 Influenza A virus NS1 targets the ubiquitin ligase TRIM25 to evade recognition by the host viral RNA sensor RIG-I. Total cell lysates were prepared from A549 cells infected with WT, E96A/E97A, or R38A/K41A viruses by lysing cells in 50 mM HEPES, pH 7.5, 1% Nonidet P-40, 0.25% sodium deoxycholate, 150 mM sodium chloride, and 10% glycerol. 2009 Cell host & microbe Method IV E96A;E97A;R38A;K41A 67;72;81;86 71;76;85;90 19857993 Evaluation of a rapid molecular algorithm for detection of pandemic influenza A (H1N1) 2009 virus and screening for a key oseltamivir resistance (H275Y) substitution in neuraminidase. At position 823 of pJET1.2-NA-H275Y, the cytosine was replaced by a thymine, resulting in the mutant sequence. 2010 Journal of clinical virology Method IV H275Y 30 35 27 29 19857993 Evaluation of a rapid molecular algorithm for detection of pandemic influenza A (H1N1) 2009 virus and screening for a key oseltamivir resistance (H275Y) substitution in neuraminidase. For the evaluation of the primers and probes for the H275Y discrimination assay, two plasmids pJET1.2-NA-H275H and pJET1.2-NA-H275Y were constructed containing neuraminidase regions 797-836 of influenza virus strain A/NL/602/2009(v). 2010 Journal of clinical virology Method IV H275Y;H275H;H275Y 53;105;126 58;110;131 NA;NA;NA 102;123;160 104;125;173 19857993 Evaluation of a rapid molecular algorithm for detection of pandemic influenza A (H1N1) 2009 virus and screening for a key oseltamivir resistance (H275Y) substitution in neuraminidase. H275Y discrimination RT-PCR. 2010 Journal of clinical virology Method IV H275Y 0 5 19857993 Evaluation of a rapid molecular algorithm for detection of pandemic influenza A (H1N1) 2009 virus and screening for a key oseltamivir resistance (H275Y) substitution in neuraminidase. The H275Y discrimination assay compromises 20 pmol for forward and reverse primer and 5 pmol for both probes and the thermal cycling profile was similar except for the elongation temperature which was 60 C instead of 62 C. 2010 Journal of clinical virology Method IV H275Y 4 9 19857993 Evaluation of a rapid molecular algorithm for detection of pandemic influenza A (H1N1) 2009 virus and screening for a key oseltamivir resistance (H275Y) substitution in neuraminidase. The primers and probes for the H275Y discrimination assay were designed around nucleotide position 823 of the neuraminidase gene. 2010 Journal of clinical virology Method IV H275Y 31 36 110 123 19857993 Evaluation of a rapid molecular algorithm for detection of pandemic influenza A (H1N1) 2009 virus and screening for a key oseltamivir resistance (H275Y) substitution in neuraminidase. To obtain a pandemic influenza A/H1N1 neuraminidase target with a H275Y substitution in the neuraminidase, the influenza virus A/NL/602/2009 (Genbank accession number CY039528 for neuraminidase gene) was rescued as described previously. 2010 Journal of clinical virology Method IV H275Y 66 71 NA;NA;NA 38;92;180 51;105;193 19893747 Novel pandemic influenza A(H1N1) viruses are potently inhibited by DAS181, a sialidase fusion protein. The seasonal A/Hawaii/31/2007 (H1N1) and closely related A/Hawaii/21/2007 (H274Y) (H1N1) virus isolates, and the 2009 pandemic A(H1N1) virus isolates A/California/04/2009, A/Mexico/4604/2009, and A/Mexico/4108/2009 were obtained from Dr. 2009 PloS one Method IV H274Y 75 80 19905033 Design and pharmacological characterization of inhibitors of amantadine-resistant mutants of the M2 ion channel of influenza A virus. Confluent monolayers of MDCK cells were incubated with the wt Udorn virus (100 plaque forming units (p.f.u.) per well) and V27A/L38F mutant virus (1000 and 100 p.f.u. 2009 Biochemistry Method IV V27A;L38F 123;128 127;132 19905033 Design and pharmacological characterization of inhibitors of amantadine-resistant mutants of the M2 ion channel of influenza A virus. WT and mutant virus (V27A/L38F) were generated by using reverse genetics from cDNAs essentially as described previously. 2009 Biochemistry Method IV V27A;L38F 21;26 25;30 19958488 Prediction of avian influenza A binding preference to human receptor using conformational analysis of receptor bound to hemagglutinin. One of the mutated Sing-97 strains (Q222L/G224S) is known to bind Siaalpha(2,6)Gal stronger, suggesting that these mutations could be important for changing the receptor preference from avian to human. 2009 BMC genomics Method IV Q222L;G224S 36;42 41;47 19958488 Prediction of avian influenza A binding preference to human receptor using conformational analysis of receptor bound to hemagglutinin. The first set comprised four Kan-1 HA variants each with single mutations M226T, K189G, K218S, and L190P obtained as quasi-species from the source where Kan-1 was found. 2009 BMC genomics Method IV M226T;K189G;K218S;L190P 74;81;88;99 79;86;93;104 HA 35 37 19958488 Prediction of avian influenza A binding preference to human receptor using conformational analysis of receptor bound to hemagglutinin. The second set contained three mutated Puerto-34 HA variants, Q222L, G224S, and Q222L/G224S (H5 numbering). 2009 BMC genomics Method IV Q222L;G224S;Q222L;G224S 62;69;80;86 67;74;85;91 HA 49 51 19995550 X-ray structures of NS1 effector domain mutants. Both crystals of the W187A and W187Y mutant NS1-ED were grown in the same condition at 277 K using the sitting-drop method. 2010 Archives of biochemistry and biophysics Method IV W187A;W187Y 21;31 26;36 NS1 44 47 19995550 X-ray structures of NS1 effector domain mutants. Primer sequences for W187A mutant were CATCGGAGGACTTGAAGCGAATGATAACACAGTTC and GAACTGTGTTATCATTCGCTTCAAGTCCTCCGATG; primer sequences for W187Y mutant were CATCGGAGGACTTGAATATAATGATAACACAGTTC and GAACTGTGTTATCATTATATTCAAGTCCTCCGATG. 2010 Archives of biochemistry and biophysics Method IV W187A;W187Y 21;137 26;142 20303563 Substitution of lysine at 627 position in PB2 protein does not change virulence of the 2009 pandemic H1N1 virus in mice. QuikChange II Site-Directed Mutagenesis Kit (Stratagene) was used for generation of E627K mutations in PB2 gene. 2010 Virology Method IV E627K 85 90 PB2 104 107 20303563 Substitution of lysine at 627 position in PB2 protein does not change virulence of the 2009 pandemic H1N1 virus in mice. The reverse genetics-derived virus with all wild-type gene segments of CA04 was designated as CA04-RG-E while that with a single E627K substitution in PB2 gene as CA04-RG-K. 2010 Virology Method IV E627K 129 134 PB2 151 154 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. Two animals inoculated with WT, E119A, or N294S viruses were euthanized by intracardiac injection of Euthanasia V solution on day 4 post-inoculation, and tissue samples (~0.5 g each) were collected from lungs (4 lobes tested separately), nasal turbinate, trachea, spleen, liver, and small intestine. 2010 PLoS pathogens Method IV E119A;N294S 32;42 37;47 20591072 Increasing antiviral activity of surfactant protein d trimers by introducing residues from bovine serum collectins: dissociation of mannan-binding and antiviral activity. Using the wild type hSP-D-NCRD and R343V mutant we not found evidence of aggregation on storage of the proteins. 2010 Scandinavian journal of immunology Method IV R343V 35 40 20661429 Oseltamivir-resistant pandemic A/H1N1 virus is as virulent as its wild-type counterpart in mice and ferrets. Anesthetized mice were challenged by intranasal inoculation of 5x105 PFUs in 50 microl virus diluent (Minimal Essential Media (MEM), 0.3% Bovine Serum Albumin (BSA), penicillin/streptomycin) of the WT or H274Y mutant influenza virus isolate. 2010 PLoS pathogens Method IV H274Y 204 209 20661429 Oseltamivir-resistant pandemic A/H1N1 virus is as virulent as its wild-type counterpart in mice and ferrets. Five male ferrets (900-1500 g) (Triple F Farms, Sayre, PA) were lightly anesthetized by isoflurane and received by intranasal instillation 250 microl (125 microl/nare) of PBS containing 4.5log TCID50/ml of pH1N1 virus with the H274Y NA mutation. 2010 PLoS pathogens Method IV H274Y 227 232 NA;PA 233;55 235;57 20661429 Oseltamivir-resistant pandemic A/H1N1 virus is as virulent as its wild-type counterpart in mice and ferrets. Groups of five male ferrets (900-1500 g) (Triple F Farms, Sayre, PA) were lightly anesthetized by isoflurane and received by intranasal instillation 250 microl (125 microl/nare) of PBS containing 4.5log TCID50/ml of pH1N1 viruses with or without the H274Y NA mutation. 2010 PLoS pathogens Method IV H274Y 250 255 NA;PA 256;65 258;67 20661429 Oseltamivir-resistant pandemic A/H1N1 virus is as virulent as its wild-type counterpart in mice and ferrets. Kawaoka, University of Wisconsin, WI) were infected at a multiplicity of infection (MOI) of 0.001 with pandemic or seasonal A/H1N1 viruses (A/Brisbane/59/2007) containing or not the H274Y NA mutation. 2010 PLoS pathogens Method IV H274Y 182 187 188 190 20661429 Oseltamivir-resistant pandemic A/H1N1 virus is as virulent as its wild-type counterpart in mice and ferrets. The pLLBA plasmid containing the NA segment was used in PCR-mediated site-directed mutagenesis kit (Stratagene, La Jolla, CA) for the introduction of the H274Y mutation. 2010 PLoS pathogens Method IV H274Y 154 159 33 35 20689744 The PB2-E627K mutation attenuates viruses containing the 2009 H1N1 influenza pandemic polymerase. The PB2-E627K mutation attenuates viruses containing the 2009 H1N1 influenza pandemic polymerase. 2010 mBio Method IV E627K 8 13 PB2 4 7 20833142 Solution NMR structure of the V27A drug resistant mutant of influenza A M2 channel. Structure determination of the V27A mutant. 2010 Biochemical and biophysical research communications Method IV V27A 31 35 20833142 Solution NMR structure of the V27A drug resistant mutant of influenza A M2 channel. The M218-60 structure was obtained by refining a homology model derived from the WT18-60 structure against V27A NMR restraints (including 948 intra- and 60 inter-subunit NOE-derived distance restraints). 2010 Biochemical and biophysical research communications Method IV V27A 107 111 20833142 Solution NMR structure of the V27A drug resistant mutant of influenza A M2 channel. The structure of the V27A amantadine-resistant mutant has been deposited to the Protein Data Bank with PDB accession code 2KWX. 2010 Biochemical and biophysical research communications Method IV V27A 21 25 20836794 Oseltamivir-resistant influenza A 2009 H1N1 virus in immunocompromised patients. The CDC protocol was used for RT-PCR and pyrosequencing to detect the H275Y mutation of 2009 H1N1, 6 except biotinylated amplicons were analyzed using the allelic quantification (AQ) module (PyroMark Q24 AQ software; Qiagen) with a dispensation order of GATCGACTATG. 2010 Influenza and other respiratory viruses Method IV H275Y 70 75 20920297 Characterization of an H3N2 triple reassortant influenza virus with a mutation at the receptor binding domain (D190A) that occurred upon virus transmission from turkeys to pigs. In addition, we generated a virus with a mutation at residue 627 of PB2 gene (Glu627Lys) that has been shown to affect replication and transmission of influenza viruses in different species. 2010 Virology journal Method IV E627K 78 87 PB2 68 71 20970464 Structure-based design of NS2 mutants for attenuated influenza A virus vaccines. To construct pCAGGS plasmids for the expression of NS2/NEP wild-type and mutants E67S/E74S and E67S/E74S/E75S, MDCK cells were infected with recombinant viruses and harvested at 37 C for 5 h. 2011 Virus research Method IV E67S;E74S;E67S;E74S;E75S 81;86;95;100;105 85;90;99;104;109 NEP;NS2 55;51 58;54 21172786 Pandemic H1N1 2009 influenza virus with the H275Y oseltamivir resistance neuraminidase mutation shows a small compromise in enzyme activity and viral fitness. The sialidase enzyme properties of both wild-type NA and the mutant H275Y NA were assessed using a fluorescent substrate [2'-(4-methylumbelliferyl)-alpha-d-N-acetylneuraminic acid (MuNANA)] as previously described. 2011 The Journal of antimicrobial chemotherapy Method IV H275Y 68 73 NA;NA 50;74 52;76 21226922 Influenza A virus NS1 gene mutations F103L and M106I increase replication and virulence. The NS cDNA of A/HK/1/68 wt was inserted into pLLB vector by ligation independent cloning and PCR directed mutagenesis was used to introduce point mutations (F103L, M106I, and F103L + M106I) into the HK-wt NS gene. 2011 Virology journal Method IV F103L;M106I;F103L;M106I 158;165;176;184 163;170;181;189 NS;NS 4;206 6;208 21249207 Nationwide molecular surveillance of pandemic H1N1 influenza A virus genomes: Canada, 2009. Phylogenetic trees were inferred using the neighbour-joining distance method, with genetic distances calculated using Kimura's two-parameter model (K2P and bootstrapping test) in MEGA 4.0. 2011 PloS one Method IV K2P 148 151 21306576 Influenza and other respiratory viruses in three Central American countries. The following primers were used for the amplification of H1 influenza A viruses: H1F-6 (5'-AAGCAGGGGAAAATAAAA-3') and H1R-1193 (5'-GTAATCCCGTTAATGGCA3'); for H3 influenza A viruses: H3F-7 (5'-ACTATCATTGCTTTGAGC-3') and H3R-1184 (5'-ATGGCTGCTTGAGTGCTT-3'); for influenza B viruses: BHAF-36 (5'-GAAGGCAATAATTGTACT-3') and BHAR-1140 (5'-ACCAGCAATAGCTCCGAA-3'). 2011 Influenza and other respiratory viruses Method IV H1F;H1R;H3F;H3R 81;118;182;219 84;121;185;222 21349290 Development of a real-time RT-PCR assay for detection of resistance to oseltamivir in influenza A pandemic (H1N1) 2009 virus using single nucleotide polymorphism probes. Analytical sensitivity of the real-time RT-PCR was determined by testing serial dilutions of quantified in vitro transcribed RNA for both the H275 and H275Y alleles in eight replicates. 2011 Journal of virological methods Method IV H275Y 151 156 21349290 Development of a real-time RT-PCR assay for detection of resistance to oseltamivir in influenza A pandemic (H1N1) 2009 virus using single nucleotide polymorphism probes. Full length amplification of the NA gene with the H275 and H275Y alleles from pandemic (H1N1) 2009 virus was performed using primers described previously. 2011 Journal of virological methods Method IV H275Y 59 64 33 35 21349290 Development of a real-time RT-PCR assay for detection of resistance to oseltamivir in influenza A pandemic (H1N1) 2009 virus using single nucleotide polymorphism probes. The inter-assay and intra-assay variability was assessed using three clinical samples each with the H275 and H275Y alleles at three levels of viral load as determined by the cycle threshold (Ct) values. 2011 Journal of virological methods Method IV H275Y 109 114 21349290 Development of a real-time RT-PCR assay for detection of resistance to oseltamivir in influenza A pandemic (H1N1) 2009 virus using single nucleotide polymorphism probes. The probe specific for detection of the H275 allele that has been reported to lead to oseltamivir sensitivity (SOIV_Osel_SEN) was labelled with 6-carboxyfluorescein (FAM); and a probe specific for the H275Y allele that has been reported to lead to oseltamivir resistance (SOIV_Osel_RES) was labelled with VIC at the 5' end; both probes had a non-fluorescent black hole quencher (BHQ) at the 3' end. 2011 Journal of virological methods Method IV H275Y 201 206 21349290 Development of a real-time RT-PCR assay for detection of resistance to oseltamivir in influenza A pandemic (H1N1) 2009 virus using single nucleotide polymorphism probes. Three hundred and six clinical samples that tested positive for pandemic (H1N1) 2009 virus from immuno-compromised, intensive care unit cases, patients who had received oseltamivir treatment, had a travel history and from the community were selected for sequencing of the partial NA gene including the H275Y (C823T) region. 2011 Journal of virological methods Method IV H275Y;C823T 302;309 307;314 280 282 21407805 A single base-pair change in 2009 H1N1 hemagglutinin increases human receptor affinity and leads to efficient airborne viral transmission in ferrets. The mutation Ile219->Lys was created by altering the position 219 codon from ATA to AAA using Stratagene QuickChange site-directed mutagenesis kit and pDZ-Cal04-HA as template. 2011 PloS one Method IV I219K 13 24 HA 161 163 21455300 Assessing the in vitro fitness of an oseltamivir-resistant seasonal A/H1N1 influenza strain using a mathematical model. Multiple-cycle viral yield assays for the A/Brisbane/59/2007 WT and H275Y mutant were performed with . 2011 PloS one Method IV H275Y 68 73 21455300 Assessing the in vitro fitness of an oseltamivir-resistant seasonal A/H1N1 influenza strain using a mathematical model. The A/Brisbane/59/2007-like (H1N1) strains used were the oseltamivir-susceptible A/Quebec/15230/08 (WT) and the oseltamivir-resistant A/Quebec/15349/08 (NA-H275Y mutant). 2011 PloS one Method IV H275Y 156 161 153 155 21466220 Exploring the size limit of templates for inhibitors of the M2 ion channel of influenza A virus. A/M2 S31N and A/M2 V27A mutants were generated by QuikChange site-directed mutagenesis kit (Agilent Technologies). 2011 Journal of medicinal chemistry Method IV S31N;V27A 5;19 9;23 M2;M2 2;16 4;18 21504394 Oseltamivir-resistant influenza viruses get by with a little help from permissive mutations. used a computational method to predict mutations that could potentially compensate for the H274Y mutation in NA. 2011 Expert review of anti-infective therapy Method IV H274Y 91 96 109 111 21744829 Molecular dynamics simulation directed rational design of inhibitors targeting drug-resistant mutants of influenza A virus M2. 1,2-dimyristoyl-sn-glycero-3-phosphoch-line (DMPC) was used to reconstitute A27, V28 and G34 labeled A/M2(22-46)-V27A by detergent dialysis as described before. 2011 Journal of the American Chemical Society Method IV V27A 113 117 M2 103 105 21744829 Molecular dynamics simulation directed rational design of inhibitors targeting drug-resistant mutants of influenza A virus M2. A/M2(22-46)-V27A peptide with A27, V28 and G34 selectively 15N and 13C labeled were manually synthesized using Fmoc chemistry at elevated temperature (75 C for both coupling and deprotection) in a semi-automated Quest synthesizer using Rink Amide Chemmatrix resin (Matrix Innovation Inc, Canada). 2011 Journal of the American Chemical Society Method IV V27A 12 16 M2 2 4 21821881 Conservation of a crystallographic interface suggests a role for beta-sheet augmentation in influenza virus NS1 multifunctionality. The construction of the pRSFDuet plasmid expressing a His6-tagged version of PR8 NS1 ED (W187A) (residues 73-230) has been described previously (Kerry et al., 2011). 2011 Acta crystallographica. Section F, Structural biology and crystallization communications Method IV W187A 89 94 NS1 81 84 21821881 Conservation of a crystallographic interface suggests a role for beta-sheet augmentation in influenza virus NS1 multifunctionality. The previously obtained structure of PR8 NS1 ED (W187A) (PDB entry 3o9q; Kerry et al., 2011) was used for molecular replacement using Phaser (McCoy et al., 2007) in the PHENIX package (Adams et al., 2002). 2011 Acta crystallographica. Section F, Structural biology and crystallization communications Method IV W187A 49 54 NS1 41 44 21821881 Conservation of a crystallographic interface suggests a role for beta-sheet augmentation in influenza virus NS1 multifunctionality. The purified PR8 NS1 ED (W187A) was pooled and concentrated to 8.5 mg ml-1 using a 5000 MWCO Vivaspin column (Sartorius). 2011 Acta crystallographica. Section F, Structural biology and crystallization communications Method IV W187A 25 30 NS1 17 20 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. Dose dependent direct binding of CA/04 D222G virus by glycan array. 2011 PloS one Method IV D222G 39 44 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. Ocular infection of mice with CA/04 and D222G viruses was performed as previously described using 105 PFU in a 5 microl volume. 2011 PloS one Method IV D222G 40 45 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. with 105 PFU of CA/04 or D222G virus in a 50 microl volume as previously described. 2011 PloS one Method IV D222G 25 30 21980293 Multidrug resistant 2009 A/H1N1 influenza clinical isolate with a neuraminidase I223R mutation retains its virulence and transmissibility in ferrets. On day 0, 4 or 2 female ferrets were housed individually in transmission cages (30 cm x 30 cm x 55 cm, W x H x L) and inoculated intranasally with 106 TCID50 of NL/602, NL/2631-R223, recNL/602 or recNL/602-I223R respectively, divided over both nostrils (2x250 microl). 2011 PLoS pathogens Method IV I223R 206 211 21980293 Multidrug resistant 2009 A/H1N1 influenza clinical isolate with a neuraminidase I223R mutation retains its virulence and transmissibility in ferrets. The I223R mutation was introduced in the NA gene of NL/602 using QuickChange multi site-directed mutagenesis kit (Stratagene, Leusden, The Netherlands) resulting in recombinant viruses recNL/602-I223R. 2011 PLoS pathogens Method IV I223R;I223R 4;195 9;200 41 43 22138712 The 2008-2009 H1N1 influenza virus exhibits reduced susceptibility to antibody inhibition: Implications for the prevalence of oseltamivir resistant variant viruses. A Y275H substitution was introduced into the NA segment using the QuikChange II site-directed mutagenesis kit (Agilent Technologies, Santa Clara, CA, USA) according to the manufacturer's instructions. 2012 Antiviral research Method IV Y275H 2 7 45 47 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. Groups of 4 seronegative (900-1500 g) male ferrets (Triple F Farms, Sayre, PA) were lightly anesthetised by isoflurane and received an intranasal instillation of 1.25x105 PFUs of the recombinant Bris07-like WT, H275Y or H275Y/Q222R variants. 2011 PLoS pathogens Method IV H275Y;H275Y;Q222R 211;220;226 216;225;231 PA 75 77 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. Sequence analysis confirmed the presence of histidine (H), glutamine (Q), methionine (M) and asparagine (N) residues at residues 275, 222, 234 and 344 (N1 numbering), respectively, of the NA protein. 2011 PLoS pathogens Method IV N275N 92 133 M;NA 86;188 87;190 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. The amount of NA activity on the cell surface and plaque sizes of the recombinants were compared to those of the WT virus and/or the H275Y mutant by the use of unpaired two-tailed t tests. 2011 PLoS pathogens Method IV H275Y 133 138 14 16 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. The pLLBA plasmid containing the NA gene was used for the introduction of the H275Y mutation using appropriate primers and the QuikChangeTM Site-Directed Mutagenesis kit (Stratagene, La Jolla, CA). 2011 PLoS pathogens Method IV H275Y 78 83 33 35 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. The recombinant wild-type (WT) and H275Y, H275Y/Q222R, H275Y/M234V and H275Y/N344D mutant viruses were subsequently sequenced and titrated by standard plaque assays in ST6Gal1-MDCK cells. 2011 PLoS pathogens Method IV H275Y;Q222R;H275Y;M234V;H275Y;H275Y;N344D 35;48;42;61;55;71;77 40;53;47;66;60;76;82 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. The resulting pLLB-NA275Y mutant plasmid was then used for reverting potential compensatory mutations (Q222R, M234V or N344D) as described above. 2011 PLoS pathogens Method IV Q222R;M234V;N344D 103;110;119 108;115;124 19 21 22230322 Highly pathogenic avian influenza virus H5N1 controls type I IFN induction in chicken macrophage HD-11 cells: a polygenic trait that involves NS1 and the polymerase complex. The alanine to valine substitution at the amino acid position 144 of the Yama NS1 protein was introduced with PCR-based site-directed mutagenesis using the 5' phosphorylated oligonucleotides Y-NS1mutAV-R (5'-TCCTTCTTCTGTGAAAACTCTAAG-3') and Y-NS1mutAV-F (5'-GCAATCGTGGGAGAAATCTCAC-3'). 2012 Virology journal Method IV A144V 4 65 NS1 78 81 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. Five trajectories of 10 ns each were produced for the wt NP and R361A monomers, respectively. 2012 PloS one Method IV R361A 64 69 NP 57 59 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. Protein expression & purification of NP, R361A, the wt-E80A-E81A, wt-R204A-R208A and R361A-E80A-E81A, R361A-R204A-R208A mutants. 2012 PloS one Method IV R361A;E80A;E81A;R204A;R208A;R361A;E80A;E81A;R361A;R204A;R208A 41;55;60;69;75;85;91;96;102;108;114 46;59;64;74;80;90;95;100;107;113;119 NP 37 39 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. The Escherichia coli BL21 (DE3) cells carrying the plasmids were induced 4 hours by isopropyl-beta-D-thiogalactopyranoside (IPTG) at 37 C (NP) or 12 h at 28 C (R361A, the double mutant wt-E80A-E81A and the triple mutant R361A-E80A-E81A) and collected by centrifugation. 2012 PloS one Method IV R361A;E81A;E80A;R361A;E81A;E80A 160;193;188;220;231;226 165;197;192;225;235;230 NP 139 141 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. The experiments were performed at a concentration of 15 and 20 microM of NP or its R416A and R361A mutants using an XLA70 ultracentrifuge (Beckman Coulter, Palo Alto, USA), equipped with an ANTi-60 rotor. 2012 PloS one Method IV R416A;R361A 83;93 88;98 NP 73 75 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. The MD simulations of the NP, R361A monomers and NP trimer were carried out using the program NAMD with the CHARMM27 force field. 2012 PloS one Method IV R361A 30 35 NP;NP 26;49 28;51 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. The monomer and trimer solvated systems were electrostatically neutralized by adding 16 (15 for the R361A mutant) and 48 chloride ions, respectively, at points of minimal electrostatic energy. 2012 PloS one Method IV R361A 100 105 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. The NP and mutant proteins were injected at concentrations between 4 and 1000 nM (NP), and 20 and 5000 nM (E361A and wt-E80A-E81A and R361A-E80A-E81A). 2012 PloS one Method IV E361A;E81A;E80A;E81A;R361A;E80A 107;125;120;145;134;140 112;129;124;149;139;144 NP;NP 4;82 6;84 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. The NP and R361A monomers and NP trimer were centered in a box of pre-equilibrated water molecules with edge of 120 A and 155 A, respectively. 2012 PloS one Method IV R361A 11 16 NP;NP 4;30 6;32 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. The R361A single mutation and R361A-E80A-E81A, R361A-R204A-R208A triple mutations were introduced by using Pfu DNA polymerase with the QuickChange site-directed mutagenesis kit (Stratagene). 2012 PloS one Method IV R361A;R361A;E81A;E80A;R361A;R204A;R208A 4;30;41;36;47;53;59 9;35;45;40;52;58;64 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. The R416A, R361A, the double mutants wt-E80A-E81A, wt-R204A-R208A and the mutants triple R361A-E80A-E81A, R361A-R204A-R208A were purified at 300 mM NaCl. 2012 PloS one Method IV R416A;R361A;E81A;E80A;R204A;R208A;R361A;E81A;E80A;R361A;R204A;R208A 4;11;45;40;54;60;89;100;95;106;112;118 9;16;49;44;59;65;94;104;99;111;117;123 22438920 Mutations in polymerase genes enhanced the virulence of 2009 pandemic H1N1 influenza virus in mice. Mutations(PA-A36T and PB2-H357N) were introduced into the plasmids to generate mutant segments using a QuikChange Site-Directed Mutagenesis Kit (Stratagene, La Jolla, CA, USA), following the manufacturer's instructions. 2012 PloS one Method IV A36T;H357N 13;26 17;31 PA;PB2 10;22 12;25 22438920 Mutations in polymerase genes enhanced the virulence of 2009 pandemic H1N1 influenza virus in mice. Recombinant viruses SC_WT and SC_PA-A36T/ SC_PB2-H357N were generated by reverse-genetics method as described as previously. 2012 PloS one Method IV A36T;H357N 36;49 40;54 22449422 Engineering temperature sensitive live attenuated influenza vaccines from emerging viruses. PB1-Mut3 contains three mutations in PB1 (K391E, D581G, A661T). 2012 Vaccine Method IV K391E;D581G;A661T 42;49;56 47;54;61 PB1;PB1 0;37 3;40 22449422 Engineering temperature sensitive live attenuated influenza vaccines from emerging viruses. PB2-Mut1 contains an N265S mutation in PB2. 2012 Vaccine Method IV N265S 21 26 PB2;PB2 0;39 3;42 22449422 Engineering temperature sensitive live attenuated influenza vaccines from emerging viruses. PB2-Mut4 contains four mutations (P112S, N265S, N556D, Y658H). 2012 Vaccine Method IV P112S;N265S;N556D;Y658H 34;41;48;55 39;46;53;60 PB2 0 3 22564359 Effect of receptor specificity of A/Hong Kong/1/68 (H3N2) influenza virus variants on replication and transmission in pigs. R2-HK differs from R1-HK solely by the L226Q/S228G mutations in the HA, which lead to a switch in receptor specificity from preferential binding of Siaalpha2,6-galactose (R1-HK) to preferential recognition of Siaalpha2,3-galactose (R2-HK). 2013 Influenza and other respiratory viruses Method IV L226Q;S228G 39;45 44;50 HA 68 70 22809692 Both influenza hemagglutinin and polymerase acidic genes are important for delayed pandemic 2009 H1N1 virus clearance in the ferret model. Four reverse genetics (rg) viruses were generated by DNA transfection as described previously: (rg)-A/Tennessee/560/09 (TN/09), rg-A/Tennessee/560/09-PA L295P mutant (PAmut), rg-A/Tennessee/560/09-HA K154Q mutant (HAmut, H1 numbering), and rg-A/Tennessee/560/09-HA K154Q mutant and PAL295P mutant (HAmutPAmut). 2012 Virology Method IV L295P;K154Q;K154Q 153;200;265 158;205;270 HA;HA;PA;PA 197;262;150;282 199;264;152;284 22809862 Treatment of oseltamivir-resistant influenza A (H1N1) virus infections in mice with antiviral agents. Influenza A/HK-H275Y virus was provided by Kwok-Yung Yuen, The University of Hong Kong, Hong Kong Special Administrative Region, People's Republic of China. 2012 Antiviral research Method IV H275Y 15 20 22809862 Treatment of oseltamivir-resistant influenza A (H1N1) virus infections in mice with antiviral agents. Influenza A/MS-H275Y was obtained from the Neuraminidase Inhibitor Surveillance Network (Melbourne, Australia). 2012 Antiviral research Method IV H275Y 15 20 43 56 22809862 Treatment of oseltamivir-resistant influenza A (H1N1) virus infections in mice with antiviral agents. The mouse-adapted viruses were partially sequenced in the neuraminidase gene and found to contain the H275Y mutation, as did the parental viruses. 2012 Antiviral research Method IV H275Y 102 107 58 71 22952752 Molecular evolutionary analysis of pH1N1 2009 influenza virus in Reunion Island, South West Indian Ocean region: a cohort study. M1E, "M2E" and "M3E" refer to the first, second or third sampling performed at days 0, 3 or 8 post ILI report, respectively. 2012 PloS one Method IV M1E;M2E;M3E 0;7;17 4;11;21 22952752 Molecular evolutionary analysis of pH1N1 2009 influenza virus in Reunion Island, South West Indian Ocean region: a cohort study. For households that were sampled twice because of the recurrence of ILI alerts, pH1N1 viruses identified in the three successive sampling events were designated as "M4E" "M5E" or "M6E". 2012 PloS one Method IV M4E;M5E;M6E 164;170;179 168;174;183 22952752 Molecular evolutionary analysis of pH1N1 2009 influenza virus in Reunion Island, South West Indian Ocean region: a cohort study. Reunion Island sequences were labelled according to the origin of the sample, whilst retaining anonymity of the participants : For example, "2133-5-M1E" corresponds to the fifth member of the family designated as number "2133", whereas "2133-6-M1E" refers to the sixth household member. 2012 PloS one Method IV M1E;M1E 148;244 151;247 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. Diffraction images were integrated using iMOSLFM or DENZO and scaled with SCALA or SCALEPACK for the ligand-free I223R structure. 2012 PLoS pathogens Method IV I223R 113 118 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. The reservoir solution of the I223R crystal in complex with zanamivir consisted of 18% PEG3350, 0.2 M Sodium Fluoride and 0.1 M bis-TRIS Propane buffer (pH 6.5). 2012 PLoS pathogens Method IV I223R 30 35 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. The reservoir solution of the I223R ligand-free crystal consisted of 20% PEG1000, 0.6 M Ammonium Phosphate and 0.1 M Sodium Acetate (pH 4.6). 2012 PLoS pathogens Method IV I223R 30 35 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. 2 (TOYOBO) and the following primers: BsmBI-R8A vNP fwd, 5'-CGTCTCNGGGAGCAAAAGCAGGTCACTCACAGAGTGACATCGAAATCATGGCGACCAAAGGCACCAAAGCATCTTACGAACAGATG-3'; BsmBI-S9A vNP fwd, 5'-CGTCTCNGGGAGCAAAAGCAGGTCACTCACAGAGTGACATCGAAATCATGGCGACCAAAGGCACCAAACGAGCTTACGAACAGATG-3'; and BsmBI-vNP rev, and 5'-CGTCTCNTATTAGTAGAAACAAGGTTCTTTAA-3'. 2013 PloS one Method IV R8A;S9A 44;157 47;160 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. 2 (Toyobo) with a full-length first-strand NP cDNA as the template and the forward primers XhoI-R8A NP fwd or XhoI-S9A NP fwd, and the reverse primer rev: 5'-AAAGCGGCCGCTTAATTGTCGTACTCCTCT-3'. 2013 PloS one Method IV R8A;S9A 96;115 99;118 NP;NP;NP 43;100;119 45;102;121 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. A549 cells (7x105 cells) were transfected with 2 microg of pCAGGS encoding mRFP-Flag-conjugated NP110aa, NP14-110aa, T3A-, K4A-, G5A-, T6A-, K7A-, R8A-, S9A-, Y10A-, E11A-, Q12A- or M13A-NP110aa using the FuGENE HD Transfection Reagent (Roche). 2013 PloS one Method IV K4A;K7A;R8A;S9A;T3A;G5A;T6A;Y10A;E11A;Q12A;M13A 123;141;147;153;117;129;135;159;166;173;182 126;144;150;156;120;132;138;163;170;177;186 NP;NP;NP 96;105;187 98;107;189 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. After incubation, 0.5 microg of vNP-luc plasmid transfected into the cells alongside the other plasmids (0.5 microg of PB2/pCAGGS, PB1/PCAGGS, PA/pCAGGS or NP/pCAGGS, or S9A-NP/pCAGGS) using the FuGENE HD transfection reagent at 37 C for 48 h. 2013 PloS one Method IV S9A 170 173 NP;NP;PA;PB1;PB2 156;174;143;131;119 158;176;145;134;122 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. Binding of mRFP-Flag conjugated NP110aa, NP14-110aa, 8A-NP110aa or S9A-NP110aa to importin alpha was detected by Western blotting with anti-Flag M2 MAb. 2013 PloS one Method IV S9A 67 70 M2;NP;NP;NP;NP 145;32;41;56;71 147;34;43;58;73 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. COS-7 cells were transfected with 10 microg of a pCAGGS encoding mRFP-Flag-conjugated NP110aa, NP14-110aa, R8A-NP110aa, S9A-NP110aa or mRFP-Flag alone using the FuGENE HD transfection reagent for 2 days. 2013 PloS one Method IV R8A;S9A 107;120 110;123 NP;NP;NP;NP 86;95;111;124 88;97;113;126 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. HEK-293T cells were transfected with 10 microg of a pCAGGS encoding mRFP-Flag-conjugated WT full length NP, WT and S9A NP110aa using the FuGENE HD transfection reagent for 2 days. 2013 PloS one Method IV S9A 115 118 NP;NP 104;119 106;121 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. pCAGGS encoding mRFP-Flag conjugated alanine mutants of the unconventional NLS extending from amino acids 3 to 13 of NP (T3A-, K4A-, G5A-, T6A-, K7A-, R8A-, S9A-, Y10A-, E11A- Q12A and M13A-NP110aa), were generated by PCR using the following forward primers: XhoI-T3A NP fwd, 5'-AAACTCGAGATGGCGGCCAAAGGCACCAAACGA-3'; XhoI-K4A NP fwd, 5'-AAACTCGAGATGGCGACCGCAGGCACCAAACGA-3'; XhoI-G5A NP fwd, 5'-AAACTCGAGATGGCGACCAAAGCCACCAAACGA-3'; XhoI-T6A NP fwd, 5'-AAACTCGAGATGGCGACCAAAGGCGCCAAACGATCT-3'; XhoI-K7A NP fwd, 5'-AAACTCGAGATGGCGACCAAAGGCACCGCACGATCTTAC-3'; XhoI-R8A NP fwd, 5'-AAACTCGAGATGGCGACCAAAGGCACCAAAGCATCTTACGAA-3'; XhoI-S9A NP fwd, 5'-AAACTCGAGATGGCGACCAAAGGCACCAAACGAGCTTACGAACAG-3'; XhoI-Y10A NP fwd, 5'-AAACTCGAGATGGCGACCAAAGGCACCAAACGATCTGCCGAACAGATG-3; XhoI-E11A NP fwd, 5'-AAACTCGAGATGGCGACCAAAGGCACCAAACGATCTTACGCACAGATGGAG-3' and XhoI-Q12A NP fwd, 5'-AAACTCGAGATGGCGACCAAAGGCACCAAACGATCTTACGAAGCGATGGAGACT-3'; XhoI-M13A NP fwd, 5'-AAACTCGAGATGGCGACCAAAGGCACCAAACGATCTTACGAACAGGCGGAGACT-3'; and the reverse primer: Spe-NP110aa-R, 5'-AAAACTAGTAAGGATGAGTTCTCTCCTCC-3' (restriction enzyme sites underlined). 2013 PloS one Method IV K4A;K7A;R8A;S9A;K4A;K7A;R8A;S9A;T3A;G5A;T6A;Y10A;E11A;Q12A;M13A;T3A;G5A;T6A;Y10A;E11A;Q12A;M13A 127;145;151;157;322;499;563;630;121;133;139;163;170;176;185;264;380;438;700;773;853;933 130;148;154;160;325;502;566;633;124;136;142;167;174;180;189;267;383;441;704;777;857;937 NP;NP;NP;NP;NP;NP;NP;NP;NP;NP;NP;NP;NP;NP 117;190;268;326;384;442;503;567;634;705;778;858;938;1036 119;192;270;328;386;444;505;569;636;707;780;860;940;1038 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. Purified mRFP-Flag-conjugated NP110aa, NP14-110aa, R8A-NP110aa, and S9A-NP110aa proteins were incubated with the importin alpha proteins bound to GST beads at 4 C overnight. 2013 PloS one Method IV R8A;S9A 51;68 54;71 NP;NP;NP;NP 30;39;55;72 32;41;57;74 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. The binding of importin alpha to mRFP-Flag-conjugated WT full length NP, WT and S9A NP110aa was detected by Western blotting with antibodies specific for Rch1, Qip1or NPI-1. 2013 PloS one Method IV S9A 80 83 NP;NP 69;84 71;86 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. To analyze the binding specificity of importin alpha for the mRFP-Flag-conjugated NP110aa protein, 50 microM of purified Rch1, Qip1 or NPI-1 protein were added to mRFP-Flag-conjugated WT or S9A NP110aa protein bound or not bound to FLAG beads. 2013 PloS one Method IV S9A 190 193 NP;NP 82;194 84;196 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. To generate the plasmids expressing alanine-mutated viral NP genomes (R8A vNP/pHH21 and S9A vNP/pHH21), PCR was performed using NP/pHH21 as the template with KOD Plus Ver. 2013 PloS one Method IV R8A;S9A 70;88 73;91 NP;NP 58;128 60;130 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. To produce pCAGGS encoding the full-length NP mutants (R8A-NP/pCAGGS and S9A-NP/pCAGGS), PCR amplification was performed using KOD Plus Ver. 2013 PloS one Method IV R8A;S9A 55;73 58;76 NP;NP;NP 43;59;77 45;61;79 23383318 Inhibitors of the influenza A virus M2 proton channel discovered using a high-throughput yeast growth restoration assay. Compounds were tested via a two-electrode patch clamp assay using Xenopus laevis oocytes microinjected with RNA for expression of the WT, S31N or V27A M2 gene. 2013 PloS one Method IV S31N;V27A 138;146 142;150 M2 151 153 23383318 Inhibitors of the influenza A virus M2 proton channel discovered using a high-throughput yeast growth restoration assay. The coding sequences of the Udorn WT, S31N and V27A M2 genes were introduced downstream of the GAL1 promoter by PCR amplification followed by recombination cloning in yeast. 2013 PloS one Method IV S31N;V27A 38;47 42;51 M2 52 54 23397331 Influenza virus A(H1N1)pdm09 hemagglutinin polymorphism and associated disease in southern Germany during the 2010/11 influenza season. For the detection of the oseltamivir-resistance-associated mutation H275Y, a commercially available assay (TIB-Molbiol, Berlin, Germany) was used according to the manufacturer's instructions. 2013 Archives of virology Method IV H275Y 68 73 23437217 Parallel screening of wild-type and drug-resistant targets for anti-resistance neuraminidase inhibitors. Generation of Oseltamivir- and Zanamivir-resistant NA with H275Y and I223R Point Mutations. 2013 PloS one Method IV H275Y;I223R 59;69 64;74 51 53 23437217 Parallel screening of wild-type and drug-resistant targets for anti-resistance neuraminidase inhibitors. Recombinant baculoviruses -Bac-NAWT, Bac-NAH275Y, Bac-NAI223R and Bac-NAI223R/H275Y-were generated to express wild-type, H275Y, I223R and I223R/H275Y mutants of NA originating from influenza N1 neuraminidase (NIBRG14 (H5N1)). 2013 PloS one Method IV H275Y;H275Y;I223R;H275Y;I223R 78;121;128;144;138 83;126;133;149;143 NA;NA;NAI;NAI;NA 41;161;54;70;194 43;163;57;73;207 23437217 Parallel screening of wild-type and drug-resistant targets for anti-resistance neuraminidase inhibitors. The NA structure with I223R and H275Y dual-point mutations was derived using a homology-modeling server. 2013 PloS one Method IV I223R;H275Y 22;32 27;37 4 6 23437217 Parallel screening of wild-type and drug-resistant targets for anti-resistance neuraminidase inhibitors. The recombination plasmid pGEM-T easy, containing the NA gene from strain NIBRG14 (H5N1), was used as a target for I223R site-directed PCR mutagenesis of NA. 2013 PloS one Method IV I223R 115 120 NA;NA 54;154 56;156 23437217 Parallel screening of wild-type and drug-resistant targets for anti-resistance neuraminidase inhibitors. To construct the I223R and H275Y double mutation expression plasmid, recombinant plasmid pGEM-T easy, containing the single point mutation H275Y NA gene (H5N1), was used as the target for site-directed PCR mutagenesis of NA. 2013 PloS one Method IV I223R;H275Y;H275Y 17;27;139 22;32;144 NA;NA 145;221 147;223 23437217 Parallel screening of wild-type and drug-resistant targets for anti-resistance neuraminidase inhibitors. To generate I223R-specific mutations, two primer sets were designed as follows: I223R-F; (5'- GAG TTG GAG GAA CAA CAG ACT GAG AAC TCA AGA GTC TG -3'), and I223R-R; (5'- CAG CTC TTG AGT TCT CAG TCT GTT GTT CCT CCA ACT C -3'). 2013 PloS one Method IV I223R;I223R;I223R 12;80;155 17;85;160 23451169 Simultaneous detection of oseltamivir- and amantadine-resistant influenza by oligonucleotide microarray visualization. Moreover, microarray probes ranging from 17 to 21 nucleotides were designed to detect H275Y, E119V, V27A, and S31N mutations, respectively, of the three influenza subtypes. 2013 PloS one Method IV H275Y;E119V;V27A;S31N 86;93;100;110 91;98;104;114 23555270 Monomeric nucleoprotein of influenza A virus. Because of non-specific polymerization of the S165D mutant NP, the sensorgrams could not be fitted by global analysis to determine the rate constants. 2013 PLoS pathogens Method IV S165D 46 51 NP 59 61 23555270 Monomeric nucleoprotein of influenza A virus. The R416A mutant protein was crystallized by vapor diffusion using the sitting drop method. 2013 PLoS pathogens Method IV R416A 4 9 23555270 Monomeric nucleoprotein of influenza A virus. The R416A, Y148A and S165D mutations were introduced by using PfuUltra DNA polymerase with the QuikChange II site-directed mutagenesis kit (Stratagene). 2013 PLoS pathogens Method IV R416A;Y148A;S165D 4;11;21 9;16;26 23555270 Monomeric nucleoprotein of influenza A virus. The S165D mutant was injected at concentrations between 0 and 8 microM. 2013 PLoS pathogens Method IV S165D 4 9 23593230 Effect of cysteine mutations in the extracellular domain of CM2 on the influenza C virus replication. For the generation of a CM2 mutant virus (rC1620A), pPolI/CM2-C1620A, instead of pPolI/M, was transfected into 293T cells together with the 15 remaining plasmids. 2013 PloS one Method IV C1620A 62 68 CM2;CM2 24;58 27;61 23593230 Effect of cysteine mutations in the extracellular domain of CM2 on the influenza C virus replication. For the generation of C1620A-VLPs, 293T cells were transfected with the same combination of plasmids as for the WT-VLPs, except that pME18S/CM2-C1620A was used instead of pME18S/Met-CM2-YA. 2013 PloS one Method IV C1620A;C1620A 22;144 28;150 CM2;CM2 140;182 143;185 23593230 Effect of cysteine mutations in the extracellular domain of CM2 on the influenza C virus replication. The pME18S/CM2-C1620A plasmid for the expression of the mutant CM2 protein (CM2-C1620A), in which the cysteines at residue 1, 6 and 20 were substituted to alanines, was constructed based on pPolI/CM2-C1620A. 2013 PloS one Method IV C1620A;C1620A;C1620A 15;80;200 21;86;206 CM2;CM2;CM2;CM2 11;63;76;196 14;66;79;199 23593230 Effect of cysteine mutations in the extracellular domain of CM2 on the influenza C virus replication. The pPolI/CM2-C1620A plasmid, used to generate virus RNA (vRNA) encoding M1 and CM2-C1620A (see below), was generated based on pPolI/M. 2013 PloS one Method IV C1620A;C1620A 14;84 20;90 CM2;CM2;M1 10;80;73 13;83;75 23626667 Quantitative characterization of glycan-receptor binding of H9N2 influenza A virus hemagglutinin. The linearized Hill equation was plotted for the seven wild type and mutant HAs, WF10, mWF10:T189A, and mWF10:L226Q, Qa88, mQa88:T189A, mQa88:Q226L and mQa88:Q226L/T189A HA were generated to calculate n and Kd' (Figure S2 and S3). 2013 PloS one Method IV T189A;L226Q;T189A;Q226L;T189A;Q226L 93;110;129;142;164;158 98;115;134;147;169;163 HA 170 172 23626667 Quantitative characterization of glycan-receptor binding of H9N2 influenza A virus hemagglutinin. The mutagenesis reaction was carried out using the QuikChange Multi Site-Directed Mutagenesis Kit (Stratagene, CA) WF10, Qa88, mWF10:T189A, mQa88:T189A, mQa88:Q226L and the double mutant mQa88:T189A/Q226L baculoviruses were created from their respective plasmids, using Baculogold system (BD Biosciences, CA) as per the manufacturer's instructions. 2013 PloS one Method IV T189A;T189A;Q226L;T189A;Q226L 133;146;159;193;199 138;151;164;198;204 23626667 Quantitative characterization of glycan-receptor binding of H9N2 influenza A virus hemagglutinin. Using pAcGp67-WF10-HA and pAcGp67-Qa88-HA as templates the gene was mutated to yield pAcGp67-L-HA [Gln226Leu], pAcGp67-TL-HA [Thr189Ala, Gln226Leu] and pAcGp67-T-HA [Thr189Ala]. 2013 PloS one Method IV Q226L;T189A;Q226L;T189A 99;126;137;166 108;135;146;175 HA;HA;HA;HA;HA 19;39;95;122;162 21;41;97;124;164 23638404 Virtual screening for oseltamivir-resistant a (H5N1) influenza neuraminidase from traditional Chinese medicine database: a combined molecular docking with molecular dynamics approach. The native and mutant (H274Y) type coordinates of NA were taken from the Brookhaven Protein Data Bank (Berman et al.). 2013 SpringerPlus Method IV H274Y 23 28 50 52 23646055 Occurrence and characterization of oseltamivir-resistant influenza virus in children between 2007-2008 and 2008-2009 seasons. For the genotypic analysis, mutations of amino acid regions related to drug resistance (E119V, R152K, H274Y, R292K, and N294S) were examined, via sequence analysis of NA gene. 2013 Korean journal of pediatrics Method IV E119V;R152K;H274Y;R292K;N294S 88;95;102;109;120 93;100;107;114;125 167 169 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. A 350 bp region of the HA1 gene flanking amino acid positions 142 and 156 was amplified from plasmid mixtures and from cDNA from ferret peak day nasal wash samples using MyTaq HS Mix (Bioline) with biotinylated forward primer (5'Biotin-GCAATTGAGCTCAGTGTCATC) and reverse primer (5'TTCCGGCTTGAACTTCTTGC) (for the WT/N156K assay) or forward primer (5'GCAATTGAGCTCAGTGTCATC) and biotinylated reverse primer (5'Biotin-TTCCGGCTTGAACTTCTTGC) (for the N156K/K142N+N156K assay), according to the manufacturer's instructions. 2013 PLoS pathogens Method IV N156K;K142N;N156K 315;451;457 320;456;462 HA1 23 26 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. DNA sequencing was performed with M13 primers (M13F-5' TGTAAAACGACGGCCAGT and M13R 5' CAGGAAACAGCTATGACC) or plasmid-specific primers in a 96-well plate format using the BigDye Terminator v3.1 Cycle Sequencing Kit (Life Technologies), followed by the removal of excess dye terminators with a BigDye XTerminator purification kit (Applied Biosystems). 2013 PLoS pathogens Method IV M13F;M13R 47;78 51;82 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. Ferret antisera binding to virus-infected cells was analyzed by comparing the relative proportion from wildtype and N156K-infected cells for each antiserum using Spearman's rank correlation co-efficient. 2013 PLoS pathogens Method IV N156K 116 121 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. L191I and R223Q were then introduced to generate ferret-adapted pHW-2000-A/Tasmania/2004/2009 HA vector. 2013 PLoS pathogens Method IV L191I;R223Q 0;10 5;15 HA 94 96 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. Mixtures of pGEMT plasmids with A/Tasmania/2004/2009-HA1 and A/Tasmania/2004/2009-HA1-N156K or A/Tasmania/2004/2009-HA1-N156K and A/Tasmania/2004/2009-HA1-K142N+ N156K inserts were prepared at different molar ratios (100:0, 80:20, 50:50, 20:80, 0:100), at multiple concentrations (1, 0.1, 0.001 pg total). 2013 PLoS pathogens Method IV N156K;N156K;K142N;N156K 86;120;155;162 91;125;160;167 HA1;HA1;HA1;HA1 53;82;116;151 56;85;119;154 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. Pyrosequencing assay to quantify the proportion of the wildtype, N156K or K142N+N156K mutants. 2013 PLoS pathogens Method IV N156K;K142N;N156K 65;74;80 70;79;85 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. S203T, Q223R and H496N were introduced into the HA gene to generate pHW-2000-A/Tasmania/2004/2009 HA vector. 2013 PLoS pathogens Method IV S203T;Q223R;H496N 0;7;17 5;12;22 HA;HA 48;98 50;100 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. S388T was introduced into the NA gene to generate pHW-2000-A/Tasmania/2004/2009 NA vector. 2013 PLoS pathogens Method IV S388T 0 5 NA;NA 30;80 32;82 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. The first quantified the proportion of the N156 (wildtype) vs the N156K mutant (WT/N156K). 2013 PLoS pathogens Method IV N156K;N156K 66;83 71;88 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. The N156K mutation generates a quadruplicate run of adenosines, which does not quantify absolutely by this technology, thus the detection limit was 5-10% for N156K. 2013 PLoS pathogens Method IV N156K;N156K 4;158 9;163 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. The pyrosequencing reaction was performed as previously described, using internal primers 5'GGATTTGCTGAGCTTTGGGT and 5'CTCATGCTGGAGCAAA, specific for the N156K and K142N mutations, respectively. 2013 PLoS pathogens Method IV N156K;K142N 154;164 159;169 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. The second assay quantified the proportion of K142 vs K142N mutant (N156K/K142N+N156K). 2013 PLoS pathogens Method IV K142N;K142N;N156K 54;74;80 59;79;85 23717200 Prolonged influenza virus shedding and emergence of antiviral resistance in immunocompromised patients and ferrets. As determined by full-genome Sanger sequencing, the mutant virus contained, additional to mutation H275Y in the neuraminidase, an L233M mutation in PB2 and a V541L mutation in HA. 2013 PLoS pathogens Method IV H275Y;L233M;V541L 99;130;158 104;135;163 HA;NA;PB2 176;112;148 178;125;151 23717200 Prolonged influenza virus shedding and emergence of antiviral resistance in immunocompromised patients and ferrets. Influenza A virus and the H275Y oseltamivir resistance mutation were detected by reverse transcriptase RT-PCR assays. 2013 PLoS pathogens Method IV H275Y 26 31 23717200 Prolonged influenza virus shedding and emergence of antiviral resistance in immunocompromised patients and ferrets. Wild type influenza virus A/Netherlands/1715b/2009 (genbank ID code: CY065810) and H275Y mutant virus were isolated from the original quasispecies by co-cultivation of a respiratory sample in a Madin-Darby Canine Kidney (MDCK) cell culture in a single passage. 2013 PLoS pathogens Method IV H275Y 83 88 23759670 Virological self-sampling to monitor influenza antiviral susceptibility in a community cohort. Influenza A(H1N1)pdm09-positive specimens were screened by pyrosequencing for the H275Y mutation (a CAC to TAC nucleotide substitution) in the viral neuraminidase. 2013 The Journal of antimicrobial chemotherapy Method IV H275Y 82 87 149 162 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. At each temperature, the relative activity of WT polymerase was set at 100%, and the activities of the PB2-D701N were determined relative to that of the WT. 2013 PloS one Method IV D701N 107 112 PB2 103 106 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. Briefly, HEK-293T cells in 24-well plates were cotransfected with 0.2 microg each of pPolI-NS-Luc plasmid (pBZ81A36) and plasmids to express the NY1682 PB2 (PB2-WT or PB2-D701N), PB1, PA, and NP proteins, and to control for transfection efficiency, 0.02 microg of the Renilla luciferase plasmid pRL-TK (Promega, Madison, WI) was also cotransfected. 2013 PloS one Method IV D701N 171 176 NP;NS;PA;PB1;PB2;PB2;PB2 192;91;184;179;152;157;167 194;93;186;182;155;160;170 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. Recombination-based In-Fusion cloning method was used to mutate the NY1682 PB2 plasmid to generate the PB2-D701N mutant reverse genetics construct. 2013 PloS one Method IV D701N 107 112 PB2;PB2 75;103 78;106 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. The cells were inoculated at a multiplicity of infection (MOI) of 0.01 TCID50/cell with recombinant NY1682 WT or NY1682 D701N viruses. 2013 PloS one Method IV D701N 120 125 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. The primary cultured alveolar type I-like cells were infected with the rNY1682-WT or rNY1682-D701N viruses at an MOI of 0.01 PFU/cell and washed twice with medium after 1 h of incubation at 37oC. 2013 PloS one Method IV D701N 93 98 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. The recombinant rNY1682-WT and rNY1682-D701N viruses were generated using the rescue protocol described previously. 2013 PloS one Method IV D701N 39 44 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. Three ferrets were inoculated intranasally with 1 ml of 106 PFU of the NY1682-WT or NY1682-D701N virus. 2013 PloS one Method IV D701N 91 96 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. To determine virus replication in vivo, six-week-old female BALB/cJ mice (n=3/group/time-point, Jackson Laboratory, Bar Harbor, ME) were anesthetized with isoflurane and inoculated intranasally with 50 microl EMEM diluent containing 103 TCID50 of rNY1682-WT or rNY1682-D701N. 2013 PloS one Method IV D701N 269 274 23860768 Resistance to neuraminidase inhibitors conferred by an R292K mutation in a human influenza virus H7N9 isolate can be masked by a mixed R/K viral population. Resistance to neuraminidase inhibitors conferred by an R292K mutation in a human influenza virus H7N9 isolate can be masked by a mixed R/K viral population. 2013 mBio Method IV R292K 55 60 14 27 23951116 Resistance mutation R292K is induced in influenza A(H6N2) virus by exposure of infected mallards to low levels of oseltamivir. All R292K mutants showed relatively low NA activity and were diluted 1:2 while wild type virus samples were further diluted. 2013 PloS one Method IV R292K 4 9 40 42 23951116 Resistance mutation R292K is induced in influenza A(H6N2) virus by exposure of infected mallards to low levels of oseltamivir. Sequencing of the HA gene was performed on 8 selected samples, among which 6 were evaluable, from the 12 microg/L experiment that were NA sequenced as wild type, R292K, R292K and D113N, R292K and D141N prior to and after egg propagation. 2013 PloS one Method IV R292K;R292K;D113N;R292K;D141N 162;169;179;186;196 167;174;184;191;201 HA;NA 18;135 20;137 24074585 Mutation from arginine to lysine at the position 189 of hemagglutinin contributes to the antigenic drift in H3N2 swine influenza viruses. The R189K in hemagglutinin of 09SW64 and K189R in hemagglutinin of 11SW347 were introduced using the QuickChange II site-directed mutagenesis kit (Stratagene, Inc., La Jolla, CA) according to manufacturer's protocols. 2013 Virology Method IV R189K;K189R 4;41 9;46 HA;HA 13;50 26;63 24139991 Asp44 stabilizes the Trp41 gate of the M2 proton channel of influenza A virus. All spectra were recorded at 313 K on Varian 600 MHz for WT or 900 MHz spectrometer for D44N, both equipped with a cryogenic probe. 2013 Structure (London, England Method IV D44N 88 92 24139991 Asp44 stabilizes the Trp41 gate of the M2 proton channel of influenza A virus. Simulations were performed for four different protonation states of the WT (+1, +2, +3, +4) and three mutants in the 2+ state: D44A, D44C, and D44N. 2013 Structure (London, England Method IV D44A;D44C;D44N 127;133;143 131;137;147 24165891 Characterization of two distinct neuraminidases from avian-origin human-infecting H7N9 influenza viruses. The structure of Anhui N9 was solved by molecular replacement using the A/tern/Australia/G70C/1975 H11N9 N9 molecule (PDB 7NN9) as the search model with Phaser in the CCP4 program suite. 2013 Cell research Method IV G70C 89 93 N9;N9 23;105 25;107 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. Additionally, the Man9 chain had to be remodeled because WT binds to the reducing end of the mannose-9 (Man9) chain (circle in vertical stripes), while D325A+R343V binds to the non-reducing end (circle in horizontal stripes) as shown in the schematic diagram of Figure 1. 2013 Biochemistry Method IV D325A;R343V 152;158 157;163 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. Crystals of D325A+R343V were grown in hanging drops by mixing equal amounts of purified D325A+R343V (12-15 mg/ml in 20 mM HEPES buffer, pH 7.5, 150 mM NaCl, and 10 mM calcium acetate) and reservoir solution (0.1 M HEPES buffer, pH 7.5, 0.25 M NaCl, and 20-22% w/v PEG 3350) on a siliconized coverslip and equilibrating over a sealed well containing 0.5 ml reservoir solution at 17 C. 2013 Biochemistry Method IV R343V;D325A;D325A;R343V 18;12;88;94 23;17;93;99 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. Figure 1 shows the resulting model of the Man9 component of the D325A+R343V/HA complex. 2013 Biochemistry Method IV D325A;R343V 64;70 69;75 HA 76 78 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. Figure 2 shows the protein system that was simulated for the present study: the HA trimer glycosylated with one Man9 and complexed with one trimer of SP-D (either WT or D325A+R343V) with bound calcium ions. 2013 Biochemistry Method IV D325A;R343V 169;175 174;180 HA 80 82 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. Since the objective of the molecular dynamics (MD) simulations is to compare the WT/HA and D325A+R343V/HA complexes, the starting coordinates of both models need to be chosen as similar as possible. 2013 Biochemistry Method IV D325A;R343V 91;97 96;102 HA;HA 84;103 86;105 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. The structure was solved by molecular replacement using the previously solved structure of R343V SP-D complexed with alpha-1,2-dimannose, less the waters and ligands and incorporating the expected D325A mutation as well as the truncation of the construct, as a search model using the AutoMR program in Phenix . 2013 Biochemistry Method IV R343V;D325A 91;197 96;202 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. Therefore, we used the coordinates of the D325A+R343V/HA complex as a template to obtain the starting model for WT. 2013 Biochemistry Method IV D325A;R343V 42;48 47;53 HA 54 56 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. To attach the SPD trimer, the mannose chain present in the D325A+R343V crystal structure (comprising MAN505A, MAN504A, and MAN503A) was extended by one mannose (equivalent to residue BMA 502) using the computational tools in Maestro (Schrodinger, LLC, New York, NY, USA). 2013 Biochemistry Method IV D325A;R343V 59;65 64;70 24237039 3-Azatetracyclo[5.2.1.1(5,8).0(1,5)]undecane derivatives: from wild-type inhibitors of the M2 ion channel of influenza A virus to derivatives with potent activity against the V27A mutant. A/M2 S31N and A/M2 V27A mutants were generated by QuikChange site-directed mutagenesis kit (Agilent Technologies). 2013 Journal of medicinal chemistry Method IV S31N;V27A 5;19 9;23 M2;M2 2;16 4;18 24312396 Conformational polymorphism of m7GTP in crystal structure of the PB2 middle domain from human influenza A virus. Coordinates and structure factors of PB2 middle domain with two amino acids mutation (P453H and I471T) have been deposited in the Protein Data Bank. 2013 PloS one Method IV P453H;I471T 86;96 91;101 PB2 37 40 24312396 Conformational polymorphism of m7GTP in crystal structure of the PB2 middle domain from human influenza A virus. To obtain more soluble domain, we introduced two mutations on the surface of this domain: P453H and I471T. 2013 PloS one Method IV P453H;I471T 90;100 95;105 24503069 The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus. Because Asn194 was not stable in MDCK cells, only viruses with Asn194 Asp and Phe95 Tyr/Asn194 Asp in HA were used in our subsequent studies. 2014 Virology Method IV N194D 63 73 HA 102 104 24503069 The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus. For the replication in mice, six to eight-week old female BALB/C mice (Charles River Laboratories) were administered intranasally with 104 PFU recombinant viruses harboring Asn194 Asp or Phe95 Tyr/Asn194 Asp HA, or with sterile PBS as negative controls (four mice per group). 2014 Virology Method IV N194D 173 183 HA 208 210 24503069 The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus. For virus with Phe95 Tyr or Phe95 Tyr/Asn194 Asp in HA, 1 mug/mL neuraminiase (NA) from Clostridium perfringens (Sigma) was added to accommodate the increased binding affinity of HA. 2014 Virology Method IV F95Y 15 24 HA;HA;NA 52;179;79 54;181;81 24503069 The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus. Site-directed mutagenesis was used to introduce the Phe95 Tyr, Asn194 Asp and Phe95 Tyr/Asn194 Asp mutants into the gene of B/Lee/40 HA (Agilent Technologies). 2014 Virology Method IV F95Y;N194D 52;63 61;73 HA 133 135 24503069 The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus. Site-directed mutagenesis was used to make the Phe95 Tyr, Asn194 Asp and Phe95 Tyr/Asn194 Asp mutants (Agilent Technologies). 2014 Virology Method IV F95Y;N194D 47;58 56;68 24503069 The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus. The viruses with Phe95 Tyr, Asn194 Asp and Phe95 Tyr/Asn194 Asp all had the expected sequences in HA. 2014 Virology Method IV F95Y;N194D 17;28 26;38 HA 98 100 24524021 Generation and Characterization of Recombinant Influenza A(H1N1) Viruses Resistant to Neuraminidase Inhibitors. To investigate mutations at NA key residues (N1 numbering: I117V, I117M, E119V, I223V, Y275H, R293K, N295S, and S334N), site-directed mutagenesis was conducted on the NA gene cloned plasmid using the QuickChange Site-Directed Mutagenesis Kit (Stratagene, Santa Clara, CA, USA). 2013 Osong public health and research perspectives Method IV I117V;I117M;E119V;I223V;Y275H;R293K;N295S;S334N 59;66;73;80;87;94;101;112 64;71;78;85;92;99;106;117 NA;NA 28;167 30;169 24558492 Study of oseltamivir and zanamivir resistance-related mutations in influenza viruses isolated from wild mallards in Sweden. The literature describing NAI resistance mutations has been reviewed, whereupon nine OC (V116A, I117V, E119V, D198N, I222V, H274Y, R292K, N294S and I314V) and ten ZA (V116A, R118K, E119G/A/D, Q136K, D151E/G/N, R152K, R224K, E276D, R292K and R371K) NAI resistance-related mutations were identified (N2 numbering). 2014 PloS one Method IV V116A;I117V;E119V;D198N;I222V;H274Y;R292K;N294S;I314V;V116A;R118K;E119G;E119A;E119D;Q136K;D151E;D151G;D151N;R152K;R224K;E276D;R292K;R371K 89;96;103;110;117;124;131;138;148;167;174;181;181;181;192;199;199;199;210;217;224;231;241 94;101;108;115;122;129;136;143;153;172;179;190;190;190;197;208;208;208;215;222;229;236;246 NAI;NAI 26;248 29;251 24563658 Synergistic combinations of favipiravir and oseltamivir against wild-type pandemic and oseltamivir-resistant influenza A virus infections in mice. Influenza A/Mississippi/3/2001 (H1N1) containing an H275Y mutation in the neuraminidase gene was obtained from the Neuraminidase Inhibitor Surveillance Network (Melbourne, Australia). 2013 Future virology Method IV H275Y 52 57 NA;NA 74;115 87;128 24563658 Synergistic combinations of favipiravir and oseltamivir against wild-type pandemic and oseltamivir-resistant influenza A virus infections in mice. It is >1000-fold more resistant to oseltamivir carboxylate in cell culture than influenza A/California/04/2009 (H1N1pdm) virus, which is similar to the resistance found in an influenza A/Hong Kong/2369/2009 (H1N1pdm) H275Y virus. 2013 Future virology Method IV H275Y 217 222 24563658 Synergistic combinations of favipiravir and oseltamivir against wild-type pandemic and oseltamivir-resistant influenza A virus infections in mice. The mouse-adapted virus was genetically analyzed and confirmed to be a homogeneous population of H275Y-containing virus. 2013 Future virology Method IV H275Y 97 102 24569063 An investigational antiviral drug, DAS181, effectively inhibits replication of zoonotic influenza A virus subtype H7N9 and protects mice from lethality. Because these influenza A(H7N9) isolates contained a mixed viral population, plaque purification was performed in MDCK-SIAT1 cells to separate the oseltamivir-resistant virus variant carrying R292K from the wild-type virus with R292. 2014 The Journal of infectious diseases Method IV R292K 192 197 24569063 An investigational antiviral drug, DAS181, effectively inhibits replication of zoonotic influenza A virus subtype H7N9 and protects mice from lethality. Sanger sequencing analyses of the plaque-purified viruses confirmed that R292K was the only amino acid difference between the NAs of wild-type and R292K virus variant. 2014 The Journal of infectious diseases Method IV R292K;R292K 147;73 152;78 126 129 24569063 An investigational antiviral drug, DAS181, effectively inhibits replication of zoonotic influenza A virus subtype H7N9 and protects mice from lethality. The HA of the Shanghai/1 R292K variant had a mixture of 151A/S (2013 H7 numbering) and 209G/E, while that of the Taiwan/1 R292K variant showed a D340G substitution, compared with characteristics of the respective wild-type viruses. 2014 The Journal of infectious diseases Method IV R292K;R292K;D340G 25;122;145 30;127;150 HA 4 6 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. Each RT-PCR assay produced double-stranded DNA fragments which encompassed the NA H275Y, V241I or N369K mutation sites. 2014 PLoS pathogens Method IV H275Y;V241I;N369K 82;89;98 87;94;103 79 81 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. Following validation of the assays used in this study we determined a similar accuracy range using purified plasmids (at a concentration range of 10-2 to 10-6 DNA copies) for each of the NA H275Y, V241I or N369K pyrosequencing assays. 2014 PLoS pathogens Method IV H275Y;V241I;N369K 190;197;206 195;202;211 187 189 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. Full genome sequence analysis revealed a high degree of amino acid similarity between this pair of viruses (New17 OR:New163 OS = 99.5%) and no amino acid differences that have previously been associated with virulence, receptor binding, antiviral resistance or other aspects of viral function, other than the OR NA H275Y mutation. 2014 PLoS pathogens Method IV H275Y 317 322 314 316 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. The drug resistance H275Y and the N386S mutations were also kept for reference. 2014 PLoS pathogens Method IV H275Y;N386S 20;34 25;39 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. To generate the figure that illustrates the evolution timeline of the NA V241I and N369K mutations, the NA sequence from A/California/07/2009 was used as reference and the percentages of occurrences for each of the mutations were calculated on a monthly basis since April 2009. 2014 PLoS pathogens Method IV V241I;N369K 73;83 78;88 NA;NA 70;104 72;106 24751348 PCR for detection of oseltamivir resistance mutation in influenza A(H7N9) virus. Seven of 11 samples had positive results in the R292K assay: 5 samples positive in the 292K assay and 2 samples positive in both assays. 2014 Emerging infectious diseases Method IV R292K 48 53 24751348 PCR for detection of oseltamivir resistance mutation in influenza A(H7N9) virus. The NA R292K assay has 2 reactions with 1 pair of primers. 2014 Emerging infectious diseases Method IV R292K 7 12 4 6 24795482 A novel I221L substitution in neuraminidase confers high-level resistance to oseltamivir in influenza B viruses. A 1-step allelic discrimination real-time RT-qPCR was adapted for the studied influenza B viruses: the real-time RT-qPCR conditions were identical to conditions previously described for detecting the H275Y-conferring mutation in N1 genes. 2014 The Journal of infectious diseases Method IV H275Y 200 205 24795482 A novel I221L substitution in neuraminidase confers high-level resistance to oseltamivir in influenza B viruses. Detection of Mutated (I221L) NA Virus Subpopulations by NA Inhibition Assay of Virus Isolates. 2014 The Journal of infectious diseases Method IV I221L 22 27 NA;NA 29;56 31;58 24795482 A novel I221L substitution in neuraminidase confers high-level resistance to oseltamivir in influenza B viruses. Quantification of Viruses With a Wild-Type or I221L-Substituted NA in Clinical Specimens. 2014 The Journal of infectious diseases Method IV I221L 46 51 64 66 24795482 A novel I221L substitution in neuraminidase confers high-level resistance to oseltamivir in influenza B viruses. The apparent IC50 values for oseltamivir in the sample mixtures were plotted (using Sigma Plot) as a function of the mutant (I221L) concentration to obtain a nonlinear regression equation. 2014 The Journal of infectious diseases Method IV I221L 125 130 24795482 A novel I221L substitution in neuraminidase confers high-level resistance to oseltamivir in influenza B viruses. The first virus isolate with a 100% wild-type NA (B/Lyon/CHU/12.88/2011 (P2 MDCK)) and virus isolates that presented the highest oseltamivir IC50 with 100% I221L substituted NA (B/Lyon/CHU/15.216/2011 (P3 MDCK) and B/Lyon/CHU/16.167/2011 (P2 MDCK)) were selected for plaque assays. 2014 The Journal of infectious diseases Method IV I221L 156 161 NA;NA 46;174 48;176 24795482 A novel I221L substitution in neuraminidase confers high-level resistance to oseltamivir in influenza B viruses. The sensitivity of this RT-qPCR was 1-10 copies for the detection of viruses bearing Ile or Leu at position 221 in NA, and it could detect the presence of at least 10% mutant (I221L) virus in a mixed-virus population. 2014 The Journal of infectious diseases Method IV I221L 176 181 115 117 24795482 A novel I221L substitution in neuraminidase confers high-level resistance to oseltamivir in influenza B viruses. Two probes specifically detect the presence of an isoleucine (Ile) or leucine (L) at position 221 of the NA for the studied influenza B viruses. 2014 The Journal of infectious diseases Method IV L221L 69 98 105 107 24854981 Solid phase assay for comparing reactivation rates of neuraminidases of influenza wild type and resistant mutants after inhibitor removal. Stocks of the following viruses were grown in Madin Darby Canine Kidney Cells, (MDCK): A/Mississippi/03/01 H1N1 wild type and oseltamivir resistant H274Y mutant,, A/Fukui/45/04 H3N2 wild type and E119V oseltamivir resistant mutant, B/Perth/211/01 influenza B wild type and D197E mutant with decreased susceptibility to all NAIs, NWS/G70C H1N9 wild type and E119G mutant with decreased susceptibility to zanamivir and peramivir. 2014 Antiviral research Method IV H274Y;E119V;D197E;G70C;E119G 148;196;273;333;357 153;201;278;337;362 NAI 323 327 24889237 Enhanced human receptor binding by H5 haemagglutinins. By PCR, Ser227Asn, Gln196Arg, Asn186Lys, Gly143Arg in H3 numbering (Ser223Asn, Gln192Arg, Asn182Lys, Gly139Arg in matured H5 HA numbering) and selected combinations Ser227Asn/Gln196Arg and Asn186Lys/Gly143Arg were introduced into the VN1194 HA cDNA. 2014 Virology Method IV Q196R;G143R;S227N;Q196R;N186K;G143R;S223N;Q192R;N182K;G139R;S227N;N186K;S227Q;S227R;N186G;N186R 175;199;8;19;30;41;68;79;90;101;165;189;165;165;189;189 184;208;17;28;39;50;77;88;99;110;174;198;174;174;198;198 HA;HA 125;241 127;243 24889237 Enhanced human receptor binding by H5 haemagglutinins. Delta133, Ile155Thr and Ser125Asn (Delta129, Ile151Thr, Ser121Asn mutations in H5 numbering) and combinations of them, were introduced in tyTy HA cDNA. 2014 Virology Method IV I155T;S125N;I151T;S121N 10;24;45;56 19;33;54;65 HA 143 145 24889237 Enhanced human receptor binding by H5 haemagglutinins. tyTy Delta133/Ile155Thr HA was expressed in Sf-9 insect cells and purified using previously published methods. 2014 Virology Method IV I155T 14 23 HA 24 26 24889237 Enhanced human receptor binding by H5 haemagglutinins. tyTy Delta133/Ile155Thr mutant HA was initially crystallised from Bis-tris propane pH 7.5, 0.2 M K/NaPO4 (pH 7.0), 20% PEG 3350, and crystals were improved by seeding in Bis-tris propane pH 7.5, 0.05-0.15 M K/NaPO4 (pH 7.0), 15-18% PEG 3350. 2014 Virology Method IV I155T 14 23 HA 31 33 24889237 Enhanced human receptor binding by H5 haemagglutinins. VN1194 Asn186Lys/Gly143Arg mutant HA was crystallised from 0.1 M MOPS pH 7.0, 12% PEG 4000. 2014 Virology Method IV G143R;N186K;N186G;N186R 17;7;7;7 26;16;16;16 HA 34 36 24889237 Enhanced human receptor binding by H5 haemagglutinins. VN1194 HAs containing Ser227Asn/Gln196Arg, Asn186Lys, Asn186Lys/Gly143Arg, and Gln196Arg substitutions, were purified from recombinant viruses grown in chicken eggs as published before. 2014 Virology Method IV Q196R;G143R;S227N;N186K;N186K;Q196R;S227Q;S227R;N186G;N186R 32;64;22;43;54;79;22;22;54;54 41;73;31;52;63;88;31;31;63;63 24889237 Enhanced human receptor binding by H5 haemagglutinins. VN1194 Ser227Asn/Gln196Arg, Asn186Lys, and Gln196Arg mutant HAs were crystallised from 0.1 M HEPES/MOPS pH 7.0, 0.05 M MgCl2, 28-30% PEG 550 MME using crushed wild-type VN1194 HA crystals as seeds. 2014 Virology Method IV Q196R;S227N;N186K;Q196R;S227Q;S227R 17;7;28;43;7;7 26;16;37;52;16;16 HA 176 178 24928037 The R35 residue of the influenza A virus NS1 protein has minimal effects on nuclear localization but alters virus replication through disrupting protein dimerization. Forward and reverse primers FluA6 and FluA5 were used along with mutagenesis primers NS1 R35A f and NS1 R35A r 2 for the R35A mutation, NS1 R37A F and NS1 R37A r 2 for R37A, and NS1 K41A f and NS1 K41A r for the K41A mutation. 2014 Virology Method IV R35A;R35A;R35A;R37A;R37A;R37A;K41A;K41A;K41A 89;104;121;140;155;168;182;197;212 93;108;125;144;159;172;186;201;216 NS1;NS1;NS1;NS1;NS1;NS1 85;100;136;151;178;193 88;103;139;154;181;196 24928037 The R35 residue of the influenza A virus NS1 protein has minimal effects on nuclear localization but alters virus replication through disrupting protein dimerization. NS1 R35A D39X mutations were introduced into a NS1-myc cDNA expression plasmid by amplifying NS1 sequences from virus with 5' primers WSN 5' NS1 into PC or WSN 5' NS1 into PC EcoR1 (for R35A D39A) and 3' primer WSN 3' NS1 into PC and introduced into a pCAGGS NS1-myc plasmid by restriction enzyme digest and ligation. 2014 Virology Method IV R35A;D39X;R35A;D39A 4;9;186;191 8;13;190;195 NS1;NS1;NS1;NS1;NS1;NS1;NS1 0;47;93;141;163;218;259 3;50;96;144;166;221;262 24941437 Easily accessible polycyclic amines that inhibit the wild-type and amantadine-resistant mutants of the M2 channel of influenza A virus. A 25 A layer of TIP3P water molecules was set up at both sides of the bilayer, and K+ cations and Cl- anions were added to achieve an ionic strength of 150 mM. 2014 Journal of medicinal chemistry Method IV A25A 0 6 24941437 Easily accessible polycyclic amines that inhibit the wild-type and amantadine-resistant mutants of the M2 channel of influenza A virus. A/M2 S31N and A/M2 V27A mutants were generated by QuikChange site-directed mutagenesis kit (Agilent Technologies). 2014 Journal of medicinal chemistry Method IV S31N;V27A 5;19 9;23 M2;M2 2;16 4;18 24941437 Easily accessible polycyclic amines that inhibit the wild-type and amantadine-resistant mutants of the M2 channel of influenza A virus. The binding mode of Amt and compound 18 to the wt M2 channels and its V27A variant embedded on a model bilayer of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) was studied by molecular dynamics simulations. 2014 Journal of medicinal chemistry Method IV V27A 70 74 M2 50 52 25043638 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2012-2013. Although treatment information was unavailable for one of the cases, two of the E119V variant viruses came from patients undergoing oseltamivir treatment. 2014 Antiviral research Method IV E119V 80 85 25043638 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2012-2013. An A(H3N2) virus with a R292K NA substitution was also recovered from an oseltamivir-treated patient. 2014 Antiviral research Method IV R292K 24 29 30 32 25043638 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2012-2013. Analysis of the available sequences also identified two N1 sequences containing D199N substitution and one influenza B NA sequence containing D197N substitution (Table 4). 2014 Antiviral research Method IV D199N;D197N 80;142 85;147 119 121 25043638 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2012-2013. Because former seasonal A(H1N1) viruses possessing NA H275Y substitution spread globally in 2008, and a cluster of A(H1N1)pdm09 viruses with NA H275Y substitution was detected in untreated community cases in Australia in 2011, there has been significant concern that such variant viruses, with HRI, may acquire the ability to spread widely. 2014 Antiviral research Method IV H275Y;H275Y 54;144 59;149 NA;NA 51;141 53;143 25043638 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2012-2013. For example, the list currently requires the inclusion of the B NA I221V substitution that was present in a cluster of influenza B viruses detected in North and South Carolina, United States of America, in 2011/2012 and the B NA I221L substitution that emerged in an immunocompromised patient treated with oseltamivir and yielded viruses showing HRI. 2014 Antiviral research Method IV I221V;I221L 67;229 72;234 NA;NA 64;226 66;228 25043638 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2012-2013. H275Y) or HRI/RI in vitro, and (ii have been confirmed to occur in patient clinical specimens (not just virus isolates). 2014 Antiviral research Method IV H275Y 0 5 25043638 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2012-2013. However the merits of including substitutions such as D199N in N1 described below, that confer only a few fold increase in IC50, and therefore remain classified as showing NI, requires further discussion. 2014 Antiviral research Method IV D199N 54 59 25043638 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2012-2013. However, there were six NA H275Y variant viruses from Brazil (n = 3), Sweden (n = 1), India (n = 1) and Lao People's Democratic Republic (n = 1) that were present in the sequence databases that had not been analysed/reported within the GISRS network and therefore not included in the WHO CCs IC50 dataset. 2014 Antiviral research Method IV H275Y 27 32 24 26 25043638 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2012-2013. Including the six NA H275Y viruses reported in the sequence database only and the two NA H275Y viruses reported in the WHO CC dataset only (1 from China and 1 from Singapore), the 24 NA H275Y viruses were derived from 14 countries worldwide and specimens collected throughout the reporting period. 2014 Antiviral research Method IV H275Y;H275Y;H275Y 21;89;186 26;94;191 NA;NA;NA 18;86;183 20;88;185 25043638 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2012-2013. NA amino acid substitutions D151E, Q136K and Q136R were detected, once each, in viruses with altered NAI susceptibility, but such substitutions can emerge during MDCK cell culture. 2014 Antiviral research Method IV D151E;Q136K;Q136R 28;35;45 33;40;50 NA;NAI 0;101 2;104 25043638 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2012-2013. No clear clustering was found, although the two NA H275Y viruses from the Netherlands were associated with possible transmission at a holiday location and the four NA H275Y viruses from Brazil were associated with possible community transmission in the south of the country. 2014 Antiviral research Method IV H275Y;H275Y 51;167 56;172 NA;NA 48;164 50;166 25043638 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2012-2013. Of the 1083 N1 sequences 1054 (97%) contained V241I substitution, and 1050 (97%) N369 K substitution, which are compensatory for H275Y substitution, thereby increasing the risk of emergence of fit oseltamivir HRI A(H1N1)pdm09 viruses that could spread worldwide. 2014 Antiviral research Method IV V241I;N369K;H275Y 46;81;129 51;87;134 25043638 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2012-2013. Of the 18 H275Y variants, six were from the Western Pacific, six from the Americas, five from Europe and one from South-East Asia, from 11 countries in total. 2014 Antiviral research Method IV H275Y 10 15 25043638 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2012-2013. Of the H275Y variant viruses detected in 2012-2013 where patient setting and antiviral treatment information was available, 80% were from non-hospitalised patients that had not been treated with oseltamivir, suggesting that there is potential for spontaneous emergence and spread of these resistant viruses in the community. 2014 Antiviral research Method IV H275Y 7 12 25043638 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2012-2013. Of the nine clinical specimens for which sequence results were available, all contained the H275Y substitution. 2014 Antiviral research Method IV H275Y 92 97 25043638 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2012-2013. One A(H1N1)pdm09 virus isolate from Argentina, A/Salta/1341/2012, contained a N295S amino acid substitution which conferred HRI by oseltamivir but had only a mild effect on zanamivir susceptibility. 2014 Antiviral research Method IV N295S 78 83 25043638 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2012-2013. The clinical specimens yielding two of these isolates were unavailable, but the specimen yielding the Q136R isolate did not contain the mutation conferring the amino acid substitution prior to cell culture. 2014 Antiviral research Method IV Q136R 102 107 25043638 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2012-2013. The E119V and R292K substitutions were also detected in the corresponding clinical specimens. 2014 Antiviral research Method IV E119V;R292K 4;14 9;19 25043638 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2012-2013. The E119V substitution conferred increases in oseltamivir IC50 values ranging from 120- to 454-fold compared to that of A(H3N2) viruses showing NI, while retaining NI by zanamivir, laninamivir and peramivir. 2014 Antiviral research Method IV E119V 4 9 25043638 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2012-2013. The H275Y substitution conferred 207- to 4010-fold higher oseltamivir IC50 values and 157- to 1672-fold higher peramivir IC50 values compared to wild type viruses, but had little or no effect on zanamivir or laninamivir susceptibility (Table 2). 2014 Antiviral research Method IV H275Y 4 9 25043638 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2012-2013. The influenza B virus containing the NA D197N substitution showed only a 2-fold increase in oseltamivir IC50 (therefore classified as NI), although in the AVWG table, it is listed that the substitution confers 4- to 10-fold increases in IC50 based on previous studies. 2014 Antiviral research Method IV D197N 40 45 37 39 25043638 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2012-2013. The most commonly detected NA amino acid substitution was E119V, present in three of the five viruses for which sequences were available (Table 2), two from the Americas and one from the Western Pacific. 2014 Antiviral research Method IV E119V 58 63 27 29 25043638 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2012-2013. The most commonly detected NA amino acid substitution was H275Y, present in 18 viruses showing RI or HRI by oseltamivir (22 viruses tested) and peramivir (13 viruses tested). 2014 Antiviral research Method IV H275Y 58 63 27 29 25043638 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2012-2013. The NA N295S substitution was subsequently confirmed in the clinical specimen from which A/Salta/1341/2012 was isolated. 2014 Antiviral research Method IV N295S 7 12 4 6 25043638 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2012-2013. The viruses with the D199N substitution showed 2- to 3-fold increases in oseltamivir IC50, values similar to the 3-fold increase listed in the AVWG table based on a previous study, however they were below the threshold of RI by definition. 2014 Antiviral research Method IV D199N 21 26 25043638 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2012-2013. This NA N295S substitution has been reported previously in clinical specimens. 2014 Antiviral research Method IV N295S 8 13 5 7 25043638 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2012-2013. Twenty-two of the 1083 (2%) N1 sequences from A(H1N1)pdm09 viruses contained the H275Y substitution (Table 3), of which 16 had been analysed by NA inhibition assay at one of the WHO CCs and are included in the viruses shown in. 2014 Antiviral research Method IV H275Y 81 86 144 146 25043638 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2012-2013. Two NA sequences identified in the databases, one with an N2 E119V substitution and the other a B NA I221T substitution (Table 4), were not among the viruses tested by phenotypic assays at the WHO CCs. 2014 Antiviral research Method IV E119V;I221T 61;101 66;106 NA;NA 4;98 6;100 25043638 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2012-2013. Two viruses from epidemiologically related cases in the Western Pacific Region contained NA H273Y substitutions which conferred 210- to 322-fold increases in peramivir IC50 but had no effect on susceptibility to the other NAIs. 2014 Antiviral research Method IV H273Y 92 97 NA;NAI 89;222 91;226 25066276 Development and clinical testing of a simple, low-density gel element array for influenza identification, subtyping, and H275Y detection. 3.8 Influenza typing, subtyping, and H275Y variant detection. 2014 Journal of virological methods Method IV H275Y 37 42 25066276 Development and clinical testing of a simple, low-density gel element array for influenza identification, subtyping, and H275Y detection. Assay targets included primers and probes for influenza A (M gene), influenza B (NS gene), seasonal H1 and H3 subtyping (HA gene), pandemic influenza A H1 (2009 pandemic NP and HA genes), H275Y variants of seasonal and pandemic H1N1 (NA genes), and a sample collection, extraction, amplification, and inhibition control (human GAPDH). 2014 Journal of virological methods Method IV H275Y 188 193 HA;HA;M;NA;NP;NS 121;177;59;234;170;81 123;179;60;236;172;83 25066276 Development and clinical testing of a simple, low-density gel element array for influenza identification, subtyping, and H275Y detection. Due to a lack of available clinical H1pdm09 samples containing the H275Y variant, pH275Y viral isolates were spiked into influenza-negative sample matrix to obtain the 30 total pH275Y samples (one pH275Y clinical sample was available for testing). 2014 Journal of virological methods Method IV H275Y 67 72 M 147 153 25066276 Development and clinical testing of a simple, low-density gel element array for influenza identification, subtyping, and H275Y detection. GenBank accessible sequences include CY173087-CY173094 (A/NY/1128/2008(H3N2)), CY173063-CY173070 (A/NY/1124/2008(H1N1)), CY39893-CY39890 (A/NY/1669/2009(H1N1)), and CY175289-CY175296 (B/NY/1195/2008)); sequences for the seasonal and pandemic H275Y positive control variants are not yet available. 2014 Journal of virological methods Method IV H275Y 242 247 25066276 Development and clinical testing of a simple, low-density gel element array for influenza identification, subtyping, and H275Y detection. To determine LoDs and the ability of the array to distinguish seasonal or pandemic oseltamivir-resistant H275Y variants from their corresponding wild-type virus (WT) in a mixed population, quantified RNA from cultured isolates of sH275Y or pH275Y were mixed with WT RNA in ratios from 0:100 to 100:0 to achieve a total of 1 x 105 gc per asymmetric-RT-PCR reaction. 2014 Journal of virological methods Method IV H275Y 105 110 25066276 Development and clinical testing of a simple, low-density gel element array for influenza identification, subtyping, and H275Y detection. Two hundred nasopharyngeal swab samples in commercially-available, standard viral transport medium (collected between 2007 and 2012) were selected to evaluate test performance and identify signal-to-noise ratio (SNR) thresholds for detecting the H275Y variant. 2014 Journal of virological methods Method IV H275Y 246 251 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. As an alternative method of measuring the actual ratio in the inoculums and passage-one viral progeny cultures, plaque assays were performed for the isolation of 32 clones for each population, and then RT-PCR of the PB1 gene region containing the V43I signature mutation was performed separately using the above primers to distinguish the wild-type from the mutant viruses using Sanger sequencing. 2014 Nature communications Method IV V43I 247 251 PB1 216 219 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. Cells were then infected with recombinant Wuhan95 or VN04 wild-type or PB1-V43I mutant viruses at an MOI of 0.1 for both drugs (Wuhan95), 0.1 for ribavirin (VN04), and 0.001 for favipiravir (VN04) and incubated for 1 hour. 2014 Nature communications Method IV V43I 75 79 PB1 71 74 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. Introducing the PB1-V43I mutation into the VN04 virus was anticipated to reduce viral virulence, as was indeed observed, with viruses with a high-fidelity RdRP exhibiting reduced pathogenicity in the mouse model . 2014 Nature communications Method IV V43I 20 24 PB1 16 19 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. Log-rank test was performed to compare the survival rate of mice inoculated with the VN04 wild-type and PB1-V43I mutant viruses. 2014 Nature communications Method IV V43I 108 112 PB1 104 107 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. One-step growth curves were determined for wild-type and the PB1-V43I mutant viruses in MDCK cells. 2014 Nature communications Method IV V43I 65 69 PB1 61 64 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. Pathogenicity of VN04 wild-type and V43I viruses in mice. 2014 Nature communications Method IV V43I 36 40 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. To compare the differences between wild-type and PB1-V43I mutant to replicate at suboptimal temperatures (33 C and 37 C), 0.5% agarose was used and triplicates of 6-wells were used to incubate for 48 hours at these temperatures. 2014 Nature communications Method IV V43I 53 57 PB1 49 52 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. To determine if the difference among wild-type and PB1-V43I viruses is statistically significant for at least one of the experiments, a 2x2 contingency table was formulated comparing the categories of the number of sequences with no mutation and those with at least one mutation. 2014 Nature communications Method IV V43I 55 59 PB1 51 54 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. To determine the Mouse Lethal Dose (MLD50) of VN04 wild-type and PB1-V43I viruses, 6-week-old female BALB/c mice were anesthetized with ketamine and xylazine and inoculated intra-nasally with 10-fold serial diluted wild-type or the PB1-V43I viruses in 25 muL of PBS. 2014 Nature communications Method IV V43I;V43I 69;236 73;240 PB1;PB1 65;232 68;235 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. To determine the survival curve groups of mice were inoculated with wild-type or PB1-V43I viruses at 100 or 10 pfu per mice in 25muL of PBS. 2014 Nature communications Method IV V43I 85 89 PB1 81 84 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. To quantify the luciferase mRNA copy numbers by quantitative real-time PCR, 293T cells transfected with wild-type or PB1-V43I polymerase complexes under increasing concentration of guanosine were lysed to extract total RNA using RNEasy kit (Qiagen). 2014 Nature communications Method IV V43I 121 125 PB1 117 120 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. Triplicates of 32-48 clones for each of wild-type or PB1-V43I virus were picked and grown in Luria Broth with ampicillin. 2014 Nature communications Method IV V43I 57 61 PB1 53 56 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. Wild-type and PB1-V43I mutant viruses were mixed into three different ratios to infect MDCK cells in triplicate 6-wells at an MOI of 0.1. 2014 Nature communications Method IV V43I 18 22 PB1 14 17 25191344 Prevalence of Oseltamivir-Resistant 2009 H1N1 Influenza Virus among Patients with Pandemic 2009 H1N1 Influenza infection in NRITLD, Tehran, Iran. The Viral load and H275Y mutation were determined using the Primer Design Quantification of Swine H1N1 Influenza Human Pandemic Strain kit and Primer Design Tami flu resistance genotyping kit (Primer Design TM Ltd, UK), respectively. 2011 Tanaffos Method IV H275Y 19 24 25409547 The K526R substitution in viral protein PB2 enhances the effects of E627K on influenza virus replication. Full-length PB2 sequences of human and avian H5N1, H9N2, H7N7 and H7N9 viruses from the National Center for Biotechnology Information (NCBI) Influenza Virus Resource Database, together with all influenza A H7N9 human isolates in the Global Initiative on Sharing All Influenza Data (GISAID) database (http://gisaid.org) were analysed for prevalence of the K526R substitution. 2014 Nature communications Method IV K526R 355 360 PB2 12 15 25470189 Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel. 11 was placed in the channel with the bromo-thiophene moiety facing H37 and V27 in the WT M2-TM and S31N mutant, respectively. 2014 Journal of the American Chemical Society Method IV S31N 100 104 M2 90 92 25470189 Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel. All compounds were initially tested in TEVC assay using Xenopus laevis frog oocytes microinjected with RNA expressing either the WT or the S31N mutant of M2 as described in a previous report. 2014 Journal of the American Chemical Society Method IV S31N 139 143 M2 154 156 25470189 Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel. For A/M2-S31N (19-49) VANIG, calcd MS: 1549.3 (+2H), 1033.2 (+3H). 2014 Journal of the American Chemical Society Method IV S31N 9 13 M2 6 8 25470189 Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel. Isotopically labeled peptides used in this study, A/M2-WT (19-49) VASIGH and A/M2-S31N (19-49) VANIG, were synthesized using the optimized solid phase synthesis protocol as described previously. 2014 Journal of the American Chemical Society Method IV S31N 82 86 M2;M2 52;79 54;81 25470189 Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel. Models were calculated with those peptide-drug NOEs in addition to distance constraints and backbone dihedral angle constraints from the S31N-WJ332 (2) structure. 2014 Journal of the American Chemical Society Method IV S31N 137 141 25470189 Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel. The final NMR sample conditions are the following: for S31N, 2 mM A/M2-S31N (19-49) (monomer), 20 mM 11, 100 mM deuterated DPC, and 50 mM sodium phosphate buffer in 10% D2O, 90% H2O, pH 6.8; for WT, 2 mM A/M2-WT (19-49) (monomer), 2.5 mM 11, 100 mM deuterated DPC (Cambridge Isotope Laboratories), and 50 mM sodium phosphate buffer in 10% D2O, 90% H2O, pH 7.5. 2014 Journal of the American Chemical Society Method IV S31N;S31N 55;71 59;75 M2;M2 68;206 70;208 25470189 Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel. To obtain assignments, 2D 15N and 13C HSQC for both WT (19-49) VASIGH and S31N (19-49) VANIG M2 in the absence/presence of 11, and 2D 13C-(13C)-1H TOCSY experiments for both M2 samples in the presence of 11 were carried out. 2014 Journal of the American Chemical Society Method IV S31N 74 78 M2;M2 93;174 95;176 25470189 Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel. WT M2-expressing A/Udorn/72 and M2-S31N-expressing A/WSN/33 were used to infect MDCK cells in the presence or absence of compounds to evaluate their antiviral activity. 2014 Journal of the American Chemical Society Method IV S31N 35 39 M2;M2 3;32 5;34 25701593 Influenza A viruses of swine circulating in the United States during 2009-2014 are susceptible to neuraminidase inhibitors but show lineage-dependent resistance to adamantanes. (accessed 10/23/2014) were screened for the presence of known molecular markers (N2 numbering) of NAI resistance that demonstrated clinical relevance in human influenza A viruses of N1 (D198N, I222R, H274Y, N294S) or N2 (E119V, R292K, N294S) subtypes, and for NA markers reported in surveillance studies or in recombinant viruses of N1 (V116A, I117V, E119V, Q136L/K, V149A, Y155H, I222V/M/K, S246N/G) or N2 (E119I, Q136K, D151E/V, S246P) subtypes. 2015 Antiviral research Method IV D198N;I222R;H274Y;N294S;E119V;R292K;N294S;V116A;I117V;E119V;Q136L;Q136K;V149A;Y155H;I222V;I222M;I222K;S246N;S246G;E119I;Q136K;D151E;D151V;S246P 186;193;200;207;221;228;235;337;344;351;358;358;367;374;381;381;381;392;392;408;415;422;422;431 191;198;205;212;226;233;240;342;349;356;365;365;372;379;390;390;390;399;399;413;420;429;429;436 NA;NAI 260;98 262;101 25701593 Influenza A viruses of swine circulating in the United States during 2009-2014 are susceptible to neuraminidase inhibitors but show lineage-dependent resistance to adamantanes. Additionally, we screened N1 IAV-S sequences for permissive substitutions that maintained full NA function in the presence of the H274Y-NA. 2015 Antiviral research Method IV H274Y 130 135 NA;NA 95;136 97;138 25713566 PB2 segment promotes high-pathogenicity of H5N1 avian influenza viruses in mice. Likewise, mutant QL90 viruses were designated 90-Lys39Gln, 90-Val649Ile, 90-Ala684Thr, and 90-Asn715Ser, respectively. 2015 Frontiers in microbiology Method IV K39Q;V649I;A684T;N715S 49;62;76;94 57;71;85;103 25713566 PB2 segment promotes high-pathogenicity of H5N1 avian influenza viruses in mice. Mutant DK212 viruses containing a substitution of the PB2 amino acid residue at position Gln39Lys, Ile649Val, Thr684Ala, and Ser715Asn were designated 212-Gln39Lys, 212-Ile649Val, 212-Thr684Ala, and 212-Ser715Asn. 2015 Frontiers in microbiology Method IV Q39K;I649V;T684A;S715N;Q39K;I649V;T684A;S715N 155;169;184;203;89;99;110;125 163;178;193;212;97;108;119;134 PB2 54 57 25713566 PB2 segment promotes high-pathogenicity of H5N1 avian influenza viruses in mice. To detect the polymerase activity of viruses, the plasmid pMD18T-NP-LUCI was constructed. 2015 Frontiers in microbiology Method IV P18T;M18T;D18T 58;58;58 64;64;64 NP 65 67 25721488 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2013-2014. 2 and Table 1), of which the NA amino acid substitution H275Y was present in 169 of those. 2015 Antiviral research Method IV H275Y 56 61 29 31 25721488 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2013-2014. 4B) gene sequences showed, in both phylogenetic trees, that the H275Y variant viruses did not emerge from a common source. 2015 Antiviral research Method IV H275Y 64 69 25721488 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2013-2014. Analysis of the available sequences also identified 25 N1 sequences from A(H1N1)pdm09 viruses containing D199N substitution, of which seven originated from Bulgaria, and four influenza B NA sequences containing D197N substitution (Table 3). 2015 Antiviral research Method IV D199N;D197N 105;211 110;216 187 189 25721488 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2013-2014. Based on available antiviral treatment information, 10 of the 12 H275Y/H mixed variants were recovered from patients during or after treatment with oseltamivir or peramivir. 2015 Antiviral research Method IV H275Y;H275H 65;65 72;72 25721488 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2013-2014. H275Y in A(H1N1)pdm09 viruses), or are known to occur clinically. 2015 Antiviral research Method IV H275Y 0 5 25721488 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2013-2014. However, NA Q136K substitution has been reported previously in clinical specimens. 2015 Antiviral research Method IV Q136K 12 17 9 11 25721488 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2013-2014. However, the H275Y variants from China were genetically similar to those from the Hokkaido cluster. 2015 Antiviral research Method IV H275Y 13 18 25721488 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2013-2014. In China, nine H275Y variant viruses were detected in nine provinces, while the oseltamivir exposure history of four patients was unknown, the remaining five had no exposure to oseltamivir. 2015 Antiviral research Method IV H275Y 15 20 25721488 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2013-2014. In the AVWG table, it is listed that the NA E119V substitution confers 18-fold (RI) to 2057-fold (HRI) increases in oseltamivir IC50. 2015 Antiviral research Method IV E119V 44 49 41 43 25721488 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2013-2014. Indeed, a cluster of A(H1N1)pdm09 viruses with the NA H275Y substitution was detected in 39 (29%) of 135 untreated community cases in Sapporo, capital of Hokkaido, Japan (described in detail in). 2015 Antiviral research Method IV H275Y 54 59 51 53 25721488 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2013-2014. NA amino acid substitutions N151S and D197N were detected in B/Yamagata-lineage HA - B/Victoria-lineage NA reassortants. 2015 Antiviral research Method IV N151S;D197N 28;38 33;43 HA;NA;NA 80;0;104 82;2;106 25721488 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2013-2014. NA amino acid substitutions N151T and S249N were detected in viruses with elevated IC50 values (Table 1). 2015 Antiviral research Method IV N151T;S249N 28;38 33;43 0 2 25721488 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2013-2014. NA amino acid substitutions T148K, N329K, S331R and V215I were detected in viruses with IC50 fold-change values that were close to the intersect between NI and RI categories for oseltamivir and/or zanamivir. 2015 Antiviral research Method IV T148K;N329K;S331R;V215I 28;35;42;52 33;40;47;57 0 2 25721488 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2013-2014. NA T148K and D151G substitutions can emerge during culturing of A(H3N2) viruses. 2015 Antiviral research Method IV T148K;D151G 3;13 8;18 0 2 25721488 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2013-2014. Of 1328 N1 sequences from A(H1N1)pdm09 viruses, 165 (12%) contained NA H275Y substitution, of which 16 showed NA 275Y/H polymorphism and one carried NA H275Y/I223R dual substitutions (Table 2). 2015 Antiviral research Method IV H275Y;I223R;H275Y 71;158;152 76;163;157 NA;NA;NA 68;110;149 70;112;151 25721488 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2013-2014. Of the H275Y variant viruses detected in 2013-2014 where patient setting information was available, 82% were from non-hospitalised patients (Table 1). 2015 Antiviral research Method IV H275Y 7 12 25721488 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2013-2014. Of the remaining H275Y variants recovered, 82% were from patients had not been treated with NAIs before specimen collection, suggesting that there is potential for spontaneous emergence and spread of these resistant viruses in the community. 2015 Antiviral research Method IV H275Y 17 22 NAI 92 96 25721488 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2013-2014. One A(H3N2) virus from the United States contained a NA E119V substitution which conferred HRI by oseltamivir but had no effect on susceptibility to the other NAIs. 2015 Antiviral research Method IV E119V 56 61 NA;NAI 53;159 55;163 25721488 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2013-2014. One B/Victoria-lineage virus from Bangladesh with a NA E117G substitution showed HRI by three of the four NAIs tested with a 2326-fold increase in peramivir IC50, a 1010-fold increase in zanamivir IC50, a 649-fold increase in laninamivir IC50 and RI with a 12-fold increase in oseltamivir IC50 compared to values for B/Victoria-lineage viruses displaying NI by the four NAIs (Table 1). 2015 Antiviral research Method IV E117G 55 60 NA;NAI;NAI 52;106;370 54;110;374 25721488 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2013-2014. One B/Yamagata-lineage virus from Macau, China contained an NA H273Y substitution which conferred HRI (103-fold increase) by peramivir and RI (7.1-fold increase) by oseltamivir but had no effect on susceptibility to zanamivir and laninamivir (Table 1). 2015 Antiviral research Method IV H273Y 63 68 60 62 25721488 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2013-2014. One H275Y variant with an additional NA I223R substitution was detected in Japan from a hospitalised patient treated with peramivir; this dual substitution has been reported previously by the United States, in a child after prolonged treatment with oseltamivir. 2015 Antiviral research Method IV H275Y;I223R 4;40 9;45 37 39 25721488 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2013-2014. One of the two D197N variant viruses, came from a patient during treatment with zanamivir, but no information was available for the second patient. 2015 Antiviral research Method IV D197N 15 20 25721488 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2013-2014. Other NA amino acid substitutions (D199E, I223K, I223T, I223R and S247G) were detected in viruses with elevated IC50 values. 2015 Antiviral research Method IV D199E;I223K;I223T;I223R;S247G 35;42;49;56;66 40;47;54;61;71 6 8 25721488 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2013-2014. Seven H275Y variant viruses were in the sequence database but not present in the WHO CCs IC50 dataset. 2015 Antiviral research Method IV H275Y 6 11 25721488 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2013-2014. The 165 H275Y variant viruses were derived from 11 countries. 2015 Antiviral research Method IV H275Y 8 13 25721488 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2013-2014. The A(H1N1)pdm09 viruses with NA D199N substitution showed NI. 2015 Antiviral research Method IV D199N 33 38 30 32 25721488 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2013-2014. The clinical specimen yielding the N151T variant did not contain the substitution. 2015 Antiviral research Method IV N151T 35 40 25721488 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2013-2014. The clinical specimen yielding the S249N variant also contained the substitution. 2015 Antiviral research Method IV S249N 35 40 25721488 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2013-2014. The clinical specimens yielding four of these isolates were available and all contained the corresponding substitutions; no matching clinical specimen was available for the viruses carrying NA D199E or NA I223R substitutions. 2015 Antiviral research Method IV D199E;I223R 193;205 198;210 NA;NA 190;202 192;204 25721488 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2013-2014. The E119V variant virus came from an oseltamivir-treated patient. 2015 Antiviral research Method IV E119V 4 9 25721488 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2013-2014. The H275Y variants were detected between weeks 24/2013 and 15/2014. 2015 Antiviral research Method IV H275Y 4 9 25721488 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2013-2014. The H275Y/H mixed variants showed 5.4- to 584-fold higher oseltamivir IC50 values and 4.8- to 599-fold higher peramivir IC50 values, depending on the proportion of the H275Y variant in the mixed population. 2015 Antiviral research Method IV H275H;H275Y;H275Y 4;4;168 11;11;173 25721488 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2013-2014. The H275Y/I223R variant showed HRI with very high increases in oseltamivir (10,739-fold) and peramivir (7709-fold) IC50 values and RI by zanamivir and laninamivir, with 18.1- and 22-fold IC50 increases respectively, compared to values for A(H1N1)pdm09 viruses displaying NI by the four NAIs. 2015 Antiviral research Method IV H275Y;I223R 4;10 9;15 NAI 286 290 25721488 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2013-2014. The H275Y/I223R variant virus had been analysed by NA inhibition assay at a WHO CC and is included in. 2015 Antiviral research Method IV H275Y;I223R 4;10 9;15 51 53 25721488 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2013-2014. The IC50 fold-changes for virus with the dual substitution NA H275Y/I223R compared to those of viruses with NA H275Y or NA I223R only. 2015 Antiviral research Method IV H275Y;I223R;H275Y;I223R 62;68;111;123 67;73;116;128 NA;NA;NA 59;108;120 61;110;122 25721488 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2013-2014. The influenza B viruses containing NA D197N substitution showed RI to one or more of the NAIs. 2015 Antiviral research Method IV D197N 38 43 NA;NAI 35;89 37;93 25721488 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2013-2014. The NA D197N substitution has been observed before in B/Yamagata-lineage virus and shown to confer RI by zanamivir and peramivir. 2015 Antiviral research Method IV D197N 7 12 4 6 25721488 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2013-2014. The NA E119V substitution was detected in the corresponding clinical specimen. 2015 Antiviral research Method IV E119V 7 12 4 6 25721488 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2013-2014. The NA H275Y substitution conferred 151- to 2212-fold higher oseltamivir IC50 values and 87- to 2045-fold higher peramivir IC50 values compared to wild type viruses, but had little or no effect on zanamivir or laninamivir susceptibility (Table 1). 2015 Antiviral research Method IV H275Y 7 12 4 6 25721488 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2013-2014. The NA H275Y substitution was confirmed in 58 clinical specimens for which sequence results were available and the NA I223R substitution was confirmed in the clinical specimen from which the H275Y/I223R variant virus was isolated (Table 1). 2015 Antiviral research Method IV H275Y;I223R;H275Y;I223R 7;118;191;197 12;123;196;202 NA;NA 4;115 6;117 25721488 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2013-2014. The timing of specimen collection and geographic distribution of the 169 H275Y variant viruses are shown in. 2015 Antiviral research Method IV H275Y 73 78 25721488 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2013-2014. The two viruses carrying NA D197N substitution yielded different patterns of NI and RI by all NAIs, around the intersect between NI and RI categories; only for peramivir did both show RI. 2015 Antiviral research Method IV D197N 28 33 NA;NAI 25;94 27;98 25721488 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2013-2014. Three of these had a NA Q136K amino acid substitution (Table 1). 2015 Antiviral research Method IV Q136K 24 29 21 23 25721488 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2013-2014. Twelve of the 169 H275Y variants harboured a mixed population of H275Y variant virus and H275 wild type virus. 2015 Antiviral research Method IV H275Y;H275Y 18;65 23;70 25721488 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2013-2014. Twentyone of the 25 N1 D199N variants and three of the four B NA D197N variants had been analysed by NA inhibition assay at the WHO CCs. 2015 Antiviral research Method IV D199N;D197N 23;65 28;70 NA;NA 62;101 64;103 25721488 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2013-2014. Two N2 sequences contained E119V substitution, with no evidence for 119E/V mixtures, and both E119V variants were analysed by NA inhibition assay at the WHO CCs. 2015 Antiviral research Method IV E119V;E119V 27;94 32;99 126 128 25742269 Oseltamivir-resistant influenza A(H1N1)pdm2009 strains found in Brazil are endowed with permissive mutations, which compensate the loss of fitness imposed by antiviral resistance. Sequences with the mutation H275Y found in our analysis were deposited in GenBank (accessions KC984901, KC984933, KJ493404 and KJ493405). 2015 Memorias do Instituto Oswaldo Cruz Method IV H275Y 28 33 25768797 Adamantane-resistant influenza a viruses in the world (1902-2013): frequency and distribution of M2 gene mutations. The frequencies of the appearance of recognized adamantine resistance-associated amino acids (L26F, V27A, A30T, A30V, S31N, G34E, and L38F) were identified and tabulated. 2015 PloS one Method IV L26F;V27A;A30T;A30V;S31N;G34E;L38F 94;100;106;112;118;124;134 98;104;110;116;122;128;138 25876137 SNPer: an R library for quantitative variant analysis on single nucleotide polymorphisms among influenza virus populations. For example, the first SNP at location 51 is A51G (VIROAF1 contains allele G while reference contains allele A at position 51 of HA gene fragment). 2015 PloS one Method IV A51G 45 49 HA 129 131 25939747 Two polar residues within C-terminal domain of M1 are critical for the formation of influenza A Virions. Amplification was performed by polymerase chain reaction (PCR) with Pfu polymerase and primers containing the appropriate base changes generating plasmids pET-30a-M1-L181A, pET-30a-M1-S183A, pET-30a-M1-T184A, pET-30a-M1-T185A, pET-30a-M1-K187A, pET-30a-M1-M189A, pET-30a-M1-E190A, pET-30a-M1-Q191A, pET-30a-M1-M192A, pET-30a-M1-S183A/T185A. 2015 Cellular microbiology Method IV L181A;S183A;T184A;T185A;K187A;M189A;E190A;Q191A;M192A;S183A;T185A 166;184;202;220;238;256;274;292;310;328;334 171;189;207;225;243;261;279;297;315;333;339 M1;M1;M1;M1;M1;M1;M1;M1;M1;M1 163;181;199;217;235;253;271;289;307;325 165;183;201;219;237;255;273;291;309;327 25939747 Two polar residues within C-terminal domain of M1 are critical for the formation of influenza A Virions. Briefly, uninfected MDCK cells and MDCK cells infected with WSN or WSN-M1-S183A or WSN-M1-T185A viruses at MOI 0.5 were fixed with 3% glutaraldehyde in 0.1 M cacodylate buffer at 16 h post-infection and post-fixed with 2% osmium tetroxide in the same buffer. 2015 Cellular microbiology Method IV S183A;T185A 74;90 79;95 M1;M1 71;87 73;89 25939747 Two polar residues within C-terminal domain of M1 are critical for the formation of influenza A Virions. pHH21-M1-S183A, pHH21-M1-T185A and pHH21-M1-S183A/T185A derived from pHH21-M1 in the 12 plasmid system of A/WSN/1933 virus. 2015 Cellular microbiology Method IV S183A;T185A;S183A;T185A 9;25;44;50 14;30;49;55 M1;M1;M1;M1 6;22;41;75 8;24;43;77 25939747 Two polar residues within C-terminal domain of M1 are critical for the formation of influenza A Virions. The recovered viruses were named based on their mutated M1 as follows: WSN-M1-S183A and WSN-M1-T185A. 2015 Cellular microbiology Method IV S183A;T185A 78;95 83;100 M1;M1;M1 56;75;92 58;77;94 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. 2.63nM), and a 980-fold increase for the MUT-H275Y (IC50 = 451.9nM). 2015 PloS one Method IV H275Y 45 50 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. Previous work has measured a 6-fold increase in oseltamivir resistance for the MUT-I223V single-mutant (IC50 = 0.46nM vs. 2015 PloS one Method IV I223V 83 88 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. Recombinant H1N1pdm09 WT-I223 (wild-type) and MUT-I223V (mutant) viruses were rescued by reverse genetics from the first sample of 2009 pandemic influenza A (H1N1pdm09) isolate in Quebec, Canada (A/Quebec/144147/09) as described previously. 2015 PloS one Method IV I223V 50 55 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. The specific probes for the I223V discrimination assay were designed with Exiquon LNA Oligo design tools and follow the guideline for design of LNA probes that improve mismatch discrimination. 2015 PloS one Method IV I223V 28 33 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. The specific WT-I223 probe (5'-ACA A T A TA T TG A GAA C6-FAM/BHQ-1) and MUT-I223V probe (5'-ACA A TG TA T TG A GAA C-Cy5/BHQ-2) were designed around nucleotide position 667 of the NA gene. 2015 PloS one Method IV I223V 77 82 181 183 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. The WT-I223 and MUT-I223V differ only by a single isoleucine-to-valine amino acid substitution at residue 223 of the N1 NA protein. 2015 PloS one Method IV I223V;I223V 20;50 25;109 120 122 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. The WT-I223 is identical to the H1N1pdm09 WT-H275 strain previously analyzed, and the MUT-H275Y differs from the wild-type by only a single histidine-to-tyrosine substitution at residue 275. 2015 PloS one Method IV H275Y;H275Y 90;140 95;189 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. These viral yield experiments were conducted on Madin-Darby canine kidney (MDCK) cells modified to express alpha-2,6 sialic acid receptors (MDCKalpha2,6) at levels more consistent with those found on the surface of epithelial cells in the human upper respiratory tract, as in the previous experiment that examined the same H1N1pdm09 wild-type (WT-H275) and the MUT-H275Y single mutant. 2015 PloS one Method IV H275Y 365 370 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. We performed single-cycle (SC), multiple-cycle (MC), and mock-yield (MY) assays on both the H1N1pdm09 strain A/Quebec/144147/09 (WT-I223) and its mutant counterpart (MUT-I223V). 2015 PloS one Method IV I223V 170 175 26038410 Adaptive mutation in influenza A virus non-structural gene is linked to host switching and induces a novel protein by alternative splicing. A549 infected with rHK-wt or rHK-NS-D125G cell lysate harvested 8 hpi were incubated with NS1 antibody-conjugated beads for 1 h at room temperature while rocking, then were washed with NP-40 lysis buffer. 2012 Emerging microbes & infections Method IV D125G 36 41 NP;NS;NS1 185;33;90 187;35;93 26038410 Adaptive mutation in influenza A virus non-structural gene is linked to host switching and induces a novel protein by alternative splicing. Monolayers of M1 cells were infected with each of the following rHK viruses NS1-wt, NS1-M124I, NS1-D125G and NS1-M124I+D125G at an MOI of 1 and overlaid with serum-free MEM. 2012 Emerging microbes & infections Method IV M124I;D125G;M124I;D125G 88;99;113;119 93;104;118;124 M1;NS1;NS1;NS1;NS1 14;76;84;95;109 16;79;87;98;112 26038410 Adaptive mutation in influenza A virus non-structural gene is linked to host switching and induces a novel protein by alternative splicing. NS1 (wt and D125G(GAT GGT)) and NS3 genes were inserted into the bidirectional pLLB plasmid for expression in vitro using the TnT T7 Quick-Coupled Transcription/Translation System (Promega, Thermo Fisher Scientific) in the presence of 10 microCi 35S-methionine and cysteine (Express 35S Protein Labeling Mix; Perkin Elmer, Waltham, MA, USA). 2012 Emerging microbes & infections Method IV D125G 12 17 NS;NS1 32;0 34;3 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. A TaqMan single nucleotide polymorphisms (SNPs) assay for detecting the NA R292K oseltamivir-resistance mutation was established, with primers (forward: 5'-CAT GTT ACG GGR ARC GAA CAG G-3', reverse: 5'-TGG TCT ATT TGA GCC CTG CC A-3'), and probes (K292: FAM5'-CAC ATG CAA GGA CAA-3'MGB; R292: VIC5'-CAC ATG CAG GGA CAA-3'MGB). 2014 Emerging microbes & infections Method IV R292K 75 80 72 74 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. An R292K mutation was later found in throat swab samples starting from day 4 after oseltamivir treatment using genotypic analysis. 2014 Emerging microbes & infections Method IV R292K 3 8 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. Briefly, confluent cells in 96-well plates were inoculated with SH5190 or SH5190 R292K diluted in DMEM (50 PFU/well) at 37 C for 1 h. 2014 Emerging microbes & infections Method IV R292K 81 86 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. Confluent MDCK cells in six well plates were infected with SH5190 or SH5190 R292K at an multiplicity of infection (MOI) of 0.001 PFU per cell. 2014 Emerging microbes & infections Method IV R292K 76 81 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. Confluent MDCK cells in six-well plates were infected with SH5190 or SH5190 R292K and diluted to 100 plague forming unit (PFU) per well in dulbecco's modified eagle medium (DMEM). 2014 Emerging microbes & infections Method IV R292K 76 81 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. MDCKcells were infected with SH5190 R292K or SH5190 at an MOI of 0.001 and were overlaid with medium containing oseltamivir carboxylate, zanamivir, peramivir, T705, ribavirin and NT-300 alone or in combination (as indicated) at fixed molar ratios (for SH5190 R292K: T-705/zanamivir=1:3, ribavirin/zanamivi=1:4, NT-300/zanamivir=1:20, T-705/peramivir=1:9, ribavirin/peramivir=1:9, NT-300/peramivir=1:60, NT-300/ribavirin=1:5, T705/ribavirin=4:5, T-705/NT-300=4:1; for SH5190 wild-type:/T-705/OC=25:3, ribavirin/OC=9:1, NT-300/OC=1:3, T-705/zanamivir=25:4, ribavirin/zanamivir=27:4, NT-300/zanamivir=1:4, T-705/peramivir=250:6, ribavirin/peramivir=270:6, NT-300/peramivir=5:3, NT-300/Ribavirin=1:27, T705/Ribavirin=25:27, T-705/NT-300=25:1). 2014 Emerging microbes & infections Method IV R292K;R292K 36;259 41;264 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. Mice (n=16-18) were inoculated intranasally with 103 or 105 PFU of SH5190 or SH5190 R292K in 50 microL phosphate buffered saline (PBS) under isoflurane anesthesia. 2014 Emerging microbes & infections Method IV R292K 84 89 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. The genome sequences of SH5190 R292K (KF997839-KF-997846) and SH5190 wild-type (KF997831-KF997838) are available at NCBI. 2014 Emerging microbes & infections Method IV R292K 31 36 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. The R292K variant (SH5190 R292K) was derived after serial passages and plaque purification. 2014 Emerging microbes & infections Method IV R292K;R292K 4;26 9;31 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. The sensitivity of the wild-type and the R292K variant to NAIs and non-NAIs were evaluated in MDCK cells against the following ranges of drugs: oseltamivir carboxylate (0.03-100 microM for wild-type, 0.3-1000 microM for mutant), peramivir (0.03-100 microM for wild-type, 0.3-1000 microM for mutant), zanamivir (0.03-100 microM for wild-type, 0.23-500 microM for mutant), ribavirin (0.03-100 microM), NT-300 (0.03-100 microM) and T705 (0.03-100 microM). 2014 Emerging microbes & infections Method IV R292K 41 46 NAI;NAI 58;71 62;75 26056814 Molecular Characterisation of the Haemagglutinin Glycan-Binding Specificity of Egg-Adapted Vaccine Strains of the Pandemic 2009 H1N1 Swine Influenza A Virus. Side-chain residues were rigid with the exception of the Q226R mutants, where a number of potential rotamers of R226 where described and included in the docking run. 2015 Molecules (Basel, Switzerland) Method IV Q226R 57 62 26056814 Molecular Characterisation of the Haemagglutinin Glycan-Binding Specificity of Egg-Adapted Vaccine Strains of the Pandemic 2009 H1N1 Swine Influenza A Virus. The D225G, Q226R, D225G/Q226R and K123N/Q226R RBS mutants were constructed by site-directed mutagenesis using the QuikChange II site-directed mutagenesis kit (Agilent Technologies, Mulgrave, Australia). 2015 Molecules (Basel, Switzerland) Method IV D225G;Q226R;D225G;Q226R;Q226R;K123N 4;11;18;24;40;34 9;16;23;29;45;39 26056814 Molecular Characterisation of the Haemagglutinin Glycan-Binding Specificity of Egg-Adapted Vaccine Strains of the Pandemic 2009 H1N1 Swine Influenza A Virus. Utilising the macromolecular model building program Coot mutants of 3UBE where built including D225G, Q226R and D225G/Q226R. 2015 Molecules (Basel, Switzerland) Method IV D225G;Q226R;D225G;Q226R 95;102;112;118 100;107;117;123 26077257 Influenza A(H7N9) virus acquires resistance-related neuraminidase I222T substitution when infected mallards are exposed to low levels of oseltamivir in water. Ten NA I222T isolates and three wild-type isolates were tested. 2015 Antimicrobial agents and chemotherapy Method IV I222T 7 12 4 6 26077257 Influenza A(H7N9) virus acquires resistance-related neuraminidase I222T substitution when infected mallards are exposed to low levels of oseltamivir in water. The hypothesis of no difference in mean IC50s of OC and ZA between wild-type virus and NA-I222T mutated virus was tested with a two-sample t test for independent samples with calculations of 95% confidence intervals (95% CI) for differences in means using Statistica v12 software (StatSoft). 2015 Antimicrobial agents and chemotherapy Method IV I222T 90 95 87 89 26391278 Dual E627K and D701N mutations in the PB2 protein of A(H7N9) influenza virus increased its virulence in mammalian models. Dual E627K and D701N mutations in the PB2 protein of A(H7N9) influenza virus increased its virulence in mammalian models. 2015 Scientific reports Method IV E627K;D701N 5;15 10;20 PB2 38 41 26391278 Dual E627K and D701N mutations in the PB2 protein of A(H7N9) influenza virus increased its virulence in mammalian models. Mutations were introduced into the pHW2000-AH1-PB2 plasmid using the QuikChange II Site-Directed Mutagenesis Kit (Stratagene) to generate the K627E, D701N and the double mutations (627E plus 701N). 2015 Scientific reports Method IV K627E;D701N 143;150 148;155 PB2 47 50 26422258 Oseltamivir Resistance in Influenza A(H6N2) Caused by an R292K Substitution in Neuraminidase Is Not Maintained in Mallards without Drug Pressure. Five samples with the NA R292K substitution (one or two from each experiment) and six wild type samples (two from each experiment) were tested regarding NA inhibition by OC and zanamivir. 2015 PloS one Method IV R292K 25 30 NA;NA 22;153 24;155 26422258 Oseltamivir Resistance in Influenza A(H6N2) Caused by an R292K Substitution in Neuraminidase Is Not Maintained in Mallards without Drug Pressure. Hypothesis testing on difference of IC50 values between R292K and wild type samples was done with the non-parametric Mann-Whitney U-test on difference in median values. 2015 PloS one Method IV R292K 56 61 26422258 Oseltamivir Resistance in Influenza A(H6N2) Caused by an R292K Substitution in Neuraminidase Is Not Maintained in Mallards without Drug Pressure. Three different isolates of oseltamivir resistant influenza A(H6N2) virus containing the NA amino acid substitution R292K (N2 numbering) were used. 2015 PloS one Method IV R292K 116 121 89 91 26422258 Oseltamivir Resistance in Influenza A(H6N2) Caused by an R292K Substitution in Neuraminidase Is Not Maintained in Mallards without Drug Pressure. viruses used in the experiments had the NA amino acid variants R292K, or R292K plus D113N, or R292K plus D141N. 2015 PloS one Method IV R292K;R292K;D113N;R292K;D141N 63;73;84;94;105 68;78;89;99;110 40 42 26583707 Influenza A(H6N1) Virus in Dogs, Taiwan. A primer set (M52C/M253R) specific for a highly conserved region of matrix (M) gene was used for detection of influenza A virus nucleotides. 2015 Emerging infectious diseases Method IV M253R;M52C 19;14 24;18 M;M 76;68 77;74 26583707 Influenza A(H6N1) Virus in Dogs, Taiwan. G228S substitution (H3 numbering) on the receptor binding site for HA was also observed for this virus, which indicated increased virus binding ability for the alpha2-6 sialic acid receptor . 2015 Emerging infectious diseases Method IV G228S 0 5 HA 67 69 26583707 Influenza A(H6N1) Virus in Dogs, Taiwan. In the M2 protein, A/canine/Taiwan/E01/2014 had an S31N substitution, which suggested resistance to admantanes . 2015 Emerging infectious diseases Method IV S31N 51 55 M2 7 9 26583707 Influenza A(H6N1) Virus in Dogs, Taiwan. Other major signatures associated with replication ability in a mammalian host or pathogenicity were also observed, including E627K in the PB2 and the PDZ ligand domain at the C-terminal region of NS1 of this virus. 2015 Emerging infectious diseases Method IV E627K 126 131 NS1;PB2 197;139 200;142 26583707 Influenza A(H6N1) Virus in Dogs, Taiwan. The amino acid H275Y substitution (oseltamivir resistance marker) in NA was not found in this virus. 2015 Emerging infectious diseases Method IV H275Y 15 20 69 71 26738596 Species difference in ANP32A underlies influenza A virus polymerase host restriction. The PB2 E627K substitution was made to 50-92, Ty05 (K627E) by overlapping PCR of the PB2 plasmid as previously described . 2016 Nature Method IV E627K;K627E 8;52 13;57 PB2;PB2 4;85 7;88 26845764 Genomic Signatures for Avian H7N9 Viruses Adapting to Humans. Site-directed mutagenesis was performed using pFLAG-CMV5.1-H7N9-PB2 to generate -K627E, -V139I&K627E, -K191E&K627E, -V511I&K627E, -M535L&K627E, -N559T&K627E, -M570I&K627E, -Q591K&K627E, -I647V&K627E, -M676V&K627E, and -D701N&K627E plasmids by mutagenic primer sets (S2 Table). 2016 PloS one Method IV K627E;V139I;K627E;K191E;K627E;V511I;K627E;M535L;K627E;N559T;K627E;K627E;M570I;K627E;Q591K;K627E;I647V;K627E;M676V;K627E;D701N 81;89;95;103;109;117;123;131;137;145;151;165;159;179;173;193;187;207;201;225;219 86;94;100;108;114;122;128;136;142;150;156;170;164;184;178;198;192;212;206;230;224 PB2 64 67 26847414 Amino acid changes in PB2 and HA affect the growth of a recombinant influenza virus expressing a fluorescent reporter protein. Briefly, HEK293 cells were transfected with viral protein expression plasmids for PB1, PA, NP and wild-type PB2 or PB2-E712D, with a plasmid expressing a reporter vRNA encoding the firefly luciferase gene under the control of the human RNA polymerase I promoter [pPolI/NP(0)Fluc(0)], and pRL-null (Promega), which expresses Renilla luciferase, as a transfection control. 2016 Scientific reports Method IV E712D 119 124 NP;NP;PA;PB1;PB2;PB2 91;269;87;82;108;115 93;271;89;85;111;118 26847414 Amino acid changes in PB2 and HA affect the growth of a recombinant influenza virus expressing a fluorescent reporter protein. HEK293 cells were infected with wild-type PR8 or PR8 possessing the HA-T380A mutation in DMEM containing 10% FCS at an MOI of 10. 2016 Scientific reports Method IV T380A 71 76 HA 68 70 27097026 Novel Polymerase Gene Mutations for Human Adaptation in Clinical Isolates of Avian H5N1 Influenza Viruses. Furthermore, a mouse infection study was performed after observing no increase in progeny vRNA production of the selected viruses carrying mutations compared to previously published studies, and the PB2-D701N mutant virus was excluded from the in vivo mouse infection study although this mutant showed reduced progeny vRNA production in human cells compared to EG/D1 (wt) virus. 2016 PLoS pathogens Method IV D701N 203 208 PB2 199 202 27097026 Novel Polymerase Gene Mutations for Human Adaptation in Clinical Isolates of Avian H5N1 Influenza Viruses. In this study, all the mutations introduced into recombinant EG/D1 virus (clade 2.2.1) were naturally detected as single/multiple intra-segment mutations or inter-segment combinations of the mutations in clade 2.2.1 viruses isolated from patients, except artificial mutation PB2-D701N. 2016 PLoS pathogens Method IV D701N 279 284 PB2 275 278 27405392 G45R mutation in the nonstructural protein 1 of A/Puerto Rico/8/1934 (H1N1) enhances viral replication independent of dsRNA-binding activity and type I interferon biology. coli strain BL21 transformed with pQE plasmids containing the amino acid 1-73 of the RBD of PR8 NS1 including WT or mutants G45R and AA were grown in Luria broth with 100 mg/ml ampicillin (Invitrogen). 2016 Virology journal Method IV G45R 124 128 NS1 96 99 27405392 G45R mutation in the nonstructural protein 1 of A/Puerto Rico/8/1934 (H1N1) enhances viral replication independent of dsRNA-binding activity and type I interferon biology. The plasmids expressing IFNbeta-promoter (-125) firefly luciferase, Renilla Luciferase vector (pRL-TK; Promega), RIG-I and each PR8 NS1 (WT, G45R and AA) were co-transfected into 293 T cells grown in 24-well plate as previously described with some modifications. 2016 Virology journal Method IV G45R 141 145 NS1 132 135 27405392 G45R mutation in the nonstructural protein 1 of A/Puerto Rico/8/1934 (H1N1) enhances viral replication independent of dsRNA-binding activity and type I interferon biology. The plasmids used were as follows; NS1 from PR8 (WT or mutated PR8 NSs; G45R, K55E, I68V, K70E and AA), HA and NA from X31 or A/Hong Kong/1/1968 (H3N2) and the remaining five genes were from PR8. 2016 Virology journal Method IV G45R;K55E;I68V;K70E 72;78;84;90 76;82;88;94 HA;NA;NS1;NS 104;111;35;67 106;113;38;70 27405392 G45R mutation in the nonstructural protein 1 of A/Puerto Rico/8/1934 (H1N1) enhances viral replication independent of dsRNA-binding activity and type I interferon biology. The rescued viruses with different PR8 NS1 (WT, G45R or AA/NS1s) were used to infect A549 cells grown in 6-well plates in triplicate wells at an MOI of 0.01 or 2. 2016 Virology journal Method IV G45R 48 52 NS1;NS1 39;59 42;63 27405392 G45R mutation in the nonstructural protein 1 of A/Puerto Rico/8/1934 (H1N1) enhances viral replication independent of dsRNA-binding activity and type I interferon biology. The viruses encoding WT, G45R and AA/NS1s were used to infect WT or IFNARnull Let1 cells grown in 6-well plates in triplicate at an MOI of 1 or 1. 2016 Virology journal Method IV G45R 25 29 NS1 37 41 27405392 G45R mutation in the nonstructural protein 1 of A/Puerto Rico/8/1934 (H1N1) enhances viral replication independent of dsRNA-binding activity and type I interferon biology. Total RNA was isolated from A549 cells infected with the rX31 viruses encoding PR8 NS1 (WT and G45R) using Trizol reagent (Invitrogen) following the manufacturer's instruction. 2016 Virology journal Method IV G45R 95 99 NS1 83 86 27413002 Pulmonary changes in Norwegian fatal cases of pandemic influenza H1N1 (2009) infection: a morphologic and molecular genetic study. A pyrosequencing assay was used to detect D222G mutations in the HA1 gene in the Norwegian A(H1N1)pdm09 cases as described previously.30 Briefly, a 110-nucleotide amplicon encompassing the HA 222 amino acid region was generated from 5 muL specimen RNA combined with each of primers pyro-H1 forward: 5'-AGTTCAAGCCGGAAATAGCA-3' and pyro-H1 reverse: 5'-biotin-TTTCCAGTTGCTTCGAATGTT-3' and reagents from the SuperScript III One-Step RT-PCR System with Platinum Taq High Fidelity kit (ThermoFisher Scientific, Waltham, MA, USA) in a 25 muL reaction and subjected to the following cycling conditions: 30 minutes at 50 C, 2 minutes at 94 C; 45 cycles of 15 seconds denaturation at 94 C, 30 seconds annealing at 55 C and 1 minute extension at 68 C; finally, 5 minutes at 68 C for final extension. 2016 Influenza and other respiratory viruses Method IV D222G 42 47 HA;HA1 189;65 191;68 27535054 NS1 Protein Mutation I64T Affects Interferon Responses and Virulence of Circulating H3N2 Human Influenza A Viruses. To introduce mutations E26K, I64T, and R224K into the NS1 protein of 1918 NS1, overlapping PCRs were performed using the primers described in Table 2, using as the template the pCAGGS-HA NH2 NS1-1918 plasmid. 2016 Journal of virology Method IV E26K;I64T;R224K 23;29;39 27;33;44 HA;NS1;NS1;NS1 184;54;74;191 186;57;77;194 27572837 The hemifusion structure induced by influenza virus haemagglutinin is determined by physical properties of the target membranes. cells were transfected with 2.5 microg pCAGGS-HA(wt) or HA(G1S) using Trans-IT LT1 (Mirus) according to the manufacturer's instructions. 2016 Nature microbiology Method IV G1S 59 62 HA;HA 46;56 48;58 27572837 The hemifusion structure induced by influenza virus haemagglutinin is determined by physical properties of the target membranes. Nucleotide mutations resulting in G1S mutant in HA (A/Aichi/2/68), was introduced by QuikChange II XL site-directed mutagenesis kit (Agilent). 2016 Nature microbiology Method IV G1S 34 37 HA 48 50 27572837 The hemifusion structure induced by influenza virus haemagglutinin is determined by physical properties of the target membranes. VLP were produced using the following quantities: 2.5 microg pCAGGS-HA(wt) or HA(G1S), 0.5 microg pCAGGS-NA, 1 microg pCAGGS-M1, and 0.25 microg of pCAGGS-M2. 2016 Nature microbiology Method IV G1S 81 84 HA;HA;M1;M2;NA 68;78;125;155;105 70;80;127;157;107 27657178 Discovery of Potent Antivirals against Amantadine-Resistant Influenza A Viruses by Targeting the M2-S31N Proton Channel. The compounds were tested in a two-electrode voltage clamp assay using Xenopus laevis frog oocytes microinjected with RNA expressing the S31N mutant of the A/M2 protein, as previously reported. 2016 ACS infectious diseases Method IV S31N 137 141 M2 158 160 27657178 Discovery of Potent Antivirals against Amantadine-Resistant Influenza A Viruses by Targeting the M2-S31N Proton Channel. The viruses used for this assay were A/WSN/33 (H1N1), A/Switzerland/9715293/2013 (H1N1), and A/California/07/2009 (H1N1), all of which contain the M2-S31N mutant. 2016 ACS infectious diseases Method IV S31N 150 154 M2 147 149 27733236 Risk of resistant avian influenza A virus in wild waterfowl as a result of environmental release of oseltamivir. Despite the H274Y resistance substitution, leading to highly reduced OC susceptibility, infectivity and transmissibility between mallards was maintained. 2016 Infection ecology & epidemiology Method IV H274Y 12 17 27733236 Risk of resistant avian influenza A virus in wild waterfowl as a result of environmental release of oseltamivir. Different permissive mutations have been identified for OC-resistant human A(H1N1) viruses in which the resistance is conferred by the H274Y substitution, including the seasonal virus in 2007-2009 and OC-resistant A(H1N1)/2009pdm/H274Y community clusters in Australia and Japan. 2016 Infection ecology & epidemiology Method IV H274Y;H274Y 135;230 140;235 27733236 Risk of resistant avian influenza A virus in wild waterfowl as a result of environmental release of oseltamivir. In a subsequent study in the same experimental model with the resistant A(H1N1)/H274Y variant in which drug exposure was removed from infected mallards, the resistant variant persisted without drug pressure. 2016 Infection ecology & epidemiology Method IV H274Y 80 85 27733236 Risk of resistant avian influenza A virus in wild waterfowl as a result of environmental release of oseltamivir. In another in vivo mallard model, selection for the framework NA substitution E119V in a low pathogenic A(H5N2) virus was demonstrated when infected ducks were exposed to 1 microg/L of OC in water. 2016 Infection ecology & epidemiology Method IV E119V 78 83 62 64 27733236 Risk of resistant avian influenza A virus in wild waterfowl as a result of environmental release of oseltamivir. In the same in vivo mallard model an A(H6N2) virus acquired high-level OC resistance conferred by the R292K substitution when ducks were exposed to 12 microg/L of OC, while a low pathogenic A(H7N9) virus acquired the resistance-related I222T framework substitution at 2.5 microg/L of OC exposure. 2016 Infection ecology & epidemiology Method IV R292K;I222T 102;236 107;241 27733236 Risk of resistant avian influenza A virus in wild waterfowl as a result of environmental release of oseltamivir. Infectivity and transmissibility between mallards was maintained during drug pressure by both of the viruses, but when the resistant A(H6N2)/R292K variant was allowed to replicate in mallards without drug pressure it reverted to wild type, confirming a reduced viral fitness of the resistant variant. 2016 Infection ecology & epidemiology Method IV R292K 141 146 27733236 Risk of resistant avian influenza A virus in wild waterfowl as a result of environmental release of oseltamivir. The different propensity is influenced by the subtype-specific resistance substitutions, as a framework substitution like H274Y may be compensated for more easily without compromising viral fitness than an active site residue, like R292K. 2016 Infection ecology & epidemiology Method IV H274Y;R292K 122;232 127;237 27733236 Risk of resistant avian influenza A virus in wild waterfowl as a result of environmental release of oseltamivir. The resistant A(H5N2)/E119V variant dominated the viral population and was transmissible between mallards, but it was outcompeted by wild-type virus when drug exposure was removed. 2016 Infection ecology & epidemiology Method IV E119V 22 27 27733236 Risk of resistant avian influenza A virus in wild waterfowl as a result of environmental release of oseltamivir. When mallards experimentally infected with an avian A(H1N1) virus were exposed to 0.95 microg/L of OC in their water, OC resistance conferred by the H274Y substitution in NA evolved. 2016 Infection ecology & epidemiology Method IV H274Y 149 154 171 173 27849220 Surveillance of antiviral resistance markers in Argentina: detection of E119V neuraminidase mutation in a post-treatment immunocompromised patient. It was essentially a qRT-PCR assay conducted using a reaction mixture that included specific primers for influenza A(H3N2) NA segment with the E119V coding region and a pair of dual-labelled probes for the detection of the E119 and V119 variants. 2016 Memorias do Instituto Oswaldo Cruz Method IV E119V 143 148 123 125 27849220 Surveillance of antiviral resistance markers in Argentina: detection of E119V neuraminidase mutation in a post-treatment immunocompromised patient. Molecular antiviral assays - In 2014, a rapid genotypic screening was implemented at the NIC to identify the single nucleotide polymorphism (SNP) encoding E119V substitution in clinical specimens that contained A(H3N2) influenza virus. 2016 Memorias do Instituto Oswaldo Cruz Method IV E119V;E119V 156;155 161;160 27849220 Surveillance of antiviral resistance markers in Argentina: detection of E119V neuraminidase mutation in a post-treatment immunocompromised patient. Sanger sequencing and phylogenetic analysis - The NA segment (1-1052 bp) of the viruses from pre- and post-treatment samples was sequenced to confirm the results obtained by E119V SNP screening. 2016 Memorias do Instituto Oswaldo Cruz Method IV E119V;E119V 175;174 180;179 50 52 27849220 Surveillance of antiviral resistance markers in Argentina: detection of E119V neuraminidase mutation in a post-treatment immunocompromised patient. The haemagglutinin (HA) segment of the E119V variant was also sequenced (1-986 bp). 2016 Memorias do Instituto Oswaldo Cruz Method IV E119V 39 44 HA;HA 20;4 22;18 27933797 Nuclear Magnetic Resonance and Molecular Dynamics Simulation of the Interaction between Recognition Protein H7 of the Novel Influenza Virus H7N9 and Glycan Cell Surface Receptors. The LSTa:H7sm and LSTc:H7sm complexes were generated from the LSTa:H7 and LSTc:H7 complexes, respectively, by applying a "virtual" mutation, G228S; under this condition, the structure surrounding each ligand was preserved. 2016 Biochemistry Method IV G228S 141 146 28087313 An M2-V27A channel blocker demonstrates potent in vitro and in vivo antiviral activities against amantadine-sensitive and -resistant influenza A viruses. All compounds were initially tested in a TEVC assay using Xenopus laevis frog oocytes microinjected with RNA expressing either the WT or the V27A mutant of A/Udorn/72-M2, as described in a previous report. 2017 Antiviral research Method IV V27A 141 145 M2 167 169 28087313 An M2-V27A channel blocker demonstrates potent in vitro and in vivo antiviral activities against amantadine-sensitive and -resistant influenza A viruses. Influenza A/WSN/33 (M2-N31S) (H1N1) and A/WSN/33 (M2-N31S + V27A) (H1N1) viruses were generated by reverse genetics of the A/WSN/33 (H1N1) virus. 2017 Antiviral research Method IV N31S;N31S;V27A 23;53;60 27;57;64 M2;M2 20;50 22;52 28087313 An M2-V27A channel blocker demonstrates potent in vitro and in vivo antiviral activities against amantadine-sensitive and -resistant influenza A viruses. M2-WT-expressing A/Udorn/72 (H3N2), A/WSN/33 (M2-N31S) (H1N1), A/Solomon Islands/3/2006 (H1N1), and M2-V27A-expressing A/WSN/33 (M2-N31S + V27A) (H1N1) were used to infect MDCK cells (American Type Culture Collection, Manassas, VA) in the presence or absence of compounds to evaluate their antiviral activity. 2017 Antiviral research Method IV N31S;V27A;N31S;V27A 49;103;132;139 53;107;136;143 M2;M2;M2;M2 0;46;100;129 2;48;102;131 28087313 An M2-V27A channel blocker demonstrates potent in vitro and in vivo antiviral activities against amantadine-sensitive and -resistant influenza A viruses. M2-WT-expressing A/Udorn/72 (H3N2), A/WSN/33 (M2-N31S) (H1N1), A/Solomon Islands/3/2006 (H1N1), and M2-V27A-expressing A/WSN/33 (M2-N31S + V27A) (H1N1) were used to infect MDCK cells in the presence or absence of compounds to evaluate their antiviral activity. 2017 Antiviral research Method IV N31S;V27A;N31S;V27A 49;103;132;139 53;107;136;143 M2;M2;M2;M2 0;46;100;129 2;48;102;131 28100622 Glycosylation of the Hemagglutinin Protein of H5N1 Influenza Virus Increases Its Virulence in Mice by Exacerbating the Host Immune Response. The microarray assay was performed by using a low-RNA-input linear amplification kit (Agilent Technologies, Santa Clara, CA) and Agilent's whole mouse genome microarray kit, 4 x 44 K (G4122F), as described elsewhere. 2017 Journal of virology Method IV G4122F 184 190 28102191 A broadly protective therapeutic antibody against influenza B virus with two mechanisms of action. At 72 h post- infection, mice received a single treatment of 46B8, 46B8 N297G or the control IgG intravenously at 15 mg kg-1. 2017 Nature communications Method IV N297G 72 77 28102191 A broadly protective therapeutic antibody against influenza B virus with two mechanisms of action. Grids were blocked with a blocking solution (Aurion Electron Microscopy Sciences) for 30 min followed by incubation with the control IgG, 34B5, 46B8 or 46B8 N297G for 1 h at room temperature. 2017 Nature communications Method IV N297G 157 162 28102191 A broadly protective therapeutic antibody against influenza B virus with two mechanisms of action. Target cells were incubated with varying concentrations of 46B8, 46B8 N297G (an Fc mutant that does not engage FcgammaR generated by site-directed mutagenesis of 46B8), Rituximab (a negative control mAb that binds to CD20) or Cetuximab (a positive control mAb that binds to EGFR) for 30 min. 2017 Nature communications Method IV N297G 70 75 28128091 Development of oseltamivir and zanamivir resistance in influenza A(H1N1)pdm09 virus, Denmark, 2014. Detection of the H275Y mutation using allele-specific real-time reverse transcription-PCR. 2017 Euro surveillance Method IV H275Y 17 22 28128091 Development of oseltamivir and zanamivir resistance in influenza A(H1N1)pdm09 virus, Denmark, 2014. For rapid initial screening of the oseltamivir resistance conferring single nt polymorphism (SNP) mutation H275Y, an allele specific real-time RT-PCR was applied to the samples, following a protocol designed by the National Influenza Center Denmark (Statens Serum Institut, Copenhagen, Denmark). 2017 Euro surveillance Method IV H275Y 107 112 28132927 Antigenic and genetic characterization of influenza viruses circulating in Bulgaria during the 2015/2016 season. Screening of A(H1N1)pdm09 viruses for the presence of point mutations conferring H275Y oseltamivir resistance was carried out using a Real Time RT-PCR assay that allowed discrimination of a single nucleotide difference between oseltamivir sensitive and resistant viruses. 2017 Infection, genetics and evolution Method IV H275Y 81 86 28182419 Expeditious Lead Optimization of Isoxazole-Containing Influenza A Virus M2-S31N Inhibitors Using the Suzuki-Miyaura Cross-Coupling Reaction. The compounds were tested in a two-electrode voltage clamp assay using Xenopus laevis frog oocytes microinjected with RNA expressing either the AM2-WT or the AM2-S31N mutant of the AM2 protein, as previously reported. 2017 Journal of medicinal chemistry Method IV S31N 162 166 28182419 Expeditious Lead Optimization of Isoxazole-Containing Influenza A Virus M2-S31N Inhibitors Using the Suzuki-Miyaura Cross-Coupling Reaction. The viruses used for this assay were A/California/07/2009 (H1N1), A/Washington/29/2009 (H1N1), A/Denmark/528/2009 (H1N1) and A/Switzerland/9715293/2013 (H3N2), all of which contain the AM2-S31N mutant in their AM2 genes. 2017 Journal of medicinal chemistry Method IV S31N 189 193 28252002 NEDDylation of PB2 Reduces Its Stability and Blocks the Replication of Influenza A Virus. A549 cells were infected with wild-type A/WSN/33 (H1N1) or mutant virus WSN-PB2 K699R at an MOI of 0.01. 2017 Scientific reports Method IV K699R 80 85 PB2 76 79 28252002 NEDDylation of PB2 Reduces Its Stability and Blocks the Replication of Influenza A Virus. For the generation of recombinant WSN viruses, HEK293T cells were cotransfected with eight viral genome-expressing plasmids (pHH21 PB2 for wild type WSN virus, or pHH21 PB2-K699R for WSN-PB2 K699R virus) and four pCAGGS protein expression plasmids encoding the viral polymerase subunits PB1, PB2 and PA (pCAGGS PB2 for wild type WSN virus, or pCAGGS PB2-K699R for WSN-PB2 K699R virus) as well as NP. 2017 Scientific reports Method IV K699R;K699R;K699R;K699R 173;191;354;372 178;196;359;377 NP;PA;PB1;PB2;PB2;PB2;PB2;PB2;PB2;PB2 396;300;287;131;169;187;292;311;350;368 398;302;290;134;172;190;295;314;353;371 28252002 NEDDylation of PB2 Reduces Its Stability and Blocks the Replication of Influenza A Virus. Plasmids pHH21-PB2 K699R and pCAGGS-PB2 K699R for generating mutant WSN-PB2 K669R virus were created by site specific mutagenesis with FastPfu DNA Polymerase (TransGen Biotech). 2017 Scientific reports Method IV K699R;K699R;K669R 19;40;76 24;45;81 PB2;PB2;PB2 15;36;72 18;39;75 28282440 H1N1 influenza viruses varying widely in hemagglutinin stability transmit efficiently from swine to swine and to ferrets. The Y17H and R106K mutants were previously described. 2017 PLoS pathogens Method IV Y17H;R106K 4;13 8;18 28323816 An NS-segment exonic splicing enhancer regulates influenza A virus replication in mammalian cells. A pair of H9N2 viruses containing WT or NS-A540G were made with the genome from the strain A/HongKong/308/2014. 2017 Nature communications Method IV A540G 43 48 NS 40 42 28323816 An NS-segment exonic splicing enhancer regulates influenza A virus replication in mammalian cells. For reassortant rH9N2-WT or rH9N2-NS-A540G viruses, HA and NA surface genes were derived from A/HongKong/308/2014 (H9N2), whereas internal genes were identical to H7N9-WT or H7N9-NS-A540G. 2017 Nature communications Method IV A540G;A540G 37;182 42;187 HA;NA;NS;NS 52;59;34;179 54;61;36;181 28323816 An NS-segment exonic splicing enhancer regulates influenza A virus replication in mammalian cells. Mini-gene expression plasmid pSMN-1, dysfunctional mutant pSMN-2, pSMN-H7N9-WT containing the putative ESE of H7N9 or pSMN-H7N9-A540G was transiently transfected into HEK293T cells for 24 h. 2017 Nature communications Method IV A540G 128 133 28323816 An NS-segment exonic splicing enhancer regulates influenza A virus replication in mammalian cells. Six- to 8-week-old female BALB/c mice were intranasally inoculated with the indicated doses of H7N9-WT or H7N9-NS-A540G diluted in PBS. 2017 Nature communications Method IV A540G 114 119 NS 111 113 28410396 Evolution of the neuraminidase gene of seasonal influenza A and B viruses in Thailand between 2010 and 2015. A real-time RT-PCR assay for detection of oseltamivir-resistant A(H1N1)pdm09 (H275Y) strains has been published previously. 2017 PloS one Method IV H275Y 78 83 28410396 Evolution of the neuraminidase gene of seasonal influenza A and B viruses in Thailand between 2010 and 2015. From 707 samples found to be positive for A(H1N1)pdm09 between November 2010 and December 2015, a total of 485 were randomly chosen for analysis of oseltamivir resistance (H275Y mutation in the NA gene) using real-time reverse transcription polymerase chain reaction (RT-PCR) for the NA gene and direct sequencing. 2017 PloS one Method IV H275Y 172 177 NA;NA 194;284 196;286 28410396 Evolution of the neuraminidase gene of seasonal influenza A and B viruses in Thailand between 2010 and 2015. We analyzed for the presence of NA substitutions associated with either NAI-resistant genotype in different NA subtypes (E119V/I/A/G, H274Y, R292K, and N294S: N2 numbering) or reduced susceptibility genotype to NAIs (Q136K, D151E/V/D, D198N/G/E/Y, I222V/T/K/R/M, S246N, E276D, and R371K: N2 numbering) among influenza A and B viruses. 2017 PloS one Method IV E119V;E119I;E119A;E119G;H274Y;R292K;N294S;Q136K;D151E;D151V;D151D;D198N;D198G;D198E;D198Y;I222V;I222T;I222K;I222R;I222M;S246N;E276D;R371K 121;121;121;121;134;141;152;217;224;224;224;235;235;235;235;248;248;248;248;248;263;270;281 132;132;132;132;139;146;157;222;233;233;233;246;246;246;246;261;261;261;261;261;268;275;286 NA;NA;NAI;NAI 32;108;72;211 34;110;75;215 28418242 Slow but Steady Wins the Race: Dissimilarities among New Dual Inhibitors of the Wild-Type and the V27A Mutant M2 Channels of Influenza A Virus. A/M2 S31N and A/M2 V27A mutants were generated by QuikChange site-directed mutagenesis kit (Agilent Technologies). 2017 Journal of medicinal chemistry Method IV S31N;V27A 5;19 9;23 M2;M2 2;16 4;18 28418242 Slow but Steady Wins the Race: Dissimilarities among New Dual Inhibitors of the Wild-Type and the V27A Mutant M2 Channels of Influenza A Virus. The PRA with A/WSN/33 N31S/V27A (H1N1) virus was carried out similarly as previously described. 2017 Journal of medicinal chemistry Method IV N31S;V27A 22;27 26;31 28433777 Design and expeditious synthesis of organosilanes as potent antivirals targeting multidrug-resistant influenza A viruses. The compounds were tested in a two-electrode voltage clamp assay using Xenopus laevis frog oocytes microinjected with RNA expressing either the AM2-WT or the AM2-S31N mutant of the A/M2 proteins, as previously reported. 2017 European journal of medicinal chemistry Method IV S31N 162 166 M2 183 185 28433777 Design and expeditious synthesis of organosilanes as potent antivirals targeting multidrug-resistant influenza A viruses. The solution NMR structure of AM2-S31N (PDB: 2LY0) was used for the docking. 2017 European journal of medicinal chemistry Method IV S31N 34 38 28498306 A Conserved Residue, Tyrosine (Y) 84, in H5N1 Influenza A Virus NS1 Regulates IFN Signaling Responses to Enhance Viral Infection. Additional lungs were harvested on days 1 (wt, n = 5; Y84F, n = 4) and 3 (wt, n = 5; Y84F, n = 3) post-infection for histology. 2017 Viruses Method IV Y84F;Y84F 54;85 58;89 28498306 A Conserved Residue, Tyrosine (Y) 84, in H5N1 Influenza A Virus NS1 Regulates IFN Signaling Responses to Enhance Viral Infection. C57BL/6 mice 8-10 weeks of age were anesthetized by intraperitoneal injection with ketamine (Ketalean, Bimeda, Cambridge, ON, Canada) and xylazine (Rompun, Bayer, Mississauga, ON, Canada), and infected intranasally with 1 x 105 plaque-forming units (PFU) of rA/WSN/33-GH-NS1-wt, or rA/WSN/33-GH-NS1-Y84F diluted in 50 muL of PBS. 2017 Viruses Method IV Y84F 299 303 NS1;NS1 271;295 274;298 28498306 A Conserved Residue, Tyrosine (Y) 84, in H5N1 Influenza A Virus NS1 Regulates IFN Signaling Responses to Enhance Viral Infection. Cells were transfected with 1.25 mug/well of pBudCE4.1-GFP (vector), pBudCE4.1-NS1-HA-GFP (NS1-wt), or pBudCE4.1-NS1-Y84F-HA-GFP (NS1-Y84F) using Lipofectamine LTX Reagent (Invitrogen) following the manufacturer's protocol and as previously described. 2017 Viruses Method IV Y84F;Y84F 117;134 121;138 HA;HA;NS1;NS1;NS1;NS1 83;122;79;91;113;130 85;124;82;94;116;133 28498306 A Conserved Residue, Tyrosine (Y) 84, in H5N1 Influenza A Virus NS1 Regulates IFN Signaling Responses to Enhance Viral Infection. Complimentary oligonucleotide primers (forward 5'GCCGGCTTCACGCTTCCTAACTGACATGAC3', reverse 5'GTCATGTCAGTTAGGAAGCG TGAAGCCGGC3') containing the desired Y84F mutation were synthesized by ACGT Corporation (Toronto, ON, Canada). 2017 Viruses Method IV Y84F 151 155 28498306 A Conserved Residue, Tyrosine (Y) 84, in H5N1 Influenza A Virus NS1 Regulates IFN Signaling Responses to Enhance Viral Infection. pLLB-A/Grey Heron/Hong Kong/837/2004 [H5N1] NS and pLLB-A/Grey Heron/Hong Kong/837/2004 [H5N1] NS-Y84F were used in place of pLLB-A/WSN/33 [H1N1] NS to generate rWSN-GH-NS1-wt and rWSN-GH-NS1-Y84F respectively. 2017 Viruses Method IV Y84F;Y84F 98;192 102;196 NS;NS;NS;NS1;NS1 44;95;146;169;188 46;97;148;172;191 28498306 A Conserved Residue, Tyrosine (Y) 84, in H5N1 Influenza A Virus NS1 Regulates IFN Signaling Responses to Enhance Viral Infection. Site-directed mutagenesis was performed to introduce a Y84F mutation in pBudCE4.1-NS1-HA-GFP and pLLB-A/Grey Heron/Hong Kong/837/2004 [H5N1]-NS using the QuikChange Site-Directed Mutagenesis Kit and XL1-Blue supercompetent cells purchased from Agilent Technologies (Santa Clara, CA, USA) following the manufacturer's protocol. 2017 Viruses Method IV Y84F 55 59 HA;NS;NS1 86;141;82 88;143;85 28498306 A Conserved Residue, Tyrosine (Y) 84, in H5N1 Influenza A Virus NS1 Regulates IFN Signaling Responses to Enhance Viral Infection. The resulting pBudCE4.1-NS1-Y84F-HA-GFP plasmid and pLLB-A/Grey Heron/Hong Kong/837/2004 [H5N1] NS-Y84F gene were sequenced by ACGT Corporation to confirm the Y84F mutation. 2017 Viruses Method IV Y84F;Y84F;Y84F 28;99;159 32;103;163 HA;NS;NS1 33;96;24 35;98;27 28588133 Novel Nonreplicating Vaccinia Virus Vector Enhances Expression of Heterologous Genes and Suppresses Synthesis of Endogenous Viral Proteins. The strong intermediate I1L promoter (sequence, TTTGTATTTGTATTTAAAAGTTGTTTGGTGAACTTAA) was joined to the lac repressor ORF by PCR and inserted into the RB21 plasmid. 2017 mBio Method IV I1L 24 27 28588133 Novel Nonreplicating Vaccinia Virus Vector Enhances Expression of Heterologous Genes and Suppresses Synthesis of Endogenous Viral Proteins. This plasmid, containing both the T7 RNA polymerase gene controlled by the early TK promoter and the lac repressor gene controlled by an intermediate I1L promoter, was designated pRB21/WX52, and all cloning was carried out in BL21 Star (DE3)pLysS One Shot competent cells (Invitrogen). 2017 mBio Method IV I1L 150 153 28588133 Novel Nonreplicating Vaccinia Virus Vector Enhances Expression of Heterologous Genes and Suppresses Synthesis of Endogenous Viral Proteins. To remove VACV intermediate transcription factor gene A23R, DNA generated by overlapping PCR consisting of (i) 180 bp of the C-terminal end of the A22R ORF, (ii) a dsRed screening marker controlled by the P11 VACV promoter, and (iii) 46 bp of the A24L promoter embedded in the C-terminal end of the A23R ORF and 201 bp of the A24L ORF was inserted into T7/luc to delete the A23R ORF. 2017 mBio Method IV A23R;A22R;A24L;A23R;A24L;A23R 54;147;247;299;326;374 58;151;251;303;330;378 28744280 Amino Acid Substitution K470R in the Nucleoprotein Increases the Virulence of H5N1 Influenza A Virus in Mammals. Briefly, the NP gene from A/environment/Qinghai/1/2008 (H5N1) (as wild type) or the NP gene with the mutation K91R, K198R, K227R, K229R, or K470R was co-transfected with the plasmids encoding the other seven genes from the A/environment/Qinghai/1/2008 (H5N1) virus into 293T cells and MDCK cells. 2017 Frontiers in microbiology Method IV K91R;K198R;K227R;K229R;K470R 110;116;123;130;140 114;121;128;135;145 NP;NP 13;84 15;86 28790432 Conformational modulation of influenza virus hemagglutinin: characterization and in vivo efficacy of monomeric form. Plasmids encoding each mutant HA gene (S199F of HA1 and G47E, R75L, F88E, V91W, R106E, and F88E/V91W of HA2) was amplified in Escherichia coli strain DH5alpha and the recombinant bacmid was generated according to the Bac-to-Bac expression system protocol (Invitrogen). 2017 Scientific reports Method IV S199F;G47E;R75L;F88E;V91W;R106E;V91W;F88E 39;56;62;68;74;80;96;91 44;60;66;72;78;85;100;95 HA;HA;HA1 30;104;48 32;106;51 28790432 Conformational modulation of influenza virus hemagglutinin: characterization and in vivo efficacy of monomeric form. The CU44 HA in this study showed 3 mutations different from the original CU44 HA: HA1 M116I and HA2 I91V and N169S, which was however used as the wild-type and these mutations also exist in nature. 2017 Scientific reports Method IV M116I;I91V;N169S 86;100;109 91;104;114 HA;HA;HA;HA1 9;78;96;82 11;80;98;85 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. A different AAS at the same position, G104R/G, was previously reported in a B/Victoria-lineage virus that displayed RI by peramivir. 2017 Antiviral research Method IV G104R;G104G 38;38 45;45 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. A single virus, collected in the Russian Federation, carried NA S247R AAS that conferred RI/HRI by all four NAIs (Tables 1 and S4). 2017 Antiviral research Method IV S247R 64 69 NA;NAI 61;108 63;112 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. A substitution at the neighbouring residue was detected in B/South Australia/48/2015 as a mixed population, NA E105K/E, associated with HRI by peramivir; the mixed population was also detected in the clinical specimen (Tables 2 and S2). 2017 Antiviral research Method IV E105K;E105E 111;111 118;118 108 110 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. All viruses harboured NA K249E AAS, which has previously been seen in viruses displaying a borderline RI by oseltamivir. 2017 Antiviral research Method IV K249E 25 30 22 24 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. Although five of these sequences were reported as E119K, it is likely that an E119K/E mix was present in the virus isolate tested; clean E119K AAS, was shown to drastically diminish NA activity. 2017 Antiviral research Method IV E119K;E119K;E119E;E119K 50;78;78;137 55;85;85;142 182 184 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. Among 1147 B/Victoria-lineage NA sequences, nine (0.7%) had the following AASs: E105K, D197N, I221V, K360E, D432G or N294S (Table S4). 2017 Antiviral research Method IV E105K;D197N;I221V;K360E;D432G;N294S 80;87;94;101;108;117 85;92;99;106;113;122 30 32 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. Analysis of B/Victoria-lineage NA sequences revealed five viruses with the following AASs: G104E/G, E105K/E, G243D/G or G407S (Table S3). 2017 Antiviral research Method IV G104E;G104G;E105K;E105E;G243D;G243G;G407S 91;91;100;100;109;109;120 98;98;107;107;116;116;125 31 33 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. Another AAS at the same NA residue, H134Y, was detected in B/Christchurch/558/2015 (Tables 2 and S2) and associated with HRI by peramivir (76-fold) and NI by the other NAIs. 2017 Antiviral research Method IV H134Y 36 41 NA;NAI 24;168 26;172 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. Another AAS at the same residue, K152M, was reported in a B/Victoria-lineage virus exhibiting RI by oseltamivir. 2017 Antiviral research Method IV K152M 33 38 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. Another AAS in the same residue, S247N, was previously shown to have a mild effect on inhibition by oseltamivir (5- to 8-fold). 2017 Antiviral research Method IV S247N 33 38 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. due to a novel NA H134N AAS, which was detected in these corresponding clinical specimens (Table S2). 2017 Antiviral research Method IV H134N 18 23 15 17 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. E119V is known to confer HRI by oseltamivir, while R292K confers HRI by oseltamivir/peramivir and RI by zanamivir/laninamivir. 2017 Antiviral research Method IV E119V;R292K 0;51 5;56 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. Eight of 74 viruses harboured mixed populations of H275Y variant and H275 wild type viruses (Table S1); five of these were from Japanese patients treated with oseltamivir (n = 4) or peramivir (n = 1). 2017 Antiviral research Method IV H275Y 51 56 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. Finally, a single virus (B/Darwin/83/2015) containing the NA AAS I221T exhibited RI by peramivir (~8-fold); this AAS was not detected in the clinical specimen. 2017 Antiviral research Method IV I221T 65 70 58 60 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. Finally, two viruses exhibited RI and contained the NA AASs D151N/D and Q136R/Q previously associated with adaptation to cell culture (Tables 1 and S1). 2017 Antiviral research Method IV D151N;D151D;Q136R;Q136Q 60;60;72;72 67;67;79;79 52 54 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. Five viruses containing D197N NA AAS were collected in widely-dispersed parts of the world (Tables 2 and S2). 2017 Antiviral research Method IV D197N 24 29 30 32 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. In addition to RI by oseltamivir, two viruses (A/India/1819/2016 and A/Tennessee/24/2016) exhibited RI/HRI by the other three NAIs (Tables 1 and S1) and carried S247R (Table 1). 2017 Antiviral research Method IV S247R 161 166 NAI 126 130 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. In addition, A/Argentina/22/2015, contained NA I223T AAS, which conferred RI by oseltamivir in another A(H1N1)pdm09 virus. 2017 Antiviral research Method IV I223T 47 52 44 46 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. Indeed, sequences of four A(H1N1)pdm09 virus isolates from Japan contained a NA H275Y/H mix; these viruses were collected from patients treated with oseltamivir (Table S3). 2017 Antiviral research Method IV H275Y;H275H 80;80 87;87 77 79 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. It was shown that I223R narrows the NA active site pocket that accommodates the hydrophobic pentoxyl group of oseltamivir and it is likely that I223K produces a similar effect. 2017 Antiviral research Method IV I223R;I223K 18;144 23;149 36 38 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. Moreover, two B/Yamagata-lineage NA sequences contained D197N or H134Y AAS. 2017 Antiviral research Method IV D197N;H134Y 56;65 61;70 33 35 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. NA I221T AAS has been shown to confer RI by peramivir in B/Victoria-lineage viruses. 2017 Antiviral research Method IV I221T 3 8 0 2 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. NA residue 147 is located in the 150-loop; it is possible that G147R alters the conformation of the 150-loop due to the larger size and positive charge of the side chain, thus adversely affecting the binding of NAIs and having a synergistic effect with H275Y. 2017 Antiviral research Method IV G147R;H275Y 63;253 68;258 NA;NAI 0;211 2;215 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. Notably, NA H134Y AAS in a B/Victoria-lineage virus (Table 2) conferred HRI by peramivir indicating a lineage-specific effect. 2017 Antiviral research Method IV H134Y 12 17 9 11 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. Notably, sequencing allowed the detection of oseltamivir-resistant NA H275Y AAS subpopulations in virus isolates exhibiting NI and revealed selection of NA variants due to tissue-culture selection. 2017 Antiviral research Method IV H275Y 70 75 NA;NA 67;153 69;155 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. Notably, the two H275Y viruses displaying the highest fold increases in IC50 each contained an addition NA AAS. 2017 Antiviral research Method IV H275Y 17 22 104 106 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. Of 2371 A(H1N1)pdm09 sequences, 40 (1.7%) contained H275Y, five of which were H275Y/H mixtures with one containing a dual AAS, H275Y/H + S247S/N (Table S4). 2017 Antiviral research Method IV H275Y;H275H;S247N;H275Y;H275H;H275Y;S247S 52;127;137;78;78;127;137 57;134;144;85;85;134;144 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. Of 365 B/Yamagata-lineage sequences, two (0.5%) contained D197N or N294S AASs (Table S4). 2017 Antiviral research Method IV D197N;N294S 58;67 63;72 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. Of 815 A(H3N2) NA sequences analysed, one (0.1%), collected in the United Kingdom, had E119V AAS (Table S4). 2017 Antiviral research Method IV E119V 87 92 15 17 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. One B/Victoria- and one B/Yamagata-lineage virus contained NA H273Q or H273N AAS, respectively. 2017 Antiviral research Method IV H273Q;H273N 62;71 67;76 59 61 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. One virus, A/Bayern/151/2015 exhibited borderline RI (10-fold) by zanamivir and carried I117R (confirmed in the matching clinical specimen), which has not been described before. 2017 Antiviral research Method IV I117R 88 93 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. One virus, B/Malaysia/0471/2016 exhibited HRI by all NAIs and harboured NA G104E AAS, which has not been described before, but neither patient information nor clinical specimen was available (Tables 2 and S2). 2017 Antiviral research Method IV G104E 75 80 NA;NAI 72;53 74;57 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. Q136K has been previously associated with virus adaptation to cell culture. 2017 Antiviral research Method IV Q136K 0 5 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. The combination of H275Y with I223K/R has been detected previously. 2017 Antiviral research Method IV H275Y;I223K;I223R 19;30;30 24;37;37 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. The first virus A/Hiroshima/13/2016 contained a novel NA dual AAS, H275Y + G147R, which conferred a 2649-fold increase in IC50. 2017 Antiviral research Method IV H275Y;G147R 67;75 72;80 54 56 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. The first virus contained the I221V NA AAS, previously reported in B/Victoria-lineage viruses circulating widely in North Carolina during 2011. 2017 Antiviral research Method IV I221V 30 35 36 38 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. The H134N viruses replicated well in Normal Human Bronchial Epithelial (NHBE) cells and ferrets. 2017 Antiviral research Method IV H134N 4 9 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. The isolate and matching clinical specimen harboured NA Q391K AAS. 2017 Antiviral research Method IV Q391K 56 61 53 55 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. The majority of these viruses exhibited RI/HRI by oseltamivir (n = 77; 15- to 20,324-fold) and peramivir (n = 65; 10- to 6270- fold), and most of them (n = 74) contained the NA H275Y AAS. 2017 Antiviral research Method IV H275Y 177 182 174 176 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. The NA G147R AAS occurs at a low frequency in N1 subtype viruses, and confers RI by oseltamivir and zanamivir in A(H5N1) viruses. 2017 Antiviral research Method IV G147R 7 12 4 6 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. The second virus, A/Ibaraki/54/2016, was collected from a patient treated with oseltamivir, peramivir and laninamivir and contained NA H275Y + I223K dual AAS conferring 20,324-fold increase in IC50 (Tables 1 and S1). 2017 Antiviral research Method IV H275Y;I223K 135;143 140;148 132 134 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. The second virus, B/Florida/05/2016 (isolate and clinical specimen) contained the K152N NA AAS (Tables 2 and S2), which has not been previously reported. 2017 Antiviral research Method IV K152N 82 87 88 90 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. These isolates and their respective clinical specimens contained NA H273Y AAS. 2017 Antiviral research Method IV H273Y 68 73 65 67 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. Three sequences of A(H3N2) viruses displaying NI contained the following AASs: E119V/E, R292K/R and Q136K/Q (Table S3). 2017 Antiviral research Method IV E119V;E119E;R292K;R292R;Q136K;Q136Q 79;79;88;88;100;100 86;86;95;95;107;107 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. Two other viruses showed RI by zanamivir (14-17-fold) and contained the dual NA AAS of T106L + P165L and K186R + I262T, while a single virus showed borderline RI by zanamivir and contained the NA AAS G243S/G as a mixed population (Tables 2 and S2). 2017 Antiviral research Method IV T106L;P165L;K186R;I262T;G243S;G243G 87;95;105;113;200;200 92;100;110;118;207;207 NA;NA 77;193 79;195 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. Two viruses exhibited RI/HRI by peramivir and contained the NA D432G AAS. 2017 Antiviral research Method IV D432G 63 68 60 62 28814518 A Single-Amino-Acid Substitution at Position 225 in Hemagglutinin Alters the Transmissibility of Eurasian Avian-Like H1N1 Swine Influenza Virus in Guinea Pigs. pCAGGS-GX/18-HA, pCAGGS-GX/18-HA-E225G, pCAGGS-GX/18-NA, pCAGGS-GX/18-M1, pCAGGS-HLJ/27-HA, pCAGGS-HLJ/27-HA-G225E, pCAGGS-HLJ/27-NA, and pCAGGS-HLJ/27-M1 were constructed by inserting the corresponding cDNAs into the SacI/NheI sites of the pCAGGS vector. 2017 Journal of virology Method IV E225G;G225E 33;109 38;114 HA;HA;HA;HA;M1;M1;NA;NA 13;30;88;106;70;152;53;130 15;32;90;108;72;154;55;132 28814737 Susceptibility of influenza A(H1N1)/pdm2009, seasonal A(H3N2) and B viruses to Oseltamivir in Guangdong, China between 2009 and 2014. Here, 4 structures with the PDB IDs 4B7Q, 3NSS, 4QNP and 4B7R were used as templates to construct the mutated NA proteins (V241I, H275Y, I321V, N369K, N386S, N386K and K432E, either alone or in combination). 2017 Scientific reports Method IV V241I;H275Y;I321V;N369K;N386S;N386K;K432E 123;130;137;144;151;158;168 128;135;142;149;156;163;173 110 112 28815216 Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity. Two rounds of PCR were performed using Phusion high-fidelity DNA polymerase with pHW2000 plasmids encoding either PB1 or PA from the PR8 virus as a template, the inner mutagenic primers for PB1 D27N (forward [Fwd], 5'-CCCTTATACTGGAAACCCTCCTTACAGC-3'; reverse [Rev], 5'-GCTGTAAGGAGGGTTTCCAGTATAAGGG-3') PB1 V43I (Fwd, 5'-CACCATGGATACTATCAACAGGACAC-3'; Rev, 5'-GTGTCCTGTTGATAGTATCCATGGTG-3'), PB1 T123A (Fwd, 5'-GTAGACAAGCTGGCACAAGGCCGAC-3'; Rev, 5'-GTCGGCCTTGTGCCAGCTTGTCTAC-3'), PB1 M645I (Fwd, 5'-CAATGCAGTGATAATGCCAGCACATGG-3'; Rev, 5'-CCATGTGCTGGCATTATCACTGCATTG-3'), and PA T97I (Fwd, 5'-CAGTATTTGCAACATTACAGGGGCTGAG-3'; Rev, 5'-CTCAGCCCCTGTAATGTTGCAAATACTG-3') and the outer primers containing AarI or BsmBI restriction sites for PB1 (Fwd, 5'-TATTCACCTGCCTCAGGGAGCGAAAGCAGGCA-3'; Rev, 5'-ATATCACCTGCCTCGTATTAGTAGAAACAAGGCATTT-3') and PA (Fwd, 5'-TATTCGTCTCAGGGAGCGAAAGCAGGTAC-3'; Rev, 5'-ATATCGTCTCGTATTAGTAGAAACAAGGTACTT-3'). 2017 mSphere Method IV D27N;V43I;T123A;M645I;T97I 194;306;395;483;578 198;310;400;488;582 PA;PA;PA;PB1;PB1;PB1;PB1;PB1;PB1 121;575;839;114;190;302;391;479;735 123;577;841;117;193;305;394;482;738 28860626 Topological N-glycosylation and site-specific N-glycan sulfation of influenza proteins in the highly expressed H1N1 candidate vaccines. Egg-derived monovalent influenza vaccines derived (inactivated, split virion) from the virus strains of NIBRG-121xp (HA: K136N, D239G; NA: N88G) and NYMC-X181A (HA: K236T, Q240R) were collected as reported previously. 2017 Scientific reports Method IV K136N;D239G;N88G;X181A;K236T;Q240R 121;128;139;154;165;172 126;133;143;159;170;177 HA;HA;NA 117;161;135 119;163;137 28951584 Identification of neuraminidase inhibitors against dual H274Y/I222R mutant strains. Recombinant baculoviruses were generated to express the wild-type, H274Y, H274Y and I222R mutants of NA originating from influenza N1 neuraminidase (NIBRG14 (H5N1)). 2017 Scientific reports Method IV H274Y;H274Y;I222R 67;74;84 72;79;89 NA;NA 101;134 103;147 28951584 Identification of neuraminidase inhibitors against dual H274Y/I222R mutant strains. The assay was conducted in 96-well plates containing active wild-type, H274Y, H274Y and I222R mutants of NA and 100 muM fluorogenic substrate per well in reaction buffer. 2017 Scientific reports Method IV H274Y;H274Y;I222R 71;78;88 76;83;93 105 107 28951584 Identification of neuraminidase inhibitors against dual H274Y/I222R mutant strains. The NA structure with I222R and H274Y dual-point mutations was derived using a homology-modeling server. 2017 Scientific reports Method IV I222R;H274Y 22;32 27;37 4 6 28951584 Identification of neuraminidase inhibitors against dual H274Y/I222R mutant strains. The oseltamivir-resistant NA contains a H274Y single point mutation for strain H1N1, which was obtained as described as Hung et al. 2017 Scientific reports Method IV H274Y 40 45 26 28 28951584 Identification of neuraminidase inhibitors against dual H274Y/I222R mutant strains. The oseltamivir-resistant NA with H274Y and I222R dual-point mutations for strain NIBRG14 (H5N1) was obtained as described as Hung et al. 2017 Scientific reports Method IV H274Y;I222R 34;44 39;49 26 28 28951584 Identification of neuraminidase inhibitors against dual H274Y/I222R mutant strains. The wild-type, H274Y, H274Y and I222R mutants of NA recombinant proteins are derived from baculovirus insect expression system. 2017 Scientific reports Method IV H274Y;H274Y;I222R 15;22;32 20;27;37 49 51 29209052 Maintaining pH-dependent conformational flexibility of M1 is critical for efficient influenza A virus replication. The wild-type (wt) WSN and M1 triple mutants M(NLS-88R) and M(NLS-88E), bearing R101S and R105S in NLS 101RKLKR105 and an additional mutation G88R or G88E in the adjacent region, were generated by reverse genetics. 2017 Emerging microbes & infections Method IV R101S;R105S;G88R;G88E 80;90;142;150 85;95;146;154 M;M;M1 45;60;27 46;61;29 29299533 Cooperating H3N2 Influenza Virus Variants Are Not Detectable in Primary Clinical Samples. The computer code that performs the analyses is available at GitHub (https://github.com/ksxue/D151G-clinical-public). 2018 mSphere Method IV D151G 94 99 29312300 Histone Deacetylase 1 Plays an Acetylation-Independent Role in Influenza A Virus Replication. For the multiple growth curves, the A549 cells were infected with rWT, rK103A, or K103R virus at an MOI of 0.1, and the procedures were the same as those for the single growth curve experiments. 2017 Frontiers in immunology Method IV K103R 82 87 29312300 Histone Deacetylase 1 Plays an Acetylation-Independent Role in Influenza A Virus Replication. In brief, The pHW2000-NP plasmid (as wild-type) or NP gene with mutation K103A and K103R was co-transfected with the other seven plasmids pHW2000-PB1, -PB2, -PA, -HA, -NA, -NS, and -M genes from A/environment/Qinghai/1/2008(H5N1) virus into MDCK cells and 293T cells. 2017 Frontiers in immunology Method IV K103A;K103R 73;83 78;88 HA;M;NA;NP;NP;NS;PA;PB1;PB2 163;182;168;22;51;173;158;146;152 165;183;170;24;53;175;160;149;155 29312300 Histone Deacetylase 1 Plays an Acetylation-Independent Role in Influenza A Virus Replication. The K103A and K103R mutations of NP in the generated viruses were confirmed by sequencing. 2017 Frontiers in immunology Method IV K103A;K103R 4;14 9;19 NP 33 35 29489903 Design and synthesis of constrained bicyclic molecules as candidate inhibitors of influenza A neuraminidase. A/Chicken/HongKong/G9/1997 H9N2 and A/Anhui/1/2005 H5N1 (wild-type and H274Y mutation) were purchased from SinoBiochemical. 2018 PloS one Method IV H274Y 71 76 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. For viral competition assays against AM2-S31N/L26I/A30T viruses, the average area of the two peaks (corresponding to the L26I and A30T mutations) were used to generate the error bars. 2018 Antiviral research Method IV A30T;L26I;S31N;L26I;A30T 51;46;41;121;130 55;50;45;125;134 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. For viral competition assays, A/California/07/2009 (H1N1) or recombinant A/Udorn/1972 (rH3N2) containing the AM2-S31N were co-infected with either AM2-S31N/V27I, AM2-S31N/L26I, or AM2-S31N/L26I/A30T viruses at an MOI ratio of 1:100 (2.0 x 10-5:2.0 x 10-3) in ST6Gal1-expressing MDCK cells. 2018 Antiviral research Method IV S31N;V27I;S31N;S31N;L26I;A30T;S31N;L26I 113;156;151;166;171;194;184;189 117;160;155;170;175;198;188;193 29587786 Effects of the S42 residue of the H1N1 swine influenza virus NS1 protein on interferon responses and virus replication. Mutations were introduced into the plasmid pBD-NS using overlap-PCR to generate the three mutant NS segments: pBD-NS S42P, pBD-NS D42E, and pBD-NS S42P/D92E. 2018 Virology journal Method IV S42P;D42E;S42P;D92E 117;130;147;152 121;134;151;156 NS;NS;NS;NS;NS 47;97;114;127;144 49;99;116;129;146 29587786 Effects of the S42 residue of the H1N1 swine influenza virus NS1 protein on interferon responses and virus replication. The recombinant virus rSIV, rSIV NS1 S42P, rSIV NS1 D92E and rSIV NS1 S42P/ D92E were generated by co-transfection of eight reverse-genetic plasmids with or without the substitution plasmids pBD-NS into 293 T cells. 2018 Virology journal Method IV S42P;D92E;S42P;D92E 37;52;70;76 41;56;74;80 NS;NS1;NS1;NS1 195;33;48;66 197;36;51;69 29587792 Major contribution of the RNA-binding domain of NS1 in the pathogenicity and replication potential of an avian H7N1 influenza virus in chickens. Briefly, four groups of 24 (wt), 22 (R38A-K41A), 23 (A149V) and 10 (mock) birds were inoculated intra-tracheally with 5 x 105 EID50 (0.1 ml) of each virus, along with 106 EID50 (0.2 ml) in the choanal cleft, while in the mock group the virus suspension was replaced by PBS. 2018 Virology journal Method IV R38A;K41A;A149V 37;42;53 41;46;58 29587792 Major contribution of the RNA-binding domain of NS1 in the pathogenicity and replication potential of an avian H7N1 influenza virus in chickens. The double substitution R38A-K41A was introduced using a primer pair harbouring two modified codons (codon 38 AGA > GCC and codon 41 AAG > GCG), while substitution A149V was introduced by changing codon GCA > GTG. 2018 Virology journal Method IV R38A;K41A;A149V;R38A;K41A 24;29;164;101;124 28;33;169;119;142 29587792 Major contribution of the RNA-binding domain of NS1 in the pathogenicity and replication potential of an avian H7N1 influenza virus in chickens. The R38A-K41A double substitution was introduced using the QuikChange kit. 2018 Virology journal Method IV R38A;K41A 4;9 8;13 29587792 Major contribution of the RNA-binding domain of NS1 in the pathogenicity and replication potential of an avian H7N1 influenza virus in chickens. The three recombinant IAVs (wt, 3841AA and A149V) were rescued by reverse genetics as described previously. 2018 Virology journal Method IV A149V 43 48 29643248 A Single Amino Acid in the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses. The minigenome plasmid with various combinations of viral polymerase complex plasmids (PB2, PB1, and NP), including WT PA or PA K338R, were transfected into 293T or MDCK cells using X-tremeGENE (Roche). 2018 Journal of virology Method IV K338R 128 133 NP;PA;PA;PB1;PB2 101;119;125;92;87 103;121;127;95;90 29688498 Dynamic Variation and Reversion in the Signature Amino Acids of H7N9 Virus During Human Infection. Validation Test of the NA R292K Mutation. 2018 The Journal of infectious diseases Method IV R292K 26 31 23 25 29688498 Dynamic Variation and Reversion in the Signature Amino Acids of H7N9 Virus During Human Infection. We used a single-nucleotide polymorphism (SNP)-specific RT-PCR assay to validate the NA R292K mutation detected by NGS. 2018 The Journal of infectious diseases Method IV R292K 88 93 85 87 29743603 Unexpected infection outcomes of China-origin H7N9 low pathogenicity avian influenza virus in turkeys. L235Q fwd: 5'-ATTCCCGCAGATGACTAAG-3' 2018 Scientific reports Method IV L235Q 0 5 29743603 Unexpected infection outcomes of China-origin H7N9 low pathogenicity avian influenza virus in turkeys. L235Q fwd: 5'-ATTCCCGCAGATGACTAAG-3'. 2018 Scientific reports Method IV L235Q 0 5 29743603 Unexpected infection outcomes of China-origin H7N9 low pathogenicity avian influenza virus in turkeys. L235Q rev: 5'-ACTGCCCTGCTATCTATGTT-3' 2018 Scientific reports Method IV L235Q 0 5 29743603 Unexpected infection outcomes of China-origin H7N9 low pathogenicity avian influenza virus in turkeys. L235Q rev: 5'-ACTGCCCTGCTATCTATGTT-3'. 2018 Scientific reports Method IV L235Q 0 5 29743603 Unexpected infection outcomes of China-origin H7N9 low pathogenicity avian influenza virus in turkeys. Raw sequence data was obtained in both orientations from the HA CS and L235Q conventional. 2018 Scientific reports Method IV L235Q 71 76 HA 61 63 29743603 Unexpected infection outcomes of China-origin H7N9 low pathogenicity avian influenza virus in turkeys. The EP6 H7N9 was full-genome sequenced and confirmed as identical to the original GenBank sequence submission (accession numbers: CY187618-CY187625) except for an amino acid change in the HA, namely N141D (complete gene numbering). 2018 Scientific reports Method IV N141D 199 204 HA 188 190 29743603 Unexpected infection outcomes of China-origin H7N9 low pathogenicity avian influenza virus in turkeys. This L235Q primer pair substituted for the GK7.3/GK7.4 primers in the above conventional RT-PCR with identical thermocycling to produce a 436 bp amplicon. 2018 Scientific reports Method IV L235Q 5 10 29743603 Unexpected infection outcomes of China-origin H7N9 low pathogenicity avian influenza virus in turkeys. To investigate the L235Q mammalian/avian adaptation polymorphism in the HA gene, two primers specific for H7N9 wt were designed which flanked this region. 2018 Scientific reports Method IV L235Q 19 24 29750015 Symmetric dimeric adamantanes for exploring the structure of two viroporins: influenza virus M2 and hepatitis C virus p7. M2: Inhibitors were tested in a two-electrode voltage-clamp assay using Xenopus laevis frog oocytes microinjected with RNA expressing either the wild type (WT) or the S31N mutant of the A/M2 protein, as previously reported. 2018 Drug design, development and therapy Method IV S31N 167 171 M2;M2 0;188 2;190 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. Mice pre-inoculated with PBS or NS1 R38A/K41A virus in the previous experiments were infected with 103.88 PFU of WT WSN virus at 17 d p.i. 2018 Frontiers in cellular and infection microbiology Method IV K41A;R38A 41;36 45;40 NS1 32 35 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. The full-length NS1 mutants (R38A, K41A, and R38A/K41A), either in pHH21 or pCMV-MYC, were generated with a Newpep site-directed mutagenesis kit (China) using the following primers: NS1-R38A-F, 5'-GACTTCTGATCTGCGCGAAGCCGAT-3'; NS1-R38A-R, 5'-ATTCCTTGATCGGCTTCGCGCAGAT-3'; NS1-K41A-F, 5'-TCCTCTTAGGGATGCCTGATCTCGG-3'; NS1-K41A-R, 5'-TTCGCCGAGATCAGGCATCCCTAAG-3'; NS1-R38A/K41A-F, 5'-CTCTTAGGGATGCCTGATCTGCGCG-3'; and NS1-R38A/K41A-R, 5'-TTCGCGCAGATCAGGCATCCCTAAG-3'. 2018 Frontiers in cellular and infection microbiology Method IV R38A;K41A;K41A;R38A;R38A;R38A;K41A;K41A;R38A;K41A;R38A;K41A 29;35;50;45;186;231;276;321;366;371;420;425 33;39;54;49;190;235;280;325;370;375;424;429 NS1;NS1;NS1;NS1;NS1;NS1;NS1 16;182;227;272;317;362;416 19;185;230;275;320;365;419 29783694 Adaptive Mutations in Influenza A/California/07/2009 Enhance Polymerase Activity and Infectious Virion Production. pHW-C72(T156A,F740L) and pHW-C73(E349G) were substituted for pHW-C72 and pHW-C73 constructs, respectively, to produce CA/07-PA,PB1-MA virus. 2018 Viruses Method IV T156A;F740L;E349G 8;14;33 13;19;38 PA;PB1 124;127 126;130 29783694 Adaptive Mutations in Influenza A/California/07/2009 Enhance Polymerase Activity and Infectious Virion Production. Subsequently, T156A and F740L amino acid substitutions were introduced into the PB1 construct to create pHW-C72(T156A,F740L) and E349G in the PA construct to create pHW-C73(E349G) using the Phusion site-directed mutagenesis PCR protocol (NEB). 2018 Viruses Method IV T156A;F740L;T156A;F740L;E349G;E349G 14;24;112;118;129;173 19;29;117;123;134;178 PA;PB1 142;80 144;83 29882021 Lethal Influenza in Two Related Adults with Inherited GATA2 Deficiency. Luciferase reporter assays were carried out in in HEK293T cells transfected with EV and with plasmids containing the GATA2-WT isoform 1 or the R396L and R398W variants. 2018 Journal of clinical immunology Method IV R396L;R398W 143;153 148;158 29882021 Lethal Influenza in Two Related Adults with Inherited GATA2 Deficiency. Western Blots of GATA-2 were performed on HEK293T cells transfected with plasmids containing GATA2-WT isoform 1 (Origene RC208554), GATA2-WT isoform 2 (Origene RC208514), mutated plasmids containing the variants R396L, R396Q and R398W generated by site-directed mutagenesis (QuickChange II XL Site-Directed Mutagenesis Kit: Agilent 200521-5) or with empty vectors (EV). 2018 Journal of clinical immunology Method IV R396L;R396Q;R398W 212;219;229 217;224;234 29933553 Kinetic, Thermodynamic, and Structural Analysis of Drug Resistance Mutations in Neuraminidase from the 2009 Pandemic Influenza Virus. A 3-fold molar excess of oseltamivir was used for the I223V, S247N, and S247N/H275Y mutants; a 12-fold excess for the H275Y mutant; and a 10-fold excess for the I223V/H275Y mutant. 2018 Viruses Method IV I223V;S247N;S247N;H275Y;H275Y;I223V;H275Y 54;61;72;78;118;161;167 59;66;77;83;123;166;172 29933553 Kinetic, Thermodynamic, and Structural Analysis of Drug Resistance Mutations in Neuraminidase from the 2009 Pandemic Influenza Virus. The 40 microL reactions contained 17 nM wt NA2009; 200 nM H275Y, S247N, H275Y/I223V, or H275Y/S247N NA2009; or 53 nM I223V NA2009 (calculated for monomer) and increasing substrate concentrations. 2018 Viruses Method IV H275Y;S247N;H275Y;I223V;H275Y;S247N;I223V 58;65;72;78;88;94;117 63;70;77;83;93;99;122 NA;NA;NA 43;100;123 45;102;125 29933553 Kinetic, Thermodynamic, and Structural Analysis of Drug Resistance Mutations in Neuraminidase from the 2009 Pandemic Influenza Virus. The following protein and inhibitor concentrations were used: 6.2 microM I223V NA2009 or 8.7 microM S247N NA2009 with 125 microM oseltamivir, and 9.6 microM H275Y NA2009 with 180 microM oseltamivir. 2018 Viruses Method IV I223V;S247N;H275Y 73;100;157 78;105;162 NA;NA;NA 79;106;163 81;108;165 29933553 Kinetic, Thermodynamic, and Structural Analysis of Drug Resistance Mutations in Neuraminidase from the 2009 Pandemic Influenza Virus. The reservoir solutions for the NA2009 mutants were as follows: I223V-0.1 M HEPES pH 6.75, 7% PEG 8000; S247N-0.1 M HEPES pH 6.7, 8.5% PEG 8000; H275Y-0.1 M HEPES pH 7.0, 8% PEG 8000; I223V/H275Y-0.1 M HEPES pH 7.0, 7% PEG 8000; and S247N/H275Y-0.1 M HEPES pH 7.5, 5% PEG 8000. 2018 Viruses Method IV I223V;S247N;H275Y;I223V;H275Y;S247N;H275Y 64;104;145;184;190;233;239 69;109;150;189;195;238;244 32 34 29933553 Kinetic, Thermodynamic, and Structural Analysis of Drug Resistance Mutations in Neuraminidase from the 2009 Pandemic Influenza Virus. The sequences of the primers used for mutagenesis were as follows: H275Y:5'CCCTAATTATTACTATGAGGAAT3' and 5'ATTCCTCATAGTAATAATTAGGG3'; I223V:5'GGAGAAACAATGTATTGAGAACAC3' and 5'GTGTTCTCAATACATTGTTTCTCC3'; S247N:5'CGATGGACCAAATAATGGACAGG3' and 5'CCTGTCCATTATTTGGTCCATCG3'. 2018 Viruses Method IV H275Y;I223V;S247N 67;134;203 72;139;208 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. Coordinates and structure factors for PA-FluA WT and I38T and PA-FluB WT and I38T in complex with BXA have been deposited in the wwPDB under accession codes 6FS6, 6FS7, 6FS8 and 6FS9 respectively and 6FSB for the ligand-free PA-FluB I38T variant. 2018 Scientific reports Method IV I38T;I38T;I38T 53;77;233 57;81;237 PA;PA;PA 38;62;225 40;64;227 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. FluA I38T BXA: 0.2 M (NH4)2SO4, 0.1 M Na(CH3)2AsO2 pH 6.5, 30% (w/v) PEG 8000. 2018 Scientific reports Method IV I38T 5 9 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. FluA or FluB endonuclease co-crystals with BXA were prepared at 20 C using either the hanging-drop (FluA WT) or sitting-drop technique (FluA I38T, FluB). 2018 Scientific reports Method IV I38T 142 146 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. FluB I38T BXA: 0.2 M CaCl2, 0.1 M MES pH 6.0, 20% (w/v) PEG 6000. 2018 Scientific reports Method IV I38T 5 9 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. FluB I38T-no ligand: 0.04 M KH2PO4, 16% (w/v) PEG 8000, 20% (v/v) glycerol. 2018 Scientific reports Method IV I38T 5 9 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. Point mutations encoding for the substitution I38T in both FluA and FluB were introduced by site-directed mutagenesis. 2018 Scientific reports Method IV I38T 46 50 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. Single crystals were fished and washed in a reservoir solution supplemented with 20% glycerol for cryoprotection (except FluB I38T-no ligand) and immediately frozen in liquid nitrogen. 2018 Scientific reports Method IV I38T 126 130 29976861 Anti-Influenza A Viral Butenolide from Streptomyces sp. Smu03 Inhabiting the Intestine of Elephas maximus. Influenza virus including A/FM/1/47 (H1N1) mouse adapted strain, A/Puerto Rico/8/34 (H1N1), A/Puerto Rico/8/34 (H1N1) with NA-H274Y mutation and A/Aichi/2/68 (H3N2), clinical isolates of 690 (H3 subtype), 699 (H3 subtype), and the influenza B virus. 2018 Viruses Method IV H274Y 126 131 123 125 30050898 Structurally Diverse Polyketides From the Mangrove-Derived Fungus Diaporthe sp. SCSIO 41011 With Their Anti-influenza A Virus Activities. Meanwhile, different influenza A virus subtypes, including A/Puerto Rico/8/34 H274Y (H1N1), A/FM-1/1/47 (H1N1), and A/Aichi/2/68 (H3N2), were multiplied in 10-day-old chick embryo at 37 C. 2018 Frontiers in chemistry Method IV H274Y 78 83 30111290 Development of a quadruple qRT-PCR assay for simultaneous identification of highly and low pathogenic H7N9 avian influenza viruses and characterization against oseltamivir resistance. Regions covering the insertion mutation in HA cleavage site and the NAI-resistance mutation (R292K) in NA were chosen as the targets for the primer design. 2018 BMC infectious diseases Method IV R292K 93 98 HA;NA;NAI 43;103;68 45;105;71 30141905 The Stabilities of the Soluble Ectodomain and Fusion Peptide Hairpins of the Influenza Virus Hemagglutinin Subunit II Protein Are Positively Correlated with Membrane Fusion. Purifications from cells expressing WT-, G1E-, and I173E-FHA2 were based on earlier work, and is denoted protocol A. 2018 Biochemistry Method IV G1E;I173E 41;51 44;56 30141905 The Stabilities of the Soluble Ectodomain and Fusion Peptide Hairpins of the Influenza Virus Hemagglutinin Subunit II Protein Are Positively Correlated with Membrane Fusion. The G1E and I173E mutants of FHA2 and HA2 were generated by PCR using DNA primers and confirmed by DNA sequencing. 2018 Biochemistry Method IV G1E;I173E 4;12 7;17 HA 38 40 30141905 The Stabilities of the Soluble Ectodomain and Fusion Peptide Hairpins of the Influenza Virus Hemagglutinin Subunit II Protein Are Positively Correlated with Membrane Fusion. Weakly-bound proteins were removed from the resin by washes (4x) with buffer A, with wash volumes of 1 mL (WT-FHA2) or 2 mL (G1E- and I173E-FHA2). 2018 Biochemistry Method IV G1E;I173E 125;134 128;139 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. In this study, all the mutations introduced into the recombinant VN/HN virus (clade 2.3.4) have been detected as single or multiple mutations in H5N1 viruses isolated from patients, except the PB2-E627K mutation. 2018 Scientific reports Method IV E627K 197 202 PB2 193 196 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. The PB2-E627K mutant virus was excluded from the mouse infection experiments in this study. 2018 Scientific reports Method IV E627K 8 13 PB2 4 7 30186261 Acquisition of Innate Inhibitor Resistance and Mammalian Pathogenicity During Egg Adaptation by the H9N2 Avian Influenza Virus. N133T was predicted to abolish a potential glycosylation site (133-135). 2018 Frontiers in microbiology Method IV N133T 0 5 30186261 Acquisition of Innate Inhibitor Resistance and Mammalian Pathogenicity During Egg Adaptation by the H9N2 Avian Influenza Virus. To replace asparagine (N) with threonine (T) at position 133 (N133T), site-directed mutagenesis was performed using a Muta-direct Site Directed Mutagenesis Kit (iNtRON, Korea) as per the manufacturer's protocol using the primers 01310-HA-N133T-F: 5'-CTTGGAATGTGACTTT CACTGGGACAAGCAAAGC-3', and 5'-01310-HA-N133T-R: GCTTTGCTTGTCCCAGTGAA AGTCACATTCCAAG-3'. 2018 Frontiers in microbiology Method IV N133T;N133T;N133T 62;238;306 67;243;311 HA;HA 235;303 237;305 30201817 Characterization of Influenza B Virus Variants with Reduced Neuraminidase Inhibitor Susceptibility. A B/Yamagata/16/88-like influenza B virus with the D197N NA substitution, designated B/Singapore/GP702/2015 (MUT-N197), was isolated from a 8-year-old female patient not receiving NAI therapy and was submitted to the WHO Collaborating Centre for Reference and Research on Influenza, Melbourne, Australia, by the Ministry of Health, Singapore. 2018 Antimicrobial agents and chemotherapy Method IV D197N 51 56 NA;NAI 57;180 59;183 30201817 Characterization of Influenza B Virus Variants with Reduced Neuraminidase Inhibitor Susceptibility. Another B/Yamagata/16/88-like virus with the H273Y NA substitution, designated B/Perth/136/2015 (MUT-Y273), was isolated from a 61-year-old female patient not receiving NAI therapy and was submitted during routine surveillance. 2018 Antimicrobial agents and chemotherapy Method IV H273Y 45 50 NA;NAI 51;169 53;172 30201817 Characterization of Influenza B Virus Variants with Reduced Neuraminidase Inhibitor Susceptibility. The WT-D197-MUT-N197 pair had identical gene sequences except for the desired D197N mutation in the NA gene, one amino acid difference in the NS gene, and one amino acid difference in the PA gene Similarly, the WT-H273-MUT-Y273 virus had two amino acid changes in the NP gene, one change in the PB1 gene, and one change in the PA gene. 2018 Antimicrobial agents and chemotherapy Method IV D197N 78 83 NA;NP;NS;PA;PA;PB1 100;268;142;188;327;295 102;270;144;190;329;298 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. The H7N9 NS1 mutants, NS1 (R55E), NS1 (H63Q), NS1 (E70K), NS1 (P87S), NS1 (S114P), NS1 (A143T), NS1 (I178V) and NS1 (S212P) were generated by site-directed mutagenesis with the QuickChange XL system (Stratagene, La Jolla, CA, USA). 2018 Veterinary research Method IV R55E;H63Q;E70K;P87S;S114P;A143T;I178V;S212P 27;39;51;63;75;88;101;117 31;43;55;67;80;93;106;122 NS1;NS1;NS1;NS1;NS1;NS1;NS1;NS1;NS1 9;22;34;46;58;70;83;96;112 12;25;37;49;61;73;86;99;115 30301950 Tree shrew as a new animal model to study the pathogenesis of avian influenza (H9N2) virus infection. H9N2 virus A/duck/Hong Kong/Y280/97 (Y280-wt) and its PB2-E627K mutant (Y280-PB2-E627K) were grown in 9- to 11-day-old specific-pathogen-free (SPF) chicken eggs. 2018 Emerging microbes & infections Method IV E627K;E627K 58;81 63;86 PB2;PB2 54;77 57;80 30301950 Tree shrew as a new animal model to study the pathogenesis of avian influenza (H9N2) virus infection. The animals were first anesthetized via intraperitoneal injection of 3% pentobarbital sodium dissolved in PBS and inoculated intranasally with Y280-wt or Y280-PB2-E627K virus (day 0). 2018 Emerging microbes & infections Method IV E627K 163 168 PB2 159 162 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. BSD, EGFP and ISG15 were separated using ribosome skipping 2A sequences (P2A and T2A). 2018 PLoS pathogens Method IV P2A;T2A 73;81 76;84 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. Independent validation of the SNP variant that gives rise to the K154E substitution in HsIFNlambda4 was obtained from gnomAD (http://grch37.ensembl.org/Homo_sapiens/Variation/Population?db=core;r=19:39737353-39738353;v=rs377155886;vdb=variation;vf=58909380 and https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=rs377155886). 2018 PLoS pathogens Method IV K154E 65 70 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. To validate the L79F variant, genomic DNA isolated from Epstein-Barr virus-immortalised B-cell lymphoblastoid cell lines from individuals (HG03095 and NA19658) identified through the 1000 Genomes Project and International HAPMAP project as probands with the L79F substitution (rs564293856 G>A SNP) were obtained from the Coriell Institute for Medical Research. 2018 PLoS pathogens Method IV L79F;L79F 16;258 20;262 151 153 30353004 Genome-wide characterization of the seasonal H3N2 virus in Shanghai reveals natural temperature-sensitive strains conferred by the I668V mutation in the PA subunit. Mutations in PB2 (R229K, R340K) and PA (I668V) were introduced by site-directed mutagenesis. 2018 Emerging microbes & infections Method IV R229K;R340K;I668V 18;25;40 23;30;45 PA;PB2 36;13 38;16 30400276 Combination Therapy with Oseltamivir and Favipiravir Delays Mortality but Does Not Prevent Oseltamivir Resistance in Immunodeficient Mice Infected with Pandemic A(H1N1) Influenza Virus. Stock viruses (rec H1N1pdm09 WT or H275Y used as controls) and viruses isolated from mouse lungs on days 8, 12, and 15 p.i. 2018 Viruses Method IV H275Y 35 40 30463209 A PB1-K577E Mutation in H9N2 Influenza Virus Increases Polymerase Activity and Pathogenicity in Mice. Human 293T and chicken DF-1 cells were transfected with pPolI-NP(0)Fluc(0) or pPolGG-NP(0)Fluc(0), together with pRL-null and pCAGGS plasmids expressing wild-type PB2, PB1, PA, and NP, or mutant PB1 K577E or PB2 E627K, by using polyethylenimine (PEI; Polysciences, Inc., Warrington, PA, USA). 2018 Viruses Method IV K577E;E627K 199;212 204;217 NP;NP;NP;PA;PA;PB1;PB1;PB2;PB2 62;85;181;173;283;168;195;163;208 64;87;183;175;285;171;198;166;211 30466301 Activity of enisamium, an isonicotinic acid derivative, against influenza viruses in differentiated normal human bronchial epithelial cells. Influenza A/Georgia/20/2006 (H1N1) H275Y (oseltamivir-resistant), A/Brisbane/59/2007 (H1N1), A/Tennessee/1-560/2009 (H1N1)pdm09, A/Perth/16/2009 (H3N2), A/Vietnam/1203/2004 (H5N1), A/Anhui/1/2003 (H7N9), and B/Texas/06/2011 viruses were obtained from the Influenza Division at the Centers for Disease Control and Prevention, and St Jude Children's Research Hospital. 2018 Antiviral chemistry & chemotherapy Method IV H275Y 35 40 30509291 Conserved methionine 165 of matrix protein contributes to the nuclear import and is essential for influenza A virus replication. Plasmids pHW187-M encoding the mutant M1 proteins R163A, Q164A, M165A, and V166A were prepared using Phusion Site-Directed Mutagenesis Kit (Finnzymes). 2018 Virology journal Method IV R163A;Q164A;M165A;V166A 50;57;64;75 55;62;69;80 M;M1 16;38 17;40 30509291 Conserved methionine 165 of matrix protein contributes to the nuclear import and is essential for influenza A virus replication. Plasmids pHW187-M encoding the mutant M1 proteins R163A, Q164A, M165A, and V166A were used to rescue of mutant viruses. 2018 Virology journal Method IV R163A;Q164A;M165A;V166A 50;57;64;75 55;62;69;80 M;M1 16;38 17;40 30509291 Conserved methionine 165 of matrix protein contributes to the nuclear import and is essential for influenza A virus replication. Significant differences in the expression of proteins between the control group (M1) and M165A were calculated using the unpaired Student's t-test. 2018 Virology journal Method IV M165A 89 94 M1 81 83 30518648 HDAC6 Restricts Influenza A Virus by Deacetylation of the RNA Polymerase PA Subunit. The following primers were used: PA-K281R-F (5'-GTT CTC AGC GGT CCA GAT TCC TGC TGA TGG AT-3') and PA-K281R-R (5'-ATC CAT CAG CAG GAA TCT GGA CCG CTG AGA AC-3'), PA-K497R-F (5'-AGG AGG GAA GGC GAA GGA CCA ATT TGT ACG G-3') and PA-K497R-R (5'-CCG TAC AAA TTG GTC CTT CGC CTT CCC TCC T-3'), PA-K643R-F (5'-AAC TTT ATT GGC AAG GTC GGT ATT CAA CAG C-3') and PA-K643R-R (5'-GCT GTT GAA TAC CGA CCT TGC CAA TAA AGT T-3'), PA-K664R-F (5'-TCA GCT GAA TCA AGA AGA CTG CTT CTT ATC GTT C-3') and PA-K664R-R (5'-GAA CGA TAA GAA GCA GTC TTC TTG ATT CAG CTG A-3'), and PA-K664Q-F (5'-TCA GCT GAA TCA AGA CAA CTG CTT CTT ATC GTT C-3') and PA-K664Q-R (5'-GAA CGA TAA GAA GCA GTT GTC TTG ATT CAG CTG A-3'). 2019 Journal of virology Method IV K281R;K281R;K497R;K497R;K643R;K643R;K664R;K664R;K664Q;K664Q 36;102;165;230;292;357;419;488;558;627 41;107;170;235;297;362;424;493;563;632 PA;PA;PA;PA;PA;PA;PA;PA;PA;PA 33;99;162;227;289;354;416;485;555;624 35;101;164;229;291;356;418;487;557;626 30574137 Susceptibility of Influenza Viruses to the Novel Cap-Dependent Endonuclease Inhibitor Baloxavir Marboxil. A/PR/8/34 possessing the PA I38T substitution (A/PR/8/34-PA/I38T) was generated by using the QuikChange Lightning Site-Directed Mutagenesis Kit (Agilent). 2018 Frontiers in microbiology Method IV I38T;I38T 28;60 32;64 PA;PA 25;57 27;59 30619194 Influenza A Virus NS1 Protein Suppresses JNK1-Dependent Autophagosome Formation Mediated by Rab11a Recycling Endosomes. The delNS1 virus harboring an amantadine sensitive mutation, N31S, in M2 protein (M2-N31S del NS1), NS1-R38AK41A, and NS1-Y89F mutant viruses were generated by reverse genetics using co-culture of HEK293T cells with MDCK cells stably expressing NS1 protein. 2018 Frontiers in microbiology Method IV N31S;N31S;Y89F 61;85;122 65;89;126 M2;M2;NS1;NS1;NS1;NS1 70;82;94;100;118;245 72;84;97;103;121;248 30619194 Influenza A Virus NS1 Protein Suppresses JNK1-Dependent Autophagosome Formation Mediated by Rab11a Recycling Endosomes. The viral titer of each virus was 2.0 x 108 FFU/ml for wild-type PR8, 3.5 x 107 FFU/ml for delNS1, 3.5 x 107 FFU/ml for M2-N31S delNS1, 1.1 x 107 FFU/ml for R38AK41A, 6.4 x 107 FFU/ml for Y89F, respectively. 2018 Frontiers in microbiology Method IV N31S;Y89F 123;188 127;192 M2 120 122 30640922 Molecular characterization of influenza A(H1N1)pdm09 in Cameroon during the 2014-2016 influenza seasons. Samples were considered positive for influenza A and A(H1N)2009 at a threshold cycle below 37 and only those with lower threshold cycles (below 30) were eligible for sequencing. 2019 PloS one Method IV H1N 55 58 30909490 The PB2 Polymerase Host Adaptation Substitutions Prime Avian Indonesia Sub Clade 2.1 H5N1 Viruses for Infecting Humans. Full length PB2 sequences of human and avian H5N1 viruses from the NCBI Influenza Virus Resource Database, together with all influenza A H5N1 human isolates in GISAID , were analyzed for prevalence of the K526R substitution. 2019 Viruses Method IV K526R 205 210 PB2 12 15 30996301 Bacterial glycosyltransferase-mediated cell-surface chemoenzymatic glycan modification. CHO, CHO-Lec2, and CHO-Lec 8 cells were labeled by Pm2,3ST-M144D, Pd2,6ST, or Hp1,3FT with CMP-SiaNAz-biotin or GDP-FucAz-biotin for 30 mins at 37 C, washed twice with PBS, and lysed on ice in NP-40 lysis buffer. 2019 Nature communications Method IV M144D 59 64 NP 194 196 30996301 Bacterial glycosyltransferase-mediated cell-surface chemoenzymatic glycan modification. For Hp1,3FT, Pd2,6ST, and Pm2,3ST-M144D, the enzymes were added at a concentration of 0.15 mug/muL, and the reaction time was 30 min. 2019 Nature communications Method IV M144D 34 39 30996301 Bacterial glycosyltransferase-mediated cell-surface chemoenzymatic glycan modification. For one-step biotin labeling of LacNAc containing glycans in tissues, slides were incubated with HBSS (pH 7.4) buffer with 3 mM HEPES, 20 mM MgSO4 and 100 muM CMP-SiaNAz-biotin, and 0.3 mug/mL enzymes (Pm2,3ST-M144D or Pd2,6ST) or without enzymes, for 30 mins at 37 C. 2019 Nature communications Method IV M144D 210 215 31008587 Hydrogen-Deuterium Exchange Supports Independent Membrane-Interfacial Fusion Peptide and Transmembrane Domains in Subunit 2 of Influenza Virus Hemagglutinin Protein, a Structured and Aqueous-Protected Connection between the Fusion Peptide and Soluble Ectodomain, and the Importance of Membrane Apposition by the Trimer-of-Hairpins Structure. SHA2_TM includes a N-terminal G20C mutation done for future native-chemical ligation (not part of the present study). 2019 Biochemistry Method IV G20C 30 34 31008587 Hydrogen-Deuterium Exchange Supports Independent Membrane-Interfacial Fusion Peptide and Transmembrane Domains in Subunit 2 of Influenza Virus Hemagglutinin Protein, a Structured and Aqueous-Protected Connection between the Fusion Peptide and Soluble Ectodomain, and the Importance of Membrane Apposition by the Trimer-of-Hairpins Structure. The G1E- and I173E-HA2 constructs were also studied. 2019 Biochemistry Method IV G1E;I173E 4;13 7;18 HA 19 21 31008587 Hydrogen-Deuterium Exchange Supports Independent Membrane-Interfacial Fusion Peptide and Transmembrane Domains in Subunit 2 of Influenza Virus Hemagglutinin Protein, a Structured and Aqueous-Protected Connection between the Fusion Peptide and Soluble Ectodomain, and the Importance of Membrane Apposition by the Trimer-of-Hairpins Structure. The HDX-MS apparatus included an incubated auto-sampler (Waters 2777), external pump (Shimadzu LC-20AD), UPLC pump system (Waters Acquity Binary Solvent Manager), and mass spectrometer (Waters Xevo G2S QTof) operating with electrospray ionization in positive ion mode, and continuum-mode m/z = 50 - 2000. 2019 Biochemistry Method IV G2S 198 201 31008587 Hydrogen-Deuterium Exchange Supports Independent Membrane-Interfacial Fusion Peptide and Transmembrane Domains in Subunit 2 of Influenza Virus Hemagglutinin Protein, a Structured and Aqueous-Protected Connection between the Fusion Peptide and Soluble Ectodomain, and the Importance of Membrane Apposition by the Trimer-of-Hairpins Structure. The sequences are from the X31 strain of influenza virus with mutation of all native Cys residues, specifically C137S, C144A, C148A, C195A, C199A, C210A, and C220A. 2019 Biochemistry Method IV C137S;C144A;C148A;C195A;C199A;C210A;C220A 112;119;126;133;140;147;158 117;124;131;138;145;152;163 31150476 Pathogenicity of the H1N1 influenza virus enhanced by functional synergy between the NPV100I and NAD248N pair. 293T cells were transfected with the pCAGGS WSN PB2, pCAGGS WSN PB1, pCAGGS WSN PA, pCAGGS WSN NP 0/14 (WT or V100I), pCAGGS and WSN NA (WT or D248N) expression vectors along with the pHH21 WSN NS-GFP reporter plasmid. 2019 PloS one Method IV V100I;D248N 110;143 115;148 NA;NP;NS;PA;PB1;PB2 133;95;194;80;64;48 135;97;196;82;67;51 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. Diffraction-quality crystals for Bris07 G186V/L194P (10 mg/ml) were obtained from 0.1 M CAPS pH 10.5 and 29% PEG 400 at 20 C. 2019 Cell host & microbe Method IV G186V;L194P 40;46 45;51 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. Chimeric PA genes, single or multiple point mutants of the PA genes, and the PB2 E627K mutant (generated by using a PCR approach) were cloned into vectors pCAGGS and pHH21. 2019 mBio Method IV E627K 81 86 PA;PA;PB2 9;59;77 11;61;80 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. Low polymerase activity attributed to PA drives the acquisition of the PB2 E627K mutation of H7N9 avian influenza virus in mammals. 2019 mBio Method IV E627K 75 80 PA;PB2 38;71 40;74 31266524 Highly pathogenic avian influenza H7N9 viruses with reduced susceptibility to neuraminidase inhibitors showed comparable replication capacity to their sensitive counterparts. A virus containing amino acid substitutions in sites related to potentially reduced susceptibility to NAIs in HPAI H7N9 viruses, including R292 K, E119V, A246T and H274Y, was constructed in this study. 2019 Virology journal Method IV R292K;E119V;A246T;H274Y 139;147;154;164 145;152;159;169 NAI 102 106 31266524 Highly pathogenic avian influenza H7N9 viruses with reduced susceptibility to neuraminidase inhibitors showed comparable replication capacity to their sensitive counterparts. NA A246T Forward, caccgatgggcctacaactggacctgcag. 2019 Virology journal Method IV A246T 3 8 31266524 Highly pathogenic avian influenza H7N9 viruses with reduced susceptibility to neuraminidase inhibitors showed comparable replication capacity to their sensitive counterparts. NA A246T Reverse, gtggctacccggatgttgacctggacgtc. 2019 Virology journal Method IV A246T 3 8 31266524 Highly pathogenic avian influenza H7N9 viruses with reduced susceptibility to neuraminidase inhibitors showed comparable replication capacity to their sensitive counterparts. NA E119V Forward, gtcgcatgaaacatagggtactcttgtgactaaaacatc. 2019 Virology journal Method IV E119V 3 8 31266524 Highly pathogenic avian influenza H7N9 viruses with reduced susceptibility to neuraminidase inhibitors showed comparable replication capacity to their sensitive counterparts. NA E119V Reverse, gatgttttagtcacaagagtaccctatgtttcatgcgac. 2019 Virology journal Method IV E119V 3 8 31266524 Highly pathogenic avian influenza H7N9 viruses with reduced susceptibility to neuraminidase inhibitors showed comparable replication capacity to their sensitive counterparts. NA H274Y Forward, ggaactgctaagtacattgaagaatg. 2019 Virology journal Method IV H274Y 3 8 31266524 Highly pathogenic avian influenza H7N9 viruses with reduced susceptibility to neuraminidase inhibitors showed comparable replication capacity to their sensitive counterparts. NA H274Y Reverse, ccttgacgattcatgtaacttcttac. 2019 Virology journal Method IV H274Y 3 8 0 2 31266524 Highly pathogenic avian influenza H7N9 viruses with reduced susceptibility to neuraminidase inhibitors showed comparable replication capacity to their sensitive counterparts. NA K292R Forward, ccctgccaattgtccctgcatgtgcaggtaatc. 2019 Virology journal Method IV K292R 3 8 31266524 Highly pathogenic avian influenza H7N9 viruses with reduced susceptibility to neuraminidase inhibitors showed comparable replication capacity to their sensitive counterparts. NA K292R Reverse, gattacctgcacatgcagggacaattggcaggg. 2019 Virology journal Method IV K292R 3 8 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. For rgGD17, the HA and NA genes from the highly pathogenic A/Guangdong/17SF003/2016 (GD17WT) were initially PCR amplified and cloned into cloning vector pGEM-T Easy (Promega, Madison, WI) for modification, with which we deleted the codon for the multibasic cleavage site RKRT from the HA gene and generated K292R (N2 numbering) mutation in NA to restore the neuraminidase inhibitor (NAi) sensitivity. 2019 Journal of virology Method IV K292R 307 312 HA;HA;NA;NA;NAI;NA 16;285;23;340;383;358 18;287;25;342;386;371 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. Louis, MO) in PBS containing 5 mM Ca2+ for 1 h, followed by washing with PBS, and subsequently inoculated with rgSH2WT or rgSH2-G218E (MOI of 0.002) for 1 h at 37 C. 2019 Journal of virology Method IV G218E 128 133 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. with 1.0 ml of rgGD17 (8.7 x 106 PFU); and (iii) rgGD17-G218E-immunized ferrets, where each ferret was inoculated i.n. 2019 Journal of virology Method IV G218E 56 61 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. with 1.0 ml of rgGD17-G218E (8.7 x 106 PFU), followed by monitoring of temperature and body weight for 2 weeks. 2019 Journal of virology Method IV G218E 22 27 31329089 Biological properties of influenza A virus mutants with amino acid substitutions in the HA2 glycoprotein of the HA1/HA2 interaction region. Mutations were introduced into the plasmid pHW2000 HA by site-directed mutagenesis to generate mutant viruses 64 (T642H substitution in the HA2 subunit; H1 numbering - position 407 in HA); 66 (V662H substitution in the HA2 subunit; H1 numbering - position 409 in HA) and D (T642H and V662H substitutions in the HA2 subunit). 2019 The Journal of general virology Method IV T642H;V662H;T642H;V662H 114;193;274;284 119;198;279;289 HA;HA;HA;HA;HA;HA 51;140;184;219;263;311 53;142;186;221;265;313 31420169 The structure and conformational plasticity of the nonstructural protein 1 of the 1918 influenza A virus. NS1-ED W187R was expressed in BL21 (DE3) E. 2019 Biochemical and biophysical research communications Method IV W187R 7 12 NS1 0 3 31436527 Human-to-Human Transmission of Influenza A(H3N2) Virus with Reduced Susceptibility to Baloxavir, Japan, February 2019. Both viruses possessed the PA I38T substitution and did not contain wild-type 38I. 2019 Emerging infectious diseases Method IV I38T 30 34 PA 27 29 31436527 Human-to-Human Transmission of Influenza A(H3N2) Virus with Reduced Susceptibility to Baloxavir, Japan, February 2019. The mutant virus encoding the PA I38T substitution showed normal inhibition with all 4 NA inhibitors but exhibited a 186-fold higher IC50 value (236 nmol/L) to baloxavir compared with the median IC50 value of influenza A(H3N2) viruses isolated in the 2018-19 season in Japan (1.27 nmol/L; Table 2). 2019 Emerging infectious diseases Method IV I38T 33 37 NA;PA 87;30 89;32 31436527 Human-to-Human Transmission of Influenza A(H3N2) Virus with Reduced Susceptibility to Baloxavir, Japan, February 2019. These results indicate that the mutant virus we isolated carrying the PA I38T substitution had reduced susceptibility to baloxavir but remained susceptible to NA inhibitors. 2019 Emerging infectious diseases Method IV I38T 73 77 NA;PA 159;70 161;72 31477028 A study of the relationship between human infection with avian influenza a (H5N6) and environmental avian influenza viruses in Fujian, China. The sequencing primers were M13F (5'-TGTAAAACGACGGCCAGT-3') and M13R (5'-CAGGAAACAGCTATG ACC-3'). 2019 BMC infectious diseases Method IV M13F;M13R 28;64 32;68 31538644 Baloxavir Marboxil in Japanese Pediatric Patients With Influenza: Safety and Clinical and Virologic Outcomes. In post hoc analyses, the baseline factors associated with emergence of viruses with PA/I38T/M substitutions were identified using a logistic regression model for patients with A(H3N2) virus, because such variants were only detected in those with A(H3N2) infection. 2020 Clinical infectious diseases Method IV I38M;I38T 88;88 94;94 PA 85 87 31538644 Baloxavir Marboxil in Japanese Pediatric Patients With Influenza: Safety and Clinical and Virologic Outcomes. Sanger sequencing of the PA gene was conducted on paired pre- and last post-treatment swab samples to detect PA/I38X-substituted viruses (Supplementary Materials). 2020 Clinical infectious diseases Method IV I38X 112 116 PA;PA 25;109 27;111 31575766 Influenza Virus Polymerase Mutation Stabilizes a Foreign Gene Inserted into the Virus Genome by Enhancing the Transcription/Replication Efficiency of the Modified Segment. MDCK cells were infected with WT-Venus-PR8 or Venus-PR8-PB2-E712D at an MOI of 1 or mock infected with medium. 2019 mBio Method IV E712D 60 65 PB2 56 59 31575766 Influenza Virus Polymerase Mutation Stabilizes a Foreign Gene Inserted into the Virus Genome by Enhancing the Transcription/Replication Efficiency of the Modified Segment. Statistically significant differences between WT-Venus-PR8 and Venus-PR8-PB2-E712D were assessed by using a two-tailed unpaired Student t test. 2019 mBio Method IV E712D 77 82 PB2 73 76 31575766 Influenza Virus Polymerase Mutation Stabilizes a Foreign Gene Inserted into the Virus Genome by Enhancing the Transcription/Replication Efficiency of the Modified Segment. WT-PR8, PR8-PB2-E712D, PR8-PB1-V43I, and PR8-PB1-T123A were generated by reverse genetics, and MDCK cells were infected at an MOI of 0.001. 2019 mBio Method IV E712D;V43I;T123A 16;31;49 21;35;54 PB1;PB1;PB2 27;45;12 30;48;15 31581279 Influenza virus polymerase subunits co-evolve to ensure proper levels of dimerization of the heterotrimer. Next-generation sequencing was performed by the P2M facility at Institut Pasteur, using the Nextera XT DNA Library Preparation kit (Illumina), the NextSeq 500 sequencing systems (Illumina), and the CLC Genomics Workbench 9 software (Qiagen) for analysis. 2019 PLoS pathogens Method IV P2M 48 51 31581279 Influenza virus polymerase subunits co-evolve to ensure proper levels of dimerization of the heterotrimer. When minigenome assays were performed with the trans-complementing pCI plasmids expressing the PR8-PB2 mutants E361A and R142A, luciferase activities were measured at 48 h post-transfection. 2019 PLoS pathogens Method IV E361A;R142A 111;121 116;126 PB2 99 102 31600274 Adaptation of H3N2 canine influenza virus to feline cell culture. Briefly, wild-type virus or mutant viruses bearing HA1-K299R or HA2-T107I were diluted to 4x106 PFU/mL and divided into six aliquots of 180 muL each. 2019 PloS one Method IV K299R;T107I 55;68 60;73 HA;HA1 64;51 66;54 31600274 Adaptation of H3N2 canine influenza virus to feline cell culture. MDCK cells were co-transfected with wild-type HA or mutant HA (HA1-K299R or HA2-T107I) expression plasmids, as well as with a fluorescent protein (Venus) expression plasmid (pcDNA3.1-Venus) by using polyethylenimine (PEI; Polysciences, Inc., Warrington, PA, USA). 2019 PloS one Method IV K299R;T107I 67;80 72;85 HA;HA;HA;HA1;PA 46;59;76;63;254 48;61;78;66;256 31600274 Adaptation of H3N2 canine influenza virus to feline cell culture. The cDNA of HA of wild-type virus or mutant viruses bearing HA1-K299R or HA2-T107I mutations were cloned into the protein expression plasmid, pCAGGS. 2019 PloS one Method IV K299R;T107I 64;77 69;82 HA;HA;HA1 12;73;60 14;75;63 31608791 Insights into species-specific regulation of ANP32A on the mammalian-restricted influenza virus polymerase activity. 293T cells were cotransfected with Myc-tagged PB2 627E or 627K, PB1 or PB1 (D446Y), PA and NP as well as ANP32A and cNA-Luc template for 24 h. 2019 Emerging microbes & infections Method IV D446Y 76 81 NP;PA;PB1;PB1;PB2 91;84;64;71;46 93;86;67;74;49 31608791 Insights into species-specific regulation of ANP32A on the mammalian-restricted influenza virus polymerase activity. 293T cells were transfected with chANP32A-X1 (0.5 mug/well) using Lipofectamine 2000 (Invitrogen) for 24 h, infected with PR8-PB2 K627E virus for 1 h at 37 C (MOI = 0.01) and cultured for indicated time point. 2019 Emerging microbes & infections Method IV K627E 130 135 PB2 126 129 31608791 Insights into species-specific regulation of ANP32A on the mammalian-restricted influenza virus polymerase activity. The C3U and G8A mutation at 5' promoter, A3G and U8C mutation at 3' promoter of cRNA were created by the inverse PCR technique and confirmed by sequencing. 2019 Emerging microbes & infections Method IV A3G;G8A 41;12 44;15 31608791 Insights into species-specific regulation of ANP32A on the mammalian-restricted influenza virus polymerase activity. The PB2 K627E substitution of pBD-PB2 was performed by site-directed mutagenesis by PCR. 2019 Emerging microbes & infections Method IV K627E 8 13 PB2;PB2 4;34 7;37 31608791 Insights into species-specific regulation of ANP32A on the mammalian-restricted influenza virus polymerase activity. The recombinant PR8 viruses carrying PB2 627K or K627E were rescued in 293T cells in the 8-plasmid system by the reverse genetics technique. 2019 Emerging microbes & infections Method IV K627E 49 54 PB2 37 40 31608791 Insights into species-specific regulation of ANP32A on the mammalian-restricted influenza virus polymerase activity. The recombinant virus was confirmed by sequencing and its growth curve analysis was performed by infecting 293T cells with PR8-PB2 K627E or PB2 627K virus (MOI = 0.01). 2019 Emerging microbes & infections Method IV K627E 131 136 PB2;PB2 127;140 130;143 31669761 Discovery of M2 channel blockers targeting the drug-resistant double mutants M2-S31N/L26I and M2-S31N/V27A from the influenza A viruses. M2-S31N inhibitors. 2020 European journal of pharmaceutical sciences Method IV S31N 3 7 M2 0 2 31749796 Enhanced Antiviral Activity of Human Surfactant Protein D by Site-Specific Engineering of the Carbohydrate Recognition Domain. Round 2, Asp324Asn: 2FOR, CA GGG GAG CCC AAC AAT GAT GGC GGC AGC AGC GGG TCA GAG GAC with 2REV, GTC CTC TGA CCC GCT GCC GCC GCC ATC ATT GTT GGG CTC CCC TG. 2019 Frontiers in immunology Method IV D324N 9 18 31749796 Enhanced Antiviral Activity of Human Surfactant Protein D by Site-Specific Engineering of the Carbohydrate Recognition Domain. Round 3, Asp330Asn: 3FOR, GGC GGC AGC AGC GGG TCA GAG AAC TGT GTG GAG ATC TTC ACC with 3REV, GGT GAA GAT CTC CAC ACA GTT CTC TGA CCC GCT GCT GCC GCC. 2019 Frontiers in immunology Method IV D330N 9 18 31749796 Enhanced Antiviral Activity of Human Surfactant Protein D by Site-Specific Engineering of the Carbohydrate Recognition Domain. Round 4, Val251Glu: 4FOR, G ATT TTC AAG ACA GCA GGC TTT GAA AAA CCA TTT ACG GAG GCA CAG with CTG TGC CTC CGT AAA TGG TTT TTC AAA GCC TGC TGT CTT GAA AAT C. 2019 Frontiers in immunology Method IV V251E 9 18 31749796 Enhanced Antiviral Activity of Human Surfactant Protein D by Site-Specific Engineering of the Carbohydrate Recognition Domain. Round 5, Lys287Gln + Glu289Lys (both mutations were generated in a single round of site-directed mutagenesis): 5FOR, G CAA CAG CTG GTC GTA GCT CAG AAC AAG GCT GCT TTC CTG AGC ATG with 5REV, CAT GCT CAG GAA AGC AGC CTT GTT CTG AGC TAC GAC CAG CTG TTG C. 2019 Frontiers in immunology Method IV K287Q;E289K 9;21 18;30 31805964 The tyrosine 73 and serine 83 dephosphorylation of H1N1 swine influenza virus NS1 protein attenuates virus replication and induces high levels of beta interferon. Furthermore, RIG-I interference dramatically impaired the induction of IFN-beta and ISG56 in NS1 Y73F and S83A mutant-infected cells. 2019 Virology journal Method IV Y73F;S83A 97;106 101;110 NS1 93 96 31805964 The tyrosine 73 and serine 83 dephosphorylation of H1N1 swine influenza virus NS1 protein attenuates virus replication and induces high levels of beta interferon. However, at 24 hpi, the NS1 protein expression was reduced dramatically in the cells infected with the NS1 Y73F and NS1 S83A mutant viruses compared with those infected with the wt virus, showing reductions of approximately 40% (Y73F) and 44% (S83A). 2019 Virology journal Method IV Y73F;S83A;Y73F;S83A 107;120;229;244 111;124;233;248 NS1;NS1;NS1 24;103;116 27;106;119 31805964 The tyrosine 73 and serine 83 dephosphorylation of H1N1 swine influenza virus NS1 protein attenuates virus replication and induces high levels of beta interferon. However, infection with the rSIV NS1 Y73F or S83A virus induced significantly higher levels of IFN-beta expression (4.06-fold and 4.49-fold, respectively) at 24 h after infection. 2019 Virology journal Method IV Y73F;S83A 37;45 41;49 NS1 33 36 31805964 The tyrosine 73 and serine 83 dephosphorylation of H1N1 swine influenza virus NS1 protein attenuates virus replication and induces high levels of beta interferon. Likewise, the expression of ISG56 upregulated by approximately 7.96-fold (rSIV NS1 Y73F virus) and 8.34-fold (rSIV NS1 S83A virus) compared to that in MDCK cells at 24 hpi. 2019 Virology journal Method IV Y73F;S83A 83;119 87;123 NS1;NS1 79;115 82;118 31805964 The tyrosine 73 and serine 83 dephosphorylation of H1N1 swine influenza virus NS1 protein attenuates virus replication and induces high levels of beta interferon. Mutations were introduced into the plasmid pBD-NS using overlap-PCR to generate the mutant NS segments: pBD-NS Y73F and pBD-NS S83A. 2019 Virology journal Method IV Y73F;S83A 111;127 115;131 NS;NS;NS;NS 47;91;108;124 49;93;110;126 31805964 The tyrosine 73 and serine 83 dephosphorylation of H1N1 swine influenza virus NS1 protein attenuates virus replication and induces high levels of beta interferon. Overall, the subcellular localization of the NS1 Y73F and the NS1 S83A mutant proteins was very similar to that of the wt NS1 protein; thus, these point mutations are insufficient to alter nuclear localization. 2019 Virology journal Method IV Y73F;S83A 49;66 53;70 NS1;NS1;NS1 45;62;122 48;65;125 31805964 The tyrosine 73 and serine 83 dephosphorylation of H1N1 swine influenza virus NS1 protein attenuates virus replication and induces high levels of beta interferon. Recombinant viruses encoding NS1 with Y-to-F substitution at position 73 and S-to-A substitution at position 83 were generated and denoted the rSIV NS1 Y73F and rSIV NS1 S83A viruses, respectively. 2019 Virology journal Method IV Y73F;S83A;S83A 152;170;77 156;174;111 NS1;NS1;NS1 29;148;166 32;151;169 31805964 The tyrosine 73 and serine 83 dephosphorylation of H1N1 swine influenza virus NS1 protein attenuates virus replication and induces high levels of beta interferon. recombinant wt virus infection exerted an inhibitory effect on RIG-I transcription; however, over 3-fold greater RIG-I expression was observed in Y73F and S83A mutant infected cells then in control cells at 24 hpi. 2019 Virology journal Method IV Y73F;S83A 146;155 150;159 31805964 The tyrosine 73 and serine 83 dephosphorylation of H1N1 swine influenza virus NS1 protein attenuates virus replication and induces high levels of beta interferon. RIG-I contributes to IFN-beta production during infection with the Y73F and S83A mutants. 2019 Virology journal Method IV Y73F;S83A 67;76 71;80 31805964 The tyrosine 73 and serine 83 dephosphorylation of H1N1 swine influenza virus NS1 protein attenuates virus replication and induces high levels of beta interferon. The pCAGGS-(SH/2014)-NS1 and pCAGGS-(SH/2014)-NS1 mutants Y73F, S76A, S83A, S151A, S161A and S195A were constructed by inserting the corresponding cDNAs into the EcoI/NheI sites of the pCAGGS vector. 2019 Virology journal Method IV Y73F;S76A;S83A;S151A;S161A;S195A 58;64;70;76;83;93 62;68;74;81;88;98 NS1;NS1 21;46 24;49 31805964 The tyrosine 73 and serine 83 dephosphorylation of H1N1 swine influenza virus NS1 protein attenuates virus replication and induces high levels of beta interferon. The recombinant viruses rSIV, rSIV NS1 Y73F and rSIV NS1 S83A were generated by cotransfection of 293 T cells with eight reverse-genetic plasmids with or without the substitution plasmid pBD-NS. 2019 Virology journal Method IV Y73F;S83A 39;57 43;61 NS;NS1;NS1 191;35;53 193;38;56 31805964 The tyrosine 73 and serine 83 dephosphorylation of H1N1 swine influenza virus NS1 protein attenuates virus replication and induces high levels of beta interferon. To further confirm our observation that RIG-I mediates IFN-beta production during infection by NS1 Y73F and S83A mutants, we collected RIG-I knockdown cells and subjected them to real-time PCR for IFN-beta and ISG56 quantification. 2019 Virology journal Method IV Y73F;S83A 99;108 103;112 NS1 95 98 31805964 The tyrosine 73 and serine 83 dephosphorylation of H1N1 swine influenza virus NS1 protein attenuates virus replication and induces high levels of beta interferon. To investigate whether the growth defects were correlated with any deficiencies in viral protein expression, we also analyzed the NS1 expression level of NS1 Y73F and NS1 S83A mutants in virus-infected cells by western blotting. 2019 Virology journal Method IV Y73F;S83A 158;171 162;175 NS1;NS1;NS1 130;154;167 133;157;170 31805964 The tyrosine 73 and serine 83 dephosphorylation of H1N1 swine influenza virus NS1 protein attenuates virus replication and induces high levels of beta interferon. Viruses with NS1 Y73F and NS1 S83A dephosphorylation show similar subcellular localization. 2019 Virology journal Method IV Y73F;S83A 17;30 21;34 NS1;NS1 13;26 16;29 31810278 Equine Mx1 Restricts Influenza A Virus Replication by Targeting at Distinct Site of its Nucleoprotein. Briefly, after 24 hr, the culture medium was removed and the cells were gently washed twice with preheated phosphate-buffered saline (PBS) and then infected for 1 hr at 37 C with wild-type (H3N8JL89) and/or mutant viruses (JL89-H52N-NP) at a multiplicity of infection (MOI) of 0.001. 2019 Viruses Method IV H52N 229 233 NP 234 236 31810278 Equine Mx1 Restricts Influenza A Virus Replication by Targeting at Distinct Site of its Nucleoprotein. Briefly, MDCK cells were infected with wild-type (H3N8JL89) and/or mutant viruses (JL89-H52N-NP) at an MOI of 0.001 and collected supernatants were used to infect MDCK cells in 96-well plates at various dilutions for 48 hr. 2019 Viruses Method IV H52N 88 92 NP 93 95 31810278 Equine Mx1 Restricts Influenza A Virus Replication by Targeting at Distinct Site of its Nucleoprotein. HEK293T cells were then co-transfected with p3XFLAG-tagged eqMx1 (4 mug) together with PB1, PB2 (2 mug each), PA, FF-Luc (1 mug each), and NP expression plasmids either from (1) H7N9, and its mutants H7N9-S34G and N52H; or (2) H3N8JL89 and its mutants JL89-G34S and H52N; or (3) an empty control vector (4 mug each) by using PolyJet In Vitro DNA transfection reagent (SignaGen, Rockville, MD, USA) according to the manufacturer's instructions. 2019 Viruses Method IV S34G;N52H;G34S;H52N 205;214;257;266 209;218;261;270 NP;PA;PB1;PB2 139;110;87;92 141;112;90;95 31810278 Equine Mx1 Restricts Influenza A Virus Replication by Targeting at Distinct Site of its Nucleoprotein. The generated wild-type virus and JL89-H52N-NP mutant virus were further propagated in 9-day-old embryonated chicken eggs at 35 C for 72 hr, and allantoic fluid was harvested and centrifuged, and a hemagglutination test was performed to confirm the presence of the virus. 2019 Viruses Method IV H52N 39 43 NP 44 46 31842256 Antiviral Activity of Benzoic Acid Derivative NC-5 Against Influenza A Virus and Its Neuraminidase Inhibition. Influenza viruses H1N1, H1N1-H275Y, and H3N2 or CHO-expressed viral NAs H5N1, H7N9 and H7N9-R294K were incubated with NC-5 at different concentrations at 37 C for 10 min. 2019 International journal of molecular sciences Method IV H275Y;R294K 29;92 34;97 68 71 31842256 Antiviral Activity of Benzoic Acid Derivative NC-5 Against Influenza A Virus and Its Neuraminidase Inhibition. MDCK cells were cultured in 96-well microplates at a density of 5 x 103 cells/well for 24 h and infected with 100 TCID50 H1N1, H1N1-H275Y or H3N2 virus for 2 h. 2019 International journal of molecular sciences Method IV H275Y 132 137 31842256 Antiviral Activity of Benzoic Acid Derivative NC-5 Against Influenza A Virus and Its Neuraminidase Inhibition. Mice were anesthetized by inhalation of diethyl ether and then intranasally infected with 50 muL of a suspension of 8 x LD50 of the mouse-adapted influenza A/FM1/1/47 (H1N1), A/FM/1/47-H275Y virus diluted in phosphate-buffered saline (PBS). 2019 International journal of molecular sciences Method IV H275Y 185 190 31842256 Antiviral Activity of Benzoic Acid Derivative NC-5 Against Influenza A Virus and Its Neuraminidase Inhibition. Plasmid construction: The recombinant plasmids pcDNA3.1(+), which can stably express NA protein sequences of A/Vietnam/1203/2004 (H5N1), A/Anhui/1/2013 (H7N9) and A/Anhui/1/2013-R294K (H7N9-R294K) were transfected into CHO-K1 cells using Lipofectamine 2000 Reagent (Invitrogen , Carlsbad, CA, USA). 2019 International journal of molecular sciences Method IV R294K;R294K 178;190 183;195 85 87 31842256 Antiviral Activity of Benzoic Acid Derivative NC-5 Against Influenza A Virus and Its Neuraminidase Inhibition. Virus production: The influenza A virus used in this study, containing A/FM/1/47 (H1N1), A/Beijing/32/92 (H3N2) and the H1N1 oseltamivir-resistant mutant strain A/FM/1/47-H275Y (H1N1-H275Y) (by introducing a histidine-to-tyrosine substitution at position 275 into NA), were propagated in 10-day-old embryonated chicken eggs. 2019 International journal of molecular sciences Method IV H275Y;H275Y 171;183 176;188 264 266 31894969 X-ray Crystal Structures of the Influenza M2 Proton Channel Drug-Resistant V27A Mutant Bound to a Spiro-Adamantyl Amine Inhibitor Reveal the Mechanism of Adamantane Resistance. M2(22-46) V27A and M2(21-61) V27A were synthesized using Fmoc chemistry with an optimized solid phase synthesis protocol and purified using reverse phase HPLC. 2020 Biochemistry Method IV V27A;V27A 10;29 14;33 M2;M2 0;19 2;21 31894969 X-ray Crystal Structures of the Influenza M2 Proton Channel Drug-Resistant V27A Mutant Bound to a Spiro-Adamantyl Amine Inhibitor Reveal the Mechanism of Adamantane Resistance. The M2(22-46) V27A - spiro-adamantylamine complex was embedded in a hydrated POPC lipid bilayer and the system was subjected to all-atom MD simulations using Desmond. 2020 Biochemistry Method IV V27A 14 18 M2 4 6 31894969 X-ray Crystal Structures of the Influenza M2 Proton Channel Drug-Resistant V27A Mutant Bound to a Spiro-Adamantyl Amine Inhibitor Reveal the Mechanism of Adamantane Resistance. The X-ray crystal structure of M2(22-46) WT in complex with spiro-adamantylamine molecule (PDB ID 6BMZ) was used as the starting structure after mutating Val27 to Ala. 2020 Biochemistry Method IV V27A 154 166 M2 31 33 31906790 Contribution of Fc-dependent cell-mediated activity of a vestigial esterase-targeting antibody against H5N6 virus infection. 9F4-WT, 9F4-LALA, 9F4-K322A and 1A4 were prepared at 5-fold serial dilutions, starting at a concentration of 5 microg/ml and added to the plated target cells for 45 min at RT. 2020 Emerging microbes & infections Method IV K322A 22 27 31906790 Contribution of Fc-dependent cell-mediated activity of a vestigial esterase-targeting antibody against H5N6 virus infection. Amino acid substitution K322A in the fragment crystallisable region (Fc region) of 9F4-pFUSEss-CHIg-mG2a was introduced by site-directed mutagenesis. 2020 Emerging microbes & infections Method IV K322A 24 29 31906790 Contribution of Fc-dependent cell-mediated activity of a vestigial esterase-targeting antibody against H5N6 virus infection. Briefly, 293 suspension cells cultured in baffled flasks were diluted to 1.0 x 106 cells/ml and co-transfected with 0.6 mug/ml of pFUSEss-CHIg-mG2a cloning vector containing VH of 9F4-WT or -K322A and 0.9 mug/ml of pFUSE2ss-CLIg-mK cloning vector containing VL gene of 9F4. 2020 Emerging microbes & infections Method IV K322A 191 196 31906790 Contribution of Fc-dependent cell-mediated activity of a vestigial esterase-targeting antibody against H5N6 virus infection. To assess the protective capabilities of 9F4-WT, 9F4-LALA and 9F4-K322A against H5N6 infections, rgPR8 H5N6 infected mice were given a single 10 mg/kg dose of 9F4-WT, 9F4-LALA, 9F4-K322A or an irrelevant isotype control 1A4 as a therapeutic via 200 microl intraperitoneal injections 24 h post-infection (hpi). 2020 Emerging microbes & infections Method IV K322A;K322A 66;181 71;186 Influenza A virus H5N6 infection 80 95 31932446 A molecularly engineered antiviral banana lectin inhibits fusion and is efficacious against influenza virus infection in vivo. Eight-week-old female BALB/c mice (Taconic) were anesthetized with isoflurane then injected intraperitoneally with either 50 mg/kg V66D/H84T/A100D BanLec, a variant of H84T engineered to increase solubility for biochemical assays, or with PBS (n = 5 per group). 2020 Proc Natl Acad Sci U S A Method IV V66D;A100D 131;141 135;146 31932446 A molecularly engineered antiviral banana lectin inhibits fusion and is efficacious against influenza virus infection in vivo. Eight-week-old female BALB/c mice were injected intraperitoneally with two 50-mg/kg doses of WT, H84T, or D133G BanLec administered 1 mo apart (n = 10 per group) and weighed and scored for appearance and injection site lesions. 2020 Proc Natl Acad Sci U S A Method IV D133G 106 111 31932446 A molecularly engineered antiviral banana lectin inhibits fusion and is efficacious against influenza virus infection in vivo. H84T and D133G BanLec Purification. 2020 Proc Natl Acad Sci U S A Method IV D133G 9 14 31932446 A molecularly engineered antiviral banana lectin inhibits fusion and is efficacious against influenza virus infection in vivo. Influenza A/WSN/HA(NC/2099-N225G)/1933 virus, produced as described in SI Appendix and as described previously. 2020 Proc Natl Acad Sci U S A Method IV N225G 27 32 HA 16 18 31932446 A molecularly engineered antiviral banana lectin inhibits fusion and is efficacious against influenza virus infection in vivo. MDCK cells were plated in eight-well chamber slides, pretreated for 1 h with 0.05 to 10 muM H84T, 10 muM D133G, or 40 muM ARB, and infected at 37 C with A/WSN/1933 (H1N1), A/Perth/2009 (H3N2), or A/Florida/2006 (H1N1) at a multiplicity of infection (MOI) of 0.5 in the presence of H84T, D133G, or ARB. 2020 Proc Natl Acad Sci U S A Method IV D133G;D133G 105;288 110;293 31932446 A molecularly engineered antiviral banana lectin inhibits fusion and is efficacious against influenza virus infection in vivo. Monolayers of MDCK cells in 96-well plates were treated for 24 h with H84T or D133G BanLec (0 to 15 muM) in 100 muL medium. 2020 Proc Natl Acad Sci U S A Method IV D133G 78 83 31932446 A molecularly engineered antiviral banana lectin inhibits fusion and is efficacious against influenza virus infection in vivo. Recombinant His-tagged H84T and D133G were prepared from Eschrichia coli as previously described, except that non-His-tagged H84T, which was used in experiments unless otherwise stated, was prepared using a Sephadex G-75 column instead of a Ni-NTA agarose column, as described in SI Appendix. 2020 Proc Natl Acad Sci U S A Method IV D133G 32 37 31932446 A molecularly engineered antiviral banana lectin inhibits fusion and is efficacious against influenza virus infection in vivo. Where indicated, virus alone (rather than cells) was pretreated with H84T, D133G, or ARB and uncoating examined. 2020 Proc Natl Acad Sci U S A Method IV D133G 75 80 31948040 H7N9 Influenza Virus Containing a Polybasic HA Cleavage Site Requires Minimal Host Adaptation to Obtain a Highly Pathogenic Disease Phenotype in Mice. Amino acid mutations in HA (A452T, H7 HA numbering with the signal peptide included), PA (D347G), and PB2 (M483K) were also inserted into each respective pPol vector by PCR using PrimeSTAR Max and in-fusion cloning. 2020 Viruses Method IV A452T;D347G;M483K 28;90;107 33;95;112 HA;HA;PA;PB2 24;38;86;102 26;40;88;105 32064779 Rapid detection of an I38T amino acid substitution in influenza polymerase acidic subunit associated with reduced susceptibility to baloxavir marboxil. The resulting PCR product of A/H3 was cloned using a TOPO TA Cloning Kit for Sequencing (Thermo Fisher Scientific), and those of A/H1pdm and B were cloned into the pHH21 vector.13 A mutation from T to C at nucleotide 113 was introduced into each gene using the primer pairs listed in Table S4 and the QuikChange Lightning Site-Directed Mutagenesis Kit (Agilent Technologies). 2020 Influenza and other respiratory viruses Method IV T113C 196 220 32064779 Rapid detection of an I38T amino acid substitution in influenza polymerase acidic subunit associated with reduced susceptibility to baloxavir marboxil. Three rhAmp SNP Assays (primer sets) for A/H1pdm PA_I38T rhPCR, A/H3 PA_I38T rhPCR, and B PA_I38T rhPCR were designed on the basis of the consensus PA gene sequence of A(H1N1)pdm09, A(H3N2), and B viruses isolated in the 2017/2018 influenza season using the rhAmp Genotyping Design Tool (Integrated DNA Technologies) (Table 1). 2020 Influenza and other respiratory viruses Method IV I38T;I38T;I38T 52;72;93 56;76;97 PA;PA;PA;PA 49;69;90;148 51;71;92;150 32093780 Acetylation at K108 of the NS1 protein is important for the replication and virulence of influenza virus. MDCK cells cultured on glass slides were infected with WSN-NS1-K108R, WSN-NS1-K108Q, or WSN-wt at an MOI of 1. 2020 Veterinary research Method IV K108R;K108Q 63;78 68;83 NS1;NS1 59;74 62;77 32093780 Acetylation at K108 of the NS1 protein is important for the replication and virulence of influenza virus. To generate mutant viruses, the site mutations K108R (deacetylation-mimic mutation) and K108Q (constant acetylation-mimic) were introduced into the reverse genetic plasmid pHW2000-WSN-NS by a commercial site-directed mutagenesis kit (Invitrogen, Grand Island, USA). 2020 Veterinary research Method IV K108R;K108Q 47;88 52;93 NS 184 186 32130243 Epidemic of influenza A(H1N1)pdm09 analyzed by full genome sequences and the first case of oseltamivir-resistant strain in Myanmar 2017. This assay utilizes single nucleotide polymorphisms (SNP) for detecting oseltamivir-sensitive (H275) and oseltamivir-resistant (H275Y) viruses based on the reaction curves of FAM (H275) or ROX (H275Y). 2020 PloS one Method IV H275Y;H275Y 128;194 133;199 32231159 Insertion of Basic Amino Acids in the Hemagglutinin Cleavage Site of H4N2 Avian Influenza Virus (AIV)-Reduced Virus Fitness in Chickens is Restored by Reassortment with Highly Pathogenic H5N1 AIV. For TMPRSS2 and HAT, HEK293T cells that do not express an endogenous HAT or TMPRSS2, were co-transfected with 1 microg pCAGGS plasmids containing H4N2_T327K, as well as 10 ng plasmid coding for each protease in the presence or absence of 50 microM furin inhibitior MI-1148 (kindly provided by Torsten Steinmetzer, Institute of Pharmaceutical Chemistry, Philipps-University Marburg, Marburg, Germany). 2020 International journal of molecular sciences Method IV T327K 151 156 32231159 Insertion of Basic Amino Acids in the Hemagglutinin Cleavage Site of H4N2 Avian Influenza Virus (AIV)-Reduced Virus Fitness in Chickens is Restored by Reassortment with Highly Pathogenic H5N1 AIV. Furthermore, HA of H4N2_wt, H4N2_T327R and H4N2_T327K H4N2 were cloned into the pCAGGS vector to increase protein expression. 2020 International journal of molecular sciences Method IV T327R;T327K 33;48 38;53 HA 13 15 32231159 Insertion of Basic Amino Acids in the Hemagglutinin Cleavage Site of H4N2 Avian Influenza Virus (AIV)-Reduced Virus Fitness in Chickens is Restored by Reassortment with Highly Pathogenic H5N1 AIV. In addition to the recombinant H4N2_wt, three recombinant H4N2 viruses carrying the HA4 with T327R (H4N2_T327R), T327K (H4N2_T327K) or H5N2-HACS (H4N2_H5N2-HACS) were constructed. 2020 International journal of molecular sciences Method IV T327R;T327K;T327R;T327K 93;113;105;125 98;118;110;130 HA 84 86 32231159 Insertion of Basic Amino Acids in the Hemagglutinin Cleavage Site of H4N2 Avian Influenza Virus (AIV)-Reduced Virus Fitness in Chickens is Restored by Reassortment with Highly Pathogenic H5N1 AIV. Moreover, three recombinant H4N1 viruses carrying seven gene segments from H5N1 and HA from H4N2_wt (H5N1_HA4), HA4_T327R (H5N1_HA4_T327R) or HA4_T327K (H5N1_HA4_T327K) and one H4N7 virus carrying seven gene segments from H7N7 and the HA from H4N2_wt (H7N7_HA4) were successfully generated. 2020 International journal of molecular sciences Method IV T327R;T327R;T327K;T327K 116;132;146;162 121;137;151;167 HA;HA 84;235 86;237 32231159 Insertion of Basic Amino Acids in the Hemagglutinin Cleavage Site of H4N2 Avian Influenza Virus (AIV)-Reduced Virus Fitness in Chickens is Restored by Reassortment with Highly Pathogenic H5N1 AIV. The cleavage of HA of H4N2_wt, H4N2_T327R and H4N2_T327K in the presence or absence of 2 microg/mL TPCK-treated trypsin was studied by transfecting cells with 5 microg pCAGGS plasmid coding for HA of the different viruses using Lipofectamine 2000 transfection reagent (ThermoFischer Scientific, Karlsruhe, Germany). 2020 International journal of molecular sciences Method IV T327R;T327K 36;51 41;56 HA;HA 16;194 18;196 32231159 Insertion of Basic Amino Acids in the Hemagglutinin Cleavage Site of H4N2 Avian Influenza Virus (AIV)-Reduced Virus Fitness in Chickens is Restored by Reassortment with Highly Pathogenic H5N1 AIV. The severity of pathohistological lesions and distribution of recombinant viruses in the trachea, lungs, heart, liver, pancreas, kidneys, thymus, spleen, proventriculus, gizzard, duodenum, jejunum, caecum, bursa of Fabricius and brain from at least two inoculated birds per group was analyzed at 4 dpi except for chickens inoculated with H5N1_HA4_T327K, which died at 2 dpi and were kept in the refrigerator. 2020 International journal of molecular sciences Method IV T327K 347 352 32231159 Insertion of Basic Amino Acids in the Hemagglutinin Cleavage Site of H4N2 Avian Influenza Virus (AIV)-Reduced Virus Fitness in Chickens is Restored by Reassortment with Highly Pathogenic H5N1 AIV. Using the HA encoding plasmid of H4N2_wt, three different CS motifs were generated by exchanging T327R or T327K, or by insertion of a polybasic CS resembling that of HPAIV A/chicken/Italy/8/1998 (H5N2) (designated hereafter H5N2-HACS) using the QuikChange II Site-Directed Mutagenesis Kit (Invitrogen, Carlsbad, CA, USA). 2020 International journal of molecular sciences Method IV T327R;T327K 97;106 102;111 HA 10 12 32256457 Identification of Chebulinic Acid and Chebulagic Acid as Novel Influenza Viral Neuraminidase Inhibitors. Oseltamivir-resistant influenza A/H1N1/pdm(09) virus containing NA/H274Y was provided by Beijing CDC, China, influenza A/Brisbane/10/2007(H3N2) was provided by Chinese Academy of Medical Sciences, and influenza B-Yamagata-like and B-Victoria-like strains were provided by Shandong CDC (Jinan, China). 2020 Frontiers in microbiology Method IV H274Y 67 72 64 66 32272772 Influenza PB1-F2 Inhibits Avian MAVS Signaling. Primers for the duck 2CARD construct contained two nucleotide replacements resulting in an A120D mutation, using preferred human codons. 2020 Viruses Method IV A120D 91 96 32272772 Influenza PB1-F2 Inhibits Avian MAVS Signaling. Primers for the human 2CARD construct contained a single nucleotide mutation to generate the D122A mutation, codon-optimized for expression in chicken cells. 2020 Viruses Method IV D122A 93 98 32272772 Influenza PB1-F2 Inhibits Avian MAVS Signaling. The d2CARD A120D and h2CARD D122A mutants were made using QuikChange mutagenesis to introduce mutations in the wild-type 2CARD constructs previously generated. 2020 Viruses Method IV A120D;D122A 11;28 16;33 32272772 Influenza PB1-F2 Inhibits Avian MAVS Signaling. The GST-d2CARD A120D and GST-h2CARD D122A constructs were then created using rolling circle PCR mutagenesis using the overlapping primers and Phusion polymerase, and a DpnI digest was performed to remove the non-mutated plasmids. 2020 Viruses Method IV A120D;D122A 15;36 20;41 32415096 mRNA display with library of even-distribution reveals cellular interactors of influenza virus NS1. HA-tagged WT or D92Y mutant NS1 protein was expressed in 293T cells, lysed at 2 days post transfection and bound with anti-HA overnight at 4 C. 2020 Nature communications Method IV D92Y 16 20 HA;HA;NS1 0;123;28 2;125;31 32415096 mRNA display with library of even-distribution reveals cellular interactors of influenza virus NS1. NS1 (WT and R38A/K41A mutation), PB2, PB1, PA, NP (from WSN strain), NS1 from Cal09 and GFP protein were cloned into Lenti-X Tet-one inducible expression plasmid with 2xStrep affinity tag at C-terminus. 2020 Nature communications Method IV R38A;K41A 12;17 16;21 NP;NS1;NS1;PA;PB1;PB2 47;0;69;43;38;33 49;3;72;45;41;36 32415096 mRNA display with library of even-distribution reveals cellular interactors of influenza virus NS1. NS1 protein with R38A/K41A or D92Y mutation was generated using a PCR-based site-directed mutagenesis strategy. 2020 Nature communications Method IV K41A;R38A;D92Y 22;17;30 26;21;34 NS1 0 3 32415096 mRNA display with library of even-distribution reveals cellular interactors of influenza virus NS1. WT and D92Y mutant NS1 ORFs were cloned into the pLVX-TetOne-Puro vector with 2xStrep tag at the N-terminus. 2020 Nature communications Method IV D92Y 7 11 NS1 19 22 32433222 Baloxavir Marboxil 2% Granules in Japanese Children With Influenza: An Open-label Phase 3 Study. The baseline characteristics of children with emergence of PA/I38T/M substitutions were presented. 2020 The Pediatric infectious disease journal Method IV I38T;I38M 62;62 68;68 PA 59 61 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. Screening of A(H1N1)pdm09 viruses for the presence of point mutations encoding NA H275Y amino acid substitution, known to confer oseltamivir resistance, was carried out using a real-time RT-PCR assay that allowed discrimination of a single nucleotide difference between oseltamivir sensitive and resistant viruses. 2020 Journal of medical microbiology Method IV H275Y 82 87 79 81 32486222 Antibody Neutralization of an Influenza Virus that Uses Neuraminidase for Receptor Binding. For experiments with the S364N mutant of NA, we introduced S364N into pHWCA09tc-NA-G147R to create pHWCA09tc-G147R-S364N. 2020 Viruses Method IV S364N;S364N;G147R;S364N;G147R 25;59;83;115;109 30;64;88;120;114 NA;NA 41;80 43;82 32486222 Antibody Neutralization of an Influenza Virus that Uses Neuraminidase for Receptor Binding. These viruses were generated from the following reverse genetics plasmids: for the WSN internal genes, pHW181-PB2, pHW183-PA, pHW185-NP, pHW187-M, and pHW188-NS; for the PB1 segment, pHH-PB1flank-eGFP; for the NA segment either pHWCA09tc-NA or pHWCA09tc-G147R; and for the HA segment either pHW-CA09tc-HA or pHWX31-HA-NGly12-Y98F-L194A-H183F-del221to228-K62EHA2. 2020 Viruses Method IV G147R;L194A;H183F;Y98F 254;330;336;325 259;335;341;329 HA;HA;HA;M;NA;NA;NP;NS;PA;PB1;PB2 273;302;315;144;210;238;133;158;122;170;110 275;304;317;145;212;240;135;160;124;173;113 32486222 Antibody Neutralization of an Influenza Virus that Uses Neuraminidase for Receptor Binding. This HA is derived from the A/Hong Kong/1968 H3N2 strain, and has the following mutations: Y98F, H183F, and L194A at receptor binding residues; seven potential N-linked glycosylation sites added at residues 45, 63, 122, 126, 133, 144, and 246; deletion of the receptor binding proximal loop spanning residues 221-228; and mutation K62E in the HA2 stalk (all mutations in H3 numbering). 2020 Viruses Method IV Y98F;H183F;L194A;K62E 91;97;108;331 95;102;113;335 HA;HA 5;343 7;345 32486222 Antibody Neutralization of an Influenza Virus that Uses Neuraminidase for Receptor Binding. We then added either the NAbind/HA bind virus, NAbind+S364N/HA bind virus, NAbind/HAwt virus, or NAwt/HAwt virus using an infectious dose determined to be within the linear range of detection. 2020 Viruses Method IV S364N 54 59 HA;HA 32;60 34;62 32599753 Virtual Screening Identifies Chebulagic Acid as an Inhibitor of the M2(S31N) Viral Ion Channel and Influenza A Virus. Additional preparation of M2(S31N) for ligand docking was performed using MOE as follows: first, the structure was protonated using default parameters; second, partial charges were computed for each atom of the molecule; and third, energy minimization was performed with gas phase solvation parameters using the all atom OPLS-AA force field until a gradient of 0.001 kcal/mol was attained. 2020 Molecules (Basel, Switzerland) Method IV S31N 29 33 M2 26 28 32599753 Virtual Screening Identifies Chebulagic Acid as an Inhibitor of the M2(S31N) Viral Ion Channel and Influenza A Virus. Briefly, approximately 100 plaque-forming units of either PR8M2(S31N) or PR8M2(S31) virus were mixed with test compounds and inoculated on confluent MDCK monolayers in six-well plates. 2020 Molecules (Basel, Switzerland) Method IV S31N 64 68 32599753 Virtual Screening Identifies Chebulagic Acid as an Inhibitor of the M2(S31N) Viral Ion Channel and Influenza A Virus. Briefly, Saccharomyces cerevisiae contain a multicopy plasmid for expression of M2(S31N) or M2(S31) obtained from the Udorn strain of influenza A virus under the control of a GAL1 promoter. 2020 Molecules (Basel, Switzerland) Method IV S31N 83 87 M2;M2 80;92 82;94 32599753 Virtual Screening Identifies Chebulagic Acid as an Inhibitor of the M2(S31N) Viral Ion Channel and Influenza A Virus. Docking validation was conducted with M2WJ332 (compound 4) against the M2(S31N) form and amantadine against the M2(S31) form; both docked native ligands showed RMSD values < 1.5 A with respect to the X-ray ligand structures. 2020 Molecules (Basel, Switzerland) Method IV S31N 74 78 M2;M2 71;112 73;114 32599753 Virtual Screening Identifies Chebulagic Acid as an Inhibitor of the M2(S31N) Viral Ion Channel and Influenza A Virus. P1 and P2 were separately docked towards the binding pocket of both M2(S31N) and M2(S31) around the vicinity of the co-crystalized M2WJ332 ligand using the Dock module implemented in MOE. 2020 Molecules (Basel, Switzerland) Method IV S31N 71 75 M2;M2 68;81 70;83 32599753 Virtual Screening Identifies Chebulagic Acid as an Inhibitor of the M2(S31N) Viral Ion Channel and Influenza A Virus. Pharmacophore features that may hypothetically contribute to the activity of the M2(S31N) inhibitors reported in the literature were determined by how well the pharmacophore features of the hits fit into the generated common pharmacophores. 2020 Molecules (Basel, Switzerland) Method IV S31N 84 88 M2 81 83 32599753 Virtual Screening Identifies Chebulagic Acid as an Inhibitor of the M2(S31N) Viral Ion Channel and Influenza A Virus. Preparation of M2(S31N) for Computational Docking Studies. 2020 Molecules (Basel, Switzerland) Method IV S31N 18 22 M2 15 17 32599753 Virtual Screening Identifies Chebulagic Acid as an Inhibitor of the M2(S31N) Viral Ion Channel and Influenza A Virus. The solution nuclear magnetic resonance (NMR) structure of M2(S31N) complexed with M2WJ332 was retrieved from the Protein Data Bank (PDB ID: 2LY0) and used as the starting point of all simulations. 2020 Molecules (Basel, Switzerland) Method IV S31N 62 66 M2 59 61 32599753 Virtual Screening Identifies Chebulagic Acid as an Inhibitor of the M2(S31N) Viral Ion Channel and Influenza A Virus. To test the inhibitory effect of compounds on virus replication, MDCK cell monolayers grown in 96-well plates were infected with 50x TCID50 of either PR8M2(S31N) or PR8M2(S31) in the presence of compound in DMEM+ containing 0.00075% Difco trypsin (BD Biosciences, San Jose, CA, USA) in quadruplicate, and as described previously. 2020 Molecules (Basel, Switzerland) Method IV S31N 156 160 32599753 Virtual Screening Identifies Chebulagic Acid as an Inhibitor of the M2(S31N) Viral Ion Channel and Influenza A Virus. Two PR8-derived recombinant influenza A viruses that differed only in M2 were used in this study: PR8M2(S31N) carries M2 protein with V and N at positions 27, and 31, respectively, while PR8M2(S31) carries V and S at positions 27, and 31, respectively. 2020 Molecules (Basel, Switzerland) Method IV S31N 104 108 M2;M2 70;118 72;120 32601336 Pre-existing immunity to influenza virus hemagglutinin stalk might drive selection for antibody-escape mutant viruses in a human challenge model. Molecules expected to undergo steric clash upon A388V mutation were predicted using the default clash parameter in UCSF Chimera. 2020 Nature medicine Method IV A388V 48 53 32601336 Pre-existing immunity to influenza virus hemagglutinin stalk might drive selection for antibody-escape mutant viruses in a human challenge model. The effect of the A388V mutation on the increase of viral resistance to three bNAbs (CR6261, CR9114 and FI6V3) was measured using wild-type (A388) and mutant (V388) H1N1pdm viruses generated by reverse genetics. 2020 Nature medicine Method IV A388V 18 23 32601336 Pre-existing immunity to influenza virus hemagglutinin stalk might drive selection for antibody-escape mutant viruses in a human challenge model. To measure the effect of the A388V mutation on the HA structure, full-length wild-type or mutant HAs, produced as described above, were diluted in PBS (3 mug ml-1) and added to 96-well ELISA plates (50 mul per well) (catalog no. 2020 Nature medicine Method IV A388V 29 34 HA 51 53 32601336 Pre-existing immunity to influenza virus hemagglutinin stalk might drive selection for antibody-escape mutant viruses in a human challenge model. To show that the stalk-only A388V construct closely represents the stalk structure in the full-length A388V HA, the magnitude of the structural differences between the respective wild-type and mutant constructs was compared by ELISA and the following AUC calculation as described above. 2020 Nature medicine Method IV A388V;A388V 28;102 33;107 HA 108 110 32636820 Enhanced Potency of a Broad H7N9-Neutralizing Antibody HNIgGA6 Through Structure-Based Design. The animals were intraperitoneally injected with HNIgGA6 or the S28H variant at a concentration of 5 mg kg-1, and the control group was treated with PBS which was used to dissolve the antibodies. 2020 Frontiers in microbiology Method IV S28H 64 68 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. (1) were extracted from the original AutoDock program to derive the binding modes of wt and I223R/H275Y mutant NA in the CDR of A4. 2020 Nature communications Method IV I223R;H275Y 92;98 97;103 111 113 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. 3D structure of A4 obtained in the precedent homology modeling served as the receptor model in docking simulations with wt and I223R/H275Y mutant NA. 2020 Nature communications Method IV I223R;H275Y 127;133 132;138 146 148 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. Docking simulations of wt and I223R/H275Y NA in the CDR of A4. 2020 Nature communications Method IV I223R;H275Y 30;36 35;41 42 44 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. Immunotubes (Nunc) were coated with 100 mug of wt NA or I223R/H275Y NA overnight at 4 C, washed twice with PBS, and blocked with 4% skim milk in PBS at 37 C for 1 h. 2020 Nature communications Method IV I223R;H275Y 56;62 61;67 NA;NA 50;68 52;70 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. In addition, I223R/H275Y mutation was introduced within the NA fragment by the forward primer: 5'-TATTCGTCTCAGGGATGAAGACTATCATTGCTTTGAGCTACATT-3' and reverse primer: 5'-ATATCGTCTCGTATTTGTTTTTAATTAATGCACTCAAATGCAAA-3'. 2020 Nature communications Method IV I223R;H275Y 13;19 18;24 60 62 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. In detail, a microtiter plate was coated with 100 ng of I223R/H275Y NA in coating buffer (0.05 M carbonate buffer, pH 9.6) and incubated at 4 C overnight. 2020 Nature communications Method IV I223R;H275Y 56;62 61;67 68 70 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. The culture supernatant of each clone was subjected to ELISA to screen anti-I223R/H275Y NA antibodies. 2020 Nature communications Method IV I223R;H275Y 76;82 81;87 88 90 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. The I223R/H275 and wt viruses were diluted in PBS buffer with various concentration and added to the prepared immune substrates for 6 h at 4 C with shaking. 2020 Nature communications Method IV I223R 4 9 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. The pH1N1/H275Y mutant virus (H275Y mutation A/Korea2785/2009 pdm: NCCP 42017) was obtained from the National Culture Collection for Pathogens (NCCP) operated by the Korea National Institute of Health. 2020 Nature communications Method IV H275Y;H275Y 10;30 15;35 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. The reverse genetics system was used to generate different subtypes of the I223R/H275Y influenza virus. 2020 Nature communications Method IV I223R;H275Y 75;81 80;86 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. The subtracted phages were then incubated with I223R/H275Y NA at 37 C for 1 h. 2020 Nature communications Method IV I223R;H275Y 47;53 52;58 59 61 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. The wt NA and mutant NA (I223R/H275Y) genes derived from A/H1N1 2009 pandemic influenza virus were amplified by PCR. 2020 Nature communications Method IV I223R;H275Y 25;31 30;36 NA;NA 7;21 9;23 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. To screen individual clones for specific binding to I223R/H275Y NA, 500 colonies were randomly selected from the output plate after the third or fourth round of panning, cultured in Superbroth medium containing 100 mug mL-1 ampicillin until optical density of 0.5, and induced for Fab expression in Escherichia coli TG1 cells at 30 C overnight by adding isopropyl beta-d-1-thiogalactopyranoside to a final concentration of 1 mM. 2020 Nature communications Method IV I223R;H275Y 52;58 57;63 64 66 32677963 Influenza A virus NS1 optimises virus infectivity by enhancing genome packaging in a dsRNA-binding dependent manner. The NS1 R38A mutant expression plasmid was generated from the parental pEF-Bos-NS1 plasmid using KOD-plus site directed mutagenesis (Toyobo) according to the manufacturer's instructions. 2020 Virology journal Method IV R38A 8 12 NS1;NS1 4;79 7;82 32721992 Differential Viral-Host Immune Interactions Associated with Oseltamivir-Resistant H275Y and Wild-Type H1N1 A(pdm09) Influenza Virus Pathogenicity. The A/Baleares/RR6121/2009 and A/Madrid/RR7495/2011 viruses bear the OR H275Y mutation and are hereafter referred to as R6 and R7, respectively. 2020 Viruses Method IV H275Y 72 77 32873642 Dynamic PB2-E627K substitution of influenza H7N9 virus indicates the in vivo genetic tuning and rapid host adaptation. The ratio of K/E (sequence depths of 627K to 627E) and ratio of N/D (sequence depths of 701N to 701D) were used to characterize the relative abundance of 627K compared with 627E in the specimens and to quantify the substitution of E627K and D701N in the viruses. 2020 Proc Natl Acad Sci U S A Method IV E627K;D701N 231;241 236;246 32929001 RNA-seq accuracy and reproducibility for the mapping and quantification of influenza defective viral genomes. Recombinant A/WSN/33 influenza viruses (NCBI:txid382835), either wild-type or bearing single mutations in the PA polymerase subunit (PA-K635A and PA-R638A), were used. 2020 RNA (New York, N.Y.) Method IV K635A;R638A 136;149 141;154 PA;PA;PA 110;133;146 112;135;148 32929001 RNA-seq accuracy and reproducibility for the mapping and quantification of influenza defective viral genomes. The Illumina library construction and sequencing were performed by the P2M platform at Institut Pasteur. 2020 RNA (New York, N.Y.) Method IV P2M 71 74 32962203 PA from a Recent H9N2 (G1-Like) Avian Influenza a Virus (AIV) Strain Carrying Lysine 367 Confers Altered Replication Efficiency and Pathogenicity to Contemporaneous H5N1 in Mammalian Systems. Briefly, 293T (2 x 106 cells/well) were seeded in 6-well plates and co-transfected with 1 microg of each pMPccdB expression plasmid encoding the individual viral ribonucleoprotein complex (vRNP; PB2, PA, PB1 and NP) components of H5N1EGY, or H9N2EGY, or H7N9Anhui, or vRNP components of H5N1EGY expressing individually the mutated PA_R367K of H5N1EGY or PA_K367R of H9N2EGY. 2020 Viruses Method IV R367K;K367R 334;357 339;362 NP;PA;PA;PA;PB1;PB2 212;200;331;354;204;195 214;202;333;356;207;198 32962203 PA from a Recent H9N2 (G1-Like) Avian Influenza a Virus (AIV) Strain Carrying Lysine 367 Confers Altered Replication Efficiency and Pathogenicity to Contemporaneous H5N1 in Mammalian Systems. The highly pathogenic avian influenza virus A/chicken/Egypt/N12640A/2016(H5N1), designated hereafter as H5N1EGY, and the low pathogenic virus A/chicken/Egypt/S12568C/2016(H9N2), designated hereafter as H9N2EGY, were isolated from infected chicken in Egypt in 2016 by the Center of Scientific Excellence for Influenza Viruses (CSEIV), National Research Centre, Egypt. 2020 Viruses Method IV N12640A;S12568C 60;158 67;165 32962203 PA from a Recent H9N2 (G1-Like) Avian Influenza a Virus (AIV) Strain Carrying Lysine 367 Confers Altered Replication Efficiency and Pathogenicity to Contemporaneous H5N1 in Mammalian Systems. Variant viruses H5N1EGY_R367K and H5N1PA-H9N2Egy_K367R carrying polymerase acidic (PA)-encoding segments with specific mutations were rescued individually by transfecting a co-culture of 293T/MDCK cells with eight pMPccdB plasmids corresponding to the unchanged seven segments of the virus and the mutated one (7 WT viral segments + 1 mutant PA viral segment), using Trans-IT2020 (Mirus Bio, Madison, WI, USA) as described previously. 2020 Viruses Method IV R367K;K367R 24;49 29;54 PA;PA;PA 83;342;64 85;344;81 33024040 Structure-Based Modification of an Anti-neuraminidase Human Antibody Restores Protection Efficacy against the Drifted Influenza Virus. In the therapeutic experiments, each group received doses of Z2B3 or Z2B3-D102R antibody (10 or 20 mg/kg) 12 hours after intranasal infection with 1,000 LD50 of A/Serbia/NS-601/2014 (H1N1). 2020 mBio Method IV D102R 74 79 NS 170 172 33024040 Structure-Based Modification of an Anti-neuraminidase Human Antibody Restores Protection Efficacy against the Drifted Influenza Virus. The crystal structures of Z2B3-18N1, Z2B3-N9, and Z2B3-D102R-Serbia N1 have been deposited in the Protein Data Bank under accession codes 6LXI, 6LXJ, and 6LXK, respectively. 2020 mBio Method IV D102R 55 60 N9 42 44 33024040 Structure-Based Modification of an Anti-neuraminidase Human Antibody Restores Protection Efficacy against the Drifted Influenza Virus. The interactions between Z2B3 or Z2B3-D102R with purified 18N1, Serbia N1, or AH-N9 were measured by SPR using a BIAcore 3000 system (GE Healthcare) at 25 C. 2020 mBio Method IV D102R 38 43 N9 81 83 33024040 Structure-Based Modification of an Anti-neuraminidase Human Antibody Restores Protection Efficacy against the Drifted Influenza Virus. The purified NA protein was mixed with Z2B3 or Z2B3-D102R Fab at a 4.5:1 molar ratio and incubated on ice for 1 hour. 2020 mBio Method IV D102R 52 57 13 15 33024040 Structure-Based Modification of an Anti-neuraminidase Human Antibody Restores Protection Efficacy against the Drifted Influenza Virus. Two-fold serial dilutions of Z2B3 Fab or Z2B3-D102R Fab were prepared and sequentially injected at a flow rate of 30 mul/min for 60 s, followed a dissociation step for 300 s. 2020 mBio Method IV D102R 46 51 33024040 Structure-Based Modification of an Anti-neuraminidase Human Antibody Restores Protection Efficacy against the Drifted Influenza Virus. Two-fold serially diluted MAbs (Z2B3 or Z2B3-D102R) were mixed with an equal volume of 100 TCID50 virus for 1 h at 37 C. 2020 mBio Method IV D102R 45 50 33024040 Structure-Based Modification of an Anti-neuraminidase Human Antibody Restores Protection Efficacy against the Drifted Influenza Virus. Z2B3 or Z2B3-D102R antibody after acclimatization for 3 days. 2020 mBio Method IV D102R 13 18 33024040 Structure-Based Modification of an Anti-neuraminidase Human Antibody Restores Protection Efficacy against the Drifted Influenza Virus. Z2B3-D102R Fab-Serbia N1 complex crystals were obtained in a solution consisting of 0.1 M magnesium acetate, 0.1 M 2-(N-morpholino)ethanesulfonic acid (MES) (pH 6.5), and 10% (wt/vol) PEG10000. 2020 mBio Method IV D102R 5 10 33063654 Detection and discrimination of influenza B Victoria lineage deletion variant viruses by real-time RT-PCR. Analytical sensitivity of the Vic 2_Del and Vic No_Del assays was determined using two V1A-2DEL and V1A viruses. 2020 Euro surveillance Method IV V1A;V1A 87;100 90;103 33063654 Detection and discrimination of influenza B Victoria lineage deletion variant viruses by real-time RT-PCR. In order to demonstrate rRT-PCR performance of the VIC deletion assay, five B/VIC lineage viruses and two B/YAM lineage viruses from recent circulating genetic groups, including the WHO-recommended influenza B vaccine viruses B/Colorado/6/2017 (V1A-2DEL), B/Brisbane/60/2008 (V1A) and B/Phuket/3073/2013 (B/Yam) were selected for assay evaluation (Figure). 2020 Euro surveillance Method IV V1A;V1A 245;276 248;279 33063654 Detection and discrimination of influenza B Victoria lineage deletion variant viruses by real-time RT-PCR. Influenza B virus isolates used to evaluate analytical performance included B/Maryland/15/2016 and B/Colorado/6/2017 (V1A-2DEL), B/Hong Kong/269/2017 and B/Washington/02/2019 (V1A-3DEL) as well as no-deletion viruses B/Florida/103/2016 and B/Brisbane/60/2008 (V1A). 2020 Euro surveillance Method IV V1A;V1A;V1A 118;176;260 121;179;263 33063654 Detection and discrimination of influenza B Victoria lineage deletion variant viruses by real-time RT-PCR. The three probes, targeted to the deletion region of the HA gene of influenza B viruses, were designed to specifically detect and differentiate V1A-2DEL, V1A-3DEL and the V1A genetic group (no-deletion) viruses (B/VIC No_Del), respectively (Table 1). 2020 Euro surveillance Method IV V1A;V1A;V1A 144;154;171 147;157;174 HA 57 59 33063654 Detection and discrimination of influenza B Victoria lineage deletion variant viruses by real-time RT-PCR. The Vic 3_Del assay was evaluated by using the V1A-3DEL virus B/Hong Kong/269/2017 and B/Washington/02/2019. 2020 Euro surveillance Method IV V1A 47 50 33063654 Detection and discrimination of influenza B Victoria lineage deletion variant viruses by real-time RT-PCR. The Vic 3_Del probe was labelled at the 5'-end with the reporter molecule 6-carboxyfluorescein (FAM) and BHQ1 at the 3'-end, and included a triplet of locked nucleic acids (LNA) that centred on the mismatch bases from V1A-2DEL and V1A viruses. 2020 Euro surveillance Method IV V1A;V1A 218;231 221;234 33099886 Comprehensive assessment of amino acid substitutions in the trimeric RNA polymerase complex of influenza A virus detected in clinical trials of baloxavir marboxil. In the CAPSTONE-2 study, next-generation sequencing (NGS) was also employed with the samples meeting the following criteria: (a) subjects shedding A(H3N2) viruses with PA/I38T substitution, (b) virology data (viral titer and RNA) are available at days 1, 2, 3 or 4, and 5 or 6, and (c) virus rebound was detected, defined as >1.5 log10TCID50/mL increases in viral titer from previous adjacent time point. 2021 Influenza and other respiratory viruses Method IV I38T 171 175 PA 168 170 33202790 Identification of Novel Influenza Polymerase PB2 Inhibitors Using a Cascade Docking Virtual Screening Approach. Influenza A PR/8 (H1N1), ZX/1109 (H1N1), the PR/8-R292K mutant (H1N1, oseltamivir-resistant, recombinant strain), the PR/8-I38T mutant (H1N1, baloxavir-resistant, recombinant strain), A/WSN/33 (H1N1), HK/68 (H3N2), and influenza B/Lee/40 were propagated in 8- to 10-day-old embryonated chicken eggs or MDCK cells for 3 days at 37 C. 2020 Molecules (Basel, Switzerland) Method IV R292K;I38T 50;123 55;127 33208942 Host ANP32A mediates the assembly of the influenza virus replicase. pcDNA-huANP32A 176-183, pcDNA-PB2 T609A, pcDNA-PB2 P132A, pcDNA-PA D529A/R531A/E533A, pcDNA-PA K413A, pcDNA-PA K324A/H326A/E327A and pcDNA-PA K339A/Q340A were generated from pcDNA-huANP32A, pcDNA-PB2 and pcDNA-PA by site-directed PCR mutagenesis and validated by Sanger sequencing. 2020 Nature Method IV T609A;P132A;D529A;R531A;E533A;K413A;K324A;H326A;E327A;K339A;Q340A 34;51;67;73;79;95;111;117;123;142;148 39;56;72;78;84;100;116;122;128;147;153 PA;PA;PA;PA;PA;PB2;PB2;PB2 64;92;108;139;210;30;47;196 66;94;110;141;212;33;50;199 33208942 Host ANP32A mediates the assembly of the influenza virus replicase. pcDNA-PB1, pcDNA-PB1a (catalytically inactive; D445A/D446A), pcDNA-PB2, pcDNA-PB2 K627E, pcDNA-PA, pcDNA-NP and pPOLI-NA, which encodes an NA vRNA segment, are derived from influenza A/WSN/33 virus and have been described previously. 2020 Nature Method IV D445A;D446A;K627E 47;53;82 52;58;87 NA;NA;NP;PA;PB1;PB2;PB2 118;139;105;95;6;67;78 120;141;107;97;9;70;81 33270431 Colorimetric Detection of SARS-CoV-2 and Drug-Resistant pH1N1 Using CRISPR/dCas9. pH1N1 and pH1N1/H275Y virus titers were determined using a one-step real-time PCR kit (Promega, Madison, WI) in accordance with the manufacturer's instructions. 2020 ACS sensors Method IV H275Y 16 21 33270431 Colorimetric Detection of SARS-CoV-2 and Drug-Resistant pH1N1 Using CRISPR/dCas9. SARS-CoV-2 (BetaCoV/Korea/KCDC03/2020) and pH1N1/H275Y mutant virus (H275Y mutation; A/Korea2785/2009 pdm: NCCP 42017) were provided by the National Culture Collection for Pathogens (NCCP), which is operated by the Korea National Institute of Health. 2020 ACS sensors Method IV H275Y;H275Y 49;69 54;74 33281788 Altering Intracellular Localization of the RNA Interference Factors by Influenza A Virus Non-structural Protein 1. Individual point mutations were introduced into the NS segment of PR8 (D101H, A155T, and D189N of PR8 NS1 protein, see below) and the mutant viruses rescued by standard procedures using an eight-plasmid reverse genetics system. 2020 Frontiers in microbiology Method IV D101H;A155T;D189N 71;78;89 76;83;94 NS;NS1 52;102 54;105 33281788 Altering Intracellular Localization of the RNA Interference Factors by Influenza A Virus Non-structural Protein 1. The lungs of BALB/c mice inoculated intranasally with PR8 WT, PR8 D101H, or PBS were harvested 3 d.p.i., fixed in 10% neutral-buffered formalin, transferred to 70% alcohol, and embedded in paraffin. 2020 Frontiers in microbiology Method IV D101H 66 71 33424035 The Effect of I155T, K156Q, K156E and N186K Mutations in Hemagglutinin on the Virulence and Reproduction of Influenza A/H5N1 Viruses. In the system that we used, HA differs from the original A/Vietnam/1203/2004(H5N1) (GenBank, AY818135) by the A138V substitution and the shortened cutting site: QIETRG instead of QRERRRKKRG. 2020 Molecular biology Method IV A138V 110 115 HA 28 30 33451024 Identification of Important N-Linked Glycosylation Sites in the Hemagglutinin Protein and Their Functional Impact on DC-SIGN Mediated Avian Influenza H5N1 Infection. The pHW1203-HA with different N-linked glycosylation mutations including N26Q, N27Q, N39Q, N170Q, N181Q, N209Q, N302Q, N500Q, N599Q and other combination of mutations were generated. 2021 International journal of molecular sciences Method IV N26Q;N27Q;N39Q;N170Q;N181Q;N209Q;N302Q;N500Q;N599Q 73;79;85;91;98;105;112;119;126 77;83;89;96;103;110;117;124;131 HA 12 14 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. Briefly, HEK293T cells were transfected with a plasmid expressing Flag-tagged truncated PB1494-757 or PB1494-757/K612R or with pCAGGS-Flag vector as a control. 2021 PLoS pathogens Method IV K612R 113 118 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. By using a PCR approach, a K612R mutation was introduced into different viral PB1 genes, which were then cloned into the pHH21 vector. 2021 PLoS pathogens Method IV K612R 27 32 PB1 78 81 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. HEK293T cells were transfected with pCAGGS constructs expressing viral PB2, PB1 (wild-type or K612R mutant), PA, and NP proteins (0.5 mug each), the construct pHH21-SC09NS F-Luc (0.1 mug), and an internal control pRL-TK (0.05 mug, Promega) by using Lipofectamine LTX & Plus reagents (Invitrogen). 2021 PLoS pathogens Method IV K612R 94 99 NP;PA;PB1;PB2 117;109;76;71 119;111;79;74 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. Mutant viruses with the PB1/K612R mutation (AAA at positions 1858-1860 of PB1 gene were mutated to CGA) in the WSN (H1N1), VN/1180 (H5N1), AH/1 (H7N9) and FZ/1(H1N1) background were generated by using the reverse genetics system as described previously. 2021 PLoS pathogens Method IV K612R 28 33 PB1;PB1 24;74 27;77 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. Plasmids expressing the WSN-H1PB1 mutants, including WSN-H1PB1/K379R, WSN-H1PB1/K612R, and WSN-H1PB1/K736R, were derived from pCAGGS-Flag-WSN-H1PB1 by PCR-based site-directed mutagenesis. 2021 PLoS pathogens Method IV K379R;K612R;K736R 63;80;101 68;85;106 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. Truncation constructs of the three different PB1 proteins, WSN-H1PB1494-757, VN/1180-H5PB1494-757, AH/1-H7PB1494-757, as well as the corresponding K612R mutants, were generated by using a PCR approach. 2021 PLoS pathogens Method IV K612R 147 152 PB1 45 48 33647314 The active form of the influenza cap-snatching endonuclease inhibitor baloxavir marboxil is a tight binding inhibitor. For IC50 determinations, various concentrations of FluB-ht WT or FluB-ht PA I38T were incubated with 1.7 muM vRNA and increasing concentrations of BXA at 30 C in buffer A and 5% DMSO for 5 minutes. 2021 The Journal of biological chemistry Method IV I38T 76 80 PA 73 75 33647314 The active form of the influenza cap-snatching endonuclease inhibitor baloxavir marboxil is a tight binding inhibitor. In total, 55 nM FluB-ht WT or FluB-ht PA I38T and 100 nM capped 20-nt substrate were mixed as specified with and without 75 nM BXA in buffer A with 5% DMSO and incubated at 30 C for 1 hour to allow for complex formation. 2021 The Journal of biological chemistry Method IV I38T 41 45 PA 38 40 33647314 The active form of the influenza cap-snatching endonuclease inhibitor baloxavir marboxil is a tight binding inhibitor. In total, 55 nM of FluB-ht WT or FluB-ht PA I38T was incubated with 75 nM BXA, 5% DMSO and 1.7 muM vRNA in buffer A at 30 C for 3, 6, 9, 12, 15, 18, 21, 24, or 27 min. 2021 The Journal of biological chemistry Method IV I38T 44 48 PA 41 43 33673017 Structural and Thermodynamic Analysis of the Resistance Development to Pimodivir (VX-787), the Clinical Inhibitor of Cap Binding to PB2 Subunit of Influenza A Polymerase. After several days, crystals of PB2-WT appeared using crystallization reservoir solution: 30 microM sodium fluoride, 30 microM sodium bromide, 30 microM sodium iodide, 20% (v/v) PEG 500 MME, 10% (w/v) PEG 20000, 0.1 M imidazole/MES, pH 6.5; for PB2-F404Y and PB2-M431I: 30 microM magnesium chloride, 30 microM calcium chloride, 20% (v/v) PEG 500 MME, 10% (w/v) PEG 20000, 0.1 M bicine/Tris, pH 8.5; and for PB2-H357N: 0.2 M magnesium chloride, 20% (w/v) PEG 8000, 0.1 M Tris, pH 8.5. 2021 Molecules (Basel, Switzerland) Method IV F404Y;M431I;H357N 249;263;411 254;268;416 PB2;PB2;PB2;PB2 32;245;259;407 35;248;262;410 33673017 Structural and Thermodynamic Analysis of the Resistance Development to Pimodivir (VX-787), the Clinical Inhibitor of Cap Binding to PB2 Subunit of Influenza A Polymerase. Crystal of PB2-F404Y diffracted up to 1.50 A; PB2-WT up to 1.55 A; PB2-H357N up to 1.63 A and PB2-M431I up to 1.75 A. 2021 Molecules (Basel, Switzerland) Method IV F404Y;H357N;M431I 15;71;98 20;76;103 PB2;PB2;PB2;PB2 11;46;67;94 14;49;70;97 33673017 Structural and Thermodynamic Analysis of the Resistance Development to Pimodivir (VX-787), the Clinical Inhibitor of Cap Binding to PB2 Subunit of Influenza A Polymerase. Purified PB2 variants were dialyzed to the crystallization buffer (10 mM Tris-HCl, pH 8.0, 1 mM TCEP) and concentrated to 2.5 mg/mL (PB2-WT), 3.2 mg/mL (PB2-F404Y), 3.8 mg/mL (PB2-M431I) and 5.2 mg/mL (PB2-H357N) using Amicon 10 kDa centrifugal filter units (MilliporeSigma, Burlington, MA, USA). 2021 Molecules (Basel, Switzerland) Method IV F404Y;M431I;H357N 157;180;206 162;185;211 PB2;PB2;PB2;PB2;PB2 9;133;153;176;202 12;136;156;179;205 33673017 Structural and Thermodynamic Analysis of the Resistance Development to Pimodivir (VX-787), the Clinical Inhibitor of Cap Binding to PB2 Subunit of Influenza A Polymerase. The crystal of PB2-H357N belonged to the P3121 space group and had also one molecule in asymmetric unit with a solvent content approximately 48%. 2021 Molecules (Basel, Switzerland) Method IV H357N 19 24 PB2 15 18 33673017 Structural and Thermodynamic Analysis of the Resistance Development to Pimodivir (VX-787), the Clinical Inhibitor of Cap Binding to PB2 Subunit of Influenza A Polymerase. The crystals of PB2-WT, PB2-F404Y, PB2-M431I belonged to the P1 space group and all of them contained one molecule in asymmetric unit, with a solvent content of approximately 39%. 2021 Molecules (Basel, Switzerland) Method IV F404Y;M431I 28;39 33;44 PB2;PB2;PB2 16;24;35 19;27;38 33673017 Structural and Thermodynamic Analysis of the Resistance Development to Pimodivir (VX-787), the Clinical Inhibitor of Cap Binding to PB2 Subunit of Influenza A Polymerase. The following protein and inhibitor concentrations were used: 6 microM PB2-WT with 65 microM pimodivir, 8 microM PB2-F404Y with 100 microM pimodivir, 3.4 microM PB2-M431I with 45 microM pimodivir, and 9 microM PB2-H357N with 75 microM pimodivir. 2021 Molecules (Basel, Switzerland) Method IV F404Y;M431I;H357N 117;165;214 122;170;219 PB2;PB2;PB2;PB2 71;113;161;210 74;116;164;213 33673017 Structural and Thermodynamic Analysis of the Resistance Development to Pimodivir (VX-787), the Clinical Inhibitor of Cap Binding to PB2 Subunit of Influenza A Polymerase. The reported crystal structures of pimodivir with WT, F404Y, M431I, and H357N variants of PB2 were used for molecular modeling. 2021 Molecules (Basel, Switzerland) Method IV F404Y;M431I;H357N 54;61;72 59;66;77 PB2 90 93 33673017 Structural and Thermodynamic Analysis of the Resistance Development to Pimodivir (VX-787), the Clinical Inhibitor of Cap Binding to PB2 Subunit of Influenza A Polymerase. The WT sequence in the plasmid was mutated by PCR mutagenesis to PB2 variants PB2-M431I, PB2-F404Y, and PB2-H357N. 2021 Molecules (Basel, Switzerland) Method IV M431I;F404Y;H357N 82;93;108 87;98;113 PB2;PB2;PB2;PB2 65;78;89;104 68;81;92;107 33679636 Improved in vitro Efficacy of Baloxavir Marboxil Against Influenza A Virus Infection by Combination Treatment With the MEK Inhibitor ATR-002. Briefly, the complete set of eight vectors encoding the vRNA of wild type and variant rgA/Victoria/3/75 (rgH3N2-WT, rgH3N2-PA-I38T) and rgA/Giessen/6/2009 (rgH1N1-WT, rgH1N1-PA-I38T) were co-transfected into a co-culture of 293T/MDCK-II cells. 2021 Frontiers in microbiology Method IV I38T;I38T 126;177 130;181 PA;PA 123;174 125;176 33679636 Improved in vitro Efficacy of Baloxavir Marboxil Against Influenza A Virus Infection by Combination Treatment With the MEK Inhibitor ATR-002. PA I38T mutation in pMP-PA-Gi /-Vic and absence of PCR introduced errors in purified plasmid DNA was confirmed by sequencing using gene-specific primers and vector-specific primers (Supplementary Table 2). 2021 Frontiers in microbiology Method IV I38T 3 7 PA;PA 0;24 2;26 33679636 Improved in vitro Efficacy of Baloxavir Marboxil Against Influenza A Virus Infection by Combination Treatment With the MEK Inhibitor ATR-002. Relevant primer pairs (Supplementary Table 1) were used for site-directed mutagenesis to introduce PA segment I38T mutation into the pMP-PA-Gi/-Vic plasmid. 2021 Frontiers in microbiology Method IV I38T 110 114 PA;PA 99;137 101;139 33679636 Improved in vitro Efficacy of Baloxavir Marboxil Against Influenza A Virus Infection by Combination Treatment With the MEK Inhibitor ATR-002. Two recombinant wild type influenza virus rgA/Giessen/6/2009 (H1N1-WT) and rgA/Victoria/3/75 (H3N2-WT) and their variants rgA/Giessen/6/2009 (H1N1-PA-I38T), rgA/Victoria/3/75 (H3N2-PA-I38T) harboring the BXA-resistance mutation PA-I38T were generated using a reverse genetic system as previously described by. 2021 Frontiers in microbiology Method IV I38T;I38T;I38T 150;184;231 154;188;235 PA;PA;PA 147;181;228 149;183;230 33782012 Discovery of a Novel Respiratory Syncytial Virus Replication Inhibitor. F_K394R mutant viruses were plaque purified from RSV long strain viruses after multiple passages in the presence of an RSV fusion inhibitor (unpublished data). 2021 Antimicrobial agents and chemotherapy Method IV K394R 2 7 33782012 Discovery of a Novel Respiratory Syncytial Virus Replication Inhibitor. L(T1684A) mutant plasmid was constructed with a QuikChange II XL site-directed mutagenesis kit (Agilent) using the following primers: T1684A-F, 5'-CTTCTCAGATAATGCTCATCTATTAAC-3', and T1684A-R, 5'-GTTAATAGATGAGCATTATCTGAGAAG-3'. 2021 Antimicrobial agents and chemotherapy Method IV T1684A;T1684A;T1684A 2;134;183 8;140;189 33975931 Analysis of the Evolution of Pandemic Influenza A(H1N1) Virus Neuraminidase Reveals Entanglement of Different Phenotypic Characteristics. Hemagglutination assays were performed with membrane vesicles containing similar amounts of NA activity of either the indicated H1N1pdm09 NAs or NAs (N1Hunan and N1432E) from H5N1 viruses (Du et al., submitted) as described previously. 2021 mBio Method IV N1432E 162 168 NA;NA;NA 92;138;145 94;141;148 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. The local immune responses of mice infected with WT or Y17H IAVs were measured and compared with those of PBS-treated mice. 2021 PloS one Method IV Y17H 55 59 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. We divided the mice into three groups of five and intranasally inoculated them with 30 muL of the acid-stable 2009 pandemic H1N1 virus (WT 750), acid-destabilized H1N1 virus (HA1-Y17H 750 or HA1-Y17H 375K), or PBS. 2021 PloS one Method IV Y17H;Y17H 179;195 183;199 HA1;HA1 175;191 178;194 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. We inoculated mice with 750 PFU HA1-Y17H, 750 PFU WT, or 375,000 PFU HA1-H17H. 2021 PloS one Method IV Y17H;H17H 36;73 40;77 HA1;HA1 32;69 35;72 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. Wild-type A/Tennessee/1-560/2009 (H1N1), A/California/04/09 (H1N1), and A/England/195/2009 (H1N1) have been reported to have HA activation pH values of 5.5, while the Y17H mutation increases the activation pH to 5.9-6.0. 2021 PloS one Method IV Y17H 167 171 HA 125 127 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. Favipiravir resistant Eng195 virus (K229R + P653L) containing a K229R mutation in PB1 and a P653L mutation in PA was constructed as described previously. 2021 PLoS pathogens Method IV K229R;P653L;K229R;P653L 36;44;64;92 41;49;69;97 PA;PB1 110;82 112;85 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. In the baseline model, Eng195, K229R, P653L and K229R + P653L were assigned a relative fitness, with default values equal to 1, 0.01, 1.25 and 1 respectively. 2021 PLoS pathogens Method IV K229R;P653L;K229R;P653L 31;38;48;56 36;43;53;61 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. P653L proportions in sequenced viruses. 2021 PLoS pathogens Method IV P653L 0 5 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. Plasmids containing the K229R PB1, N321K PA and P653L PA mutations were constructed by site-directed mutagenesis. 2021 PLoS pathogens Method IV K229R;N321K;P653L 24;35;48 29;40;53 PA;PA;PB1 41;54;30 43;56;33 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. The model tracked the proportion of free virions of the wild-type virus Eng195, the resistant virus K229R + P653L and viruses containing a single mutation, K229R or P653L. 2021 PLoS pathogens Method IV K229R;P653L;K229R;P653L 100;108;156;165 105;113;161;170 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. The model was initialised with 106 virions, a mix of K229R + P653L virus and Eng195 in the ratio 95:5, as in the inoculum, and assumes a well-mixed population with virions infecting cells randomly. 2021 PLoS pathogens Method IV K229R;P653L 53;61 58;66 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. The virus inoculum was ~10,000 plaque forming units consisting of a mix of K229R + P653L virus and Eng195 in the ratio 95:5. 2021 PLoS pathogens Method IV K229R;P653L 75;83 80;88 34068322 Dual R108K and G189D Mutations in the NS1 Protein of A/H1N1 Influenza Virus Counteract Host Innate Immune Responses. Correct insertion of the viral segments into pHW2000 and presence of the R108K and G189D mutations were confirmed by sequencing. 2021 Viruses Method IV R108K;G189D 73;83 78;88 34068322 Dual R108K and G189D Mutations in the NS1 Protein of A/H1N1 Influenza Virus Counteract Host Innate Immune Responses. The R108K and G189D mutations were inserted into the NS1 gene using the Q5 site-directed mutagenesis kit (NEB; E0554S) and the following primers: NS1-R108K_F: 5'-CTTATGCCTAaGCAAAAGATAATAG-3'; NS1-R108K_R: 5'-CATGAACCAGTCTCGTGAC-3'; NS1-G189D_F: 5'-AAGTGGAATGaTAACACGGTTC-3'; and NS1-G189D_R: 5'-AAGTCCTCCGATGAGGAC-3'). 2021 Viruses Method IV R108K;G189D;E0554S;R108K;R108K;G189D;G189D 4;14;111;150;196;236;283 9;19;117;155;201;241;288 NS1;NS1;NS1;NS1;NS1 53;146;192;232;279 56;149;195;235;282 34131512 Identification of H3N2 NA and PB1-F2 genetic variants and their association with disease symptoms during the 2014-15 influenza season. A/Columbia/P0041/2014 (Co14) has the NAg-F2H genotype while A/Bethesda/P0055/2015 (Be15) has the NAg+F2P genotype. 2021 Virus evolution Method IV F2H;F2P 41;101 44;104 34131512 Identification of H3N2 NA and PB1-F2 genetic variants and their association with disease symptoms during the 2014-15 influenza season. The sequences of virus stocks were compared with the WGS consensus sequences and the HA of both Co14 and Be15 were found to have the non-synonymous nucleotide mutation C478A, which encoded the mutation T160K (H3 Numbering). 2021 Virus evolution Method IV C478A;T160K 168;202 173;207 HA 85 87 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. Binding free energies were estimated for OTV complexed with WT and H274Y mutant NA using the Molecular Mechanics Poisson Boltzmann Surface Area (MM-PBSA) method in the Amber 20 package, MMPBSA.py (). 2021 PeerJ Method IV H274Y 67 72 80 82 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. By repeatedly applying the above procedure, the dRINs were constructed based on the sets of residue interactions and close contacts obtained from the MD simulations for the WT and H274Y mutant NA-OTV complexes. 2021 PeerJ Method IV H274Y 180 185 193 195 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. Residue interactions were analyzed for 2,000 three-dimensional structures of the WT and H274Y mutant NA-OTV complexes generated in the 40-ns production phase of the MD simulations. 2021 PeerJ Method IV H274Y 88 93 101 103 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. The complexes of the WT and H274Y mutant NA with OTV were solvated in a truncated octahedral box of TIP3P water molecules with a distance of at least 10 A around them. 2021 PeerJ Method IV H274Y 28 33 41 43 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. The crystal structures of wild-type (WT) avian influenza virus A/H5N1 NA and its H274Y mutant in complex with OTV were obtained from the Protein Data Bank (PDB code: 2HU4 and 3CL0) (), using a single monomer for modeling. 2021 PeerJ Method IV H274Y 81 86 70 72 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. The time series of RMSD for the backbone atoms in the WT and H274Y mutant NA are shown in. 2021 PeerJ Method IV H274Y 61 66 74 76 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. The total number of atoms in the complexes of the WT and H274Y mutant NA were 30,252 and 29,635, respectively. 2021 PeerJ Method IV H274Y 57 62 70 72 34253060 In Vivo Therapy with M2e-Specific IgG Selects for an Influenza A Virus Mutant with Delayed Matrix Protein 2 Expression. Determination of M2e sequence in viral stocks of PR8, PR8-M2-P10H, PR8-M2-P10L, and PR8-M2-I11T. 2021 mBio Method IV P10H;P10L;I11T 61;74;91 65;78;95 M2;M2;M2 58;71;88 60;73;90 34253060 In Vivo Therapy with M2e-Specific IgG Selects for an Influenza A Virus Mutant with Delayed Matrix Protein 2 Expression. HEK293T cells (seeded at 60,000 cells per well in 24-well plates) were transfected in triplicate with the expression plasmids pHW-PB1; pHW-PB2, pHW-PB2 I504V, pHW-PB2 K443R, pHW-PB2 R493K; pHW-PB2 I373T or pHW-PB2 D309N; pHW-PA, pHW-PA I550T, pHW-PA V127I, and S405N or pHW-PA M374K and Q556H; and pHW-NP (80 ng each); luciferase reporter pHW-NSLuc (80 ng); and pRL-CMV (25 ng) using polyethyleneimine as shown in. 2021 mBio Method IV I504V;K443R;R493K;I373T;D309N;I550T;V127I;S405N;M374K;Q556H 152;167;182;197;214;236;250;261;277;287 157;172;187;202;219;241;255;266;282;292 NP;PA;PA;PA;PA;PB1;PB2;PB2;PB2;PB2;PB2;PB2 302;225;233;247;274;130;139;148;163;178;193;210 304;227;235;249;276;133;142;151;166;181;196;213 34253060 In Vivo Therapy with M2e-Specific IgG Selects for an Influenza A Virus Mutant with Delayed Matrix Protein 2 Expression. In addition, the Val458Met variant in HA can be neglected, since this mutation was already present for 95% in the PR8 virus stock and is possibly the result of plaque purification. 2021 mBio Method IV V458M 17 26 HA 38 40 34253060 In Vivo Therapy with M2e-Specific IgG Selects for an Influenza A Virus Mutant with Delayed Matrix Protein 2 Expression. Sixteen hours later, the cells were infected with a multiplicity of infection (MOI) of 1 of PR8 virus or with the PR8-M2e mutant viruses (PR8-M2-P10H, PR8-M2-P10L, or PR8-M2-I11T). 2021 mBio Method IV P10H;P10L;I11T 145;158;174 149;162;178 M2;M2;M2 142;155;171 144;157;173 34253060 In Vivo Therapy with M2e-Specific IgG Selects for an Influenza A Virus Mutant with Delayed Matrix Protein 2 Expression. The HA segment carrying the G679A (silent), G743T (Ala231Ser), A1135G (Ile361Met), and G1424A (Val458Met) mutations was introduced by Gibson cloning into the pHW2000 vector. 2021 mBio Method IV G679A;G743T;A231S;A1135G;I361M;G1424A;V458M 28;44;51;63;71;87;95 33;49;60;69;80;93;104 HA 4 6 34358217 Mutation E48K in PB1 Polymerase Subunit Improves Stability of a Candidate Live Attenuated Influenza B Virus Vaccine. The B/Bris PB1 3M (K391E, E580G, S660A, and the HA tag) virus was rescued in our previous study. 2021 Vaccines Method IV K391E;E580G;S660A 19;26;33 24;31;38 HA;PB1 48;11 50;14 34358217 Mutation E48K in PB1 Polymerase Subunit Improves Stability of a Candidate Live Attenuated Influenza B Virus Vaccine. The B/Bris PB1att 4M (E48K, K391E, E580G, and S660A) virus was generated by reverse genetics, as previously described, in co-cultured 293T and MDCK cells. 2021 Vaccines Method IV E48K;K391E;E580G;S660A 22;28;35;46 26;33;40;51 34358217 Mutation E48K in PB1 Polymerase Subunit Improves Stability of a Candidate Live Attenuated Influenza B Virus Vaccine. The E48K mutation was introduced into the PB1 gene segment by site-directed mutagenesis with the QuikChange II XL kit (Agilent, Santa Clara, CA, USA) to generate the PB1 4M plasmid. 2021 Vaccines Method IV E48K 4 8 PB1;PB1 42;166 45;169 34358217 Mutation E48K in PB1 Polymerase Subunit Improves Stability of a Candidate Live Attenuated Influenza B Virus Vaccine. The reverse genetics plasmid encoding the PB1 segment of the B/Bris att strain containing three amino acid mutations (K391E, E580G, and S660A) was previously described in. 2021 Vaccines Method IV K391E;E580G;S660A 118;125;136 123;130;141 PB1 42 45 34358217 Mutation E48K in PB1 Polymerase Subunit Improves Stability of a Candidate Live Attenuated Influenza B Virus Vaccine. with a 50 microL inoculum containing 107 EID50/mouse of the lethal strain B/Bris PB2-F406Y. 2021 Vaccines Method IV F406Y 85 90 PB2 81 84 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. Confluent MDCK cells seeded in 96-well plates were washed twice with PBS and infected with H1N1 WSN wild-type and the K235R mutant viruses. 2021 Nucleic acids research Method IV K235R 118 123 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. Confluent MDCK cells seeded in six-well plates were washed twice with PBS and infected with H1N1 WSN wild-type and the K235R mutant viruses. 2021 Nucleic acids research Method IV K235R 119 124 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. K235 and R239 mutations were introduced by site-direct mutagenesis kit (NEB E0554S) according to the protocol. 2021 Nucleic acids research Method IV E0554S 76 82 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. Media containing P3 wild-type and K235R mutant viruses were collected and concentrated. 2021 Nucleic acids research Method IV K235R 34 39 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. NGS sequencing of wild-type and PB1-K235R recombinant live viruses. 2021 Nucleic acids research Method IV K235R 36 41 PB1 32 35 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. The growth kinetics curves were determined for H1N1 WSN wild-type and the K235R mutant viruses. 2021 Nucleic acids research Method IV K235R 74 79 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. The NGS collection was constructed using 2 ng DNA from two separate cultures of P3 wild-type and K235R mutant IAV mediated by the Tn5-tagmentation method, which was then fed into the MGI DNBSEQ-G400 platform. 2021 Nucleic acids research Method IV K235R 97 102 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. We generated the wild-type and PB1-K235R mutant A/WSN/1933 (H1N1) recombinant virus from eight pHW2000 plasmids encoding each of the IAV genome segments including either the wild-type or mutant K235 PB1 gene and the viruses were amplified to passage 3. 2021 Nucleic acids research Method IV K235R 35 40 PB1;PB1 31;199 34;202 34702977 Ancestral sequence reconstruction pinpoints adaptations that enable avian influenza virus transmission in pigs. PB1-Q621R and NP-R351K) are conserved among influenza A viruses, the PB1 of 74,095 influenza A viruses and NP of 80,188 influenza A viruses isolated from 1933 to 2019, respectively, were downloaded from GISAID. 2021 Nature microbiology Method IV Q621R;R351K 4;17 9;22 NP;NP;PB1;PB1 14;107;0;69 16;109;3;72 17922571 A single mutation in the PB1-F2 of H5N1 (HK/97) and 1918 influenza A viruses contributes to increased virulence. Alignment of the proteins with other PB1-F2 sequences available in the database revealed that with the exception of the N66S substitution, all of the described mutations were previously present in other influenza viral strains. 2007 PLoS pathogens Result IV N66S 120 124 PB1F2 37 43 17922571 A single mutation in the PB1-F2 of H5N1 (HK/97) and 1918 influenza A viruses contributes to increased virulence. All three cytokines were detected at significantly higher levels (p <= 0.5, analysis of variance) in 1918 wild-type-infected than in 1918 S66N mutant-infected mice. 2007 PLoS pathogens Result IV S66N 138 142 17922571 A single mutation in the PB1-F2 of H5N1 (HK/97) and 1918 influenza A viruses contributes to increased virulence. At days 7 and 8 after infection, TNF-alpha levels in mice infected with WH N66S virus had a two times higher increase over levels in WH-infected mice (Figure 5B). 2007 PLoS pathogens Result IV N66S 75 79 17922571 A single mutation in the PB1-F2 of H5N1 (HK/97) and 1918 influenza A viruses contributes to increased virulence. Determination of IL-1alpha, IFN-gamma, and TNF-alpha levels demonstrated that these cytokines were produced above their constitutive levels 4 d after infection with both 1918 S66N mutant and wild-type virus (Figure 5C). 2007 PLoS pathogens Result IV S66N 175 179 17922571 A single mutation in the PB1-F2 of H5N1 (HK/97) and 1918 influenza A viruses contributes to increased virulence. Given these findings, we proceeded to determine whether the PB1-F2 mutation in position 66 (N66S) in the 1997 H5N1 viruses contributed to viral pathogenicity. 2007 PLoS pathogens Result IV N66S 92 96 PB1F2 60 66 17922571 A single mutation in the PB1-F2 of H5N1 (HK/97) and 1918 influenza A viruses contributes to increased virulence. However, virus levels in the lung were equal on day 7, suggesting that the continued weight loss of WH N66S-infected mice is partially the result of increased cytokine production in the lung. 2007 PLoS pathogens Result IV N66S 103 107 17922571 A single mutation in the PB1-F2 of H5N1 (HK/97) and 1918 influenza A viruses contributes to increased virulence. IFN-gamma levels were observed to be higher in mice infected with WH N66S virus, especially at days 7 and 8 after infection, when the levels were approximately two times higher than the levels in the WH virus-infected mice (Figure 5A). 2007 PLoS pathogens Result IV N66S 69 73 17922571 A single mutation in the PB1-F2 of H5N1 (HK/97) and 1918 influenza A viruses contributes to increased virulence. In contrast to the highly virulent wild-type 1918 virus infection, higher amounts of inoculating virus (105 and 106 PFU) were required to cause severe disease and weight loss among the mice infected with 1918 S66N mutant virus (Figure 4B). 2007 PLoS pathogens Result IV S66N 209 213 17922571 A single mutation in the PB1-F2 of H5N1 (HK/97) and 1918 influenza A viruses contributes to increased virulence. Increased viral load and slowed viral clearance during WH N66S infection could suggest an impaired cellular immune response. 2007 PLoS pathogens Result IV N66S 58 62 17922571 A single mutation in the PB1-F2 of H5N1 (HK/97) and 1918 influenza A viruses contributes to increased virulence. Infection of mice with the 104 PFU of 1918 S66N mutant virus resulted in lung virus titers, on days 2 and 3 after infection, that were at least 12-fold lower than those of mice infected with the same dose of wild-type 1918 virus (Figure 4C). 2007 PLoS pathogens Result IV S66N 43 47 17922571 A single mutation in the PB1-F2 of H5N1 (HK/97) and 1918 influenza A viruses contributes to increased virulence. Site-directed mutagenesis was used to introduce the N66S mutation in PB1-F2 without changing the amino acid sequence of the PB1 protein (WH N66S). 2007 PLoS pathogens Result IV N66S;N66S 52;140 56;144 PB1;PB1F2 124;69 127;75 17922571 A single mutation in the PB1-F2 of H5N1 (HK/97) and 1918 influenza A viruses contributes to increased virulence. The location of the N66S mutation in the structure of PB1-F2 and its presence in the C-terminal region supports the hypothesis that this aa change could impact PB1-F2's effects in vivo. 2007 PLoS pathogens Result IV N66S 20 24 PB1F2;PB1F2 54;160 60;166 17922571 A single mutation in the PB1-F2 of H5N1 (HK/97) and 1918 influenza A viruses contributes to increased virulence. The N66S mutation was of a particular interest, since it was found only to be present in the highly virulent 1997 H5N1 group, in the PB1-F2 proteins of some avian isolates, and in the 1918 A/Brevig Mission/18 PB1-F2 (Figure 1). 2007 PLoS pathogens Result IV N66S 4 8 PB1F2;PB1F2 133;209 139;215 17922571 A single mutation in the PB1-F2 of H5N1 (HK/97) and 1918 influenza A viruses contributes to increased virulence. The r1918 and r1918 S66N viruses also have similar growth kinetics in MDCK cells when inoculated at MOIs of .01 and .001 (Figure 2B). 2007 PLoS pathogens Result IV S66N 20 24 17922571 A single mutation in the PB1-F2 of H5N1 (HK/97) and 1918 influenza A viruses contributes to increased virulence. The WH N66S virus caused the mice to start losing weight at day 3, and weight loss continued in all WH N66S-infected mice until day 8, resulting in 50% of the mice succumbing to infection. 2007 PLoS pathogens Result IV N66S;N66S 103;7 107;11 17922571 A single mutation in the PB1-F2 of H5N1 (HK/97) and 1918 influenza A viruses contributes to increased virulence. The WH N66S virus was found to replicate to higher titers in the lungs and exhibited peak virus titers 2 d earlier than the WH virus. 2007 PLoS pathogens Result IV N66S 7 11 17922571 A single mutation in the PB1-F2 of H5N1 (HK/97) and 1918 influenza A viruses contributes to increased virulence. These were (low-virulence versus high-virulence) E6D, R53K, N66S, and R75H. 2007 PLoS pathogens Result IV E6D;R53K;N66S;R75H 49;54;60;70 52;58;64;74 17922571 A single mutation in the PB1-F2 of H5N1 (HK/97) and 1918 influenza A viruses contributes to increased virulence. To evaluate the virulence and pathogenicity of the 1918 S66N mutant virus, the morbidity (measured by weight loss), virus replication, and LD50 titers were determined in BALB/c mice and compared with a group of animals infected with wild-type 1918 virus, previously shown to be highly lethal in mice. 2007 PLoS pathogens Result IV S66N 56 60 17922571 A single mutation in the PB1-F2 of H5N1 (HK/97) and 1918 influenza A viruses contributes to increased virulence. To examine this aa in the context of a fully reconstructed 1918 virus, a single aa change was made (S66N) in PB1-F2 without changing the aa sequence of PB1. 2007 PLoS pathogens Result IV S66N 100 104 PB1;PB1F2 152;109 155;115 17922571 A single mutation in the PB1-F2 of H5N1 (HK/97) and 1918 influenza A viruses contributes to increased virulence. WH N66S replication in the lungs was significantly higher than WH on days 2, 5, and 8 after infection, with WH N66S replicating to almost 100 times higher titers on each day (Figure 3B). 2007 PLoS pathogens Result IV N66S;N66S 3;111 7;115 17922571 A single mutation in the PB1-F2 of H5N1 (HK/97) and 1918 influenza A viruses contributes to increased virulence. WH N66S-infected mice exhibited slower viral clearance with persisting high viral titers, whereas the WH virus was cleared more effectively from the lung, with 3 out of 4 mice completely clearing the virus by day 8 (Figure 3B). 2007 PLoS pathogens Result IV N66S 3 7 18188421 Identification of a casein kinase II phosphorylation domain in NS1 protein of H5N1 influenza virus. Almost all the mutations in NS1 showed the change in secondary structure conformation of the mutated AA and those in contact with mutated AA, except for P223S mutation in A/chicken/Viet Nam/KG-076/2004 and L33I in A/chicken/Viet Nam/LD-080/2004, where only the conformation of residues in contact with these AAs was changed and not of that particular AA. 2007 Bioinformation Result IV P223S;L33I 154;207 159;211 NS1 28 31 18188421 Identification of a casein kinase II phosphorylation domain in NS1 protein of H5N1 influenza virus. Analysis of residue contacts in rna-binding domain structure (1NS1) at position 33 where the mutation I33L in A/chicken/Viet Nam/LD-080/2004 is observed, shows that the AAs VAL23, ALA30, PRO31, PHE32, ASP34, ARG35, LEU36 and ARG37 (Additional file RC at http://www.geocities.com/amubioinfo/InfluenzaAVirus.htm) are binding with LEU33 (Figure 1). 2007 Bioinformation Result IV I33L 102 106 18188421 Identification of a casein kinase II phosphorylation domain in NS1 protein of H5N1 influenza virus. In strains A/chicken/VietNam/KG-076/2004, A/chicken/Viet Nam/LD-080/2004 and A/chicken/VietNam/TG-023/2004 mutation A132T was a change from hydrophilic to hydrophobic AA that altered the secondary structure from coil to helix. 2007 Bioinformation Result IV A132T 117 122 18188421 Identification of a casein kinase II phosphorylation domain in NS1 protein of H5N1 influenza virus. In A/chicken/Vietnam/27/2003, G148E mutation, glutamic acid that is hydrophilic AA was replaced by hydrophobic glycine and the secondary structure was altered from helix to coil. 2007 Bioinformation Result IV G148E 30 35 18188421 Identification of a casein kinase II phosphorylation domain in NS1 protein of H5N1 influenza virus. In A/chicken/VietNam/TG-023/2004 mutation E147K involved change of hydrophilic AA, which altered the secondary structure from coil to helix. 2007 Bioinformation Result IV E147K 42 47 18188421 Identification of a casein kinase II phosphorylation domain in NS1 protein of H5N1 influenza virus. Mutation L33I in A/chicken/Viet Nam/LD-080/2004 involved change of hydrophobic residues. 2007 Bioinformation Result IV L33I 9 13 18188421 Identification of a casein kinase II phosphorylation domain in NS1 protein of H5N1 influenza virus. Mutation T151I is reported at the Casein kinase II phosphorylation site. 2007 Bioinformation Result IV T151I 9 14 18188421 Identification of a casein kinase II phosphorylation domain in NS1 protein of H5N1 influenza virus. Mutation V81A is responsible for change in secondary structure from coil to helix at this position. 2007 Bioinformation Result IV V81A 9 13 18188421 Identification of a casein kinase II phosphorylation domain in NS1 protein of H5N1 influenza virus. On comparing sequence of NS1 protein of A/Hatay/2004/(H5N1) with the other homologous sequences described in method section, by using the program MAP MUTATION, it was observed that mutations at positions V81A, I151T, I171N and P223S were common in all the strains used in this study (Table 1 in supplementary material). 2007 Bioinformation Result IV V81A;I151T;I171N;P223S 205;211;218;228 209;216;223;233 NS1 25 28 18188421 Identification of a casein kinase II phosphorylation domain in NS1 protein of H5N1 influenza virus. P223S was a change from an uncharged to hydrophilic AA. 2007 Bioinformation Result IV P223S 0 5 18188421 Identification of a casein kinase II phosphorylation domain in NS1 protein of H5N1 influenza virus. T151I involves the change of hydrophobic to hydrophilic AA. 2007 Bioinformation Result IV T151I 0 5 18188421 Identification of a casein kinase II phosphorylation domain in NS1 protein of H5N1 influenza virus. The mutation at I171N changed the amino acid from hydrophilic to hydrophobic which changed the secondary structure change from helix to strand. 2007 Bioinformation Result IV I171N 16 21 18188421 Identification of a casein kinase II phosphorylation domain in NS1 protein of H5N1 influenza virus. This mutation (I151T) was reported at the Casein kinase II (CKII) phosphorylation site. 2007 Bioinformation Result IV I151T 15 20 18248089 Interaction of polymerase subunit PB2 and NP with importin alpha1 is a determinant of host range of influenza A virus. In 293T cells transfected with PB2 of SC35M or PB2 D701N, 4 to 7 times more importin alpha1 was bound than in cells transfected with PB2 of SC35 (Figure 1A and 1C). 2008 PLoS pathogens Result IV D701N 51 56 PB2;PB2;PB2 31;47;133 34;50;136 18248089 Interaction of polymerase subunit PB2 and NP with importin alpha1 is a determinant of host range of influenza A virus. SC35 PB2 displays two amino acid substitutions contributing to increased mouse virulence (D701N and S714R). 2008 PLoS pathogens Result IV D701N;S714R 90;100 95;105 PB2 5 8 18248089 Interaction of polymerase subunit PB2 and NP with importin alpha1 is a determinant of host range of influenza A virus. Since SC35M NP differs from SC35 NP only by one amino acid substitution (N319K), it can be concluded that this mutation contributes to nuclear accumulation of importin. 2008 PLoS pathogens Result IV N319K 73 78 NP;NP 12;33 14;35 18248089 Interaction of polymerase subunit PB2 and NP with importin alpha1 is a determinant of host range of influenza A virus. Taken together, these observations indicate that, in mammalian cells, mutations PB2 D701N and NP N319K enhance the efficiency of the nuclear import of PB2 and NP as well as importin alpha1. 2008 PLoS pathogens Result IV D701N;N319K 84;97 89;102 NP;NP;PB2;PB2 94;159;80;151 96;161;83;154 18248089 Interaction of polymerase subunit PB2 and NP with importin alpha1 is a determinant of host range of influenza A virus. These findings indicate that mouse adaptation mutations PB2 D701N and NP N319K promote nuclear accumulation of importin alpha1 in mammalian cells. 2008 PLoS pathogens Result IV D701N;N319K 60;73 65;78 NP;PB2 70;56 72;59 18248089 Interaction of polymerase subunit PB2 and NP with importin alpha1 is a determinant of host range of influenza A virus. These observations indicate that the adaptive mutations PB2 D701N and NP N319K specifically improve the binding of PB2 and NP to mammalian importin alpha1 adaptor protein. 2008 PLoS pathogens Result IV D701N;N319K 60;73 65;78 NP;NP;PB2;PB2 70;123;56;115 72;125;59;118 18404209 Human-like receptor specificity does not affect the neuraminidase-inhibitor susceptibility of H5N1 influenza viruses. A/Vietnam/1203/04 (H5N1) virus carrying the triple N158S/Q226L/N248D HA mutation and grown in MDCK-SIAT1 cells was genetically stable and demonstrated the switch from avian to human receptor specificity (Figure 1B). 2008 PLoS pathogens Result IV N158S;Q226L;N248D 51;57;63 56;62;68 HA 69 71 18404209 Human-like receptor specificity does not affect the neuraminidase-inhibitor susceptibility of H5N1 influenza viruses. After observing a discrepancy in the receptor affinity of two N158S/Q226L/N248D HA triple mutants that were independently obtained by passaging in MDCK-SIAT1 cells (Figure S1) or by transfection of 293T-MDCK cells (Figure 1B), we investigated whether the host cell type can determine viral binding properties. 2008 PLoS pathogens Result IV N158S;Q226L;N248D 62;68;74 67;73;79 HA 80 82 18404209 Human-like receptor specificity does not affect the neuraminidase-inhibitor susceptibility of H5N1 influenza viruses. However, the introduced N158S, T160A, R229S, N158S/N248D, and Q226L/N248D HA mutations could not be stably maintained in A/Vietnam/1203/04 virus after one passage in MDCK cells in two independent experiments because additional HA mutations were observed (Table S2). 2008 PLoS pathogens Result IV N158S;T160A;R229S;N158S;N248D;N248D;Q226L 24;31;38;45;51;68;62 29;36;43;50;56;73;67 HA;HA 74;227 76;229 18404209 Human-like receptor specificity does not affect the neuraminidase-inhibitor susceptibility of H5N1 influenza viruses. However, virus with the Q226L substitution had acquired two additional HA mutations, N158S (which eliminates a glycosylation site at position 158) and N248D, after five passages with or without compound. 2008 PLoS pathogens Result IV Q226L;N158S;N248D 24;85;151 29;90;156 HA 71 73 18404209 Human-like receptor specificity does not affect the neuraminidase-inhibitor susceptibility of H5N1 influenza viruses. However, we were unable to assay the drug susceptibility of the mutants carrying the double N158S/Q226L and triple N158S/Q226L/N248D HA mutations, because their replication was undetectable. 2008 PLoS pathogens Result IV N158S;Q226L;N158S;Q226L;N248D 92;98;115;121;127 97;103;120;126;132 HA 133 135 18404209 Human-like receptor specificity does not affect the neuraminidase-inhibitor susceptibility of H5N1 influenza viruses. In A549 cells, but not in MDCK and MDCK-SIAT1 cells, only double mutants with the Y161H or K222I HA substitution plus the H274Y NA mutation showed resistance significantly greater (EC50 increased by a factor of 10-106) than that of the H274Y virus to both NA inhibitors (Figure 3A). 2008 PLoS pathogens Result IV Y161H;K222I;H274Y;H274Y 82;91;122;236 87;96;127;241 HA;NA;NA 97;128;256 99;130;258 18404209 Human-like receptor specificity does not affect the neuraminidase-inhibitor susceptibility of H5N1 influenza viruses. In addition, to gain insight into how combinations of HA and NA mutations can affect the sensitivity of H5N1 virus to NA inhibitors, we rescued viruses carrying the 15 HA changes together with the H274Y NA substitution. 2008 PLoS pathogens Result IV H274Y 197 202 HA;HA;NA;NA;NA 54;168;61;118;203 56;170;63;120;205 18404209 Human-like receptor specificity does not affect the neuraminidase-inhibitor susceptibility of H5N1 influenza viruses. In differentiated cultures of NHBE cells (primarily human-type SAalpha2,6-receptors), none of the HA mutations resulted in increased resistance to oseltamivir or zanamivir, and there was no difference in susceptibility between viruses carrying only the H274Y NA mutation and those carrying HA mutations as well (Figure 3B). 2008 PLoS pathogens Result IV H274Y 253 258 HA;HA;NA 98;290;259 100;292;261 18404209 Human-like receptor specificity does not affect the neuraminidase-inhibitor susceptibility of H5N1 influenza viruses. In MDCK cells, which express predominantly SAalpha2,3 (avian-type) receptors, all HA mutants except those with the S159N and N158S/Q226L substitutions were significantly more resistant to oseltamivir and to zanamivir than the wild-type strain (P<0.01) (Figure 2A). 2008 PLoS pathogens Result IV S159N;N158S;Q226L 115;125;131 120;130;136 HA 82 84 18404209 Human-like receptor specificity does not affect the neuraminidase-inhibitor susceptibility of H5N1 influenza viruses. Interestingly, A/Vietnam/1203/04 virus simultaneously carrying the Q226L HA mutation and the H274Y NA mutation was genetically unstable, since the stock virus contained a mixture of viruses with Q or L at HA residue 226 as well as a K222I HA substitution. 2008 PLoS pathogens Result IV Q226L;H274Y;K222I 67;93;233 72;98;238 HA;HA;HA;NA 73;205;239;99 75;207;241;101 18404209 Human-like receptor specificity does not affect the neuraminidase-inhibitor susceptibility of H5N1 influenza viruses. Introduction of the NA H274Y mutation markedly reduced the sensitivity of the recombinant H5N1 viruses to oseltamivir (mean EC50, 270 times that of the wild-type strain) but did not alter their susceptibility to zanamivir. 2008 PLoS pathogens Result IV H274Y 23 28 20 22 18404209 Human-like receptor specificity does not affect the neuraminidase-inhibitor susceptibility of H5N1 influenza viruses. Previous studies had shown that two HA substitutions (Q226L and G228S) are likely to modulate receptor specificity in the H5 serotype. 2008 PLoS pathogens Result IV Q226L;G228S 54;64 59;69 HA 36 38 18404209 Human-like receptor specificity does not affect the neuraminidase-inhibitor susceptibility of H5N1 influenza viruses. Sequence analysis of the entire HA and NA genes revealed no additional mutations in virus with the G228S substitution after five sequential passages in the presence or absence of the drug. 2008 PLoS pathogens Result IV G228S 99 104 HA;NA 32;39 34;41 18404209 Human-like receptor specificity does not affect the neuraminidase-inhibitor susceptibility of H5N1 influenza viruses. Surprisingly, H5N1 mutants carrying the triple mutation N158S/Q226L/N248D exhibited very weak SAalpha2,6Gal binding, whereas virus with the double mutation N158S/Q226L did not bind to any SAalpha2,3Gal sialosides but showed enhanced binding affinity to SAalpha2,6Gal-substrate (Figure 1B). 2008 PLoS pathogens Result IV N248D;N158S;Q226L;N158S;Q226L 68;56;62;156;162 73;61;67;161;167 18404209 Human-like receptor specificity does not affect the neuraminidase-inhibitor susceptibility of H5N1 influenza viruses. The combined HA and NA (H274Y) substitutions therefore reduced oseltamivir sensitivity synergistically in MDCK cells. 2008 PLoS pathogens Result IV H274Y 24 29 HA;NA 13;20 15;22 18404209 Human-like receptor specificity does not affect the neuraminidase-inhibitor susceptibility of H5N1 influenza viruses. The receptor specificity of this triple-mutant (N158S/Q226L/N248D) virus was determined by measuring its binding affinity to sialoglycopolymers possessing either SAalpha2,3Gal (p3'SL) or SAalpha2,6Gal (p6'SL) (Table S1). 2008 PLoS pathogens Result IV Q226L;N158S;N248D 54;48;60 59;53;65 18404209 Human-like receptor specificity does not affect the neuraminidase-inhibitor susceptibility of H5N1 influenza viruses. This H5N1 variant exhibited enhanced affinity for human-like SAalpha2,6-linked receptor and was unable to bind the avian-like SAalpha2,3-linked receptor (Figure S1); therefore, the N158S/Q226L/N248D triple mutation is sufficient to completely switch the host receptor specificity of A/Vietnam/1203/04 (H5N1) virus from avian to human. 2008 PLoS pathogens Result IV Q226L;N158S;N248D 187;181;193 192;186;198 18404209 Human-like receptor specificity does not affect the neuraminidase-inhibitor susceptibility of H5N1 influenza viruses. Viruses with Q226L, G228S and Q226L/G228S substitutions, which enhanced binding affinity for SAalpha2,6Gal receptors (Figure 1B), were as sensitive to both NA inhibitors as the wild-type virus in MDCK-SIAT1 cells but not in MDCK cells (Figure 2). 2008 PLoS pathogens Result IV Q226L;G228S;Q226L;G228S 13;20;30;36 18;25;35;41 156 158 18404209 Human-like receptor specificity does not affect the neuraminidase-inhibitor susceptibility of H5N1 influenza viruses. We prepared virus stocks by transfecting MDCK-SIAT1 cells, rather than MDCK cells, with the two H5N1 viruses carrying the double N158S/Q226L and triple N158S/Q226L/N248D HA substitutions. 2008 PLoS pathogens Result IV N158S;Q226L;N158S;Q226L;N248D 129;135;152;158;164 134;140;157;163;169 HA 170 172 18404209 Human-like receptor specificity does not affect the neuraminidase-inhibitor susceptibility of H5N1 influenza viruses. We therefore passaged the wild-type virus (rgVN1203) and two HA mutants (Q226L and G228S) in MDCK-SIAT1 cells (Madin Darby canine kidney cells altered to express predominantly human-type SAalpha2,6 receptors). 2008 PLoS pathogens Result IV Q226L;G228S 73;83 78;88 HA 61 63 18404209 Human-like receptor specificity does not affect the neuraminidase-inhibitor susceptibility of H5N1 influenza viruses. We used the fluorometric NA enzyme inhibition assay to test the susceptibility to oseltamivir and zanamivir of the 20 recombinant H5N1 viruses carrying either HA mutations or both HA and NA (H274Y) changes. 2008 PLoS pathogens Result IV H274Y 191 196 HA;HA;NA;NA 159;180;25;187 161;182;27;189 18442378 Application of bioinformatics-coupled experimental analysis reveals a new transport-competent nuclear localization signal in the nucleoprotein of influenza A virus strain. It is noteworthy that the obpNLS of NP-L is present in 9 other influenza virus strains (out of a total of 500 NP sequences screened) suggesting that the Met to Arg change (M105R) does occur naturally and that this single aa change results in the conversion of the region between aa 90 to 121 to a 32-residue obpNLS (Table 2). 2008 BMC cell biology Result IV M105R 172 177 NP;NP 36;110 38;112 18442378 Application of bioinformatics-coupled experimental analysis reveals a new transport-competent nuclear localization signal in the nucleoprotein of influenza A virus strain. The analyses indicated that a single aa change (M105R) resulted in converting the flanking regions (between aa 90-121) into two overlapping bipartite nuclear localizing signals (obpNLS). 2008 BMC cell biology Result IV M105R 48 53 18601954 Treatment of influenza A (H1N1) virus infections in mice and ferrets with cyanovirin-N. Mice infected with the influenza A/WSN/33 HAnc-Asp225Gly (H1N1) virus were treated with doses of CV-N starting 4 h prior to virus exposure (Table 1). 2008 Antiviral research Result IV D225G;H225G;A225G;N225G;C225G 47;47;47;47;47 56;56;56;56;56 18613963 A broad spectrum, one-step reverse-transcription PCR amplification of the neuraminidase gene from multiple subtypes of influenza A virus. There are other residues that confer resistance to the NA inhibitors, but for the purpose of this study we focused on the H274Y mutation (an NA mutation that appears to be increasing significantly in frequency and distribution). 2008 Virology journal Result IV H274Y 122 127 NA;NA 55;141 57;143 18613963 A broad spectrum, one-step reverse-transcription PCR amplification of the neuraminidase gene from multiple subtypes of influenza A virus. virus subtype N1: amino acid H274Y). 2008 Virology journal Result IV H274Y 29 34 18769709 Host determinant residue lysine 627 lies on the surface of a discrete, folded domain of influenza virus polymerase PB2 subunit. The structure of the K627E mutant domain is essentially identical (RMSD of 0.34 A for all Calpha atoms of residues 539-675), with the Glu627 side-chain (not visible beyond Cgamma) again pointing into solvent. 2008 PLoS pathogens Result IV K627E 21 26 18769709 Host determinant residue lysine 627 lies on the surface of a discrete, folded domain of influenza virus polymerase PB2 subunit. To assess the structural impact of the typically avian glutamate at this position, the K627E mutation was engineered into the 538-693 construct, the corresponding protein crystallized and its structure also determined. 2008 PLoS pathogens Result IV K627E 87 92 19008377 The human H5N1 influenza A virus polymerase complex is active in vitro over a broad range of temperatures, in contrast to the WSN complex, and this property can be attributed to the PB2 subunit. 5b and d, respectively) and found, that an E627K mutation slightly shifted the temperature optimum from 37 C to 39 C. 2008 The Journal of general virology Result IV E627K 43 48 19008377 The human H5N1 influenza A virus polymerase complex is active in vitro over a broad range of temperatures, in contrast to the WSN complex, and this property can be attributed to the PB2 subunit. Interestingly, in both assays an E627K mutation in the avian PB2 resulted in a slight increase in activity. 2008 The Journal of general virology Result IV E627K 33 38 PB2 61 64 19014974 Aurintricarboxylic acid inhibits influenza virus neuraminidase. An in vitro selection study demonstrated that the mutation R292K is the most common substitution in Group 2 NAs resistant to oseltamivir. 2009 Antiviral research Result IV R292K 59 64 108 111 19014974 Aurintricarboxylic acid inhibits influenza virus neuraminidase. ATA inhibited the wild-type NA and H274Y oseltamivir-resistant NA. 2009 Antiviral research Result IV H274Y 35 40 NA;NA 28;63 30;65 19014974 Aurintricarboxylic acid inhibits influenza virus neuraminidase. In our assay, the H274Y mutation in NA of the H1N1 and H5N1 subtypes, i.e., NAH274Y(WSN)and NAH274(H5N1), resulted in resistance to oseltamivir carboxylate (GS4071), the active ingredient of oseltamivir, as indicated by a 191- and 885-fold increase in the IC50 values, respectively (not shown). 2009 Antiviral research Result IV H274Y 18 23 NA;NA;NA 36;76;92 38;78;94 19014974 Aurintricarboxylic acid inhibits influenza virus neuraminidase. Such results are largely consistent with a previous report indicating that the H274Y mutation in NAWT(WSN) conferred a 754-fold increase in the IC50 of oseltamivir. 2009 Antiviral research Result IV H274Y 79 84 19014974 Aurintricarboxylic acid inhibits influenza virus neuraminidase. The H274Y mutation could perturb the rearrangement space of E276, leading to increased resistance to GS4071. 2009 Antiviral research Result IV H274Y 4 9 19014974 Aurintricarboxylic acid inhibits influenza virus neuraminidase. Thus, ATA remained equally potent in inhibiting the activity of the H274Y mutant forms and the wild-type NAs derived from either the H5N1 or the H1N1 influenza subtypes. 2009 Antiviral research Result IV H274Y 68 73 105 108 19014974 Aurintricarboxylic acid inhibits influenza virus neuraminidase. We were interested in examining whether ATA is also effective in inhibiting the oseltamivir-resistant of H5N1 and H1N1 NAs due to a H274Y mutation in NAs. 2009 Antiviral research Result IV H274Y 132 137 NA;NA 119;150 122;153 19119420 Transmission of influenza virus in a mammalian host is increased by PB2 amino acids 627K or 627E/701N. Again, sequencing of the PB2 gene of one transmitted virus indicated that both the K627E and D701N mutations were retained. 2009 PLoS pathogens Result IV K627E;D701N 83;93 88;98 PB2 25 28 19119420 Transmission of influenza virus in a mammalian host is increased by PB2 amino acids 627K or 627E/701N. Growth in the lungs was affected to a lesser extent by the K627E and D701N mutations than growth in the nasal passages. 2009 PLoS pathogens Result IV K627E;D701N 59;69 64;74 19119420 Transmission of influenza virus in a mammalian host is increased by PB2 amino acids 627K or 627E/701N. Partial rescue of the transmission defect was observed when the PB2 D701N change was also present: rPan99 627E 701N virus transmitted to ten of twelve exposed guinea pigs (Figure 4C). 2009 PLoS pathogens Result IV D701N 68 73 PB2 64 67 19119420 Transmission of influenza virus in a mammalian host is increased by PB2 amino acids 627K or 627E/701N. Reverse genetics systems for Pan99 and VN1203 viruses were used to generate recombinant viruses which encode the mutations K627E alone or K627E and D701N combined, in their respective PB2 segments. 2009 PLoS pathogens Result IV K627E;K627E;D701N 123;138;148 128;143;153 PA;PB2 29;184 31;187 19119420 Transmission of influenza virus in a mammalian host is increased by PB2 amino acids 627K or 627E/701N. The PB2 gene of the transmitted virus was subjected to RT PCR and sequencing and the introduced mutation, K627E, was found to be maintained. 2009 PLoS pathogens Result IV K627E 106 111 PB2 4 7 19119420 Transmission of influenza virus in a mammalian host is increased by PB2 amino acids 627K or 627E/701N. These results suggest that, in MDCK cell culture, the attenuated phenotype of a K627E mutant is partially rescued by the D701N mutation. 2009 PLoS pathogens Result IV K627E;D701N 80;121 85;126 19119420 Transmission of influenza virus in a mammalian host is increased by PB2 amino acids 627K or 627E/701N. Thus, in the background of a human H3N2 isolate, mutation of PB2 residue 627 from K to E decreases the efficiency of transmission, while the introduction of D701N alongside K627E results in a phenotype more similar to that of the wild-type virus. 2009 PLoS pathogens Result IV D701N;K627E 157;173 162;178 PB2 61 64 19119420 Transmission of influenza virus in a mammalian host is increased by PB2 amino acids 627K or 627E/701N. Thus, the amino acid change PB2 D701N favors the transmission of an H5N1 virus in a mammalian host and this mutation fully compensates for the lack of a lysine at position 627 in terms of transmission by the contact route. 2009 PLoS pathogens Result IV D701N 32 37 PB2 28 31 19119420 Transmission of influenza virus in a mammalian host is increased by PB2 amino acids 627K or 627E/701N. To test whether the introduction of K627E or K627E D701N mutations would also alter the transmissibility of the rVN1203 virus, contact transmission experiments were performed in guinea pigs. 2009 PLoS pathogens Result IV K627E;K627E;D701N 36;45;51 41;50;56 19119420 Transmission of influenza virus in a mammalian host is increased by PB2 amino acids 627K or 627E/701N. While this result suggests that this single amino acid change - PB2 K627E - reduces the transmission potential of a highly pathogenic avian influenza virus in a mammalian species (p = 0.09, Student's t-test), an increased number of replicates would be required to prove a statistically significant reduction in transmission. 2009 PLoS pathogens Result IV K627E 68 73 PB2 64 67 19249874 Recognition of mannosylated ligands and influenza A virus by human surfactant protein D: contributions of an extended site and residue 343. Although 246-02 blocked the HA inhibitory activity of R343V, 246-05 was ineffective, consistent with poor binding of the antibody to this mutant. 2009 Biochemistry Result IV R343V 54 59 HA 28 30 19249874 Recognition of mannosylated ligands and influenza A virus by human surfactant protein D: contributions of an extended site and residue 343. Although R343A showed no neutralizing activity at the same concentrations as used for R343V, doserelated neutralizing activity was observed at considerably higher protein concentrations (Figure 8, right panel). 2009 Biochemistry Result IV R343A;R343V 9;86 14;91 19249874 Recognition of mannosylated ligands and influenza A virus by human surfactant protein D: contributions of an extended site and residue 343. By contrast, the substitution of valine for Arg343 (R343V) showed little effect on binding to PI or LPS. 2009 Biochemistry Result IV R343V;R343V 52;33 57;50 19249874 Recognition of mannosylated ligands and influenza A virus by human surfactant protein D: contributions of an extended site and residue 343. Crystal structures of the trimeric NCRD complexes were obtained at 1.8A and 2.3A resolution for wild-type or R343V proteins, respectively. 2009 Biochemistry Result IV R343V 109 114 19249874 Recognition of mannosylated ligands and influenza A virus by human surfactant protein D: contributions of an extended site and residue 343. Crystallographic complexes show differential interactions of alpha1-2DM with wild-type or R343V hNCRDs. 2009 Biochemistry Result IV R343V 90 95 19249874 Recognition of mannosylated ligands and influenza A virus by human surfactant protein D: contributions of an extended site and residue 343. Despite marked increases in binding of R343V to Phil82 IAV, there was no alteration in binding or neutralization of PR8 (data not shown), an SP-D resistant strain that lacks high-mannose glycans on the head of the HA. 2009 Biochemistry Result IV R343V 39 44 HA 214 216 19249874 Recognition of mannosylated ligands and influenza A virus by human surfactant protein D: contributions of an extended site and residue 343. Despite these effects, R343V showed no significant increase in affinity for D-mannose (Figure 2B). 2009 Biochemistry Result IV R343V 23 28 19249874 Recognition of mannosylated ligands and influenza A virus by human surfactant protein D: contributions of an extended site and residue 343. For example, substitution of lysine for Arg343 (R343K) greatly increased binding to PI and E. 2009 Biochemistry Result IV R343K;R343K 48;29 53;46 19249874 Recognition of mannosylated ligands and influenza A virus by human surfactant protein D: contributions of an extended site and residue 343. However, the apparent affinity for R343V for mannan was increased by 2 to 3-fold (Figure 2A). 2009 Biochemistry Result IV R343V 35 40 19249874 Recognition of mannosylated ligands and influenza A virus by human surfactant protein D: contributions of an extended site and residue 343. In one experiment, R343A showed a similar but less marked increase in affinity (I50=362 microM). 2009 Biochemistry Result IV R343A 19 24 19249874 Recognition of mannosylated ligands and influenza A virus by human surfactant protein D: contributions of an extended site and residue 343. In particular, R343V showed a 7-fold increase in affinity for alpha1-2 DM (I50=210 +- 60 microM, n=5), as compared to wild-type. 2009 Biochemistry Result IV R343V 15 20 19249874 Recognition of mannosylated ligands and influenza A virus by human surfactant protein D: contributions of an extended site and residue 343. Ligand binding preferences of wild-type hNCRD and R343V were examined in array experiments using a small panel of mannoses, mannose-rich oligosaccharides, and selected other simple sugars covalently linked to the slide (Figure 1B and Figure 4). 2009 Biochemistry Result IV R343V 50 55 19249874 Recognition of mannosylated ligands and influenza A virus by human surfactant protein D: contributions of an extended site and residue 343. Notably, a human loss-of-function mutant (E321K) with a point mutation at Glu321 and abnormal coordination of calcium at the sugar binding site consistently showed negligible binding to all ligands (Figure 4). 2009 Biochemistry Result IV E321K 42 47 19249874 Recognition of mannosylated ligands and influenza A virus by human surfactant protein D: contributions of an extended site and residue 343. R343A showed a much smaller increase in hemagglutination inhibition (Table 2). 2009 Biochemistry Result IV R343A 0 5 19249874 Recognition of mannosylated ligands and influenza A virus by human surfactant protein D: contributions of an extended site and residue 343. R343K also showed a detectable increase in affinity for alpha1-2 DM (I50 = 552 +- 35 microM, average of 3 determinations); however, this finding must be interpreted with some caution given the markedly lower levels of total binding of R343K mannan. 2009 Biochemistry Result IV R343K;R343K 0;235 5;240 19249874 Recognition of mannosylated ligands and influenza A virus by human surfactant protein D: contributions of an extended site and residue 343. R343V and R343A show increased antiviral activity. 2009 Biochemistry Result IV R343V;R343A 0;10 5;15 19249874 Recognition of mannosylated ligands and influenza A virus by human surfactant protein D: contributions of an extended site and residue 343. R343V showed very different interactions with the dimannose (Figure 5C). 2009 Biochemistry Result IV R343V 0 5 19249874 Recognition of mannosylated ligands and influenza A virus by human surfactant protein D: contributions of an extended site and residue 343. Significantly, R343V, and to a lesser extent R343A, bound to virus (Figure 7). 2009 Biochemistry Result IV R343V;R343A 15;45 20;50 19249874 Recognition of mannosylated ligands and influenza A virus by human surfactant protein D: contributions of an extended site and residue 343. The binding profile of R343V was generally similar to the wild-type protein. 2009 Biochemistry Result IV R343V 23 28 19249874 Recognition of mannosylated ligands and influenza A virus by human surfactant protein D: contributions of an extended site and residue 343. The more conservative R343K mutation caused a less pronounced reduction of binding to 246-05. 2009 Biochemistry Result IV R343K 22 27 19249874 Recognition of mannosylated ligands and influenza A virus by human surfactant protein D: contributions of an extended site and residue 343. The R343K mutant showed no significant binding (data not shown) and no detectable hemagglutination inhibition (Table 2) or neutralizing activity (Figure 8)), despite its greatly enhanced interactions with PI and inositol, as well as rough LPS. 2009 Biochemistry Result IV R343K 4 9 19331731 Oseltamivir-resistant influenza virus A (H1N1), Europe, 2007-08 season. A degree of heterogeneity was observed, especially among ORVs from the United Kingdom; however, the NA sequences in these smaller clusters, represented by, for example, A/Scotland/5/2008 (and A/Hawaii/21/2007) or A/England/654/2007, are not distinguished from those of OSVs by any common amino acid differences other than H275Y. 2009 Emerging infectious diseases Result IV H275Y 322 327 100 102 19331731 Oseltamivir-resistant influenza virus A (H1N1), Europe, 2007-08 season. Although the D344N substitution in NA has been associated with increases in the enzyme activity, this amino acid is common to both clades 2B and 2C, and none of the clade-specific differences between the NA (13 amino acids) or HA (6 amino acids) can readily account for the greater proportion of ORVs in clade 2B over clade 2C viruses. 2009 Emerging infectious diseases Result IV D344N 13 18 HA;NA;NA 227;35;204 229;37;206 19331731 Oseltamivir-resistant influenza virus A (H1N1), Europe, 2007-08 season. None of 237 ORVs tested for M2I sensitivity had any of the common resistance substitutions in the M2 protein. 2009 Emerging infectious diseases Result IV M2I 28 31 M2 98 100 19331731 Oseltamivir-resistant influenza virus A (H1N1), Europe, 2007-08 season. Of the 2,949 viruses tested, 712 (24%) were oseltamivir resistant either by presence of the H275Y substitution (n = 548) or an IC50 >100 nmol/L for oseltamivir (n = 463) (Figure 3). 2009 Emerging infectious diseases Result IV H275Y 92 97 19331731 Oseltamivir-resistant influenza virus A (H1N1), Europe, 2007-08 season. The NA sequences of most European ORVs form a cluster, characterized by a difference in amino acid residue 354 (D354G), as well as 275 (H275Y) compared with OSVs, including some ORVs from the United States and Japan. 2009 Emerging infectious diseases Result IV D354G;H275Y 112;136 117;141 4 6 19394063 The origin and global emergence of adamantane resistant A/H3N2 influenza viruses. Again, given the geographic and temporal proximity of these phylogenetically related isolates, we infer that this occurrence of the S31N mutation has disseminated locally in New Zealand (Table 1). 2009 Virology Result IV S31N 132 136 19394063 The origin and global emergence of adamantane resistant A/H3N2 influenza viruses. Despite the global dominance of adamantane resistant influenza viruses from 2005-2007, a phylogenetically distinct lineage of the M1/2 segment that for the most part lacks the S31N substitution co-circulates from 2004-2007. 2009 Virology Result IV S31N 176 180 M1 130 132 19394063 The origin and global emergence of adamantane resistant A/H3N2 influenza viruses. Following this last introduction of the S31N mutation in the summer of 2005, all adamantane resistant influenza viruses hereon are associated with the 'N-lineage', strongly suggesting that this clade has a major fitness advantage. 2009 Virology Result IV S31N 40 44 19394063 The origin and global emergence of adamantane resistant A/H3N2 influenza viruses. Given the time and distance separating these three isolates, it is possible that each isolate represents a separate introduction of the S31N mutation, although there is insufficient phylogenetic resolution in this section of the M1/2 phylogeny to distinguish between the single versus multiple introductions of these three isolates. 2009 Virology Result IV S31N 136 140 M1 229 231 19394063 The origin and global emergence of adamantane resistant A/H3N2 influenza viruses. However, it is possible that these S31N both arose de novo and represent independent introductions, rather than being transmitted through a network of New York State viruses not sampled in our study population. 2009 Virology Result IV S31N 35 39 19394063 The origin and global emergence of adamantane resistant A/H3N2 influenza viruses. In 2002 the S31N mutation is first detected in Oceania (Introduction #5), involving the two A/Sydney/5/1997-like isolates A/Wellington/71/2002 and A/Wellington/79/2002. 2009 Virology Result IV S31N 12 16 19394063 The origin and global emergence of adamantane resistant A/H3N2 influenza viruses. In addition, the four phylogenetically distinct clusters of '#7F' isolates on the HA tree suggest that A/Fujian/411/2002-like isolates may have acquired the #7 S31N introduction through multiple additional reassortment events. 2009 Virology Result IV S31N 160 164 HA 82 84 19394063 The origin and global emergence of adamantane resistant A/H3N2 influenza viruses. Introduction #6 also represents the first S31N mutation observed among A/Fujian/411/2002-like viruses. 2009 Virology Result IV S31N 42 46 19394063 The origin and global emergence of adamantane resistant A/H3N2 influenza viruses. Notably, isolate A/Hong Kong/CUHK4245/1997 is the only S31N mutant from 1997 in our data set and is related to no other adamantane resistant isolates, compatible with no or limited spread of this virus in this viral population. 2009 Virology Result IV S31N 55 59 19394063 The origin and global emergence of adamantane resistant A/H3N2 influenza viruses. Of the 1402 viral isolates sampled between 1997 and 2007 that are included in this analysis, 119 (8.5%) exhibited the S31N mutation in the M2 protein conferring resistance to adamantane antiviral drugs. 2009 Virology Result IV S31N 118 122 M2 139 141 19394063 The origin and global emergence of adamantane resistant A/H3N2 influenza viruses. Phylogenetic analysis of the M1/2 segment of A/H3N2 influenza virus isolates collected from Hong Kong, New York State, Australia, and New Zealand reveals at least 11 independent introductions (i.e., 11 separate clades) of the S31N mutation between the years 1997 - 2007. 2009 Virology Result IV S31N 226 230 M1 29 31 19394063 The origin and global emergence of adamantane resistant A/H3N2 influenza viruses. The first introduction of S31N that is observed in these data occurred in Hong Kong in 1997 (isolate A/Hong Kong/CUHK4245/1997, Introduction #1. 2009 Virology Result IV S31N 26 30 19394063 The origin and global emergence of adamantane resistant A/H3N2 influenza viruses. The first S31N introduction that exhibits possible spread between multiple localities is Introduction #6, which is detected first in Australia on 08/25/2003 (A/Queensland/34/2003) and subsequently observed twice in New York State (A/New York/1/2003, 10/28/2003; A/New York/31/2004, 01/05/2004) (Table 1). 2009 Virology Result IV S31N 10 14 19394063 The origin and global emergence of adamantane resistant A/H3N2 influenza viruses. The second emergence of the S31N substitution involves a A/Sydney/5/1997-like isolate from New York State (A/New York/512/1998, Introduction #2, Table 1. 2009 Virology Result IV S31N 28 32 19394063 The origin and global emergence of adamantane resistant A/H3N2 influenza viruses. The third independent introduction of the S31N mutation among A/Fujian/411/2002-like viruses is detected in 2004 involving three isolates from Hong Kong (Introduction #8, Table 1. 2009 Virology Result IV S31N 42 46 19394063 The origin and global emergence of adamantane resistant A/H3N2 influenza viruses. This estimate is conservative, as clusters of genetically related resistant isolates are regarded as a single introduction of the S31N replacement even though it is possible (although less parsimonious) that the mutation arose independently among these isolates rather than through viral transmission. 2009 Virology Result IV S31N 130 134 19394063 The origin and global emergence of adamantane resistant A/H3N2 influenza viruses. To be as conservative as possible in our estimate of independent introductions of the S31N mutation, we regard these two isolates as a single introduction, given the phylogenetic similarity of these two isolates, their geographic and temporal proximity, and the low number of S31N mutations detected at this time. 2009 Virology Result IV S31N;S31N 86;276 90;280 19394063 The origin and global emergence of adamantane resistant A/H3N2 influenza viruses. Two additional introductions of the S31N mutation occur among this adamantane sensitive M1/2 lineage, both involving A/California/7/2004-like isolates. 2009 Virology Result IV S31N 36 40 M1 88 90 19394063 The origin and global emergence of adamantane resistant A/H3N2 influenza viruses. Whereas the six previous introductions of the S31N mutation likely exhibit limited spread in time and space, Introduction #7 is continually detected among this viral population for more than 3.5 years (from 07/06/2003 to 03/14/2007) and gives rise to the majority of adamantane resistant isolates in our data set, including the major 'N-lineage' that is associated with the global spread of adamantane resistance that begins in 2005 (Table 1. 2009 Virology Result IV S31N 46 50 19436701 Avian Influenza virus glycoproteins restrict virus replication and spread through human airway epithelium at temperatures of the proximal airways. First, mutations in HA previously shown to switch sialic acid usage from alpha2,6 to alpha2,3 linkages (L226Q, S228G) were introduced to generate the Vic-226-228HA virus. 2009 PLoS pathogens Result IV L226Q;S228G 104;111 109;116 HA 20 22 19436701 Avian Influenza virus glycoproteins restrict virus replication and spread through human airway epithelium at temperatures of the proximal airways. Indeed, quantification of the numbers of infected cells identified by en face staining revealed that the K627E mutant virus infected a similar percentage of cells compared to wild-type virus at 24 hrs pi (Figure 4Aii) and that the mutant was capable of spread since new cells were infected by 48 hrs with similar kinetics to that of wild-type A/Victoria/3/75 at both 32 C and 37 C (Figure 4Aii). 2009 PLoS pathogens Result IV K627E 105 110 19436701 Avian Influenza virus glycoproteins restrict virus replication and spread through human airway epithelium at temperatures of the proximal airways. The K627E mutation resulted in restriction of the virus at both temperatures (Figure 4Ai), and although titer at 32 C was 1.3 logs lower than at 37 C at 24 hrs pi, this difference was no greater than the differences in growth for wild-type virus at these temperatures (1.5 logs; Figure 4Ai). 2009 PLoS pathogens Result IV K627E 4 9 19436701 Avian Influenza virus glycoproteins restrict virus replication and spread through human airway epithelium at temperatures of the proximal airways. These data indicate that the K627E mutant virus was restricted for growth in HAE but that restriction was not temperature-dependent. 2009 PLoS pathogens Result IV K627E 29 34 19436701 Avian Influenza virus glycoproteins restrict virus replication and spread through human airway epithelium at temperatures of the proximal airways. To assess the potential impact of this PB2 amino acid residue in restriction of avian influenza viruses at 32 C, we generated a recombinant A/Victoria/3/75 virus containing the PB2 K627E mutation and compared its growth with that of the isogenic wild-type virus in HAE at 32 C and 37 C. 2009 PLoS pathogens Result IV K627E 181 186 PB2;PB2 39;177 42;180 19454348 Influenza A virus NS1 targets the ubiquitin ligase TRIM25 to evade recognition by the host viral RNA sensor RIG-I. Among the three viral IFN antagonist proteins tested, influenza A virus NS1 was unique in that it potently inhibited the RIG-I 2CARD ubiquitination; whereas the other IFN antagonists Ebola virus VP35 and vaccinia virus E3L showed no effect under the same conditions. 2009 Cell host & microbe Result IV E3L 219 222 NS1 72 75 19454348 Influenza A virus NS1 targets the ubiquitin ligase TRIM25 to evade recognition by the host viral RNA sensor RIG-I. As compared to titers achieved with WT virus, the E96A/E97A virus exhibited an approximately 1.5 log reduction in titer at 72 hours post-infection. 2009 Cell host & microbe Result IV E96A;E97A 50;55 54;59 19454348 Influenza A virus NS1 targets the ubiquitin ligase TRIM25 to evade recognition by the host viral RNA sensor RIG-I. At 24 hours post-infection with 100 pfu per egg, the titers obtained for the E96A/E97A virus were comparable to those of the WT virus. 2009 Cell host & microbe Result IV E96A;E97A 77;82 81;86 19454348 Influenza A virus NS1 targets the ubiquitin ligase TRIM25 to evade recognition by the host viral RNA sensor RIG-I. Considering that the R38A/K41A NS1 mutant is defective both in sequestering viral RNA from molecular sensors and in suppressing TRIM25-mediated RIG-I ubiquitination, it is difficult to determine which NS1 function is more critical to its antagonism of the type I interferon system. 2009 Cell host & microbe Result IV K41A;R38A 26;21 30;25 NS1;NS1 31;201 34;204 19454348 Influenza A virus NS1 targets the ubiquitin ligase TRIM25 to evade recognition by the host viral RNA sensor RIG-I. Consistent with the absence of morbidity, infections with E96A/E97A and R38A/K41A viruses resulted in reduced pulmonary titers at day 3 and 5 post-infection as compared to titers achieved by WT virus. 2009 Cell host & microbe Result IV E96A;E97A;R38A;K41A 58;63;72;77 62;67;76;81 19454348 Influenza A virus NS1 targets the ubiquitin ligase TRIM25 to evade recognition by the host viral RNA sensor RIG-I. Consistent with their inability to bind TRIM25, the E96A/E97A and R38A/K41A NS1 mutants did not interfere with TRIM25 multimerization. 2009 Cell host & microbe Result IV E96A;E97A;R38A;K41A 52;57;66;71 56;61;70;75 NS1 76 79 19454348 Influenza A virus NS1 targets the ubiquitin ligase TRIM25 to evade recognition by the host viral RNA sensor RIG-I. Consistently, while NS1 WT effectively inhibited the RIG-I 2CARD-induced IFN-beta promoter activation in a dose-dependent manner, the E96A/E97A and R38A/K41A NS1 mutants showed no effect. 2009 Cell host & microbe Result IV E97A;E96A;K41A;R38A 139;134;153;148 143;138;157;152 NS1;NS1 20;158 23;161 19454348 Influenza A virus NS1 targets the ubiquitin ligase TRIM25 to evade recognition by the host viral RNA sensor RIG-I. For comparative purposes we also included R38A/K41A and DeltaNS1 viruses. 2009 Cell host & microbe Result IV R38A;K41A 42;47 46;51 19454348 Influenza A virus NS1 targets the ubiquitin ligase TRIM25 to evade recognition by the host viral RNA sensor RIG-I. Furthermore, both E96A/E97A and R38A/K41A NS1 mutants did not co-localize with over-expressed TRIM25 in HeLa cells. 2009 Cell host & microbe Result IV E96A;E97A;R38A;K41A 18;23;32;37 22;27;36;41 NS1 42 45 19454348 Influenza A virus NS1 targets the ubiquitin ligase TRIM25 to evade recognition by the host viral RNA sensor RIG-I. In agreement with these results, the R38A/K41A and E96A/E97A NS1 mutants, in contrast to NS1 WT, did not interact with full-length RIG-I. 2009 Cell host & microbe Result IV R38A;K41A;E96A;E97A 37;42;51;56 41;46;55;60 NS1;NS1 61;89 64;92 19454348 Influenza A virus NS1 targets the ubiquitin ligase TRIM25 to evade recognition by the host viral RNA sensor RIG-I. In contrast to the R38A/K41A NS1 mutant, the E96A/E97A NS1 mutant retains dsRNA-binding activity. 2009 Cell host & microbe Result IV R38A;K41A;E96A;E97A 19;24;45;50 23;28;49;54 NS1;NS1 29;55 32;58 19454348 Influenza A virus NS1 targets the ubiquitin ligase TRIM25 to evade recognition by the host viral RNA sensor RIG-I. In contrast, mutations associated with loss of multiple IFN antagonistic NS1 functions, such as R38A/K41A, result in viruses with lower but still detectable IFN-inducing properties in TRIM25-/- cells. 2009 Cell host & microbe Result IV R38A;K41A 96;101 100;105 NS1 73 76 19454348 Influenza A virus NS1 targets the ubiquitin ligase TRIM25 to evade recognition by the host viral RNA sensor RIG-I. In contrast, the E96A/E97A and R38A/K41A NS1 mutants, which had no inhibitory effect on RIG-I 2CARD ubiquitination, did not interfere with the phosphorylation or dimerization of IRF3. 2009 Cell host & microbe Result IV E97A;E96A;K41A;R38A 22;17;36;31 26;21;40;35 NS1 41 44 19454348 Influenza A virus NS1 targets the ubiquitin ligase TRIM25 to evade recognition by the host viral RNA sensor RIG-I. In line with this, NS1 WT, but not the E96A/E97A and R38A/K41A NS1 mutants, potently suppressed the ubiquitination-dependent CARD interaction between RIG-I and MAVS. 2009 Cell host & microbe Result IV E97A;E96A;K41A;R38A 44;39;58;53 48;43;62;57 NS1;NS1 19;63 22;66 19454348 Influenza A virus NS1 targets the ubiquitin ligase TRIM25 to evade recognition by the host viral RNA sensor RIG-I. Infection of A549 cells with the E96A/E97A and R38A/K41A mutant viruses resulted in substantial IFN production as compared to infection with WT virus. 2009 Cell host & microbe Result IV E96A;E97A;K41A;R38A 33;38;52;47 37;42;56;51 19454348 Influenza A virus NS1 targets the ubiquitin ligase TRIM25 to evade recognition by the host viral RNA sensor RIG-I. Infection with the E96A/E97A mutant virus resulted in detectable IFN production from wild-type and heterozygous cells. 2009 Cell host & microbe Result IV E96A;E97A 19;24 23;28 19454348 Influenza A virus NS1 targets the ubiquitin ligase TRIM25 to evade recognition by the host viral RNA sensor RIG-I. NS1 WT potently suppressed the RIG-I CARD ubiquitination, whereas the E96A/E97A and R38A/K41A NS1 mutants had no effect on the ubiquitination level of RIG-I CARDs. 2009 Cell host & microbe Result IV E97A;E96A;K41A;R38A 75;70;89;84 79;74;93;88 NS1;NS1 0;94 3;97 19454348 Influenza A virus NS1 targets the ubiquitin ligase TRIM25 to evade recognition by the host viral RNA sensor RIG-I. R38A/K41A and E96A/E97A NS1 mutants showed a complete loss of TRIM25 binding ability in Co-IP assays. 2009 Cell host & microbe Result IV R38A;K41A;E96A;E97A 0;5;14;19 4;9;18;23 NS1 24 27 19454348 Influenza A virus NS1 targets the ubiquitin ligase TRIM25 to evade recognition by the host viral RNA sensor RIG-I. Specifically, while some remaining IFN was detectable by bioassay in DeltaNS1 and R38A/K41A virus infected cells in the absence of TRIM25, these levels were approximately 10 to 100 times lower than in the presence of TRIM25, indicating that most of the IFN produced in MEFs is dependent on TRIM25 expression and suggesting that additional NS1 functions, such as dsRNA binding, are needed to fully prevent a suboptimal TRIM25-independent induction of IFN during viral infection. 2009 Cell host & microbe Result IV R38A;K41A 82;87 86;91 NS1 339 342 19454348 Influenza A virus NS1 targets the ubiquitin ligase TRIM25 to evade recognition by the host viral RNA sensor RIG-I. The E96A/E97A mutation is located in a highly conserved putative protein-protein interacting motif (S/T-x-E-E), identified by a computational analysis of the NS1 sequence using the Eukaryotic Linear Motif resource (ELM). 2009 Cell host & microbe Result IV E96A;E97A 4;9 8;13 NS1 158 161 19454348 Influenza A virus NS1 targets the ubiquitin ligase TRIM25 to evade recognition by the host viral RNA sensor RIG-I. The IFN-inducing phenotypes of the R38A/K41A and DeltaNS1 viruses were reduced in at least one order of magnitude but they were still evident in the TRIM25-/- cell line. 2009 Cell host & microbe Result IV K41A;R38A 40;35 44;39 19454348 Influenza A virus NS1 targets the ubiquitin ligase TRIM25 to evade recognition by the host viral RNA sensor RIG-I. The R38A/K41A NS1 mutant is known to be deficient in dsRNA binding activity and in IFN antagonism. 2009 Cell host & microbe Result IV R38A;K41A 4;9 8;13 NS1 14 17 19454348 Influenza A virus NS1 targets the ubiquitin ligase TRIM25 to evade recognition by the host viral RNA sensor RIG-I. The R38A/K41A NS1 mutant was previously reported to be deficient in binding dsRNA, and a recombinant influenza virus expressing this mutant NS1 protein was defective in IFN antagonism and attenuated in mice. 2009 Cell host & microbe Result IV R38A;K41A 4;9 8;13 NS1;NS1 14;140 17;143 19454348 Influenza A virus NS1 targets the ubiquitin ligase TRIM25 to evade recognition by the host viral RNA sensor RIG-I. The titers of the R38A/K41A and DeltaNS1 viruses were slightly reduced as compared to the WT virus. 2009 Cell host & microbe Result IV R38A;K41A 18;23 22;27 19454348 Influenza A virus NS1 targets the ubiquitin ligase TRIM25 to evade recognition by the host viral RNA sensor RIG-I. These data indicate that the loss of TRIM25 inhibition by the E96A/E97A mutant virus is responsible for its IFN inducing properties. 2009 Cell host & microbe Result IV E96A;E97A 62;67 66;71 19454348 Influenza A virus NS1 targets the ubiquitin ligase TRIM25 to evade recognition by the host viral RNA sensor RIG-I. These results suggest that the reduced titers obtained for the E96A/E97A virus following infection of A549 cells are attributed to IFN production and not to an intrinsic defect in NS1 function resulting in impaired virus replication. 2009 Cell host & microbe Result IV E96A;E97A 63;68 67;72 NS1 180 183 19454348 Influenza A virus NS1 targets the ubiquitin ligase TRIM25 to evade recognition by the host viral RNA sensor RIG-I. Thus, the E96A/E97A mutation in the context of a recombinant influenza virus should unveil the contribution of TRIM25 inhibition by NS1 in IFN antagonism and virulence. 2009 Cell host & microbe Result IV E96A;E97A 10;15 14;19 NS1 132 135 19454348 Influenza A virus NS1 targets the ubiquitin ligase TRIM25 to evade recognition by the host viral RNA sensor RIG-I. To determine whether the reduction in titer for the E96A/E97A virus was attributed to induction of IFN, virus production from IFN-deficient, 8-day old embryonated chicken eggs was determined. 2009 Cell host & microbe Result IV E96A;E97A 52;57 56;61 19454348 Influenza A virus NS1 targets the ubiquitin ligase TRIM25 to evade recognition by the host viral RNA sensor RIG-I. To establish whether the loss of TRIM25 regulation correlated with attenuation in pathogenicity, we assessed the replication and virulence of WT and E96A/E97A viruses in mice. 2009 Cell host & microbe Result IV E96A;E97A 149;154 153;158 19454348 Influenza A virus NS1 targets the ubiquitin ligase TRIM25 to evade recognition by the host viral RNA sensor RIG-I. We next investigated the ability of NS1 WT and mutants E96A/E97A and R38A/K41A to inhibit the TRIM25-mediated RIG-I ubiquitination and downstream signaling. 2009 Cell host & microbe Result IV E97A;E96A;K41A;R38A 60;55;74;69 64;59;78;73 NS1 36 39 19454348 Influenza A virus NS1 targets the ubiquitin ligase TRIM25 to evade recognition by the host viral RNA sensor RIG-I. We therefore generated a recombinant A/PR/8/34 virus expressing NS1 E96A/E97A and tested its replication in A549 cells, a human lung epithelial cell line, in comparison to WT virus. 2009 Cell host & microbe Result IV E96A;E97A 68;73 72;77 NS1 64 67 19454348 Influenza A virus NS1 targets the ubiquitin ligase TRIM25 to evade recognition by the host viral RNA sensor RIG-I. While the WT virus did not produce detectable amounts of IFN-beta, the E96A/E97A and R38A/K41A viruses induced between 100 to 1000 pg/mL IFN-beta from wild-type and heterozygous (TRIM25+/-) MEFs. 2009 Cell host & microbe Result IV E96A;E97A;R38A;K41A 71;76;85;90 75;80;89;94 19454348 Influenza A virus NS1 targets the ubiquitin ligase TRIM25 to evade recognition by the host viral RNA sensor RIG-I. WT NS1 but not R38A/K41A and E96A/E97A NS1 mutants inhibit TRIM25-mediated RIG-I ubiquitination and signal transduction. 2009 Cell host & microbe Result IV R38A;K41A;E96A;E97A 15;20;29;34 19;24;33;38 NS1;NS1 3;39 6;42 19517011 Novel genotypes of H9N2 influenza A viruses isolated from poultry in Pakistan containing NS genes similar to highly pathogenic H7N3 and H5N1 viruses. At residue 15, all the H9N2 UDL viruses encode isoleucine and the amino acid substitution of V15I is common within H9N2 lineages. 2009 PloS one Result IV V15I 93 97 19517011 Novel genotypes of H9N2 influenza A viruses isolated from poultry in Pakistan containing NS genes similar to highly pathogenic H7N3 and H5N1 viruses. In addition, a substitution from tryptophan to arginine at position 403 was observed in 11 of the 12 viruses recently isolated from Pakistan; this substitution was present in Qa/HK/G1/97 but not in other H9N2 viruses, including those from the UAE from 2000 to 2003 and, importantly, not in the human (e.g. 2009 PloS one Result IV W403R 33 71 19517011 Novel genotypes of H9N2 influenza A viruses isolated from poultry in Pakistan containing NS genes similar to highly pathogenic H7N3 and H5N1 viruses. It is striking that N66S in PB1-F2 is associated with increased virulence in a mouse model but viruses having S at residue 66 of PB1-F2 are rare and were not present in the H9N2 viruses in this study. 2009 PloS one Result IV N66S 20 24 PB1F2;PB1F2 28;129 34;135 19517011 Novel genotypes of H9N2 influenza A viruses isolated from poultry in Pakistan containing NS genes similar to highly pathogenic H7N3 and H5N1 viruses. Of these, three represent substitutions (E/T190A, Q226L and Q227I) when compared with the reference strains of the H9 lineage (Table 1). 2009 PloS one Result IV E190A;T190A;Q226L;Q227I 41;41;50;60 48;48;55;65 19517011 Novel genotypes of H9N2 influenza A viruses isolated from poultry in Pakistan containing NS genes similar to highly pathogenic H7N3 and H5N1 viruses. One UDL isolate Ck/Pak/UDL-02/06 lacked one potential glycosylation site at Asn 234 due to T236I substitution. 2009 PloS one Result IV T236I 91 96 19517011 Novel genotypes of H9N2 influenza A viruses isolated from poultry in Pakistan containing NS genes similar to highly pathogenic H7N3 and H5N1 viruses. The exceptions were that a single isolate (Ck/Pak/UDL-04/06) contained a S44A substitution in PB2 and all isolates had aspartic acid at position 372 in NP which has been found in avian influenza viruses isolated from humans. 2009 PloS one Result IV S44A 73 77 NP;PB2 152;94 154;97 19517011 Novel genotypes of H9N2 influenza A viruses isolated from poultry in Pakistan containing NS genes similar to highly pathogenic H7N3 and H5N1 viruses. The Qa/Hong Kong/G1/97 isolate is unusual in carrying a N402I substitution and one of the viruses characterised here (A/Ck/Pak/UDL-04/06) has serine at this position. 2009 PloS one Result IV N402I 56 61 19517011 Novel genotypes of H9N2 influenza A viruses isolated from poultry in Pakistan containing NS genes similar to highly pathogenic H7N3 and H5N1 viruses. The substitution, as seen in the viruses under study here, of Q226L at the receptor binding site in the HA allows H9N2 viruses to replicate more efficiently (with 100-fold higher peak titres) in human cells in culture and is associated with a preferential receptor binding specificity for sialic acid alpha2,6-linked galactose and was also observed in the UAE isolates analysed by Aamir. 2009 PloS one Result IV Q226L 62 67 HA 104 106 19517011 Novel genotypes of H9N2 influenza A viruses isolated from poultry in Pakistan containing NS genes similar to highly pathogenic H7N3 and H5N1 viruses. The substitutions at residue 372 from serine to alanine or, for one virus, threonine (Table 1) were similar to those detected in Parakeet/Narita/92A/98, Ck/Pak/2/99 and H9N2 viruses isolated from Iran and the United Arab Emirates. 2009 PloS one Result IV S372A 29 55 19517011 Novel genotypes of H9N2 influenza A viruses isolated from poultry in Pakistan containing NS genes similar to highly pathogenic H7N3 and H5N1 viruses. The UDL viruses showed heterogeneity at residue 37 with 5 viruses encoding valine and 7 viruses alanine but the substitution T37A/V clusters exclusively with the recent UDL H9N2 viruses from Pakistan. 2009 PloS one Result IV T37A;T37V 125;125 131;131 19517011 Novel genotypes of H9N2 influenza A viruses isolated from poultry in Pakistan containing NS genes similar to highly pathogenic H7N3 and H5N1 viruses. The viruses sequenced in this study contained an additional glycosylation site at Asn 44 due to the substitution of Pro45Ser. 2009 PloS one Result IV P45S 116 124 19857993 Evaluation of a rapid molecular algorithm for detection of pandemic influenza A (H1N1) 2009 virus and screening for a key oseltamivir resistance (H275Y) substitution in neuraminidase. In mixtures of wild type H275 and mutant H275Y RNA, up to 5% of mutant virus could be detected in a reaction with a total input of 1.0 x 105 vp/ml. 2010 Journal of clinical virology Result IV H275Y 41 46 19857993 Evaluation of a rapid molecular algorithm for detection of pandemic influenza A (H1N1) 2009 virus and screening for a key oseltamivir resistance (H275Y) substitution in neuraminidase. Performance of pandemic influenza H275Y discrimination RT-PCR. 2010 Journal of clinical virology Result IV H275Y 34 39 19857993 Evaluation of a rapid molecular algorithm for detection of pandemic influenza A (H1N1) 2009 virus and screening for a key oseltamivir resistance (H275Y) substitution in neuraminidase. Serial 10-fold dilutions of in vitro transcribed RNA containing wild type or mutant sequence were analyzed using the H275Y discrimination RT-PCR assay. 2010 Journal of clinical virology Result IV H275Y 117 122 19857993 Evaluation of a rapid molecular algorithm for detection of pandemic influenza A (H1N1) 2009 virus and screening for a key oseltamivir resistance (H275Y) substitution in neuraminidase. The assay sensitivity was tested using both RNA obtained from influenza A/NL/602/2009 virus as well as the H275Y recombinant. 2010 Journal of clinical virology Result IV H275Y 107 112 19893749 Inhibition of neuraminidase inhibitor-resistant influenza virus by DAS181, a novel sialidase fusion protein. Although a zanamivir-sensitive isolate, A/St.Louis/758/09, carries a N163T mutation, this isolate also has a unique, nearby V189A mutation that might negate the effects of the N163T mutation such that the virus remains sensitive to zanamivir (Table 3). 2009 PloS one Result IV N163T;V189A;N163T 69;124;176 74;129;181 19893749 Inhibition of neuraminidase inhibitor-resistant influenza virus by DAS181, a novel sialidase fusion protein. An N32S mutation was found in all but one zanamivir-sensitive 2009 isolate (A/St.Louis/758/09) and an I222V mutation was observed solely in two zanamivir-resistant 2009 isolates (Figure S3 and S4). 2009 PloS one Result IV N32S;I222V 3;102 7;107 19893749 Inhibition of neuraminidase inhibitor-resistant influenza virus by DAS181, a novel sialidase fusion protein. For comparison we obtained from CDC two pairs of seasonal IFV reference viruses: one pair is sensitive to both NAIs (2004 isolates) and the other pair is resistant to oseltamivir, due to the H274Y mutation in the NA (2007/08 season isolates, representative of two distinctive clades, "Hawaiian" and "Northern European"). 2009 PloS one Result IV H274Y 191 196 NA;NAI 213;111 215;115 19893749 Inhibition of neuraminidase inhibitor-resistant influenza virus by DAS181, a novel sialidase fusion protein. In the NI assay, oseltamivir failed to effectively inhibit NA activity from each of the 2007 and 2009 isolates; however, all of these isolates were equally sensitive to zanamivir, including the 2009 isolates that carry the N32S and I222V mutations (Table 2). 2009 PloS one Result IV N32S;I222V 223;232 227;237 59 61 19893749 Inhibition of neuraminidase inhibitor-resistant influenza virus by DAS181, a novel sialidase fusion protein. Non-conserved mutations at these two positions, N163K/H and D225G, thus may be sufficient to cause reduced sensitivity to NAIs in MDCK cells. 2009 PloS one Result IV N163K;N163H;D225G 48;48;60 55;55;65 NAI 122 126 19893749 Inhibition of neuraminidase inhibitor-resistant influenza virus by DAS181, a novel sialidase fusion protein. Upon sequencing the neuraminidase (NA) gene of the clinical isolates, we found that all of the tested 2007 and 2009 isolates, but not the 2004 isolates, contained the NA H274Y mutation known to confer oseltamivir resistance. 2009 PloS one Result IV H274Y 170 175 NA;NA;NA 35;167;20 37;169;33 19905033 Design and pharmacological characterization of inhibitors of amantadine-resistant mutants of the M2 ion channel of influenza A virus. Based on these findings we decided that the results of the plaque formation assay performed on the double mutant A/M2-V27A/L38F adequately represent the behavior of the single A/M2-V27A mutant. 2009 Biochemistry Result IV L38F;V27A;V27A 123;118;181 127;122;185 M2;M2 115;178 117;180 19905033 Design and pharmacological characterization of inhibitors of amantadine-resistant mutants of the M2 ion channel of influenza A virus. By contrast to the other mutations considered here, L26F does not involve a pore-lining residue, and instead involves a partially largely lipid-exposed residue that packs at the interface between the helices adjacent to the V27. 2009 Biochemistry Result IV L26F 52 56 19905033 Design and pharmacological characterization of inhibitors of amantadine-resistant mutants of the M2 ion channel of influenza A virus. Compound 8 is an even more potent inhibitor of A/M2 L26F (IC50 = 30.6 muM, Figure 2). 2009 Biochemistry Result IV L26F 52 56 M2 49 51 19905033 Design and pharmacological characterization of inhibitors of amantadine-resistant mutants of the M2 ion channel of influenza A virus. In comparison, amantadine and BL-1743 at the same concentration range failed to inhibit plaque formation of A/M2-V27A/L38F viruses (Figure 3C). 2009 Biochemistry Result IV V27A;L38F 113;118 117;122 M2 110 112 19905033 Design and pharmacological characterization of inhibitors of amantadine-resistant mutants of the M2 ion channel of influenza A virus. It is also interesting to note that the mutant V27G, which is also naturally occurring is highly resistant to all compounds tested (Table 2). 2009 Biochemistry Result IV V27G 47 51 19905033 Design and pharmacological characterization of inhibitors of amantadine-resistant mutants of the M2 ion channel of influenza A virus. On the other hand, plaque count and size resulting from infection by an influenza virus A/M2-V27A/L38F, that contains the M2-V27A mutation was reduced by 50 muM spiran amine 8 (Figure 3C). 2009 Biochemistry Result IV L38F;V27A;V27A 98;93;125 102;97;129 M2;M2 90;122 92;124 19905033 Design and pharmacological characterization of inhibitors of amantadine-resistant mutants of the M2 ion channel of influenza A virus. Other mutations deeper inside the pore than V27 (A30T and G34E) completely eliminate the ability of all drugs tested to inhibit the channel (Table 2). 2009 Biochemistry Result IV A30T;G34E 49;58 53;62 19905033 Design and pharmacological characterization of inhibitors of amantadine-resistant mutants of the M2 ion channel of influenza A virus. S31N is a highly frequent mutation, which gives rise to decreased sensitivity to amantadine (IC50 = 237.0 muM versus 15.8 muM for the wt A/M2 channel, Figure 2), and complete resistance to rimantadine (IC50 > 10mM). 2009 Biochemistry Result IV S31N 0 4 M2 139 141 19905033 Design and pharmacological characterization of inhibitors of amantadine-resistant mutants of the M2 ion channel of influenza A virus. The A/M2-V27A/L38F mutant channels were not sensitive to either amantadine, or BL1743, while being efficiently inhibited by compound 8 (A/M2-V27A/L38F IC50=78.21+-15.06; A/M2-V27A IC50= 84.92+-13.61). 2009 Biochemistry Result IV V27A;L38F;L38F;V27A;V27A 9;14;146;141;175 13;18;150;145;179 M2;M2;M2 6;138;172 8;140;174 19905033 Design and pharmacological characterization of inhibitors of amantadine-resistant mutants of the M2 ion channel of influenza A virus. The activity of the double mutant A/M2-V27A/L38F was tested by TEVC and compared to that of a single mutant A/M2-V27A. 2009 Biochemistry Result IV L38F;V27A;V27A 44;39;113 48;43;117 M2;M2 36;110 38;112 19905033 Design and pharmacological characterization of inhibitors of amantadine-resistant mutants of the M2 ion channel of influenza A virus. The inhibition of V27A mutants is particularly interesting, given that amantadine, BL-1743, and spiro piperidine 20 gave less than 10% inhibition of the mutant, when applied at 100 muM concentration. 2009 Biochemistry Result IV V27A 18 22 19905033 Design and pharmacological characterization of inhibitors of amantadine-resistant mutants of the M2 ion channel of influenza A virus. The L38F mutation is naturally found in the Weybridge strain of the virus. 2009 Biochemistry Result IV L38F 4 8 19905033 Design and pharmacological characterization of inhibitors of amantadine-resistant mutants of the M2 ion channel of influenza A virus. Thus, spiran amine 8 is capable of efficiently inhibiting not only wt A/M2 channels and A/M2-L26F and A/M2-V27A mutant channels expressed in oocytes, but it also prevents replication of wt virus and these mutant recombinant viruses. 2009 Biochemistry Result IV L26F;V27A 93;107 97;111 M2;M2;M2 72;90;104 74;92;106 19905033 Design and pharmacological characterization of inhibitors of amantadine-resistant mutants of the M2 ion channel of influenza A virus. We found that sensitivity of the double mutant channel to the tested compound was comparable to that of the single A/M2-V27A mutant. 2009 Biochemistry Result IV V27A 120 124 M2 117 119 19905033 Design and pharmacological characterization of inhibitors of amantadine-resistant mutants of the M2 ion channel of influenza A virus. We found that spiran amine 8 efficiently inhibits the activity of A/M2 wt channels and of A/M2-V27A mutants, with IC50 values of 12.6 muM and 84.9 muM respectively (Figure 2; Table 2). 2009 Biochemistry Result IV V27A 95 99 M2;M2 68;92 70;94 19958488 Prediction of avian influenza A binding preference to human receptor using conformational analysis of receptor bound to hemagglutinin. For the binding studies of avian receptor analogs with alpha(2,3)-linkage, the glycosidic linkage in trans conformation was observed during most of the simulation in all HA systems tested (Phi angle -55 degrees), albeit with some transient fluctuations to the cis conformation for the Q222L, G224S, and Q222L/G224S Sing-97 HA variants. 2009 BMC genomics Result IV Q222L;G224S;Q222L;G224S 285;292;303;309 290;297;308;314 HA;HA 170;323 172;325 19958488 Prediction of avian influenza A binding preference to human receptor using conformational analysis of receptor bound to hemagglutinin. In contrast, the cis conformation was observed (Phi = +60 degrees) for the majority of the simulation time when the analogs bound with Puerto-34 human influenza, L129V/A134V Kan-1, and Q222L/G224S Sing-97 HAs. 2009 BMC genomics Result IV L129V;A134V;Q222L;G224S 162;168;185;191 167;173;190;196 Influenza 145 160 19958488 Prediction of avian influenza A binding preference to human receptor using conformational analysis of receptor bound to hemagglutinin. In the simulation of human receptor analogs with alpha(2,6)-linkage, the trans configuration (Phi = -55 degrees) was observed in the majority during the simulation with some transient fluctuations to the cis conformation when bound to Sing-97, Sing-97 mutants Q222L, G224S and Kan-1 systems. 2009 BMC genomics Result IV Q222L;G224S 260;267 265;272 19995550 X-ray structures of NS1 effector domain mutants. 3.4 The W187Y mutant could serve as a drug screening target. 2010 Archives of biochemistry and biophysics Result IV W187Y 8 13 19995550 X-ray structures of NS1 effector domain mutants. A screen of crystallization conditions showed that both W187A and W187Y mutants form diffraction quality crystals in the same condition. 2010 Archives of biochemistry and biophysics Result IV W187A;W187Y 56;66 61;71 19995550 X-ray structures of NS1 effector domain mutants. A superposition of the mutant EDs with wild type ED (Figure 2) gives an rms distance between 123 Calpha atoms of 0.16 A and 0.39 A for W187A mutant and W187Y mutant respectively. 2010 Archives of biochemistry and biophysics Result IV W187A;W187Y 135;152 140;157 19995550 X-ray structures of NS1 effector domain mutants. As shown in Figure 5, the wild type elutes as a dimer whereas both W187A and W187Y mutant proteins eluted in a volume equivalent to a monomer. 2010 Archives of biochemistry and biophysics Result IV W187A;W187Y 67;77 72;82 19995550 X-ray structures of NS1 effector domain mutants. Both recombinant, His tagged, effector domain mutants (W187A and W187Y) can be expressed in good yield from Escherichia coli (~10 mg/ liter of cell culture). 2010 Archives of biochemistry and biophysics Result IV W187A;W187Y 55;65 60;70 19995550 X-ray structures of NS1 effector domain mutants. Conversion of Trp 187 to Tyr disrupts homodimer formation at least 100 fold, but only retards formation of a complex with F1F3 four fold. 2010 Archives of biochemistry and biophysics Result IV W187Y 14 28 19995550 X-ray structures of NS1 effector domain mutants. Converting Trp 187 to Tyr reduces binding affinity about six-fold, while converting it to Ala reduces binding by forty fold. 2010 Archives of biochemistry and biophysics Result IV W187Y 11 25 19995550 X-ray structures of NS1 effector domain mutants. Coordinates of the refined models of the W187A and W187Y crystals have been deposited in the Protein Data Bank with entry codes 3KWG and 3KWI, respectively. 2010 Archives of biochemistry and biophysics Result IV W187A;W187Y 41;51 46;56 19995550 X-ray structures of NS1 effector domain mutants. CPSF30 contains five C3H zinc finger repeats, but the second and third fingers (F2F3) are sufficient for efficient binding to NS1A. 2010 Archives of biochemistry and biophysics Result IV C3H 21 24 NS 126 128 19995550 X-ray structures of NS1 effector domain mutants. Following refinement, a Ramachandran plot of the W187A crystal showed 89.2% of residues to be in the most favorable region and 10.3% in the additionally allowed space. 2010 Archives of biochemistry and biophysics Result IV W187A 49 54 19995550 X-ray structures of NS1 effector domain mutants. In conclusion, we have engineered a W187Y mutant of NS1 effector domain, which behaves as a monomer in solution but is still able to binding CPSF30 with binding affinity close to the wild type protein. 2010 Archives of biochemistry and biophysics Result IV W187Y 36 41 NS1 52 55 19995550 X-ray structures of NS1 effector domain mutants. In contrast to the packing of the W187Y mutant, the non-crystallographic dimer of the W187A mutant is very different, as shown in Figure 3b. 2010 Archives of biochemistry and biophysics Result IV W187A;W187Y 86;34 91;39 19995550 X-ray structures of NS1 effector domain mutants. In that case, tryptophan 187 was found to be essential for the effector domain dimerization; the wild type protein eluted from a column as a dimer and a W187A mutant as a monomer. 2010 Archives of biochemistry and biophysics Result IV W187A 153 158 19995550 X-ray structures of NS1 effector domain mutants. In the W187Y mutant, the Calpha atom of the N-terminal A86 is shifted toward the antiparallel beta-sheet ~8 A; residues 136-140 are shifted up to ~2.5 A toward the N-terminus that backbone nitrogen of F138 is within hydrogen bond distance of the sulfur atom of S87. 2010 Archives of biochemistry and biophysics Result IV W187Y 7 12 19995550 X-ray structures of NS1 effector domain mutants. Solution studies were undertaken to assess the strength of the W187Y dimerization. 2010 Archives of biochemistry and biophysics Result IV W187Y 63 68 19995550 X-ray structures of NS1 effector domain mutants. The cell constants for the W187A mutant are a = 47.78, b = 48.19, c =154.59A. 2010 Archives of biochemistry and biophysics Result IV W187A 27 32 19995550 X-ray structures of NS1 effector domain mutants. The corresponding enthalpy and entropy change of the binding are -7.7 kcal/mol and 9.3 cal/mol for the wild type effector domain, -8.2 kcal/mol and -2.4 cal/mol for the W187A mutant, -9.0 kcal/mol and -1.5 cal/mol for the W187Y mutant. 2010 Archives of biochemistry and biophysics Result IV W187A;W187Y 169;222 174;227 19995550 X-ray structures of NS1 effector domain mutants. The integrated titration curves were fit to a single site binding model, and gave a Kd of 0.07 muM for the wild type effector domain, 3 muM for the W187A mutant, and 0.4 muM for the W187Y mutant. 2010 Archives of biochemistry and biophysics Result IV W187A;W187Y 148;182 153;187 19995550 X-ray structures of NS1 effector domain mutants. The only significant differences are between the W187Y mutant and wild type structures. 2010 Archives of biochemistry and biophysics Result IV W187Y 49 54 19995550 X-ray structures of NS1 effector domain mutants. The rms deviation of the independent Calpha chains is 0.18 A for the W187A mutant, and 0.29 A for the W187Y mutants. 2010 Archives of biochemistry and biophysics Result IV W187A;W187Y 69;102 74;107 19995550 X-ray structures of NS1 effector domain mutants. The Tyr side chain of the W187Y mutant should work well to define the receptor pocket during the screening of small molecule ligands. 2010 Archives of biochemistry and biophysics Result IV W187Y 26 31 19995550 X-ray structures of NS1 effector domain mutants. The W187A mutant is unable to bury the side chain of position 187 in a neighboring molecule. 2010 Archives of biochemistry and biophysics Result IV W187A 4 9 19995550 X-ray structures of NS1 effector domain mutants. The W187Y mutant dimer is similar to the wild type NS1-ED. 2010 Archives of biochemistry and biophysics Result IV W187Y 4 9 NS1 51 54 19995550 X-ray structures of NS1 effector domain mutants. The W187Y mutant forms a non-crystallographic dimer very similar to that of the wild type protein. 2010 Archives of biochemistry and biophysics Result IV W187Y 4 9 19995550 X-ray structures of NS1 effector domain mutants. The W187Y mutant has a slightly larger unit cell, a = 48.0, b = 60.24, and c = 132.66 A. 2010 Archives of biochemistry and biophysics Result IV W187Y 4 9 19995550 X-ray structures of NS1 effector domain mutants. The W87Y crystal had a Ramachandran plot with 87.6% of residues in the most favorable region and 12.4% in additionally allowed space. 2010 Archives of biochemistry and biophysics Result IV W87Y 4 8 19995550 X-ray structures of NS1 effector domain mutants. There are two molecules in the asymmetric unit of each, giving a Vm value of 2.78 A3/Da for W187A mutant, and 3.0 A3/Da for W187Y mutant. 2010 Archives of biochemistry and biophysics Result IV W187A;W187Y 92;124 97;129 19995550 X-ray structures of NS1 effector domain mutants. They show the W187Y ED protein binds only 4 fold less tightly to F1F3 than the wild type does. 2010 Archives of biochemistry and biophysics Result IV W187Y 14 19 19995550 X-ray structures of NS1 effector domain mutants. This in turn suggests that the interactions of the three aromatic rings of F2F3 in the ED receptor pocket are essentially identical between the wild type and the W187Y mutant. 2010 Archives of biochemistry and biophysics Result IV W187Y 162 167 19995550 X-ray structures of NS1 effector domain mutants. To test if the two mutant NS1A-EDs (W187A and W187Y) are able to bind CPSF30, we carried out a GST pull down assay as described by others. 2010 Archives of biochemistry and biophysics Result IV W187A;W187Y 36;46 41;51 NS 26 28 20303563 Substitution of lysine at 627 position in PB2 protein does not change virulence of the 2009 pandemic H1N1 virus in mice. Effects of PB2 E627K substitution on the growth property of CA04 on MDCK cells at different temperatures. 2010 Virology Result IV E627K 15 20 PB2 11 14 20303563 Substitution of lysine at 627 position in PB2 protein does not change virulence of the 2009 pandemic H1N1 virus in mice. Effects of PB2 E627K substitution on the viral replication and pathogenicity of A/California/04/2009 (H1N1) virus in mice. 2010 Virology Result IV E627K 15 20 PB2 11 14 20303563 Substitution of lysine at 627 position in PB2 protein does not change virulence of the 2009 pandemic H1N1 virus in mice. The E627K substitution in PB2 gene of avian H5N1 influenza virus was reported to be responsible for the increased growth efficiency in mammals, especially at lower temperatures of 32-33 C. 2010 Virology Result IV E627K 4 9 PB2 26 29 20303563 Substitution of lysine at 627 position in PB2 protein does not change virulence of the 2009 pandemic H1N1 virus in mice. To assess the potential effect of a PB2 E627K substitution on the pandemic (H1N1) 2009 virus, we constructed a recombinant virus by introducing a lysine into the 627 position of PB2 gene in the background of A/California/04/2009 (CA04). 2010 Virology Result IV E627K 40 45 PB2;PB2 36;178 39;181 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. A single F291L mutation in the HA gene was identified in 1 of 3 ferrets inoculated with either E119A or N294S mutants. 2010 PLoS pathogens Result IV F291L;E119A;N294S 9;95;104 14;100;109 HA 31 33 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. All mutants were able to maintain their plaque phenotype with the exception of those carrying mutations at positions 252 and 274: homogenous large plaques were observed for both Y252H and H274Y viruses after the third passage (Table 1). 2010 PLoS pathogens Result IV Y252H;H274Y 178;188 183;193 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. All of the viruses grew to comparable titers and formed homogeneous plaques in MDCK cells (diameter, 0.3 to 1.7 mm), although viruses with the Y252H, H274Y, and N294S NA mutations formed significantly smaller plaques than did the WT virus (P<0.01) (Table 1). 2010 PLoS pathogens Result IV Y252H;H274Y;N294S 143;150;161 148;155;166 167 169 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. All three viruses were detected in the lungs, nasal turbinate, and trachea; however, only the E119A and N294S mutants were detected in the liver (Figure 4A). 2010 PLoS pathogens Result IV E119A;N294S 94;104 99;109 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. An NA enzyme inhibition assay, a reliable phenotypic assay used to characterize the NA inhibitor susceptibility of influenza viruses, showed altered susceptibility in all recombinant H5N1 influenza viruses except that with K150N substitution. 2010 PLoS pathogens Result IV K150N 223 228 NA;NA 3;84 5;86 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. Cell counts remained at the same level in nasal washes of animals infected with either WT or I117V viruses, and they returned to normal levels in ferrets inoculated with Y252H at day 6 p.i. 2010 PLoS pathogens Result IV I117V;Y252H 93;170 98;175 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. Comparison of the protein concentrations in the nasal washes showed no significant differences among the I117V, Y252H and WT viruses, suggesting that upper respiratory tract inflammation in these groups was comparable. 2010 PLoS pathogens Result IV I117V;Y252H 105;112 110;117 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. Consistent with the more pronounced clinical signs of disease, the E119A and N294S were detected at significantly higher titers in three out of four lobes of the lungs (~4.9-6.7 log10EID50/gram tissue) and liver (~1.7-2.9 log10EID50/gram tissue) (P<0.01). 2010 PLoS pathogens Result IV E119A;N294S 67;77 72;82 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. Further, increased virulence and severity of disease caused by H5N1 viruses carrying E119A and N294S NA changes were associated with higher virus titers and more pronounced local inflammatory response in the lungs compared to WT virus. 2010 PLoS pathogens Result IV E119A;N294S 85;95 90;100 101 103 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. Histopathology and Replication of Recombinant WT, E119A, and N294S Viruses in Internal Organs of Ferrets. 2010 PLoS pathogens Result IV E119A;N294S 50;61 55;66 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. However, the ferrets inoculated with N294S recombinant had bronchopneumonia in ~ 50% of two lung lobes and in >90% of the other two lobes. 2010 PLoS pathogens Result IV N294S 37 42 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. Importantly, all clinical symptoms of disease were similar to those observed in the first experiment (Figure 3C), including a slight increase in RII for the E119A and N294S (0.3 and 0.4, respectively) and substantial weight loss (~15%) of N294S-infected ferrets. 2010 PLoS pathogens Result IV E119A;N294S;N294S 157;167;239 162;172;244 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. In contrast, inoculation of ferrets with recombinant E119A and N294S viruses caused markedly different results. 2010 PLoS pathogens Result IV E119A;N294S 53;63 58;68 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. In contrast, the Y252H NA change conferred increased susceptibility to oseltamivir carboxylate (mean IC50 decrease, 22-fold) (Table 2). 2010 PLoS pathogens Result IV Y252H 17 22 23 25 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. In the N294S-infected ferrets, alveolitis was characterized by a centrifugal progression of severity from the peribronchiole alveoli to the subpleural alveoli with pneumocyte hyperplasia and extensive infiltrates of inflammatory cells obscuring the lace-like alveolar pattern. 2010 PLoS pathogens Result IV N294S 7 12 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. Mild but prolonged illness (duration ~ 10 days, relative inactivity index, RII 0.01) was seen in ferrets infected with mutant V116A and K150N viruses (Table 3). 2010 PLoS pathogens Result IV V116A;K150N 126;136 131;141 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. Mild, short illness (duration ~ 5-6 days) was observed in ferrets inoculated with H5N1 viruses carrying I117V and Y252H NA mutations: only slight temperature elevation (mean peak increase, 0.5 to 1.2 C), mild clinical features (RII 0.05) (Table 3) and minor weight changes were detected (Figure 3B). 2010 PLoS pathogens Result IV I117V;Y252H 104;114 109;119 120 122 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. NA proteins harboring the V116A, I117V, and E119A mutations exhibited significantly lower affinity for the substrate (mean Km decrease, 4-8-fold) than did other NAs studied. 2010 PLoS pathogens Result IV V116A;I117V;E119A 26;33;44 31;38;49 NA;NA 0;161 2;164 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. No amino acid substitutions were identified in the NA gene of viruses isolated from ferrets inoculated with the WT, E119A, or N294S recombinants. 2010 PLoS pathogens Result IV E119A;N294S 116;126 121;131 51 53 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. Of the three H5N1 viruses, the E119A mutant caused very severe and extensive alveolitis with necrosis of the alveolar pneumocytes and interstitial septal walls resulting in the loss of the alveolar architecture and leading to large coalescing spaces of edema fluid, fibrin, inflammatory and hemorrhagic red blood cells (Figure 4B). 2010 PLoS pathogens Result IV E119A 31 36 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. Of the three H5N1 viruses, the N294S recombinant yielded significantly higher virus titers in the trachea (~6.2 log10EID50/gram tissue versus 4.7 log10EID50/gram tissue, P<0.01) (Figure 4A). 2010 PLoS pathogens Result IV N294S 31 36 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. Recombinant I117V and Y252H viruses replicated less efficiently in the upper respiratory tract than did the WT strain (P<0.05) (Figure 3B). 2010 PLoS pathogens Result IV I117V;Y252H 12;22 17;27 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. Taken together, our results indicated that the introduced E119A and N294S NA mutations were stably maintained in A/Turkey/15/06 (H5N1) virus background in ferrets. 2010 PLoS pathogens Result IV E119A;N294S 58;68 63;73 74 76 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. The body temperature elevation and nasal-wash inflammatory cell count were significantly higher in animals inoculated with the E119A mutant than in those inoculated with recombinant WT virus (P<0.01) (Figure 3C). 2010 PLoS pathogens Result IV E119A 127 132 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. The E119A-infected animals revealed multifocal bronchopneumonia in >90% of all four lung lobes (Figure 4B). 2010 PLoS pathogens Result IV E119A 4 9 Bronchopneumonia 47 63 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. The H274Y mutant was much more resistant to oseltamivir carboxylate (mean IC50 increase, >900-fold) and slightly less susceptible to zanamivir (mean IC50 increase, 3-fold) than WT virus. 2010 PLoS pathogens Result IV H274Y 4 9 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. the peak nasal inflammatory cell counts in nasal washes was significantly higher in groups of ferrets inoculated with V116A and K150N recombinants than in those inoculated with WT virus (P<0.01). 2010 PLoS pathogens Result IV V116A;K150N 118;128 123;133 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. The recombinant wild-type (WT) H5N1 influenza virus and seven mutants (V116A, I117V, E119A, K150N, Y252H, H274Y, and N294S) were successfully rescued. 2010 PLoS pathogens Result IV V116A;I117V;E119A;K150N;Y252H;H274Y;N294S 71;78;85;92;99;106;117 76;83;90;97;104;111;122 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. The recovery of ferrets inoculated with the N294S NA mutant was delayed, and they regained no weight during the observation period. 2010 PLoS pathogens Result IV N294S 44 49 50 52 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. The susceptibility of V116A, I117V, and N294S viruses to oseltamivir carboxylate or zanamivir was moderately reduced (mean IC50 increase, 5-63-fold and 3-33-fold, respectively) as compared to that of WT virus. 2010 PLoS pathogens Result IV V116A;I117V;N294S 22;29;40 27;34;45 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. Thus, in two independent experiments, the infection of ferrets with viruses carrying E119A or N294S NA mutations consistently caused more severe influenza disease than WT virus. 2010 PLoS pathogens Result IV E119A;N294S 85;94 90;99 100 102 Influenza 138 162 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. To characterize in more details the disease caused by recombinant E119A and N294S viruses, we increased the number of animals from three to five in each of the pathogenicity groups and repeated inoculation of ferrets with 106 EID50 of the WT, E119A, and N294S viruses (Figure S1). 2010 PLoS pathogens Result IV E119A;N294S;E119A;N294S 66;76;243;254 71;81;248;259 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. To identify characteristics that may explain the severity of infection caused by E119A and N294S H5N1 mutants compared to WT stain, we evaluated virus replication and tissue tropism in the lungs, nasal turbinate, trachea, spleen, liver, and small intestine of two inoculated ferrets per virus on day 4 p.i. 2010 PLoS pathogens Result IV E119A;N294S 81;91 86;96 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. Two NA mutations (H274Y and N294S) were selected based on case reports on the isolation of oseltamivir-resistant variants in H5N1 virus infected patients after treatment with oseltamivir or before administration of the drug. 2010 PLoS pathogens Result IV H274Y;N294S 18;28 23;33 4 6 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. Virus carrying the E119A mutation was moderately more resistant to oseltamivir carboxylate (35-fold increase in mean IC50 value) and markedly more resistant to zanamivir (>1200-fold increase in mean IC50 value) than was WT virus (Table 2). 2010 PLoS pathogens Result IV E119A 19 24 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. virus titers in nasal washes were significantly lower for animals infected with recombinant V116A and K150N viruses than those in animals inoculated with WT virus (P<0.05), but remained significantly higher on day 6 p.i. 2010 PLoS pathogens Result IV V116A;K150N 92;102 97;107 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. Virus with the H274Y NA mutation exhibited virulence comparable to that of recombinant WT virus (Table 3, Figure 3C). 2010 PLoS pathogens Result IV H274Y 15 20 21 23 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. Viruses with the R111K, I222L, S247N, and D283N NA amino acid substitutions could not be rescued in three independent experiments, clearly indicating that these mutations are not stably maintained in the clade 2.2 A/Turkey/15/06-virus background. 2010 PLoS pathogens Result IV R111K;I222L;S247N;D283N 17;24;31;42 22;29;36;47 48 50 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. We further histologically examined the tissues of inoculated ferrets to investigate the lesions associated with virus replication in infected organs and to obtain more information about the differences in virulence between recombinant WT, E119A, and N294S viruses. 2010 PLoS pathogens Result IV E119A;N294S 239;250 244;255 20591072 Increasing antiviral activity of surfactant protein d trimers by introducing residues from bovine serum collectins: dissociation of mannan-binding and antiviral activity. All of the serum collectins have a hydrophobic residue at position 343 (SP-D numbering), and we have previously shown that hSP-D-NCRDs with an R343V or R343I substitution have increased mannan binding activity and greatly increased antiviral activity. 2010 Scandinavian journal of immunology Result IV R343V;R343I 143;152 148;157 20591072 Increasing antiviral activity of surfactant protein d trimers by introducing residues from bovine serum collectins: dissociation of mannan-binding and antiviral activity. As in the case of mAb 246-02, the binding of 3C3-C-20 was greatly diminished by the RAK insertion and restored to baseline by the combined RAK+R343V mutations (Table 2). 2010 Scandinavian journal of immunology Result IV R343V 143 148 20591072 Increasing antiviral activity of surfactant protein d trimers by introducing residues from bovine serum collectins: dissociation of mannan-binding and antiviral activity. Figure 4A compares viral binding by R343V and RAK+R343V. 2010 Scandinavian journal of immunology Result IV R343V;R343V 36;50 41;55 20591072 Increasing antiviral activity of surfactant protein d trimers by introducing residues from bovine serum collectins: dissociation of mannan-binding and antiviral activity. Of interest, the combined mutant RAK+R343V had restored binding to 246-02. 2010 Scandinavian journal of immunology Result IV R343V 37 42 20591072 Increasing antiviral activity of surfactant protein d trimers by introducing residues from bovine serum collectins: dissociation of mannan-binding and antiviral activity. Similar results were obtained in comparing the RAK+R343I combined mutant to R343I (table 3 and figure 4C). 2010 Scandinavian journal of immunology Result IV R343I;R343I 51;76 56;81 20591072 Increasing antiviral activity of surfactant protein d trimers by introducing residues from bovine serum collectins: dissociation of mannan-binding and antiviral activity. The combined mutant RAK+R343V had less HA inhibitory (Table 3) and neutralizing activity (figure 4B) than R343V. 2010 Scandinavian journal of immunology Result IV R343V;R343V 24;106 29;111 HA 39 41 20591072 Increasing antiviral activity of surfactant protein d trimers by introducing residues from bovine serum collectins: dissociation of mannan-binding and antiviral activity. The RAK insertion strongly diminished binding of this mAb, whereas binding was not affected by the R343V substitution. 2010 Scandinavian journal of immunology Result IV R343V 99 104 20591072 Increasing antiviral activity of surfactant protein d trimers by introducing residues from bovine serum collectins: dissociation of mannan-binding and antiviral activity. The RAK+R343I and RAK+R343V double mutants had greatly increased mannan binding activity compared to R343I (or R343V), RAK or hSP-D-NCRD (figure 3). 2010 Scandinavian journal of immunology Result IV R343I;R343V;R343I;R343V 8;22;101;111 13;27;106;116 20591072 Increasing antiviral activity of surfactant protein d trimers by introducing residues from bovine serum collectins: dissociation of mannan-binding and antiviral activity. The RAK+R343I, RAK+R343V, R343I, R343V and RAK mutants all retained full binding to mAbs 246-08, 246-04 and 6B2 (Table 2), indicating that these mAbs probably bind to areas of the CRD distant from the lectin site. 2010 Scandinavian journal of immunology Result IV R343I;R343V;R343I;R343V 8;19;26;33 13;24;31;38 20591072 Increasing antiviral activity of surfactant protein d trimers by introducing residues from bovine serum collectins: dissociation of mannan-binding and antiviral activity. We, therefore, prepared double mutants containing both the RAK insertion and hydrophobic substitutions R343I or R343V to see if additive increases in antiviral activity could be achieved. 2010 Scandinavian journal of immunology Result IV R343I;R343V 103;112 108;117 20655872 Drug sensitivity, drug-resistant mutations, and structures of three conductance domains of viral porins. 6 shows that the PISEMA spectra of 5 15N-labeled leucine residues in the M2 TM domain do not change significantly in the presence (red) or absence (black) of amantadine for the S31N, V27A, and A30T mutants. 2011 Biochimica et biophysica acta Result IV S31N;V27A;A30T 177;183;193 181;187;197 M2 73 75 20655872 Drug sensitivity, drug-resistant mutations, and structures of three conductance domains of viral porins. For V27S a different result is observed, in which amantadine clearly binds to the tetramer and furthermore the amide resonance frequencies for the bound state are very similar to those of the wild type. 2011 Biochimica et biophysica acta Result IV V27S 4 8 20655872 Drug sensitivity, drug-resistant mutations, and structures of three conductance domains of viral porins. In order to further investigate the binding site of amantadine in M2 channels, we prepared mutants of the AM2 TM domain corresponding to the naturally occurring drug-resistant mutations, V27S, V27A, A30T, and S31N. 2011 Biochimica et biophysica acta Result IV V27S;V27A;A30T;S31N 187;193;199;209 191;197;203;213 M2 66 68 20655872 Drug sensitivity, drug-resistant mutations, and structures of three conductance domains of viral porins. Now we see that V27S binds amantadine while V27A does not. 2011 Biochimica et biophysica acta Result IV V27S;V27A 16;44 20;48 20655872 Drug sensitivity, drug-resistant mutations, and structures of three conductance domains of viral porins. So far the V27S mutation has been assayed for drug sensitive proton conductance using the full-length protein while drug binding (shown here) has been assessed using the TM domain, so there is the possibility that the full-length protein does not bind amantadine and therefore, the possibility exists that for this mutant the TM domain maybe a poor model for the full-length protein with regard to drug binding. 2011 Biochimica et biophysica acta Result IV V27S 11 15 20655872 Drug sensitivity, drug-resistant mutations, and structures of three conductance domains of viral porins. Some of the naturally occurring amantadine-resistant mutants may function to impede drug binding by reducing the size of the cavity, such as S31N and A30T. 2011 Biochimica et biophysica acta Result IV S31N;A30T 141;150 145;154 20655872 Drug sensitivity, drug-resistant mutations, and structures of three conductance domains of viral porins. suggesting that the backbone structural changes induced by the V27S mutations are minimal, both in the presence and absence of amantadine. 2011 Biochimica et biophysica acta Result IV V27S 63 67 20661429 Oseltamivir-resistant pandemic A/H1N1 virus is as virulent as its wild-type counterpart in mice and ferrets. 233.9+-0.5787 for the WT and 233.2+-0.8669 for the H274Y mutant (P = 0.5156). 2010 PLoS pathogens Result IV H274Y 51 56 20661429 Oseltamivir-resistant pandemic A/H1N1 virus is as virulent as its wild-type counterpart in mice and ferrets. A limited transmission study was conducted in ferrets and it demonstrated that the H274Y mutant strain was transmitted from ferrets experimentally infected intranasally to ferrets placed in the same cage 24 h after infection. 2010 PLoS pathogens Result IV H274Y 83 88 20661429 Oseltamivir-resistant pandemic A/H1N1 virus is as virulent as its wild-type counterpart in mice and ferrets. A pH1N1 H274Y recombinant mutant virus generated from an unrelated pH1N1 strain also exhibited high levels of resistance to oseltamivir and peramivir but remained susceptible to zanamivir and A-315675 (Table 1). 2010 PLoS pathogens Result IV H274Y 8 13 20661429 Oseltamivir-resistant pandemic A/H1N1 virus is as virulent as its wild-type counterpart in mice and ferrets. All cytokines/chemokines were equally expressed following infection with either of the two pH1N1 isolates (Figure S2), with the exception of increased expression of IL-6 and KC levels on day 1, following infection with the H274Y mutant virus (Figure 4). 2010 PLoS pathogens Result IV H274Y 223 228 20661429 Oseltamivir-resistant pandemic A/H1N1 virus is as virulent as its wild-type counterpart in mice and ferrets. Also, the mean percentage of body weight loss over time was not significantly different in animals infected with the WT or the H274Y mutant virus (Figure S4). 2010 PLoS pathogens Result IV H274Y 127 132 20661429 Oseltamivir-resistant pandemic A/H1N1 virus is as virulent as its wild-type counterpart in mice and ferrets. As shown in Table 1, the pH1N1 isolate from the index case collected before oseltamivir therapy (A/Quebec/147023/2009-WT) was susceptible to all NAIs whereas the pH1N1 isolate from the contact case recovered during post-exposure oseltamivir prophylaxis (A/Quebec/147365/2009-H274Y) was resistant to oseltamivir and peramivir. 2010 PLoS pathogens Result IV H274Y 275 280 NAI 145 149 20661429 Oseltamivir-resistant pandemic A/H1N1 virus is as virulent as its wild-type counterpart in mice and ferrets. However, some cytokines (IL-6, IL-12 and IFN-gamma) were specifically upregulated in lymph nodes of ferrets infected with the H274Y mutant. 2010 PLoS pathogens Result IV H274Y 126 131 20661429 Oseltamivir-resistant pandemic A/H1N1 virus is as virulent as its wild-type counterpart in mice and ferrets. In the second experiment, more weight loss was induced after infection with the H274Y mutant from days 3 to 8. 2010 PLoS pathogens Result IV H274Y 80 85 20661429 Oseltamivir-resistant pandemic A/H1N1 virus is as virulent as its wild-type counterpart in mice and ferrets. Increased levels of IL-6, IL-12 and IFN-gamma mRNA were observed in retropharyngeal lymph nodes of ferrets infected with the H274Y mutant compared to the WT on day 14 with ratios of 1.174, 1.38 and 1.183, respectively (not shown). 2010 PLoS pathogens Result IV H274Y 125 130 20661429 Oseltamivir-resistant pandemic A/H1N1 virus is as virulent as its wild-type counterpart in mice and ferrets. Intranasal inoculation of ferrets with the WT and H274Y mutant pH1N1 isolates resulted in a strong anti-A/California/07/2009 serum antibody response on day 14 (hemagglutination inhibition reciprocal geometric mean titers went from <20 to 4208 and from <20 to 3135, respectively). 2010 PLoS pathogens Result IV H274Y 50 55 20661429 Oseltamivir-resistant pandemic A/H1N1 virus is as virulent as its wild-type counterpart in mice and ferrets. Lung viral titers, which were determined on days 1, 3, 6 and 9 post-infection, did not significantly differ between the WT and H274Y mutant viruses when assessed by quantitative viral culture (Figure 3) and real-time RT-PCR (Figure S1). 2010 PLoS pathogens Result IV H274Y 127 132 20661429 Oseltamivir-resistant pandemic A/H1N1 virus is as virulent as its wild-type counterpart in mice and ferrets. Sequence analysis of the original clinical isolates revealed the presence of only one substitution (H274Y; N2 numbering) in the NA gene of the contact case (GenBank accession number FN434454) compared to that of the index case (accession number FN434445). 2010 PLoS pathogens Result IV H274Y 100 105 128 130 20661429 Oseltamivir-resistant pandemic A/H1N1 virus is as virulent as its wild-type counterpart in mice and ferrets. The maximum weight loss (day 7 and day 3) was 7.54% and 4.15% for the WT and H274Y mutant viruses, respectively (P = 0.0515). 2010 PLoS pathogens Result IV H274Y 77 82 20661429 Oseltamivir-resistant pandemic A/H1N1 virus is as virulent as its wild-type counterpart in mice and ferrets. The pattern of NAI resistance of the pH1N1 H274Y mutant was similar to that of another H274Y mutant from a seasonal A/H1N1 strain (A/Brisbane/59/2007-H274Y). 2010 PLoS pathogens Result IV H274Y;H274Y;H274Y 43;87;150 48;92;155 NAI 15 18 20661429 Oseltamivir-resistant pandemic A/H1N1 virus is as virulent as its wild-type counterpart in mice and ferrets. The two pH1N1 isolates produced lower viral titers than seasonal A/H1N1 viruses (A/Brisbane/59/2007) including both a WT and a H274Y mutant at 36 and 48 h. 2010 PLoS pathogens Result IV H274Y 127 132 20661429 Oseltamivir-resistant pandemic A/H1N1 virus is as virulent as its wild-type counterpart in mice and ferrets. There was significantly more perivascular (day 6) and pleural (days 6 and 12) inflammation visualized in the lungs of mice infected with the H274Y mutant compared to the WT virus (Figure 5). 2010 PLoS pathogens Result IV H274Y 141 146 20661429 Oseltamivir-resistant pandemic A/H1N1 virus is as virulent as its wild-type counterpart in mice and ferrets. Thus, the H274Y mutation resulted in either no impairment or only initial reduction in replicative capacities when inserted in seasonal and pandemic A/H1N1 backgrounds, respectively. 2010 PLoS pathogens Result IV H274Y 10 15 20667110 Isolation of mixed subtypes of influenza A virus from a bald eagle (Haliaeetus leucocephalus). One virulence-associated polymorphism in PB1-F2 (N66S) was present in the H1N1 virus (CY043317). 2010 Virology journal Result IV N66S 49 53 PB1F2 41 47 20686654 Oseltamivir-resistant pandemic H1N1/2009 influenza virus possesses lower transmissibility and fitness in ferrets. Comparison of the NA and HA amino acid sequences of A/DM/528/09 virus with sequences of other 24 H275Y mutants and around 2000 wild-type H1N1/2009 viruses available in Gene Bank did not reveal an increased frequency of any specific amino acid mutation(s) shared among the viruses analyzed (data not shown). 2010 PLoS pathogens Result IV H275Y 97 102 HA;NA 25;18 27;20 20686654 Oseltamivir-resistant pandemic H1N1/2009 influenza virus possesses lower transmissibility and fitness in ferrets. In MDCK cells, both pandemic H1N1/2009 viruses formed pinpoint-like (0.3 mm) plaque phenotype (Figure 1A), differing significantly from some seasonal H1N1 viruses, such as A/Brisbane/59/2007 (BR/59/07) virus, which formed large plaques (1.3 mm) (P<0.05) (data not shown); however, the plaque size did not differ between the oseltamivir-sensitive and -resistant viruses (Figure 1A), indicating that the H275Y NA mutation did not alter plaque morphology. 2010 PLoS pathogens Result IV H275Y 402 407 408 410 20686654 Oseltamivir-resistant pandemic H1N1/2009 influenza virus possesses lower transmissibility and fitness in ferrets. or post-contact (p.c.) were sequenced to detect the presence of the H275Y NA mutation. 2010 PLoS pathogens Result IV H275Y 68 73 74 76 20686654 Oseltamivir-resistant pandemic H1N1/2009 influenza virus possesses lower transmissibility and fitness in ferrets. Our study is the first to show reduced but not severely impaired NA enzymatic function in a resistant H1N1/2009 virus with the H275Y mutation. 2010 PLoS pathogens Result IV H275Y 127 132 65 67 20686654 Oseltamivir-resistant pandemic H1N1/2009 influenza virus possesses lower transmissibility and fitness in ferrets. Pairwise sequence analysis of the full viral genomes showed that the A/DM/524/09 and A/DM/528/09 viruses had no amino acid differences other than the H275Y NA mutation and were a highly matched pair. 2010 PLoS pathogens Result IV H275Y 150 155 156 158 20686654 Oseltamivir-resistant pandemic H1N1/2009 influenza virus possesses lower transmissibility and fitness in ferrets. Sequence analysis of the NA genes revealed that A/DM/524/09 virus encoded a conserved H residue at amino acid position 275, whereas A/DM/528/09 virus had an H275Y amino acid mutation caused by a single T-to-C nucleotide substitution at codon 275 (Table 1). 2010 PLoS pathogens Result IV H275Y 157 162 25 27 20686654 Oseltamivir-resistant pandemic H1N1/2009 influenza virus possesses lower transmissibility and fitness in ferrets. The alignment of the NA and HA sequences showed that viruses with H275Y NA substitution have some amino acid differences from certain wild-type viruses (without H275Y NA mutation), but these differences also were observed in other wild-type viruses. 2010 PLoS pathogens Result IV H275Y;H275Y 66;161 71;166 HA;NA;NA;NA 28;21;72;167 30;23;74;169 20686654 Oseltamivir-resistant pandemic H1N1/2009 influenza virus possesses lower transmissibility and fitness in ferrets. The H275Y NA mutation reduced NA affinity for substrate and NA catalytic activity, although the function of NA was not severely impaired. 2010 PLoS pathogens Result IV H275Y 4 9 NA;NA;NA;NA 10;30;60;108 12;32;62;110 20686654 Oseltamivir-resistant pandemic H1N1/2009 influenza virus possesses lower transmissibility and fitness in ferrets. The wild-type A/DM/524/09 virus was susceptible to oseltamivir carboxylate (mean IC50: 5.0 nM), but the A/DM/528/09 carrying the H275Y NA mutation had IC50 values approximately 200 times that of the wild-type virus (Table 1). 2010 PLoS pathogens Result IV H275Y 129 134 135 137 20686654 Oseltamivir-resistant pandemic H1N1/2009 influenza virus possesses lower transmissibility and fitness in ferrets. Therefore, no spontaneous H275Y NA mutation emerged in the wild-type virus and the H275Y mutation remained stable in the mutant after transmission to a new host. 2010 PLoS pathogens Result IV H275Y;H275Y 26;83 31;88 32 34 20686654 Oseltamivir-resistant pandemic H1N1/2009 influenza virus possesses lower transmissibility and fitness in ferrets. These results showed that the H275Y NA mutation conferred resistance to oseltamivir carboxylate but did not alter susceptibility to zanamivir. 2010 PLoS pathogens Result IV H275Y 30 35 36 38 20686654 Oseltamivir-resistant pandemic H1N1/2009 influenza virus possesses lower transmissibility and fitness in ferrets. These results showed that the oseltamivir-resistant H275Y mutant A/DM/528/09 virus was transmitted efficiently only by direct contact. 2010 PLoS pathogens Result IV H275Y 52 57 20686654 Oseltamivir-resistant pandemic H1N1/2009 influenza virus possesses lower transmissibility and fitness in ferrets. To determine whether the H275Y NA mutation affects virus growth in vitro, we characterized virus plaque morphology and growth kinetics in both MDCK and MDCK-SIAT1 cells. 2010 PLoS pathogens Result IV H275Y 25 30 31 33 20686654 Oseltamivir-resistant pandemic H1N1/2009 influenza virus possesses lower transmissibility and fitness in ferrets. To further evaluate the impact of the H275Y NA mutation on virus growth in vitro, we performed single- and multiple-cycle growth studies of both viruses in MDCK and MDCK-SIAT1 cells. 2010 PLoS pathogens Result IV H275Y 38 43 44 46 20686654 Oseltamivir-resistant pandemic H1N1/2009 influenza virus possesses lower transmissibility and fitness in ferrets. To understand the impact of the H275Y mutation on the NA enzymatic properties of the H1N1/2009 viruses, we determined the NA enzyme kinetics of both viruses. 2010 PLoS pathogens Result IV H275Y 32 37 NA;NA 54;122 56;124 20689744 The PB2-E627K mutation attenuates viruses containing the 2009 H1N1 influenza pandemic polymerase. A 1918RNP virus in which PB2 residue 627 was "back-adapted" to the avian glutamic acid (1918RNP-K627E) consistently grew to a 1- to 2-log-lower peak titer (P = 0.042) than the 1918RNP virus. 2010 mBio Result IV K627E 96 101 PB2 25 28 20689744 The PB2-E627K mutation attenuates viruses containing the 2009 H1N1 influenza pandemic polymerase. Again, to our surprise, introduction of the mammalian-adaptive PB2-E627K or -D701N mutation into the pandemic RNP significantly attenuated viral replication in mouse lung. 2010 mBio Result IV E627K;D701N 67;77 72;82 PB2;RNP 63;110 66;113 20689744 The PB2-E627K mutation attenuates viruses containing the 2009 H1N1 influenza pandemic polymerase. CA09RNP-E627K and CA09RNP-D701N reached approximately 2- and 1-log-lower peak titers than the wild-type CA09RNP virus, respectively (1.1 x 103 and 1.24 x 104 PFU/g versus 2.21 x 105 PFU/g; P = 0.042 and 0.049). 2010 mBio Result IV E627K;D701N 8;26 13;31 20689744 The PB2-E627K mutation attenuates viruses containing the 2009 H1N1 influenza pandemic polymerase. Compared to wild-type CA09RNP, CA09RNP-E627K and CA09RNP-D701N induced similarly mild weight losses. 2010 mBio Result IV E627K;D701N 39;57 44;62 20689744 The PB2-E627K mutation attenuates viruses containing the 2009 H1N1 influenza pandemic polymerase. Compared to wild-type S09RNP, the S09RNP-E627K virus replicated to approximately 1.5-log-greater titers on day 3 (9.9 x 105 versus 5.2 x 104 PFU/g; P = 0.025) and 3-log-greater titers on day 5 (2.27 x 105 versus 1.4 x 102 PFU/g; P = 0.023). 2010 mBio Result IV E627K 41 46 20689744 The PB2-E627K mutation attenuates viruses containing the 2009 H1N1 influenza pandemic polymerase. Conversely, 1918RNP-K627E virus replication in mouse lung on day 3 was attenuated by more than 1 log compared to the wild-type 1918 RNP-containing virus (7.73 x 105 versus 4.41 x 104 PFU/g; P = 0.019). 2010 mBio Result IV K627E 20 25 RNP 132 135 20689744 The PB2-E627K mutation attenuates viruses containing the 2009 H1N1 influenza pandemic polymerase. Conversely, mutation of PB2 residue 627 in the avian RNP S09RNP virus to the mammalian consensus residue (S09RNP-E627K) had little effect on growth in A549 cells. 2010 mBio Result IV E627K 113 118 PB2;RNP 24;53 27;56 20689744 The PB2-E627K mutation attenuates viruses containing the 2009 H1N1 influenza pandemic polymerase. Introducing the avian-like PB2-K627E change into the 1918RNP virus rendered the weight loss curve similar to that observed for rNY312. 2010 mBio Result IV K627E 31 36 PB2 27 30 20689744 The PB2-E627K mutation attenuates viruses containing the 2009 H1N1 influenza pandemic polymerase. Introduction of the PB2-E627K change into the low-pathogenicity avian S09RNP virus also altered histopathology. 2010 mBio Result IV E627K 24 29 PB2 20 23 20689744 The PB2-E627K mutation attenuates viruses containing the 2009 H1N1 influenza pandemic polymerase. Next, the impact of the PB2-E627K (CA09RNP-E627K) and D701N (CA09RNP-D701N) mutations on viruses containing the 2009 pandemic RNP was assessed. 2010 mBio Result IV E627K;E627K;D701N;D701N 28;43;54;69 33;48;59;74 PB2;RNP 24;126 27;129 20689744 The PB2-E627K mutation attenuates viruses containing the 2009 H1N1 influenza pandemic polymerase. The 1918RNP-K627E virus, for example, induced almost no inflammatory changes, resembling the findings seen with rNY312. 2010 mBio Result IV K627E 12 17 20689744 The PB2-E627K mutation attenuates viruses containing the 2009 H1N1 influenza pandemic polymerase. The introduction of either PB2-E627K or -D701N diminished these findings, resulting in a histopathological picture that was predominantly within normal limits, displaying only rare, focal inflammation. 2010 mBio Result IV E627K;D701N 31;41 36;46 PB2 27 30 20689744 The PB2-E627K mutation attenuates viruses containing the 2009 H1N1 influenza pandemic polymerase. To assess the impact of the PB2-E627K change on an RNP of nonmammalian-adapted, avian origin, we generated a virus with the appropriate segments from the low-pathogenicity avian virus A/green-winged teal/Ohio/175/1986 (H2N1) on the NY312 background, termed S09RNP. 2010 mBio Result IV E627K 32 37 PB2;RNP 28;51 31;54 20689744 The PB2-E627K mutation attenuates viruses containing the 2009 H1N1 influenza pandemic polymerase. Whereas the wild-type S09RNP virus gave rise to a focal alveolitis with viral antigen in alveolar epithelial cells, the S09RNP-E627K virus instead induced a mild bronchiolitis with increased levels of bronchiolar antigen staining and no alveolitis. 2010 mBio Result IV E627K 127 132 Bronchiolitis 162 175 20689744 The PB2-E627K mutation attenuates viruses containing the 2009 H1N1 influenza pandemic polymerase. while the introduction of the human-like PB2-E627K change into the S09RNP virus increased weight loss somewhat, albeit not significantly (4.93% versus 8.06%; P = 0.10). 2010 mBio Result IV E627K 45 50 PB2 41 44 20738882 Clinical importance and impact on the households of oseltamivir-resistant seasonal A/H1N1 influenza virus in healthy children in Italy. A resistance of A/H1N1 influenza viruses to oseltamivir (mainly due to the H275Y mutation) has recently emerged in a number of countries. 2010 Virology journal Result IV H275Y 75 80 20738882 Clinical importance and impact on the households of oseltamivir-resistant seasonal A/H1N1 influenza virus in healthy children in Italy. Among the A/H1N1 subtypes, the H275Y mutation was found in 2/126 samples (1.6%) in 2007-2008 and in all 17 samples (100%; p < 0.0001) in 2008-2009. 2010 Virology journal Result IV H275Y 31 36 20738882 Clinical importance and impact on the households of oseltamivir-resistant seasonal A/H1N1 influenza virus in healthy children in Italy. demonstrated the presence of a second mutation, the T284A substitution. 2010 Virology journal Result IV T284A 52 57 20738882 Clinical importance and impact on the households of oseltamivir-resistant seasonal A/H1N1 influenza virus in healthy children in Italy. Furthermore, it has been reported that a number of different mutations conferring various degrees of resistance, such as H126N G248R, S247N or S247G, can be found among resistant A/H1N1 influenza strains, and that the presence of the D344N substitution in neuraminidase is associated with an increase in enzyme activity. 2010 Virology journal Result IV H126N;G248R;S247N;S247G;D344N 121;127;134;143;234 126;132;139;148;239 256 269 20738882 Clinical importance and impact on the households of oseltamivir-resistant seasonal A/H1N1 influenza virus in healthy children in Italy. However, the presence of the H275Y mutation did not seem to modify the pathogenicity of A/H1N1 influenza virus in our otherwise healthy children because all the variables evaluated for the clinical importance and impact on the households of the infections due to mutated or wild-type viruses were comparable. 2010 Virology journal Result IV H275Y 29 34 20738882 Clinical importance and impact on the households of oseltamivir-resistant seasonal A/H1N1 influenza virus in healthy children in Italy. In conclusion, despite its frequency, A/H1N1 influenza virus with a single H275Y mutation is of marginal clinical importance and impact on the households in otherwise healthy children, but further studies are needed to clarify its role in children with severe influenza, as well as the relationships between different mutations and complicated clinical pictures. 2010 Virology journal Result IV H275Y 75 80 Influenza 253 269 20738882 Clinical importance and impact on the households of oseltamivir-resistant seasonal A/H1N1 influenza virus in healthy children in Italy. It is also possible that, in cases with a negative evolution, the H275Y mutation may be associated with one or more other genetic mutations. 2010 Virology journal Result IV H275Y 66 71 20738882 Clinical importance and impact on the households of oseltamivir-resistant seasonal A/H1N1 influenza virus in healthy children in Italy. Table 1 shows the demographic and clinical characteristics of the children with A/H1N1 influenza infection, by the presence or absence of the H275Y mutation, and the impact on the households of the infection on their households No statistically significant differences were found in terms of gender, age, viral load, diagnosis at enrolment, clinical outcome, pharmacological treatment or impact on the households between the children with oseltamivir-resistant seasonal A/H1N1 influenza virus and those with the wild-type. 2010 Virology journal Result IV H275Y 142 147 Influenza A virus H1N1 infection 87 106 20738882 Clinical importance and impact on the households of oseltamivir-resistant seasonal A/H1N1 influenza virus in healthy children in Italy. The A influenza virus-positive samples underwent neuraminidase gene analysis using pyrosequencing to identify mutations H275Y and N294 S in A/H1N1, and E119V, R292K, and N294 S in A/H3N2. 2010 Virology journal Result IV H275Y;N294S;E119V;R292K;N294S 120;130;152;159;170 125;136;157;164;176 49 62 20738882 Clinical importance and impact on the households of oseltamivir-resistant seasonal A/H1N1 influenza virus in healthy children in Italy. The findings of this study show that the spread of H275Y-mutated A/H1N1 seasonal influenza virus is a common phenomenon that may be unrelated to the previous use of antivirals, and that the clinical importance and impact on the households of the mutated virus is similar to that of the wild-type in an otherwise healthy pediatric population. 2010 Virology journal Result IV H275Y 51 56 20738882 Clinical importance and impact on the households of oseltamivir-resistant seasonal A/H1N1 influenza virus in healthy children in Italy. We found only the H275Y mutation in our children who developed mild or moderate influenza, whereas complete sequencing of the neuraminidase gene in adult and elderly patients with severe disease by Goosken et al. 2010 Virology journal Result IV H275Y 18 23 126 139 20833142 Solution NMR structure of the V27A drug resistant mutant of influenza A M2 channel. A comparison of the pores of the WT, V27A, and S31N structures (Figure 3) show that the overall architectures of the pores are similar among the three variants except for local changes around the mutated residues. 2010 Biochemical and biophysical research communications Result IV V27A;S31N 37;47 41;51 20833142 Solution NMR structure of the V27A drug resistant mutant of influenza A M2 channel. An obvious difference in the V27A structure is that the channel entrance is much wider than in WT. 2010 Biochemical and biophysical research communications Result IV V27A 29 33 20833142 Solution NMR structure of the V27A drug resistant mutant of influenza A M2 channel. Another interesting detail revealed by the V27A structure is the position of the Ser50 sidechain. 2010 Biochemical and biophysical research communications Result IV V27A 43 47 20833142 Solution NMR structure of the V27A drug resistant mutant of influenza A M2 channel. As in the closed channel of WT18-60, the TM helices of V27A form a four-helix bundle with a left-handed twist similar to WT. 2010 Biochemical and biophysical research communications Result IV V27A 55 59 20833142 Solution NMR structure of the V27A drug resistant mutant of influenza A M2 channel. Compared to WT, the structure ensemble of V27A shows much better defined arrangement of the AP helices relative to the pore domain (Figure 2B&D). 2010 Biochemical and biophysical research communications Result IV V27A 42 46 20833142 Solution NMR structure of the V27A drug resistant mutant of influenza A M2 channel. In addition to water near Ser31, water crosspeaks are also present near the Trp41 indol amine in WT, the S31N, and the V27A mutants. 2010 Biochemical and biophysical research communications Result IV S31N;V27A 105;119 109;123 20833142 Solution NMR structure of the V27A drug resistant mutant of influenza A M2 channel. In order to directly compare the structure of the V27A mutant with that of the WT and the S31N mutant, we examined the V27A18-60 construct under the same conditions as those used in the NMR studies of WT18-60 and S31N18-60. 2010 Biochemical and biophysical research communications Result IV V27A;S31N;S31N 50;90;213 54;94;217 20833142 Solution NMR structure of the V27A drug resistant mutant of influenza A M2 channel. In the V27A structure, the sidechain of Ala27 is too small to form strong inter-helical packing, which may be the cause of the weakened tetrameric assembly. 2010 Biochemical and biophysical research communications Result IV V27A 7 11 20833142 Solution NMR structure of the V27A drug resistant mutant of influenza A M2 channel. Indeed, structural and biochemical studies of the S31N mutant showed that replacing Ser31, which is located in the helix-helix interface, with the bulkier asparagine results in substantially weaker helix-helix packing. 2010 Biochemical and biophysical research communications Result IV S31N 50 54 20833142 Solution NMR structure of the V27A drug resistant mutant of influenza A M2 channel. Moreover, as in the case of S31N, we could not detect protein-rimantadine NOEs for the external drug pocket of the V27A mutant, suggesting that again a mutation in the N-terminal TM region can dramatically decrease drug binding to the external pocket through a long-range, allosteric effect. 2010 Biochemical and biophysical research communications Result IV S31N;V27A 28;115 32;119 20833142 Solution NMR structure of the V27A drug resistant mutant of influenza A M2 channel. Since there have been published results that are consistent with either of the two proposed sites of inhibition, the pore-blocking site and the external site for allosteric inhibition, we discuss possible mechanism of drug resistance of the V27A mutant separately for the two different inhibition sites. 2010 Biochemical and biophysical research communications Result IV V27A 241 245 20833142 Solution NMR structure of the V27A drug resistant mutant of influenza A M2 channel. Structure of the V27A drug resistant mutant. 2010 Biochemical and biophysical research communications Result IV V27A 17 21 20833142 Solution NMR structure of the V27A drug resistant mutant of influenza A M2 channel. The higher rate of conductance of V27A suggests reduction in an energy barrier for the proton transport for this mutant. 2010 Biochemical and biophysical research communications Result IV V27A 34 38 20833142 Solution NMR structure of the V27A drug resistant mutant of influenza A M2 channel. The new V27A structure suggests that the protons may exit the channel near Asp44 or Arg45 (Figure 4a&b). 2010 Biochemical and biophysical research communications Result IV V27A 8 12 20833142 Solution NMR structure of the V27A drug resistant mutant of influenza A M2 channel. The same mechanism in principle can be used to explain drug resistance conferred by the V27A mutation. 2010 Biochemical and biophysical research communications Result IV V27A 88 92 20833142 Solution NMR structure of the V27A drug resistant mutant of influenza A M2 channel. The V27A structure shows that replacing Val27 with alanine more than doubles the channel opening (Figure 3), thus it is expected that this mutation will increase proton flux rate by decreasing energy barrier for water molecules to enter. 2010 Biochemical and biophysical research communications Result IV V27A;V27A 4;40 8;58 20833142 Solution NMR structure of the V27A drug resistant mutant of influenza A M2 channel. The V27A structure shows that side chains of Ser50 are pointing along the axial direction of the channel, which would allow, upon palmitoylation, the fatty acid chains to partition naturally into the lipid bilayer of the membrane. 2010 Biochemical and biophysical research communications Result IV V27A 4 8 20833142 Solution NMR structure of the V27A drug resistant mutant of influenza A M2 channel. The weakening of the assembly can be explained by comparing the WT and V27A structures. 2010 Biochemical and biophysical research communications Result IV V27A 71 75 20833142 Solution NMR structure of the V27A drug resistant mutant of influenza A M2 channel. Thus the V27A mutation would be expected to reduce the hydrophobic interactions with the drug. 2010 Biochemical and biophysical research communications Result IV V27A 9 13 20833142 Solution NMR structure of the V27A drug resistant mutant of influenza A M2 channel. Under these conditions the V27A18-60 mutant yields NMR spectrum that is similar to those of WT and S31N, although demonstrates overall better spectral quality (Figure 1A). 2010 Biochemical and biophysical research communications Result IV S31N 99 103 20833142 Solution NMR structure of the V27A drug resistant mutant of influenza A M2 channel. Using a previously established liposomal proton flux assay, we showed that the V27A18-60 peptide reconstituted in liposomes conduct protons ~ 2 times faster than WT at pH ~6 and that addition of 50 muM rimantadine only inhibited conductance by ~1%, compared to near complete inhibition of WT18-60 by 50 muM rimantadine (Supplementary Figure S1). 2010 Biochemical and biophysical research communications Result IV V27A 79 83 20833142 Solution NMR structure of the V27A drug resistant mutant of influenza A M2 channel. We previously proposed a mechanism of inhibition by rimantadine based on the external drug binding site for the S31N mutant. 2010 Biochemical and biophysical research communications Result IV S31N 112 116 20833142 Solution NMR structure of the V27A drug resistant mutant of influenza A M2 channel. We previously showed by dithiobis[succinimidylpropionate] (DSP) crosslinking experiment that the V27A variant forms looser, more dynamic tetramer than WT. 2010 Biochemical and biophysical research communications Result IV V27A 97 101 20833142 Solution NMR structure of the V27A drug resistant mutant of influenza A M2 channel. While the C-terminal region (residues 47- 60) of the V27A structure is more compact due to the newly acquired NOE restraints, the channel pore is overall very similar to that of WT and the S31N mutant. 2010 Biochemical and biophysical research communications Result IV V27A;S31N 53;189 57;193 20836794 Oseltamivir-resistant influenza A 2009 H1N1 virus in immunocompromised patients. A reference laboratory detected the H275Y mutation in the influenza virus isolate from the BAL sample taken on day 9. 2010 Influenza and other respiratory viruses Result IV H275Y 36 41 20836794 Oseltamivir-resistant influenza A 2009 H1N1 virus in immunocompromised patients. Although BAL specimens were culture negative for influenza A virus on days 42 and 43, a sample taken on day 22 and positive for influenza A virus by DFA was sent to the CDC where on day 43, results of molecular testing demonstrated the H275Y resistance mutation. 2010 Influenza and other respiratory viruses Result IV H275Y 236 241 20836794 Oseltamivir-resistant influenza A 2009 H1N1 virus in immunocompromised patients. During our retrospective testing, the H275Y mutation was not present on admission. 2010 Influenza and other respiratory viruses Result IV H275Y 38 43 20836794 Oseltamivir-resistant influenza A 2009 H1N1 virus in immunocompromised patients. Four patients (2 1%) were found to carry the H275Y mutation (Table 1). 2010 Influenza and other respiratory viruses Result IV H275Y 45 50 20836794 Oseltamivir-resistant influenza A 2009 H1N1 virus in immunocompromised patients. Sanger sequencing was unable to detect the H275Y mutant population. 2010 Influenza and other respiratory viruses Result IV H275Y 43 48 20836794 Oseltamivir-resistant influenza A 2009 H1N1 virus in immunocompromised patients. We later demonstrated that the influenza virus present during his second admission also had the H275Y mutation. 2010 Influenza and other respiratory viruses Result IV H275Y 96 101 20920297 Characterization of an H3N2 triple reassortant influenza virus with a mutation at the receptor binding domain (D190A) that occurred upon virus transmission from turkeys to pigs. Hence, we initiated this study to evaluate the effect of Asp190Ala mutation on H3N2 TR virus behavior in vitro utilizing reverse genetics created viruses. 2010 Virology journal Result IV D190A 57 66 20920297 Characterization of an H3N2 triple reassortant influenza virus with a mutation at the receptor binding domain (D190A) that occurred upon virus transmission from turkeys to pigs. In conclusion, the Asp190Ala mutation that occurred upon virus transmission from turkeys to pigs could have been a transient or rare occurring mutation that resulted in a less fitted virus, explaining the rareness of Ala at this position in swine and turkey H3N2 influenza isolates. 2010 Virology journal Result IV D190A 19 28 20920297 Characterization of an H3N2 triple reassortant influenza virus with a mutation at the receptor binding domain (D190A) that occurred upon virus transmission from turkeys to pigs. Interestingly, Glu627Lys mutation in the PB2 gene did not affect virus replication in all three cell types (Figure 2), supporting a recent finding which indicated that Glu627Lys substitution in PB2 gene does not increase virulence nor growth rate of pandemic-H1N1 (2009) virus in mice and cell culture. 2010 Virology journal Result IV E627K;E627K 15;168 24;177 PB2;PB2 41;194 44;197 20920297 Characterization of an H3N2 triple reassortant influenza virus with a mutation at the receptor binding domain (D190A) that occurred upon virus transmission from turkeys to pigs. Next, we evaluated the effect of Asp190Ala mutation on antigenicity of H3N2 TR virus using the conventional cross-HI test (Table 1). 2010 Virology journal Result IV D190A 33 42 20920297 Characterization of an H3N2 triple reassortant influenza virus with a mutation at the receptor binding domain (D190A) that occurred upon virus transmission from turkeys to pigs. Virus with a mutation at residue 627 of the PB2 gene (Glu627Lys) was used as control, where such mutation has been shown to affect replication and host range specificity of influenza viruses. 2010 Virology journal Result IV E627K 54 63 PB2 44 47 20920297 Characterization of an H3N2 triple reassortant influenza virus with a mutation at the receptor binding domain (D190A) that occurred upon virus transmission from turkeys to pigs. We then assessed the effect of Asp190Ala mutation on binding efficiency of the TK04 virus to PMP from primary tracheal cells of human, pig and turkey origin (Figure 3). 2010 Virology journal Result IV D190A 31 40 20970464 Structure-based design of NS2 mutants for attenuated influenza A virus vaccines. An addition mutation in this glutamate cluster (triple mutant; E67S/E74S/E75S) further reduced this activity. 2011 Virus research Result IV E67S;E74S;E75S 63;68;73 67;72;77 20970464 Structure-based design of NS2 mutants for attenuated influenza A virus vaccines. Based on the crystal structure of the C-terminal M1-binding domain of NS2/NEP, we used reverse genetics to generate a W78S mutant as well as a series of glutamate mutants including single (E75S), double (E67S/E74S), or triple (E67S/E74S/E75S) mutations to look for phenotypic changes in virus replication. 2011 Virus research Result IV W78S;E75S;E67S;E74S;E75S;E67S;E74S 118;189;204;209;237;227;232 122;193;208;213;241;231;236 M1;NEP;NS2 49;74;70 51;77;73 20970464 Structure-based design of NS2 mutants for attenuated influenza A virus vaccines. Double (E67S/E74S) mutations at the cluster of NS2/NEP glutamates reduced NS2/NEP the ability to inhibit the polymerase activity. 2011 Virus research Result IV E67S;E74S 8;13 12;17 NEP;NEP;NS2;NS2 51;78;47;74 54;81;50;77 20970464 Structure-based design of NS2 mutants for attenuated influenza A virus vaccines. Of note, due to gene overlapping, the NS2/NEP E67S mutation caused G224V/T225A mutations in NS1 and the NS2/NEP E74S mutation suppressed the stop codon of NS1, resulting in the addition of seven residues (termed the "tail" here, residues 231-237) to the C-terminus of NS1. 2011 Virus research Result IV E67S;G224V;T225A;E74S 46;67;73;112 50;72;78;116 NEP;NEP;NS1;NS1;NS1;NS2;NS2 42;108;92;155;268;38;104 45;111;95;158;271;41;107 21048522 Oseltamivir-resistant influenza A and B viruses pre- and postantiviral therapy in children and young adults with cancer. An E119V substitution in the NA was detected in all three resistant influenza A (H3N2) strains obtained from patients 2, 6 and 7. 2011 The Pediatric infectious disease journal Result IV E119V 3 8 29 31 21048522 Oseltamivir-resistant influenza A and B viruses pre- and postantiviral therapy in children and young adults with cancer. For patient 12, influenza B virus harboring an N294S mutation in the NA was detected before therapy. 2011 The Pediatric infectious disease journal Result IV N294S 47 52 69 71 21048522 Oseltamivir-resistant influenza A and B viruses pre- and postantiviral therapy in children and young adults with cancer. In patient 6, a viral isolate collected on day 7 of therapy revealed a mixed population of wild-type virus and E119V mutant quasi-species. 2011 The Pediatric infectious disease journal Result IV E119V 111 116 21048522 Oseltamivir-resistant influenza A and B viruses pre- and postantiviral therapy in children and young adults with cancer. Susceptibility to adamantanes was tested for all oseltamivir-resistant influenza A (H3N2) viruses by sequence analysis of the M gene; all strains had an S31N mutation in the transmembrane region of the M2 protein and were therefore resistant to these drugs (data not shown). 2011 The Pediatric infectious disease journal Result IV S31N 153 157 M;M2 126;202 127;204 21048522 Oseltamivir-resistant influenza A and B viruses pre- and postantiviral therapy in children and young adults with cancer. The E119V mutant then emerged as the dominant strain in the next isolate collected on day 9 of therapy. 2011 The Pediatric infectious disease journal Result IV E119V 4 9 21116343 Does pandemic A/H1N1 virus have the potential to become more pathogenic? A polymerase basic 2 (PB2) protein D87N mutation was observed in all the clones recovered from the group with an initial predominance of NJ/15. 2010 mBio Result IV D87N 35 39 PB2 22 25 21116343 Does pandemic A/H1N1 virus have the potential to become more pathogenic? At least in the case of G2, it appears that the PB2 D87N mutation may play a role in viral replication and that this mutation functions by increasing polymerase activity. 2010 mBio Result IV D87N 52 56 PB2 48 51 21116343 Does pandemic A/H1N1 virus have the potential to become more pathogenic? Given the preferential binding of human H1N1 viruses to a 6'-SLN receptor, our findings suggest that the HA K154Q mutation is a mammal-associated change that leads to better refinement of receptor-binding properties of currently circulating pandemic A/H1N1 viruses. 2010 mBio Result IV K154Q 108 113 HA 105 107 21116343 Does pandemic A/H1N1 virus have the potential to become more pathogenic? HA K154Q (H1 numbering) and/or polymerase acid (PA) protein L295P mutations were observed in two groups with an initial 50% or 90% proportion of TN/560 (Table 1). 2010 mBio Result IV K154Q;L295P 3;60 8;65 HA;PA 0;48 2;50 21116343 Does pandemic A/H1N1 virus have the potential to become more pathogenic? In contrast, the G1 variant (with the HA K154Q substitution) exhibited an affinity for the 6'-SLN sialic polymer similar to that observed for TN/560 but was unable to bind to 6'-SL, indicating that G1 discriminated both alpha2,6-linked receptors. 2010 mBio Result IV K154Q 41 46 HA 38 40 21116343 Does pandemic A/H1N1 virus have the potential to become more pathogenic? The G1 RNP complex, carrying the PA L295P mutation, showed ~20% more polymerase activity than TN/560 at 37 C (and comparable activities at 33 C and 39 C). 2010 mBio Result IV L295P 36 41 PA;RNP 33;7 35;10 21116343 Does pandemic A/H1N1 virus have the potential to become more pathogenic? The two A/H1N1 strains that represented two major genotypes isolated from coinfected NHBE cells were designated G1 (TN/560-like virus with PA L295P and HA K154Q) and G2 (reassortant NJ/15 HA in a TN/560 backbone with PB2 D87N) and were further analyzed (Table 1). 2010 mBio Result IV L295P;K154Q;D87N 142;155;221 147;160;225 HA;HA;PA;PB2 152;188;139;217 154;190;141;220 21116343 Does pandemic A/H1N1 virus have the potential to become more pathogenic? To test whether the acquired HA K154Q mutation changed the antigenic specificity of the pandemic TN/560 virus, we determined the antigenic properties of all A/H1N1 viruses in a hemagglutination inhibition (HI) test using postinfection ferret antisera and monoclonal antibodies (MAbs) raised against a selection of currently circulating seasonal, pandemic, and swine H1 isolates (see Table S2 in the supplemental material). 2010 mBio Result IV K154Q 32 37 HA 29 31 21172786 Pandemic H1N1 2009 influenza virus with the H275Y oseltamivir resistance neuraminidase mutation shows a small compromise in enzyme activity and viral fitness. Effect of H275Y on the growth kinetics of pH1N1 in vitro. 2011 The Journal of antimicrobial chemotherapy Result IV H275Y 10 15 21172786 Pandemic H1N1 2009 influenza virus with the H275Y oseltamivir resistance neuraminidase mutation shows a small compromise in enzyme activity and viral fitness. Furthermore, the EC50 of oseltamivir for virus containing wild-type NA was between 10 and 100 nM, whereas for the H275Y mutant this value was >10 microM since the virus still formed plaques at this concentration of drug (data not shown). 2011 The Journal of antimicrobial chemotherapy Result IV H275Y 114 119 68 70 21172786 Pandemic H1N1 2009 influenza virus with the H275Y oseltamivir resistance neuraminidase mutation shows a small compromise in enzyme activity and viral fitness. Mutation H275Y in A/England/195/09 NA confers resistance to oseltamivir. 2011 The Journal of antimicrobial chemotherapy Result IV H275Y 9 14 35 37 21172786 Pandemic H1N1 2009 influenza virus with the H275Y oseltamivir resistance neuraminidase mutation shows a small compromise in enzyme activity and viral fitness. Recombinant virus with the NA mutation H275Y shows decreased red cell elution. 2011 The Journal of antimicrobial chemotherapy Result IV H275Y 39 44 27 29 21172786 Pandemic H1N1 2009 influenza virus with the H275Y oseltamivir resistance neuraminidase mutation shows a small compromise in enzyme activity and viral fitness. The ability of the wild-type pH1N1 to elute virus from red blood cells was 4-fold greater than that of the H275Y isogenic mutant (Table 1). 2011 The Journal of antimicrobial chemotherapy Result IV H275Y 107 112 21172786 Pandemic H1N1 2009 influenza virus with the H275Y oseltamivir resistance neuraminidase mutation shows a small compromise in enzyme activity and viral fitness. The N1 NA of pH1N1 that carried the H275Y mutation showed an ~300-fold increase in oseltamivir IC50 values (Table 1), but the mutation did not confer resistance to zanamivir. 2011 The Journal of antimicrobial chemotherapy Result IV H275Y 36 41 7 9 21172786 Pandemic H1N1 2009 influenza virus with the H275Y oseltamivir resistance neuraminidase mutation shows a small compromise in enzyme activity and viral fitness. The two viruses were used to co-infect triplicate wells of either MDCK or HAE cells at defined ratios and after 72 h released virus was analysed for the presence of H275Y mutation. 2011 The Journal of antimicrobial chemotherapy Result IV H275Y 165 170 21226922 Influenza A virus NS1 gene mutations F103L and M106I increase replication and virulence. 12 and 24 hpi), whereas at later time points (48 and 72 hpi) there was a trend to increased yield for the NS1 mutants where the rPR8-HK-NS-M106I and rPR8-HK-NS-F103L + M106I mutants demonstrate statistically significant enhanced growth compared to rPR8-HK-NS-wt at 48 hpi (P < 0.05) (Figure 1b). 2011 Virology journal Result IV M106I;F103L;M106I 139;160;168 144;165;173 NS;NS;NS;NS1 136;157;256;106 138;159;258;109 21226922 Influenza A virus NS1 gene mutations F103L and M106I increase replication and virulence. A single mutation (F103L) introduced to the HK-wt NS gene resulted in 40% mortality in BALB/c, while the infection with the viruses possessing M106I and F103L + M106I mutations resulted in a 20% mortality rate by 4 and 7 dpi respectively. 2011 Virology journal Result IV F103L;M106I;F103L;M106I 19;143;153;161 24;148;158;166 NS 50 52 21226922 Influenza A virus NS1 gene mutations F103L and M106I increase replication and virulence. All the mutants had a significantly increased ability to grow in MDCK cells compared to rPR8-HK-NS-wt with the rPR8-HK-NS-M106I and rPR8-HK-NS-F103L + M106I mutants growing to higher titers than the rPR8-HK-NS-F103L mutant (Figure 1a). 2011 Virology journal Result IV M106I;F103L;M106I;F103L 122;143;151;210 127;148;156;215 NS;NS;NS;NS 96;119;140;207 98;121;142;209 21226922 Influenza A virus NS1 gene mutations F103L and M106I increase replication and virulence. As both the F103L and M106I mutations were associated with greater levels of growth than the double mutant at later times following IFN-beta pretreatment, we assessed the amount of IFN-beta production during infection, which could explain the differences in mutant gene functions among these mutants. 2011 Virology journal Result IV F103L;M106I 12;22 17;27 21226922 Influenza A virus NS1 gene mutations F103L and M106I increase replication and virulence. Because the F103L and M106I mutations have been associated with increased IFN-beta induction in reassortants of the A/Hong Kong/156/97(H5N1) NS1 gene on the A/Udorn/1/1972 (H3N2) backbone we measured the IFN-beta induction by the parental HK-wt and the MA20c (F103L) and MA51 (M106I) mutant viruses in mouse M1 cells. 2011 Virology journal Result IV F103L;M106I;F103L;M106I 12;22;260;277 17;27;265;282 M1;NS1 308;141 310;144 21226922 Influenza A virus NS1 gene mutations F103L and M106I increase replication and virulence. Following IFN-beta pretreatment, the rPR8-HK-NS-wt reached a peak of 3 x 103 pfu/ml at 8 hpi and all the viral mutants grew better than the rPR8-HK-NS-wt at this time (P < 0.01 for the single mutants and P < 0.05 for the double mutant) (>7 fold increase by F103L mutant). 2011 Virology journal Result IV F103L 257 262 NS;NS 45;148 47;150 21226922 Influenza A virus NS1 gene mutations F103L and M106I increase replication and virulence. Growth was particularly enhanced at early times (12 and 24 hpi) (P < 0.05) in the three mutant viruses compared to rPR8-HK-NS-wt, where the F103L mutation enhanced yields by 6 and 2 fold respectively; relative to the M106I containing, single and double, mutants that showed 20 and 9, as well as 7 and 5 fold enhanced yields for these respective viruses at 12 and 24 hpi. 2011 Virology journal Result IV F103L;M106I 140;217 145;222 NS 123 125 21226922 Influenza A virus NS1 gene mutations F103L and M106I increase replication and virulence. However, at the 48 hpi time point, only rPR8-HK-NS-M106I, and rPR8-HK-NS-F103L+M106I viruses grew significantly better than rPR8-HK-NS-wt (P < 0.05) and at 72 hpi, the double mutant was the only virus that grew to a significantly higher titer than the rPR8-HK-NS-wt virus (P < 0.05) (Figure 1a). 2011 Virology journal Result IV M106I;F103L;M106I 51;73;79 56;78;84 NS;NS;NS;NS 48;70;132;260 50;72;134;262 21226922 Influenza A virus NS1 gene mutations F103L and M106I increase replication and virulence. In addition, rPR8-HK-NS-F103L and the double mutant rPR8-HK-NS-F103L + M106I demonstrated enhanced viral growth relative to the rPR8-HK-NS-M106I mutant at 5 dpi (Figure 1c). 2011 Virology journal Result IV F103L;F103L;M106I;M106I 24;63;71;139 29;68;76;144 NS;NS;NS 21;60;136 23;62;138 21226922 Influenza A virus NS1 gene mutations F103L and M106I increase replication and virulence. Interestingly, mutating the NS1 sites 103L and 106I to L103F and I106M in either of these NS1 genes resulted in viruses of low and comparable interferon induction indicating a role of other NS1 gene mutations in the regulation of IFN-beta induction by these viruses. 2011 Virology journal Result IV L103F;I106M 55;65 60;70 NS1;NS1;NS1 28;90;190 31;93;193 21226922 Influenza A virus NS1 gene mutations F103L and M106I increase replication and virulence. M106I also enhanced viral protein synthesis at 2 hpi but not at later time points (Figure 3). 2011 Virology journal Result IV M106I 0 5 21226922 Influenza A virus NS1 gene mutations F103L and M106I increase replication and virulence. Sequence analysis of the NS1 genes of 42 mouse-adapted clones identified two groups of variants MA20-B, -C and -D as well as MA-51, -52 and -53 (Table 1) that possessed the F103L and M106I mutations respectively and thus were convergent with highly pathogenic H5N1 IAV isolated from humans in Hong Kong in 1997 (A/Hong Kong/156/97-like viruses). 2011 Virology journal Result IV F103L;M106I 173;183 178;188 NS1 25 28 21226922 Influenza A virus NS1 gene mutations F103L and M106I increase replication and virulence. The ability of the two rWSN viruses (rWSN-Ck/Bj-NS-103L + 106I and rWSN-Ck/Bj-NS-L103F + I106M) to grow in BALB/c mice was also determined by infecting groups of 8 mice intranasally at a lower infection dose of 5 x 103 pfu. 2011 Virology journal Result IV L103F;I106M 81;89 86;94 NS;NS 48;78 50;80 21226922 Influenza A virus NS1 gene mutations F103L and M106I increase replication and virulence. The extent of viral growth was thus inversely correlated with IFN-beta induction where the rPR8-HK-NS-F103L virus grew to the highest yield in M1 cells in the presence and absence of IFN-beta and induced the least amount of IFN-beta, while the double mutant grew the least with and without IFN-beta pre-treatment and induced the highest levels of IFN-beta compared to the rest of the mutants. 2011 Virology journal Result IV F103L 102 107 M1;NS 143;99 145;101 21226922 Influenza A virus NS1 gene mutations F103L and M106I increase replication and virulence. The growth was also more persistent at 7 dpi with >2 logs increased lung titer due to the presence of F103L + M106I mutations (P < 0.05) (Figure 6b). 2011 Virology journal Result IV F103L;M106I 102;110 107;115 21226922 Influenza A virus NS1 gene mutations F103L and M106I increase replication and virulence. The NS1 mutants showed an increased extent of alveolar tissue infection with larger foci in the lungs that was more pronounced in the single mutants rPR8-HK-NS-F103L and rPR8-HK-NS-M106I compared to rPR8-HK-NS-wt (Figure 2b, c, d, e), whereas no bronchiolar infections were observed for any of the mutants. 2011 Virology journal Result IV F103L;M106I 160;181 165;186 NS;NS;NS;NS1 157;178;207;4 159;180;209;7 21226922 Influenza A virus NS1 gene mutations F103L and M106I increase replication and virulence. The presence of the H9N2 NS1 103L + 106I residues increased growth in BALB/c lungs by 100 fold at 1 dpi and >10 fold at 3 and 5 dpi relative to the L103F + I106M mutant that was significantly different by paired t-test (P <= 0.01) (Figure 6b). 2011 Virology journal Result IV L103F;I106M 148;156 153;161 NS1 25 28 21226922 Influenza A virus NS1 gene mutations F103L and M106I increase replication and virulence. The rate of viral protein synthesis was enhanced by the F103L mutation at all time points as demonstrated for the M1 and NS1 bands with the most dramatic increase shown early after infection (at 2 hpi). 2011 Virology journal Result IV F103L 56 61 M1;NS1 114;121 116;124 21226922 Influenza A virus NS1 gene mutations F103L and M106I increase replication and virulence. The rPR8-H5N1-NS-L103F + I106M did not cause any mortality in mice, LD50 of >104.5 (Figure 5a); in addition, the infected mice only lost 4% of their body weight (Figure 5b). 2011 Virology journal Result IV L103F;I106M 17;25 22;30 NS 14 16 21226922 Influenza A virus NS1 gene mutations F103L and M106I increase replication and virulence. The rPR8-HK-NS-wt recombinant also induced low levels of IFN-beta (22 pg/ml) whereas each of the recombinants rPR8-HK-NS-F103L or rPR8-HK-NS-M106I induced 2 and 3 fold more IFN-beta respectively compared to rPR8-HK-NS-wt (40 and 68 pg/ml respectively) while the double mutations together had a cumulative effect on increasing IFN-beta induction to 113 pg/ml (P < 0.001) (Figure 7). 2011 Virology journal Result IV F103L;M106I 121;141 126;146 NS;NS;NS;NS 12;118;138;215 14;120;140;217 21226922 Influenza A virus NS1 gene mutations F103L and M106I increase replication and virulence. Therefore, the NS1 mutations increased viral replication and growth in vitro compared to the rPR8-HK-NS-wt in MDCK and, in the case of rPR8-HK-NS-M106I and rPR8-HK-NS-F103L + M106I mutants, in A549 cells and thus demonstrate their adaptive nature in both human and canine cells. 2011 Virology journal Result IV M106I;F103L;M106I 146;167;175 151;172;180 NS;NS;NS;NS1 101;143;164;15 103;145;166;18 21226922 Influenza A virus NS1 gene mutations F103L and M106I increase replication and virulence. These data indicated that each of the F103L and M106I mutations resulted in more rapid gene expression seen at the level of protein synthesis, but that these mutations in combination were not as effective at enhancing protein synthesis. 2011 Virology journal Result IV F103L;M106I 38;48 43;53 21226922 Influenza A virus NS1 gene mutations F103L and M106I increase replication and virulence. This indicated that both of the mouse adaptive mutations, F103L and M106I, were associated with increased replication in mouse lungs such that they grew faster and to a higher yield as well as persisted longer in the mouse lung compared to rPR8-HK-NS-wt. 2011 Virology journal Result IV F103L;M106I 58;68 63;73 NS 248 250 21226922 Influenza A virus NS1 gene mutations F103L and M106I increase replication and virulence. Thus the Ck/Bj/95 NS1 F103L + M106I mutations conferred both increased replication and virulence in mouse lungs. 2011 Virology journal Result IV F103L;M106I 22;30 27;35 NS1 18 21 21226922 Influenza A virus NS1 gene mutations F103L and M106I increase replication and virulence. Thus, following IFN-beta treatment, the rPR8-HK-NS-F103L and rPR8-HK-NS-M106I mutants had demonstrated enhanced growth throughout infection relative to rPR8-HK-NS-wt, but enhanced growth was only seen at early times for the double mutant. 2011 Virology journal Result IV F103L;M106I 51;72 56;77 NS;NS;NS 48;69;160 50;71;162 21226922 Influenza A virus NS1 gene mutations F103L and M106I increase replication and virulence. To compare the growth kinetics of viruses that differed due to specific change in their NS1 genes, rPR8-HK-NS-wt, rPR8-HK-NS F103L, rPR8-HK-NS-M106I, and rPR8-HK-NS-F103L + M106I were used to infect MDCK and A549 epithelial cells, in triplicate, at a low MOI (0.001) to initiate multicycle replication. 2011 Virology journal Result IV F103L;M106I;F103L;M106I 125;143;165;173 130;148;170;178 NS;NS;NS;NS;NS1 107;122;140;162;88 109;124;142;164;91 21226922 Influenza A virus NS1 gene mutations F103L and M106I increase replication and virulence. To test the role of F103L and M106I mutations on growth, we first generated viruses possessing the HK-wt (106F + 106M), or F103L, M106I and F103L + M106I mutations on the A/PR/8/34 backbone. 2011 Virology journal Result IV F103L;M106I;F103L;M106I;F103L;M106I 20;30;123;130;140;148 25;35;128;135;145;153 21226922 Influenza A virus NS1 gene mutations F103L and M106I increase replication and virulence. We also assessed the extent of lung infection using immunofluorescent staining of infected lung sections to show that the presence of L103F and I106M mutations in the Ck/Bj/95 H9N2-NS1 gene on the WSN backbone resulted in lung infection that was restricted to specific foci in the bronchiolar epithelium (Figure 6c). 2011 Virology journal Result IV L103F;I106M 134;144 139;149 NS1 181 184 21226922 Influenza A virus NS1 gene mutations F103L and M106I increase replication and virulence. We then mutated the 103L and 106L sites back to consensus and generated a PR8 recombinant possessing the H5N1-NS-L103F + I106M. 2011 Virology journal Result IV L103F;I106M 113;121 118;126 NS 110 112 21226922 Influenza A virus NS1 gene mutations F103L and M106I increase replication and virulence. We then mutated the Ck/Bj/95 (H9N2) NS gene to possess L103F + I106M to generate the consensus sequence at these sites. 2011 Virology journal Result IV L103F;I106M 55;63 60;68 NS 36 38 21226922 Influenza A virus NS1 gene mutations F103L and M106I increase replication and virulence. When both sites were mutated to L103F + I106M, the virus lost its ability to cause fatal infection at this dose in the mouse, as the virus did not cause any mortality throughout 14 dpi, thus the LD50 was reduced by >10 fold (Figure 6a). 2011 Virology journal Result IV L103F;I106M 32;40 37;45 21226922 Influenza A virus NS1 gene mutations F103L and M106I increase replication and virulence. Without prior IFN-beta treatment, the rPR8-HK-NS-wt reaches a peak of 3.8 x 104 pfu/ml at 24 hpi that was comparable to each of the single mutants at that time, while each of the mutations (103L and 106I) enhanced growth at the earliest (8 hpi) (by > 6 fold and >4 fold for the F103L and M106I mutants respectively) and at the latest time point (48 hpi) compared to rPR8-HK-NS-wt (P < 0.01) (Figure 4a). 2011 Virology journal Result IV F103L;M106I 278;288 283;293 NS;NS 46;374 48;376 21249207 Nationwide molecular surveillance of pandemic H1N1 influenza A virus genomes: Canada, 2009. A sporadic HA variant of note, E374K (residue 391 in HA propeptide), was observed in 8 Canadian viruses from 5 Canadian regions spanning outbreak weeks 17 to 36. 2011 PloS one Result IV E374K 31 36 HA;HA 11;53 13;55 21249207 Nationwide molecular surveillance of pandemic H1N1 influenza A virus genomes: Canada, 2009. All six of the R205K Ca1 variants were clade 6 viruses isolated in southwestern ON during wave 2 (weeks 20, 24, 26, 27 and 29); thus, could have emerged from a regional single point introduction. 2011 PloS one Result IV R205K 15 20 21249207 Nationwide molecular surveillance of pandemic H1N1 influenza A virus genomes: Canada, 2009. Amino acid substitutions were observed in a limited number (9) of the Canadian viruses at characterized hemagglutinin antigenic sites: Ca (7) - R205K in Ca1 (6) and P137S Ca2 (1); S74N in Cb (1); and A186T in Sb (1) (Table S2). 2011 PloS one Result IV R205K;P137S;S74N;A186T 144;165;180;200 149;170;184;205 HA 104 117 21249207 Nationwide molecular surveillance of pandemic H1N1 influenza A virus genomes: Canada, 2009. As noted elsewhere, all NA S286G clade 2 virus variants from 4 regions (BC, MB, NFL, and PQ) co-varied with PB1 K480R. 2011 PloS one Result IV S286G;K480R 27;112 32;117 NA;PB1 24;108 26;111 21249207 Nationwide molecular surveillance of pandemic H1N1 influenza A virus genomes: Canada, 2009. Aside from the co-varying clade 7-marker loci (HA-S203T and NP-V100I), we observed that PB1 N158S co-varied with NA V394I in a regional manner (15/16 of the Alberta NA V394I clade 7 viruses). 2011 PloS one Result IV S203T;V100I;N158S;V394I;V394I 50;63;92;116;168 55;68;97;121;173 HA;NA;NA;NP;PB1 47;113;165;60;88 49;115;167;62;91 21249207 Nationwide molecular surveillance of pandemic H1N1 influenza A virus genomes: Canada, 2009. Characterized by two amino acid substitutions relative to ancestor sequences: PA (M581L) and NP (T373I), clade 2 viruses quickly disseminated worldwide, and nationwide (this study). 2011 PloS one Result IV M581L;T373I 82;97 87;102 NP;PA 93;78 95;80 21249207 Nationwide molecular surveillance of pandemic H1N1 influenza A virus genomes: Canada, 2009. Clade 5, characterized by amino acid changes in the NP (V100I) and NA (V106I and N248D) was only observed twice in Canada (RV1758/09 and RV1954/09) in PQ during outbreak weeks 06 and 08, respectively (Figures 1 and 3; Table S2) with inferred ancestries in the same week 06. 2011 PloS one Result IV V100I;V106I;N248D 56;71;81 61;76;86 NA;NP 67;52 69;54 21249207 Nationwide molecular surveillance of pandemic H1N1 influenza A virus genomes: Canada, 2009. Clade 6, characterized by two non-epitope, unique amino acid substitutions in HA (K-15E [K2E] and Q293H [Q310H]), appeared later in Canada starting in week 06 (RV1765/09 - MB). 2011 PloS one Result IV K2E;Q293H;Q310H 89;98;105 92;103;110 HA 78 80 21249207 Nationwide molecular surveillance of pandemic H1N1 influenza A virus genomes: Canada, 2009. Clade 7 sequences, characterized by fixed amino acid changes in the NP (V100I) and NA (V106I and N248D) that are also found in clades 5 and 6 as well as by unique amino acid changes in mature HA (S203T) and NS1 (I123V), first appeared in Canada in ON (RV1526/09, RV1527/09, and RV1529/09) during global outbreak week 04 (Table S3). 2011 PloS one Result IV V100I;V106I;N248D;S203T;I123V 72;87;97;196;212 77;92;102;201;217 HA;NA;NP;NS1 192;83;68;207 194;85;70;210 21249207 Nationwide molecular surveillance of pandemic H1N1 influenza A virus genomes: Canada, 2009. Few glycosylation variants were noted in the Canadian sampled viruses, and most generated loss of N-glycosylation sequons (N87K; RV1532/09; residue 104 in propeptide) or loss of potential "Cand1" glycosylation sites (N56D; N228D; Y230H in the HA1 globular head, and a mixed site N473N/R in HA2 (RV2810/09; residue 490 in propeptide). 2011 PloS one Result IV N87K;N56D;N228D;Y230H;N473N;N473R 123;217;223;230;279;279 127;221;228;235;286;286 HA;HA1 290;243 292;246 21249207 Nationwide molecular surveillance of pandemic H1N1 influenza A virus genomes: Canada, 2009. Five of the Manitoba NA S286G variants were isolated during outbreak weeks 08, 09, and 11 and were associated with severe disease. 2011 PloS one Result IV S286G 24 29 21 23 21249207 Nationwide molecular surveillance of pandemic H1N1 influenza A virus genomes: Canada, 2009. HA-S203T represents a clade 7-defining variation located near the HA monomer-monomer interface. 2011 PloS one Result IV S203T 3 8 HA;HA 0;66 2;68 21249207 Nationwide molecular surveillance of pandemic H1N1 influenza A virus genomes: Canada, 2009. In addition, HA Q293H (55 Canadawide) co-varied with HA K402T (37 Canadawide) in 36 clade 6 viruses in four regions (AB (1), MB (32), NB (2), and SK (1)). 2011 PloS one Result IV Q293H;K402T 16;56 21;61 HA;HA;NB 13;53;134 15;55;136 21249207 Nationwide molecular surveillance of pandemic H1N1 influenza A virus genomes: Canada, 2009. NA V394I co-varied with PB1 N158S in 15/16 clade 7 viruses from AB. 2011 PloS one Result IV V394I;N158S 3;28 8;33 NA;PB1 0;24 2;27 21249207 Nationwide molecular surveillance of pandemic H1N1 influenza A virus genomes: Canada, 2009. NA V394I was present in 16 clade 7 viruses (AB) and one clade 3 virus (PQ). 2011 PloS one Result IV V394I 3 8 0 2 21249207 Nationwide molecular surveillance of pandemic H1N1 influenza A virus genomes: Canada, 2009. No NA V394I variants were encountered in the severe population (P = 0.041; Table 2). 2011 PloS one Result IV V394I 6 11 3 5 21249207 Nationwide molecular surveillance of pandemic H1N1 influenza A virus genomes: Canada, 2009. Of note, all 16 S286G variants were clade 2 (36% of Canadian clade 2 viruses; n = 45 sampled) isolated during wave 1 in BC (1), MB (11), NFL (3), and PQ (1). 2011 PloS one Result IV S286G 16 21 21249207 Nationwide molecular surveillance of pandemic H1N1 influenza A virus genomes: Canada, 2009. Only six coding substitutions were observed within the HA receptor-binding site (RBS): one A186T variant in the 190-helix (184-191); and 5 residue 222 variants (D222E and D222G) in the 220-loop (mature peptide residues 218-225). 2011 PloS one Result IV A186T;D222E;D222G 91;161;171 96;166;176 HA 55 57 21249207 Nationwide molecular surveillance of pandemic H1N1 influenza A virus genomes: Canada, 2009. Polymorphisms in Canada were numerous that delineated clades 5 through 7, namely NA V106I (49) variants and N248D (48); however, these also appeared early during the global pandemic. 2011 PloS one Result IV V106I;N248D 84;108 89;113 81 83 21249207 Nationwide molecular surveillance of pandemic H1N1 influenza A virus genomes: Canada, 2009. Presence in all Canadian sequences of non-clade 1 mutations (namely HA (P83S [P100S], and I321V [I338V]) and PA (P224S)) agrees with prior reports of limited geographic dissemination of clade 1 isolates. 2011 PloS one Result IV P83S;P100S;I321V;I338V;P224S 72;78;90;97;113 76;83;95;102;118 HA;PA 68;109 70;111 21249207 Nationwide molecular surveillance of pandemic H1N1 influenza A virus genomes: Canada, 2009. Substitutions within these sites were observed in only 2 Canadian A/H1N1pdm viruses, namely NA E119K (RV2984/09 sampled in global outbreak week 29) and N295S (1: RV0005-10/2009 sampled in week 36). 2011 PloS one Result IV E119K;N295S 95;152 100;157 92 94 21249207 Nationwide molecular surveillance of pandemic H1N1 influenza A virus genomes: Canada, 2009. The NA S286G variation was only seen with accompanying co-variation in PB1 (K480R), which is located in the region of PB1 that interacts with virus complementary RNA (cRNA). 2011 PloS one Result IV S286G;K480R 7;76 12;81 NA;PB1;PB1 4;71;118 6;74;121 21249207 Nationwide molecular surveillance of pandemic H1N1 influenza A virus genomes: Canada, 2009. These eight HA E374K viruses were associated with mild infection (1) or cases of unknown severity (7). 2011 PloS one Result IV E374K 15 20 HA 12 14 21249207 Nationwide molecular surveillance of pandemic H1N1 influenza A virus genomes: Canada, 2009. These variants were V83M (1); S95G (4); V106I (49); E119K (1); I163V (1); I188V (1); N189S (1); V264I (1); H275Y (5); S286G (16); E287K (1); N295S (1); T332A (2); S388L (1); V394I (17), and E462G (1) (summarized in Table S2). 2011 PloS one Result IV V83M;S95G;V106I;E119K;I163V;I188V;N189S;V264I;H275Y;S286G;E287K;N295S;T332A;S388L;V394I;E462G 20;30;40;52;63;74;85;96;107;118;130;141;152;163;174;190 24;34;45;57;68;79;90;101;112;123;135;146;157;168;179;195 21249207 Nationwide molecular surveillance of pandemic H1N1 influenza A virus genomes: Canada, 2009. This virus genome revealed confirmed heterozygote bases that caused coding changes, namely, M1 Y240Y/F; M2 T11T/S; NA S35S/T, and PB2 D567D/G (Table S2). 2011 PloS one Result IV T11S;S35T;Y240Y;Y240F;T11T;S35S;D567D;D567G 107;118;95;95;107;118;134;134 113;124;102;102;113;124;141;141 M1;M2;NA;PB2 92;104;115;130 94;106;117;133 21249207 Nationwide molecular surveillance of pandemic H1N1 influenza A virus genomes: Canada, 2009. When analysis of positive selection was conducted, only two viral sites located in HA (namely D222G/E and E374K) displayed evidence of adaptive evolution, corresponding to the HA RBS and HA2-subunit position 47, respectively. 2011 PloS one Result IV D222G;D222E;E374K 94;94;106 101;101;111 HA;HA;HA 83;176;187 85;178;189 21306576 Influenza and other respiratory viruses in three Central American countries. The analyses show that all influenza B (n = 10) samples were sensitive to oseltamivir, and all influenza A/H3N2 (n = 10) samples were resistant to amantadine (mutation S31N) and sensitive to oseltamivir. 2011 Influenza and other respiratory viruses Result IV S31N 168 172 21349290 Development of a real-time RT-PCR assay for detection of resistance to oseltamivir in influenza A pandemic (H1N1) 2009 virus using single nucleotide polymorphism probes. Limit-of-detection limit for the assay was determined by testing 10-fold serial dilutions of quantified RNA in triplicate, resulting in 47.6 copies and 52.9 copies for the H275 and the H275Y alleles per reaction, respectively. 2011 Journal of virological methods Result IV H275Y 185 190 21349290 Development of a real-time RT-PCR assay for detection of resistance to oseltamivir in influenza A pandemic (H1N1) 2009 virus using single nucleotide polymorphism probes. Linear amplification of template was observed between 4.76 x 101 to 4.76 x 108 and 5.29 x 102 to 5.29 x 109 copies per reaction for H275 and H275Y alleles, respectively. 2011 Journal of virological methods Result IV H275Y 141 146 21349290 Development of a real-time RT-PCR assay for detection of resistance to oseltamivir in influenza A pandemic (H1N1) 2009 virus using single nucleotide polymorphism probes. Samples with the H275Y allele were present either as 823T (n = 15) or admixtures of C823 and 823T (n = 9). 2011 Journal of virological methods Result IV H275Y 17 22 21349290 Development of a real-time RT-PCR assay for detection of resistance to oseltamivir in influenza A pandemic (H1N1) 2009 virus using single nucleotide polymorphism probes. The 24 specimens containing the H275Y allele and H275/H275Y admixtures populations were from 10 patients belong to immuno-compromised and intensive care unit cases identified in the described screening process previously. 2011 Journal of virological methods Result IV H275Y;H275Y 32;54 37;59 21349290 Development of a real-time RT-PCR assay for detection of resistance to oseltamivir in influenza A pandemic (H1N1) 2009 virus using single nucleotide polymorphism probes. The inter-assay variability ranged from 0.56% to 2.13% and 0.27-1.01% with the H275 and H275Y alleles, respectively. 2011 Journal of virological methods Result IV H275Y 88 93 21349290 Development of a real-time RT-PCR assay for detection of resistance to oseltamivir in influenza A pandemic (H1N1) 2009 virus using single nucleotide polymorphism probes. There was no non-specific detection of the H275 or H275Y alleles, thus both probes were 100% specific (Table 2a, Table 2b). 2011 Journal of virological methods Result IV H275Y 51 56 21349290 Development of a real-time RT-PCR assay for detection of resistance to oseltamivir in influenza A pandemic (H1N1) 2009 virus using single nucleotide polymorphism probes. This parameter ranged from 0.08% to 6.06% with the H275 allele and 0.02-2.95% for H275Y samples. 2011 Journal of virological methods Result IV H275Y 82 87 21364825 Identification of sequence mutations affecting hemagglutinin specificity to sialic acid receptor in influenza A virus subtypes. These mutation patterns are those occurring in positions 190 and 225 (E190 D and G225D) in the pandemic H1N1 strains and those in positions 226 and 228 (Q226L and G228S) in the H2N2 and H3N2 subtypes respectively. 2010 Bioinformation Result IV E190D;G225D;Q226L;G228S 71;82;155;165 77;87;160;170 21407805 A single base-pair change in 2009 H1N1 hemagglutinin increases human receptor affinity and leads to efficient airborne viral transmission in ferrets. Despite the differences in transmissibility of the parental rgCA04/09 virus and the rgCA04/09 HA Ile219Lys mutant virus, similar virus replication kinetics, and comparable levels of fever induction and weight loss in ferrets were observed with both viruses ( Table 1 ). 2011 PloS one Result IV I219K 97 106 HA 94 96 21407805 A single base-pair change in 2009 H1N1 hemagglutinin increases human receptor affinity and leads to efficient airborne viral transmission in ferrets. However this would involve at least two amino acid substitutions, Ser186 Pro and Glu227 Ala, to make this interaction network similar to that observed in SC18 HA (Figure S1). 2011 PloS one Result IV S186P;E227A 66;81 76;91 HA 159 161 21407805 A single base-pair change in 2009 H1N1 hemagglutinin increases human receptor affinity and leads to efficient airborne viral transmission in ferrets. Mutation of the HA at amino acid position 219 (Ile219->Lys) resulted in a virus (rgCA04/09 HA Ile219Lys) that efficiently transmitted via respiratory droplets to all of the contact ferrets which shed virus by day 3 post-contact (p.c.) ( Figure 3 ). 2011 PloS one Result IV I219K;I219K 94;47 103;58 HA;HA 16;91 18;93 21407805 A single base-pair change in 2009 H1N1 hemagglutinin increases human receptor affinity and leads to efficient airborne viral transmission in ferrets. Rationale for designing Ile219 Lys mutation on CA04/09 HA. 2011 PloS one Result IV I219K 24 34 21407805 A single base-pair change in 2009 H1N1 hemagglutinin increases human receptor affinity and leads to efficient airborne viral transmission in ferrets. The rgCA04/09 virus shedding showed similar kinetics to mutant virus harboring the Ile219 Lys amino acid mutation in HA, which was sustained for 5 days in ferrets at titers of >=104.3 PFU/ml. 2011 PloS one Result IV I219K 83 93 HA 117 119 21407805 A single base-pair change in 2009 H1N1 hemagglutinin increases human receptor affinity and leads to efficient airborne viral transmission in ferrets. To correct the mismatched combination of residues in the RBS of CA04/09 HA, our strategy was to generate a single mutant; Ile219 Lys (CA04/09mut1), that would generate a stable ionic interaction between Lys219 and Glu227. 2011 PloS one Result IV I219K 122 132 HA 72 74 21407805 A single base-pair change in 2009 H1N1 hemagglutinin increases human receptor affinity and leads to efficient airborne viral transmission in ferrets. We also verified that the dose-dependent binding profile of recombinant CA04/09mut1 HA was consistent with that of the whole virus harboring the Ile219 Lys HA mutation on our glycan array platform (Figure S2). 2011 PloS one Result IV I219K 145 155 HA;HA 84;156 86;158 21455300 Assessing the in vitro fitness of an oseltamivir-resistant seasonal A/H1N1 influenza strain using a mathematical model. Figure 1 shows representative plaques for the WT and H275Y mutant strains of A/Brisbane/59/2007 (H1N1) viruses at each time point. 2011 PloS one Result IV H275Y;H275Y 54;53 59;58 21455300 Assessing the in vitro fitness of an oseltamivir-resistant seasonal A/H1N1 influenza strain using a mathematical model. Figures 6A and 6D show the values of the kinetics parameters most consistent with the measured plaque velocities of the A/Brisbane/59/2007 WT and H275Y mutant strains, respectively. 2011 PloS one Result IV H275Y;H275Y 147;146 152;151 21455300 Assessing the in vitro fitness of an oseltamivir-resistant seasonal A/H1N1 influenza strain using a mathematical model. For each replicate, the viral titer of each strain was observed to grow rapidly after 4 h post-infection, with the WT viral titer reaching a plateau at approximately 8 h post-infection and that of the H275Y mutant reaching a plateau between 10 h and 14 h post-infection. 2011 PloS one Result IV H275Y 201 206 21455300 Assessing the in vitro fitness of an oseltamivir-resistant seasonal A/H1N1 influenza strain using a mathematical model. In order to obtain two complementary views of the infection kinetics for the A/Brisbane/59/2007 WT and H275Y mutant strains, virus growth over time was observed in two different in vitro systems: the viral plaque assay and the multiple-cycle viral yield assay. 2011 PloS one Result IV H275Y 103 108 21455300 Assessing the in vitro fitness of an oseltamivir-resistant seasonal A/H1N1 influenza strain using a mathematical model. Looking at Figure 2, one can see that at 36 h, the plaque radius of both A/Brisbane/59/2007 WT and its H275Y mutant counterpart are comparable in size. 2011 PloS one Result IV H275Y 103 108 21455300 Assessing the in vitro fitness of an oseltamivir-resistant seasonal A/H1N1 influenza strain using a mathematical model. The delay in the peak of viral titer between the two strains is qualitatively consistent with the model predictions of the previous section: the H275Y mutant strain appears to have a longer latent infection period than the WT strain. 2011 PloS one Result IV H275Y 145 150 21455300 Assessing the in vitro fitness of an oseltamivir-resistant seasonal A/H1N1 influenza strain using a mathematical model. The extent of these regions, shown in Figure 6C for the A/Brisbane/59/2007 WT strain and Figure 6F for the H275Y mutant strain, is summarized in Table 2. 2011 PloS one Result IV H275Y 107 112 21455300 Assessing the in vitro fitness of an oseltamivir-resistant seasonal A/H1N1 influenza strain using a mathematical model. The fitted value of the average latent infection period, , was found to be 5.6 h for the WT strain and 7.5 h for the H275Y mutant, with fitted values of the standard deviation in the normal distribution, , of 0.5 h and 1.2 h, respectively. 2011 PloS one Result IV H275Y 117 122 21455300 Assessing the in vitro fitness of an oseltamivir-resistant seasonal A/H1N1 influenza strain using a mathematical model. The longer latent infection period predicted for the H275Y mutant strain, could be the result of poorer NA activity. 2011 PloS one Result IV H275Y 53 58 104 106 21455300 Assessing the in vitro fitness of an oseltamivir-resistant seasonal A/H1N1 influenza strain using a mathematical model. The region of intersection suggests that the latent infection period for the H275Y mutant ( h) is longer than that of the WT strain (1-3 h), while the infecting time of the mutant ( 5 min) is much shorter than that of the WT (30-80 min). 2011 PloS one Result IV H275Y 77 82 21455300 Assessing the in vitro fitness of an oseltamivir-resistant seasonal A/H1N1 influenza strain using a mathematical model. The results of these experiments for the WT and H275Y mutant strains are shown in Figure 3. 2011 PloS one Result IV H275Y 48 53 21455300 Assessing the in vitro fitness of an oseltamivir-resistant seasonal A/H1N1 influenza strain using a mathematical model. The values of obtained for the WT and H275Y mutant strains were and , respectively. 2011 PloS one Result IV H275Y 39 44 21455300 Assessing the in vitro fitness of an oseltamivir-resistant seasonal A/H1N1 influenza strain using a mathematical model. The viral titer growth rate of the H275Y mutant was , slightly greater than that of the WT which was . 2011 PloS one Result IV H275Y 35 40 21455300 Assessing the in vitro fitness of an oseltamivir-resistant seasonal A/H1N1 influenza strain using a mathematical model. This result, demonstrating a higher affinity of the WT neuraminidase for the substrate than that of the H275Y mutant, agrees both qualitatively and quantitatively with previously published results on A/Brisbane/59/2007 -like (H1N1) strains, where the average value for susceptible strains from the 2007-2008 influenza season was and the average for resistant strains was . 2011 PloS one Result IV H275Y 104 109 55 68 21455300 Assessing the in vitro fitness of an oseltamivir-resistant seasonal A/H1N1 influenza strain using a mathematical model. Thus, it would appear from the viral titer growth rate alone, that the H275Y mutant has a replicative advantage over the WT strain, in contrast with the findings using the plaque velocity extracted from the plaque assay alone. 2011 PloS one Result IV H275Y 71 76 21455300 Assessing the in vitro fitness of an oseltamivir-resistant seasonal A/H1N1 influenza strain using a mathematical model. Thus, using plaque velocity alone, it would appear that the WT strain has a replicative fitness advantage over the H275Y mutant. 2011 PloS one Result IV H275Y 115 120 21455300 Assessing the in vitro fitness of an oseltamivir-resistant seasonal A/H1N1 influenza strain using a mathematical model. To demonstrate this concept using the A/Brisbane/59/2007 (H1N1) WT and H275Y mutant strains, we have plotted the experimentally-measured values of plaque velocity and viral titer growth rate as functions of the infecting time and latent infection period, using the model dependence determined above (Figure 6). 2011 PloS one Result IV H275Y 71 76 21455300 Assessing the in vitro fitness of an oseltamivir-resistant seasonal A/H1N1 influenza strain using a mathematical model. To investigate whether the H275Y mutant had poorer NA activity compared to the WT, we directly measured the enzymatic activity of the NA of each virus strain using the fluorescent substrate 4-MUNANA, providing information independent of virus-cell infection dynamics. 2011 PloS one Result IV H275Y 27 32 NA;NA 51;134 53;136 21455300 Assessing the in vitro fitness of an oseltamivir-resistant seasonal A/H1N1 influenza strain using a mathematical model. Using this method, the measured plaque growth was more rapid for the WT than the H275Y mutant, with a plaque velocity of compared to , where is the diameter of one cell. 2011 PloS one Result IV H275Y 81 86 21455300 Assessing the in vitro fitness of an oseltamivir-resistant seasonal A/H1N1 influenza strain using a mathematical model. Yet at 60 h, the WT strain has significantly larger plaques than the H275Y mutant, and the situation is reversed at 96 h. 2011 PloS one Result IV H275Y 69 74 21504394 Oseltamivir-resistant influenza viruses get by with a little help from permissive mutations. A computational method was used to identify R194G as a potential compensatory mutation that could possibly rescue the negative effect of H274Y. 2011 Expert review of anti-infective therapy Result IV R194G;H274Y 44;137 49;142 21504394 Oseltamivir-resistant influenza viruses get by with a little help from permissive mutations. Could compensatory mutations in more modern H1N1 strains minimize the negative effects of H274Y? 2011 Expert review of anti-infective therapy Result IV H274Y 90 95 21504394 Oseltamivir-resistant influenza viruses get by with a little help from permissive mutations. Could compensatory mutations in more modern H1N1 strains minimize the negative effects of H274Y. 2011 Expert review of anti-infective therapy Result IV H274Y 90 95 21504394 Oseltamivir-resistant influenza viruses get by with a little help from permissive mutations. From this analysis they identified several potential compensatory mutations and since these mutations preceded the emergence of the H274Y mutation in the human population, they termed these 'permissive' mutations. 2011 Expert review of anti-infective therapy Result IV H274Y 132 137 21504394 Oseltamivir-resistant influenza viruses get by with a little help from permissive mutations. Indeed, NAs possessing the H274Y mutation exhibited decreased enzymatic activity and this correlated with reduced levels of NA cell surface expression. 2011 Expert review of anti-infective therapy Result IV H274Y 27 32 NA;NA 124;8 126;11 21504394 Oseltamivir-resistant influenza viruses get by with a little help from permissive mutations. Introduction of H274Y into NAs from viruses from 1991 and 1999 led to decreased NA activity, but interestingly, the introduction of this mutation into an NA from 2006 did not have as drastic an effect. 2011 Expert review of anti-infective therapy Result IV H274Y 16 21 NA;NA;NA 80;154;27 82;156;30 21504394 Oseltamivir-resistant influenza viruses get by with a little help from permissive mutations. More importantly, viruses possessing only H274Y replicated poorly, while viruses possessing both H274Y and R194G replicated similar to parent viruses. 2011 Expert review of anti-infective therapy Result IV H274Y;H274Y;R194G 42;97;107 47;102;112 21504394 Oseltamivir-resistant influenza viruses get by with a little help from permissive mutations. Mutant NAs expressing both R194G and H274Y were created and the results were crystal clear: the addition of R194G completely negated the effect seen previously with NAs possessing only H274Y. 2011 Expert review of anti-infective therapy Result IV R194G;H274Y;R194G;H274Y 27;37;108;185 32;42;113;190 NA;NA 7;165 10;168 21504394 Oseltamivir-resistant influenza viruses get by with a little help from permissive mutations. The authors began by hypothesizing that H274Y negatively affects NA folding or stability rather than enzymatic activity. 2011 Expert review of anti-infective therapy Result IV H274Y 40 45 65 67 21504394 Oseltamivir-resistant influenza viruses get by with a little help from permissive mutations. These initial studies demonstrated the proof-of-principle that secondary mutations can compensate for negative effects associated with H274Y. 2011 Expert review of anti-infective therapy Result IV H274Y 135 140 21504394 Oseltamivir-resistant influenza viruses get by with a little help from permissive mutations. These mutations were sequentially introduced into a 1999 NA and two of these mutations, V234M and R222Q, were found to counterbalance the negative effects of H274Y. 2011 Expert review of anti-infective therapy Result IV V234M;R222Q;H274Y 88;98;158 93;103;163 57 59 21504394 Oseltamivir-resistant influenza viruses get by with a little help from permissive mutations. To address this, they introduced the H274Y mutation into NAs from H1N1 viruses isolated from the years 1933 and 1934. 2011 Expert review of anti-infective therapy Result IV H274Y 37 42 57 60 21504394 Oseltamivir-resistant influenza viruses get by with a little help from permissive mutations. Viruses possessing H274Y and these two permissive mutations were able to replicate to high titers both in the presence and absence of oseltamivir. 2011 Expert review of anti-infective therapy Result IV H274Y 19 24 21555520 Biophysical analysis of influenza A virus RNA promoter at physiological temperatures. 3 demonstrate that the 3'-G3U and G3U/C8A mutations do not decrease, and possibly increase, the stability of the promoter duplex. 2011 The Journal of biological chemistry Result IV C8A 38 41 21555520 Biophysical analysis of influenza A virus RNA promoter at physiological temperatures. Both 3'-G3U and 3'-G3U/C8A promoters yielded structures with a slightly higher Tm and more favorable DeltaG than the wild-type promoter, supporting that these mutant promoters do not form less stable duplexes than the wild-type promoter. 2011 The Journal of biological chemistry Result IV C8A 23 26 21555520 Biophysical analysis of influenza A virus RNA promoter at physiological temperatures. It was previously shown that the 3'-G3U mutation inactivated IAV promoter function whereas the combined 3'-G3U/C8A mutations, which restored a proposed base pair in the corkscrew model, showed wild-type levels of reporter gene expression. 2011 The Journal of biological chemistry Result IV C8A 111 114 21555520 Biophysical analysis of influenza A virus RNA promoter at physiological temperatures. Next, we investigated the effects of two previously characterized promoter mutations on duplex formation, 3'-G3U and 3'-G3U/C8A. 2011 The Journal of biological chemistry Result IV C8A 124 127 21555520 Biophysical analysis of influenza A virus RNA promoter at physiological temperatures. Our trFRET analysis revealed that both 3'-G3U and 3'-G3U/C8A mutant RNAs were able to form a duplex with the 5'-vRNA at temperatures up to 42 C, as observed for the wild-type sequences (data not shown). 2011 The Journal of biological chemistry Result IV C8A 57 60 21555520 Biophysical analysis of influenza A virus RNA promoter at physiological temperatures. These 3'-vRNA self-structures may also be destabilized by the G3U and G3U/C8A 3' sequences, which could explain the slightly higher Tm observed for these sequences when compared with the wild-type sequence (Table 1). 2011 The Journal of biological chemistry Result IV C8A 74 77 21572517 Mutation analysis of 2009 pandemic influenza A(H1N1) viruses collected in Japan during the peak phase of the pandemic. As Figure 2 demonstrates, samples "I" and "II" were clearly distinguished by two clusters, where both HA S220T and NA N248D were identified as the major non-synonymous mutations that discriminate the samples between the two clusters. 2011 PloS one Result IV S220T;N248D 105;118 110;123 HA;NA 102;115 104;117 21572517 Mutation analysis of 2009 pandemic influenza A(H1N1) viruses collected in Japan during the peak phase of the pandemic. In our clinical study carried out in Tokyo, the NA-H275Y mutation was found in a patient (6 years old) who had influenza-induced brain edema and severe pneumonia with little response to oseltamivir (4 mg/kg/day). 2011 PloS one Result IV H275Y 51 56 48 50 Influenza encephalopathy;Pneumonia 129;152 140;161 21572517 Mutation analysis of 2009 pandemic influenza A(H1N1) viruses collected in Japan during the peak phase of the pandemic. In our study, however, clusters 1 and 1.2 are not distinguished, because the amino acid substitution NA-V106I that discriminates these two clusters (Table 3) was not involved in the sequence analysis of this study. 2011 PloS one Result IV V106I 104 109 101 103 21572517 Mutation analysis of 2009 pandemic influenza A(H1N1) viruses collected in Japan during the peak phase of the pandemic. Oseltamivir-resistance associated mutations: H275Y and N295S in NA. 2011 PloS one Result IV H275Y;N295S 45;55 50;60 64 66 21572517 Mutation analysis of 2009 pandemic influenza A(H1N1) viruses collected in Japan during the peak phase of the pandemic. The NA-H275Y mutation was found in two of these patients, whereas the NA-N295S mutation was found in one. 2011 PloS one Result IV H275Y;N295S 7;73 12;78 NA;NA 4;70 6;72 21572517 Mutation analysis of 2009 pandemic influenza A(H1N1) viruses collected in Japan during the peak phase of the pandemic. The NA-N295S mutation was originally reported in drug-resistant H5N1 viruses. 2011 PloS one Result IV N295S 7 12 4 6 21572517 Mutation analysis of 2009 pandemic influenza A(H1N1) viruses collected in Japan during the peak phase of the pandemic. Thus, we first examined the two major non-synonymous mutations, i.e., HA-S220T and NA-N248D. 2011 PloS one Result IV S220T;N248D 73;86 78;91 HA;NA 70;83 72;85 21572517 Mutation analysis of 2009 pandemic influenza A(H1N1) viruses collected in Japan during the peak phase of the pandemic. To our knowledge, the NA-N295S mutation is the first case so far reported for oseltamivir-resistance in the 2009 pdm influenza A(H1N1) viruses. 2011 PloS one Result IV N295S 25 30 22 24 21586098 Recent avian influenza virus A/H5N1 evolution in vaccinated and unvaccinated poultry from farms in Southern Vietnam, January-March 2010. Five new amino acid changes were located in previously identified antigenic sites (T36A, D45G, P136S, S155N/G and A185E). 2011 Transboundary and emerging diseases Result IV T36A;D45G;P136S;S155N;S155G;A185E 83;89;95;102;102;114 87;93;100;109;109;119 21586098 Recent avian influenza virus A/H5N1 evolution in vaccinated and unvaccinated poultry from farms in Southern Vietnam, January-March 2010. The 2010 clade is characterized by a substitution from isoleucine to valine at position 514 (I514V; H5 numbering as in and), with four new amino acid changes observed in at least two sequences (Table 1). 2011 Transboundary and emerging diseases Result IV I514V;I514V 93;55 98;91 21586098 Recent avian influenza virus A/H5N1 evolution in vaccinated and unvaccinated poultry from farms in Southern Vietnam, January-March 2010. Three amino acid changes (A184G, A185E and A214S) occurred within predicted loop structures of the receptor-binding domain, and the S155N/G mutations remove a potential N-linked glycosylation site. 2011 Transboundary and emerging diseases Result IV A184G;A185E;A214S;S155N;S155G 26;33;43;132;132 31;38;48;139;139 21586098 Recent avian influenza virus A/H5N1 evolution in vaccinated and unvaccinated poultry from farms in Southern Vietnam, January-March 2010. Two previously polymorphic sites (K48R and N168D) exhibited dramatic increases in frequency in the 2010 clade as compared to the 2007 clade. 2011 Transboundary and emerging diseases Result IV K48R;N168D 34;43 38;48 21744829 Molecular dynamics simulation directed rational design of inhibitors targeting drug-resistant mutants of influenza A virus M2. Although compound 2 was ineffective against V27A, ssNMR characterization of this compound in complex with WT A/M2 in bilayers showed that this spiro-piperidine 2 had a greater impact on the dynamics and magnetic environment of the pore than amantadine, and that it interacted over a more extended site within the channel. 2011 Journal of the American Chemical Society Result IV V27A 44 48 M2 111 113 21744829 Molecular dynamics simulation directed rational design of inhibitors targeting drug-resistant mutants of influenza A virus M2. Although its apolar portion is more effectively dehydrated than amanatadine in V27A, the diffuse density of the upper ring of 1, when bound to V27A (Figure 3d), indicates that it averages between multiple orientations and does not fully fill the cavity. 2011 Journal of the American Chemical Society Result IV V27A;V27A 79;143 83;147 21744829 Molecular dynamics simulation directed rational design of inhibitors targeting drug-resistant mutants of influenza A virus M2. Amantadine failed to bind a unique site when placed within V27A, and instead bound with its ammonium occupying either the upper or the lower aqueous sites. 2011 Journal of the American Chemical Society Result IV V27A 59 63 21744829 Molecular dynamics simulation directed rational design of inhibitors targeting drug-resistant mutants of influenza A virus M2. As a negative control, amantadine showed no inhibition of A/M2-V27A virus replication even at 50 muM concentration. 2011 Journal of the American Chemical Society Result IV V27A 63 67 M2 60 62 21744829 Molecular dynamics simulation directed rational design of inhibitors targeting drug-resistant mutants of influenza A virus M2. As a negative control, the 6-membered aliphatic ring of compound 3 was converted to the five-membered ring in 6, which only showed minimal inhibition against V27A mutant. 2011 Journal of the American Chemical Society Result IV V27A 158 162 21744829 Molecular dynamics simulation directed rational design of inhibitors targeting drug-resistant mutants of influenza A virus M2. As expected, the drug shifted its position upward in V27A, to allow its alkyl group to fill the larger cavity near the channel entrance (Figure 3e). 2011 Journal of the American Chemical Society Result IV V27A 53 57 21744829 Molecular dynamics simulation directed rational design of inhibitors targeting drug-resistant mutants of influenza A virus M2. As was the case for binding spirane inhibitors to WT M2TM, incubation of V27A with 9 or 1 sharpened the peak, altered the intensity ratios, and shifted the chemical shift positions for the resonances associated with G34 in V27A (Figure 6b, c). 2011 Journal of the American Chemical Society Result IV V27A;V27A 73;223 77;227 21744829 Molecular dynamics simulation directed rational design of inhibitors targeting drug-resistant mutants of influenza A virus M2. By contrast, incubation of A/M2TM-V27A with the weaker-binding 1 resulted in two partially overlapping peaks: the less intense peak has a chemical shift close to that seen in the absence of the inhibitor, indicative of either less complete binding or a minor conformation that is similar to the one found in the uncomplexed form. 2011 Journal of the American Chemical Society Result IV V27A 34 38 21744829 Molecular dynamics simulation directed rational design of inhibitors targeting drug-resistant mutants of influenza A virus M2. Combining these substitutions in the bis-cycloheptyl-spirane amine, 1, resulted in a compound with a two-fold higher potency than amantadine against WT A/M2, and great potency against the amantadine-insensitive mutant V27A with IC50 of 11.3 +- 0.7 muM. 2011 Journal of the American Chemical Society Result IV V27A 218 222 M2 154 156 21744829 Molecular dynamics simulation directed rational design of inhibitors targeting drug-resistant mutants of influenza A virus M2. Design and synthesis of inhibitors targeting A/M2-V27A. 2011 Journal of the American Chemical Society Result IV V27A 50 54 M2 47 49 21744829 Molecular dynamics simulation directed rational design of inhibitors targeting drug-resistant mutants of influenza A virus M2. Design of potent spiro-adamantane inhibitor of A/M2-V27A and L26F. 2011 Journal of the American Chemical Society Result IV V27A;L26F 52;61 56;65 M2 49 51 21744829 Molecular dynamics simulation directed rational design of inhibitors targeting drug-resistant mutants of influenza A virus M2. Direct binding of spirane amine to the TM domain of V27A. 2011 Journal of the American Chemical Society Result IV V27A 52 56 21744829 Molecular dynamics simulation directed rational design of inhibitors targeting drug-resistant mutants of influenza A virus M2. Encouragingly, 4 and 5 had potencies similar to amantadine against WT; more importantly they had similar low IC50 values against V27A, which amantadine is completely unable to inhibit. 2011 Journal of the American Chemical Society Result IV V27A 129 133 21744829 Molecular dynamics simulation directed rational design of inhibitors targeting drug-resistant mutants of influenza A virus M2. Furthermore, this inhibitor was also highly active against another amantadine-resistant mutant L26F (Figure 4c), consistent with homology modeling and MD results showing that L26F and V27A have similarly expanded central cavities. 2011 Journal of the American Chemical Society Result IV L26F;L26F;V27A 95;175;184 99;179;188 21744829 Molecular dynamics simulation directed rational design of inhibitors targeting drug-resistant mutants of influenza A virus M2. In the case of WT and L26F, compound 9 was pushed lower toward H37 and forms water mediated hydrogen bonding with H37. 2011 Journal of the American Chemical Society Result IV L26F 22 26 21744829 Molecular dynamics simulation directed rational design of inhibitors targeting drug-resistant mutants of influenza A virus M2. Indeed, a one carbon extension of the spiro-piperidine 2 gave spirane amine 3, which was the first molecule to show weak but saturable inhibition of V27A (IC50 = 84.9 +- 13.6 muM). 2011 Journal of the American Chemical Society Result IV V27A 149 153 21744829 Molecular dynamics simulation directed rational design of inhibitors targeting drug-resistant mutants of influenza A virus M2. It is noted that high density of 9 was observed in all three variants (including L26F, not shown), suggesting tight binding with each mutant. 2011 Journal of the American Chemical Society Result IV L26F 81 85 21744829 Molecular dynamics simulation directed rational design of inhibitors targeting drug-resistant mutants of influenza A virus M2. It was found that 9 had a similar pose as 1 in V27A with the hydrophobic adamantane filling in the extra space near A27. 2011 Journal of the American Chemical Society Result IV V27A 47 51 21744829 Molecular dynamics simulation directed rational design of inhibitors targeting drug-resistant mutants of influenza A virus M2. Its ammonium group occupies the lower aqueous site in WT, where it forms solvent-mediated hydrogen bonds with the carbonyl of G34, versus A30 in V27A (Figure 3d,e). 2011 Journal of the American Chemical Society Result IV V27A 145 149 21744829 Molecular dynamics simulation directed rational design of inhibitors targeting drug-resistant mutants of influenza A virus M2. MD simulations at room temperature of both the G34A mutant of the crystal structure33 and the WT protein confirm that the two tetrads are both mobile, but water molecules associated to G34 and H37 are more stable than those associated to A30. 2011 Journal of the American Chemical Society Result IV G34A 47 51 21744829 Molecular dynamics simulation directed rational design of inhibitors targeting drug-resistant mutants of influenza A virus M2. MD simulations were used to further probe the mode of binding of amantadine and the potent bis-cycloheptyl-spirane amine 1 to both WT and V27A. 2011 Journal of the American Chemical Society Result IV V27A 138 142 21744829 Molecular dynamics simulation directed rational design of inhibitors targeting drug-resistant mutants of influenza A virus M2. Moreover, its apolar adamantane cage was significantly less well dehydrated in V27A versus WT, explaining the loss in potency for the mutant. 2011 Journal of the American Chemical Society Result IV V27A 79 83 21744829 Molecular dynamics simulation directed rational design of inhibitors targeting drug-resistant mutants of influenza A virus M2. Spiroadamantane 9 proved to be the most potent V27A inhibitor-showing more than 280-fold lower IC50 for V27A than 3 (Figure 4c). 2011 Journal of the American Chemical Society Result IV V27A;V27A 47;104 51;108 21744829 Molecular dynamics simulation directed rational design of inhibitors targeting drug-resistant mutants of influenza A virus M2. The inhibitory effect of four of the most potent inhibitors on A/M2-V27A mutant was confirmed by plaque reduction assay of influenza A virus. 2011 Journal of the American Chemical Society Result IV V27A 68 72 M2 65 67 21744829 Molecular dynamics simulation directed rational design of inhibitors targeting drug-resistant mutants of influenza A virus M2. The V27A and L26F mutants have larger, more solvent-exposed N-terminal pores. 2011 Journal of the American Chemical Society Result IV V27A;L26F 4;13 8;17 21744829 Molecular dynamics simulation directed rational design of inhibitors targeting drug-resistant mutants of influenza A virus M2. Their ability to inhibit proton currents was measured in Xenopus laevis oocytes expressing either WT A/M2 or A/M2-V27A. 2011 Journal of the American Chemical Society Result IV V27A 114 118 M2;M2 103;111 105;113 21744829 Molecular dynamics simulation directed rational design of inhibitors targeting drug-resistant mutants of influenza A virus M2. These findings indicate a direct interaction of the drug with V27A, and suggest that the 10-fold higher potency of 9 compared to 1 is a result of a tighter and more extended interaction between the drug and the channel. 2011 Journal of the American Chemical Society Result IV V27A 62 66 21744829 Molecular dynamics simulation directed rational design of inhibitors targeting drug-resistant mutants of influenza A virus M2. This apparent flexibility provided a crucial insight to enable design of dual-specificity inhibitors for WT as well as V27A. 2011 Journal of the American Chemical Society Result IV V27A 119 123 21744829 Molecular dynamics simulation directed rational design of inhibitors targeting drug-resistant mutants of influenza A virus M2. This inhibitor was simulated against WT, V27A and L26F (Figure 3f,g). 2011 Journal of the American Chemical Society Result IV V27A;L26F 41;50 45;54 21744829 Molecular dynamics simulation directed rational design of inhibitors targeting drug-resistant mutants of influenza A virus M2. Thus, it appeared to be an attractive scaffold upon which to build functional groups to fill in the more spacious vestibule created by the V27A mutation. 2011 Journal of the American Chemical Society Result IV V27A 139 143 21744829 Molecular dynamics simulation directed rational design of inhibitors targeting drug-resistant mutants of influenza A virus M2. Thus, the challenge was to design molecules that were larger than amantadine and able to fill the increased volume of the upper pore created by V27A and L26F mutant, while still being accommodated within the WT structure. 2011 Journal of the American Chemical Society Result IV V27A;L26F 144;153 148;157 21744829 Molecular dynamics simulation directed rational design of inhibitors targeting drug-resistant mutants of influenza A virus M2. Thus, the inhibitory potency of the compounds against amantadine-resistant A/M2-V27A mutant channels seen in electrophysiology assays results in potent inhibition of the replication of influenza A virus. 2011 Journal of the American Chemical Society Result IV V27A 80 84 M2 77 79 21744829 Molecular dynamics simulation directed rational design of inhibitors targeting drug-resistant mutants of influenza A virus M2. To investigate how V27A and L26F mutations affect the size and shape of the binding site, we built theoretical models of these mutants in the drug-free form using the recently solved high resolution structure of A/M2 (PDB: 3LBW) as an initial configuration. 2011 Journal of the American Chemical Society Result IV V27A;L26F 19;28 23;32 M2 214 216 21744829 Molecular dynamics simulation directed rational design of inhibitors targeting drug-resistant mutants of influenza A virus M2. We synthesized A/M2-V27A TM peptide (22-46, M2TM) containing uniformly 15N, 13C-labeled A27, V28 and G34 (Supporting information). 2011 Journal of the American Chemical Society Result IV V27A 20 24 M2 17 19 21821881 Conservation of a crystallographic interface suggests a role for beta-sheet augmentation in influenza virus NS1 multifunctionality. However, it is intriguing to observe that the strand-strand dimer is conserved among all three PR8 NS1 ED (W187A) structures that have now been solved. 2011 Acta crystallographica. Section F, Structural biology and crystallization communications Result IV W187A 107 112 NS1 99 102 21821881 Conservation of a crystallographic interface suggests a role for beta-sheet augmentation in influenza virus NS1 multifunctionality. In contrast to the majority of NS1 structures, only one molecule of PR8 NS1 ED (W187A) was present within the asymmetric unit, although a strand-strand interface homologous to those observed for previous structures obtained using this construct was observed between symmetry-related monomers. 2011 Acta crystallographica. Section F, Structural biology and crystallization communications Result IV W187A 80 85 NS1;NS1 31;72 34;75 21821881 Conservation of a crystallographic interface suggests a role for beta-sheet augmentation in influenza virus NS1 multifunctionality. The novel crystal form of PR8 NS1 ED (W187A) shows the alpha/beta fold common to all structures of NS1 ED (Bornholdt & Prasad, 2006; Kerry et al., 2011). 2011 Acta crystallographica. Section F, Structural biology and crystallization communications Result IV W187A 38 43 NS1;NS1 30;99 33;102 21821881 Conservation of a crystallographic interface suggests a role for beta-sheet augmentation in influenza virus NS1 multifunctionality. Therefore, since the PR8 NS1 ED W187A mutant is monomeric in vitro (Kerry et al., 2011), it appears highly likely that the helix-helix dimer is the predominant interface for ED homodimerization. 2011 Acta crystallographica. Section F, Structural biology and crystallization communications Result IV W187A 32 37 NS1 25 28 21821881 Conservation of a crystallographic interface suggests a role for beta-sheet augmentation in influenza virus NS1 multifunctionality. W187Y (PDB entry 3kwi) and W187A (PDB entry 3kwg); Xia & Robertus, 2010]. 2011 Acta crystallographica. Section F, Structural biology and crystallization communications Result IV W187Y;W187A 0;27 5;32 21821881 Conservation of a crystallographic interface suggests a role for beta-sheet augmentation in influenza virus NS1 multifunctionality. While the W187R mutation present within the monomer used to collect these NMR data is likely to disrupt ED dimerization, it is located within the helix-helix interface and is unlikely to influence any strand-strand interactions. 2011 Acta crystallographica. Section F, Structural biology and crystallization communications Result IV W187R 10 15 21935413 Genetic structure of human A/H1N1 and A/H3N2 influenza virus on Corsica Island: phylogenetic analysis and vaccine strain match, 2006-2010. All groups were characterized by two variations (K264P and S265H) compared to the vaccine strain A/Brisbane/10/2007 (vaccine strain for the 2008-2009 season in the Northern Hemisphere) and by five altered amino acids (K62E, K144N, N158K, K189N and S214I) with respect to A/Perth/16/2009 (vaccine strain for the 2009-2010 season in the Northern Hemisphere). 2011 PloS one Result IV K264P;S265H;K62E;K144N;N158K;K189N;S214I 49;59;218;224;231;238;248 54;64;222;229;236;243;253 21935413 Genetic structure of human A/H1N1 and A/H3N2 influenza virus on Corsica Island: phylogenetic analysis and vaccine strain match, 2006-2010. All isolates were characterized by the substitution H156Q. 2011 PloS one Result IV H156Q 52 57 21935413 Genetic structure of human A/H1N1 and A/H3N2 influenza virus on Corsica Island: phylogenetic analysis and vaccine strain match, 2006-2010. Both clades were characterized by the N39D and I189D (antigenic site B) with respect to A/Brisbane/59/2007 (vaccine strain of the 2008-2009 season in the Northern Hemisphere) (Table 2). 2011 PloS one Result IV N39D;I189D 38;47 42;52 21935413 Genetic structure of human A/H1N1 and A/H3N2 influenza virus on Corsica Island: phylogenetic analysis and vaccine strain match, 2006-2010. Clade II was characterized by the A62G, S125N (antigenic site B), W127G, C139S and S140C (antigenic site A), Y209F (at antigenic site D) and E246Q (Table 2). 2011 PloS one Result IV A62G;S125N;W127G;C139S;S140C;Y209F;E246Q 34;40;66;73;83;109;141 38;45;71;78;88;114;146 21935413 Genetic structure of human A/H1N1 and A/H3N2 influenza virus on Corsica Island: phylogenetic analysis and vaccine strain match, 2006-2010. Several strains were characterized by H156Q associated with at least one of these three additional substitutions: R142G, L157S and K173E (clade I. 2011 PloS one Result IV H156Q;R142G;L157S;K173E 38;114;121;131 43;119;126;136 21935413 Genetic structure of human A/H1N1 and A/H3N2 influenza virus on Corsica Island: phylogenetic analysis and vaccine strain match, 2006-2010. The H1 phylogeny showed that the amino acid substitutions P83S and S203T were found in all of the Corsican isolates. 2011 PloS one Result IV P83S;S203T 58;67 62;72 21935413 Genetic structure of human A/H1N1 and A/H3N2 influenza virus on Corsica Island: phylogenetic analysis and vaccine strain match, 2006-2010. The isolate A/Corsica/7/2007 was characterized by the substitutions I189D (antigenic site B) and G240R with respect to A/Brisbane/59/2007. 2011 PloS one Result IV I189D;G240R 68;97 73;102 21935413 Genetic structure of human A/H1N1 and A/H3N2 influenza virus on Corsica Island: phylogenetic analysis and vaccine strain match, 2006-2010. The K144N mutation was located at antigenic site A, while the N158K and K189N mutations were located at site B, the S241I and Q173K mutations were at site D and the K264P and S265H mutations were at site E. 2011 PloS one Result IV K144N;N158K;K189N;S241I;Q173K;K264P;S265H 4;62;72;116;126;165;175 9;67;77;121;131;170;180 21935413 Genetic structure of human A/H1N1 and A/H3N2 influenza virus on Corsica Island: phylogenetic analysis and vaccine strain match, 2006-2010. The largest p epitope value was 0.095 (epitope B; substitutions Q156H and L157S), suggesting that two mutations in dominant epitope B would lead to a rate of worst-case VE against these strains of 50.1% (E = 23.5% of 47%, p epitope = 0) of that of a perfect match between vaccine and virus. 2011 PloS one Result IV Q156H;L157S 64;74 69;79 21935413 Genetic structure of human A/H1N1 and A/H3N2 influenza virus on Corsica Island: phylogenetic analysis and vaccine strain match, 2006-2010. The sub-clade III was characterized by the Q173K mutation with respect to A/Perth/16/2009. 2011 PloS one Result IV Q173K 43 48 21935413 Genetic structure of human A/H1N1 and A/H3N2 influenza virus on Corsica Island: phylogenetic analysis and vaccine strain match, 2006-2010. The sub-clade IV showed one supplementary variation compared to A/Perth/16/2009 (Q173K and L194D). 2011 PloS one Result IV Q173K;L194D 81;91 86;96 21935413 Genetic structure of human A/H1N1 and A/H3N2 influenza virus on Corsica Island: phylogenetic analysis and vaccine strain match, 2006-2010. The sub-clade V was characterized by the supplementary mutation S54N when compared to A/Brisbane/10/2007 and A/Perth/16/2009. 2011 PloS one Result IV S54N 64 68 21935413 Genetic structure of human A/H1N1 and A/H3N2 influenza virus on Corsica Island: phylogenetic analysis and vaccine strain match, 2006-2010. The substitution D222E was identified in 99% of the A/H1N1pdm viruses (Table 3). 2011 PloS one Result IV D222E 17 22 21935413 Genetic structure of human A/H1N1 and A/H3N2 influenza virus on Corsica Island: phylogenetic analysis and vaccine strain match, 2006-2010. The substitution P83S were assigned to epitope E and the substitutions S203T and D222E to epitope D. 2011 PloS one Result IV P83S;S203T;D222E 17;71;81 21;76;86 21935413 Genetic structure of human A/H1N1 and A/H3N2 influenza virus on Corsica Island: phylogenetic analysis and vaccine strain match, 2006-2010. These two strains were not characterized by the mutation H156Q. 2011 PloS one Result IV H156Q 57 62 21935413 Genetic structure of human A/H1N1 and A/H3N2 influenza virus on Corsica Island: phylogenetic analysis and vaccine strain match, 2006-2010. Using the p epitope method, we found the largest p epitope value was 0.045 (dominant epitope = E; substitutions K264P and S265H), suggesting a rate of worst-case VE against these strains of 76% (E = 35.9% of 47%, p epitope = 0) of that of a perfect match (p epitope = 0) vaccine. 2011 PloS one Result IV K264P;S265H 112;122 117;127 21935413 Genetic structure of human A/H1N1 and A/H3N2 influenza virus on Corsica Island: phylogenetic analysis and vaccine strain match, 2006-2010. We calculated the antigenic distance from the 2007-2008 vaccine strain A/Salomon Island/3/2006 (H1N1) and A/H1N1 Corsican strains characterized by the mutation S125N (epitope B). 2011 PloS one Result IV S125N 160 165 21935413 Genetic structure of human A/H1N1 and A/H3N2 influenza virus on Corsica Island: phylogenetic analysis and vaccine strain match, 2006-2010. We calculated the antigenic distance from the vaccine strain of the Northern Hemisphere in 2009-2010, A/California/7/2009 and the A/H1N1pdm strains having the substitution P83S, S183T and D222E. 2011 PloS one Result IV P83S;S183T;D222E 172;178;188 176;183;193 21951678 Comparative safety, immunogenicity, and efficacy of several anti-H5N1 influenza experimental vaccines in a mouse and chicken models (Testing of killed and live H5 vaccine). Replacements such as Asp54/Asn in HA1, Val48/Ile and Lys131/Glu in HA2, and Ala46/Thr in NA are more typical for HA and NA proteins from wild duck viruses because most of ancient duck H5 viruses had Asn54 in HA1 and Ile48 in HA2; H3 and H4 duck viruses have Glu131 in HA2. 2012 Influenza and other respiratory viruses Result IV D54N;V48I;K131E;A46T 21;39;53;76 30;48;63;85 HA;HA;HA;HA;HA1;HA1;NA;NA 67;113;225;268;34;208;89;120 69;115;227;270;37;211;91;122 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. A recent report indicated that the presence of D222G enhanced the ability of a 2009 H1N1 virus to cause ocular disease in mice, with virus detected in the eye of one mouse following intranasal inoculation. 2011 PloS one Result IV D222G 47 52 Ocular disease 104 118 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. A recent study demonstrated that the introduction of D222G in a 2009 H1N1 virus did not alter the pathogenicity or transmissibility of a 2009 H1N1 isolate A/Netherlands/602/09 in ferrets. 2011 PloS one Result IV D222G 53 58 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. Both CA/04 and D222G viruses were detected at low levels (<3 log10 PFU/ml) through 72 hrs p.i. 2011 PloS one Result IV D222G 15 20 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. D222G mutation does not alter 2009 H1N1 virus tropism in human respiratory and ocular cells. 2011 PloS one Result IV D222G 0 5 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. D222G virus replicated efficiently in the upper respiratory tract of inoculated ferrets, reaching peak mean titers of 7.5+-0.2 log10 PFU/ml day 1 p.i., significantly higher than CA/04 virus at this time (p<0.03). 2011 PloS one Result IV D222G 0 5 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. D222G virus was detected in the ferret upper respiratory tract (6.7+-0.2 log10 PFU/ml nasal turbinates) and the lower respiratory tract (6.3+-0.6 log10 PFU/g lung tissue) at similar titers as 2009 H1N1 wild-type viruses day 3 p.i. 2011 PloS one Result IV D222G 0 5 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. D222G virus-infected ferrets further exhibited a mild, transient lymphopenia (22% decrease in circulating lymphocytes on day 3 p.i.) which was comparable to ferrets infected with other 2009 H1N1 viruses. 2011 PloS one Result IV D222G 0 5 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. Effect of D222G mutation on pathogenesis and respiratory droplet transmission. 2011 PloS one Result IV D222G 10 15 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. Effect of D222G mutation on the receptor binding properties of HA. 2011 PloS one Result IV D222G 10 15 HA 63 65 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. Enhanced virulence of D222G virus in mice by the intranasal but not intraocular route. 2011 PloS one Result IV D222G 22 27 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. Ferrets inoculated with the D222G virus exhibited similar clinical signs as CA/04 wild-type virus and a reverse-genetics derived CA/04 virus, with ferrets exhibiting transient weight loss (mean maximum weight loss of 11.3% on day 6-7 p.i.) and fever (mean maximum fever 1.9 C over baseline day 2 p.i.) before returning to baseline levels. 2011 PloS one Result IV D222G 28 33 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. However, at 48 and 72 hrs p.i., D222G virus replicated to significantly higher titer than CA/04 virus in the human respiratory cells (p<0.0005). 2011 PloS one Result IV D222G 32 37 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. However, to better assess the ability of the D222G mutation to cause ocular disease in mice, we inoculated mice by the ocular route with both viruses. 2011 PloS one Result IV D222G 45 50 Ocular disease 69 83 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. In contrast, the 2009 H1N1 CA/04 virus, which exhibits reduced transmissibility in the ferret model compared with seasonal H1N1 viruses, and previously enabled us to identify an HA mutation which conferred efficient transmission by respiratory droplets in ferrets was used in this study to more stringently assess the impact of D222G on virus transmission. 2011 PloS one Result IV D222G 328 333 HA 178 180 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. Mice inoculated with D222G virus by the intranasal route exhibited greater weight loss than CA/04 virus-inoculated mice; one mouse from the D222G group was euthanatized on day 11 p.i. 2011 PloS one Result IV D222G;D222G 21;140 26;145 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. Moreover, the D222G mutant virus was detected in the intestinal tract of 1/3 ferrets day 3 p.i. 2011 PloS one Result IV D222G 14 19 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. Our analysis showed that D222G mutation resulted in a modest reduction in the binding avidity to alpha2-6 sialylated glycans (6'SLN and, to a lesser extent, 6'SLN-LN) in comparison with the wild-type virus. 2011 PloS one Result IV D222G 25 30 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. Similar to a previous study, we observed a slight delay in D222G virus replication in Calu-3 cells at 24 hrs p.i., with titers of D222G virus being 10-fold lower than CA/04 virus (p<0.02). 2011 PloS one Result IV D222G;D222G 59;130 64;135 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. Similar to CA/04 virus, D222G mutant virus was detected in NW of two of three contact ferrets, with virus titers >7 log10 PFU/ml on day 3 p.c. 2011 PloS one Result IV D222G 24 29 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. Taken together, these findings indicate that the D222G mutation confers enhanced replication in respiratory epithelial cells but does not alter the ocular tropism of 2009 H1N1 virus. 2011 PloS one Result IV D222G 49 54 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. The notable difference in glycan-binding properties was the substantial increase in binding of D222G mutant virus to alpha2-3 sialylated glycans (relative to its alpha2-6 binding) compared with that of wild-type virus. 2011 PloS one Result IV D222G 95 100 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. Therefore a D222G mutation is likely to affect the molecular contacts of this key residue position with the glycan receptor. 2011 PloS one Result IV D222G 12 17 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. These results indicate that CA/04 virus is not well suited to infect mice by the ocular route, and the presence of D222G does not confer an ocular tropism in this model. 2011 PloS one Result IV D222G 115 120 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. These results with CA/04 virus are consistent with previous observations demonstrating an increase in alpha2-3 binding of other 2009 H1N1 viruses carrying the D222G mutation. 2011 PloS one Result IV D222G 159 164 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. This pattern of D222G virus transmission by respiratory droplets was confirmed in a duplicate experiment that resulted in virus detection in NW in two of three contact ferrets and seroconversion of all contact ferrets (data not shown). 2011 PloS one Result IV D222G 16 21 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. To determine whether the D222G mutation conferred heightened virulence of a 2009 H1N1 virus in a mouse model, we inoculated mice i.n. 2011 PloS one Result IV D222G 25 30 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. To evaluate the transmissibility of D222G virus by respiratory droplets, three ferrets were inoculated with 106 PFU of virus. 2011 PloS one Result IV D222G 36 41 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. To investigate the effect of D222G mutation on glycan-receptor binding properties of CA/04 virus, we analyzed the binding of both wild-type and mutant virus in a dose-dependent fashion to representative alpha2-3 and alpha2-6 sialylated glycans on a glycan array platform (Figure 1). 2011 PloS one Result IV D222G 29 34 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. To rule out the possibility that the D222G mutation confers an ocular tropism not observed in our murine model, we compared the ability of CA/04 and D222G viruses to replicate in primary human corneal epithelial cells (HCEpiC), which predominantly express alpha2-3 linked sialic acids. 2011 PloS one Result IV D222G;D222G 37;149 42;154 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. We did not observe extrapulmonary spread of virus to the eyes of mice following intranasal inoculation with either CA/04 or D222G virus, and ocular disease was not observed during visual examination of mice during the course of infection (data not shown). 2011 PloS one Result IV D222G 124 129 Ocular disease 141 155 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. While both viruses replicated efficiently in the lungs of mice on days 3 and 6 p.i., D222G virus replicated to a significantly higher mean titer compared with CA/04 virus at day 6 p.i. 2011 PloS one Result IV D222G 85 90 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. with 105 PFU of either CA/04 or D222G virus. 2011 PloS one Result IV D222G 32 37 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. Zeng, personal communication), but did not support efficient replication of either CA/04 or D222G viruses. 2011 PloS one Result IV D222G 92 97 21980293 Multidrug resistant 2009 A/H1N1 influenza clinical isolate with a neuraminidase I223R mutation retains its virulence and transmissibility in ferrets. A recombinant derivative of NL/602 with the I223R mutation in NA (recNL/602-I223R) replicated to lower peak titers in both cell lines compared to recNL/602 and NL/2631-R223. 2011 PLoS pathogens Result IV I223R;I223R 44;76 49;81 62 64 21980293 Multidrug resistant 2009 A/H1N1 influenza clinical isolate with a neuraminidase I223R mutation retains its virulence and transmissibility in ferrets. At day 5 p.e., the presence of the I223R mutation was confirmed by sequencing the NA gene of virus isolated from the throat swabs of the positive animals. 2011 PLoS pathogens Result IV I223R 35 40 82 84 21980293 Multidrug resistant 2009 A/H1N1 influenza clinical isolate with a neuraminidase I223R mutation retains its virulence and transmissibility in ferrets. By studying these isolates, a direct comparison could be made between a NAI susceptible and a novel I223R resistant virus, but such comparison does not address the impact of the single I223R mutation directly. 2011 PLoS pathogens Result IV I223R;I223R 100;185 105;190 NAI 72 75 21980293 Multidrug resistant 2009 A/H1N1 influenza clinical isolate with a neuraminidase I223R mutation retains its virulence and transmissibility in ferrets. Full genome sequencing of this clinical isolate A/NL/2631_1202/2010 (NL/2631-R223, GenBank accession numbers JF906180-906187) harboring an I223R mutation in the neuraminidase was performed. 2011 PLoS pathogens Result IV I223R 139 144 161 174 21980293 Multidrug resistant 2009 A/H1N1 influenza clinical isolate with a neuraminidase I223R mutation retains its virulence and transmissibility in ferrets. I223R harboring isolate is not attenuated in vitro . 2011 PLoS pathogens Result IV I223R 0 5 21980293 Multidrug resistant 2009 A/H1N1 influenza clinical isolate with a neuraminidase I223R mutation retains its virulence and transmissibility in ferrets. I223R harboring isolate is not attenuated in vitro. 2011 PLoS pathogens Result IV I223R 0 5 21980293 Multidrug resistant 2009 A/H1N1 influenza clinical isolate with a neuraminidase I223R mutation retains its virulence and transmissibility in ferrets. I223R harboring isolate is transmissible via aerosols or respiratory droplets. 2011 PLoS pathogens Result IV I223R 0 5 21980293 Multidrug resistant 2009 A/H1N1 influenza clinical isolate with a neuraminidase I223R mutation retains its virulence and transmissibility in ferrets. I223R mutant transmits as well as parental reference virus. 2011 PLoS pathogens Result IV I223R 0 5 21980293 Multidrug resistant 2009 A/H1N1 influenza clinical isolate with a neuraminidase I223R mutation retains its virulence and transmissibility in ferrets. In addition, initial virus replication of recNL/602-I223R was delayed by 6 to 12 hours in MDCK-SIAT1 cells. 2011 PLoS pathogens Result IV I223R 52 57 21980293 Multidrug resistant 2009 A/H1N1 influenza clinical isolate with a neuraminidase I223R mutation retains its virulence and transmissibility in ferrets. In contrast to the results obtained in MDCK cells, recNL/602-I223R replicated and transmitted as well as recNL/602 when evaluated in the ferret transmission model. 2011 PLoS pathogens Result IV I223R 61 66 21980293 Multidrug resistant 2009 A/H1N1 influenza clinical isolate with a neuraminidase I223R mutation retains its virulence and transmissibility in ferrets. It was expected that reduced replication in ferrets would impede the virus to transmit to naive animals, thereby suggesting that compensatory mutations are needed to balance the fitness loss induced by the I223R mutation. 2011 PLoS pathogens Result IV I223R 206 211 21980293 Multidrug resistant 2009 A/H1N1 influenza clinical isolate with a neuraminidase I223R mutation retains its virulence and transmissibility in ferrets. Moderate pathogenicity of I223R harboring isolate. 2011 PLoS pathogens Result IV I223R 26 31 21980293 Multidrug resistant 2009 A/H1N1 influenza clinical isolate with a neuraminidase I223R mutation retains its virulence and transmissibility in ferrets. onwards and transmission was detected in 4 out of 4 (recNL/602), or 2 out of 2 (recNL/602-I223R) naive animals from day 2 onwards (Figure 5). 2011 PLoS pathogens Result IV I223R 90 95 21980293 Multidrug resistant 2009 A/H1N1 influenza clinical isolate with a neuraminidase I223R mutation retains its virulence and transmissibility in ferrets. Pair-wise comparison revealed, in addition to the amino acid change I223R, 5 amino acid differences in NA (V106I, V108I, N248D, N386D and I407V) and 1 in HA (S203T). 2011 PLoS pathogens Result IV I223R;V106I;V108I;N248D;N386D;I407V;S203T 68;107;114;121;128;138;158 73;112;119;126;133;143;163 HA;NA 154;103 156;105 21980293 Multidrug resistant 2009 A/H1N1 influenza clinical isolate with a neuraminidase I223R mutation retains its virulence and transmissibility in ferrets. Sequence analysis confirmed the presence of the I223R mutation in the respiratory samples collected at day 7 p.i. 2011 PLoS pathogens Result IV I223R 48 53 21980293 Multidrug resistant 2009 A/H1N1 influenza clinical isolate with a neuraminidase I223R mutation retains its virulence and transmissibility in ferrets. The presence of the I223R mutation in the recNL/602 backbone was confirmed in throat samples obtained from these animals at day 5 p.e. 2011 PLoS pathogens Result IV I223R 20 25 21980293 Multidrug resistant 2009 A/H1N1 influenza clinical isolate with a neuraminidase I223R mutation retains its virulence and transmissibility in ferrets. Therefore, we introduced the I223R mutation in the recNL/602 backbone, resulting in the drug-resistant recNL602-I223R, to evaluate the impact of the single I223R mutation on virus replication, virus shedding from the upper respiratory tract and transmissibility in the ferret model. 2011 PLoS pathogens Result IV I223R;I223R;I223R 29;112;156 34;117;161 21980293 Multidrug resistant 2009 A/H1N1 influenza clinical isolate with a neuraminidase I223R mutation retains its virulence and transmissibility in ferrets. This reference virus is a representative of pandemic H1N1 viruses that circulated in 2009, with only amino acid changes I108V and V407I (N1 numbering) in NA being unusual among the deposited sequences in the Influenza Research Database. 2011 PLoS pathogens Result IV I108V;V407I 120;130 125;135 154 156 21980293 Multidrug resistant 2009 A/H1N1 influenza clinical isolate with a neuraminidase I223R mutation retains its virulence and transmissibility in ferrets. To address if this difference in in vitro replication capacity could be extrapolated to reduced replication in vivo, the ability of recNL/602-I223R to transmit in the ferret model was studied. 2011 PLoS pathogens Result IV I223R 142 147 21980293 Multidrug resistant 2009 A/H1N1 influenza clinical isolate with a neuraminidase I223R mutation retains its virulence and transmissibility in ferrets. When the multi-cycle replication kinetics were studied of viruses with or without the I223R substitution in MDCK cells, it was noticed that the recombinant virus in which the I223R mutation was introduced, recNL/602-I223R, replicated to lower titers than its parental virus recNL/602 (Figure 1). 2011 PLoS pathogens Result IV I223R;I223R;I223R 86;175;216 91;180;221 22022458 Minor changes in the hemagglutinin of influenza A(H1N1)2009 virus alter its antigenic properties. In addition, novel double mutations (N125D and E374K) were also found in the group II/2010-2011 viruses, namely in A/Finland/19/2010 and A/Finland/22/2010 viruses. 2011 PloS one Result IV N125D;E374K 37;47 42;52 22022458 Minor changes in the hemagglutinin of influenza A(H1N1)2009 virus alter its antigenic properties. N125D and N156K mutations in Sa epitope of HA compromise the antibody recognition induced by vaccination with pandemic influenza A(H1N1)2009 vaccine. 2011 PloS one Result IV N125D;N156K 0;10 5;15 HA 43 45 22022458 Minor changes in the hemagglutinin of influenza A(H1N1)2009 virus alter its antigenic properties. Of potential interest in respect to antibody recognition is the group I/2009-2010 virus, A/Finland/694/2009, which has N125D and N156K amino acid substitutions on the distal end of the HA molecule locating to the antigenic site Sa (Figure 2 and Figure S2). 2011 PloS one Result IV N125D;N156K 119;129 124;134 HA 185 187 22022458 Minor changes in the hemagglutinin of influenza A(H1N1)2009 virus alter its antigenic properties. One conserved change in all Finnish A(H1N1)2009 virus strains, except A/Finland/554/2009, was S203T which is located in the antigenic epitope Ca1 of HA, close to the receptor binding pocket (Figure 2). 2011 PloS one Result IV S203T 94 99 HA 149 151 22022458 Minor changes in the hemagglutinin of influenza A(H1N1)2009 virus alter its antigenic properties. The amino acid change E374K has been identified in some A(H1N1)2009 viruses isolated in Finland (Figure 1) and elsewhere. 2011 PloS one Result IV E374K 22 27 22022458 Minor changes in the hemagglutinin of influenza A(H1N1)2009 virus alter its antigenic properties. The decrease in antibody levels against A/Finland/694/2009, A/Finland/698/2009, and A/Finland/618/2009 viruses, which exhibited mutations in different antigenic epitopes (N125D and N156K, S74N, or S162R, respectively; Figure 2 and Figure S2) showed that even one or two amino acid change may significantly alter HI titers and also have an effect on seroprotection rates. 2011 PloS one Result IV N125D;N156K;S74N;S162R 171;181;188;197 176;186;192;202 22138712 The 2008-2009 H1N1 influenza virus exhibits reduced susceptibility to antibody inhibition: Implications for the prevalence of oseltamivir resistant variant viruses. A substitution at D151 (D151E/N/A) of the NA gene has been found to affect the receptor binding characteristics of human H3N2 viruses, resulting in altered agglutination of red blood cells. 2012 Antiviral research Result IV D151E;D151N;D151A 24;24;24 33;33;33 42 44 22138712 The 2008-2009 H1N1 influenza virus exhibits reduced susceptibility to antibody inhibition: Implications for the prevalence of oseltamivir resistant variant viruses. H275Y variants exhibit differential neuraminidase activity. 2012 Antiviral research Result IV H275Y 0 5 36 49 22138712 The 2008-2009 H1N1 influenza virus exhibits reduced susceptibility to antibody inhibition: Implications for the prevalence of oseltamivir resistant variant viruses. In contrast to the results using clinical isolates, when mice were infected with reverse genetically modified H1N1 viruses where the only difference between oseltamivir resistant and susceptible strains was the H275Y substitution in the NA gene, there was no apparent difference in antibody levels between the 275Y and 275H strains, suggesting that H275Y alone is not sufficient to alter the antibody response in mice (Table 5). 2012 Antiviral research Result IV H275Y;H275Y 211;349 216;354 237 239 22138712 The 2008-2009 H1N1 influenza virus exhibits reduced susceptibility to antibody inhibition: Implications for the prevalence of oseltamivir resistant variant viruses. In the HA gene, all resistant strains contain an A189T substitution that is not seen in any of the susceptible strains (Supplementary Table 2). 2012 Antiviral research Result IV A189T 49 54 HA 7 9 22138712 The 2008-2009 H1N1 influenza virus exhibits reduced susceptibility to antibody inhibition: Implications for the prevalence of oseltamivir resistant variant viruses. It has been reported previously that the oseltamivir resistant H1N1 viruses containing H275Y mutant NA replicate similarly to wild type viruses in cell culture using canine MDCK and MDCK-SIAT1 cells. 2012 Antiviral research Result IV H275Y 87 92 100 102 22138712 The 2008-2009 H1N1 influenza virus exhibits reduced susceptibility to antibody inhibition: Implications for the prevalence of oseltamivir resistant variant viruses. Notably, antibody titers from mice inoculated with oseltamivir resistant (A/Hong Kong/423432/2009) are higher than those elicited by susceptible (A/California/07/2009) strains of the 2009 pandemic H1N1 virus (Table 5), further suggesting that the oseltamivir resistant 2009 pandemic H1N1 virus does not possess similar antigenic properties to the 2008-2009 H1N1 NA-H275Y virus. 2012 Antiviral research Result IV H275Y 365 370 362 364 22138712 The 2008-2009 H1N1 influenza virus exhibits reduced susceptibility to antibody inhibition: Implications for the prevalence of oseltamivir resistant variant viruses. Only one oseltamivir susceptible isolate, A/Hong Kong/02181/2008, was found to contain a D151E substitution. 2012 Antiviral research Result IV D151E 89 94 22138712 The 2008-2009 H1N1 influenza virus exhibits reduced susceptibility to antibody inhibition: Implications for the prevalence of oseltamivir resistant variant viruses. Previous studies showed that H275Y substitution in the NA gene caused changes in the enzymatic properties of the neuraminidase proteins of H1N1 and H5N1 viruses. 2012 Antiviral research Result IV H275Y 29 34 NA;NA 55;113 57;126 22138712 The 2008-2009 H1N1 influenza virus exhibits reduced susceptibility to antibody inhibition: Implications for the prevalence of oseltamivir resistant variant viruses. Sequence comparison of NA genes from 275H and 275Y H1N1 strains found that there is a D354G substitution in all resistant strains (Supplementary Table 1). 2012 Antiviral research Result IV D354G 86 91 23 25 22138712 The 2008-2009 H1N1 influenza virus exhibits reduced susceptibility to antibody inhibition: Implications for the prevalence of oseltamivir resistant variant viruses. The impact of NA D354G, HA A189T and other variations detected in the HA gene on viral fitness and antigenic properties remains to be investigated. 2012 Antiviral research Result IV D354G;A189T 17;27 22;32 HA;HA;NA 24;70;14 26;72;16 22138712 The 2008-2009 H1N1 influenza virus exhibits reduced susceptibility to antibody inhibition: Implications for the prevalence of oseltamivir resistant variant viruses. These results suggest that changes in the NA molecule associated with the H275Y substitution may contribute to the lower antibody reactivity of the 275Y variant. 2012 Antiviral research Result IV H275Y 74 79 42 44 22138712 The 2008-2009 H1N1 influenza virus exhibits reduced susceptibility to antibody inhibition: Implications for the prevalence of oseltamivir resistant variant viruses. To further characterize the effect of the H275Y substitution on reactivity between antibodies and resistant strains, we constructed a pair of recombinant viruses with HA and NA either directly derived from an oseltamivir resistant seasonal H1N1 virus, A/Hong Kong/62768/2008, or with the same HA but the NA of the resistant strain reverse-mutated from 275Y to 275H. 2012 Antiviral research Result IV H275Y 42 47 HA;HA;NA;NA 167;293;174;304 169;295;176;306 22138712 The 2008-2009 H1N1 influenza virus exhibits reduced susceptibility to antibody inhibition: Implications for the prevalence of oseltamivir resistant variant viruses. Zanamivir binds to a different site on the NA protein than oseltamivir and its action is unaffected by the H275Y substitution in the NA protein of H1N1 virus (; Hurt et al., 2009a). 2012 Antiviral research Result IV H275Y 107 112 NA;NA 43;133 45;135 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. 5A, mean viral titers in nasal wash samples collected on day 2 PI from ferrets infected with the recombinant WT and the single H275Y mutant were comparable (4x105+-2.9x104 PFU/ml for the WT and 2.6x105+-8.7x104 PFU/ml for the H275Y mutant) whereas the H275Y/Q222R mutant had a reduced mean viral titer (4.6x104+-4.2x103 PFU/ml; P<0.05 vs WT). 2011 PLoS pathogens Result IV H275Y;H275Y;H275Y;Q222R 127;226;252;258 132;231;257;263 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. 6.81+-1.19 for the WT virus, 5.99+-1.9 for the H275Y/Q222R mutant and 7.26+-0.55 for the H275Y mutant. 2011 PLoS pathogens Result IV Q222R;H275Y;H275Y 53;47;89 58;52;94 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. A febrile response could be observed on days 4 and 5 in the WT and the H275Y groups, respectively, but not in the H275Y/Q222R group. 2011 PLoS pathogens Result IV H275Y;H275Y;Q222R 71;114;120 76;119;125 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. All contact ferrets seroconverted for A/Brisbane/59/2007 when tested 14 days after contact, with geometrical mean hemagglutination inhibition (HAI) titers of 160+-33, 145+-119 and 95+-55 for the WT, H275Y and H275Y/Q222R recombinant viruses, respectively. 2011 PLoS pathogens Result IV H275Y;H275Y;Q222R 199;209;215 204;214;220 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. all studied mutations were associated with a significant reduction of total surface NA activity compared to the WT with relative total surface activities of 66% (P<0.01), 9.72% (P<0.001), 32.07% (P<0.001) and 54.89% (P<0.01) for the H275Y, H275Y/Q222R, H275Y/M234V and H275Y/N344D mutant proteins, respectively. 2011 PLoS pathogens Result IV H275Y;Q222R;H275Y;H275Y;M234V;H275Y;N344D 233;246;240;253;259;269;275 238;251;245;258;264;274;280 84 86 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. As expected, the presence of the H275Y mutation was associated with resistance to oseltamivir (mean fold increase of 2627 in IC50 values) and peramivir (mean fold increase of 998) with no impact on zanamivir susceptibility (Table 2). 2011 PLoS pathogens Result IV H275Y 33 38 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. As shown in Table 1, the single H275Y mutation had no significant impact on NA affinity and activity compared to the WT virus in the context of the Bris07 background. 2011 PLoS pathogens Result IV H275Y 32 37 76 78 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. By contrast, and in accordance with plaque size data, the double H275Y/Q222R mutant was associated with a significant reduction in viral titers at 36 h (P<0.001) and 48 h (P<0.05) PI compared to the WT. 2011 PLoS pathogens Result IV Q222R;H275Y 71;65 76;70 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. By contrast, the double H275Y/Q222R mutation was associated with a significant reduction of both NA affinity (Km of 40.31 vs 11.95 microM, P<0.001) and relative NA activity (7.01 vs 28.19 U/sec, P<0.001) compared to the WT (Table 1 and. 2011 PLoS pathogens Result IV H275Y;Q222R 24;30 29;35 NA;NA 97;161 99;163 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. In contrast, the H275Y/Q222R mutant was associated with significantly lower mean viral titers compared to WT on both day 4 (2.7x102+-1.2x102 vs 1.2x104+-3.5x103 PFU/ml, P<0.01) and day 6 PI (3.8x103+-2.1x103 vs 1.2x104+-2.5x103 PFU/ml, P<0.01). 2011 PLoS pathogens Result IV H275Y;Q222R 17;23 22;28 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. In replication kinetics experiments, the peak viral titers for all recombinants were obtained at 36 h post-infection (PI) with viral titers ranging from 5.6x106 PFU/ml (H275Y/Q222R) to 5.3x107 PFU/ml (WT). 2011 PLoS pathogens Result IV Q222R;H275Y 175;169 180;174 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. In the present study, five recombinant Bris07 influenza viruses were generated i.e., the WT virus (containing the putative permissive mutations) that briefly circulated during the 2007-08 season, the single H275Y oseltamivir-resistant variant and three double mutants containing the H275Y mutation as well as reversion of potential permissive mutations (H275Y/Q222R, H275Y/M234V and H275Y/N344D). 2011 PLoS pathogens Result IV H275Y;H275Y;H275Y;Q222R;M234V;H275Y;H275Y;N344D 207;283;354;360;373;367;383;389 212;288;359;365;378;372;388;394 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. Interestingly, comparison of the levels of resistance for the double recombinant mutants versus the single H275Y mutant revealed a significant reduction in the level of resistance to peramivir for the double H275Y/Q222R mutant (IC50 of 35.25 nM vs 59.85 nM, P<0.01). 2011 PLoS pathogens Result IV H275Y;H275Y;Q222R 107;208;214 112;213;219 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. Intranasal inoculation of ferrets with the WT and two mutant (H275Y and H275Y/Q222R) Bris07 recombinant viruses resulted in a febrile response that peaked on day 2 PI. 2011 PLoS pathogens Result IV H275Y;H275Y;Q222R 62;72;78 67;77;83 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. Mean viral titers were comparable for the H275Y mutant and the WT virus on days 4 and 6 PI. 2011 PLoS pathogens Result IV H275Y 42 47 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. Of note, the reduction in plaque size for the H275Y/Q222R mutant was also significant compared to that of the single H275Y mutant (P<0.001). 2011 PLoS pathogens Result IV Q222R;H275Y;H275Y 52;46;117 57;51;122 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. On the other hand, the three recombinants were associated with comparable mean viral titers on day 6 PI (2x102+-4.6x101 PFU/ml for the WT, 1.1x102+-5.8x101 PFU/ml for the H275Y/Q222R and 1.3x102+-8.1x10PFU/ml for the H275Y). 2011 PLoS pathogens Result IV H275Y;Q222R;H275Y 171;177;217 176;182;222 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. Similarly, mean viral titers in nasal wash samples of ferrets infected with the H275Y/Q222R were significantly lower than those of the H275Y mutant (P<0.05) and WT virus (P<0.01) on day 4 PI (3.4x103+-1.7x103, 1.1x104+-6.7x103 and 1.5x104+-9.6x102 PFU/ml, respectively). 2011 PLoS pathogens Result IV Q222R;H275Y;H275Y 86;80;135 91;85;140 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. The AUC of temperatures between days 2 and 6 PI was similar between groups of ferrets infected with the recombinant WT (5.29+-0.34) and its H275Y variant (4.54+-0.19) whereas the AUC of the H275Y/Q222R group was significantly lower than that of the WT group (4.09+-0.96; P<0.05). 2011 PLoS pathogens Result IV H275Y;H275Y;Q222R 140;190;196 145;195;201 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. The double H275Y/Q222R mutant produced viral plaques with a significantly reduced area compared to the recombinant WT (0.13 mm2 vs 0.53 mm2, P<0.001) whereas the remaining recombinants generated plaques of comparable sizes (Table 1). 2011 PLoS pathogens Result IV Q222R;H275Y 17;11 22;16 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. The H275Y/M234V mutant had a Km value comparable to that of the WT, whereas its relative NA activity was significantly reduced (Vmax of 21.89 vs 28.19 U/sec, P<0.05). 2011 PLoS pathogens Result IV M234V;H275Y 10;4 15;9 89 91 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. The H275Y/N344D mutant showed a significantly reduced affinity (Km of 50.77 vs 11.95 microM, P<0.001) with no change in NA activity compared to the WT. 2011 PLoS pathogens Result IV H275Y;N344D 4;10 9;15 120 122 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. The WT, the single (H275Y) and the double (H275Y/N344D) mutants had comparable viral titers at all time points. 2011 PLoS pathogens Result IV H275Y;H275Y;N344D 20;43;49 25;48;54 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. There was also a significant reduction in the viral titer obtained at 36 h PI for the double H275Y/M234V mutant compared to the WT (P<0.001). 2011 PLoS pathogens Result IV H275Y;M234V 93;99 98;104 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. When compared to the single (H275Y) mutant, viral titers of the double H275Y/Q222R and H275Y/M234V mutants were significantly lower at 36 h (P<0.001). 2011 PLoS pathogens Result IV H275Y;Q222R;H275Y;H275Y;M234V 29;77;71;87;93 34;82;76;92;98 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. When compared to the single H275Y mutant, H275Y/Q222R (P<0.001), H275Y/M234V (P<0.001) and H275Y/N344D (P<0.05) double mutants also had significantly reduced surface NA activities. 2011 PLoS pathogens Result IV H275Y;Q222R;H275Y;H275Y;M234V;H275Y;N344D 28;48;42;65;71;91;97 33;53;47;70;76;96;102 166 168 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. When comparing the double mutants to the single H275Y mutant, the Km values were significantly increased for the H275Y/Q222R and H275Y/N344D mutants (P<0.001) whereas only the double H275Y/Q222R mutant had a significantly lower relative NA activity (P<0.001). 2011 PLoS pathogens Result IV H275Y;H275Y;Q222R;H275Y;N344D;H275Y;Q222R 48;113;119;129;135;183;189 53;118;124;134;140;188;194 237 239 22217077 Surveillance in Eastern India (2007-2009) revealed reassortment event involving NS and PB1-F2 gene segments among co-circulating influenza A subtypes. All 31 A/KOL/H1N1 showed an alternative start codon (AUG) at positions 119 to 121 in the PB1 gene, which translated into Met (M) and marked the beginning 6 of PB1-F2 ORF. 2012 Virology journal Result IV A119G 52 74 PB1;PB1F2 89;159 92;165 22217077 Surveillance in Eastern India (2007-2009) revealed reassortment event involving NS and PB1-F2 gene segments among co-circulating influenza A subtypes. In addition, Trp (W) at position 78 of 5 NEP/NS2 which is implicated in NEP-M1 interaction and nuclear export of viral ribonucleoprotein complexes was conserved in all the eastern Indian strains but these five strains had an additional PR8-like G63E substitution in the NEP/NS2 region (Figure 4). 2012 Virology journal Result IV G63E;W78W 245;12 249;36 M1;NEP;NEP;NEP;NS2;NS2 76;41;72;270;45;274 78;44;75;273;48;277 22217077 Surveillance in Eastern India (2007-2009) revealed reassortment event involving NS and PB1-F2 gene segments among co-circulating influenza A subtypes. The NS1 polypeptides of three 2007 and two 2009 eastern India H1N1 strains showed sequence homology with the prototype H1N1 strain [A/PR/8/34(H1N1)] with A/PR/8/34(H1N1)-like mutations in both RNA-binding (H4N, Q21R, A22V, K44R, N53D, C59R and V60A) and effector (F103S and M106I) domains, whereas, other strains from this region were more similar to the concurrent vaccine strains (Figure 2). 2012 Virology journal Result IV H4N;Q21R;A22V;K44R;N53D;C59R;V60A;F103S;M106I 206;211;217;223;229;235;244;264;274 209;215;221;227;233;239;248;269;279 NS1 4 7 22230322 Highly pathogenic avian influenza virus H5N1 controls type I IFN induction in chicken macrophage HD-11 cells: a polygenic trait that involves NS1 and the polymerase complex. A reassortant Vac-derived virus with the Yama HA segment (Vac-Yama/HA), and a Yama mutant carrying an NS1 A144V substitution (Yama-NS1A144V) corresponding to that described for A/goose/Guangdong/1/96 (H5N1) at position 149 were generated. 2012 Virology journal Result IV A144V;A144V 106;134 111;139 HA;HA;NS1;NS1 46;67;102;131 48;69;105;134 22230322 Highly pathogenic avian influenza virus H5N1 controls type I IFN induction in chicken macrophage HD-11 cells: a polygenic trait that involves NS1 and the polymerase complex. Interestingly, the Vac PB2 and Yama PB2 amino acid sequences differ only by four amino acids (M64I, I67V, T108A and K339T). 2012 Virology journal Result IV M64I;I67V;T108A;K339T 94;100;106;116 98;104;111;121 PB2;PB2 23;36 26;39 22238617 Mutational analyses of the influenza A virus polymerase subunit PA reveal distinct functions related and unrelated to RNA polymerase activity. At 20 hpi, when wild-type virus had reached a titer of 106 pfu/ml, the titers of K378A and D478A were 3 and 4 fold lower, respectively, and E656A was not yet producing detectable plaques. 2012 PloS one Result IV K378A;D478A;E656A 81;91;140 86;96;145 22238617 Mutational analyses of the influenza A virus polymerase subunit PA reveal distinct functions related and unrelated to RNA polymerase activity. At 28 hpi, titers of E656A and K378A each lagged the wild-type by ~50 fold, while that of D478A lagged by 300 fold. 2012 PloS one Result IV E656A;K378A;D478A 21;31;90 26;36;95 22238617 Mutational analyses of the influenza A virus polymerase subunit PA reveal distinct functions related and unrelated to RNA polymerase activity. Consistent with the earlier report, E656A yielded a virus titer more than 2 logs lower than wild type, and it formed tiny plaques ( Figure 4A ). 2012 PloS one Result IV E656A 36 41 22238617 Mutational analyses of the influenza A virus polymerase subunit PA reveal distinct functions related and unrelated to RNA polymerase activity. In summary, among this group of nine single-codon mutations targeting residues that lie close to the J10 locus in the native PA structure, we found two (K378A and D478A) that markedly reduced infectivity without compromising RNA synthesis - the phenotype shared by L3, L5, L8, L9, and L10, and first observed in J10. 2012 PloS one Result IV K378A;D478A 153;163 158;168 PA 125 127 22238617 Mutational analyses of the influenza A virus polymerase subunit PA reveal distinct functions related and unrelated to RNA polymerase activity. K378A gave indistinct plaques and a 25-fold reduced titer, and D478A produced a mixture of large and small plaques. 2012 PloS one Result IV K378A;D478A 0;63 5;68 22238617 Mutational analyses of the influenza A virus polymerase subunit PA reveal distinct functions related and unrelated to RNA polymerase activity. We have reported that the bi-codon mutation J10 (G507A-R508A) in PA has little or no apparent effect on viral RNA synthesis but severely impairs infectivity and viral particle yield in a spreading-infection assay. 2012 PloS one Result IV G507A;R508A 49;55 54;60 PA 65 67 22238617 Mutational analyses of the influenza A virus polymerase subunit PA reveal distinct functions related and unrelated to RNA polymerase activity. We targeted eight individual residues within positions 361-480, in each case substituting alanine for a single charged, polar, or bulky native residue (i.e., K361, K362, K367, E372, K378, K385, D478, and F480); in addition, we recreated the mutant E656A which had been reported by other investigators to form tiny plaques despite normal viral RNA synthesis, a phenotype reminiscent of J10. 2012 PloS one Result IV E656A 248 253 22238617 Mutational analyses of the influenza A virus polymerase subunit PA reveal distinct functions related and unrelated to RNA polymerase activity. When tested for polymerase activity using the 5-plasmid assay, E656A was the only mutant in this group that showed any defect, as evidenced by modest reductions both in luciferase expression and in RNA synthesis as measured by the primer-extension assay ( Figure 4C ). 2012 PloS one Result IV E656A 63 68 22252168 Susceptibility of avian influenza viruses of the N6 subtype to the neuraminidase inhibitor oseltamivir. The I222V NA mutation has been shown to confer reduced susceptibility of human influenza viruses of the N1 and N2 NA subtypes to oseltamivir in phenotypic assays. 2012 Antiviral research Result IV I222V 4 9 NA;NA 10;114 12;116 22252168 Susceptibility of avian influenza viruses of the N6 subtype to the neuraminidase inhibitor oseltamivir. These two isolates possess the I222V NA mutation (I222V, N2 numbering; and I223V, N1 numbering). 2012 Antiviral research Result IV I222V;I222V;I223V 31;50;75 36;55;80 37 39 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. Analysis of loop 1 in R361A. 2012 PloS one Result IV R361A 22 27 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. Characterization of RNA-free wt NP, wt-E80A-E81A, wt-R204A-R208A, R361A and R361A-E80A-E81A, R361A-R204A-R208A mutants. 2012 PloS one Result IV E80A;E81A;R204A;R208A;R361A;R361A;E80A;E81A;R361A;R204A;R208A 39;44;53;59;66;76;82;87;93;99;105 43;48;58;64;71;81;86;91;98;104;110 NP 32 34 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. Comparison between the fluctuations of NP and R361A monomers. 2012 PloS one Result IV R361A 46 51 NP 39 41 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. Consequently, loop 1 of the R361A mutant was unstructured and more elongated than in NP (30.6 A and 37.6 A for wt NP and R361A respectively) which allowed loop-loop contacts. 2012 PloS one Result IV R361A;R361A 28;121 33;126 NP;NP 85;114 87;116 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. Figure 2 highlights the large structural difference between NP and R361A in the relative position of loops 1 and 2. 2012 PloS one Result IV R361A 67 72 NP 60 62 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. Figure 2 shows the superimposed structure of the loops 1 and 2 of the R361A mutant represented in green on NP monomer structure shown in red. 2012 PloS one Result IV R361A;R361A 71;70 76;75 NP 107 109 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. Figure 2 shows the superimposed structure of the loops 1 and 2 of the R361A mutant represented in green on NP monomer structure. 2012 PloS one Result IV R361A 70 75 NP 107 109 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. However, the ability to form RNA-NP oligomers of normal size was partly recovered in R361A-R204A-R208A for which the oligomers had a diameter of Dh = 14+-1 nm, compared to Dh = 11+-1 nm observed in the presence R361A. 2012 PloS one Result IV R204A;R208A;R361A;R361A 91;97;85;211 96;102;90;216 NP 33 35 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. In contrast with the ability of the loop 1-double mutant to form oligomers with an apparent diameter of Dh = 16+-1 nm as NP did, wt- R204A- R208A oligomers had a smaller size of Dh = 12+-1 nm (Figure 7b and data not shown). 2012 PloS one Result IV R204A;R208A 133;140 138;145 NP 121 123 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. In contrast, the signal of the R361A-E80A-E81A triple mutant was about twice larger than that of R361A. 2012 PloS one Result IV R361A;E80A;E81A;R361A 31;37;42;97 36;41;46;102 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. In contrast, the triple mutant R361A-E80A-E81A formed oligomers of Dh = 16+-2 nm, recovered an oligomerization rate similar to that of NP, in contrast with R361A-RNA oligomers (Figure 6C). 2012 PloS one Result IV E81A;R361A;E80A;R361A 42;31;37;156 46;36;41;161 NP 135 137 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. In contrast, this distance was drastically reduced to a value of 2.5 A in the R361A mutant, consistent with the formation of strong interactions bridging the two loops, in agreement with the formation of a salt bridge and hydrophobic contacts (Figure 2). 2012 PloS one Result IV R361A 78 83 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. In R361A, the flexibility of loop 3 also presented a relative decrease. 2012 PloS one Result IV R361A 3 8 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. Indeed, R361A has a lower affinity for RNA and a reduced ability to oligomerize (see below). 2012 PloS one Result IV R361A 8 13 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. L79 of loop 1 made hydrophobic interactions with W207 and the aliphatic portion of R208 (carbons Cbeta and Cgamma) of loop 2 which drove and stabilized the loop-loop interactions in R361A. 2012 PloS one Result IV R361A 182 187 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. Loop 1 became unstructured in R361A and came in close contact with loop 2, stabilized by a salt bridge between E80 and R208 (Figure 2, inset). 2012 PloS one Result IV R361A 30 35 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. Loop 1 became unstructured in R361A. 2012 PloS one Result IV R361A 30 35 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. NP was eluted at a similar retention volume than R416A mutant, known to be monomeric. 2012 PloS one Result IV R416A 49 54 NP 0 2 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. The affinity of the R361A-R204A-R208A mutant for RNA was lower than that of R361A, Kd = 1.1+-0.1 microM and 565+-60 nM, respectively. 2012 PloS one Result IV R204A;R208A;R361A;R361A 26;32;20;76 31;37;25;81 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. The apparent equilibrium dissociation constants were found to be Kd = 41+-7 nM, 240+-26 nM and 565+-60 nM for NP, R361A-E80A-E81A and R361A respectively. 2012 PloS one Result IV R361A;E81A;E80A;R361A 114;125;120;134 119;129;124;139 NP 110 112 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. The extent of RNA-induced oligomerization of R361A was lower than that of NP: once formed, R361A-RNA oligomers had an apparent smaller size of Dh = 11+-1 nm than Dh = 16+-1 nm observed for the NP-RNA oligomers (Figure 6A and B). 2012 PloS one Result IV R361A;R361A 45;91 50;96 NP;NP 74;193 76;195 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. The flexibility of loop 2 was reduced by the R361A mutation, located on a linker of the RNA binding domain. 2012 PloS one Result IV R361A 45 50 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. The formation of the salt bridge is consistent with the RMSF decrease of loop 2 in R361A relative to that of NP (Figure 1B). 2012 PloS one Result IV R361A 83 88 NP 109 111 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. The insert of Figure 5 shows that the association of NP to RNA resulted in a fast NP-RNA complex, in contrast with the slower association of the R361A mutant to RNA yielding to a ca three times lower signal using a protein concentration of 400 nM. 2012 PloS one Result IV R361A 145 150 NP;NP 53;82 55;84 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. The R361A mutant was eluted into two main peaks at 81.6 ml and 70.4 ml, resembling the chromatographic profile of NP, but required 300 mM NaCl for elution from the size-exclusion column. 2012 PloS one Result IV R361A 4 9 NP 114 116 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. The RMSF value decreased markedly in loop 2 while it increased somewhat in loop 1 of R361A compared to loops 1 and 2 of NP monomer respectively (Figure 1B). 2012 PloS one Result IV R361A 85 90 NP 120 122 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. The single-point mutation R361A, located in the RNA binding groove, was created from the wt structure and used for testing the relationships between flexibility, RNA binding and RNA-induced oligomerization. 2012 PloS one Result IV R361A 26 31 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. The size of the NP - RNA oligomers was comparable to that formed with wt-E80A-E81A in the presence of RNA (data not shown). 2012 PloS one Result IV E81A;E80A 78;73 82;77 NP 16 18 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. The triple mutant recovered part of the affinity for RNA that was lost in the single mutant R361A. 2012 PloS one Result IV R361A 92 97 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. The wt monomer and R361A mutant were simulated over runs of 50 ns for each protein in explicit solvent conditions to insure correct electrostatic interactions in these highly charged proteins. 2012 PloS one Result IV R361A 19 24 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. The wt NP protein and the R361A, wt-E80A-E81A, wt-R204A-R208A and R361A-E80A-E81A, R361A-R204A-R208A mutants were expressed as C-terminal His-tagged proteins in E. 2012 PloS one Result IV R361A;E81A;E80A;R204A;R208A;E81A;R361A;E80A;R204A;R208A;R361A 26;41;36;50;56;77;66;72;89;95;83 31;45;40;55;61;81;71;76;94;100;88 NP 7 9 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. The wt- R204A- R208A protein in which the mutation belongs to loop 2 had a RNA binding affinity of Kd = 350+-40 nM, close to Kd = 280+-40 nM observed for the wt-E80A-E81A mutant. 2012 PloS one Result IV R204A;R208A;E81A;E80A 8;15;166;161 13;20;170;165 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. Therefore, the remaining affinity difference between R361A-E80A-E81A and wt NP was due to the E80A-E81A mutation without contribution of the R361A single mutation. 2012 PloS one Result IV R361A;E81A;E80A;E81A;E80A;R361A 53;64;59;99;94;141 58;68;63;103;98;146 NP 76 78 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. This mainly resulted from a lower association rate constant for the R361A monomer compared to that of the wt. 2012 PloS one Result IV R361A 68 73 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. This reduced flexibility was caused, at least partly, by interactions between loops 1 and 2, mediated by a salt bridge between E80 and R208 and additional hydrophobic interactions (Figure 2), thus the gate for RNA accessing its binding groove was narrowed from 12 A in NP to 2.5 A in R361A (Figures 2, 3). 2012 PloS one Result IV R361A 284 289 NP 269 271 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. This result comforts the hypothesis of the salt bridge between R208 and E80 in R361A that reduced access to RNA for its binding groove, leading in R361A to an increase of the apparent Kd (loss of affinity) and a decrease of the association rate constant to RNA compared to NP (Figure 5A, insert). 2012 PloS one Result IV R361A;R361A 79;147 84;152 NP 273 275 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. To test this model, we expressed the recombinant NP, R361A, wt- E80A- E81A and R361A- E80A-E81A proteins. 2012 PloS one Result IV R361A;E80A;E81A;R361A;E81A;E80A 53;64;70;79;91;86 58;68;74;84;95;90 NP 49 51 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. We also tested the E80A E81A mutation in the context of wt NP: its affinity for RNA was identical within experimental error to that observed with the triple mutant Kd = 280+-40 nM (Figure 5B). 2012 PloS one Result IV E80A;E81A 19;24 23;28 NP 59 61 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. We expected improved RNA binding and RNA-induced oligomerization in this triple mutant as compared to that in R361A. 2012 PloS one Result IV R361A 110 115 22363521 Frequency of D222G and Q223R hemagglutinin mutants of pandemic (H1N1) 2009 influenza virus in Japan between 2009 and 2010. A homology modeling and docking study also showed that D222G and Q223R mutants had reduced affinity for the alpha2,6 sialic acid-linked receptor (Figure S4). 2012 PloS one Result IV D222G;Q223R 55;65 60;70 22363521 Frequency of D222G and Q223R hemagglutinin mutants of pandemic (H1N1) 2009 influenza virus in Japan between 2009 and 2010. Among these substitutions, D222G and Q223R had already been shown to be critical for receptor binding and to cause a shift from alpha2,6 to alpha2,3 sialic acid receptor specificity. 2012 PloS one Result IV D222G;Q223R 27;37 32;42 22363521 Frequency of D222G and Q223R hemagglutinin mutants of pandemic (H1N1) 2009 influenza virus in Japan between 2009 and 2010. By contrast, the N125D mutation could still be detected (0.66-2.15%; average, 1.42%) (Table 2). 2012 PloS one Result IV N125D 17 22 22363521 Frequency of D222G and Q223R hemagglutinin mutants of pandemic (H1N1) 2009 influenza virus in Japan between 2009 and 2010. D222G and/or Q223R substitutions were detected at even higher rates in the early passaged (P1) viruses (Table 3) than in the parental viruses (Table 1). 2012 PloS one Result IV D222G;Q223R 0;13 5;18 22363521 Frequency of D222G and Q223R hemagglutinin mutants of pandemic (H1N1) 2009 influenza virus in Japan between 2009 and 2010. Deep sequencing analysis of H1N1pdm HA D222G or Q223R mutants from the second wave of the outbreak. 2012 PloS one Result IV D222G;Q223R 39;48 44;53 HA 36 38 22363521 Frequency of D222G and Q223R hemagglutinin mutants of pandemic (H1N1) 2009 influenza virus in Japan between 2009 and 2010. Deep sequencing of more than 3,000 clones (reads) per specimen showed high rates of amino acid diversity, with the K119N, N125D, D222G, and Q223R substitutions in specimens #1-#3 (Table 2). 2012 PloS one Result IV K119N;N125D;D222G;Q223R 115;122;129;140 120;127;134;145 22363521 Frequency of D222G and Q223R hemagglutinin mutants of pandemic (H1N1) 2009 influenza virus in Japan between 2009 and 2010. Four substitutions, K119N, N125D, D222G, and Q223R, were detected in more than 2.0% of the samples (Table 1). 2012 PloS one Result IV K119N;N125D;D222G;Q223R 20;27;34;45 25;32;39;50 22363521 Frequency of D222G and Q223R hemagglutinin mutants of pandemic (H1N1) 2009 influenza virus in Japan between 2009 and 2010. In addition, the D187E substitution could be critical for the human-to-avian-type receptor switch. 2012 PloS one Result IV D187E 17 22 22363521 Frequency of D222G and Q223R hemagglutinin mutants of pandemic (H1N1) 2009 influenza virus in Japan between 2009 and 2010. K119N, N125D and D187E mutations were also detected at higher ratios in the P5 or P6 passages than in the P1 passage, suggesting that these mutations were being selected for effective growth in avian cells. 2012 PloS one Result IV K119N;N125D;D187E 0;7;17 5;12;22 22363521 Frequency of D222G and Q223R hemagglutinin mutants of pandemic (H1N1) 2009 influenza virus in Japan between 2009 and 2010. More than half (98.6%, 95.0%, and 59.7% in #1, #2, and #3, respectively) possessed either D222G or Q223R substitutions (Table 3). 2012 PloS one Result IV D222G;Q223R 90;99 95;104 22363521 Frequency of D222G and Q223R hemagglutinin mutants of pandemic (H1N1) 2009 influenza virus in Japan between 2009 and 2010. The D187E substitution was also identified in two specimens through deep sequencing analysis; however, the substitution rate was only slightly increased in one of these (by 0.72% in specimen #2) (Table 2). 2012 PloS one Result IV D187E 4 9 22363521 Frequency of D222G and Q223R hemagglutinin mutants of pandemic (H1N1) 2009 influenza virus in Japan between 2009 and 2010. The K119N mutation frequency also shifted to an undetectable level except for one specimen (#8). 2012 PloS one Result IV K119N 4 9 22363521 Frequency of D222G and Q223R hemagglutinin mutants of pandemic (H1N1) 2009 influenza virus in Japan between 2009 and 2010. The results showed low substitution rates for D222G and Q223R (0.01-0.11% and 0.1-0.41%, respectively), consistent with the results of the second epidemic, in H1N1pdm. 2012 PloS one Result IV D222G;Q223R 46;56 51;61 22363521 Frequency of D222G and Q223R hemagglutinin mutants of pandemic (H1N1) 2009 influenza virus in Japan between 2009 and 2010. These results are coincident with the homology modeling and docking of D222G and Q223R mutants (Figure S4). 2012 PloS one Result IV D222G;Q223R 71;81 76;86 22363521 Frequency of D222G and Q223R hemagglutinin mutants of pandemic (H1N1) 2009 influenza virus in Japan between 2009 and 2010. To elucidate how the genomic diversity (and population) of the RBS, including the D222G and/or Q223R substitutions, might change, we inoculated these specimens into embryonated chicken eggs and serially passaged them five or six times in eggs. 2012 PloS one Result IV D222G;Q223R 82;95 87;100 22438920 Mutations in polymerase genes enhanced the virulence of 2009 pandemic H1N1 influenza virus in mice. Amino acid at position 357 in PB2 or 36 in PA displayed polymorphic, and the substitutions similar to SC_PB2-H357N and SC_PA-A36T were rare (Table 1). 2012 PloS one Result IV H357N;A36T 109;125 114;129 PA;PB2 43;30 45;33 22438920 Mutations in polymerase genes enhanced the virulence of 2009 pandemic H1N1 influenza virus in mice. Approximately 30% weight loss was detected in SC_PB2-H357N-infected mice together with an 80% mortality rate. 2012 PloS one Result IV H357N 53 58 22438920 Mutations in polymerase genes enhanced the virulence of 2009 pandemic H1N1 influenza virus in mice. In contrast to SC_PA-A36T and SC_WT (105 and 105.5 TCID50 causing 50% mice death, respectively), PB2-H357N has an MLD50 of 103.5 TCID50. 2012 PloS one Result IV A36T;H357N 21;101 25;106 PB2 97 100 22438920 Mutations in polymerase genes enhanced the virulence of 2009 pandemic H1N1 influenza virus in mice. In contrast, the SC_PA-A36T and SC_WT viruses caused around 20% weight loss with no significant difference. 2012 PloS one Result IV A36T 23 27 22438920 Mutations in polymerase genes enhanced the virulence of 2009 pandemic H1N1 influenza virus in mice. In line with viral replication in LA-4 cells, titer of SC_PB2-H357N was significant higher than that of WT at all the tested time points, and peaked (>107 TCID50/ml) at 48 hpi. 2012 PloS one Result IV H357N 62 67 22438920 Mutations in polymerase genes enhanced the virulence of 2009 pandemic H1N1 influenza virus in mice. In order to investigate whether the PA-A36T or PB2-H357N mutations affect the enzymatic activity of RdRp, we analyzed the reconstituted ribonucleoprotein complexes polymerase activities (composed of PB2, PB1, PA, and NP) in 293T cells at different temperatures using a mini-genome replication assay as described previously. 2012 PloS one Result IV A36T;H357N 39;51 43;56 NP;PA;PA;PB1;PB2;PB2 217;36;209;204;47;199 219;38;211;207;50;202 22438920 Mutations in polymerase genes enhanced the virulence of 2009 pandemic H1N1 influenza virus in mice. Mice were inoculated intranasally with 104 TCID50 of SC_WT, SC_PB2-H357N, and SC_PA-A36T. 2012 PloS one Result IV H357N;A36T 67;84 72;88 22438920 Mutations in polymerase genes enhanced the virulence of 2009 pandemic H1N1 influenza virus in mice. Multi-cycle growth assay of recombinant viruses containing PA-A36T or PB2-H357N mutation was performed in human, porcine and murine epithelial cell lines at 35 or 39 C at a MOI of 0.0001. 2012 PloS one Result IV A36T;H357N 62;74 66;79 PA;PB2 59;70 61;73 22438920 Mutations in polymerase genes enhanced the virulence of 2009 pandemic H1N1 influenza virus in mice. Notably, the strongest RNP activity of PA-A36T than PB2-357N and WT was detected at both 37 and 39 C, and was nearly 10-, and 20-fold increase as compared with WT, respectively (p<0.001; n = 3). 2012 PloS one Result IV A36T 42 46 PA;PB2;RNP 39;52;23 41;55;26 22438920 Mutations in polymerase genes enhanced the virulence of 2009 pandemic H1N1 influenza virus in mice. Our study showed that the SC_PB2-H357N mutant displayed marked replication activity in mice and caused severe infection and high mortality. 2012 PloS one Result IV H357N 33 38 22438920 Mutations in polymerase genes enhanced the virulence of 2009 pandemic H1N1 influenza virus in mice. PA-A36T or PB2-H357N mutant replicated efficiently in human, porcine and murine cells. 2012 PloS one Result IV A36T;H357N 3;15 7;20 PA;PB2 0;11 2;14 22438920 Mutations in polymerase genes enhanced the virulence of 2009 pandemic H1N1 influenza virus in mice. Recombinant viruses containing PA-A36T or PB2-357N mutation enhanced virulence in mice. 2012 PloS one Result IV A36T 34 38 PA;PB2 31;42 33;45 22438920 Mutations in polymerase genes enhanced the virulence of 2009 pandemic H1N1 influenza virus in mice. RNP complex with PA-A36T or PB2-H357N mutation enhanced the polymerase activity at different temperatures. 2012 PloS one Result IV A36T;H357N 20;32 24;37 PA;PB2;RNP 17;28;0 19;31;3 22438920 Mutations in polymerase genes enhanced the virulence of 2009 pandemic H1N1 influenza virus in mice. Significantly higher virus titer of SC_PB2-H357N mutant than SC_WT was found in PK15 cells at 24 hpi. 2012 PloS one Result IV H357N 43 48 22438920 Mutations in polymerase genes enhanced the virulence of 2009 pandemic H1N1 influenza virus in mice. Similar to viral replication in A549 and PK15 cells , significantly higher titers of SC_PA-A36T were detected at early stage, i.e., 24 hpi. 2012 PloS one Result IV A36T 91 95 22438920 Mutations in polymerase genes enhanced the virulence of 2009 pandemic H1N1 influenza virus in mice. The mutation of PA-A36T exhibited significantly elevated growth ability in both A549 and PK15 cells with virus titers of more than 10-fold higher than those of SC_WT at 24 hpi and the trend maintained throughout the time course. 2012 PloS one Result IV A36T 19 23 PA 16 18 22438920 Mutations in polymerase genes enhanced the virulence of 2009 pandemic H1N1 influenza virus in mice. To determine if SC_PB2-H357N/SC_PA-A36T replicated more efficiently than SC_WT virus in vivo, we inoculated mice with 104 TCID50 of each virus and analyzed virus titers in lung at various time points post inoculation. 2012 PloS one Result IV H357N;A36T 23;35 28;39 22438920 Mutations in polymerase genes enhanced the virulence of 2009 pandemic H1N1 influenza virus in mice. To determine whether the amino acid substitutions observed in SC_PA-A36T and SC_PB2-H357N also exist in field strains, we checked all public available sequences from GenBank. 2012 PloS one Result IV A36T;H357N 68;84 72;89 22438920 Mutations in polymerase genes enhanced the virulence of 2009 pandemic H1N1 influenza virus in mice. To elucidate the contribution of the PB2-H357N and PA-A36T mutations to virulence in mice, we used recombinant viruses to determine the MLD50. 2012 PloS one Result IV H357N;A36T 41;54 46;58 PA;PB2 51;37 53;40 22449422 Engineering temperature sensitive live attenuated influenza vaccines from emerging viruses. 2D), indicating that the additional mutations (P112S, N556D, Y658H) engineered into the PB2 gene of rNY1682-TS2 conferred an enhanced ts phenotype and restricted the virus completely. 2012 Vaccine Result IV P112S;N556D;Y658H 47;54;61 52;59;66 PB2 88 91 22449422 Engineering temperature sensitive live attenuated influenza vaccines from emerging viruses. An infectious clone set was created directly from clinical specimen using M-RTPCR and recombination-based cloning technologies, and the TS1 mutations (PB1-K391E, D581G, A661T, and PB2-N265S) or TS2 mutations (PB1-K391E, D581G, A661T, and PB2-P112S, N265S, N556D, Y658H) were introduced into this seasonal H1N1 influenza A strain (A/New York/1692/2009 [NY1692]), creating LAIV candidates rNY1692-TS1 and rNY1692-TS2. 2012 Vaccine Result IV K391E;D581G;A661T;N265S;K391E;D581G;A661T;P112S;N265S;N556D;Y658H 155;162;169;184;213;220;227;242;249;256;263 160;167;174;189;218;225;232;247;254;261;268 M;PB1;PB1;PB2;PB2 74;151;209;180;238 75;154;212;183;241 22449422 Engineering temperature sensitive live attenuated influenza vaccines from emerging viruses. No mutation was introduced into the NP vRNA because the NY1682 wild-type virus already contained NP-D34G, which was shown to play a role in the ts phenotype of ca A/AA/6/60. 2012 Vaccine Result IV D34G 100 104 NP;NP 36;97 38;99 22449422 Engineering temperature sensitive live attenuated influenza vaccines from emerging viruses. The rNY1682-TS2 LAIV candidate was designed to incorporate these additional PB2 mutations (PB2-Mut4: P112S, N265S, N556D, Y658H) into the rNY1682 genome. 2012 Vaccine Result IV P112S;N265S;N556D;Y658H 101;108;115;122 106;113;120;127 PB2;PB2 76;91 79;94 22449422 Engineering temperature sensitive live attenuated influenza vaccines from emerging viruses. There are six amino acid differences (S100P, K136E, A203D, D239G, D293N, and V338I, amino acid positions are based on the use of the start codon and include the signal peptide) between the HA's of rNY1682-viruses and the MDCK propagated FluMist -H1N1pdm LAIV. 2012 Vaccine Result IV S100P;K136E;A203D;D239G;D293N;V338I 38;45;52;59;66;77 43;50;57;64;71;82 HA 189 191 22449422 Engineering temperature sensitive live attenuated influenza vaccines from emerging viruses. These amino acid mutations include three mutations in PB1 (PB1-Mut3: K391E, D581G, A661T) and one mutation in PB2 (PB2-Mut1: N265S) (Fig.1A). 2012 Vaccine Result IV K391E;D581G;A661T;N265S 69;76;83;125 74;81;88;130 PB1;PB1;PB2;PB2 54;59;110;115 57;62;113;118 22449422 Engineering temperature sensitive live attenuated influenza vaccines from emerging viruses. Thus, to enhance attenuation and safety of the TS-LAIV prototype (NY1682-TS1) we also introduced three additional PB2 mutations (P112S, N556D, Y658H), which were previously identified and confirmed as ts markers in tsA/Ud/307/72 and tsA/GL/0389/65 . 2012 Vaccine Result IV P112S;N556D;Y658H 129;136;143 134;141;148 PB2 114 117 22615752 Functional analysis of conserved motifs in influenza virus PB1 protein. 3 ); the K480R mutant was included as a second 'positive control' since it directed efficient genome amplification and would thus be expected to be expressed stably. 2012 PloS one Result IV K480R 9 14 22615752 Functional analysis of conserved motifs in influenza virus PB1 protein. Among the 25 PB1 mutants tested, only K480R increased the replicative ability of the BHG polymerase complex in minireplicon assays. 2012 PloS one Result IV K480R 38 43 PB1 13 16 22615752 Functional analysis of conserved motifs in influenza virus PB1 protein. As detected in human 293T cells, mutant K480R once again augmented transcription and replication activity slightly. 2012 PloS one Result IV K480R 40 45 22615752 Functional analysis of conserved motifs in influenza virus PB1 protein. As found in the background of BHG, the K480R mutation slightly increased polymerase activities relative to wild-type in both cell lines . 2012 PloS one Result IV K480R 39 44 22615752 Functional analysis of conserved motifs in influenza virus PB1 protein. Comparison of the four conserved motifs revealed lower variability in motifs I and II (14 and 29 mutations, respectively) than in motif III (48 mutations) and motif IV (144 mutations, of which 88 encode K480R, see above) ( Table 1 ). 2012 PloS one Result IV K480R 203 208 22615752 Functional analysis of conserved motifs in influenza virus PB1 protein. For the other mutants tested, the levels of viral replication products overall correlated with the levels of luciferase expression: the N306T and D439E mutants yielded reduced levels of vRNA, cRNA, and mRNA, whereas the remaining mutants did not catalyze the synthesis of appreciable amounts of viral replication products. 2012 PloS one Result IV N306T;D439E 136;146 141;151 22615752 Functional analysis of conserved motifs in influenza virus PB1 protein. In contrast, mutation K480R (motif IV) slightly increased transcription/replication activity relative to wild-type polymerase activity. 2012 PloS one Result IV K480R 22 27 22615752 Functional analysis of conserved motifs in influenza virus PB1 protein. Overall, we observed the same trends of polymerase activity ( Table 3 ); however, two mutant PB1 proteins (T303I and A448V) showed higher activity in chicken than in human cells, while the inverse effect was observed for the D439E and Q442L mutants. 2012 PloS one Result IV T303I;A448V;D439E;Q442L 107;117;225;235 112;122;230;240 PB1 93 96 22615752 Functional analysis of conserved motifs in influenza virus PB1 protein. Polymerase Complex Activity and Virus Replication of PB1-K480R in Pandemic H1N1 Virus Background. 2012 PloS one Result IV K480R 57 62 PB1 53 56 22615752 Functional analysis of conserved motifs in influenza virus PB1 protein. Sequence analysis of the PB1 gene isolated from mutant viruses after replication in Calu-3 cells indicated that the K480R mutation was maintained in the viral population. 2012 PloS one Result IV K480R 116 121 PB1 25 28 22615752 Functional analysis of conserved motifs in influenza virus PB1 protein. The K480R mutant yielded increased levels of viral replication products compared to wild-type PB1; this increase was even more pronounced than that detected in luciferase assays. 2012 PloS one Result IV K480R 4 9 PB1 94 97 22615752 Functional analysis of conserved motifs in influenza virus PB1 protein. The K480R mutation may have originated in pig influenza viruses, where it has been found more frequently than in human and avian virus PB1 proteins. 2012 PloS one Result IV K480R 4 9 PB1 135 138 22615752 Functional analysis of conserved motifs in influenza virus PB1 protein. The most frequently observed deviation was K480R (motif IV), which was found in 33 human, 40 swine, and 15 avian virus PB1 proteins (i.e., in 0.45%, 4.21%, and 0.24% of the evaluated human, swine, and avian virus PB1 proteins, respectively). 2012 PloS one Result IV K480R 43 48 PB1;PB1 119;213 122;216 22615752 Functional analysis of conserved motifs in influenza virus PB1 protein. Therefore, despite slightly enhanced polymerase activity in the minireplicon assays, the K480R mutation did not significantly affect the replication of a pandemic (H1N1) 2009 virus in human airway epithelial cells. 2012 PloS one Result IV K480R 89 94 22615752 Functional analysis of conserved motifs in influenza virus PB1 protein. To further assess the significance of the K480R mutation for virus replication, we generated wild-type CA04 virus and a mutant encoding PB1-K480R. 2012 PloS one Result IV K480R;K480R 42;140 47;145 PB1 136 139 22615752 Functional analysis of conserved motifs in influenza virus PB1 protein. We found that the S444P and D445G mutations rendered the protein unstable; however, other mutations at position 445 (tested in combination with mutations at position 446, or at positions 447 and 449) resulted in detectable protein, suggesting that the nature of the amino acid at this position is critical. 2012 PloS one Result IV S444P;D445G 18;28 23;33 22621130 The new temperature-sensitive mutation PA-F35S for developing recombinant avian live attenuated H5N1 influenza vaccine. All these data showed that the single-mutation recombinant virus C4/W1-PA (F35S) as well as virus ts-C4/W1 was non-pathogenic to chickens and highly impaired in growth in chickens, which was critically important as LAIV. 2012 Virology journal Result IV F35S 75 79 PA 71 73 22621130 The new temperature-sensitive mutation PA-F35S for developing recombinant avian live attenuated H5N1 influenza vaccine. Although the ts mutations of the avian H9N2 LAIV were not identified, some of the amino acid mutations (PB2N265S, PB1K391E/E581G/A661T and NPD34G) were similar to the ts mutations of the MDV A/Ann Arbor/6/60 (H2N2). 2012 Virology journal Result IV E581G;A661T 123;129 128;134 NP;PB1;PB2 139;114;104 141;117;107 22621130 The new temperature-sensitive mutation PA-F35S for developing recombinant avian live attenuated H5N1 influenza vaccine. As shown in Figure 1, four of the five single-mutation recombinant viruses including C4/W1-PB1(K698N), C4/W1-HA(H119Y), C4/W1-M1(R174K) and C4/W1-NS1(K108N) did not display ts phenotype, they grew up to similar titers at 37 C or 41 C. 2012 Virology journal Result IV K698N;H119Y;R174K;K108N 95;112;129;150 100;117;134;155 HA;M1;NS1;PB1 109;126;146;91 111;128;149;94 22621130 The new temperature-sensitive mutation PA-F35S for developing recombinant avian live attenuated H5N1 influenza vaccine. As shown in Table 1, virus C4/W1-PA (F35S) and virus ts-C4/W1 were more attenuated (MLD50 > 8.0 log10EID50/50 mul) in mice than virus C4/W1 (MLD50 = 6.5 log10EID50/50 mul). 2012 Virology journal Result IV F35S 37 41 PA 33 35 22621130 The new temperature-sensitive mutation PA-F35S for developing recombinant avian live attenuated H5N1 influenza vaccine. As shown in Table 2, virus C4/W1-PA (F35S) induced detectable HI antibody titers and can provide efficient protection against the same clade or cross-clade H5N1 HPAIV with undetectable viral titers from tracheal or cloacal swabs at 3 days p.c., while all the chickens received with virus ts-C4/W1 or PBS died. 2012 Virology journal Result IV F35S 37 41 PA 33 35 22621130 The new temperature-sensitive mutation PA-F35S for developing recombinant avian live attenuated H5N1 influenza vaccine. Effects of the ts mutation PA (F35S) on polymerase activity was analyzed at different temperatures (37 C and 41 C) using minigenome reconstitution assay as described previously (Sun et al., 2010). 2012 Virology journal Result IV F35S 31 35 PA 27 29 22621130 The new temperature-sensitive mutation PA-F35S for developing recombinant avian live attenuated H5N1 influenza vaccine. Here, mice were used to assess the virulence of virus C4/W1-PA (F35S). 2012 Virology journal Result IV F35S 64 68 PA 60 62 22621130 The new temperature-sensitive mutation PA-F35S for developing recombinant avian live attenuated H5N1 influenza vaccine. However, at 41 C, the Luciferase activity of the RNP components of virus C4/W1 was 5.3-fold that of virus C4/W1-PA(F35S) (data not shown). 2012 Virology journal Result IV F35S 115 119 PA;RNP 112;49 114;52 22621130 The new temperature-sensitive mutation PA-F35S for developing recombinant avian live attenuated H5N1 influenza vaccine. However, transferring these ts mutations (PB2N265S, PB1K391E/E581G/A661T and NPD34G) into the corresponding internal genes of an avian H9N2 influenza virus A/Guinea Fowl/Hong Kong/WF10/99 could not sufficiently result in an avian live attenuated H9N2 influenza backbone, further introduction of an HA tag into PB1 gene was needed. 2012 Virology journal Result IV E581G;A661T 61;67 66;72 HA;NP;PB1;PB1;PB2 298;77;52;310;42 300;79;55;313;45 22621130 The new temperature-sensitive mutation PA-F35S for developing recombinant avian live attenuated H5N1 influenza vaccine. In light of rare LAIV used for poultry, we highlighted the potential of the new and simple ts mutation PA (F35S) in developing recombinant avian H5N1 LAIV with avian H9N2 influenza virus as backbone. 2012 Virology journal Result IV F35S 107 111 PA 103 105 22621130 The new temperature-sensitive mutation PA-F35S for developing recombinant avian live attenuated H5N1 influenza vaccine. The intravenous pathogenicity index (IVPI) was performed and indicated that virus C4/W1-PA (F35S) (IVPI = 0) as well as virus ts-C4/W1 (IVPI = 0) was more attenuated than virus C4/W1 (IVPI = 0.8). 2012 Virology journal Result IV F35S 92 96 PA 88 90 22621130 The new temperature-sensitive mutation PA-F35S for developing recombinant avian live attenuated H5N1 influenza vaccine. The position 35 was near the endonuclease active site 41 of PA (Yuan et al., 2009), whether the amino acid mutation PA(F35S) restricted the endonuclease activity of PA to some extent under thermal stress needed to be identified. 2012 Virology journal Result IV F35S 119 123 PA;PA;PA 60;116;165 62;118;167 22621130 The new temperature-sensitive mutation PA-F35S for developing recombinant avian live attenuated H5N1 influenza vaccine. The rest single-mutation recombinant virus C4/W1-PA (F35S) grew efficiently at C (8.9 log10 EID50/ml) in chicken eggs, but was highly impaired in growth at 41 C(under limited detection). 2012 Virology journal Result IV F35S 53 57 PA 49 51 22621130 The new temperature-sensitive mutation PA-F35S for developing recombinant avian live attenuated H5N1 influenza vaccine. The results showed that viruses C4/W1-PA (F35S) and ts-C4/W1 grew up to lower titers than that of virus C4/W1 at 3 or 6 days p.i. 2012 Virology journal Result IV F35S 42 46 PA 38 40 22621130 The new temperature-sensitive mutation PA-F35S for developing recombinant avian live attenuated H5N1 influenza vaccine. The RNP components of virus C4/W1 and C4/W1-PA(F35S) showed similar Luciferase activity at 37 C. 2012 Virology journal Result IV F35S 47 51 PA;RNP 44;4 46;7 22621130 The new temperature-sensitive mutation PA-F35S for developing recombinant avian live attenuated H5N1 influenza vaccine. These results indicated that PA (F35S) was the ts mutation. 2012 Virology journal Result IV F35S 33 37 PA 29 31 22621130 The new temperature-sensitive mutation PA-F35S for developing recombinant avian live attenuated H5N1 influenza vaccine. They were PB1 (K698N), PA (F35S), HA (H119Y), M1 (R174K) and NS1 (K108N) (data not shown). 2012 Virology journal Result IV K698N;F35S;H119Y;R174K;K108N 15;27;38;50;66 20;31;43;55;71 HA;M1;NS1;PA;PB1 34;46;61;23;10 36;48;64;25;13 22621130 The new temperature-sensitive mutation PA-F35S for developing recombinant avian live attenuated H5N1 influenza vaccine. To assess growth property, groups of 3-week-old White Leghorn chickens were inoculated intranasally (i.n.) with 0.2 ml 106 EID50 of the single-mutation recombinant virus C4/W1-PA (F35S), ts-C4/W1 or C4/W1, At 3 and 5 days post-inoculation (p.i.), four chickens in each group were sacrificed, tracheal swabs, cloacal swabs and lungs were collected in 1 ml phosphate buffered saline (PBS) containing penicillin and streptomycin, lungs were homogenized. 2012 Virology journal Result IV F35S 180 184 PA 176 178 22621130 The new temperature-sensitive mutation PA-F35S for developing recombinant avian live attenuated H5N1 influenza vaccine. To determine whether recombinant virus with the ts mutation PA (F35S) was attenuated in chickens, pathogenicity and growth property of the single-mutation recombinant virus C4/W1-PA (F35S) was assessed, viruses ts-C4/W1 and C4/W1 were used as comparison. 2012 Virology journal Result IV F35S;F35S 64;183 68;187 PA;PA 60;179 62;181 22621130 The new temperature-sensitive mutation PA-F35S for developing recombinant avian live attenuated H5N1 influenza vaccine. Virus C4/W1 caused maximum 20% of initial body weight loss, while no apparent body weight loss was observed when mice infected with virus C4/W1-PA (F35S) or ts-C4/W1 (Data not shown). 2012 Virology journal Result IV F35S 148 152 PA 144 146 22621130 The new temperature-sensitive mutation PA-F35S for developing recombinant avian live attenuated H5N1 influenza vaccine. Virus C4/W1 grew efficiently in chickens and could be detected in tracheal swabs, cloacal swabs and lungs of inoculated chickens with high viral titers at 3 and 5 days p.i.; virus ts-C4/W1 couldn't be detected in any swabs or lungs of the inoculated chickens; while virus C4/W1-PA (F35S) could only be detected in the tracheal swabs of inoculated chickens at 3 days p.i. 2012 Virology journal Result IV F35S 282 286 PA 278 280 22621130 The new temperature-sensitive mutation PA-F35S for developing recombinant avian live attenuated H5N1 influenza vaccine. with 0.2 ml 106 EID50 of the virus C4/W1-PA (F35S), ts-C4/W1 or 0.2 ml PBS. 2012 Virology journal Result IV F35S 45 49 PA 41 43 22621130 The new temperature-sensitive mutation PA-F35S for developing recombinant avian live attenuated H5N1 influenza vaccine. with 50 mul 106 EID50 of virus C4/W1-PA (F35S), ts-C4/W1 or C4/W1. 2012 Virology journal Result IV F35S 41 45 PA 37 39 22661221 Intrahost emergent dynamics of oseltamivir-resistant virus of pandemic influenza A (H1N1) 2009 in a fatally immunocompromised patient. 1), indicating the presence of H257Y mutant population. 2012 Journal of infection and chemotherapy Result IV H257Y 31 36 22661221 Intrahost emergent dynamics of oseltamivir-resistant virus of pandemic influenza A (H1N1) 2009 in a fatally immunocompromised patient. All H275Y mutants, except for the L7 clone, had additional common mutations at V80M and S82P, which were parsimony-informative sites (Table 2), suggesting that V80M and S82P might be important for the microevolution of oseltamivir-resistant virus. 2012 Journal of infection and chemotherapy Result IV H275Y;V80M;S82P;V80M;S82P 4;79;88;160;169 9;83;92;164;173 22661221 Intrahost emergent dynamics of oseltamivir-resistant virus of pandemic influenza A (H1N1) 2009 in a fatally immunocompromised patient. From the tree, the H275Y mutant was predicted to be derived from an oseltamivir-sensitive L2 clone, because the L2 clone was most closely related to the H275Y mutant and had common mutations at V80M and S82P. 2012 Journal of infection and chemotherapy Result IV H275Y;H275Y;V80M;S82P 19;153;194;203 24;158;198;207 22661221 Intrahost emergent dynamics of oseltamivir-resistant virus of pandemic influenza A (H1N1) 2009 in a fatally immunocompromised patient. However, the H275Y mutation was detected in 13 of 22 clones from the left lung. 2012 Journal of infection and chemotherapy Result IV H275Y 13 18 22661221 Intrahost emergent dynamics of oseltamivir-resistant virus of pandemic influenza A (H1N1) 2009 in a fatally immunocompromised patient. Intrahost evolution of H275Y mutant. 2012 Journal of infection and chemotherapy Result IV H275Y 23 28 22661221 Intrahost emergent dynamics of oseltamivir-resistant virus of pandemic influenza A (H1N1) 2009 in a fatally immunocompromised patient. No H275Y mutant was detected in all 42 clones tested (Table 2). 2012 Journal of infection and chemotherapy Result IV H275Y 3 8 22661221 Intrahost emergent dynamics of oseltamivir-resistant virus of pandemic influenza A (H1N1) 2009 in a fatally immunocompromised patient. The H275Y mutation was also detected in autopsy tissues from the right lung. 2012 Journal of infection and chemotherapy Result IV H275Y 4 9 22661221 Intrahost emergent dynamics of oseltamivir-resistant virus of pandemic influenza A (H1N1) 2009 in a fatally immunocompromised patient. The H275Y mutation was detected in all clones tested in 12 clones from the right lung and 11 clones from the nasopharynx (Table 2). 2012 Journal of infection and chemotherapy Result IV H275Y 4 9 22661221 Intrahost emergent dynamics of oseltamivir-resistant virus of pandemic influenza A (H1N1) 2009 in a fatally immunocompromised patient. The parsimony-informative amino acid of this L7 clone was the same as those of L1, except H275Y. 2012 Journal of infection and chemotherapy Result IV H275Y 90 95 22661221 Intrahost emergent dynamics of oseltamivir-resistant virus of pandemic influenza A (H1N1) 2009 in a fatally immunocompromised patient. These results indicated that the H275Y mutant was the predominant population in both nasopharynx and right lung, whereas the H275Y mutant virus in the left lung was distributed with an equivalent population of oseltamivir-sensitive clones. 2012 Journal of infection and chemotherapy Result IV H275Y;H275Y 33;125 38;130 22661221 Intrahost emergent dynamics of oseltamivir-resistant virus of pandemic influenza A (H1N1) 2009 in a fatally immunocompromised patient. To analyze the intrahost evolution of H275Y oseltamivir-resistant virus in case 1, we constructed a minimum spanning tree that provides a better understanding of sequence relationships for microevolution than standard phylogenetic tree representation. 2012 Journal of infection and chemotherapy Result IV H275Y 38 43 22661221 Intrahost emergent dynamics of oseltamivir-resistant virus of pandemic influenza A (H1N1) 2009 in a fatally immunocompromised patient. We detected the H275Y mutation by direct sequencing from the nasopharyngeal samples on day 13 (Table 1) and confirmed it was resistant to oseltamivir. 2012 Journal of infection and chemotherapy Result IV H275Y 16 21 22788742 Comprehensive global amino acid sequence analysis of PB1F2 protein of influenza A H5N1 viruses and the influenza A virus subtypes responsible for the 20th-century pandemics. Alignment of the amino acid sequences of the Indian strains revealed that five of the 32 strains showed a mutation at the 84 position from aspargine to serine (designated as N84S). 2013 Influenza and other respiratory viruses Result IV N84S 174 178 22788742 Comprehensive global amino acid sequence analysis of PB1F2 protein of influenza A H5N1 viruses and the influenza A virus subtypes responsible for the 20th-century pandemics. Among the 58 avian strains having N84S mutation, 46 (79%) were from HPAI, because they harbored the polybasic HA cleavage site. 2013 Influenza and other respiratory viruses Result IV N84S 34 38 HA 110 112 22788742 Comprehensive global amino acid sequence analysis of PB1F2 protein of influenza A H5N1 viruses and the influenza A virus subtypes responsible for the 20th-century pandemics. Further analysis revealed that N66S mutation was present only 1 24% of the strains from human and 77 94% of the avian strains. 2013 Influenza and other respiratory viruses Result IV N66S 31 35 22788742 Comprehensive global amino acid sequence analysis of PB1F2 protein of influenza A H5N1 viruses and the influenza A virus subtypes responsible for the 20th-century pandemics. Global data analysis of the N84S mutation in PB1F2 protein of H5N1 isolates revealed that 86 (9 35%) strains harbored this mutation Table 3. 2013 Influenza and other respiratory viruses Result IV N84S 28 32 PB1F2 45 50 22788742 Comprehensive global amino acid sequence analysis of PB1F2 protein of influenza A H5N1 viruses and the influenza A virus subtypes responsible for the 20th-century pandemics. Global database analysis of the PB1F2 sequence of influenza A H5N1 isolates revealed that N66S mutation was present in only 35 (3 8%) strains that included 17 from avian species, 12 from environment, and six from human hosts (Table 3). 2013 Influenza and other respiratory viruses Result IV N66S 90 94 PB1F2 32 37 22788742 Comprehensive global amino acid sequence analysis of PB1F2 protein of influenza A H5N1 viruses and the influenza A virus subtypes responsible for the 20th-century pandemics. However, all the six human isolates having N66S mutation in PB1F2 protein isolated from Hong Kong (five in 1997; one in 2001) were found to be highly pathogenic (Table 3). 2013 Influenza and other respiratory viruses Result IV N66S 43 47 PB1F2 60 65 22788742 Comprehensive global amino acid sequence analysis of PB1F2 protein of influenza A H5N1 viruses and the influenza A virus subtypes responsible for the 20th-century pandemics. Mutational analysis for the N66S mutation in the 83 H2N2 strains revealed that 24 (28 91%) harbored the mutation (Table 4). 2013 Influenza and other respiratory viruses Result IV N66S 28 32 22788742 Comprehensive global amino acid sequence analysis of PB1F2 protein of influenza A H5N1 viruses and the influenza A virus subtypes responsible for the 20th-century pandemics. N66S mutation in the PB1F2 protein has been earlier reported in H5N1 strains isolated in 1997 Hong Kong outbreak and H1N1 virus of the 1918 Spanish flu and found to contribute to the increased virulence in mice. 2013 Influenza and other respiratory viruses Result IV N66S 0 4 PB1F2 21 26 22788742 Comprehensive global amino acid sequence analysis of PB1F2 protein of influenza A H5N1 viruses and the influenza A virus subtypes responsible for the 20th-century pandemics. N66S mutational analysis for the H3N2 strains revealed that this mutation was present in only 3 96% of the strains (Table 4). 2013 Influenza and other respiratory viruses Result IV N66S 0 4 22788742 Comprehensive global amino acid sequence analysis of PB1F2 protein of influenza A H5N1 viruses and the influenza A virus subtypes responsible for the 20th-century pandemics. Phylogenetic tree drawn using the Neighbor-Joining method (mega 5.0) of 32 Indian strains with few reference strains showed that five strains with N84S mutation branched out as shown in the Figure 2. 2013 Influenza and other respiratory viruses Result IV N84S 147 151 22808250 Mouse-adapted H9N2 influenza A virus PB2 protein M147L and E627K mutations are critical for high virulence. Among the six mutants, only SD16-M147L/E627K virus had similar virulence (MLD50 = 103.8 pfu ) to SD16:MA PB2 (MLD50 = 103.5 pfu). 2012 PloS one Result IV M147L;E627K 33;39 38;44 PB2 106 109 22808250 Mouse-adapted H9N2 influenza A virus PB2 protein M147L and E627K mutations are critical for high virulence. Collectively, our findings showed that efficient polymerase activity (>6-fold increase, P<0.05) was ~achieved by PB2 E627K mutation that was similar for all mutant combinations that contained this mutation, PB2 E627K/M147L, PB2 E627K/V250G and PB2 E627K/M147L/V250G. 2012 PloS one Result IV E627K;M147L;E627K;E627K;V250G;M147L;V250G;E627K 117;217;211;228;234;254;260;248 122;222;216;233;239;259;265;253 PB2;PB2;PB2;PB2 113;207;224;244 116;210;227;247 22808250 Mouse-adapted H9N2 influenza A virus PB2 protein M147L and E627K mutations are critical for high virulence. For the six mutated viruses, SD16-M147L/E627K and SD16-V250G/E627K grew more efficiently than the other four viruses (P<0.05), reaching maximum titers of more than 7.7 log10 pfu/ml at 48 hpi. 2012 PloS one Result IV M147L;E627K;E627K;V250G 34;40;61;55 39;45;66;60 22808250 Mouse-adapted H9N2 influenza A virus PB2 protein M147L and E627K mutations are critical for high virulence. In combination the M147L and V250G only possessed a marginally increased polymerase activity to ~127% that of SD16. 2012 PloS one Result IV M147L;V250G 19;29 24;34 22808250 Mouse-adapted H9N2 influenza A virus PB2 protein M147L and E627K mutations are critical for high virulence. In contrast, the combination of E627K plus M147L, and E627K plus V250G enhanced polymerase activity to ~620% and 622% respectively, indicating an attenuating effect of the mutations in combination with E627K. 2012 PloS one Result IV E627K;M147L;E627K;V250G;E627K 32;43;54;65;202 37;48;59;70;207 22808250 Mouse-adapted H9N2 influenza A virus PB2 protein M147L and E627K mutations are critical for high virulence. Moreover, lung virus titer for SD16-M147L/E627K was approximately 0.7 and 0.8 log10 pfu higher than SD16-147L and SD16-627K, respectively, and approximately 1.4 log10 pfu higher than SD16 virus (Table 1 and 2). 2012 PloS one Result IV M147L;E627K 36;42 41;47 22808250 Mouse-adapted H9N2 influenza A virus PB2 protein M147L and E627K mutations are critical for high virulence. PB2 E627K is as a host range determinant that determines the pathogenicity of H5N1 influenza viruses in mice. 2012 PloS one Result IV E627K 4 9 PB2 0 3 22808250 Mouse-adapted H9N2 influenza A virus PB2 protein M147L and E627K mutations are critical for high virulence. PB2 E627K mutation increased polymerase activity of SD16 RNP complex to ~805%, whereas M147L and V250G did not significantly increase polymerase activity as PB2 E627K. 2012 PloS one Result IV E627K;M147L;V250G;E627K 4;87;97;161 9;92;102;166 PB2;PB2;RNP 0;157;57 3;160;60 22808250 Mouse-adapted H9N2 influenza A virus PB2 protein M147L and E627K mutations are critical for high virulence. SD16-MA carrying PB2 M147L, V250G, and E627K had polymerase activities that was ~630% relative to wild-type SD16 virus (100%). 2012 PloS one Result IV M147L;V250G;E627K 21;28;39 26;33;44 PB2 17 20 22808250 Mouse-adapted H9N2 influenza A virus PB2 protein M147L and E627K mutations are critical for high virulence. Sequence analysis identified five mutations among 3 genes that were involved in adaptation of SD16 strain to mice; specifically PB2 (M147L, V250G, and E627K), HA (L226Q), and M (R210K). 2012 PloS one Result IV M147L;V250G;E627K;L226Q;R210K 133;140;151;163;178 138;145;156;168;183 HA;M;PB2 159;175;128 161;176;131 22808250 Mouse-adapted H9N2 influenza A virus PB2 protein M147L and E627K mutations are critical for high virulence. Single amino acid substitution PB2 M147L or V250G did not increase the pathogenicity of SD16 in mice with MLD50 >106.5 pfu, while PB2 E627K slightly increased pathogenicity with MLD50 reduced more than 10-fold compared to wild-type virus (Table 2). 2012 PloS one Result IV M147L;V250G;E627K 35;44;134 40;49;139 PB2;PB2 31;130 34;133 22808250 Mouse-adapted H9N2 influenza A virus PB2 protein M147L and E627K mutations are critical for high virulence. The L226Q (H3 numbering) mutation in HA occurred the receptor-binding site (RBS). 2012 PloS one Result IV L226Q 4 9 HA 37 39 22808250 Mouse-adapted H9N2 influenza A virus PB2 protein M147L and E627K mutations are critical for high virulence. The M1 R210K mutation was in a region (165-252aa) that had been shown to bind ribonucleoprotein (RNP). 2012 PloS one Result IV R210K 7 12 M1;RNP 4;97 6;100 22808250 Mouse-adapted H9N2 influenza A virus PB2 protein M147L and E627K mutations are critical for high virulence. The PB2 M147L mutation resided in the N-terminal NP binding region (1-269aa) and PB2 V250G mapped to a site involved in the host 7methyl guanosine cap binding domain (242-282aa) and NP binding region. 2012 PloS one Result IV M147L;V250G 8;85 13;90 NP;NP;PB2;PB2 49;182;4;81 51;184;7;84 22808250 Mouse-adapted H9N2 influenza A virus PB2 protein M147L and E627K mutations are critical for high virulence. These results suggested that M1 R210K, PB2 147L/627K and 250G/627K combination could enhance viral replication in vitro. 2012 PloS one Result IV R210K 32 37 M1;PB2 29;39 31;42 22808250 Mouse-adapted H9N2 influenza A virus PB2 protein M147L and E627K mutations are critical for high virulence. Thus, these single and double mutants clearly demonstrated that only the combination of PB2 M147L and E627K could increase the virulence of the H9N2 virus in BALB/c mice. 2012 PloS one Result IV M147L;E627K 92;102 97;107 PB2 88 91 22809692 Both influenza hemagglutinin and polymerase acidic genes are important for delayed pandemic 2009 H1N1 virus clearance in the ferret model. HA D222G altered the receptor binding properties of the virus, and PA F35L increased its polymerase activity; the mutant virus was therefore similar to our G1 or HAmutPAmut strain. 2012 Virology Result IV D222G;F35L 3;70 8;74 HA;PA 0;67 2;69 22809692 Both influenza hemagglutinin and polymerase acidic genes are important for delayed pandemic 2009 H1N1 virus clearance in the ferret model. HA K119N, G155E, S183P, R221K, D222G, and D225G lead to increased virulence in mice. 2012 Virology Result IV K119N;G155E;S183P;R221K;D222G;D225G 3;10;17;24;31;42 8;15;22;29;36;47 HA 0 2 22809692 Both influenza hemagglutinin and polymerase acidic genes are important for delayed pandemic 2009 H1N1 virus clearance in the ferret model. However, a synergistic role of influenza HA and PA proteins has recently been reported with HA D222G, HA K163E, and PA F35L together increasing A(H1N1)pdm09 virulence in mice. 2012 Virology Result IV D222G;K163E;F35L 95;105;119 100;110;123 HA;HA;HA;PA;PA 41;92;102;48;116 43;94;104;50;118 22809692 Both influenza hemagglutinin and polymerase acidic genes are important for delayed pandemic 2009 H1N1 virus clearance in the ferret model. If real, this virus replication advantage conferred by PA L295P at both temperatures could explain why this mutation prevails in all A(H1N1)pdm09 strains. 2012 Virology Result IV L295P 58 63 PA 55 57 22809692 Both influenza hemagglutinin and polymerase acidic genes are important for delayed pandemic 2009 H1N1 virus clearance in the ferret model. In conclusion for the in vivo experiments, both HA K154Q and PA L295P mutations contribute to increasing A(H1N1)pdm09 pathogenicity, and they are both necessary for delayed virus clearance. 2012 Virology Result IV K154Q;L295P 51;64 56;69 HA;PA 48;61 50;63 22809692 Both influenza hemagglutinin and polymerase acidic genes are important for delayed pandemic 2009 H1N1 virus clearance in the ferret model. In our previous study, G1 (TN/09 with HA K154Q and PA L295P mutations) showed an increased virulence and delayed clearance in vivo in the ferret model. 2012 Virology Result IV K154Q;L295P 41;54 46;59 HA;PA 38;51 40;53 22809692 Both influenza hemagglutinin and polymerase acidic genes are important for delayed pandemic 2009 H1N1 virus clearance in the ferret model. Mutations of HA have been linked with an increased binding to alpha2,6-sialyl receptors 90D and 225D, T200A and E227A synergistically, E227A, and I219K or a decreased binding for D222G. 2012 Virology Result IV T200A;E227A;E227A;I219K;D222G 102;112;135;146;179 107;117;140;151;184 HA 13 15 22809692 Both influenza hemagglutinin and polymerase acidic genes are important for delayed pandemic 2009 H1N1 virus clearance in the ferret model. The observed reduced binding to a few receptors might explain why HA K154Q does not seem prevalent in nature: of 8546 A(H1N1)pdm09 HA sequences available on GenBank, only 2 have K154Q: A/Arequipa/WRAIR9939F/2009 (accession number: ADX97028) and A/Dakar/WRAIR0020T/2010 (accession number: ADX96288). 2012 Virology Result IV K154Q;K154Q 69;178 74;183 HA;HA 66;131 68;133 22809692 Both influenza hemagglutinin and polymerase acidic genes are important for delayed pandemic 2009 H1N1 virus clearance in the ferret model. The role of HA K154Q and PA L295P in modification of receptor binding affinity and increased pathogenicity has so far been described only in our previous study. 2012 Virology Result IV K154Q;L295P 15;28 20;33 HA;PA 12;25 14;27 22809692 Both influenza hemagglutinin and polymerase acidic genes are important for delayed pandemic 2009 H1N1 virus clearance in the ferret model. Therefore, our results showed that both single mutations HA K154Q and PA L295P confer significantly higher replication of A/Tennessee/560/09 strain in human epithelial cells (P<0.05). 2012 Virology Result IV K154Q;L295P 60;73 65;78 HA;PA 57;70 59;72 22809692 Both influenza hemagglutinin and polymerase acidic genes are important for delayed pandemic 2009 H1N1 virus clearance in the ferret model. We could speculate that although no increase in polymerase activity was observed with PA L295P mutation at 33 C, the mutation may still contribute to increasing the level of RNA transcription for example. 2012 Virology Result IV L295P 89 94 PA 86 88 22809692 Both influenza hemagglutinin and polymerase acidic genes are important for delayed pandemic 2009 H1N1 virus clearance in the ferret model. We previously observed similar polymerase activities for G1 (with the PA L295P mutation) and TN/09 viruses at 33 C. 2012 Virology Result IV L295P 73 78 PA 70 72 22809862 Treatment of oseltamivir-resistant influenza A (H1N1) virus infections in mice with antiviral agents. Against the H275Y viruses, oseltamivir carboxylate was inactive at 100 muM, peramivir exhibited protection at about 8 muM, and zanamivir was inhibitory at 0.24-0.36 muM. 2012 Antiviral research Result IV H275Y 12 17 22809862 Treatment of oseltamivir-resistant influenza A (H1N1) virus infections in mice with antiviral agents. Amantadine and rimantadine were both highly active against A/MS-H275Y (although rimantadine exhibited toxicity at 22 muM), but were not active against A/HK-H275Y. 2012 Antiviral research Result IV H275Y;H275Y 64;156 69;161 22809862 Treatment of oseltamivir-resistant influenza A (H1N1) virus infections in mice with antiviral agents. Amantadine and rimantadine were tested for their ability to prevent or delay the time to death in mice challenged with the A/MS-H275Y virus. 2012 Antiviral research Result IV H275Y 128 133 22809862 Treatment of oseltamivir-resistant influenza A (H1N1) virus infections in mice with antiviral agents. Body weights were determined during the A/HK-H275Y virus infection. 2012 Antiviral research Result IV H275Y 45 50 22809862 Treatment of oseltamivir-resistant influenza A (H1N1) virus infections in mice with antiviral agents. Efficacy of oseltamivir and ribavirin against influenza A/HK-H275Y virus infection in mice. 2012 Antiviral research Result IV H275Y 61 66 22809862 Treatment of oseltamivir-resistant influenza A (H1N1) virus infections in mice with antiviral agents. Oseltamivir and ribavirin were used to treat an A/HK-H275Y virus infection starting treatment at -2 h relative to virus challenge. 2012 Antiviral research Result IV H275Y 53 58 22809862 Treatment of oseltamivir-resistant influenza A (H1N1) virus infections in mice with antiviral agents. Oseltamivir and zanamivir were evaluated for efficacy against influenza A/MS-H275Y virus infections in mice. 2012 Antiviral research Result IV H275Y 77 82 22809862 Treatment of oseltamivir-resistant influenza A (H1N1) virus infections in mice with antiviral agents. Oseltamivir carboxylate was ineffective against the two H275Y enzymes at 100 nM. 2012 Antiviral research Result IV H275Y 56 61 22809862 Treatment of oseltamivir-resistant influenza A (H1N1) virus infections in mice with antiviral agents. Six compounds representing different classes [viral M2 channel blockers: amantadine and rimantadine; viral neuraminidase inhibitors: oseltamivir carboxylate, peramivir, and zanamivir; and a viral polymerase inhibitor: ribavirin], were evaluated for anti-influenza virus activity in cell culture against oseltamivir-sensitive influenza A/California/07/2009 (H1N1) virus, and oseltamivir-resistant influenza A/MS-H275Y and A/HK-H275Y viruses (Table 1). 2012 Antiviral research Result IV H275Y;H275Y 411;426 416;431 M2;NA 52;107 54;120 22809862 Treatment of oseltamivir-resistant influenza A (H1N1) virus infections in mice with antiviral agents. The protective activity of ribavirin was studied in mice infected with influenza A/MS-H275Y virus. 2012 Antiviral research Result IV H275Y 86 91 22809862 Treatment of oseltamivir-resistant influenza A (H1N1) virus infections in mice with antiviral agents. The three inhibitors of viral neuraminidase were tested for inhibitory activity against one oseltamivir-sensitive and two oseltamivir-resistant (H275Y) viral neuraminidases (Table 2). 2012 Antiviral research Result IV H275Y 145 150 NA;NA 30;158 43;172 22809862 Treatment of oseltamivir-resistant influenza A (H1N1) virus infections in mice with antiviral agents. These survival results for oseltamivir treatment were similar to those obtained in treating the A/MS-H275Y virus infection. 2012 Antiviral research Result IV H275Y 101 106 22809862 Treatment of oseltamivir-resistant influenza A (H1N1) virus infections in mice with antiviral agents. These values are comparable to the published values against the non-mouse-adapted influenza A/MS-H275Y virus. 2012 Antiviral research Result IV H275Y 97 102 22851656 Emergence of fatal avian influenza in New England harbor seals. In avian H3 viruses, phenylalanine (Phe/F) is consistently seen, while seal H3N8 uses Ser (F110S). 2012 mBio Result IV F110S 91 96 22851656 Emergence of fatal avian influenza in New England harbor seals. Mutations at positions 226 and 228 (H3 numbering) in the H3 HA can also affect receptor-binding preferences and can either completely abrogate (Q226L) or reduce (G228S) affinity for the avian-preferred SAalpha-2,3 interaction. 2012 mBio Result IV Q226L;G228S 144;162 149;167 HA 60 62 22851656 Emergence of fatal avian influenza in New England harbor seals. The seal H3N8 virus from the 2011 outbreak has naturally acquired this D701N substitution (Table 1), which was confirmed by clonal sequencing directly from infected tissue (50 clones/animal) to be the only phenotype present in all five animals. 2012 mBio Result IV D701N 71 76 22851656 Emergence of fatal avian influenza in New England harbor seals. The significance of this (if any) is currently unknown; however, previous work has suggested that this amino acid (position 110) is a critical component of the influenza fusion peptide, and given the essential role of fusion in viral replication and the host-specific differences that presumably exist in this process, the F110S substitution may well represent further adaption of this virus to mammalian replication. 2012 mBio Result IV F110S 323 328 22851656 Emergence of fatal avian influenza in New England harbor seals. These are NA-W399R, PB2-I382V, and PA-S184N (Table 1). 2012 mBio Result IV W399R;I382V;S184N 13;24;38 18;29;43 NA;PA;PB2 10;35;20 12;37;23 22851656 Emergence of fatal avian influenza in New England harbor seals. This D701N mutation has been experimentally introduced into an adapted version of the H7N7 seal influenza virus isolated in 1982 (1, 2) and was shown to increase the pathogenicity of the virus to mice. 2012 mBio Result IV D701N 5 10 22851656 Emergence of fatal avian influenza in New England harbor seals. While the seal virus contains the same conserved S152, it also harbors a neighboring G151E mutation (Table 1), which introduces a large residue capable of both donating and receiving hydrogen bonds with residues in close proximity to the ligand-binding pocket. 2012 mBio Result IV G151E 85 90 22952752 Molecular evolutionary analysis of pH1N1 2009 influenza virus in Reunion Island, South West Indian Ocean region: a cohort study. All clade RUN sequences also exhibited a fixed amino acid mutation in HA (D239E) and a silent mutation in NA (g873a). 2012 PloS one Result IV D239E 74 79 HA;NA 70;106 72;108 22952752 Molecular evolutionary analysis of pH1N1 2009 influenza virus in Reunion Island, South West Indian Ocean region: a cohort study. Fixed mutations were also observed for RUN-B sequences in PB2 (a807g and V414I), PA (c1794t), NA (a48t) and M (t823c). 2012 PloS one Result IV V414I 73 78 M;NA;PA;PB2 108;94;81;58 109;96;83;61 22952752 Molecular evolutionary analysis of pH1N1 2009 influenza virus in Reunion Island, South West Indian Ocean region: a cohort study. In addition, mutations NP (V100I) and NA (N248D), which are not systematically detected within clade 7 isolates were seen to be fixed in all sequences from clade RUN. 2012 PloS one Result IV V100I;N248D 27;42 32;47 NA;NP 38;23 40;25 22952752 Molecular evolutionary analysis of pH1N1 2009 influenza virus in Reunion Island, South West Indian Ocean region: a cohort study. RUN-A sequences were characterized by mutations in NS1 (N133D), NP (a366g), HA (c42a and t333c) and PB2 (g120a and g1665a), whereas RUN-B sequences lacked all these mutations (Table 3b). 2012 PloS one Result IV N133D 56 61 HA;NP;NS1;PB2 76;64;51;100 78;66;54;103 22952752 Molecular evolutionary analysis of pH1N1 2009 influenza virus in Reunion Island, South West Indian Ocean region: a cohort study. Sequences belonging to clade 7 can be characterized by fixed amino acid changes in HA (S220T), NA (V106I) and NS1 (I123V) (Table 3a). 2012 PloS one Result IV S220T;V106I;I123V 87;99;115 92;104;120 HA;NA;NS1 83;95;110 85;97;113 22958470 Molecular and phylogenetic analysis of matrix gene of avian influenza viruses isolated from wild birds and live bird markets in the USA. Of these 17 isolates, 16 had S31N change and one isolate had V27A mutation (Table 2). 2013 Influenza and other respiratory viruses Result IV S31N;V27A 29;61 33;65 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. Although the KM-values for MUNANA are increased about equally for both the I223R and H275Y single mutants, the change in oseltamivir inhibitor constant for the H275Y mutant relative to wild type, is approximately 10 times greater than for the I223R mutant (Table 1). 2012 PLoS pathogens Result IV I223R;H275Y;H275Y;I223R 75;85;160;243 80;90;165;248 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. As previously suggested, suboptimal drug levels in the patient's respiratory tract, due to the route of administration (IV versus inhaled) as well as the immune status of the patient may have contributed to the emergence and persistence of the I223R mutant virus. 2012 PLoS pathogens Result IV I223R 244 249 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. Both the single and the S247N/H275Y double mutant viruses were found not to be compromised in a ferret model suggesting that the mutant neuraminidases retain most of their normal activity. 2012 PLoS pathogens Result IV S247N;H275Y 24;30 29;35 136 150 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. By comparison to the oseltamivir inhibitor constant (KI) of wild type NA, the KI of the I223R mutant increased 48 times and the I223R/H275Y double mutant KI more than 7500 times. 2012 PLoS pathogens Result IV I223R;H275Y;I223R 88;134;128 93;139;133 70 72 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. Changes in oseltamivir binding by the I223R change. 2012 PLoS pathogens Result IV I223R 38 43 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. Enzyme kinetics of the I223R and H275Y mutant neuraminidases. 2012 PLoS pathogens Result IV I223R;H275Y 23;33 28;38 46 60 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. Furthermore, the binding of oseltamivir by the I223R/H275Y double mutant becomes even less energetically favorable than by either of the two single mutant proteins. 2012 PLoS pathogens Result IV I223R;H275Y 47;53 52;58 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. In addition to the I223R change, isoleucine 223 changes to valine (I223V) and lysine (I223K) accompanying the H275Y change have also been reported. 2012 PLoS pathogens Result IV I223R;I223V;I223K;H275Y;I223V 19;67;86;110;33 24;72;91;115;65 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. In brief, the introduction of the bulkier tyrosine residue perturbs the position and the reorientation of the acidic side chain of E277 required for oseltamivir binding, such that the hydrophobic pentoxyl substituent of oseltamivir is translated out of the active site towards the pocket occupied in the I223R structure by the side chain of the arginine residue (Figure 2B). 2012 PLoS pathogens Result IV I223R 304 309 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. In the 2007-2008 influenza H1N1 season, naturally occurring H275Y variants had emerged, which were not attenuated in virus growth or transmissibility. 2012 PLoS pathogens Result IV H275Y 60 65 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. In the I223R neuraminidase, this pocket is occupied by the side chain of R223. 2012 PLoS pathogens Result IV I223R 7 12 13 26 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. In the I223R single or double mutant neuraminidases, somewhat different interactions are made by the glycerol moiety: one hydrogen bond is formed with E277 and another hydrogen bond is formed with S247 (Figure 3A). 2012 PLoS pathogens Result IV I223R 7 12 37 51 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. Interestingly, a serine to asparagine change at position 247 (S247N) has also been linked to oseltamivir resistance. 2012 PLoS pathogens Result IV S247N;S247N 62;17 67;60 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. It contained the mutation I223R. 2012 PLoS pathogens Result IV I223R 26 31 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. Like the I223R change, the S247N mutation also causes enhanced resistance to oseltamivir when accompanied by the H275Y change. 2012 PLoS pathogens Result IV I223R;S247N;H275Y 9;27;113 14;32;118 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. Moreover, the reorientation of the side-chain of E277, which is required for oseltamivir binding to wild-type neuraminidase, is presumably made even less energetically favorable in the I223R mutant by the need to disrupt the hydrogen bond between S247 and E277. 2012 PLoS pathogens Result IV I223R 185 190 110 123 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. Our observations suggest that, as was observed with the non-attenuated H275Y variants in the 2007-2008 season, the occurrence of viable NAI resistant pandemic influenza A/H1N1 viruses is not an unlikely event. 2012 PLoS pathogens Result IV H275Y 71 76 NAI 136 139 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. Our structural data therefore provide an explanation for the 1750-fold poorer binding of oseltamivir by the I223R/H275Y double mutant by comparison with the wild-type neuraminidase (Table 1). 2012 PLoS pathogens Result IV H275Y;I223R 114;108 119;113 167 180 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. Our structural studies help to explain how the single I223R and I223R/H275Y double mutant neuraminidases bind zanamivir almost as well as wild type. 2012 PLoS pathogens Result IV I223R;I223R;H275Y 54;64;70 59;69;75 90 104 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. Relative to wild type NA, KM values increased marginally for the I223R and H275Y single mutants. 2012 PLoS pathogens Result IV I223R;H275Y 65;75 70;80 22 24 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. S247 therefore plays an important role in the decreased sensitivity of the I223R neuraminidase to inhibitors. 2012 PLoS pathogens Result IV I223R 75 80 81 94 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. Since the single I223R change described here resulted in only a 9-fold increase in the KI for zanamivir, it is interesting to consider why the I223R mutant virus persisted in the IV zanamivir treated immunocompromised patient. 2012 PLoS pathogens Result IV I223R;I223R 17;143 22;148 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. Since this change has been reported both as a single mutation as well as in combination with the substitution H275Y, virus recombinants were constructed containing the wild type NA, the I223R or H275Y single mutants and the I223R, H275Y double mutant. 2012 PLoS pathogens Result IV H275Y;I223R;H275Y;I223R;H275Y 110;186;195;224;231 115;191;200;229;236 178 180 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. Structural changes in the I223R/H275Y double mutant. 2012 PLoS pathogens Result IV I223R;H275Y 26;32 31;37 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. The change in the KI for I223R (48-fold) was largely accounted for by an increased dissociation rate constant for the enzyme-inhibitor complex (15-fold) rather than by a reduced association rate constant (kon) (3-fold). 2012 PLoS pathogens Result IV I223R 25 30 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. The change in the KI for I223R (9-fold) was in this case accounted for by a reduced association rate constant (4-fold) and a slightly increased dissociation rate constant (2-fold). 2012 PLoS pathogens Result IV I223R 25 30 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. The crystals yielded high-resolution diffraction data and the structures were solved by molecular replacement and refined by standard procedures (Table 2.) The first striking feature from these data is that the 150-loop in the ligand-free I223R NA adopts an open conformation, as seen in the first reported N1 structure, but in contrast to the closed conformation of this loop seen in the recently reported crystal structure of the 2009 pandemic A/H1N1 NA (Figure 1A). 2012 PLoS pathogens Result IV I223R 239 244 NA;NA 245;453 247;455 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. The I223R mutation, therefore, appears to restrict the alternative position that the pentoxyl substituent adopts in the H275Y mutant. 2012 PLoS pathogens Result IV I223R;H275Y 4;120 9;125 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. The mechanism whereby the H275Y mutant neuraminidase binds substantially more weakly to oseltamivir than wild type has been described previously. 2012 PLoS pathogens Result IV H275Y 26 31 39 52 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. The polarity of the zanamivir glycerol substituent correlates with the smaller effect of the I223R mutation on zanamivir binding. 2012 PLoS pathogens Result IV I223R 93 98 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. Therefore, although there is no structural information in that case we speculate that, like the I223R change, the resistance mechanism of the S247N change also may involve shrinkage of the hydrophobic pocket. 2012 PLoS pathogens Result IV I223R;S247N 96;142 101;147 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. These changes in the structure of the I223R neuraminidase result in shrinkage at the edge of the active site pocket that accommodates the hydrophobic pentoxyl group of oseltamivir. 2012 PLoS pathogens Result IV I223R 38 43 44 57 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. This interaction is unaffected in the H275Y mutant (Figure 3). 2012 PLoS pathogens Result IV H275Y 38 43 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. This may explain why the H275Y change may be the more likely resistance change in oseltamivir monotherapy and of course, to date, the H275Y mutation is the most frequently detected oseltamivir resistance mutation. 2012 PLoS pathogens Result IV H275Y;H275Y 25;134 30;139 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. Thus the binding of oseltamivir to the active site of the I223R mutant results not only in changes in the conformation of the side chain of S247 but also in the side-chain of R223 being translated about 1.1 A out of the active site compared to the mutant ligand-free structure (Figure 2A). 2012 PLoS pathogens Result IV I223R 58 63 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. Thus the I223R mutation has a markedly greater effect on NA inhibition by oseltamivir than by zanamivir. 2012 PLoS pathogens Result IV I223R 9 14 57 59 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. Thus, oseltamivir binding to the active site of I223R neuraminidase requires the reorientation of the S247 and R223 side chains. 2012 PLoS pathogens Result IV I223R 48 53 54 67 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. To study the effects of the single mutations I223R and H275Y, and the double mutant on the enzymatic properties of NA, Michaelis-Menten (KM) constants were determined using MUNANA as a substrate. 2012 PLoS pathogens Result IV I223R;H275Y 45;55 50;60 115 117 23029425 Multiple distinct forms of CD8+ T cell cross-reactivity and specificities revealed after 2009 H1N1 influenza A virus infection in mice. Each of the CANP366 and CAPA224 epitopes from CA/E3/09 virus have one substitution in peptide position 6 and 1, M371V and S224P respectively, which may affect both potential H2-Db binding affinity and T cell recognition. 2012 PloS one Result IV M371V;S224P 112;122 117;127 23029425 Multiple distinct forms of CD8+ T cell cross-reactivity and specificities revealed after 2009 H1N1 influenza A virus infection in mice. However, single M371V replacement in the CANP366 significantly disrupted the peptide's ability to induce IFN-gamma production by CD8 cells from X31 infected mice. 2012 PloS one Result IV M371V 16 21 23029425 Multiple distinct forms of CD8+ T cell cross-reactivity and specificities revealed after 2009 H1N1 influenza A virus infection in mice. Thus, the tetramer staining data presented here further supported the observation that the single M371V substitution in the CA/E3/09 virus results in minimal cross-reactivity between the related epitopes, though it remains immunogenic. 2012 PloS one Result IV M371V 98 103 23280098 Genetic characterization of influenza virus circulating in Brazilian pigs during 2009 and 2010 reveals a high prevalence of the pandemic H1N1 subtype. All 2009-2010 Brazilian swine and human isolates contained residues of the swine lineage in the receptor-binding pockets, with no substitutions in those sites relative to the A/Mexico/4108/09 strain, except for the substitutions A134T and D222N in isolates A/swine/Brazil/19/2010 and A/swine/Brazil/20/2010. 2013 Influenza and other respiratory viruses Result IV A134T;D222N 229;239 234;244 23280098 Genetic characterization of influenza virus circulating in Brazilian pigs during 2009 and 2010 reveals a high prevalence of the pandemic H1N1 subtype. Interestingly, the amino acid substitution S203T in HA1 and both the V106I and N248D mutations in NA (data not shown) were observed in all but two 2009-2010 Brazilian pandemic H1N1 isolates. 2013 Influenza and other respiratory viruses Result IV S203T;V106I;N248D 43;69;79 48;74;84 HA1;NA 52;98 55;100 23280098 Genetic characterization of influenza virus circulating in Brazilian pigs during 2009 and 2010 reveals a high prevalence of the pandemic H1N1 subtype. None of the 2009-2010 Brazilian pandemic H1N1 isolates had the H275Y or N295S substitutions in NA (data not shown), which are known to confer resistance to oseltamivir.26 . 2013 Influenza and other respiratory viruses Result IV H275Y;N295S 63;72 68;77 95 97 23280098 Genetic characterization of influenza virus circulating in Brazilian pigs during 2009 and 2010 reveals a high prevalence of the pandemic H1N1 subtype. None of the 2009-2010 Brazilian pandemic H1N1 isolates had the H275Y or N295S substitutions in NA (data not shown), which are known to confer resistance to oseltamivir.26. 2013 Influenza and other respiratory viruses Result IV H275Y;N295S 63;72 68;77 23280098 Genetic characterization of influenza virus circulating in Brazilian pigs during 2009 and 2010 reveals a high prevalence of the pandemic H1N1 subtype. The isolate A/swine/Brazil/7/2009 had the Q293H substitution in HA1 and both the V106I and N248D mutations in NA, while isolate A/swine/Brazil/14/2009 contained the S203T substitution in HA1 but only the V106I substitution in NA. 2013 Influenza and other respiratory viruses Result IV Q293H;V106I;N248D;S203T;V106I 42;81;91;165;204 47;86;96;170;209 HA1;HA1;NA;NA 64;187;110;226 67;190;112;228 23289789 Genetic analysis of influenza B viruses isolated in Uganda during the 2009-2010 seasons. All B/Victoria-like Ugandan viruses possessed the N75K, N165K and S172P substitutions, characteristics of clade 1 B/Victoria viruses (Figure 1). 2013 Virology journal Result IV N75K;N165K;S172P 50;56;66 54;61;71 23289789 Genetic analysis of influenza B viruses isolated in Uganda during the 2009-2010 seasons. Its HA sequence clustered with clade 3 Yamagata viruses such as B/Bangladesh/3333/2007 characterized by S150I and N166Y substitutions (Figure 1). 2013 Virology journal Result IV S150I;N166Y 104;114 109;119 HA 4 6 23289789 Genetic analysis of influenza B viruses isolated in Uganda during the 2009-2010 seasons. The 2009 viruses could be differentiated from the 2010 viruses by a D35G substitution on NA. 2013 Virology journal Result IV D35G 68 72 89 91 23326573 An assay suitable for high throughput screening of anti-influenza drugs. Another two compounds 180 and 206, which are more potent than 34 and 35 in inhibiting V27A in electrophysiology assay, show higher viral inhibition activities at 10 microM. 2013 PloS one Result IV V27A 86 90 23326573 An assay suitable for high throughput screening of anti-influenza drugs. As summarized in tabe1, Compound 180 and 206 appear to be the best two inhibitors for M2 (V27A) mutant ion channel, which exhibit 82.7% and 94.5% inhibition of channel conductivity, respectively (Tabel 1). 2013 PloS one Result IV V27A 90 94 M2 86 88 23326573 An assay suitable for high throughput screening of anti-influenza drugs. In consistent with the electrophysiology assay, compound 34 also inhibits the replication of virus harboring A/M2-V27A mutation when tested at 50 microM. 2013 PloS one Result IV V27A 114 118 M2 111 113 23326573 An assay suitable for high throughput screening of anti-influenza drugs. It was found that Ac-GFP-M2 (V27A) was well expressed only in the presence of compound 180 or 206 (Figure 3C). 2013 PloS one Result IV V27A 29 33 M2 25 27 23326573 An assay suitable for high throughput screening of anti-influenza drugs. Next, we tested if the same compounds are able to inhibit the M2 (V27A) mutant channel, which is known to be resistant to amantadine. 2013 PloS one Result IV V27A 66 70 M2 62 64 23326573 An assay suitable for high throughput screening of anti-influenza drugs. Remarkably, the most potent compound 206 completely inhibits V27A virus replication at 5 microM concentration. 2013 PloS one Result IV V27A 61 65 23326573 An assay suitable for high throughput screening of anti-influenza drugs. The V27A mutation was introduced to pColdIIAcGFP-M2 (sp-4) by site-directed PCR mutagenesis. 2013 PloS one Result IV V27A 4 8 M2 49 51 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. As a result, the recombinant virus possessing the R8A NP mutant, which showed a 50% reduction in NP nuclear localization activity, was still not rescued at 72 h after transfection into HEK-293T/MDCK cells. 2013 PloS one Result IV R8A 50 53 NP;NP 54;97 56;99 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. Because S9A NP110aa mainly localized to the nucleus, the reduction in viral growth observed for the S9A mutant may be due to other functions of the unconventional NLS, which do not relate to nuclear transport. 2013 PloS one Result IV S9A;S9A 8;100 11;103 NP 12 14 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. By contrast, the bindings of WT and S9A NP110aa to Qip1 did not reduced comparing with WT full length NP. 2013 PloS one Result IV S9A 36 39 NP;NP 40;102 42;104 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. By contrast, the interaction between S9A NP110aa and Qip1 was almost the same as that observed for WT NP110aa; however, it bound very weakly to Rch1 and NPI-1. 2013 PloS one Result IV S9A 37 40 NP;NP 41;102 43;104 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. By contrast, the R8A NP110aa mutant showed only diffuse cytoplasmic staining in 54% of cells. 2013 PloS one Result IV R8A 17 20 NP 21 23 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. Despite the finding that S9A NP localized to the nucleus at the same level as WT-NP, the luciferase activity generated by S9A NP was only half that generated by WT NP after 48 h. 2013 PloS one Result IV S9A;S9A 25;122 28;125 NP;NP;NP;NP 29;81;126;164 31;83;128;166 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. Expression of K7A NP110aa was observed in the nuclei of 82% of transfected cells, and showed cytoplasmic staining in only 18%. 2013 PloS one Result IV K7A 14 17 NP 18 20 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. Furthermore, luciferase activity was significantly reduced by approximately 30% in Qip1-silenced cells compared to negative control siRNA treated cells using S9A NP plasmid (p<0.05). 2013 PloS one Result IV S9A 158 161 NP 162 164 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. Furthermore, we examined the viral growth of the WT and the S9A mutant virus in Qip1-silenced cells. 2013 PloS one Result IV S9A 60 63 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. However, virus possessing the S9A NP mutation, which predominantly localized in the nucleus, was able to generate progeny at the same level as the WT NP virus (5x106 PFU/ml vs. 2013 PloS one Result IV S9A 30 33 NP;NP 34;150 36;152 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. In addition, S9A mutation in unconventional NLS of NP110aa resulted in obvious reduction in affinity bindings for Rch1. 2013 PloS one Result IV S9A 13 16 NP 51 53 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. In the S9A virus, the viral titer was similar to those of control and Qip1-silenced cells (1.1x103 PFU/ml vs. 2013 PloS one Result IV S9A 7 10 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. Next, we determined the nuclear localization of WT and S9A NP110aa in A549 cells, in which Qip1 had been knocked-down. 2013 PloS one Result IV S9A 55 58 NP 59 61 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. Nine of the mutants (the exceptions were R8A NP110aa and K7A NP110aa) mainly localized in the nucleus 48 h after transfection into A549 cells. 2013 PloS one Result IV R8A;K7A 41;57 44;60 NP;NP 45;61 47;63 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. Plasmids encoding WT NP or S9A NP were transfected into HEK-293 cells together with expression plasmids encoding the viral polymerase subunits and a vNP-luc/pHH21 plasmid. 2013 PloS one Result IV S9A 27 30 NP;NP 21;31 23;33 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. Qip1 is important for transcription and growth of S9A virus via a nuclear localization-independent mechanism. 2013 PloS one Result IV S9A 50 53 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. R8A NP110aa lost the ability to bind Qip1 and NPI-1 but still showed very weak binding to Rch1. 2013 PloS one Result IV R8A 0 3 NP 4 6 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. Recombinant GST-tagged importin alpha isoforms (Rch1, Qip1 and NPI-1) were immobilized on glutathione-Sepharose beads and incubated with mRFP-Flag-tagged NP110aa or its mutants NP14-110aa, R8A NP110aa and S9A NP110aa followed by purification from vertebrate cells. 2013 PloS one Result IV R8A;S9A 189;205 192;208 NP;NP;NP;NP 154;177;193;209 156;179;195;211 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. Taken together, Qip1 preferentially bound to S9A NP110aa comparing with Rch1 and NPI-1 in vitro and vivo. 2013 PloS one Result IV S9A 45 48 NP 49 51 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. The amounts of WT and S9A mutant viruses in the cell culture supernatant were measured after 24, 48 and 72 h of infection using a plaque assay. 2013 PloS one Result IV S9A 22 25 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. The growth of S9A NP mutant virus was attenuated compared with that of the WT virus (4x108 PFU/ml vs. 2013 PloS one Result IV S9A 14 17 NP 18 20 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. The luciferase activity was reduced by approximately 50% in negative control siRNA treated cells using S9A NP plasmid compare to WT NP plasmid. 2013 PloS one Result IV S9A 103 106 NP;NP 107;132 109;134 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. The nuclear localization of WT and S9A NP110aa was not changed by Qip1 silencing. 2013 PloS one Result IV S9A 35 38 NP 39 41 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. Therefore, we next examined the binding affinity of WT NP110aa and S9A NP110aa for the three importin alpha isoforms using a compatitive binding assay. 2013 PloS one Result IV S9A 67 70 NP;NP 55;71 57;73 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. This result clearly shows that the production of mutant virus was completely inhibited by the R8A mutation, which also reduced NP nuclear localization activity. 2013 PloS one Result IV R8A 94 97 NP 127 129 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. To demonstrate the role of the unconventional NLS of NP on viral production, we generated mutant viruses with amino acid substitutions R8A or S9A using a reverse-genetics approach. 2013 PloS one Result IV R8A;S9A 135;142 138;145 NP 53 55 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. To determine whether Qip1 is involved in viral multiplication, viral transcription and replication of the WT and the S9A NP mutant were examined in A549 cells and in HEK-293 cells in which Qip1 expression had been knocked down. 2013 PloS one Result IV S9A 117 120 NP 121 123 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. To examine the role of amino acid residue 9 on the replication of influenza virus, A549 cells were infected with S9A NP mutant or WT NP viruses (produced by reverse-genetics) at a multiplicity of infection of 1 (MOI 1), and the viral titers were determined using a plaque assay 24 h later. 2013 PloS one Result IV S9A 113 116 NP;NP 117;133 119;135 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. When all three importin alpha proteins were incubated with WT or S9A NP110aa-conjugated beads, subsequent Western blot analysis detected bindings of WT and S9A NP110aa to Qip1. 2013 PloS one Result IV S9A;S9A 65;156 68;159 NP;NP 69;160 71;162 23383318 Inhibitors of the influenza A virus M2 proton channel discovered using a high-throughput yeast growth restoration assay. Amantadine did not increase the growth of the S31N and V27A strains (Figs 1C, 1D), as expected since these mutated channels are amantadine-resistant. 2013 PloS one Result IV S31N;V27A 46;55 50;59 23383318 Inhibitors of the influenza A virus M2 proton channel discovered using a high-throughput yeast growth restoration assay. cerevisiae strains were generated containing a multicopy plasmid for expression of the wild-type, S31N-mutated, or V27A-mutated M2 gene from the Udorn strain of influenza A controlled by the inducible GAL1 promoter (designated WT, S31N and V27A respectively), or an empty plasmid. 2013 PloS one Result IV S31N;V27A;S31N;V27A 98;115;231;240 102;119;235;244 M2 128 130 23383318 Inhibitors of the influenza A virus M2 proton channel discovered using a high-throughput yeast growth restoration assay. Compound 16 showed significant activity against the V27A mutant (EC50 = 7 microM) and was inactive against S31N while all other compounds were inactive against V27A or S31N. 2013 PloS one Result IV V27A;S31N;V27A;S31N 52;107;160;168 56;111;164;172 23383318 Inhibitors of the influenza A virus M2 proton channel discovered using a high-throughput yeast growth restoration assay. Compounds 14, 18, and 20-34 were also tested at 100 microM against the S31N and V27A mutant channels in the TEVC assay and were found to be inactive. 2013 PloS one Result IV S31N;V27A 71;80 75;84 23383318 Inhibitors of the influenza A virus M2 proton channel discovered using a high-throughput yeast growth restoration assay. Expression of amantadine-resistant S31N M2 reduced yeast growth to 60% of the control strain while expression of V27A M2 reduced growth to 55% of control. 2013 PloS one Result IV S31N;V27A 35;113 39;117 M2;M2 40;118 42;120 23383318 Inhibitors of the influenza A virus M2 proton channel discovered using a high-throughput yeast growth restoration assay. Given the high prevalence of amantadine-resistant mutations in seasonal flu strains, it was of interest to determine whether any of the compounds found to be active against WT M2 also showed activity towards the S31N or V27A mutant channels. 2013 PloS one Result IV S31N;V27A 212;220 216;224 M2 176 178 23383318 Inhibitors of the influenza A virus M2 proton channel discovered using a high-throughput yeast growth restoration assay. In accordance with these expectations, spiroadamantane amine clearly increased growth of the V27A strain at 0.01 microM and above, with an EC50 of 0.3 microM. 2013 PloS one Result IV V27A 93 97 23383318 Inhibitors of the influenza A virus M2 proton channel discovered using a high-throughput yeast growth restoration assay. This compound inhibits the V27A mutant channel as well as the WT channel in the two electrode voltage clamp (TVEC) assay of M2 channel conductance with IC50 of 0.3 and 18.7 microM respectively, and also inhibits replication of recombinant viruses bearing the V27A mutation in a plaque reduction assay. 2013 PloS one Result IV V27A;V27A 27;259 31;263 M2 124 126 23397331 Influenza virus A(H1N1)pdm09 hemagglutinin polymorphism and associated disease in southern Germany during the 2010/11 influenza season. All of the viruses analysed displayed the amino acid changes P83S and S203T in the HA1 region as well as I321V and E 374 K in the HA2 region. 2013 Archives of virology Result IV P83S;S203T;I321V;E374K 61;70;105;115 65;75;110;122 HA;HA1 130;83 132;86 23397331 Influenza virus A(H1N1)pdm09 hemagglutinin polymorphism and associated disease in southern Germany during the 2010/11 influenza season. Also in this case, two additional amino acid changes (K130R and M344L, GenBank accession number JX483122) were detected in the BAL sample. 2013 Archives of virology Result IV K130R;M344L 54;64 59;69 23397331 Influenza virus A(H1N1)pdm09 hemagglutinin polymorphism and associated disease in southern Germany during the 2010/11 influenza season. Double mutations characteristic of group 3 (A134T, S183P), and group 2 (N31D, S162N) were not observed. 2013 Archives of virology Result IV A134T;S183P;N31D;S162N 44;51;72;78 49;56;76;83 23397331 Influenza virus A(H1N1)pdm09 hemagglutinin polymorphism and associated disease in southern Germany during the 2010/11 influenza season. Finally, 3 of the 33 sequences (9 %) clustered within group 7 and were characterized by the mutations S185T, S143G, and A197T. 2013 Archives of virology Result IV S185T;S143G;A197T 102;109;120 107;114;125 23397331 Influenza virus A(H1N1)pdm09 hemagglutinin polymorphism and associated disease in southern Germany during the 2010/11 influenza season. Group 4, characterized by amino acid mutations N125D included four sequences, all obtained from the same patient. 2013 Archives of virology Result IV N125D 47 52 23397331 Influenza virus A(H1N1)pdm09 hemagglutinin polymorphism and associated disease in southern Germany during the 2010/11 influenza season. However, in two patients, two additional glycosylation sites were detected at residue 119 (lysine to asparagine) in one case and at residue162 (serine to asparagine) in the other case. 2013 Archives of virology Result IV K119N 86 112 23397331 Influenza virus A(H1N1)pdm09 hemagglutinin polymorphism and associated disease in southern Germany during the 2010/11 influenza season. In detail, 16 of the 33 sequences (48 %) belonged to genetic group 6, characterized by the double mutation D97N and S185T. 2013 Archives of virology Result IV D97N;S185T 107;116 111;121 23397331 Influenza virus A(H1N1)pdm09 hemagglutinin polymorphism and associated disease in southern Germany during the 2010/11 influenza season. In this group, three also had the H138Q mutation. 2013 Archives of virology Result IV H138Q 34 39 23397331 Influenza virus A(H1N1)pdm09 hemagglutinin polymorphism and associated disease in southern Germany during the 2010/11 influenza season. Interestingly, the K119N mutation, representing an additional potential N-glycosylation site, was present only in the BAL sample. 2013 Archives of virology Result IV K119N 19 24 23397331 Influenza virus A(H1N1)pdm09 hemagglutinin polymorphism and associated disease in southern Germany during the 2010/11 influenza season. Moreover, 3 of these 6 showed an additional S84I mutation (as influenza A/Delaware/AF21764/2010), and one of them had a P159S mutation. 2013 Archives of virology Result IV S84I;P159S 44;120 48;125 23397331 Influenza virus A(H1N1)pdm09 hemagglutinin polymorphism and associated disease in southern Germany during the 2010/11 influenza season. Ten of the 33 sequences (30 %) belonged to genetic group 5, characterized by the mutations D97N, R205K, I216V and V249L. 2013 Archives of virology Result IV D97N;R205K;I216V;V249L 91;97;104;114 95;102;109;119 23397331 Influenza virus A(H1N1)pdm09 hemagglutinin polymorphism and associated disease in southern Germany during the 2010/11 influenza season. The oseltamivir-resistance-associated mutation H275Y was detected in 1 (20 %) of the 5 treated patients, a one-year-old child with a genetic disorder, who was treated for 21 days with oseltamivir. 2013 Archives of virology Result IV H275Y 47 52 23437033 Quantitative description of glycan-receptor binding of influenza A virus H7 hemagglutinin. Given that FC and CC HA differ by a single amino acid change at RBS, CC HA was generated by introducing a Thr135 Ala mutation through site-directed mutagenesis. 2013 PloS one Result IV T135A 106 116 HA;HA 21;72 23;74 23437033 Quantitative description of glycan-receptor binding of influenza A virus H7 hemagglutinin. Therefore the Ala135 Thr mutation was introduced on NY/107 HA and this mutant HA showed the identical binding profile in a dose-dependent fashion as that of the wild type HA (Figure 1D). 2013 PloS one Result IV A135T 14 24 HA;HA;HA 59;78;171 61;80;173 23437033 Quantitative description of glycan-receptor binding of influenza A virus H7 hemagglutinin. Therefore the loss in binding to avian receptor by Gln-226 Leu mutation is compensated in part by binding of Ser-228 to avian receptor. 2013 PloS one Result IV Q226L 51 62 23437217 Parallel screening of wild-type and drug-resistant targets for anti-resistance neuraminidase inhibitors. Because of the I223R mutation, the ketone moiety of tetrahydroanthracene switches its hydrogen-bond partner from R152 of the S3 subsite to R223 of the S4 subsite. 2013 PloS one Result IV I223R 15 20 23437217 Parallel screening of wild-type and drug-resistant targets for anti-resistance neuraminidase inhibitors. Structure comparison of WT and MDR NAs shows striking differences in volume and polarity of S4 subsites, which are mainly caused by the I223R mutation. 2013 PloS one Result IV I223R 136 141 35 38 23437217 Parallel screening of wild-type and drug-resistant targets for anti-resistance neuraminidase inhibitors. Unlike the high conservation of the S1, S2, and S3 subsites, the S4 subsite has relatively low residue conservation and acquires drug resistant mutations such as H275Y and I223R. 2013 PloS one Result IV H275Y;I223R 162;172 167;177 23451169 Simultaneous detection of oseltamivir- and amantadine-resistant influenza by oligonucleotide microarray visualization. V27A sites of two cases of 2009 influenza A (H1N1) (27V confirmed by sequencing) were not detected by microarray, while 31N and 275H were consistent with sequencing. 2013 PloS one Result IV V27A 0 4 23555270 Monomeric nucleoprotein of influenza A virus. All results for the monomeric wt and mutant proteins are identical and different from those for the oligomeric form thus, it is likely that monomeric wt NP has a similar structure as the R416A mutant NP. 2013 PLoS pathogens Result IV R416A 187 192 NP;NP 153;200 155;202 23555270 Monomeric nucleoprotein of influenza A virus. All spectra of monomeric NP (wt NP at 50 mM salt and R416A mutant NP at both 50 and 300 mM salt) were identical. 2013 PLoS pathogens Result IV R416A 53 58 NP;NP;NP 25;32;66 27;34;68 23555270 Monomeric nucleoprotein of influenza A virus. Figure 2 shows the comparison of the structures of trimeric wt and monomeric R416A NP. 2013 PLoS pathogens Result IV R416A 77 82 NP 83 85 23555270 Monomeric nucleoprotein of influenza A virus. Figure 3 compares the H1N1 R416A monomer structure with the trimer structures of H1N1 and H5N1. 2013 PLoS pathogens Result IV R416A;R416A 28;27 33;32 23555270 Monomeric nucleoprotein of influenza A virus. However, in the structure of R416A, the chain is visible until the penultimate residue and points into the RNA binding surface, reducing the space for RNA binding and changing the electrostatic characteristics of this surface (compare figures 3C, F and I, blue is positively charged). 2013 PLoS pathogens Result IV R416A 29 34 23555270 Monomeric nucleoprotein of influenza A virus. However, when studied by DLS at higher concentrations, the S165D mutant showed a much higher cooperativity upon RNA binding than wt NP. 2013 PLoS pathogens Result IV S165D 59 64 NP 132 134 23555270 Monomeric nucleoprotein of influenza A virus. In the R416A structure, E339 makes hydrogen bonds with R461 and the mutated R416A points towards R461; if the wt monomer structure were the same as the R416A structure there could be a clash between arginines 416 and 461. 2013 PLoS pathogens Result IV R416A;R416A;R416A 7;76;152 12;81;157 23555270 Monomeric nucleoprotein of influenza A virus. In the trimer structures, R416 makes an ionic bond with E339 and it was assumed that R416A and E339A formed monomers because this bond in the trimer was disrupted. 2013 PLoS pathogens Result IV R416A;E339A 85;95 90;100 23555270 Monomeric nucleoprotein of influenza A virus. Influenza A/WSN/33 R416A mutant NP was concentrated to 10 mg/ml and crystallised by vapour diffusion using the sitting drop method. 2013 PLoS pathogens Result IV R416A 19 24 NP 32 34 23555270 Monomeric nucleoprotein of influenza A virus. Monomeric R416A and monomeric wt NP stabilised at low salt have an identical sedimentation behaviour with an S20,w of 4.3 S. 2013 PLoS pathogens Result IV R416A 10 15 NP 33 35 23555270 Monomeric nucleoprotein of influenza A virus. NP-RNA complexes formed immediately upon mixing of S165D NP with a 51 nt RNA oligo (Figure 5C, T = 0) whereas complex formation with wt NP was slower (Figure 1). 2013 PLoS pathogens Result IV S165D 51 56 NP;NP;NP 0;57;136 2;59;138 23555270 Monomeric nucleoprotein of influenza A virus. S165D NP polymerisation onto a 24-mer RNA oligonucleotide reached a plateau in 30 minutes compared to 2 hours for wt NP (Figure 5B). 2013 PLoS pathogens Result IV S165D 0 5 NP;NP 6;117 8;119 23555270 Monomeric nucleoprotein of influenza A virus. The circular dichroism spectrum of the trimer form of the wt protein is identical to that of the obligate Y148A trimer, both at 50 and 300 mM NaCl (Figure 4A). 2013 PLoS pathogens Result IV Y148A 106 111 23555270 Monomeric nucleoprotein of influenza A virus. The Kd for RNA of S165D was determined by surface plasmon resonance (SPR) using a 24 nt oligoribonucleotide and by a filter binding assay using a radioactive panhandle RNA. 2013 PLoS pathogens Result IV S165D 18 23 23555270 Monomeric nucleoprotein of influenza A virus. Therefore, the R416A mutation may both stabilise the monomer and destabilise the trimer. 2013 PLoS pathogens Result IV R416A 15 20 23555270 Monomeric nucleoprotein of influenza A virus. This means that the exchange domain of the wild type monomer does not extend out in solution in the same conformation as in the oligomeric form but must be close to the core of the protein like in the R416A structure. 2013 PLoS pathogens Result IV R416A 201 206 23555270 Monomeric nucleoprotein of influenza A virus. Thus, although the Kd for RNA is lower for the S165D mutant than for wt NP, the kinetics of assembly on RNA is more rapid. 2013 PLoS pathogens Result IV S165D 47 52 NP 72 74 23555270 Monomeric nucleoprotein of influenza A virus. We produced the S165D mutant mimicking the phosphorylation of Ser165. 2013 PLoS pathogens Result IV S165D 16 21 23555270 Monomeric nucleoprotein of influenza A virus. We then crystallised the obligate monomeric R416A mutant of NP. 2013 PLoS pathogens Result IV R416A 44 49 NP 60 62 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. All influenza A(H1N1)pdm09 viruses tested for peramivir (n = 326) were sensitive to the drug, with the exception of the two extreme outliers mentioned above, which contained the H275Y change, A/Puerto Rico/09/2011 and A/Alberta/RV1242/2011, whose IC50s that were ~300- and ~100-fold greater than the mean IC50 for the drug (0 06 +- 0 08 nm; Table 3), respectively. 2013 Influenza and other respiratory viruses Result IV H275Y 178 183 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. Among influenza B viruses of the Yamagata lineage, only one extreme outlier for oseltamivir was detected (Table 4), the isolate B/Ontario/006876/2011 with H273Y mutation, which was also an extreme outlier for peramivir but not for zanamivir. 2013 Influenza and other respiratory viruses Result IV H273Y 155 160 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. Among viruses of the Victoria lineage, only two outliers for oseltamivir were detected (Table 4), B/Dominican Republic/5506/2011 with H273Y and B/Ontario/1256/2011, which had previously uncharacterized changes in the NA, G140R and N144K. 2013 Influenza and other respiratory viruses Result IV H273Y;G140R;N144K 134;221;231 139;226;236 217 219 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. Another extreme outlier for oseltamivir, the isolate A/Santiago/14689/2011, which exhibited the least fold difference in IC50 for oseltamivir (19-fold) compared with the mean IC50 for the drug, did not have the H275Y mutation. 2013 Influenza and other respiratory viruses Result IV H275Y 211 216 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. Another influenza B isolate, B/Guatemala/16/2011, had the S244P (S245P in N2 numbering) mutation in the NA and was a mild outlier for zanamivir (threefold), but was sensitive to oseltamivir and peramivir (Table 4). 2013 Influenza and other respiratory viruses Result IV S244P;S245P 58;65 63;70 104 106 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. Another isolate, B/Dominican Republic/5506/2011, had the H273Y mutation in the NA, but its IC50 for oseltamivir (23 71 nm) was only approximately twofold higher than the mean IC50 of the drug for B viruses (10 43 +- 5 24 nm). 2013 Influenza and other respiratory viruses Result IV H273Y 57 62 79 81 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. Full NA sequence analysis showed that B/Ontario/006876/2011 had H273Y (H274Y in N2 numbering) mutation, while B/Ontario/1256/20 had two amino acid changes, G140R and N144K (G142R and N146K in N2 numbering). 2013 Influenza and other respiratory viruses Result IV H273Y;H274Y;G140R;N144K;G142R;N146K 64;71;156;166;173;183 69;76;161;171;178;188 5 7 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. Genetic analysis showed that the isolate A/Puerto Rico/09/2011 harbored the oseltamivir resistance conferring H275Y mutation in the NA, while the isolate A/Alberta/RV1242/2011 consisted of a mixed population of H275 wild-type virus and H275Y variants (H275H/Y), in addition to a mix of D199 wild-type and D199N variants (D199D/N; D198D/N in N2 numbering). 2013 Influenza and other respiratory viruses Result IV H275Y;H275Y;H275H;H275Y;D199N;D199D;D199N;D198D;D198N 110;236;252;252;305;321;321;330;330 115;241;259;259;310;328;328;337;337 132 134 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. However, it is unknown whether the N325K substitution was present before the virus' passage in MDCK cells due to unavailability of clinical material. 2013 Influenza and other respiratory viruses Result IV N325K 35 40 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. In addition, six mild outliers to peramivir were detected, including A/Santiago/14689/2011 with N325K mutation and A/Brazil/568/2011 with S247N mutation, both showing a threefold increase in IC50 compared with that of peramivir-susceptible viruses. 2013 Influenza and other respiratory viruses Result IV N325K;S247N 96;138 101;143 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. In addition, three mild outliers for oseltamivir were detected among B viruses of the Yamagata lineage, including B/British Columbia/RV1383/2011, which had a T106N (T110N in N2 numbering) amino acid change in the NA. 2013 Influenza and other respiratory viruses Result IV T106N;T110N 158;165 163;170 213 215 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. Instead, this virus contained a previously unreported substitution in the NA, N325K (N1 and N2 numbering). 2013 Influenza and other respiratory viruses Result IV N325K 78 83 74 76 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. Mild outliers for zanamivir included the two viruses mentioned above that were extreme outliers for oseltamivir, A/Alberta/RV1242/2011 with the mixed double mutations H275H/Y and D199D/N, and A/Santiago/14689/2011 with N325K mutation, which showed three- and eightfold increases in IC50 compared with the mean for the drug (0 23 +- 0 05 nm), respectively. 2013 Influenza and other respiratory viruses Result IV H275H;H275Y;D199D;D199N;N325K 167;167;179;179;219 174;174;186;186;224 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. Of note, IC50 values for oseltamivir (69 92 nm) and peramivir (6 48 nm) for this virus were approximately threefold less than those for the isolate A/Puerto Rico/09/2011 with the dominant H275Y mutation, respectively (Table 4). 2013 Influenza and other respiratory viruses Result IV H275Y 188 193 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. Other influenza A(H1N1)pdm09 outliers for oseltamivir were A/Dominican Republic/5507/2011 and A/Brazil/568/2011, both with S247N (S246N in N2 numbering) mutation in the NA, as well as A/Puerto Rico/05/2011 and A/Bolivia/258/2011, both of which had D199N (D198N in N2 numbering) mutation. 2013 Influenza and other respiratory viruses Result IV S247N;S246N;D199N;D198N 123;130;248;255 128;135;253;260 169 171 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. Other mild outliers for zanamivir were A/Vietnam/108/2011 with F147V and A/Bolivia/258/2011 with D199N mutation; both isolates were also mild outliers for oseltamivir. 2013 Influenza and other respiratory viruses Result IV F147V;D199N 63;97 68;102 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. Overall, the frequency of oseltamivir resistance was low (0 6%) among influenza A(H1N1)pdm09 viruses collected globally (n = 326), with the detection of only two viruses harboring H275Y substitution in the NA. 2013 Influenza and other respiratory viruses Result IV H275Y 180 185 206 208 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. Some of these outliers showed genetic changes in the NA (Table 4), including A/Vietnam/108/2011 with F147V (F143V in N2 numbering) mutation and A/Santiago/15706/2011 with G460S (G461S in N2 numbering) mutation, which exhibited six- and fourfold increases in IC50, respectively, compared with the mean IC50 for the drug. 2013 Influenza and other respiratory viruses Result IV F147V;F143V;G460S;G461S 101;108;171;178 106;113;176;183 53 55 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. The H275H/Y mix comprised of 54 2% wild-type virus and 45 8% variants, while the D199D/N mix comprised of 43% wild-type virus and 57% variants. 2013 Influenza and other respiratory viruses Result IV H275H;H275Y;D199D;D199N 4;4;81;81 11;11;88;88 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. The isolate B/Dominican Republic/5506/2011 exhibited H273Y, but was an outlier for neither oseltamivir nor peramivir, based on IC50 analysis of all type B viruses. 2013 Influenza and other respiratory viruses Result IV H273Y 53 58 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. The matching clinical samples were unavailable testing, and thus, the presence of the G140R and N144K substitutions prior to the virus culturing could not be ascertained. 2013 Influenza and other respiratory viruses Result IV G140R;N144K 86;96 91;101 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. The only other country where a H275Y virus was detected was Canada, from where only three A(H1N1)pdm09 viruses were submitted to the CDC in the time period covered by this study. 2013 Influenza and other respiratory viruses Result IV H275Y 31 36 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. Virus isolates of the A(H3N2) subtype that were tested for oseltamivir, zanamivir, and peramivir (n = 407) were all sensitive to the three NAIs, with exception of 5 mild outliers for zanamivir; two of which exhibited mutations at residue 151 of the NA, D151G and a mixed D151D/G/N mutations, respectively (Table 4). 2013 Influenza and other respiratory viruses Result IV D151G;D151N;D151G;D151D 271;271;253;271 280;280;258;280 NA;NAI 249;139 251;143 23593230 Effect of cysteine mutations in the extracellular domain of CM2 on the influenza C virus replication. 5(E), there was no significant difference in the total copy number of GFP-vRNA in the cells just after the incubation for 30 min at 4 C between WT- and C1620A-VLP-infected cells, indicating that an equal amount of GFP-vRNAs was used for infection. 2013 PloS one Result IV C1620A 152 158 23593230 Effect of cysteine mutations in the extracellular domain of CM2 on the influenza C virus replication. After incubation at 33 C for 60 min, the copy number of GFP-vRNA in the nuclear fraction of WT-VLP-infected cells significantly increased (p<0.05), whereas that of C1620A-VLP-infected cells was unchanged. 2013 PloS one Result IV C1620A 164 170 23593230 Effect of cysteine mutations in the extracellular domain of CM2 on the influenza C virus replication. As described in the Materials and Methods section, the pPolI/CM2-C1620A plasmid was transfected to 293T cells together with the six remaining Pol I plasmids and nine protein-expressing plasmids. 2013 PloS one Result IV C1620A 65 71 CM2 61 64 23593230 Effect of cysteine mutations in the extracellular domain of CM2 on the influenza C virus replication. At 48 h p.i., the expression level of GFP in the C1620A-VLP-infected cells was lower (30%) than that in the WT-VLP-infected cells. 2013 PloS one Result IV C1620A 49 55 23593230 Effect of cysteine mutations in the extracellular domain of CM2 on the influenza C virus replication. Furthermore, after incubation for 60 min, a significant difference in the copy numbers in the nuclear fraction was observed between WT-VLP- and C1620A-VLP-infected cells (p<0.05). 2013 PloS one Result IV C1620A 144 150 23593230 Effect of cysteine mutations in the extracellular domain of CM2 on the influenza C virus replication. Furthermore, the amounts of Luc expressed in the C1620A-VLP-infected cells were constantly lower than those in the WT-VLP-infected cells at 3, 6, 9 and 12 h p.i. 2013 PloS one Result IV C1620A 49 55 23593230 Effect of cysteine mutations in the extracellular domain of CM2 on the influenza C virus replication. Furthermore, the tetrameric CM2-C1620A could not be detected on film even at longer exposure times (data not shown). 2013 PloS one Result IV C1620A 32 38 CM2 28 31 23593230 Effect of cysteine mutations in the extracellular domain of CM2 on the influenza C virus replication. Growth of the Recombinant C1620A Virus. 2013 PloS one Result IV C1620A 26 32 23593230 Effect of cysteine mutations in the extracellular domain of CM2 on the influenza C virus replication. HMV-II cells were infected with VLPs so that the copy number of GFP-vRNA included in the WT-VLPs was equal to that in C1620A-VLPs; i.e., cells were infected with VLP preparations containing three times as many C1620A-VLPs as WT-VLPs. 2013 PloS one Result IV C1620A;C1620A 118;210 124;216 23593230 Effect of cysteine mutations in the extracellular domain of CM2 on the influenza C virus replication. Immunofluorescence analysis of CM2-expressing COS cells has shown that C1620A-CM2 was transported to the cell surface in a manner similar to that of wild-type CM2. 2013 PloS one Result IV C1620A 71 77 CM2;CM2;CM2 31;78;159 34;81;162 23593230 Effect of cysteine mutations in the extracellular domain of CM2 on the influenza C virus replication. In contrast, in the rC1620A-infected cells the cross-linked dimers of CM2-C1620A were detected even in the absence of DSP (approximately 25% that of rWT). 2013 PloS one Result IV C1620A;C1620A 74;20 80;27 CM2 70 73 23593230 Effect of cysteine mutations in the extracellular domain of CM2 on the influenza C virus replication. In order to examine the possibility that the mutant CM2-C1620A protein may form a dimer or tetramer that is held together weakly by non-covalent forces, an experiment using a chemical cross-linker was performed. 2013 PloS one Result IV C1620A 56 62 CM2 52 55 23593230 Effect of cysteine mutations in the extracellular domain of CM2 on the influenza C virus replication. In particular, a mutant protein, CM2-C1620A, in which all three cysteines were substituted to alanines, lacked the ability to form disulfide-linked oligomers, although it was transported to the cell surface. 2013 PloS one Result IV C1620A 37 43 CM2 33 36 23593230 Effect of cysteine mutations in the extracellular domain of CM2 on the influenza C virus replication. It should be noted that the tetrameric form of CM2-C1620A could be detected at less than trace amounts in the presence of DSP. 2013 PloS one Result IV C1620A 51 57 CM2 47 50 23593230 Effect of cysteine mutations in the extracellular domain of CM2 on the influenza C virus replication. The amount of NP contained in the C1620A-VLPs appeared to be smaller than that in WT-VLPs, a finding suggesting the presence of less GFP-vRNA in the C1620A-VLPs. 2013 PloS one Result IV C1620A;C1620A 34;149 40;155 NP 14 16 23593230 Effect of cysteine mutations in the extracellular domain of CM2 on the influenza C virus replication. The amount of protein of the purified WT-VLPs generated from a given number of VLP-producing 293T cells was identical to that of C1620A-VLPs (WT-VLP:C1620A-VLP = 1.00:1.05), which is consistent with our previous finding that CM2 mutation did not affect the efficiency of VLP formation. 2013 PloS one Result IV C1620A;C1620A 129;149 135;155 CM2 225 228 23593230 Effect of cysteine mutations in the extracellular domain of CM2 on the influenza C virus replication. the mutant CM2-C1620A protein matured properly in virus-infected cells, but its tetramer formation was impaired. 2013 PloS one Result IV C1620A 15 21 CM2 11 14 23593230 Effect of cysteine mutations in the extracellular domain of CM2 on the influenza C virus replication. These findings are consistent with the hypothesis that the transport of the GFP-vRNA from the uncoated VLPs occurred less efficiently in the C1620A-VLP-infected cells than in the WT-VLP-infected cells, suggesting that the uncoating of C1620A-VLP occurs less efficiently. 2013 PloS one Result IV C1620A;C1620A 141;235 147;241 23593230 Effect of cysteine mutations in the extracellular domain of CM2 on the influenza C virus replication. This finding was consistent with that reported for the CM2-C1620A protein expressed in COS cells. 2013 PloS one Result IV C1620A 59 65 CM2 55 58 23593230 Effect of cysteine mutations in the extracellular domain of CM2 on the influenza C virus replication. This observation indicates that the packaging of GFP-vRNA into the C1620A-VLPs occurred less efficiently than that into WT-VLPs, since there were no differences in the amount of virus proteins or GFP-vRNA expressed in the VLP-producing 293T cells (data not shown). 2013 PloS one Result IV C1620A 67 73 23593230 Effect of cysteine mutations in the extracellular domain of CM2 on the influenza C virus replication. Thus, it is unlikely that the CM2-C1620A protein forms a tetramer at a level comparable to that of the authentic CM2 in virus-infected cells. 2013 PloS one Result IV C1620A 34 40 CM2;CM2 30;113 33;116 23593230 Effect of cysteine mutations in the extracellular domain of CM2 on the influenza C virus replication. Thus, these findings suggest that the uncoating process of C1620A-VLPs occurred less efficiently than does that of WT-VLPs. 2013 PloS one Result IV C1620A 59 65 23593230 Effect of cysteine mutations in the extracellular domain of CM2 on the influenza C virus replication. To examine reporter gene expression in the infected cells, HMV-II cells were infected with three times as much C1620A-VLP-preparation as WT-VLP-preparation, based on the difference in the amount of GFP-vRNA contained in the VLPs. 2013 PloS one Result IV C1620A 111 117 23593230 Effect of cysteine mutations in the extracellular domain of CM2 on the influenza C virus replication. To investigate whether C1620A-CM2 is incorporated into progeny virions, aliquots of the purified virions were subjected to immunoblotting with anti-CM2 serum under reducing. 2013 PloS one Result IV C1620A 23 29 CM2;CM2 30;148 33;151 23593230 Effect of cysteine mutations in the extracellular domain of CM2 on the influenza C virus replication. To obtain further evidence for the impaired uncoating of the C1620A-VLPs, we quantified the incoming GFP-vRNA transported to the nucleus of VLP-infected cells according to the procedure reported previously. 2013 PloS one Result IV C1620A 61 67 23593230 Effect of cysteine mutations in the extracellular domain of CM2 on the influenza C virus replication. To obtain VLPs possessing the mutant CM2 protein (C1620A-VLP), pME18S/CM2-C1620A, instead of pME18S/Met-CM2-YA, was transfected together with the nine other plasmids. 2013 PloS one Result IV C1620A;C1620A 50;74 56;80 CM2;CM2;CM2 37;70;104 40;73;107 23593230 Effect of cysteine mutations in the extracellular domain of CM2 on the influenza C virus replication. upper panel), whereas the amount of surface CM2-C1620A on the rC1620A-infected cells was less than that of CM2 on rWT-infected cells. 2013 PloS one Result IV C1620A;C1620A 48;62 54;69 CM2;CM2 44;107 47;110 23593230 Effect of cysteine mutations in the extracellular domain of CM2 on the influenza C virus replication. was also confirmed using VLPs containing Luc-vRNA; WT-VLP:C1620A-VLP = 1.0:0.35 (data not shown). 2013 PloS one Result IV C1620A 58 64 23593230 Effect of cysteine mutations in the extracellular domain of CM2 on the influenza C virus replication. We analyzed HMV-II cells infected with WT- or C1620A-VLPs by flow cytometry, and found that the attachment and internalization of C1620A-VLPs occurred as efficiently as did those of WT-VLPs (data not shown). 2013 PloS one Result IV C1620A;C1620A 46;130 52;136 23593230 Effect of cysteine mutations in the extracellular domain of CM2 on the influenza C virus replication. We then quantified the amount of GFP-vRNA in the VLPs using real-time PCR, and found that the amount (copies per microg VLP protein) of GFP-vRNA in the C1620A-VLPs was approximately 31% of that in WT-VLPs. 2013 PloS one Result IV C1620A 152 158 23626667 Quantitative characterization of glycan-receptor binding of H9N2 influenza A virus hemagglutinin. Both these mutant HAs showed extensive staining to apical surface of human tracheal epithelium consistent with their human-receptor binding properties on the glycan array ( Figure 4D ; data for mQa88:Q226L not shown). 2013 PloS one Result IV Q226L 200 205 23626667 Quantitative characterization of glycan-receptor binding of H9N2 influenza A virus hemagglutinin. Consistent with its glycan array-binding properties, mQa88:T189A also showed extensive staining to human alveolar tissues ( Figure 4D ). 2013 PloS one Result IV T189A 59 64 23626667 Quantitative characterization of glycan-receptor binding of H9N2 influenza A virus hemagglutinin. In fact the Kd' of mQa88:Q226L is in the same range as that of HAs from seasonal influenza strains. 2013 PloS one Result IV Q226L 25 30 23626667 Quantitative characterization of glycan-receptor binding of H9N2 influenza A virus hemagglutinin. In the case of H3 HA, Gly-228 Ser is another hallmark amino acid change. 2013 PloS one Result IV G228S 22 33 HA 18 20 23626667 Quantitative characterization of glycan-receptor binding of H9N2 influenza A virus hemagglutinin. In the case of Qa88 HA, a single amino acid change in the mQa88:Q226L mutant completely changed its glycan-binding preference from avian to human receptors (6'SLN-LN) ( Figure 4A ). 2013 PloS one Result IV Q226L 64 69 HA 20 22 23626667 Quantitative characterization of glycan-receptor binding of H9N2 influenza A virus hemagglutinin. In the case of Qa88 HA, we defined three mutant forms; mQa88:T189A (to establish if changes to Thr-189 would affect avian receptor-binding), mQa88:Q226L (to determine if Gln-226 Leu mutation would change its binding preference from avian to human receptor), and mQa88:Q226L/T189A (to explore if the additional Thr189 Ala mutation would further modulate human receptor-binding of mQa88:Q226L). 2013 PloS one Result IV T189A;Q226L;T189A;Q226L;Q226L;Q226L;T189A 61;147;274;268;385;170;310 66;152;279;273;390;181;320 HA 20 22 23626667 Quantitative characterization of glycan-receptor binding of H9N2 influenza A virus hemagglutinin. mWF10:T189A showed a more specific binding to 6'SLN-LN than WF10 HA where binding to other representative glycan receptors at >40 microg/ml concentration was minimal when compared to WF10 HA at the same concentration ( Figure 3A ). 2013 PloS one Result IV T189A 6 11 HA;HA 65;188 67;190 23626667 Quantitative characterization of glycan-receptor binding of H9N2 influenza A virus hemagglutinin. Notably, both WF10 and mQa88:Q226L viruses showed similar pattern of binding to both avian and human receptors in the glycan array screening assays performed earlier. 2013 PloS one Result IV Q226L 29 34 23626667 Quantitative characterization of glycan-receptor binding of H9N2 influenza A virus hemagglutinin. One of the observed mutations in WF10 HA in the reassorted virus that shows airborne transmission in ferrets is Thr-189 Ala. 2013 PloS one Result IV T189A 112 123 HA 38 40 23626667 Quantitative characterization of glycan-receptor binding of H9N2 influenza A virus hemagglutinin. Staining of mWF10:T189A HA on human tracheal tissue sections revealed a pattern similar to that observed with WT WF10 with extensive binding of the protein to the apical side and weak to no binding to the human deep lung alveolar tissue ( Figure 3A ). 2013 PloS one Result IV T189A 18 23 HA 24 26 23626667 Quantitative characterization of glycan-receptor binding of H9N2 influenza A virus hemagglutinin. The additional Thr-189 Ala change in the mQa88:Q226L/T189A mutant leads to an increase in the binding specificity to 6'SLN-LN where binding to other glycan receptors at 40 microg/ml was minimal when compared to mQa88:Q226L at the same concentration. 2013 PloS one Result IV Q226L;T189A;Q226L;T189A 47;53;217;15 52;58;222;26 23626667 Quantitative characterization of glycan-receptor binding of H9N2 influenza A virus hemagglutinin. The Kd' ~60 pM for 6'SLN-LN binding of mQa88:Q226L/T189A was in the same range as that of mQa88:Q226L. 2013 PloS one Result IV Q226L;T189A;Q226L 45;51;96 50;56;101 23626667 Quantitative characterization of glycan-receptor binding of H9N2 influenza A virus hemagglutinin. The single amino acid change in mWF10:L226Q mutant, on the other hand, completely reversed its glycan-binding preference from human to avian receptors (with Kd' ~30 pM for 3'SLN-LN and 3'SLN-LN-LN) ( Figure 3B ). 2013 PloS one Result IV L226Q 38 43 23626667 Quantitative characterization of glycan-receptor binding of H9N2 influenza A virus hemagglutinin. The third mutant mQa88:T189A increased specificity to 3'SLN-LN and 3'SLN-LN-LN without altering the Kd' (~30 pM) when compared to that calculated for the wild-type Qa88 HA ( Figure 4C ). 2013 PloS one Result IV T189A 23 28 HA 169 171 23626667 Quantitative characterization of glycan-receptor binding of H9N2 influenza A virus hemagglutinin. Therefore, we postulated that the Thr-189 Ala mutation, in the context of a given HA, would alter binding to both avian and human receptors by affecting side chain orientation of residues (in a given HA) that make contact with these receptors. 2013 PloS one Result IV T189A 34 45 HA;HA 82;200 84;202 23626667 Quantitative characterization of glycan-receptor binding of H9N2 influenza A virus hemagglutinin. We designed two mutant forms of WF10 HA; mWF10:T189A (to investigate the effect of Thr-189 Ala mutation on human receptor-binding) and mWF10:L226Q (to determine if Leu-226 Gln mutation would change its binding preference from human to avian receptor). 2013 PloS one Result IV T189A;L226Q;T189A;L226Q 47;141;83;164 52;146;94;175 HA 37 39 23638404 Virtual screening for oseltamivir-resistant a (H5N1) influenza neuraminidase from traditional Chinese medicine database: a combined molecular docking with molecular dynamics approach. Despite the H274Y mutation in the structure of NA, neoglucobrassicin were retained the interaction with the residues R-371 and R-152 as like the wild type NA. 2013 SpringerPlus Result IV H274Y 12 17 NA;NA 47;155 49;157 23638404 Virtual screening for oseltamivir-resistant a (H5N1) influenza neuraminidase from traditional Chinese medicine database: a combined molecular docking with molecular dynamics approach. It is evident from the figure that H274Y mutation alters the confirmations of the NA binding pocket. 2013 SpringerPlus Result IV H274Y 35 40 82 84 23646055 Occurrence and characterization of oseltamivir-resistant influenza virus in children between 2007-2008 and 2008-2009 seasons. Amino acid mutations (S158N, G202A, and A206T) were shown in all the domestic isolates, but they were unlikely to affect antigenicity to vaccine strain. 2013 Korean journal of pediatrics Result IV S158N;G202A;A206T 22;29;40 27;34;45 23646055 Occurrence and characterization of oseltamivir-resistant influenza virus in children between 2007-2008 and 2008-2009 seasons. NA gene analysis was conducted on influenza viruses isolated from 51 patients (group A, 29 patients; group B, 22 patients) during the first study period in order to examine the drug resistance-related mutation of NA inhibitor (E119V, R152K, H274Y, R292K, N294S). 2013 Korean journal of pediatrics Result IV E119V;R152K;H274Y;R292K;N294S 227;234;241;248;255 232;239;246;253;260 NA;NA 0;213 2;215 23646055 Occurrence and characterization of oseltamivir-resistant influenza virus in children between 2007-2008 and 2008-2009 seasons. The result showed that H275Y (N1 numbering) mutation was observed in all of A/H1N1 virus strains isolated from 39 patients during the second study period, showing NI resistance, and that D354G of NA gene was observed in most isolates. 2013 Korean journal of pediatrics Result IV H275Y;D354G 23;187 28;192 196 198 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. Adaptations K153E and G155E are also antigenically distinct from each other. 2013 PLoS pathogens Result IV K153E;G155E 12;22 17;27 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. Adding K153E to N156K reduces the positive electrostatic potential of the HA head domain ( Figure 5D ) as does the addition of G155E to N156K (Figure S3C). 2013 PLoS pathogens Result IV K153E;N156K;G155E;N156K 7;16;127;136 12;21;132;141 HA 74 76 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. Addition of G155E to N156K increased 6'SL binding, while the addition of K153E to N156K did not alter the binding preference. 2013 PLoS pathogens Result IV G155E;N156K;K153E;N156K 12;21;73;82 17;26;78;87 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. Addition of oseltamivir carboxylate did not improve hemagglutination titres for N156K either (data not shown), indicating no binding effect of the NA. 2013 PLoS pathogens Result IV N156K 80 85 147 149 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. All reverse genetics viruses used contained the ferret-specific adaptations L191I and R223Q in the HA protein. 2013 PLoS pathogens Result IV L191I;R223Q 76;86 81;91 HA 99 101 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. Although gene sequencing detected five amino acid differences between the HA of A/Tasmania/2004/2009 (GISAID EPI_ISL_129743) and A/California/7/2009 (GenBank: CY058519) (N38N/S, P83S, S203T, T209K, I321V, Table 2 ), none were in the major antigenic regions. 2013 PLoS pathogens Result IV N38S;N38N;P83S;S203T;T209K;I321V 170;170;178;184;191;198 176;176;182;189;196;203 HA 74 76 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. Although the K142N mutation on its own had no effect, addition of this mutation to viruses with mutation/s at positions 153-156 reduced their titre at least four-fold further ( Table 5 ). 2013 PLoS pathogens Result IV K142N 13 18 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. Analysis of all A(H1N1)pdm09 sequences from 2009-2012 in GISAID and GenBank found N156K, K153E and N156D at similar low frequencies (0.15, 0.20 and 0.27%, respectively); G155E has been reported more often (1.30%, Table 4 ). 2013 PLoS pathogens Result IV N156K;K153E;N156D;G155E 82;89;99;170 87;94;104;175 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. Antisera from MIV-, MIV+IFA-immunized ferrets or from ferrets infected with wildtype virus recognized cells infected with N156K virus less efficiently than cells infected with wildtype virus. 2013 PLoS pathogens Result IV N156K 122 127 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. As folding of the mutated HA protein may be temperature dependent, infection and culture of MDCK-SIAT1 cells with N156K mutant viruses was also attempted at different temperatures (33, 35 and 37 C), yet similar cell culture adaptations in the HA protein were observed (data not shown). 2013 PLoS pathogens Result IV N156K 114 119 HA;HA 26;243 28;245 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. Attempts to isolate the N156K mutant virus in a variety of other cell lines (MDCK, Beas-2B, Vero, A549) as well as embryonated hen's eggs, were unsuccessful. 2013 PLoS pathogens Result IV N156K 24 29 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. Binding was more restricted compared to the original egg inoculum virus, presumably due to the mutations L191I and R223Q ( Figure 4C ). 2013 PLoS pathogens Result IV L191I;R223Q 105;115 110;120 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. Both reverse genetics mutant N156E as well as surveillance viruses with mutations and adaptations at N156 showed reduced HI titre compared to wildtype virus, indicating the antigenic importance of amino acid 156. 2013 PLoS pathogens Result IV N156E 29 34 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. Cell culture adaptations may disguise the effect of N156K on the antigenic profile of A/Tasmania/2004/2009 virus. 2013 PLoS pathogens Result IV N156K 52 57 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. Cloning revealed that L191 and R223 were mixed populations (L191L/I and R223R/Q) in the original inoculum. 2013 PLoS pathogens Result IV L191L;L191I;R223R;R223Q 60;60;72;72 67;67;79;79 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. Computer modeling with alpha-2,6- and alpha-2,3-linked Neu5Ac receptors was performed to enable a structural basis for the N156K mutation and subsequent cell culture adaptations. 2013 PLoS pathogens Result IV N156K 123 128 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. Culture adaptations of the HA protein were detected at residues 153, 155 and 156, most commonly as a mixed population at position 156 (N156K/E) or with mutations at positions 153 or 155 in addition to N156K (K153E+N156K or G155E+N156K) ( Figure 3A , Table 3 ). 2013 PLoS pathogens Result IV N156K;N156E;N156K;K153E;N156K;N156K;G155E 135;135;201;208;214;229;223 142;142;206;213;219;234;228 HA 27 29 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. Culture of virus from peak day samples containing mixed populations of wildtype (N156) and N156K viruses resulted in outgrowth of the wildtype N156 virus as determined by RNA extraction and sequencing (data not shown). 2013 PLoS pathogens Result IV N156K 91 96 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. D14E, identified in one of the MIV+IFA passage lines, lies outside predicted antigenic sites, does not alter glycosylation and was not tested further. 2013 PLoS pathogens Result IV D14E 0 4 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. Detection of N156K and culture adaptations in influenza surveillance data. 2013 PLoS pathogens Result IV N156K 13 18 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. Direct binding assays using antisera from immunized and virus-infected ferrets were used to assess the antigenicity of the N156K mutant virus. 2013 PLoS pathogens Result IV N156K 123 128 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. Following inoculation of donor ferrets (D0) with egg-grown A/Tasmania/2004/2009, we detected amino acid substitutions in the HA at residues 191 (L191I) and 223 (R223Q) ( Table 2 ). 2013 PLoS pathogens Result IV L191I;R223Q 145;161 150;166 HA 125 127 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. Furthermore, it is likely that the wildtype antiserum contains a high level of antibodies directed towards the N156 region of the HA protein, whilst the N156K and K142N+N156K antisera contains antibodies that are directed towards a region of the HA protein, common to both wildtype and N156K HA. 2013 PLoS pathogens Result IV N156K;N156K;K142N;N156K 153;169;163;286 158;174;168;291 HA;HA;HA 130;246;292 132;248;294 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. G131S creates a potential glycosylation site and D187 has been associated with host specificity. 2013 PLoS pathogens Result IV G131S 0 5 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. Genetic analysis found no changes in the HA protein of virus isolated from the R7 ferret of N156K line A compared to inoculum (D14E+N156K). 2013 PLoS pathogens Result IV N156K;N156K;D14E 92;132;127 97;137;131 HA 41 43 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. HA and matrix protein were also detected on the surface of N156K-infected cells ( Figure 3A ) and CPE was visible (data not shown), indicating that N156K mutant virus was present, even in the absence of RBC agglutination. 2013 PLoS pathogens Result IV N156K;N156K 59;148 64;153 HA;M 0;7 2;13 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. However, an additional mutation was detected (K142N in R4) and became fixed in the HA of passage line B (K142N+N156K, Table 2 ). 2013 PLoS pathogens Result IV K142N;N156K;K142N 46;111;105 51;116;110 HA 83 85 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. However, as the K142N mutation was acquired in only one of the two lines of passaging the N156K virus seven times in naive ferrets (Table S1), it is not essential for replication and transmission in the ferret model. 2013 PLoS pathogens Result IV K142N;N156K 16;90 21;95 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. However, isolates from ferrets of the MIV+IFA and N156K naive passage lines (herein referred to as N156K mutant virus) had only low hemagglutination titres (HA<=4). 2013 PLoS pathogens Result IV N156K;N156K 50;99 55;104 HA 157 159 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. In both lines, pyrosequencing and sequencing of clones showed N156K persisted at approximately 100% in each sample and did not revert to wildtype N156 ( Figure 2E , Tables 2 , S1). 2013 PLoS pathogens Result IV N156K 62 67 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. In contrast, K153E and G155E adaptations were strongly associated with growth in MDCK cells ( Table 4 ). 2013 PLoS pathogens Result IV K153E;G155E 13;23 18;28 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. In contrast, N156E significantly reconfigures the distribution of charge ( Figure 5C ). 2013 PLoS pathogens Result IV N156E 13 18 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. In contrast, post-infection antisera from ferrets infected with N156K or K142N+N156K viruses bound cells infected with wildtype or N156K mutant virus to a similar degree ( Figure 4B ). 2013 PLoS pathogens Result IV N156K;N156K;K142N;N156K 64;79;73;131 69;84;78;136 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. In line B, the N156K mutant emerged earlier, in R1, and became dominant in R2, persisting through to R7 ( Figure 2D ). 2013 PLoS pathogens Result IV N156K 15 20 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. Introduction of the N156K mutation to the ferret adapted virus resulted in binding to only 6'SLN, indicating a strong preference for alpha-2,6-linked Neu5Ac receptors containing GlcNAc rather than galactose ( Figure 4C , N156K, D14E+N156K, K142N+N156K). 2013 PLoS pathogens Result IV N156K;N156K;D14E;N156K;K142N;N156K 20;221;228;233;240;246 25;226;232;238;245;251 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. It also suggests that the K142N mutation, when added to N156K, gives a selective advantage. 2013 PLoS pathogens Result IV K142N;N156K 26;56 31;61 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. K142N and N156E displayed a similar profile to N156K. 2013 PLoS pathogens Result IV K142N;N156E;N156K 0;10;47 5;15;52 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. K142N is not predicted to alter glycosylation. 2013 PLoS pathogens Result IV K142N 0 5 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. K153E showed weak binding to 6'SLN, G155E showed binding to 6'SL and 6'SLN. 2013 PLoS pathogens Result IV K153E;G155E 0;36 5;41 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. Mutations arose in the naive passage lines (G131S, D187E, Table 2 ) and in the MIV passage line (D187V, Table 2 ). 2013 PLoS pathogens Result IV G131S;D187E;D187V 44;51;98 49;56;103 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. N156D has been detected following passage of A(H1N1)pdm09 virus in embryonated hen's eggs under immune pressure. 2013 PLoS pathogens Result IV N156D 0 5 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. N156K A/Tasmania/2004/2009 HA mutant virus is fit in naive ferrets. 2013 PLoS pathogens Result IV N156K 0 5 HA 27 29 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. N156K and K142N (and K153E, R223Q) are located in regions on the HA protein proposed to contact sugars beyond Neu5Ac on cell surface receptors. 2013 PLoS pathogens Result IV N156K;K142N;K153E;R223Q 0;10;21;28 5;15;26;33 HA 65 67 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. N156K is at the interface of three previously crystallized antibody binding sites (Figure S3B). 2013 PLoS pathogens Result IV N156K 0 5 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. N156K is predicted to prefer alpha-2,6-linked receptors ( Figure 5E ), whilst in our models it is more favorable for the N156E mutation to bind to alpha-2,3-linked receptors ( Figure 5E ). 2013 PLoS pathogens Result IV N156K;N156E 0;121 5;126 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. N156K was detected only in virus samples collected from ferrets in the MIV+IFA immunization group; proportions were similar by cloning and pyrosequencing assay ( Figure 2D and Table S1). 2013 PLoS pathogens Result IV N156K 0 5 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. N156K was not able to be isolated without culture adaptations in the presence of exogenous neuraminidase, or oseltamivir carboxylate (data not shown). 2013 PLoS pathogens Result IV N156K 0 5 91 104 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. Neither the N156K alone nor K142N+N156K virus could be rescued as a pure population without adaptation. 2013 PLoS pathogens Result IV N156K;N156K;K142N 12;34;28 17;39;33 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. Our observation that N156K mutant viruses were not detected by hemagglutination and did not persist without adaptation in vitro suggested an alteration in receptor binding specificity. 2013 PLoS pathogens Result IV N156K 21 26 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. Real time RT-PCR for the matrix gene indicated that levels of viral RNA in the N156K mutant virus culture supernatant at 72 h post-infection were similar to those in control samples from naive or PBS+IFA-immunized ferrets (herein referred to as wildtype viruses) ( Figure 3A , P1). 2013 PLoS pathogens Result IV N156K 79 84 M 25 31 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. The A/Tasmania/2004/2009 original inoculum and ferret-adapted wildtype viruses were recognized by mAb174, but binding was greatly reduced in the presence of the N156K mutation and cell culture adaptations ( Figure 4A ). 2013 PLoS pathogens Result IV N156K 161 166 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. The addition of K153E to N156K (and G155E to N156K) appears compensatory, allowing stronger binding to alpha-2,3 receptors compared to N156K alone ( Figure 5F , Figure S3C,D). 2013 PLoS pathogens Result IV K153E;N156K;G155E;N156K;N156K 16;25;36;45;135 21;30;41;50;140 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. The emergence of the N156K mutation did not result in a change of virus kinetics (peak viral load, growth rate or serial interval) compared to N156 wildtype virus (data not shown). 2013 PLoS pathogens Result IV N156K 21 26 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. The G131S, D187E and D187V viruses were antigenically indistinguishable from the wildtype virus in HI assays with serum from ferrets infected with egg-grown A/Tasmania/2004/2009 (data not shown). 2013 PLoS pathogens Result IV G131S;D187E;D187V 4;11;21 9;16;26 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. The HA antigenicity and receptor binding profile are altered in the N156K A/Tasmania/2004/2009 HA mutant virus. 2013 PLoS pathogens Result IV N156K 68 73 HA;HA 4;95 6;97 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. The introduction of the K142N mutation did not result in a change of virus kinetics peak viral load, growth rate or serial interval) compared to N156K alone virus (data not shown). 2013 PLoS pathogens Result IV K142N;N156K 24;145 29;150 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. The K142N mutation had no effect ( Table 5 ). 2013 PLoS pathogens Result IV K142N 4 9 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. The K142N+N156K virus outgrew the N156K virus after one or two transmission events ( Figure 2G ). 2013 PLoS pathogens Result IV N156K;K142N;N156K 10;4;34 15;9;39 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. The N156K A/Tasmania/2004/2009 HA mutant virus does not agglutinate red blood cells and adapts rapidly in vitro . 2013 PLoS pathogens Result IV N156K 4 9 HA 31 33 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. The N156K A/Tasmania/2004/2009 HA mutant virus does not agglutinate red blood cells and adapts rapidly in vitro. 2013 PLoS pathogens Result IV N156K 4 9 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. The N156K mutant emerged in R4 of line A, persisted at a similar proportion in R5, and became dominant by R6. 2013 PLoS pathogens Result IV N156K 4 9 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. The N156K mutation arose in both passage lines of MIV+IFA-immunized ferrets ( Table 2 ). 2013 PLoS pathogens Result IV N156K 4 9 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. The N156K mutation has been detected in human A(H1N1)pdm09 clinical samples (analyzed for surveillance purposes at the WHO Collaborating Centre for Reference and Research on Influenza, Melbourne), both alone and in conjunction with N125D, which is located in antigenic site Sa ) ( Table 3 and Figure 3C, D ). 2013 PLoS pathogens Result IV N156K;N125D 4;232 9;237 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. The N156K mutation noticeably adds positive charge potential compared to wildtype HA ( Figure 5A, B ). 2013 PLoS pathogens Result IV N156K 4 9 HA 82 84 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. The N156K mutation was found more commonly in original specimens than in cell isolates. 2013 PLoS pathogens Result IV N156K 4 9 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. The N156K virus outgrew the N156 wildtype virus after one or two transmission events, in duplicate experiments ( Figure 2F ), as in the original experiment ( Figure 2D ). 2013 PLoS pathogens Result IV N156K 4 9 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. The relative proportions of the N156K mutant and wildtype N156 viruses were quantified in samples from both passage lines of MIV+IFA-immunized ferrets using a pyrosequencing assay. 2013 PLoS pathogens Result IV N156K 32 37 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. The serial interval between transmission events was similar for wildtype and N156K virus passaged in naive ferrets ( Figure 2C ). 2013 PLoS pathogens Result IV N156K 77 82 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. These data suggest that the N156K virus is antigenically distinct from wildtype virus. 2013 PLoS pathogens Result IV N156K 28 33 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. This effect was specific for viruses with mutations in the Sa/Sb antigenic region as the virus with K142N mutation alone was still recognized by mAb174. 2013 PLoS pathogens Result IV K142N 100 105 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. This suggests that the N156K variant fitter than the N156 wildtype virus in the ferret model. 2013 PLoS pathogens Result IV N156K 23 28 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. To assess the ability of the N156K mutant virus to transmit and persist in vivo, N156K variant viruses (from MIV+IFA R7 ferrets) were passaged a further seven times by contact transmission in naive ferrets (passage lines N156K naive A and B). 2013 PLoS pathogens Result IV N156K;N156K;N156K 29;81;221 34;86;226 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. To confirm the pyrosequencing data and to determine whether the N156K mutation was present in the original inoculum, the proportion of the N156K mutant was quantified by cloning and sequencing the HA1 gene from the original inoculum (n = 480) and from samples from the R7 ferret in each passage line, and the ferrets in which the N156K mutation was first detected (MIV+IFA R4, line A and R1, line B) (n = 96 for each) (Table S1). 2013 PLoS pathogens Result IV N156K;N156K;N156K 64;139;330 69;144;335 HA1 197 200 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. To directly compare the fitness of the wildtype, N156K and K142N+N156K viruses in the absence of immune pressure, naive ferrets were infected with mixtures of either N156 wildtype and N156K viruses (42:58% ratio from line B R1 ( Figure 2D , and Table S1, MIV+IFA B R1)) or N156K and K142N+N156K viruses (76:24% ratio by pyrosequencing). 2013 PLoS pathogens Result IV N156K;N156K;K142N;N156K;N156K;N156K;K142N 49;65;59;184;273;289;283 54;70;64;189;278;294;288 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. Two mutations were detected in the NA protein: M15I emerged in the MIV passage line A and I46F in the MIV+IFA passage line B ( Table 2 ). 2013 PLoS pathogens Result IV M15I;I46F 47;90 51;94 35 37 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. Upon further passage in MDCK-SIAT1 cells, the N156K mutant virus was detected only at high HA titres (HA>=16) when additional HA mutations were present ( Figure 3A , P2). 2013 PLoS pathogens Result IV N156K 46 51 HA;HA;HA 91;102;126 93;104;128 23717200 Prolonged influenza virus shedding and emergence of antiviral resistance in immunocompromised patients and ferrets. Emergence of oseltamivir resistance was studied in the animals infected with wild type virus (groups 1, 2 and 3) using an RT-PCR assay specifically detecting the H275Y oseltamivir resistance mutation (Figure 4). 2013 PLoS pathogens Result IV H275Y 162 167 23717200 Prolonged influenza virus shedding and emergence of antiviral resistance in immunocompromised patients and ferrets. From day 8 onward, the H275Y mutation emerged in the virus population of all oseltamivir treated animals in both the nose and throat. 2013 PLoS pathogens Result IV H275Y 23 28 23717200 Prolonged influenza virus shedding and emergence of antiviral resistance in immunocompromised patients and ferrets. In 5 (7%) of the immunocompromised patients with an influenza pH1N1 virus infection the oseltamivir resistance mutation H275Y in the neuraminidase was detected by RT-PCR during oseltamivir mono or oseltamivir/zanamivir combination therapy. 2013 PLoS pathogens Result IV H275Y 120 125 133 146 Influenza A virus H1N1 infection 52 83 23717200 Prolonged influenza virus shedding and emergence of antiviral resistance in immunocompromised patients and ferrets. The animals of groups 1, 2 and 3 had been inoculated with oseltamivir sensitive (wild type; H275) and the animals in groups 4, 5 and 6 with oseltamivir resistant virus (mutant; H275Y) (Figure 2A and 3). 2013 PLoS pathogens Result IV H275Y 177 182 23717200 Prolonged influenza virus shedding and emergence of antiviral resistance in immunocompromised patients and ferrets. The H275Y mutant became the major genotype 2 or 3 days later. 2013 PLoS pathogens Result IV H275Y 4 9 23717200 Prolonged influenza virus shedding and emergence of antiviral resistance in immunocompromised patients and ferrets. To this end, 6 groups of ferrets were inoculated intratracheally on day 0 with a wild type or H275Y mutant pH1N1 virus (Figure 2A). 2013 PLoS pathogens Result IV H275Y 94 99 23759670 Virological self-sampling to monitor influenza antiviral susceptibility in a community cohort. Screening for this H275Y substitution was performed by pyrosequencing on a total of 1312 influenza A(H1N1)pdm09-positive samples. 2013 The Journal of antimicrobial chemotherapy Result IV H275Y 19 24 23759670 Virological self-sampling to monitor influenza antiviral susceptibility in a community cohort. The minority H275Y quasi-species was maintained in the primary isolates for two of the three samples, but no shift in IC50 was detected (Table 2). 2013 The Journal of antimicrobial chemotherapy Result IV H275Y 13 18 23759670 Virological self-sampling to monitor influenza antiviral susceptibility in a community cohort. The most common mechanism of oseltamivir resistance is a single amino acid substitution, histidine to tyrosine at position 275 (H275Y) in the N1 neuraminidase. 2013 The Journal of antimicrobial chemotherapy Result IV H275Y;H275Y 128;89 133;126 145 158 23759670 Virological self-sampling to monitor influenza antiviral susceptibility in a community cohort. To determine the baseline incidence in the community, samples from the sentinel GP scheme were also screened for H275Y (738 samples), one of which had a quasi-species of H275Y at 18% Tyr-275; this had been taken in week 44 from a 15-year-old child who had had no known antiviral treatment or contact (Table 2). 2013 The Journal of antimicrobial chemotherapy Result IV H275Y;H275Y 113;170 118;175 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. Additionally, we performed a similar experiment (one donor) using an MOI of 3 and detected the same trend in IFN-lambda response (rNY1682-D701N lower than rNY1682-WT, data not shown). 2013 PloS one Result IV D701N 138 143 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. Although the increased RNA polymerase activity conferred by PB2-D701N was fairly modest in comparison to other mutations (e.g., E627K, and E158G), seemingly small differences in RNA polymerase activity may still influence transmission or pathogenesis. 2013 PloS one Result IV D701N;E627K;E158G 64;128;139 69;133;144 PB2 60 63 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. Although the mini-genome assay results indicate that the D701N substitution increases the polymerase activity in human kidney and lung cell lines (HEK-293T and A549), rNY1682-WT and rNY1682-D701N showed similar growth kinetics in the human lung Calu-3 cell line at 33oC and 37oC (Figure 2C and D). 2013 PloS one Result IV D701N;D701N 57;190 62;195 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. Although viral titer from different donors varied, we found that the rNY1682-D701N virus always replicated to modestly higher titers than the rNY1682-WT virus (Figure 3A). 2013 PloS one Result IV D701N 77 82 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. At both time points and all temperatures, the PB2-D701N substitution resulted in a significantly higher level of relative luciferase activity compared to the PB2-WT (p<0.05, t-test) (Figure 1), indicating that the D701N substitution in the PB2 protein enhances activity of the H1N1pdm RdRp. 2013 PloS one Result IV D701N;D701N 50;214 55;219 PB2;PB2;PB2 46;158;240 49;161;243 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. Compared to rNY1682-WT, rNY1682-D701N replicated more rapidly and had 40-fold higher titers in the lungs as early as 24 hpi (Figure 4A). 2013 PloS one Result IV D701N 32 37 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. Compared to the rNY1682-WT infected cells, rNY1682-D701N infected cells secreted significantly lower amount of IFN-lambda (Figure 3B), which represents important virus induced antiviral type III interferon (IL28/29). 2013 PloS one Result IV D701N 51 56 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. Ferrets inoculated with rNY1682-WT and rNY1682-D701N viruses exhibited similar clinical signs including transient weight loss and fever before returning to baseline levels (data not shown). 2013 PloS one Result IV D701N 47 52 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. However, mean nasal wash virus titers from the rNY1682-D701N inoculated ferrets were significantly higher than that from the rNY1682-WT inoculated ferrets on day 3 and day 5 post inoculation (P<0.001, Figure 6A and 6B), consistent with the replication advantage of the rNY1682-D701N virus has in cells (human primary ATI-like cells, Calu-3 cells, and mouse CMT-93) and mice. 2013 PloS one Result IV D701N;D701N 55;277 60;282 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. Human embryonic kidney-293T cells (HEK-293T) were co-transfected with plasmids expressing the NY1682 PB2 (either WT or D701N), PB1, PA, NP proteins, and a pPolI-NS-Luc reporter plasmid. 2013 PloS one Result IV D701N 119 124 NP;NS;PA;PB1;PB2 136;161;132;127;101 138;163;134;130;104 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. In contrast, rNY1682-WT and rNY1682-D701N infected cells secreted comparable levels of CCL5 (Figure 3C), IL-6 (Figure 3D), and IL-8 (Figure 3E). 2013 PloS one Result IV D701N 36 41 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. In contrast, the group of mice infected by rNY1682-D701N continued to lose weight throughout the experiment and all of these animals succumbed to infection by 7 dpi (Figure 5A and 5B). 2013 PloS one Result IV D701N 51 56 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. In contrast, the rNY1682-D701N replicated faster and to higher titer than rNY1682-WT virus in ATI-like cells. 2013 PloS one Result IV D701N 25 30 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. In contrast, the rNY1682-D701N virus transmitted efficiently to all of the three contact ferrets (Figure 6B) and all of them were seroconverted (data now shown). 2013 PloS one Result IV D701N 25 30 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. In that study, we again found that the rNY1682-D701N virus transmitted to all three of the contact ferrets and with similar kinetics of transmission as was observed in the first study (in total 6/6 for PB2-701N on day 3 verses 4/6 for PB2-701D on day 7, Figure 6B and data not shown). 2013 PloS one Result IV D701N 47 52 PB2;PB2 202;235 205;238 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. In the CMT-93 cells, the rNY1682-D701N replicated more efficiently than rNY1682-WT, and the titers of rNY1682-D701N were significantly higher (~8-fold) than that of rNY1682-WT at 48, 72 and 96 hpi (p<0.001, ANOVA) (Figure 2B). 2013 PloS one Result IV D701N;D701N 33;110 38;115 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. Interestingly, at 39oC, rNY1682-D701N replicated faster and the viral titer was modestly higher than rNY1682-WT at 48 hpi (p<0.001, ANOVA) (Figure 2E). 2013 PloS one Result IV D701N 32 37 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. It is possible that at the optimal temperature (37 C), the rNY1682-WT virus replicated to very high titers (107.8 TCID50/ML) in the Calu-3 cells (Figure 2D), to which the rNY1682-D701N virus was unable to surpass. 2013 PloS one Result IV D701N 179 184 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. Mice inoculated with rNY1682-WT, rNY1682-E627K and rNY1682-D701N, began to lose weight by 3 dpi; and more significant weight loss was observed in the mice inoculated with rNY1682-D701N than in mice inoculated with rNY1682-WT or rNY1682-E627K as early as 4 dpi (p<0.01, ANOVA) (Figure 4A). 2013 PloS one Result IV E627K;D701N;D701N;E627K 41;59;179;236 46;64;184;241 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. Notably, in contrast to the largely delayed transmission of the rNY1682-WT virus, the rNY1682-D701N virus transmitted to contact ferrets as early as 1 dpc and all the ferrets showed relatively high virus titers by 3 dpc (Figure 6B). 2013 PloS one Result IV D701N 94 99 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. PB2-D701N enhances lung replication and pathogenicity of the H1N1pdm virus in a mouse model. 2013 PloS one Result IV D701N 4 9 PB2 0 3 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. PB2-D701N increases the transmissibility of the H1N1pdm virus in a ferret model. 2013 PloS one Result IV D701N 4 9 PB2 0 3 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. PB2-D701N reduces induction of IFN-lambda and enhances virus replication in primary human alveolar epithelial cells. 2013 PloS one Result IV D701N 4 9 PB2 0 3 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. PB2-D701N substitution increases viral RNA polymerase activity in vitro . 2013 PloS one Result IV D701N 4 9 PB2 0 3 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. PB2-D701N substitution increases viral RNA polymerase activity in vitro. 2013 PloS one Result IV D701N 4 9 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. Previous studies have shown that D701N substitution in the PB2 protein of H5N1 virus can improve virus growth in mammalian cells. 2013 PloS one Result IV D701N 33 38 PB2 59 62 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. Statistical analysis of the data demonstrated that the rNY1682-D701N infected mice had significantly higher titers at 12 and 24 hpi (p<0.05, ANOVA), whereas the modest titer differences in the nasal washes at 24 and 48 hpi (Figure 4B) were not statistically significant compared to the rNY1682-WT (p>0.05, ANOVA). 2013 PloS one Result IV D701N 63 68 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. Taken together, the rNY1682-D701N virus consistently demonstrated similar or enhanced replication kinetics compared to the rNY1682-WT (Figures 2 and 3). 2013 PloS one Result IV D701N 28 33 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. The dramatic increase in viral titer in the lungs of mice infected by rNY1682-D701N indicate that this substitution has a stronger impact on replication in vivo than in the mouse CMT-93 cell line, which didn't show a difference between rNY1682-WT and rNY1682-D701N until 48 hpi (Figure 2B). 2013 PloS one Result IV D701N;D701N 78;259 83;264 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. The growth advantage of the rNY1682-D701N virus in ATI-like cells could be the result of interaction between the viral factor, PB2-D701N, and multiple host factors. 2013 PloS one Result IV D701N;D701N 36;131 41;136 PB2 127 130 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. The growth kinetics of the rNY1682-WT and rNY1682-D701N viruses was almost identical in MDCK cells, and both viruses reached peak titers of 107.7 TCID50/ml by 24 hpi (Figure 2A). 2013 PloS one Result IV D701N 50 55 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. The lower level of IFN-lambda Induced by the rNY1682-D701N virus may give the virus a replication advantage in the type I-like cells. 2013 PloS one Result IV D701N 53 58 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. The mice inoculated with rNY1682-WT or rNY1682-E627K had an average maximum weight loss of approximately 12% and began to recover by 8 dpi (Figure 5A). 2013 PloS one Result IV E627K 47 52 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. The MLD50 of rNY1682-D701N was 2X104 TCID50, which is at least 300-fold lower than that of the parental virus rNY1682-WT (>6X106 TCID50) and 33-fold higher than that of the rNY1682-E158G virus (6X102 TCID50). 2013 PloS one Result IV D701N;E158G 21;181 26;186 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. The PB2-D701N substitution also increased the H1N1pdm polymerase activity in A549 cells, a human lung epithelial cell line (data not shown). 2013 PloS one Result IV D701N 8 13 PB2 4 7 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. The rapid and robust replication of rNY1682-D701N in mouse respiratory tract warranted further evaluation of the effect of PB2-D701N on the pathogenicity of H1N1pdm virus. 2013 PloS one Result IV D701N;D701N 44;127 49;132 PB2 123 126 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. The rNY1682-D701N virus replicates more efficiently in mouse epithelial cells and in human lung epithelial cells at an elevated temperature. 2013 PloS one Result IV D701N 12 17 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. Therefore, the ATI-like cells may be more sensitive than the Calu-3 cells for the detection of the effects from the PB2-D701N mutation (compare to Figure 2D). 2013 PloS one Result IV D701N 120 125 PB2 116 119 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. Therefore, the effects of the PB2-D701N substitution on virus replication, pathogenesis, and transmission were investigated. 2013 PloS one Result IV D701N 34 39 PB2 30 33 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. These data show that rNY1682-D701N is more virulent than either rNY1682-WT or rNY1682-E627K, and that it is less virulent than the highly pathogenic rNY1682-E158G virus. 2013 PloS one Result IV D701N;E627K;E158G 29;86;157 34;91;162 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. Three ferrets were inoculated intranasally with 106 PFU of the rNY1682-WT or rNY1682-D701N virus, and 24 h later three naive ferrets were each placed in a transmission cage adjacent to an inoculated ferret. 2013 PloS one Result IV D701N 85 90 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. To determine if the D701N substitution also has a similar effect on the H1N1pdm virus, we created a recombinant H1N1pdm virus that differed from the wild-type A/New York/1682/2009 (rNY1682-WT) at PB2-D701N (rNY1682-701N). 2013 PloS one Result IV D701N;D701N 20;200 25;205 PB2 196 199 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. To determine if the PB2-D701N substitution also enhances H1N1pdm virus replication in vivo, six-week-old female BALB/cJ mice were anesthetized with isoflurane and inoculated intranasally with 50 microl virus diluent containing 103 TCID50 of either rNY1682-WT or rNY1682-D701N. 2013 PloS one Result IV D701N;D701N 24;270 29;275 PB2 20 23 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. To determine if the PB2-D701N substitution influences the replication of the H1N1pdm virus in human lung cells, primary cultured ATI-like cells were prepared from lungs of seven de-identified donors as described previously, and were infected with the rNY1682-WT and rNY1682-D701N viruses at 37oC. 2013 PloS one Result IV D701N;D701N 24;274 29;279 PB2 20 23 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. To further evaluate the influence of PB2-D701N, we determined the 50% mouse lethal dose (MLD50) by intranasally inoculating BALB/cJ mice with 103, 104, 105, or 106 TCID50 of rNY1682-D701N; all of the groups of mice showed prominent weight loss (Figure 5C), and the mortality rate was 0%, 40%, 80%, and 100%, respectively (Figure 5D). 2013 PloS one Result IV D701N;D701N 41;182 46;187 PB2 37 40 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. Using the same assay, we have previously shown that introduction of E627K into NY1682-PB2 increased polymerase activity by 400% and E158G substitution in NY1682-PB2 increased activity by 1500%. 2013 PloS one Result IV E627K;E158G 68;132 73;137 PB2;PB2 86;161 89;164 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. We compared H1N1pdm viruses that expressed wild type PB2 (rNY1682-WT), PB2-E627K (rNY1682-E627K), PB2-D701N (rNY1682-D701N), or a PB2-E158G (rNY1682-E158G) substitution that we previously showed significantly increases the pathogenicity of the H1N1pdm virus. 2013 PloS one Result IV E627K;E627K;D701N;D701N;E158G;E158G 75;90;102;117;134;149 80;95;107;122;139;154 PB2;PB2;PB2;PB2 53;71;98;130 56;74;101;133 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. We used a luciferase-mediated mini-genome assay to examine the effects of the PB2-D701N substitution on the H1N1pdm viral polymerase activity. 2013 PloS one Result IV D701N 82 87 PB2 78 81 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. We used the well-established ferret respiratory droplet transmission model to evaluate the effects of PB2-D701N on the transmissibility of H1N1pdm virus by housing ferrets in adjacent cages, each with a perforated side wall that prevented direct contact but allowed spread of virus through the air. 2013 PloS one Result IV D701N 106 111 PB2 102 105 23860768 Resistance to neuraminidase inhibitors conferred by an R292K mutation in a human influenza virus H7N9 isolate can be masked by a mixed R/K viral population. 3) that bear additional HA mutations showed better dose-response curves, and a more accurate IC50 estimation conferred by the NA R292K mutation was able to be determined (Table 4). 2013 mBio Result IV R292K 129 134 HA;NA 24;126 26;128 23860768 Resistance to neuraminidase inhibitors conferred by an R292K mutation in a human influenza virus H7N9 isolate can be masked by a mixed R/K viral population. 6, which differed only by the NA R292K mutation in their HA and NA genes, were selected for further analysis. 2013 mBio Result IV R292K 33 38 HA;NA;NA 57;30;64 59;32;66 23860768 Resistance to neuraminidase inhibitors conferred by an R292K mutation in a human influenza virus H7N9 isolate can be masked by a mixed R/K viral population. Overall, our results showed that the R292K NA mutation confers resistance to zanamivir, peramivir, and oseltamivir in the novel H7N9 influenza virus and that the mutation had impaired the NA enzyme function as previously reported for the H1N9 or seasonal H3N2 influenza viruses. 2013 mBio Result IV R292K 37 42 NA;NA 43;188 45;190 23860768 Resistance to neuraminidase inhibitors conferred by an R292K mutation in a human influenza virus H7N9 isolate can be masked by a mixed R/K viral population. The R292K mutation also increased the Km value, indicating a reduced binding affinity for the MUNANA substrate. 2013 mBio Result IV R292K 4 9 23860768 Resistance to neuraminidase inhibitors conferred by an R292K mutation in a human influenza virus H7N9 isolate can be masked by a mixed R/K viral population. This observation suggests that the NA R292K mutation did not compromise the replication efficiency of the A/Shanghai/1/2013 virus in the MDCK-SIAT1 cells. 2013 mBio Result IV R292K 38 43 35 37 23860768 Resistance to neuraminidase inhibitors conferred by an R292K mutation in a human influenza virus H7N9 isolate can be masked by a mixed R/K viral population. To evaluate if the reduced NA activity conferred by the R292K mutation would compromise viral growth, we performed multicycle replication kinetics analyses for the plaque-purified A/Shanghai/1/2013 NAR292 and A/Shanghai/1/2013 NAK292 viruses in MDCK-SIAT1 cells that overexpress the alpha-2,6-linked terminal sialic acid. 2013 mBio Result IV R292K 56 61 NA;NA;NA 27;198;227 29;200;229 23860768 Resistance to neuraminidase inhibitors conferred by an R292K mutation in a human influenza virus H7N9 isolate can be masked by a mixed R/K viral population. To evaluate the effect of the R292K mutation on the NA enzyme activity, we performed the NA kinetics assay using the 2'-(4-methylumbelliferryl)-alpha-d-N-acetylneuraminic acid (MUNANA) substrate (Table 5). 2013 mBio Result IV R292K 30 35 NA;NA 52;89 54;91 23860768 Resistance to neuraminidase inhibitors conferred by an R292K mutation in a human influenza virus H7N9 isolate can be masked by a mixed R/K viral population. To monitor if any compensatory mutation might have arisen together with the NA R292K mutation, full-length hemagglutinin (HA) and NA sequences of these plaque-purified viruses were verified by Sanger sequencing. 2013 mBio Result IV R292K 79 84 HA;HA;NA;NA 122;107;76;130 124;120;78;132 23860768 Resistance to neuraminidase inhibitors conferred by an R292K mutation in a human influenza virus H7N9 isolate can be masked by a mixed R/K viral population. viruses (Table 4), it was observed that the R292K mutation confers resistance to zanamivir that is increased by 62-fold, to peramivir that is increased by 1,445-fold, and to oseltamivir carboxylate that is increased by 33,862-fold. 2013 mBio Result IV R292K 44 49 23894575 Analysis of adaptation mutants in the hemagglutinin of the influenza A(H1N1)pdm09 virus. Although mutation S143G has been reported since 2009, mutant S185T was not reported until 2010. 2013 PloS one Result IV S143G;S185T 18;61 23;66 23894575 Analysis of adaptation mutants in the hemagglutinin of the influenza A(H1N1)pdm09 virus. As can be observed in Figures 6A and 6B, wild-type HA has a marked charge distribution, with the lower part of HA predominantly negative and the top, positive; however, in E374K, the protein loses negative electrostatic potential and gains positive potential inside the fusion peptide pocket. 2013 PloS one Result IV E374K 172 177 HA;HA 51;111 53;113 23894575 Analysis of adaptation mutants in the hemagglutinin of the influenza A(H1N1)pdm09 virus. In D222E, the extra carbon in the side chain of E222 caused the glutamate's carboxyl group to move away from the RBS, rendering water-mediated polar contacts with a terminal mannose from glycosylations originating from N87 and van der Waals contacts with galactose from the receptor (Figure 4B). 2013 PloS one Result IV D222E 3 8 23894575 Analysis of adaptation mutants in the hemagglutinin of the influenza A(H1N1)pdm09 virus. In E374K, the longer hydrocarbon side chain of lysine eliminated interactions with Y433 (Figure S11), while polar contacts with N366 shifted to the amide's oxygen (Figure S10), exposing the amino group to the solvent (Figures 5A and 5B). 2013 PloS one Result IV E374K 3 8 23894575 Analysis of adaptation mutants in the hemagglutinin of the influenza A(H1N1)pdm09 virus. In this variant, mutation D222E is located in the RBS within antigenic site Ca2, whereas P297S is localized in the upper stem portion of HA (Figure 1). 2013 PloS one Result IV D222E;P297S 26;89 31;94 HA 137 139 23894575 Analysis of adaptation mutants in the hemagglutinin of the influenza A(H1N1)pdm09 virus. Interestingly, removal of the bulky side chain in S143G rendered important rearrangements in the loop. 2013 PloS one Result IV S143G 50 55 23894575 Analysis of adaptation mutants in the hemagglutinin of the influenza A(H1N1)pdm09 virus. Regarding mutant S185T, the substitution did not create or eliminate interactions because in this position, the side chain is completely exposed with the solvent and rotates freely (Figure 2B). 2013 PloS one Result IV S185T 17 22 23894575 Analysis of adaptation mutants in the hemagglutinin of the influenza A(H1N1)pdm09 virus. Regarding mutation P297S, we could not deduce a change in interactions during the molecular dynamics simulations. 2013 PloS one Result IV P297S 19 24 23894575 Analysis of adaptation mutants in the hemagglutinin of the influenza A(H1N1)pdm09 virus. Stability analysis performed with I-Mutant and CUPSAT suggested that the E374K mutation in HA would have a destabilizing structural effect (I-Mutant DeltaDeltaG = -0.65 kcal/mol; CUPSAT DeltaDeltaG = -1.58 kcal/mol). 2013 PloS one Result IV E374K 73 78 HA 91 93 23894575 Analysis of adaptation mutants in the hemagglutinin of the influenza A(H1N1)pdm09 virus. The A134T mutant established hydrogen bonds with sialic acid through the hydroxyl group of threonine (Figure 3A). 2013 PloS one Result IV A134T 4 9 23894575 Analysis of adaptation mutants in the hemagglutinin of the influenza A(H1N1)pdm09 virus. The mutations are localized in antigenic sites surrounding the RBS (Figure 1); S143G is localized at antigenic site Ca2, and S185T is within antigenic site Sb. 2013 PloS one Result IV S143G;S185T 79;125 84;130 23894575 Analysis of adaptation mutants in the hemagglutinin of the influenza A(H1N1)pdm09 virus. Thus mutation S143G changed the conformation of antigenic site Ca2 by hindering the histidine residue into loop 140. 2013 PloS one Result IV S143G 14 19 23894575 Analysis of adaptation mutants in the hemagglutinin of the influenza A(H1N1)pdm09 virus. Variant 1 (S143G, S185T) 2013 PloS one Result IV S143G;S185T 11;18 16;23 23894575 Analysis of adaptation mutants in the hemagglutinin of the influenza A(H1N1)pdm09 virus. Variant 1 (S143G, S185T). 2013 PloS one Result IV S143G;S185T 11;18 16;23 23894575 Analysis of adaptation mutants in the hemagglutinin of the influenza A(H1N1)pdm09 virus. Variant 2 (A134T) 2013 PloS one Result IV A134T 11 16 23894575 Analysis of adaptation mutants in the hemagglutinin of the influenza A(H1N1)pdm09 virus. Variant 2 (A134T). 2013 PloS one Result IV A134T 11 16 23894575 Analysis of adaptation mutants in the hemagglutinin of the influenza A(H1N1)pdm09 virus. Variant 2 possesses an A134T mutation and was present early in the pandemic, reaching a peak in 2010 and decreasing over time. 2013 PloS one Result IV A134T 23 28 23894575 Analysis of adaptation mutants in the hemagglutinin of the influenza A(H1N1)pdm09 virus. Variant 3 (D222E, P297S) 2013 PloS one Result IV D222E;P297S 11;18 16;23 23894575 Analysis of adaptation mutants in the hemagglutinin of the influenza A(H1N1)pdm09 virus. Variant 3 (D222E, P297S). 2013 PloS one Result IV D222E;P297S 11;18 16;23 23894575 Analysis of adaptation mutants in the hemagglutinin of the influenza A(H1N1)pdm09 virus. Variant 3 is a double mutant (D222E and P297S) that appeared in late 2009, reaching its maximum in 2010 but declined afterward. 2013 PloS one Result IV D222E;P297S 30;40 35;45 23894575 Analysis of adaptation mutants in the hemagglutinin of the influenza A(H1N1)pdm09 virus. Variant 4 (E374K) 2013 PloS one Result IV E374K 11 16 23894575 Analysis of adaptation mutants in the hemagglutinin of the influenza A(H1N1)pdm09 virus. Variant 4 (E374K). 2013 PloS one Result IV E374K 11 16 23894575 Analysis of adaptation mutants in the hemagglutinin of the influenza A(H1N1)pdm09 virus. Variant 4, which has an E374K mutation, was present from the beginning of the pandemic and has dominated in the current influenza viruses; this mutation is localized near the fusion peptide in the stem of HA. 2013 PloS one Result IV E374K 24 29 HA 205 207 23894575 Analysis of adaptation mutants in the hemagglutinin of the influenza A(H1N1)pdm09 virus. We focused on four variants that emerged since the beginning of the 2009 pandemic (Table 1 and Table S1): Variant 1 has two mutations, S143G and S185T. 2013 PloS one Result IV S143G;S185T 135;145 140;150 23902660 Frequency of D222G haemagglutinin mutant of pandemic (H1N1) pdm09 influenza virus in Tunisia between 2009 and 2011. E374K substitution was found in two severe cases (4%). 2013 Diagnostic pathology Result IV E374K 0 5 23902660 Frequency of D222G haemagglutinin mutant of pandemic (H1N1) pdm09 influenza virus in Tunisia between 2009 and 2011. Here we report the occurrence of an amino acid substitution, aspartic acid to glycine in position 222 (D222G) in the HA subunit of the viral haemagglutinin, in clinical specimens from 3 out of 42 cases analyzed in Tunisia with severe outcome (7%). 2013 Diagnostic pathology Result IV D222G;D222G 103;61 108;101 HA;HA 117;141 119;155 23902660 Frequency of D222G haemagglutinin mutant of pandemic (H1N1) pdm09 influenza virus in Tunisia between 2009 and 2011. Moreover, D222E was found in one out of 50 viruses studied. 2013 Diagnostic pathology Result IV D222E 10 15 23902660 Frequency of D222G haemagglutinin mutant of pandemic (H1N1) pdm09 influenza virus in Tunisia between 2009 and 2011. P83S and S203T were detected in 94% of Tunisian viruses studied. 2013 Diagnostic pathology Result IV P83S;S203T 0;9 4;14 23951116 Resistance mutation R292K is induced in influenza A(H6N2) virus by exposure of infected mallards to low levels of oseltamivir. All 9 isolates additionally had the D113N or D141N mutations that also were retained through the egg propagation (Figure 3). 2013 PloS one Result IV D113N;D141N 36;45 41;50 23951116 Resistance mutation R292K is induced in influenza A(H6N2) virus by exposure of infected mallards to low levels of oseltamivir. At 12 microg/L of OC, the resistance mutation R292K (the arginine codon AGA changed to the lysine codon AAA) in the NA occurred in the first generation of mallards 4 days pi as a mixed genotype, and dominated from day 5 pi and throughout the experiment. 2013 PloS one Result IV R292K 46 51 116 118 23951116 Resistance mutation R292K is induced in influenza A(H6N2) virus by exposure of infected mallards to low levels of oseltamivir. D113N and D141N were frequent variants, D113N in approximately 1-10% and D141N in approximately 20-40% (varying proportions with different HA subtype combination) although the mutations did not occur simultaneously. 2013 PloS one Result IV D113N;D141N;D113N;D141N 0;10;40;73 5;15;45;78 HA 139 141 23951116 Resistance mutation R292K is induced in influenza A(H6N2) virus by exposure of infected mallards to low levels of oseltamivir. E216K was present in the latest samples from the experiment. 2013 PloS one Result IV E216K 0 5 23951116 Resistance mutation R292K is induced in influenza A(H6N2) virus by exposure of infected mallards to low levels of oseltamivir. In addition to the R292K mutation, the D113N and D141N mutations evolved (the aspartic acid codon GAC changed to the asparagine codon AAC) in the 12 microg/L experiment from day 7 and 8 pi respectively. 2013 PloS one Result IV R292K;D113N;D141N 19;39;49 24;44;54 23951116 Resistance mutation R292K is induced in influenza A(H6N2) virus by exposure of infected mallards to low levels of oseltamivir. Inhibition of NA activity with OC and zanamivir (ZA) was compared between isolates with the R292K-mutation (10 evaluable isolates) and wild-type isolates (5 from 120 ng/L, 4 from 1.2 microg/L and 5 from 12 microg/L OC-levels). 2013 PloS one Result IV R292K 92 97 14 16 23951116 Resistance mutation R292K is induced in influenza A(H6N2) virus by exposure of infected mallards to low levels of oseltamivir. Mean IC50 for ZA was 5.3 nM (95% CI of median 4.5, 6.8) of R292K isolates and 0.68 (95% CI of median 0.44, 0.92) nM of wild type isolates, as well significantly different at a 95% level (P = 0.000082), corresponding to a 7.6 fold reduced sensitivity (normal according to WHO criteria). 2013 PloS one Result IV R292K 59 64 23951116 Resistance mutation R292K is induced in influenza A(H6N2) virus by exposure of infected mallards to low levels of oseltamivir. NA sequencing of the fecal samples showed either D113N or D141N, or mixed sequencing results of both mutations, but both mutations did not dominate at the same time. 2013 PloS one Result IV D113N;D141N 49;58 54;63 0 2 23951116 Resistance mutation R292K is induced in influenza A(H6N2) virus by exposure of infected mallards to low levels of oseltamivir. No sequences contained R292K. 2013 PloS one Result IV R292K 23 28 23951116 Resistance mutation R292K is induced in influenza A(H6N2) virus by exposure of infected mallards to low levels of oseltamivir. Of those, 13 of 23 isolates (56%) originally carrying R292K were successfully propagated and 13 of 15 isolates (87%) with wild-type R292. 2013 PloS one Result IV R292K 54 59 23951116 Resistance mutation R292K is induced in influenza A(H6N2) virus by exposure of infected mallards to low levels of oseltamivir. One of six examined birds was infected with the R292K-mutated virus and the rest with wild-type virus. 2013 PloS one Result IV R292K 48 53 23951116 Resistance mutation R292K is induced in influenza A(H6N2) virus by exposure of infected mallards to low levels of oseltamivir. One R292K-isolate from day 9 pi had an IC50 of 770 nM for OC and 0.32 nM for ZA. 2013 PloS one Result IV R292K 4 9 23951116 Resistance mutation R292K is induced in influenza A(H6N2) virus by exposure of infected mallards to low levels of oseltamivir. Only two isolates had other amino acids at position 292; one had R292W (a H9N2 virus isolated from a sparrow in China 2006, ADC97091) and one had a 14 amino acid sequence exchange including position 292 (a H9N2 virus isolated from a duck in China 2001, ABG27052). 2013 PloS one Result IV R292W 65 70 23951116 Resistance mutation R292K is induced in influenza A(H6N2) virus by exposure of infected mallards to low levels of oseltamivir. Sequencing of HA of 6 isolates from the 12 microg/L experiment revealed the E216K mutation (H3-numbering, the GAA codon for glutamic acid changed to AAA for lysine) in the same isolates that also harbored R292K in combination with D113N or D141N in the NA (but not in wild type isolates or isolates with only R292K). 2013 PloS one Result IV E216K;R292K;D113N;D141N;R292K 76;205;231;240;309 81;210;236;245;314 HA;NA 14;253 16;255 23951116 Resistance mutation R292K is induced in influenza A(H6N2) virus by exposure of infected mallards to low levels of oseltamivir. Sequencing of NA from water samples revealed the R292K mutation from day 5 pi and onwards. 2013 PloS one Result IV R292K 49 54 14 16 23951116 Resistance mutation R292K is induced in influenza A(H6N2) virus by exposure of infected mallards to low levels of oseltamivir. Taken together, these results suggest that either of the mutations D113N or D141N was present in a single virus, but not both mutations at the same time. 2013 PloS one Result IV D113N;D141N 67;76 72;81 23951116 Resistance mutation R292K is induced in influenza A(H6N2) virus by exposure of infected mallards to low levels of oseltamivir. The 9 following R292K isolates from generation 2, 3 and 4 retained the mutation through the propagation process. 2013 PloS one Result IV R292K 16 21 23951116 Resistance mutation R292K is induced in influenza A(H6N2) virus by exposure of infected mallards to low levels of oseltamivir. The D113N mutation was found in water samples from day 8 pi and D141N from day 12 pi, whereafter both mutations were present as mixed genotypes. 2013 PloS one Result IV D113N;D141N 4;64 9;69 23951116 Resistance mutation R292K is induced in influenza A(H6N2) virus by exposure of infected mallards to low levels of oseltamivir. The E216K mutation in HA also persisted through the egg propagation process. 2013 PloS one Result IV E216K 4 9 HA 22 24 23951116 Resistance mutation R292K is induced in influenza A(H6N2) virus by exposure of infected mallards to low levels of oseltamivir. The mean 50% inhibitory concentration (IC50) for OC was 2,900 nM (95% CI of median 2,600, 3,000) of the R292K isolates, significantly different at a 95% level to 0.21 nM (95% CI of median 0.15, 0.21) of the wild type isolates (P = 0.000082), corresponding to a 13,000 fold reduced sensitivity (highly reduced according to WHO criteria). 2013 PloS one Result IV R292K 104 109 23951116 Resistance mutation R292K is induced in influenza A(H6N2) virus by exposure of infected mallards to low levels of oseltamivir. The R292K-mutant infected bird (fecal-orally infected) and one wild-type infected bird (artificially inoculated, from the 1.2 microg/L experiment) had one section each of the intestine where weak IHC positivity was demonstrated in distal epithelial cells and monocytes. 2013 PloS one Result IV R292K 4 9 23951116 Resistance mutation R292K is induced in influenza A(H6N2) virus by exposure of infected mallards to low levels of oseltamivir. The two later generations of the 12 microg/L experiment, in which the virus was R292K mutated, had similar shedding patterns as those seen at OC levels of 120 ng/L and 1.2 microg/L (Figure 2). 2013 PloS one Result IV R292K 80 85 23951116 Resistance mutation R292K is induced in influenza A(H6N2) virus by exposure of infected mallards to low levels of oseltamivir. When re-sequencing the isolates after the propagation process we found wild-type R292 in 3 of the 13 R292K isolates, all from the first generation of birds of the 12 microg/L experiment, and in one isolate from the second generation birds we found mixed genotype after the propagation. 2013 PloS one Result IV R292K 101 106 23951116 Resistance mutation R292K is induced in influenza A(H6N2) virus by exposure of infected mallards to low levels of oseltamivir. While assaying the NA activity by the relative fluorescence measurement prior to dilution of samples for the inhibition assay, we noted an approximately 70% reduction of NA activity of the R292K isolates compared to wild type with mean RFU 8,000 of the mutant (95% CI of median 3,900, 9,000), significantly different at a 95% level to 27,000 of wild type virus (95% CI of median 24,000, 32,000) (P<0.000001). 2013 PloS one Result IV R292K 189 194 NA;NA 19;170 21;172 24074585 Mutation from arginine to lysine at the position 189 of hemagglutinin contributes to the antigenic drift in H3N2 swine influenza viruses. Antigenic cartography demonstrated that the R189K mutation could move A/swine/09SW64/2009(H3N2) from antigenic cluster H3N2SIV-alpha forward to antigenic cluster H3N2SIV-beta whereas the K189R mutation could drive A/swine/11SW347/2011(H3N2) from antigenic cluster H3N2SIV-beta toward antigenic cluster H3N2SIV-alpha (Figure 1). 2013 Virology Result IV R189K;K189R 44;187 49;192 24074585 Mutation from arginine to lysine at the position 189 of hemagglutinin contributes to the antigenic drift in H3N2 swine influenza viruses. Because these glycans might not represent the entire glycan profile in human respiratory system, it would be interesting to characterize the role of R189K in transmission of H3N2v from swine to human. 2013 Virology Result IV R189K 149 154 24074585 Mutation from arginine to lysine at the position 189 of hemagglutinin contributes to the antigenic drift in H3N2 swine influenza viruses. Compared with those isolates in antigenic cluster H3N2SIV_alpha, the H3N2 swine influenza isolates in H3N2SIV_beta have two major differences: (1) the introduction of matrix gene from 2009 H1N1 influenza A virus; (2) a consistent mutation R189K, which is located in the 190-loop of receptor binding site in H3 subtype of influenza A virus. 2013 Virology Result IV R189K 239 244 M 167 173 24074585 Mutation from arginine to lysine at the position 189 of hemagglutinin contributes to the antigenic drift in H3N2 swine influenza viruses. Instead, the R189K seemed not to affect much receptor binding profiles based on the results on six glycans (Neu5Aca2-3Galbeta1-4GlcNAcbeta1-; Neu5Aca2-6Galbeta1-4GlcNAcbeta1-; Neu5Aca2-3Galbeta1-4GlcNAcp1-3Galbeta1-4GlcNAcbeta1-; Neu5Aca2-6Galbeta1-4GlcNAcbeta1-3Galbeta1-4GlcNAcbeta1-; and Neu5Aca2-3Galbeta1-4GlcNAcbeta1-3Galbeta1-4GlcNAcbeta1-3Galbeta1-4GlcNAcbeta1-). 2013 Virology Result IV R189K 13 18 24074585 Mutation from arginine to lysine at the position 189 of hemagglutinin contributes to the antigenic drift in H3N2 swine influenza viruses. It was recently reported that K189N/D/Q/E mutations were involved in the antigenic drift of horse H3N8 isolates collected between 1968 to 2007. 2013 Virology Result IV K189D;K189Q;K189E;K189N 30;30;30;30 41;41;41;41 24074585 Mutation from arginine to lysine at the position 189 of hemagglutinin contributes to the antigenic drift in H3N2 swine influenza viruses. These HI data demonstrate that the R189K mutation in the hemagglutinin of H3N2 IAV contributed to the antigenic drift. 2013 Virology Result IV R189K 35 40 HA 57 70 24074585 Mutation from arginine to lysine at the position 189 of hemagglutinin contributes to the antigenic drift in H3N2 swine influenza viruses. This data further supported our conclusion that the single R189K mutation in the HA of swine H3N2 IAV contributed to the antigenic drift, separating these viruses into H3N2SIV-alpha to H3N2SIV-beta. 2013 Virology Result IV R189K 59 64 HA 81 83 24074585 Mutation from arginine to lysine at the position 189 of hemagglutinin contributes to the antigenic drift in H3N2 swine influenza viruses. This indicated that some other mutations (not in reported antibody binding sites of H3N2 IAVs) in HA, NA, or MP protein might affect influenza antigenicity indirectly, although R189K is the prodominant mutation leading to antigenic drift in H3N2 SIVs. 2013 Virology Result IV R189K 177 182 HA;NA 98;102 100;104 24074585 Mutation from arginine to lysine at the position 189 of hemagglutinin contributes to the antigenic drift in H3N2 swine influenza viruses. To evaluate contribution of R189K mutation to antigenic drift of H3N2 IAVs from Ohio county fairs, four reassortant viruses were generated by reverse genetics and designated as 09SW64_189R (wt), 09SW64_189K(mt), 11SW347_189K(wt) and 11SW347_189R(mt) (Table 1). 2013 Virology Result IV R189K 28 33 24074585 Mutation from arginine to lysine at the position 189 of hemagglutinin contributes to the antigenic drift in H3N2 swine influenza viruses. To evaluate the contribution of the R189K mutation in that cross-reaction, HI assay was performed on the four reassortant viruses using antisera produced against several historic seasonal human influenza virus strains with or without 189K. 2013 Virology Result IV R189K 36 41 24139991 Asp44 stabilizes the Trp41 gate of the M2 proton channel of influenza A virus. All of the Asp44 mutants exhibit strong deviations from the X-ray structure of G34A-M2TM, similar to those observed in simulations of the +3 and +4 charge states of WT. 2013 Structure (London, England Result IV G34A 79 83 24139991 Asp44 stabilizes the Trp41 gate of the M2 proton channel of influenza A virus. At the same pH, the diagnostic downfield-shifted indole NH peak from Trp41 is entirely missing in the D44N spectrum, indicating that the Cclosed state has been destabilized relative to the Copen state. 2013 Structure (London, England Result IV D44N 102 106 24139991 Asp44 stabilizes the Trp41 gate of the M2 proton channel of influenza A virus. Because the structure was resolved for the G34A mutant, we also performed a simulation of WT-M2TM under the same conditions as a control. 2013 Structure (London, England Result IV G34A 43 47 24139991 Asp44 stabilizes the Trp41 gate of the M2 proton channel of influenza A virus. However, the magnitude of this conformational change in D44A-M2 and D44C-M2 is about 50% of the one induced by low pH and that in D44N-M2TM is about 70% of that. 2013 Structure (London, England Result IV D44A;D44C;D44N 56;68;130 60;72;134 M2;M2 61;73 63;75 24139991 Asp44 stabilizes the Trp41 gate of the M2 proton channel of influenza A virus. If the changes in the spectrum seen for D44N are a result of changes in the relative energetics of the Cclosed versus the Copen states, tipping the energetic balance toward the Cclosed state should be possible by adding drug that stabilizes the Cclosed state. 2013 Structure (London, England Result IV D44N 40 44 24139991 Asp44 stabilizes the Trp41 gate of the M2 proton channel of influenza A virus. In contrast, the structures of the three mutants all follow a divergent trajectory: the rmsd of all atoms increases to about 3 A for D44A and D44C and to 4 A for D44N (Figure 6). 2013 Structure (London, England Result IV D44A;D44C;D44N 133;142;162 137;146;166 24139991 Asp44 stabilizes the Trp41 gate of the M2 proton channel of influenza A virus. In fact, the outward current was nearly as great for the Asp44 variants as for the W41F mutant. 2013 Structure (London, England Result IV W41F 83 87 24139991 Asp44 stabilizes the Trp41 gate of the M2 proton channel of influenza A virus. In Figure 6, we compare the rmsds of the four structures (WT, D44A, D44C, and D44N) from the X-ray structure, as a function of the simulated time. 2013 Structure (London, England Result IV D44A;D44C;D44N 62;68;78 66;72;82 24139991 Asp44 stabilizes the Trp41 gate of the M2 proton channel of influenza A virus. In the D44A- and D44C-M2TM simulations, p settles at around 0.45, and p settles at around 0.7 in the D44N-M2TM simulation. 2013 Structure (London, England Result IV D44A;D44C;D44N 7;17;101 11;21;105 24139991 Asp44 stabilizes the Trp41 gate of the M2 proton channel of influenza A virus. Indeed, the Asp44 mutants behaved quite similar to the W41F mutant in which the Trp44 gate has been incapacitated by mutation to Phe. 2013 Structure (London, England Result IV W41F 55 59 24139991 Asp44 stabilizes the Trp41 gate of the M2 proton channel of influenza A virus. NMR Shows the Cclosed Conformation Is Destabilized by the D44N Mutation. 2013 Structure (London, England Result IV D44N 58 62 24139991 Asp44 stabilizes the Trp41 gate of the M2 proton channel of influenza A virus. The distance between the Calpha atoms of the amino acid 44 from two neighboring monomers (approximately 12 A in the X-ray structure) increases to about 16 +- 3 A in D44A, 18 +- 4 A in D44C, and 20 +- 3 A in D44N. 2013 Structure (London, England Result IV D44A;D44C;D44N 165;184;207 169;188;211 24139991 Asp44 stabilizes the Trp41 gate of the M2 proton channel of influenza A virus. The first consequence of the Asp44 mutation is to induce proton current reverse flow at the condition of low pHin as in W41F mutant channel. 2013 Structure (London, England Result IV W41F 120 124 24139991 Asp44 stabilizes the Trp41 gate of the M2 proton channel of influenza A virus. This saturation is also seen in naturally occurring strains bearing the D44N mutation. 2013 Structure (London, England Result IV D44N 72 76 24139991 Asp44 stabilizes the Trp41 gate of the M2 proton channel of influenza A virus. To determine the effect of the D44N mutation on the stability of the Cclosed conformation, we examined the NMR spectrum of its TM domain at pH 6.0 in C14-betaine micelles, using a fragment, M219-49, that includes the channel-forming domain and a portion of the cytoplasmic helix. 2013 Structure (London, England Result IV D44N 31 35 24139991 Asp44 stabilizes the Trp41 gate of the M2 proton channel of influenza A virus. Upon returning to alkaline solution (pHout = 8.5), the oocytes expressing the M2 W41F, D44N, D44C, and D44A mutant channels conducted outward currents (arrow), but those expressing the Udorn WT M2 channel did not (Figure 3). 2013 Structure (London, England Result IV W41F;D44N;D44C;D44A 81;87;93;103 85;91;97;107 M2;M2 78;194 80;196 24139991 Asp44 stabilizes the Trp41 gate of the M2 proton channel of influenza A virus. We also examined the mutant R45C, because this residue forms a salt bridge with Asp44 (Figure 1). 2013 Structure (London, England Result IV R45C 28 32 24139991 Asp44 stabilizes the Trp41 gate of the M2 proton channel of influenza A virus. We compared these results with the previously published simulations of G34A-M2TM at charge states +1, +3, and +4. 2013 Structure (London, England Result IV G34A 71 75 24139991 Asp44 stabilizes the Trp41 gate of the M2 proton channel of influenza A virus. We performed three simulations of the transmembrane domain of M2 (M2TM) embedded in a 80 x 80 A2 hydrated palmitoyloleoyl-phosphatidylcholine (POPC) bilayer, applying the mutations D44A, D44C, and D44N. 2013 Structure (London, England Result IV D44A;D44C;D44N 181;187;197 185;191;201 M2 62 64 24147093 Emerging antigenic variants at the antigenic site Sb in pandemic A(H1N1)2009 influenza virus in Japan detected by a human monoclonal antibody. The entire HA gene was sequenced in 9/15 samples, and all harbored a D190E substitution. 2013 PloS one Result IV D190E 69 74 HA 11 13 24147093 Emerging antigenic variants at the antigenic site Sb in pandemic A(H1N1)2009 influenza virus in Japan detected by a human monoclonal antibody. When we sequenced the entire HA gene from each of these samples, we found that all harbored an A189T substitution (based on H3 numbering). 2013 PloS one Result IV A189T 95 100 HA 29 31 24162312 Adaptation of novel H7N9 influenza A virus to human receptors. Additional introduction of the G186V mutation did not drastically affect the shift in binding from alpha2-3 to alpha2-6/alpha2-8 sialosides although the extent to which several individual glycans were bound was affected by the double mutation (e.g. 2013 Scientific reports Result IV G186V 31 36 24162312 Adaptation of novel H7N9 influenza A virus to human receptors. Binding of this double mutant protein was significantly higher than that of the Q226L single mutant protein (P < 0.001). 2013 Scientific reports Result IV Q226L 80 85 24162312 Adaptation of novel H7N9 influenza A virus to human receptors. In agreement with the important role for the residues at position 186 and 226 in the teal protein for fetuin binding, reciprocal substitutions at positions 186 and 226 in the background of the human H7 protein resulted in significantly decreased (V186G) and increased (L226Q) fetuin binding. 2013 Scientific reports Result IV V186G;L226Q 247;269 252;274 24162312 Adaptation of novel H7N9 influenza A virus to human receptors. Introduction of only the G186V mutation in the teal H7 protein clearly increased binding of HA to a subset of alpha2-3 sialosides, in agreement with the fetuin assay. 2013 Scientific reports Result IV G186V 25 30 HA 92 94 24162312 Adaptation of novel H7N9 influenza A virus to human receptors. Introduction of the L226Q substitution in the human protein resulted in negligible binding to alpha2-6/alpha2-8 sialosides but resulted in increased binding to alpha2-3 SIA-containing glycans. 2013 Scientific reports Result IV L226Q 20 25 24162312 Adaptation of novel H7N9 influenza A virus to human receptors. Introduction of the Q226L mutation in the teal H7 protein resulted in decreased binding to alpha2-3 sialosides and increased binding to alpha2-6/alpha2-8 sialosides, resembling, apart from some quantitative differences, the patterns observed for the human H7 protein. 2013 Scientific reports Result IV Q226L 20 25 24162312 Adaptation of novel H7N9 influenza A virus to human receptors. Introduction of two additional substitutions in the H7 protein already carrying both G186V and Q226L did not significantly affect fetuin binding compared to the G186V and Q226L double mutant. 2013 Scientific reports Result IV G186V;Q226L;G186V;Q226L 85;95;161;171 90;100;166;176 24162312 Adaptation of novel H7N9 influenza A virus to human receptors. One mutation caused a modest but significant increase (G186V) in fetuin binding, while another mutation (Q226L) severely decreased the binding of the H7 protein. 2013 Scientific reports Result IV G186V;Q226L 55;105 60;110 24162312 Adaptation of novel H7N9 influenza A virus to human receptors. Thus, single substitutions at position 186 and 226 in the background of the human H7 protein are sufficient to obtain fetuin-binding properties that are similar to single mutant teal proteins (compare H7/Human L226Q with H7/Teal G186V [P > 0.7] and H7/Human V186G with H7/Teal Q226L [P > 0.3]). 2013 Scientific reports Result IV L226Q;G186V;V186G;Q226L 210;229;258;277 215;234;263;282 24165891 Characterization of two distinct neuraminidases from avian-origin human-infecting H7N9 influenza viruses. In the case of zanamivir, laninamivir and peramivir, the R294K mutation conferred less resistance relative to oseltamivir carboxylate (Table 1). 2013 Cell research Result IV R294K 57 62 24165891 Characterization of two distinct neuraminidases from avian-origin human-infecting H7N9 influenza viruses. The R294K substitution impairs H7N9 virus fitness and N9 enzymatic activity. 2013 Cell research Result IV R294K 4 9 N9 54 56 24165891 Characterization of two distinct neuraminidases from avian-origin human-infecting H7N9 influenza viruses. The R294K substitution in N9 from epidemic H7N9 confers multidrug resistance. 2013 Cell research Result IV R294K 4 9 N9 26 28 24165891 Characterization of two distinct neuraminidases from avian-origin human-infecting H7N9 influenza viruses. To gain insight into the structural basis of the N9-R294K drug-resistant substitution, high-resolution crystal structures of Anhui N9 and Shanghai N9 were solved. 2013 Cell research Result IV R294K 52 57 N9;N9;N9 49;131;147 51;133;149 24165891 Characterization of two distinct neuraminidases from avian-origin human-infecting H7N9 influenza viruses. To investigate the effect of the R294K substitution on H7N9 virus replication, we used reverse genetics to generate various viruses containing NA and HA from either A/Anhui/1/2013 or A/Shanghai/1/2013. 2013 Cell research Result IV R294K 33 38 HA;NA 150;143 152;145 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. Additionally, Pro319 of D325A+R343V interacts with Ala138 of HA throughout the entire trajectory. 2013 Biochemistry Result IV D325A;R343V 24;30 29;35 HA 61 63 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. As shown in Figure 3A, D325A+R343V strongly inhibited the Aichi68 strain in MDCK cells. 2013 Biochemistry Result IV R343V;D325A 29;23 34;28 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. As shown in Figure 5, both WT and D325A+R343V resulted in similar SA ASA values of approximately 150 A2 at the end of either simulation, carrying out in each case an average over three independent trajectories. 2013 Biochemistry Result IV D325A;R343V 34;40 39;45 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. As shown in Figure 6B, Ala325 of D325A+R343V is observed to interact with another hydrophobic residue of HA, Trp222. 2013 Biochemistry Result IV D325A;R343V 33;39 38;44 HA 105 107 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. D325A+R343V Crystal Structures. 2013 Biochemistry Result IV D325A;R343V 0;6 5;11 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. Despite the stability of the SP-D/HA complexes in the presence of Man9, SP-D is seen to diffuse away from the SA binding site within the first 40ns in the absence of the glycan as shown in Figure 7, though D325A+R343V without glycan is observed to diffuse back to its starting location. 2013 Biochemistry Result IV D325A;R343V 206;212 211;217 HA 34 36 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. Figure 6A illustrates the difference in average hydrophobic interaction between SP-D and HA for WT and D325A+R343V. 2013 Biochemistry Result IV D325A;R343V 103;109 108;114 HA 89 91 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. Given that the SA ASA for a fully exposed SA binding site is approximately 450 A2, it is apparent that both WT and D325A+R343V SP-D fully block the SA binding site at the end of the simulations. 2013 Biochemistry Result IV D325A;R343V 115;121 120;126 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. In D325A+R343V, as for R343V, one sugar (Man504A) is bound in the lectin site, making coordination interactions to the calcium ion through the 3 and 4 hydroxyl groups of the mannose sugar. 2013 Biochemistry Result IV D325A;R343V;R343V 3;9;23 8;14;28 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. In simulations WTS and DMS (Table 1), both WT and D325A+R343V are found to be stably bound to HA. 2013 Biochemistry Result IV D325A;R343V 50;56 55;61 HA 94 96 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. In the D325A+R343V complex with Man9, the ligand is bound in a similar conformation and location as in the alpha1,2-dimannose complex with R343V. 2013 Biochemistry Result IV D325A;R343V;R343V 7;13;139 12;18;144 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. In the D325A+R343V complex, only three mannose sugars are visible in the electron density map, all linked with alpha1-2 glycosidic bonds and therefore these sugars have been assigned as Man505A, Man504A, and Man503A of Man9 based on the connectivity. 2013 Biochemistry Result IV D325A;R343V 7;13 12;18 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. In the simulations the binding of HA with D325A+R343V, but not with WT, reveals involvement of hydrophobic interactions. 2013 Biochemistry Result IV D325A;R343V 42;48 47;53 HA 34 36 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. It is evident that the Asp-to-Ala mutation of residue 325 increases the hydrophobic interaction between D325A+R343V and HA, and provides additional stabilization to the complex. 2013 Biochemistry Result IV D325A;R343V;A325D 104;110;23 109;115;57 HA 120 122 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. Overall, the Asp325 to Ala mutation shows little effect on the binding of dimannose: the sugars have r.m.s.d. 2013 Biochemistry Result IV D325A 13 26 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. Residues 300 to 304 in the short loop (residues 297-304) show lower interaction energies for D325A+R343V, while residues 324 to 329 in the long loop (residues 307-331) indicate lower energies for WT. 2013 Biochemistry Result IV D325A;R343V 93;99 98;104 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. Residues 300 to 304 of D325A+R343V are observed to inhibit the SA binding site while residues 324 to 329 of WT inhibit this site. 2013 Biochemistry Result IV D325A;R343V 23;29 28;34 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. The 50% neutralizing concentration for D325A+R343V was ~0.25 mug/ml, whereas the corresponding concentration for native SP-D, the next best inhibitor, was ~0.50 mug/ml. 2013 Biochemistry Result IV D325A;R343V 39;45 44;50 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. The average total interaction energies between SP-D with HA and the Man9 chain are -123 +- 8 kcal/mol (WT) and -142 +- 14 kcal/mol (D325A+R343V); the interaction energies between SP-D and the Man9 chain alone are -87 +- 7 kcal/mol and -97 +- 5 kcal/mol for WT and D325A+R343V, respectively. 2013 Biochemistry Result IV D325A;R343V;D325A;R343V 132;138;264;270 137;143;269;275 HA 57 59 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. The crystal structure of D325A+R343V was solved unliganded at 2.1 A resolution and in complex with Man9 at 3.2 A resolution. 2013 Biochemistry Result IV R343V;D325A 31;25 36;30 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. The D325A+R343V crystals are in a different space group than R343V or WT and have more monomers in the asymmetric unit (12 versus 3). 2013 Biochemistry Result IV R343V;D325A;R343V 10;4;61 15;9;66 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. The protein portion of the D325A+R343V complex is structurally similar to those in the WT and R343V single mutant dimannose complexes . 2013 Biochemistry Result IV D325A;R343V;R343V 27;33;94 32;38;99 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. The strong activity of D325A+R343V was confirmed in primary HTBE cells as well (Figure 3B). 2013 Biochemistry Result IV D325A;R343V 23;29 28;34 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. The third sugar (Man503A) is less well defined in the electron density maps (and absent in two of the monomers in the asymmetric unit) and occupies space made available by the Asp325 to Ala mutation. 2013 Biochemistry Result IV D325A 176 189 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. The unliganded and complexed D325A+R343V structures are similar, with a root-mean-square-deviation (r.m.s.d.) of 0.2-0.6 A. 2013 Biochemistry Result IV D325A;R343V 29;35 34;40 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. This hydrophobic interaction may provide a basis for the enhanced HA binding by the D325A+R343V mutant compared with the HA binding by the R343V mutant. 2013 Biochemistry Result IV D325A;R343V;R343V 84;90;139 89;95;144 HA;HA 66;121 68;123 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. We note that D325A+R343V also had stronger neutralizing activity than either R343V or native SP-D or SP-A. 2013 Biochemistry Result IV D325A;R343V;R343V 13;19;77 18;24;82 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. We previously reported that D325A+R343V had equivalent neutralizing activity as native SP-D for a seasonal H3N2 strain . 2013 Biochemistry Result IV R343V;D325A 34;28 39;33 24224816 Swine influenza in Norway: a distinct lineage of influenza A(H1N1)pdm09 virus. Amino acid position 164 is within a known antigenic site,16 but antigenic characterization of one of the isolates showed that the virus was not distinguishable from viruses lacking the S164F substitution (data not shown). 2013 Influenza and other respiratory viruses Result IV S164F 185 190 24224816 Swine influenza in Norway: a distinct lineage of influenza A(H1N1)pdm09 virus. The distinct group is characterized by amino acid substitutions N31D, S84I, S164F, and N473D in the viral HA0 protein, with the substitutions at positions 31, 164, and 473 (position 146 in the HA2 subunit) appearing to be unique to this group (Table 1). 2013 Influenza and other respiratory viruses Result IV N31D;S84I;S164F;N473D 64;70;76;87 68;74;81;92 HA 193 195 24312396 Conformational polymorphism of m7GTP in crystal structure of the PB2 middle domain from human influenza A virus. This crystal contains large solvent content (70%), and two mutations P453H and I471T located on the solvent accessible surface in the crystal packing. 2013 PloS one Result IV P453H;I471T 69;79 74;84 24312396 Conformational polymorphism of m7GTP in crystal structure of the PB2 middle domain from human influenza A virus. Two mutations (P453H and I471T) were introduced because these positions are surface of the protein and far from cap-binding site. 2013 PloS one Result IV P453H;I471T 15;25 20;30 24391498 A single amino acid in the stalk region of the H1N1pdm influenza virus HA protein affects viral fusion, stability and infectivity. As predicted, the HA1-E21K change in Cal/09 lowered the threshold pH for fusion from 5.4 to 5.0, which can be explained by the introduction of the stabilizing salt bridge between HA1-K21 and HA2-E47. 2014 PLoS pathogens Result IV E21K 22 26 HA;HA1;HA1 191;18;179 193;21;182 24391498 A single amino acid in the stalk region of the H1N1pdm influenza virus HA protein affects viral fusion, stability and infectivity. Conversely, Bris/10 HA1-E21K, which eliminated the interaction between residues HA1-21 and HA2-47 in the Bris/10 HA, raised the threshold pH for fusion from 5.0 to 5.4 (Figure 2). 2014 PLoS pathogens Result IV E21K 24 28 HA;HA;HA1;HA1 91;113;20;80 93;115;23;83 24391498 A single amino acid in the stalk region of the H1N1pdm influenza virus HA protein affects viral fusion, stability and infectivity. Conversely, the HA2-K47E substitution in the HA of Bris/10 raised the threshold pH for fusion from 5.0 to 5.4. 2014 PLoS pathogens Result IV K47E 20 24 HA;HA 16;45 18;47 24391498 A single amino acid in the stalk region of the H1N1pdm influenza virus HA protein affects viral fusion, stability and infectivity. It has been predicted that the HA2-E47K change introduces an inter-monomer salt bridge between the glutamic acid residue at HA1 position 21 (E21) from one monomer to the HA2-K47 in another (Figure 2). 2014 PLoS pathogens Result IV E47K 35 39 HA;HA;HA1 31;170;124 33;172;127 24391498 A single amino acid in the stalk region of the H1N1pdm influenza virus HA protein affects viral fusion, stability and infectivity. Only the substitution of the glutamic acid at HA2 position 47 to lysine (Cal/09 HA2-E47K) effectively lowered the threshold pH of the Cal/09 HA from 5.4 to 5.0. 2014 PLoS pathogens Result IV E47K 84 88 HA;HA;HA 46;80;141 48;82;143 24391498 A single amino acid in the stalk region of the H1N1pdm influenza virus HA protein affects viral fusion, stability and infectivity. Remarkably, the Cal/09 virus with the single HA2-E47K mutation exhibited a greater defect in replication. 2014 PLoS pathogens Result IV E47K 49 53 HA 45 47 24391498 A single amino acid in the stalk region of the H1N1pdm influenza virus HA protein affects viral fusion, stability and infectivity. Taken together, these data show that the HA2-E47K mutation in Cal/09 conferred greater temperature stability across temperatures from 4 C to 57.5 C. 2014 PLoS pathogens Result IV E47K 45 49 HA 41 43 24391498 A single amino acid in the stalk region of the H1N1pdm influenza virus HA protein affects viral fusion, stability and infectivity. The global emergence and increased prevalence of the HA2-E47K change in human H1N1pdm isolates have been reported. 2014 PLoS pathogens Result IV E47K 57 61 HA 53 55 24391498 A single amino acid in the stalk region of the H1N1pdm influenza virus HA protein affects viral fusion, stability and infectivity. Thus, the HA2-E47K change in recently circulating H1N1pdm viruses increased viral infectivity in ferrets. 2014 PLoS pathogens Result IV E47K 14 18 HA 10 12 24391498 A single amino acid in the stalk region of the H1N1pdm influenza virus HA protein affects viral fusion, stability and infectivity. To confirm that the HA1-E21 and HA2-K47 inter-monomer interaction was critical for the threshold pH of fusion, an HA1-E21K change was introduced into the HA of Cal/09 (Cal/09 HA1-E21K) and Bris/10 (Bris/10 HA1-E21K), and the threshold pH for fusion was determined by the HA/GFP co-expression fusion assay. 2014 PLoS pathogens Result IV E21K;E21K;E21K 118;179;210 122;183;214 HA;HA;HA;HA1;HA1;HA1;HA1 32;154;271;20;114;175;206 34;156;273;23;117;178;209 24391498 A single amino acid in the stalk region of the H1N1pdm influenza virus HA protein affects viral fusion, stability and infectivity. To evaluate whether increased stability due to HA2-E47K conferred a fitness advantage to the H1N1pdm virus, ferret studies were carried out to compare the infectivity of the two pairs of H1N1pdm viruses: wt Cal/09 HA2-E47 and the Cal/09 HA2-K47 mutant; and wt Bris/10 HA2-K47 and the Bris/10 HA2-E47 mutant. 2014 PLoS pathogens Result IV E47K 51 55 HA;HA;HA;HA;HA 47;214;237;268;292 49;216;239;270;294 24503069 The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus. and the Phe95 Tyr mutant displays eight-fold inhibition. 2014 Virology Result IV F95Y 8 17 24503069 The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus. As seen for the single mutant Phe95 Tyr, the double mutant Phe95 Tyr/Asn194 Asp improves the binding for 6'SLN-LN receptors by about 107 times compared to Asn194 Asp. 2014 Virology Result IV F95Y;N194D 30;155 39;165 24503069 The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus. By administering 104 PFU recombinant viruses intranasally, the mice have an average viral titer of 2.2x102 pfu/mL for the Phe95 Tyr/Asn194 Asp virus, in marked contrast to the titer of 2.7x105 pfu/mL for the Asn194 Asp virus, indicating an attenuation of ~1,000 folds for the former (Table 3). 2014 Virology Result IV N194D 208 218 24503069 The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus. Clearly, compared to the modeled B/Lee/40 HA Asn194 Asp - LSTa structure, the LSTa in the B/Lee/40 HA Phe95 Tyr/Asn194 Asp extends closer to the glycosylation at HA1 230 in the 240-loop. 2014 Virology Result IV N194D 45 55 HA;HA;HA1 42;99;162 44;101;165 24503069 The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus. Compared to the wild-type HA, Phe95 Tyr HA shares the same preference for human-like Neu5Acalpha(2,6)Gal receptors, but with much higher fluorescence intensities. 2014 Virology Result IV F95Y 30 39 HA;HA 26;40 28;42 24503069 The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus. Compared to the wild-type HA, the mutation Phe95 Tyr enhances the binding for 3'SLN-LN and 6'SLN-LN by 103 and 107 times, respectively (Table 1). 2014 Virology Result IV F95Y 43 52 HA 26 28 24503069 The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus. Consequently, the following studies were only conducted on recombinant B/Lee/40 viruses harboring Asn194 Asp or Phe95 Tyr/Asn194 Asp in the HA sequence. 2014 Virology Result IV N194D 98 108 HA 140 142 24503069 The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus. Consistent to their similar affinity for 3'SLN-LN, Asn194 Asp and Phe95 Tyr/Asn194 Asp have a similar Hill coefficient. 2014 Virology Result IV N194D 51 61 24503069 The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus. Consistent with the picomolar dissociation constant of the recombinant Asn194 Asp HA protein for 3'SLN-LN receptors, the Asn194 Asp virus binds to a higher titer for chicken, turkey and guinea pig erythrocytes (containing mixed alpha(2,3)- and alpha(2,6)-linked sialic acid receptors) than for sheep, horse and bovine erythrocytes (containing predominantly alpha(2,6)-linked sialic acid receptors) (Table 2). 2014 Virology Result IV N194D;N194D 71;121 81;131 HA 82 84 24503069 The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus. For the Asn194 Asp and Phe95 Tyr/Asn194 Asp mutants, the glycosylation at HA1 194 was depleted in order to mimic the situation in some field isolates or due to egg adaptation. 2014 Virology Result IV N194D 8 18 HA1 74 77 24503069 The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus. However, the introduction of Phe95 Tyr into B/Lee/40 HA containing the Asn194 Asp mutation enhances the binding affinity for 6'SLN-LN by ~2,000 times, but at the same time decreases the binding for 3'SLN-LN by 276 folds (Table 1). 2014 Virology Result IV F95Y;N194D 29;71 38;81 HA 53 55 24503069 The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus. However, the Phe95 Tyr/Asn194 Asp virus does not bind to any of the cultured cells at the same level as the Asn194 Asp virus. 2014 Virology Result IV N194D 108 118 24503069 The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus. In conclusion, the higher binding affinity of the Phe95 Tyr and Phe95 Tyr/Asn194 Asp mutants for sialic acid receptors does allow a much stronger competition against influenza A virus infection. 2014 Virology Result IV F95Y 50 59 IAV infections 166 193 24503069 The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus. In contrast, while the loss of the glycosylation at HA1 194 increases the affinity for 3'SLN-LN by 109 times (Asn194 Asp vs. 2014 Virology Result IV N194D 110 120 HA1 52 55 24503069 The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus. In order to examine the impact of the Phe95 Tyr mutation on influenza virus infection and replication, we generated recombinant influenza B viruses by reverse genetics using all genes from influenza B/Lee/40 virus (generous gifts from Dr. 2014 Virology Result IV F95Y 38 47 IV infections 60 85 24503069 The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus. In order to understand the effects of Phe95 Tyr on binding to receptors, we determined the crystal structures of B/Lee/40 HA containing Phe95 Tyr/Asn194 Asp and its complexes with human-like LSTc and avian-like LSTa receptor analogues to 2.53, 2.63 and 2.72 A, respectively (Table 4). 2014 Virology Result IV F95Y 38 47 HA 122 124 24503069 The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus. In other words, in the double mutant Phe95 Tyr/Asn194 Asp, the enhanced binding for 3'SLN-LN is mostly brought about by Asn194 Asp, while the tighter binding for 6'SLN-LN is largely the result of Phe95 Tyr. 2014 Virology Result IV N194D;F95Y 120;196 130;205 24503069 The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus. Interestingly, by incubating the virus-erythrocyte mixtures at 37 C for 2 hours to allow the cleavage of sialic acids by viral NA protein, the majority of Asn194 Asp virus is quickly eluted from erythrocytes, while in marked contrast, the binding of the Phe95 Tyr/Asn194 Asp virus hardly changes. 2014 Virology Result IV N194D 155 165 127 129 24503069 The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus. It is interesting to notice that comparing to the wild-type HA, the Hill coefficient values of Phe95 Tyr are almost doubled for both 3'SLN-LN and 6'SLN-LN (Table 1). 2014 Virology Result IV F95Y 95 104 HA 60 62 24503069 The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus. Its binding to horse erythrocytes is particularly low, in agreement with the fact that horse erythrocytes contain 100% Neu5Gc that can not be recognized by the Asn194 Asp protein on B/Yamagata/73 HA. 2014 Virology Result IV N194D 160 170 HA 196 198 24503069 The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus. Most strikingly, while the Asn194 Asp single mutant exhibits very weak inhibition against the binding of influenza A virus, the mutant Phe95 Tyr/Asn194 Asp completely blocks the infection of influenza A virus with 400 mug. 2014 Virology Result IV N194D 27 37 24503069 The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus. On the other hand, the mutation Asn194 Asp, with the loss of the glycosylation at HA1 194, results in a preferential binding to avian-like Neu5Acalpha(2,3)Gal receptors, with overall increased fluorescence intensities relative to the wild-type HA. 2014 Virology Result IV N194D 32 42 HA;HA1 244;82 246;85 24503069 The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus. Our quantitative data reported here provide a molecular basis for this advantage: the Asn194 Asp mutant has an ~109 times higher affinity for 3'SLN-LN than the wild-type HA, while they share a similar affinity for 6'SLN-LN (Table 1). 2014 Virology Result IV N194D 86 96 HA 170 172 24503069 The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus. Phe95 Tyr, and especially Phe95 Tyr/Asn194 Asp, significantly improve the binding to all three cell lines. 2014 Virology Result IV F95Y 0 9 24503069 The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus. Relative to the titer of the Asn194 Asp virus (at 2.8x106 pfu/mL), the Phe95 Tyr/Asn194 Asp virus has a comparable titer of 3.0x106 pfu/ml (Table 3). 2014 Virology Result IV N194D 29 39 24503069 The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus. Similar to the results of B/Yamagata/73 HA, the Asn194 Asp mutation in B/Lee/40 HA exhibits ~105 times stronger binding for 3'SLN-LN than for 6'SLN-LN. 2014 Virology Result IV N194D 48 58 HA;HA 40;80 42;82 24503069 The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus. Similarly, compared to Asn194 Asp, the Phe95 Tyr/Asn194 Asp mutant has significantly enhanced binding signals to all types of Neu5Ac-containing receptors. 2014 Virology Result IV N194D 23 33 24503069 The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus. Similarly, relative to Asn194 Asp, Phe95 Tyr/Asn194 Asp has also doubled its Hill coefficient for 6'SLN-LN. 2014 Virology Result IV N194D 23 33 24503069 The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus. Since binding to cell-surface receptors is a prerequisite for infecting host cells by influenza virus, we asked whether the higher binding affinity of the Phe95 Tyr and Phe95 Tyr/Asn194 Asp mutants would allow them to compete more effectively against infection caused by influenza virus. 2014 Virology Result IV F95Y 155 164 24503069 The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus. Structural basis for the effects of Phe95 Tyr on binding to receptors. 2014 Virology Result IV F95Y 36 45 24503069 The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus. The Asn194 Asp mutant has a stronger binding to all three cell lines, with the strongest being Vero cells. 2014 Virology Result IV N194D 4 14 24503069 The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus. The B/Yamagata/73 HA Phe95 Tyr mutant competitively blocks the binding and infection of influenza A virus. 2014 Virology Result IV F95Y 21 30 24503069 The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus. The calculated apparent dissociation constants of wild-type and Phe95 Tyr HA are 5.8 x 10-3 M and 3.5 x 10-6 M for the 3'SLN-LN, 2.3 x 10-4 M and 1.6 x 10-11 M for the 6'SLN-LN, respectively (Table 1). 2014 Virology Result IV F95Y 64 73 HA 74 76 24503069 The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus. The ectodomains of the recombinant wild-type influenza B/Yamagata/73 HA and its mutants (single mutants: Phe95 Tyr, Asn194 Asp and double mutant Phe95 Tyr/Asn194 Asp) were expressed in mammalian cell CV-1 using vaccinia virus system and purified to high purity. 2014 Virology Result IV F95Y;N194D 105;116 114;126 HA 69 71 24503069 The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus. The fluorescence obtained for Asn194 Asp virus to each cell line was expressed as 100%. 2014 Virology Result IV N194D 30 40 24503069 The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus. The instability of Asn194 of recombinant wild-type B/Lee/40 virus in MDCK cells precluded a study of the wild-type and Phe95 Tyr viruses. 2014 Virology Result IV F95Y 119 128 24503069 The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus. The mutation Asn194 Asp has an apparent dissociation constant of 4.5 x 10-12 M for 3'SLN-LN, in contrast to the 7.5 x 10-5 M dissociation constant for 6'SLN-LN (Table 1). 2014 Virology Result IV N194D 13 23 24503069 The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus. The mutation Phe95 Tyr improves the binding of influenza B/Yamagata/73 HA to cultured cell lines. 2014 Virology Result IV F95Y 13 22 24503069 The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus. The mutations of Asn194 Asp and Phe95 Tyr were introduced into the coding region of B/Lee/40 HA by site-directed mutagenesis. 2014 Virology Result IV N194D;F95Y 17;32 27;41 HA 93 95 24503069 The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus. The Phe95 Tyr mutation enhances receptor-binding affinity of influenza B/Yamagata/73 HA. 2014 Virology Result IV F95Y 4 13 24503069 The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus. The Phe95 Tyr mutation introduced into B/Lee/40 HA enhances binding for human receptors but decreases binding for avian receptors. 2014 Virology Result IV F95Y 4 13 24503069 The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus. The Phe95 Tyr/Asn194 Asp virus exhibits 60~80% binding signals relative to the Asn194 Asp virus. 2014 Virology Result IV N194D 79 89 24503069 The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus. Therefore, we also expressed and purified recombinant proteins of B/Lee/40 HA containing Asn194 Asp or Phe95 Tyr/Asn194 Asp and tested their binding affinity for synthetic glycans (Table 1). 2014 Virology Result IV N194D 89 99 HA 75 77 24503069 The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus. This attenuation is in good agreement with the 276 times lower binding affinity of the Phe95 Tyr/Asn194 Asp protein, compared to Asn194 Asp, for Neu5Acalpha(2,3)Gal receptors (Table 1) that are almost exclusively found in mouse airway epithelial cells. 2014 Virology Result IV N194D 129 139 24503069 The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus. Thus, regardless of whether there is a glycosylation at HA1 194 (in the case of Phe95 Tyr) or not (in the case of Phe95 Tyr/Asn194 Asp), the mutation Phe95 Tyr consistently enhances the binding of HA for 6'SLN-LN receptors by about 107 times. 2014 Virology Result IV F95Y;F95Y 80;150 89;159 HA;HA1 197;56 199;59 24503069 The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus. Thus, the mutation Phe95 Tyr restores all three hydrogen bonds that the hydroxyl oxygen atom of Tyr-98 makes in influenza A/H3 HA. 2014 Virology Result IV F95Y 19 28 HA 127 129 24503069 The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus. To illustrate this point, we generated a modeled structure of B/Lee/40 HA Asn194 Asp - LSTa by using the conformation of LSTa in the B/Lee/40 HA Phe95 Tyr/Asn194 Asp - LSTa structure, but with the Sia-1 moiety at the higher position as observed in B/Yamanashi/98 HA. 2014 Virology Result IV N194D 74 84 HA;HA;HA 71;142;263 73;144;265 24503069 The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus. To investigate the impact of the Phe95 Tyr mutation on the receptor binding capability of HA, we carried out a glycan microarray analysis on wild-type B/Yamagata/73 HA and its three mutants. 2014 Virology Result IV F95Y 33 42 HA;HA 90;165 92;167 24503069 The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus. We next tested whether the enhanced receptor-binding affinity of the Phe95 Tyr and Phe95 Tyr/Asn194 Asp mutants allows influenza B/Yamagata/73 HA to bind host cells significantly better. 2014 Virology Result IV F95Y 69 78 HA 143 145 24521884 Mass spectrometry analysis coupled with de novo sequencing reveals amino acid substitutions in nucleocapsid protein from influenza A virus. Additionally, detection of some of the a and b series ions such as a2, a3, b2 and b3 indicated that E449 was not subject to amino acid substitution, confirming the substitution of R452 K. 2014 International journal of molecular sciences Result IV R452K 180 186 24521884 Mass spectrometry analysis coupled with de novo sequencing reveals amino acid substitutions in nucleocapsid protein from influenza A virus. However, a nominal mass shift of -43 but not -13.01 Da (N430 T) was observed for MP2 when compared to the theoretical sequence of TTIMAAFNGNTEGR (423-436), suggesting that there might be at least one additional amino acid substitution in the sequence, which resulted in an additional mass shift of -30.01 Da. 2014 International journal of molecular sciences Result IV N430T 56 62 24521884 Mass spectrometry analysis coupled with de novo sequencing reveals amino acid substitutions in nucleocapsid protein from influenza A virus. Identification of AA Substitution of R452K. 2014 International journal of molecular sciences Result IV R452K 37 42 24521884 Mass spectrometry analysis coupled with de novo sequencing reveals amino acid substitutions in nucleocapsid protein from influenza A virus. Identification of AA Substitution T423A and N430T. 2014 International journal of molecular sciences Result IV T423A;N430T 34;44 39;49 24521884 Mass spectrometry analysis coupled with de novo sequencing reveals amino acid substitutions in nucleocapsid protein from influenza A virus. Investigation of the rest of the residues of the tryptic peptide sequence (423-436) indicated that there were three amino acid residues that could result in a mass shift of -30.01 Da upon substitution: T423 A, T433 A, E434 T. 2014 International journal of molecular sciences Result IV T423A;T433A;E434T 202;210;218 208;216;224 24521884 Mass spectrometry analysis coupled with de novo sequencing reveals amino acid substitutions in nucleocapsid protein from influenza A virus. The detection of the y series ion y13 at m/z 1368.66, as well as b3-H2O, b3, b2-H2O and b2 ions, indicated that the first three residues in the peptide were ATI, thus confirming the identification of substitution of T423 A. 2014 International journal of molecular sciences Result IV T423A 216 222 24521884 Mass spectrometry analysis coupled with de novo sequencing reveals amino acid substitutions in nucleocapsid protein from influenza A virus. Therefore amino acid substitution of N430 T was identified, which resulted in a mass shift of -13.01 Da. 2014 International journal of molecular sciences Result IV N430T 37 43 24521884 Mass spectrometry analysis coupled with de novo sequencing reveals amino acid substitutions in nucleocapsid protein from influenza A virus. Therefore, the peak MP2 was identified as the tryptic peptide in the residues from 423 to 436 with the two substitutions, namely T423 A and N430 T. 2014 International journal of molecular sciences Result IV T423A;N430T 129;140 135;146 24524021 Generation and Characterization of Recombinant Influenza A(H1N1) Viruses Resistant to Neuraminidase Inhibitors. All the single and double mutants containing tyrosine (Y) at NA residue 275 of the wild-type virus except the single mutant (Chungbuk-Y275-E119V) conferred important levels of resistance to oseltamivir, whereas the wild-type virus and these mutants were associated with the susceptibility to zanamivir. 2013 Osong public health and research perspectives Result IV E119V 139 144 61 63 24524021 Generation and Characterization of Recombinant Influenza A(H1N1) Viruses Resistant to Neuraminidase Inhibitors. All the single, double, and triple mutants containing the E119V mutation were associated with the resistance to zanamivir. 2013 Osong public health and research perspectives Result IV E119V 58 63 24524021 Generation and Characterization of Recombinant Influenza A(H1N1) Viruses Resistant to Neuraminidase Inhibitors. Compared with the double Chungbuk-Y274H-N295S mutant, triple Chungbuk-Y275H-N295S-I117V, Y275H-N295S-I117M, and Y275H-N295S-I223V mutants also had slightly increased IC50 values for oseltamivir (1.5-fold, 1.3-fold, and 2.4-fold), whereas these mutants were susceptible to zanamivir. 2013 Osong public health and research perspectives Result IV N295S;Y274H;N295S;I117V;Y275H;N295S;Y275H;I117M;N295S;Y275H;I223V 40;34;76;82;70;95;89;101;118;112;124 45;39;81;87;75;100;94;106;123;117;129 24524021 Generation and Characterization of Recombinant Influenza A(H1N1) Viruses Resistant to Neuraminidase Inhibitors. Compared with the single Chungbuk-Y274-N295S mutant, double Chungbuk-Y275-N295S-I117V, Y275-N295S-I117M, and Y275-N295S-I223V mutants had slightly increased IC50 values for oseltamivir (3.1-fold, 1.1-fold, and 2.8-fold), whereas these mutants were susceptible to zanamivir. 2013 Osong public health and research perspectives Result IV N295S;N295S;I117V;N295S;I117M;N295S;I223V 39;74;80;92;98;114;120 44;79;85;97;103;119;125 24524021 Generation and Characterization of Recombinant Influenza A(H1N1) Viruses Resistant to Neuraminidase Inhibitors. Compared with the single Chungbuk-Y274H mutant, triple Chungbuk-Y275H-E119V-I117V and Y275H-E119V-I117M mutants had increased IC50 values for zanamivir (390.7- and 181.0-fold), whereas these mutants were susceptible to oseltamivir. 2013 Osong public health and research perspectives Result IV Y274H;E119V;Y275H;I117V;E119V;Y275H;I117M 34;70;64;76;92;86;98 39;75;69;81;97;91;103 24524021 Generation and Characterization of Recombinant Influenza A(H1N1) Viruses Resistant to Neuraminidase Inhibitors. For example, the recombinant Chungbuk-Y275-I117V virus contained an I V amino acid change at residue 117 of NA in the wild-type virus [A/Chungbuk/4448/2008(H1N1)] and the recombinant Chungbuk-Y275H-I117V virus contained I V and Y H amino acid changes at residues 117 and 275 of NA in the wild-type virus, respectively (numbering is based on the N1 NA protein throughout). 2013 Osong public health and research perspectives Result IV I117V;I117V;Y275H 43;198;192 48;203;197 NA;NA;NA 108;278;348 110;280;350 24524021 Generation and Characterization of Recombinant Influenza A(H1N1) Viruses Resistant to Neuraminidase Inhibitors. NA-inhibition assays showed that E119V mutation of the wild-type virus containing tyrosine (Y) at NA residue 275 (Chungbuk-Y275-E119V) and E119V mutation of the mutant virus containing histidine (H) at NA residue 275 (Chungbuk-Y275H-E119V) conferred important levels of resistance to zanamivir, with 202.5-fold and 135.7-fold increases in IC50 values compared with that of the wild-type virus (Chungbuk-Y275) and Chungbuk-Y275H mutant virus, respectively, whereas these mutants were susceptible to oseltamivir. 2013 Osong public health and research perspectives Result IV E119V;E119V;E119V;E119V;Y275H;Y275H 33;128;139;233;227;422 38;133;144;238;232;427 NA;NA;NA 0;98;202 2;100;204 24524021 Generation and Characterization of Recombinant Influenza A(H1N1) Viruses Resistant to Neuraminidase Inhibitors. The N295S mutation in the wild-type virus (Chungbuk-Y275-N295S) was associated with a reduction in oseltamivir resistance (0.2-fold decrease in IC50 compared with that of the wild-type virus), whereas N295S mutation of the mutant virus containing histidine (H) at NA residue 275 (Chungbuk-Y275H-N295S) was associated with an increase in oseltamivir resistance (40.3-fold increase in IC50 compared with that of Chungbuk-Y275H mutant virus). 2013 Osong public health and research perspectives Result IV N295S;N295S;N295S;N295S;Y275H;Y275H 4;57;201;295;289;419 9;62;206;300;294;424 264 266 24524021 Generation and Characterization of Recombinant Influenza A(H1N1) Viruses Resistant to Neuraminidase Inhibitors. The single I117V, I117M, I223V, R293K, N295S, or S334N mutation did not seem to contribute significantly to a phenotype resistant to oseltamivir as well as to zanamivir. 2013 Osong public health and research perspectives Result IV I117V;I117M;I223V;R293K;N295S;S334N 11;18;25;32;39;49 16;23;30;37;44;54 24524021 Generation and Characterization of Recombinant Influenza A(H1N1) Viruses Resistant to Neuraminidase Inhibitors. Totally, eight single mutants (Y275-I117V, Y275-I117M, Y275-E119V, Y275-I223V, Y275H, Y275-R293K, Y275-N295S, and Y275-S334N), 10 double mutants (Y275H-I117V, Y275H-I117M, Y275H-E119V, Y275H-I223V, Y275H-R293K, Y275H-N295S, Y275H-S334N, Y275-N295S-I117V, Y275-N295S-I117M, and Y275-N295S-I223V), and five triple mutants (Y275H-E119V-I117V, Y275H-E119V-I117M, Y275H-N295S-I117V, Y275H-N295S-I117M, and Y275H-N295S-I223V) were generated (Table 1). 2013 Osong public health and research perspectives Result IV I117V;I117M;E119V;I223V;Y275H;R293K;N295S;S334N;I117V;Y275H;Y275H;I117M;Y275H;E119V;Y275H;I223V;R293K;Y275H;Y275H;N295S;S334N;Y275H;I117V;N295S;I117M;N295S;I223V;N295S;I117V;Y275H;E119V;E119V;Y275H;I117M;I117V;Y275H;N295S;I117M;Y275H;N295S;Y275H;I223V;N295S 36;48;60;72;79;91;103;119;152;146;159;165;172;178;185;191;204;198;211;217;230;224;248;242;266;260;288;282;333;321;327;346;340;352;371;359;365;390;378;384;401;413;407 41;53;65;77;84;96;108;124;157;151;164;170;177;183;190;196;209;203;216;222;235;229;253;247;271;265;293;287;338;326;332;351;345;357;376;364;370;395;383;389;406;418;412 24558492 Study of oseltamivir and zanamivir resistance-related mutations in influenza viruses isolated from wild mallards in Sweden. After inhibition by ZA, the highest IC50 value (38.6 nM) was found in the N9II WT, while the lowest IC50 value (1.2 nM) belonged to the N1I WT. 2014 PloS one Result IV N1I 136 139 24558492 Study of oseltamivir and zanamivir resistance-related mutations in influenza viruses isolated from wild mallards in Sweden. All IC50 values of mutants in the N1 subtype following inhibition by ZA were higher than the corresponding mean value of the N1I WT (Figure 2A; Table 2). 2014 PloS one Result IV N1I 125 128 24558492 Study of oseltamivir and zanamivir resistance-related mutations in influenza viruses isolated from wild mallards in Sweden. Compared to WT N9I all mutants were less sensitive to NAIs while in comparison with WT N9II all mutants were more sensitive to NAIs. 2014 PloS one Result IV N9I 15 18 NAI;NAI 54;127 58;131 24558492 Study of oseltamivir and zanamivir resistance-related mutations in influenza viruses isolated from wild mallards in Sweden. Conversely, the WTs following OC inhibition were less variable (Figure 2A-D), with the exceptions of the N3I and N3II isolates, in which IC50 values of 2.8 nM and 0.4 nM (seven times difference), respectively, were detected. 2014 PloS one Result IV N3I 105 108 24558492 Study of oseltamivir and zanamivir resistance-related mutations in influenza viruses isolated from wild mallards in Sweden. Effect of the R118K mutation on different subtypes. 2014 PloS one Result IV R118K 14 19 24558492 Study of oseltamivir and zanamivir resistance-related mutations in influenza viruses isolated from wild mallards in Sweden. In this case three mutants with R118K change (3z, 4z and 14z) and one mutant with I222V change had IC50s higher than corresponding IC50s of both WTs while only mutant with D151K change had IC50 lower than IC50s of WTs. 2014 PloS one Result IV R118K;I222V;D151K 32;82;172 37;87;177 24558492 Study of oseltamivir and zanamivir resistance-related mutations in influenza viruses isolated from wild mallards in Sweden. One isolate (H8N1) with a D151K mutation and one isolate (H2N3) with R156K mutation were revealed. 2014 PloS one Result IV D151K;R156K 26;69 31;74 24558492 Study of oseltamivir and zanamivir resistance-related mutations in influenza viruses isolated from wild mallards in Sweden. The H2N3 viral isolate (Figure 2B: 6o) had a higher IC50 than that of N3II WT and a lower IC50 than that of N3I. 2014 PloS one Result IV N3I 108 111 24558492 Study of oseltamivir and zanamivir resistance-related mutations in influenza viruses isolated from wild mallards in Sweden. The mutation R118K did not influence NAI sensitivity to any of inhibitors in either the N1 or the N9 subtypes. 2014 PloS one Result IV R118K 13 18 N9;NAI 98;37 100;40 24563658 Synergistic combinations of favipiravir and oseltamivir against wild-type pandemic and oseltamivir-resistant influenza A virus infections in mice. Combinations of oseltamivir and favipiravir were used to treat an influenza A/Mississippi/3/2001 (H1N1; H275Y - viral neuraminidase mutation resulting in oseltamivir resistance) infection in mice (Table 3). 2013 Future virology Result IV H275Y 104 109 118 131 24569063 An investigational antiviral drug, DAS181, effectively inhibits replication of zoonotic influenza A virus subtype H7N9 and protects mice from lethality. Contrariwise, no effect on body weight and lung virus titer was seen in mice infected with R292K influenza A(H7N9). 2014 The Journal of infectious diseases Result IV R292K 91 96 24569063 An investigational antiviral drug, DAS181, effectively inhibits replication of zoonotic influenza A virus subtype H7N9 and protects mice from lethality. In the next experiment, mice infected with Taiwan/1 wild-type virus, its R292K variant, or influenza A(H1N1)pdm09 were treated with DAS181 starting 24, 48, or 72 hours after infection; the 2 last treatments were done at the highest DAS181 dose only. 2014 The Journal of infectious diseases Result IV R292K 73 78 24569063 An investigational antiviral drug, DAS181, effectively inhibits replication of zoonotic influenza A virus subtype H7N9 and protects mice from lethality. Infected mice given DAS181 after 48 hours showed >=75% survival, while 75% and 25% protection was seen after 72 hours in wild-type and R292K virus-infected mice, respectively. 2014 The Journal of infectious diseases Result IV R292K 135 140 24569063 An investigational antiviral drug, DAS181, effectively inhibits replication of zoonotic influenza A virus subtype H7N9 and protects mice from lethality. Next, the ability of DAS181 to inhibit replication of the R292K virus variant and its wild-type counterpart in cell culture was tested using the focus reduction assay. 2014 The Journal of infectious diseases Result IV R292K 58 63 24569063 An investigational antiviral drug, DAS181, effectively inhibits replication of zoonotic influenza A virus subtype H7N9 and protects mice from lethality. Noteworthy, no reversion to the wild type (R292) was detected, based on pyrosequencing analysis conducted on virus in lung homogenates of animals infected with either R292K virus. 2014 The Journal of infectious diseases Result IV R292K 167 172 24569063 An investigational antiviral drug, DAS181, effectively inhibits replication of zoonotic influenza A virus subtype H7N9 and protects mice from lethality. The MLD50 values for the Shanghai/1 wild-type and R292K virus variant were 103 and 2.0 x 103 TCID50, respectively. 2014 The Journal of infectious diseases Result IV R292K 50 55 24569063 An investigational antiviral drug, DAS181, effectively inhibits replication of zoonotic influenza A virus subtype H7N9 and protects mice from lethality. The plaque-purified R292K virus variants of Shanghai/1 and Taiwan/1 influenza A(H7N9) isolates exhibited highly reduced inhibition by oseltamivir carboxylate (>10 000-fold) and peramivir (1388-1587-fold) and reduced inhibition by zanamivir (51-55-fold) and laninamivir (22-24-fold) in the NA inhibition assay (Supplementary Table 1). 2014 The Journal of infectious diseases Result IV R292K 20 25 289 291 24576826 Unique reassortant of influenza A(H7N9) virus associated with severe disease emerging in Hong Kong. However the NA does not contain the R289K substitution which confers resistance to neuraminidase inhibitors. 2014 The Journal of infection Result IV R289K 36 41 NA;NA 12;83 14;96 24576826 Unique reassortant of influenza A(H7N9) virus associated with severe disease emerging in Hong Kong. However, the PB2 T271A and D701N substitutions associated with enhanced polymerase activity and mammalian adaptation were not found. 2014 The Journal of infection Result IV T271A;D701N 17;27 22;32 PB2 13 16 24576826 Unique reassortant of influenza A(H7N9) virus associated with severe disease emerging in Hong Kong. In the HA, G177V and Q217L substitutions which were reported to confer increased binding to alpha2,6-linked sialic acid receptors present in the upper respiratory tract of humans, are found. 2014 The Journal of infection Result IV G177V;Q217L 11;21 16;26 HA 7 9 24576826 Unique reassortant of influenza A(H7N9) virus associated with severe disease emerging in Hong Kong. In the PB2 polymerase subunit, A/Hong Kong/470129/2013 contains L89V and E627K substitutions which are associated with enhanced viral polymerase activity in mammalian cells. 2014 The Journal of infection Result IV L89V;E627K 64;73 68;78 PB2 7 10 24576826 Unique reassortant of influenza A(H7N9) virus associated with severe disease emerging in Hong Kong. Surprisingly, the PA L336M substitution of the polymerase subunit, which was reported in one study to be associated with enhanced polymerase activity, is found in the A/Hong Kong/470129/2013 but not other human or avian A(H7N9) isolates (Table 2 and Table 3 ). 2014 The Journal of infection Result IV L336M 21 26 PA 18 20 24576826 Unique reassortant of influenza A(H7N9) virus associated with severe disease emerging in Hong Kong. The M2 protein contains the S31N mutation which confers resistance to adamantanes. 2014 The Journal of infection Result IV S31N 28 32 M2 4 6 24576826 Unique reassortant of influenza A(H7N9) virus associated with severe disease emerging in Hong Kong. The mutations V236I, K261E, N322T, N341D, and K460R of the NA gene, that were first identified in the A/Zhejiang/22/2013 and A/Zhejiang/DTID_ZJU10/2013 strain isolated from patients in October 2013, are not found in A/Hong Kong/470129/2013. 2014 The Journal of infection Result IV V236I;K261E;N322T;N341D;K460R 14;21;28;35;46 19;26;33;40;51 59 61 24576826 Unique reassortant of influenza A(H7N9) virus associated with severe disease emerging in Hong Kong. The PB1 protein contains I368V, which enables droplet transmission in ferrets. 2014 The Journal of infection Result IV I368V 25 30 PB1 4 7 24667168 Low 2012-13 influenza vaccine effectiveness associated with mutation in the egg-adapted H3N2 vaccine strain not antigenic drift in circulating viruses. Other antigenic site mutations in 2012-13, located close to the receptor-binding site, include 21/57 (37%) viruses with R205K (seen in clade 5 sequences in 2011-12), 17/57 (30%) with A141T, and 8/57 (14%) with A186T (Table S5, Figure S3). 2014 PloS one Result IV R205K;A141T;A186T 120;183;210 125;188;215 24667168 Low 2012-13 influenza vaccine effectiveness associated with mutation in the egg-adapted H3N2 vaccine strain not antigenic drift in circulating viruses. The genetic profile of circulating A(H1N1)pdm09 viruses differs from 2011-12 when 90% of sequenced viruses clustered within clade 7, bearing the same 2AA mutations shared by all subsequent 2012-13 clade 6/7 viruses (S185T/P and S203T) but with greater additional genetic diversity observed in 2012-13. 2014 PloS one Result IV S185T;S185P;S203T 216;216;228 223;223;233 24667168 Low 2012-13 influenza vaccine effectiveness associated with mutation in the egg-adapted H3N2 vaccine strain not antigenic drift in circulating viruses. These three mutations in IVR-165, located close to the receptor binding site, include H156Q and G186V substitutions at antigenic site B, and S219Y mutation at antigenic site D. 2014 PloS one Result IV H156Q;G186V;S219Y 86;96;141 91;101;146 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. Addition of both V241I and N369K together offset these losses by approximately 70% (Figure 2B). 2014 PLoS pathogens Result IV V241I;N369K 17;27 22;32 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. An in vitro NA expression system was used to investigate the effect of the NA mutations V241I, N369K and S386N on NA surface expression and enzymatic activity. 2014 PLoS pathogens Result IV V241I;N369K;S386N 88;95;105 93;100;110 NA;NA;NA 12;75;114 14;77;116 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. Dual V241I and N369K PPMs enhance the in vitro activity and fitness of contemporary A(H1N1)pdm09 viruses in ferrets. 2014 PLoS pathogens Result IV V241I;N369K 5;15 10;20 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. Effects of individual V241I or N369K PPMs on in vitro activity and viral fitness in ferrets. 2014 PLoS pathogens Result IV V241I;N369K 22;31 27;36 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. Following inoculation in ferrets, there were no significant differences in morbidity between the groups of ferrets inoculated with pure populations of the rgNew17 OR and rgNew17 I241V, K369N OR viruses (data not shown), and both viruses replicated to similar titres (4.9+-0.4 and 5.5+-0.3 log10TCID50/ml respectively) and were shed for an equivalent duration (5.3+-0.6 days for both viruses) (Figure 3A, S5). 2014 PLoS pathogens Result IV I241V;K369N 178;185 183;190 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. Following inoculation into ferrets, there were no significant differences in morbidity between the groups of ferrets inoculated with pure populations of rgPerth261 OR and rgPerth261 V241I, N369K OR (data not shown), and both viruses replicated to similar titres of 5.8+-1.0 and 5.4+-1.2 log10TCID50/ml respectively, and were shed for a similar duration of 5.3+-0.6 and 5.7+-0.6 days respectively (Figure 4A, S8). 2014 PLoS pathogens Result IV V241I;N369K 182;189 187;194 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. Given the spread of HNE2011 H275Y OR viruses, we hypothesised that they may have had equivalent or superior fitness to similar OS strains. 2014 PLoS pathogens Result IV H275Y 28 33 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. Hence, subsequent investigations were restricted to the NA V241I and N369K mutations. 2014 PLoS pathogens Result IV V241I;N369K 59;69 64;74 56 58 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. However, rgNew17 K369N OR showed delayed replication for the first 6-8 h pi at a high MOI (Figure S4A), suggesting that removal of NA 369K had a somewhat detrimental effect upon virus growth in vitro. 2014 PLoS pathogens Result IV K369N 17 22 131 133 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. In contrast, removal of the N386S mutation from the HNE2011 NA (New17 S386N OR) enhanced the activity and surface expression by approximately 50% (Figure 2A), demonstrating that this mutation was unlikely to be having a beneficial effect upon the fitness of the New17 OR virus. 2014 PLoS pathogens Result IV N386S;S386N 28;70 33;75 60 62 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. In the four groups of ferrets inoculated with virus mixtures, a pure population of rgPerth261 V241I, N369K OR virus, that was maintained upon subsequent transmission to further recipient ferrets, was observed by the end of the infection in the donor in the 20:80 group, and in the 1st recipient in the 80:20 group, and both of the 50:50 groups (Figure 4B). 2014 PLoS pathogens Result IV V241I;N369K 94;101 99;106 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. In vitro assays demonstrated that introduction of the NA V241I and N369K mutations into an earlier A(H1N1)pdm09 OR NA protein, that did not naturally contain these mutations, resulted in enhanced enzymatic activity and NA expression (Figure 2). 2014 PLoS pathogens Result IV V241I;N369K;V241I;N369K 58;68;57;67 63;73;62;72 NA;NA;NA 54;115;219 56;117;221 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. Initial comparison of in vitro replication kinetics at low and high MOI showed that replication of the rgNew17 I241V, K369N OR virus was delayed for the first 4-6 h pi compared to the rgNew17 OR virus (Figure S4A, B). 2014 PLoS pathogens Result IV I241V;K369N 111;118 116;123 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. Modelling found that, while the rgNew17 OR virus exhibited significantly superior within-host viral replication fitness compared to the rgNew17 K369N OR virus (relative within-host fitness value [95% CI] = 3.14 [1.17; 5.30]), there was no statistical evidence for a transmission fitness difference between the viruses (Table 1). 2014 PLoS pathogens Result IV K369N 144 149 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. Modelling indicated that the rgNew17 OR virus exhibited significantly superior transmission (relative fitness value [95% CI] = 2.69 [1.00; 7.24]) and within-host viral replication fitness (relative fitness value [95% CI] = 1.82 [1.35; 7.46]), compared to the rgNew17 I241V, K369N OR virus (Table 1), demonstrating that removal of NA 241I and 369K impaired the ability of the rgNew17 I241V, K369N OR virus to out-compete the rgNew17 OR virus both during replication within hosts and upon transmission between them. 2014 PLoS pathogens Result IV I241V;K369N;I241V;K369N 267;274;383;390 272;279;388;395 330 332 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. Modelling revealed that the rgNew17 OR virus exhibited significantly superior transmission (relative transmission fitness value [95% CI] = 2.22 [1.24; 3.97]) and within-host viral replication fitness (relative within-host fitness value [95% CI] = 3.96 [1.17; 6.83]) compared to the rgNew17 I241V OR virus (Table 1), demonstrating that the V241I NA mutation is important in contemporary A(H1N1)pdm09 OR viruses for both within-host and transmission fitness. 2014 PLoS pathogens Result IV I241V;V241I 290;339 295;344 345 347 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. Modelling showed that while the rgPerth261 V241I, N369K OR virus exhibited superior within-host viral replication fitness (relative within-host fitness value [95% CI] = 1.86 [1.37; 7.24]) compared to the rgPerth261 OR virus, there was no significant difference in transmission fitness between the viruses (Table 1). 2014 PLoS pathogens Result IV V241I;N369K 43;50 48;55 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. Pure populations of the rgNew17 OR and rgNew17 K369N OR viruses replicated to 5.0+-0.5 and 4.1+-0.6 log10TCID50/ml respectively, and both viruses were shed for a similar duration of 5.0+-1.2 and 5.3+-0.6 days respectively (Figure S7A, C). 2014 PLoS pathogens Result IV K369N 47 52 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. Removal of H275Y from the New17 OR NA protein enhanced its surface expression and enzymatic activity by approximately 50% (Figure 2A), demonstrating the detrimental effect of the H275Y mutation upon surface expression and enzymatic activity. 2014 PLoS pathogens Result IV H275Y;H275Y 11;179 16;184 35 37 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. Reversal of the V241I and N369K PPMs individually from the New17 OR NA protein (New17 I241V OR and New17 K369N OR) resulted in approximately 40% and 35% reductions in NA surface expression and enzymatic activity respectively (Figure 2A). 2014 PLoS pathogens Result IV V241I;N369K;I241V;K369N 16;26;86;105 21;31;91;110 NA;NA 68;167 70;169 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. Rg viruses were generated encoding the complete Perth261 OR genome without any changes (rgPerth261 OR) and with the NA V241I and N369K mutations (rgPerth261 V241I, N369K OR). 2014 PLoS pathogens Result IV V241I;N369K;V241I;N369K 119;129;157;164 124;134;162;169 116 118 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. rgNew17 I241V OR virus pair in ferrets showed that pure populations of the two viruses replicated to 4.0+-0.5, and 5.2+-0.4 log10TCID50/ml respectively, and were shed for 5.3+-1.2 and 6.0+-1.0 days respectively (Figure S6A, C). 2014 PLoS pathogens Result IV I241V 8 13 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. Sequence analysis did not reveal any new mutations within the NA genes of this virus pair, although a HA P154S amino acid change was detected in the virus mixture within the nasal washes of the 2nd recipient ferret in this group. 2014 PLoS pathogens Result IV P154S 105 110 HA;NA 102;62 104;64 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. The in vitro replication kinetics of rgNew17 OR, rgNew17 I241V OR and rgNew17 K369N OR viruses along with the "natural" New17 OR virus was first determined in MDCK cells at a low and high MOI. 2014 PLoS pathogens Result IV I241V;K369N 57;78 62;83 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. To assess the effect of the K369N mutation, ferrets were inoculated with the rgNew17 OR and rgNew17 K369N OR viruses. 2014 PLoS pathogens Result IV K369N;K369N 28;100 33;105 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. To further evaluate the impact of both H275Y and the PPMs V241I and N369K in vitro, we introduced the mutations into an early A(H1N1)pdm09 OS virus from 2009. 2014 PLoS pathogens Result IV H275Y;V241I;N369K 39;58;68 44;63;73 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. To investigate the individual influence of the NA V241I and N369K mutations upon the fitness of recent OR A(H1N1)pdm09 viruses, rgNew17 OR was compared with isogenic rg viruses from which either the NA V241I (rgNew17 I241V OR) or N369K (rgNew17 K369N OR) mutations had been removed. 2014 PLoS pathogens Result IV V241I;N369K;V241I;I241V;N369K;K369N 50;60;202;217;230;245 55;65;207;222;235;250 NA;NA 47;199 49;201 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. V241I and N369K PPMs enhance in vitro activity and viral fitness of early A(H1N1)pdm09 viruses in ferrets. 2014 PLoS pathogens Result IV V241I;N369K 0;10 5;15 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. V241I and N369K PPMs enhance NA activity in vitro . 2014 PLoS pathogens Result IV V241I;N369K 0;10 5;15 29 31 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. V241I and N369K PPMs enhance NA activity in vitro. 2014 PLoS pathogens Result IV V241I;N369K 0;10 5;15 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. We then determined the effect of removing both V241I and N369K from a HNE2011 OR virus on in vivo within-host and transmission fitness. 2014 PLoS pathogens Result IV V241I;N369K 47;57 52;62 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. While the incorporation of H275Y into the Cal7 OS NA protein reduced its surface expression and activity by 50%, addition of the V241I and N369K mutations partially offset these losses, by approximately 40% and 20% respectively (Figure 2B). 2014 PLoS pathogens Result IV H275Y;V241I;N369K 27;129;139 32;134;144 50 52 24790833 Isolation and characterization of H9N2 influenza virus isolates from poultry respiratory disease outbreak. Additionally, all the Indian strains (excluding A/duck/India/31g/86-Q) and both the current isolates have isoleucine (I) at position 227 (H3 numbering, 235 for H9 numbering) in contrast to glutamine (Q) in all three lineage strains (Table 1). 2014 SpringerPlus Result IV I227I 105 137 24790833 Isolation and characterization of H9N2 influenza virus isolates from poultry respiratory disease outbreak. Isolate1 along with only one Indian strain (A/ck/Tripura/105131/08) also revealed a unique substitution from glutamine to arginine at position 432 when compared with strains of G1 and Y280 lineage. 2014 SpringerPlus Result IV Q432R 109 146 24790833 Isolation and characterization of H9N2 influenza virus isolates from poultry respiratory disease outbreak. Most importantly the substitution Q226L was observed in isolate 2 in present study, which is associated with mammalian adaptation of avian influenza virus. 2014 SpringerPlus Result IV Q226L 34 39 24790833 Isolation and characterization of H9N2 influenza virus isolates from poultry respiratory disease outbreak. The isolates sequenced in this study as well as most of the Indian isolates revealed an additional site at asparagine (N) 44 due to substitution of P45S. 2014 SpringerPlus Result IV P45S 148 152 24795482 A novel I221L substitution in neuraminidase confers high-level resistance to oseltamivir in influenza B viruses. Analysis of HA and NA genes revealed that the only difference between oseltamivir-resistant and oseltamivir-susceptible isolates was the mutation conferring the I221L substitution in the NA gene (Supplementary Table 1). 2014 The Journal of infectious diseases Result IV I221L 161 166 HA;NA;NA 12;19;187 14;21;189 24795482 A novel I221L substitution in neuraminidase confers high-level resistance to oseltamivir in influenza B viruses. Consistent with lower levels of inhibition of the I221L mutant virus by zanamivir, no marked changes in the conformation of zanamivir were seen (Figure 3B). 2014 The Journal of infectious diseases Result IV I221L 50 55 24795482 A novel I221L substitution in neuraminidase confers high-level resistance to oseltamivir in influenza B viruses. Crystals of the NA-I221L protein in complex with both inhibitors diffracted to high resolution, showing clearly defined density for bound oseltamivir and zanamivir (Supplementary Table 2). 2014 The Journal of infectious diseases Result IV I221L 19 24 16 18 24795482 A novel I221L substitution in neuraminidase confers high-level resistance to oseltamivir in influenza B viruses. Detection of Mutated NA (I221L) in Clinical Specimens From the Patient. 2014 The Journal of infectious diseases Result IV I221L 25 30 21 23 24795482 A novel I221L substitution in neuraminidase confers high-level resistance to oseltamivir in influenza B viruses. Five passages of wild-type and mutated NA (I221L) viruses in MDCK cells (MOI, 10-4) with no selective pressure revealed the stability of viruses bearing wild-type or mutated NA (data not shown) and neither gain nor reversion of the I221L substitution (Table 3). 2014 The Journal of infectious diseases Result IV I221L;I221L 43;232 48;237 NA;NA 39;174 41;176 24795482 A novel I221L substitution in neuraminidase confers high-level resistance to oseltamivir in influenza B viruses. One-step allelic discrimination real-time RT-qPCR was performed to assess the presence of the mutation conferring the I221L substitution in clinical specimens and determine whether the mutation was selected for and amplified during cell culture (Table 2). 2014 The Journal of infectious diseases Result IV I221L 118 123 24795482 A novel I221L substitution in neuraminidase confers high-level resistance to oseltamivir in influenza B viruses. Sequencing of the NA gene in isolates revealed a unique mutation encoding an I221L substitution in NA at a level of 100% for isolates from a NPA obtained on D34 and a nasal swab specimen obtained on D40 and at a level of 80% for the isolate from a BAL obtained on D42. 2014 The Journal of infectious diseases Result IV I221L 77 82 NA;NA 18;99 20;101 24795482 A novel I221L substitution in neuraminidase confers high-level resistance to oseltamivir in influenza B viruses. The Km revealed that the I221L NA variant had a 1.9 times lower affinity for the MUNANA substrate, and the Ki values for oseltamivir carboxylate and zanamivir showed affinities that were around 84 and 51 times lower, respectively, than that for wild-type NA (Table 1). 2014 The Journal of infectious diseases Result IV I221L 25 30 NA;NA 31;255 33;257 24795482 A novel I221L substitution in neuraminidase confers high-level resistance to oseltamivir in influenza B viruses. The structure of the NA-I221L-oseltamivir complex showed that the L side chain protrudes into the hydrophobic pocket of the active site that accommodates the pentyloxy substituent of oseltamivir, thus causing a change in the conformation of the inhibitor such that its C81 carbon moves about 2.2 A from the wild-type NA bound position (Figure 3A). 2014 The Journal of infectious diseases Result IV I221L 24 29 NA;NA 21;317 23;319 24795482 A novel I221L substitution in neuraminidase confers high-level resistance to oseltamivir in influenza B viruses. To better understand the viral fitness of viruses bearing a wild-type or mutated NA (I221L), we performed competition experiments by mixing (1:1) viruses propagated from the plaque assays of the first wild-type isolate and the isolate showing the highest oseltamivir-resistance. 2014 The Journal of infectious diseases Result IV I221L 85 90 81 83 24795482 A novel I221L substitution in neuraminidase confers high-level resistance to oseltamivir in influenza B viruses. Virus kinetics experiments performed under 1-step conditions showed wild-type viruses and mutated NA (I221L) viruses to have similar growth kinetics in MDCK cells (Figure 2). 2014 The Journal of infectious diseases Result IV I221L 102 107 98 100 24795482 A novel I221L substitution in neuraminidase confers high-level resistance to oseltamivir in influenza B viruses. We used X-ray crystallography to understand the structural basis of resistance to oseltamivir conferred by NA carrying the I221L substitution. 2014 The Journal of infectious diseases Result IV I221L 123 128 107 109 24854981 Solid phase assay for comparing reactivation rates of neuraminidases of influenza wild type and resistant mutants after inhibitor removal. Although the E119V mutation does not affect the IC50 for zanamivir, there was faster reactivation compared to the wild type virus (70 min compared to 109 min, p value < 0.005). 2014 Antiviral research Result IV E119V 13 18 24854981 Solid phase assay for comparing reactivation rates of neuraminidases of influenza wild type and resistant mutants after inhibitor removal. For the E119G virus with high zanamivir resistance, dissociation was so rapid, < 10 min, we could not determine any difference from the uninhibited virus control. 2014 Antiviral research Result IV E119G 8 13 24854981 Solid phase assay for comparing reactivation rates of neuraminidases of influenza wild type and resistant mutants after inhibitor removal. For the H1N1 H274Y, H3N2 E119V, and clade 2 H5N1 viruses with reduced oseltamivir sensitivity, dissociation was even faster, from 12 - 16 min (p < 0.001 compared to each wild type pair). 2014 Antiviral research Result IV H274Y;E119V 13;25 18;30 24854981 Solid phase assay for comparing reactivation rates of neuraminidases of influenza wild type and resistant mutants after inhibitor removal. However, although the D197E mutation reduces sensitivity to all three NAIs, (8.9 versus 258 nM for zanamivir, 144 versus 708 nM for oseltamivir and 2.8 versus 41.5 nM peramivir for wild type and mutant respectively) reactivation of the zanamivir and oseltamivir treated mutant viruses was faster compared to the zanamivir or oseltamivir treated wild type. 2014 Antiviral research Result IV D197E 22 27 NAI 70 74 24854981 Solid phase assay for comparing reactivation rates of neuraminidases of influenza wild type and resistant mutants after inhibitor removal. Interestingly T1/2 values were similar for the mutants, regardless of how high the IC50 was (H274Y 2440 nM, E119V 260 nM and clade 2 H5N1 19.6 nM, compared to wild type values of H1N1 3.1 nM, H3N2 5.3 nM and clade 1 H5N1 of 0.6 nM). 2014 Antiviral research Result IV H274Y;E119V 93;108 98;113 24854981 Solid phase assay for comparing reactivation rates of neuraminidases of influenza wild type and resistant mutants after inhibitor removal. Mutations conferring peramivir resistance had the most dramatic effect on the dissociation rate of all NAIs, with reductions in T1/2 from > 240 min to <=10 min for the E119G mutant and from > 240 min to 14 min for the H274Y mutant. 2014 Antiviral research Result IV E119G;H274Y 168;218 173;223 NAI 103 107 24854981 Solid phase assay for comparing reactivation rates of neuraminidases of influenza wild type and resistant mutants after inhibitor removal. These results are consistent with our more direct assay presented here, where all the mutants, apart from the influenza B/Perth/211/01 D197E virus with peramivir, also showed faster dissociation compared to the wild type virus. 2014 Antiviral research Result IV D197E 135 140 24854981 Solid phase assay for comparing reactivation rates of neuraminidases of influenza wild type and resistant mutants after inhibitor removal. Thus this novel assay demonstrates that there are subtle impacts on drug binding both with the H5N1 and E119V mutant not readily seen by just determining just a single IC50. 2014 Antiviral research Result IV E119V 104 109 24889237 Enhanced human receptor binding by H5 haemagglutinins. 1b), the Asn186Lys mutant virus has higher avidity for both human and avian receptors. 2014 Virology Result IV N186K 9 18 24889237 Enhanced human receptor binding by H5 haemagglutinins. 1f, g and h), indicating that both Asn186Lys and Gly143Arg substitutions have a role in improving human receptor binding. 2014 Virology Result IV N186K;G143R 35;49 44;58 24889237 Enhanced human receptor binding by H5 haemagglutinins. 1f) achieving similar levels to those observed for the Ser227Asn/Gln196Arg double mutant virus. 2014 Virology Result IV Q196R;S227N;S227Q;S227R 65;55;55;55 74;64;64;64 24889237 Enhanced human receptor binding by H5 haemagglutinins. 1j) and Ile155Thr. 2014 Virology Result IV I155T 8 17 24889237 Enhanced human receptor binding by H5 haemagglutinins. 2b) and Asn186Lys. 2014 Virology Result IV N186K 8 17 24889237 Enhanced human receptor binding by H5 haemagglutinins. 2c) mutants and the tyTy Delta133/Ile155Thr mutant. 2014 Virology Result IV I155T 34 43 24889237 Enhanced human receptor binding by H5 haemagglutinins. 3b) and Asn186Lys. 2014 Virology Result IV N186K 8 17 24889237 Enhanced human receptor binding by H5 haemagglutinins. 4d) mutants, the stabilising hydrogen bond between Asn-186 and Gln-226 is lost, either due to loss of the asparagine side-chain as a result of the Asn186Lys substitution, or to an altered Asn-186 side-chain rotamer influenced by the nearby Ser227Asn substitution. 2014 Virology Result IV N186K;S227N 147;240 156;249 24889237 Enhanced human receptor binding by H5 haemagglutinins. Although both Ser227Asn and Asn186Lys mutations switch the bound avian receptor to a cis-conformation, without changing the human receptor binding mode, they alter receptor affinities to different extents. 2014 Virology Result IV S227N;N186K 14;28 23;37 24889237 Enhanced human receptor binding by H5 haemagglutinins. and Asn186Lys. 2014 Virology Result IV N186K 4 13 24889237 Enhanced human receptor binding by H5 haemagglutinins. As described above, the alpha-2,3-glycosidic bond between Sia-1 and Gal-2 of the avian receptors bound to the Ser227Asn/Gln196Arg. 2014 Virology Result IV Q196R;S227N;S227Q;S227R 120;110;110;110 129;119;119;119 24889237 Enhanced human receptor binding by H5 haemagglutinins. BLI analyses show that virus bearing the Delta133/Ile155Thr double mutant HA. 2014 Virology Result IV I155T 50 59 HA 74 76 24889237 Enhanced human receptor binding by H5 haemagglutinins. BLI experiments with mutant clade 1 VN1194 viruses indicated that Ser227Asn. 2014 Virology Result IV S227N 66 75 24889237 Enhanced human receptor binding by H5 haemagglutinins. By contrast the affinity for human receptor of the Asn186Lys/Gly143Arg mutant increases compared with either of the two single mutants; the combined effect gives rise to a ~104-fold gain in human receptor binding avidity compared to the VN1194 wild-type. 2014 Virology Result IV G143R;N186K;N186G;N186R 61;51;51;51 70;60;60;60 24889237 Enhanced human receptor binding by H5 haemagglutinins. Compared to the Ser227Asn mutant. 2014 Virology Result IV S227N 16 25 24889237 Enhanced human receptor binding by H5 haemagglutinins. Comparison of the wild-type tyTy structure with the structure of the Delta133/Ile155Thr receptor complexes suggests that the presence of either Ala-133 or Ile-155 would restrict the occupancy of these waters due to their close proximity to the water binding sites. 2014 Virology Result IV I155T 78 87 24889237 Enhanced human receptor binding by H5 haemagglutinins. Due to this difference in linkage conformation, Gal-2 in the avian receptors bound by the Ser227Asn/Gln196Arg and Asn186Lys mutants, is rotated ~110 about the 2,3 linked glycosidic bond relative to Gal-2 in the wild-type H5 avian receptor complexes. 2014 Virology Result IV Q196R;S227N;N186K;S227Q;S227R 100;90;114;90;90 109;99;123;99;99 24889237 Enhanced human receptor binding by H5 haemagglutinins. Enhancement of human and avian receptor binding by the double mutant Delta133/Ile155Thr of clade 2 HA. 2014 Virology Result IV I155T 78 87 HA 99 101 24889237 Enhanced human receptor binding by H5 haemagglutinins. For the Asn186Lys/Gly143Arg double mutant, avian receptor binding decreases ~4-fold relative to wild-type in comparison with the ~80-fold decrease in binding by the mutant containing only the Asn186Lys substitution. 2014 Virology Result IV G143R;N186K;N186K;N186G 18;8;192;8 27;17;201;17 24889237 Enhanced human receptor binding by H5 haemagglutinins. For the Ser227Asn mutant, binding to human receptor (blue curves) is weak with an avidity slightly less than wild-type VN1194. 2014 Virology Result IV S227N 8 17 24889237 Enhanced human receptor binding by H5 haemagglutinins. Given that residue 186 does not contact any part of the receptor, it is likely that the Asn186Lys substitution makes an electrostatic contribution to compensate for the loss of avian receptor affinity by addition of positive charge in a similar manner to the Gly143Arg and the Gln196Arg substitutions. 2014 Virology Result IV N186K;G143R;Q196R 88;259;277 97;268;286 24889237 Enhanced human receptor binding by H5 haemagglutinins. Gln196Arg and Gly143Arg substitutions, located further away from the receptor binding site, modify receptor binding of the VN1194 HA in very similar ways. 2014 Virology Result IV Q196R;G143R 0;14 9;23 HA 130 132 24889237 Enhanced human receptor binding by H5 haemagglutinins. Human receptor binding by Delta133 also remains unchanged relative to wild-type tyTy, but there is a ~40-fold decrease in human receptor binding by the Ile155Thr single mutant. 2014 Virology Result IV I155T 152 161 24889237 Enhanced human receptor binding by H5 haemagglutinins. Human receptors bound by the VN1194 Ser227Asn/Gln196Arg. 2014 Virology Result IV Q196R;S227N;S227Q;S227R 46;36;36;36 55;45;45;45 24889237 Enhanced human receptor binding by H5 haemagglutinins. In both the avian and human receptor complexes of Delta133/Ile155Thr mutant, by comparison with the wild-type, two additional water molecules are observed in the vicinity of the mutant residues. 2014 Virology Result IV I155T 59 68 24889237 Enhanced human receptor binding by H5 haemagglutinins. In both the Ser227Asn/Gln196Arg. 2014 Virology Result IV Q196R;S227N;S227Q;S227R 22;12;12;12 31;21;21;21 24889237 Enhanced human receptor binding by H5 haemagglutinins. In contrast, human receptor binding by the Asn186Lys mutant increases 120-fold. 2014 Virology Result IV N186K 43 52 24889237 Enhanced human receptor binding by H5 haemagglutinins. In contrast, the other Egyptian strain specific substitution, Ser125Asn alone or in combination with the Delta133 and/or Ile155Thr mutations has no influence on the receptor binding properties. 2014 Virology Result IV S125N;I155T 62;121 71;130 24889237 Enhanced human receptor binding by H5 haemagglutinins. In contrast, the tyTy Delta133/Ile155Thr mutant exhibits increased binding for human receptor with little effect on binding of avian receptor. 2014 Virology Result IV I155T 31 40 24889237 Enhanced human receptor binding by H5 haemagglutinins. In order to understand the molecular basis of these differences in receptor binding, crystal structures of VN1194 Ser227Asn/Gln196Arg, Asn186Lys and tyTy Delta133/Ile155Thr mutant HAs in complex with receptor analogues were determined by X-ray crystallography. 2014 Virology Result IV Q196R;I155T;S227N;N186K;S227Q;S227R 124;163;114;135;114;114 133;172;123;144;123;123 24889237 Enhanced human receptor binding by H5 haemagglutinins. In the case of the Ser227Asn/Gln196Arg combination, avian receptor binding decreases ~50-fold relative to the VN1194 wild-type as opposed to the ~1200-fold decrease resulting from the Ser227Asn single mutation. 2014 Virology Result IV Q196R;S227N;S227N;S227Q;S227R 29;19;184;19;19 38;28;193;28;28 24889237 Enhanced human receptor binding by H5 haemagglutinins. In the tyTy Delta133/Ile155Thr human receptor complex, bound receptor is also shown close to the site of the deleted Ala-133 and the Ile155Thr substitution. 2014 Virology Result IV I155T;I155T 21;133 30;142 24889237 Enhanced human receptor binding by H5 haemagglutinins. Interestingly, when Delta133 and Ile155Thr were introduced simultaneously into tyTy H5, a small increase in avian receptor binding (~3-fold) and a significant increase of human receptor binding (~100-fold) were observed. 2014 Virology Result IV I155T 33 42 24889237 Enhanced human receptor binding by H5 haemagglutinins. Introduction of the double substitutions Ser227Asn/Gln196Arg and Asn186Lys/Gly143Arg, identified in viruses isolated from humans, indicated that the weakened avian receptor binding that resulted from Ser227Asn or Asn186Lys mutations alone can be partially restored by the second substitutions. 2014 Virology Result IV Q196R;G143R;S227N;N186K;S227N;N186K;S227Q;S227R;N186G;N186R 51;75;41;65;200;213;41;41;65;65 60;84;50;74;209;222;50;50;74;74 24889237 Enhanced human receptor binding by H5 haemagglutinins. Mutant VN1194 viruses containing HA substitutions - Ser227Asn, Gln196Arg, Asn186Lys, Gly143Arg and selected combinations - Ser227Asn/Gln196Arg and Asn186Lys/Gly143Arg (H3 numbering is used throughout the manuscript unless otherwise stated) and mutant A/turkey/Turkey/1/2005 (H5N1) (tyTy) viruses containing Delta133, Ile155Thr, Ser125Asn and combinations of them were generated by reverse genetics following PCR mutagenesis of their respective wild-type HA cDNAs. 2014 Virology Result IV Q196R;G143R;S227N;Q196R;N186K;G143R;S227N;N186K;I155T;S125N;S227Q;S227R;N186G;N186R 133;157;52;63;74;85;123;147;317;328;123;123;147;147 142;166;61;72;83;94;132;156;326;337;132;132;156;156 HA;HA 33;454 35;456 24889237 Enhanced human receptor binding by H5 haemagglutinins. Nevertheless, this structure confirms that the Gly143Arg substitution is 15 A away from the receptor binding site. 2014 Virology Result IV G143R 47 56 24889237 Enhanced human receptor binding by H5 haemagglutinins. Secondly, because of the Ile155Thr substitution, the hydrophobic surface, formed jointly by the side-chain of Ile-155 and the protruding Ala-133 in wild-type HA, is lost. 2014 Virology Result IV I155T 25 34 HA 158 160 24889237 Enhanced human receptor binding by H5 haemagglutinins. The crystal structure of an unbound form of the VN1194 Asn186Lys/Gly143Arg mutant was also determined, but the crystal was unsuitable for ligand soaking experiments. 2014 Virology Result IV G143R;N186K;N186G;N186R 65;55;55;55 74;64;64;64 24889237 Enhanced human receptor binding by H5 haemagglutinins. The human receptor complexes of the two VN1194 mutant HAs also illustrate that the bound receptors are in close proximity to the substitutions Ser227Asn and Asn186Lys, whereas the Gln196Arg substitution is located 17 A away from the nearest atom of the receptor. 2014 Virology Result IV S227N;N186K;Q196R 143;157;180 152;166;189 24889237 Enhanced human receptor binding by H5 haemagglutinins. The second substitutions were also found to increase human receptor binding compared with the Ser227Asn or Asn186Lys single mutants. 2014 Virology Result IV S227N;N186K 94;107 103;116 24889237 Enhanced human receptor binding by H5 haemagglutinins. The Ser227Asn/Gln196Arg and Asn186Lys/Gly143Arg mutants of VN1194 have increased binding for human receptors but reduced binding for avian receptors. 2014 Virology Result IV Q196R;G143R;S227N;N186K;S227Q;S227R;N186G;N186R 14;38;4;28;4;4;28;28 23;47;13;37;13;13;37;37 24889237 Enhanced human receptor binding by H5 haemagglutinins. The Ser227Asn/Gln196Arg mutant virus has the same avidity towards human receptor as that of the Gln196Arg single mutant, suggesting that increased human receptor binding by the double mutant is mainly brought about by the Gln196Arg substitution. 2014 Virology Result IV Q196R;S227N;Q196R;Q196R;S227Q;S227R 14;4;96;222;4;4 23;13;105;231;13;13 24889237 Enhanced human receptor binding by H5 haemagglutinins. The VN1194 mutants - Ser227Asn/Gln196Arg and Asn186Lys also exhibit significant decreases in avian receptor binding in BLI analyses. 2014 Virology Result IV Q196R;S227N;N186K;S227Q;S227R 31;21;45;21;21 40;30;54;30;30 24889237 Enhanced human receptor binding by H5 haemagglutinins. Three mutations, a deletion of residue 133 (Delta133), and two amino acid substitutions, Ile155Thr and Ser125Asn were originally identified as Egyptian strain specific mutations. 2014 Virology Result IV I155T;S125N;del 133 89;103;19 98;112;42 24889237 Enhanced human receptor binding by H5 haemagglutinins. Thus the combination of Delta133 and Ile155Thr mutations creates a more polar environment for the two extra water molecules. 2014 Virology Result IV I155T 37 46 24889237 Enhanced human receptor binding by H5 haemagglutinins. Thus, as with the Gly143Arg substitution, the Gln196Arg substitution is also likely to enhance receptor binding electrostatically, consistent with the observation that both substitutions increase the net-charge of HA by +1 and have similar enhancing effects in virus binding assays (compare. 2014 Virology Result IV G143R;Q196R 18;46 27;55 HA 214 216 24889237 Enhanced human receptor binding by H5 haemagglutinins. Unlike the VN1194 Ser227Asn/Gln196Arg and Asn186Lys mutants, the tyTy Delta133/Ile155Thr mutant shows a slight increase, rather than loss, in avian receptor binding. 2014 Virology Result IV Q196R;I155T;S227N;N186K;S227Q;S227R 28;79;18;42;18;18 37;88;27;51;27;27 24928037 The R35 residue of the influenza A virus NS1 protein has minimal effects on nuclear localization but alters virus replication through disrupting protein dimerization. 2C), no nucleolar localization was seen in the D39X infected cells. 2014 Virology Result IV D39X 47 51 24928037 The R35 residue of the influenza A virus NS1 protein has minimal effects on nuclear localization but alters virus replication through disrupting protein dimerization. 4A and B), suggesting that altered NS1 protein levels were not responsible for the reduced virus replication of rWSN NS1 D35A D39N/Y viruses. 2014 Virology Result IV D39Y;D35A;D39N 126;121;126 132;125;132 NS1;NS1 35;117 38;120 24928037 The R35 residue of the influenza A virus NS1 protein has minimal effects on nuclear localization but alters virus replication through disrupting protein dimerization. 6), indicating that the R35A mutation reduces NS1 protein levels, presumably due to greater amounts of protein degradation, and that the D39X mutations are restoring protein expression levels. 2014 Virology Result IV R35A;D39X 24;137 28;141 NS1 46 49 24928037 The R35 residue of the influenza A virus NS1 protein has minimal effects on nuclear localization but alters virus replication through disrupting protein dimerization. 7A, constructs with black NS1) or YFP1-NS1 R35A and YFP2-NS1 R35A. 2014 Virology Result IV R35A;R35A 43;61 47;65 NS1;NS1;NS1 26;39;57 29;42;60 24928037 The R35 residue of the influenza A virus NS1 protein has minimal effects on nuclear localization but alters virus replication through disrupting protein dimerization. 7B), indicating loss of NS1 dimerization in the NS1 R35A mutant protein. 2014 Virology Result IV R35A 52 56 NS1;NS1 24;48 27;51 24928037 The R35 residue of the influenza A virus NS1 protein has minimal effects on nuclear localization but alters virus replication through disrupting protein dimerization. A virus with the NS1 R38A mutation (rWSN NS1 R38A), which disrupts both NLS1 and RNA binding, was previously isolated. 2014 Virology Result IV R38A;R38A 21;45 25;49 NS1;NS1 17;41 20;44 24928037 The R35 residue of the influenza A virus NS1 protein has minimal effects on nuclear localization but alters virus replication through disrupting protein dimerization. As previously described, some of the cells infected with the rWSN NS1 R38A virus displayed punctate concentrations of NS1 throughout the cytoplasm. 2014 Virology Result IV R38A 70 74 NS1;NS1 66;118 69;121 24928037 The R35 residue of the influenza A virus NS1 protein has minimal effects on nuclear localization but alters virus replication through disrupting protein dimerization. Because a virus encoding only the NS1 R35A mutation was not rescued, it was hypothesized that the D39 mutations compensate for a loss of NS1 dimerization, as R35A was previously identified as critical for dimerization of the NS1 RNA binding domain. 2014 Virology Result IV R35A;R35A 38;158 42;162 NS1;NS1;NS1 34;137;225 37;140;228 24928037 The R35 residue of the influenza A virus NS1 protein has minimal effects on nuclear localization but alters virus replication through disrupting protein dimerization. In a portion of infected cells, all three NS1 R35A D39X viruses formed fluorescent puncta in the cytoplasm not observed in wild type rWSN-infected cells. 2014 Virology Result IV R35A;D39X 46;51 50;55 NS1 42 45 24928037 The R35 residue of the influenza A virus NS1 protein has minimal effects on nuclear localization but alters virus replication through disrupting protein dimerization. In order to study the effects of these amino acids on influenza virus replication, the basic amino acids in NLS1 were mutated to alanine, generating plasmids encoding NS1 R35A, R37A, R38A, and K41A (Table 1, top half "NLS"). 2014 Virology Result IV R35A;R37A;R38A;K41A 171;177;183;193 175;181;187;197 NS1 167 170 24928037 The R35 residue of the influenza A virus NS1 protein has minimal effects on nuclear localization but alters virus replication through disrupting protein dimerization. MDCK cells were transfected with YFP1/YFP2 constructs encoding each of the NS1 R35A D39X proteins. 2014 Virology Result IV R35A;D39X 79;84 83;88 NS1 75 78 24928037 The R35 residue of the influenza A virus NS1 protein has minimal effects on nuclear localization but alters virus replication through disrupting protein dimerization. Nucleolar localization was unaffected in rWSN NS1 R37A infected cells. 2014 Virology Result IV R37A 50 54 NS1 46 49 24928037 The R35 residue of the influenza A virus NS1 protein has minimal effects on nuclear localization but alters virus replication through disrupting protein dimerization. Plasmid expressed NS1 R35A and R35A D39X proteins show similar localizations. 2014 Virology Result IV R35A;R35A;D39X 22;31;36 26;35;40 NS1 18 21 24928037 The R35 residue of the influenza A virus NS1 protein has minimal effects on nuclear localization but alters virus replication through disrupting protein dimerization. Protein localization was examined by transfecting MDCK cells with wild type NS1, NS1 R35A, or one of the NS1 R35A D39X plasmids. 2014 Virology Result IV R35A;R35A;D39X 85;109;114 89;113;118 NS1;NS1;NS1 76;81;105 79;84;108 24928037 The R35 residue of the influenza A virus NS1 protein has minimal effects on nuclear localization but alters virus replication through disrupting protein dimerization. Similar to other viruses with mutations to NLS1, the NS1 protein was not excluded from the nucleus by R35A D39X mutations. 2014 Virology Result IV R35A;D39X 102;107 106;111 NS1 53 56 24928037 The R35 residue of the influenza A virus NS1 protein has minimal effects on nuclear localization but alters virus replication through disrupting protein dimerization. Similar to rWSN NS1 R38A- and K41A-infected cells. 2014 Virology Result IV R38A;K41A 20;30 24;34 NS1 16 19 24928037 The R35 residue of the influenza A virus NS1 protein has minimal effects on nuclear localization but alters virus replication through disrupting protein dimerization. Similar to virus infection, the expression levels of the NS1 R35A D39X proteins are not significantly different than wild type protein. 2014 Virology Result IV R35A;D39X 61;66 65;70 NS1 57 60 24928037 The R35 residue of the influenza A virus NS1 protein has minimal effects on nuclear localization but alters virus replication through disrupting protein dimerization. Subcellular localization of NS1 R35A and the NS1 R35A D39X proteins at 9 hours post transfection was similar for wild type and mutant NS1. 2014 Virology Result IV R35A;R35A;D39X 32;49;54 36;53;58 NS1;NS1;NS1 28;45;134 31;48;137 24928037 The R35 residue of the influenza A virus NS1 protein has minimal effects on nuclear localization but alters virus replication through disrupting protein dimerization. Taken together, these data indicate that viruses encoding NS1 protein with R37A and K41A mutations replicate in MDCK and Vero cells similarly to wild type virus. 2014 Virology Result IV R37A;K41A 75;84 79;88 NS1 58 61 24928037 The R35 residue of the influenza A virus NS1 protein has minimal effects on nuclear localization but alters virus replication through disrupting protein dimerization. The cells transfected with NS1 R35A D39A constructs had similar levels of YFP florescence when compared to NS1 wild type expressing cells, while the cells expressing NS1 R35A D39N or NS1 R35A D39Y expressed YFP MFI levels that were lower than that observed in NS1 wild type expressing cells. 2014 Virology Result IV D39Y;R35A;D39A;R35A;D39N;R35A 192;31;36;170;175;187 196;35;40;174;179;191 NS1;NS1;NS1;NS1;NS1 27;107;166;183;260 30;110;169;186;263 24928037 The R35 residue of the influenza A virus NS1 protein has minimal effects on nuclear localization but alters virus replication through disrupting protein dimerization. The degree of dimerization conferred by the D39X mutation seems to correlate with the overall replication of the recombinant viruses, with the NS1 R35A D39A protein having restored NS1 dimerization and recombinant virus replication more effectively on MDCK cells than either NS1 R35A D39N or NS1 R35A D39Y (Figure 3A). 2014 Virology Result IV D39X;R35A;D39A;R35A;D39N;R35A;D39Y 44;147;152;279;284;296;301 48;151;156;283;288;300;305 NS1;NS1;NS1;NS1 143;181;275;292 146;184;278;295 24928037 The R35 residue of the influenza A virus NS1 protein has minimal effects on nuclear localization but alters virus replication through disrupting protein dimerization. The distinct brightly fluorescent puncta seen in rWSN NS1 R35A D39X infected cells were not observed after cDNA expression of the proteins, indicating that the puncta form either in response to the expression of other viral proteins or are due to cellular responses to virus infection. 2014 Virology Result IV R35A;D39X 58;63 62;67 NS1 54 57 24928037 The R35 residue of the influenza A virus NS1 protein has minimal effects on nuclear localization but alters virus replication through disrupting protein dimerization. The expression of NS1 R35A was significantly lower than any of the other NS1 proteins. 2014 Virology Result IV R35A 22 26 NS1;NS1 18;73 21;76 24928037 The R35 residue of the influenza A virus NS1 protein has minimal effects on nuclear localization but alters virus replication through disrupting protein dimerization. The mutations at NS1 D39 were tested for their effects on NS1 R35A dimerization. 2014 Virology Result IV R35A 62 66 NS1;NS1 17;58 20;61 24928037 The R35 residue of the influenza A virus NS1 protein has minimal effects on nuclear localization but alters virus replication through disrupting protein dimerization. The NS1 R35A mutation reduces protein dimerization and mutations at amino acid 39 restore this activity. 2014 Virology Result IV R35A 8 12 NS1 4 7 24928037 The R35 residue of the influenza A virus NS1 protein has minimal effects on nuclear localization but alters virus replication through disrupting protein dimerization. The NS1 R38A mutation slightly attenuates virus replication, as previously demonstrated. 2014 Virology Result IV R38A 8 12 NS1 4 7 24928037 The R35 residue of the influenza A virus NS1 protein has minimal effects on nuclear localization but alters virus replication through disrupting protein dimerization. The NS1 wild type protein was found in the nucleolus of some infected cells and a loss of nucleolar localization was observed for cells infected with rWSN NS1 R38A and rWSN NS1 K41A. 2014 Virology Result IV R38A;K41A 159;177 163;181 NS1;NS1;NS1 4;155;173 7;158;176 24928037 The R35 residue of the influenza A virus NS1 protein has minimal effects on nuclear localization but alters virus replication through disrupting protein dimerization. The rWSN NS1 R35A D39A virus had similar replication kinetics and peak titers of infectious virus relative to rWSN, while the rWSN NS1 R35A D39N and rWSN R35A D39Y viruses reached significantly lower peak titers. 2014 Virology Result IV R35A;D39A;R35A;D39N;R35A;D39Y 13;18;135;140;154;159 17;22;139;144;158;163 NS1;NS1 9;131 12;134 24928037 The R35 residue of the influenza A virus NS1 protein has minimal effects on nuclear localization but alters virus replication through disrupting protein dimerization. The rWSN NS1 R35A virus was not isolated in three separate rescue attempts, but recombinant viruses with amino acid substitutions at position 39 of NS1 (D39A, D39N, or D39Y, Table 1, bottom half collectively referred to as "D39X") in addition to the R35A mutation were isolated. 2014 Virology Result IV D39X;R35A;D39A;D39N;D39Y;R35A 223;13;153;159;168;250 228;17;157;163;172;254 NS1;NS1 9;148 12;151 24928037 The R35 residue of the influenza A virus NS1 protein has minimal effects on nuclear localization but alters virus replication through disrupting protein dimerization. The rWSN NS1 R37A and rWSN NS1 K41A viruses were successfully rescued and plaque purified. 2014 Virology Result IV R37A;K41A 13;31 17;35 NS1;NS1 9;27 12;30 24928037 The R35 residue of the influenza A virus NS1 protein has minimal effects on nuclear localization but alters virus replication through disrupting protein dimerization. The viruses with NS1 R35A D39X mutations were tested for virus replication, NS1 protein expression and localization. 2014 Virology Result IV R35A;D39X 21;26 25;30 NS1;NS1 17;76 20;79 24928037 The R35 residue of the influenza A virus NS1 protein has minimal effects on nuclear localization but alters virus replication through disrupting protein dimerization. The YFP expression in each of the NS1 R35A D39X expressing cells was significantly higher than that observed in NS1 R35A expressing cells (Figure 7B bars with diagonal lines). 2014 Virology Result IV R35A;D39X;R35A 38;43;116 42;47;120 NS1;NS1 34;112 37;115 24928037 The R35 residue of the influenza A virus NS1 protein has minimal effects on nuclear localization but alters virus replication through disrupting protein dimerization. The YFP MFI for NS1 R35A constructs is similar to background fluorescence levels measured by transfecting cells with plasmids expressing YFP1 and YFP2-NS1. 2014 Virology Result IV R35A 20 24 NS1;NS1 16;151 19;154 24928037 The R35 residue of the influenza A virus NS1 protein has minimal effects on nuclear localization but alters virus replication through disrupting protein dimerization. These data supports the hypothesis that the D39 mutations partially restore the ability of NS1 R35A proteins to dimerize, thus allowing for recombinant virus replication. 2014 Virology Result IV R35A 95 99 NS1 91 94 24928037 The R35 residue of the influenza A virus NS1 protein has minimal effects on nuclear localization but alters virus replication through disrupting protein dimerization. These results indicate that rWSN NS1 R35A D39X viruses are able to replicate and express similar levels of NS1 protein compared to wild type virus but NS1 localization is affected. 2014 Virology Result IV R35A;D39X 37;42 41;46 NS1;NS1;NS1 33;107;151 36;110;154 24928037 The R35 residue of the influenza A virus NS1 protein has minimal effects on nuclear localization but alters virus replication through disrupting protein dimerization. To determine if RNA dimerization is reduced with a NS1 R35A mutation, cells were transfected with plasmids encoding YFP1-NS1 and YFP2-NS1. 2014 Virology Result IV R35A 55 59 NS1;NS1;NS1 51;121;134 54;124;137 24928037 The R35 residue of the influenza A virus NS1 protein has minimal effects on nuclear localization but alters virus replication through disrupting protein dimerization. To determine if the loss of dimerization occurs if only one of the NS1 molecules in a dimer has the R35A mutation, cells were transfected with plasmids encoding YFP1-NS1 and YFP2-NS1 R35A or YFP1-NS1 R35A with YFP2 NS1. 2014 Virology Result IV R35A;R35A;R35A 100;183;200 104;187;204 NS1;NS1;NS1;NS1;NS1 67;166;179;196;215 70;169;182;199;218 24928037 The R35 residue of the influenza A virus NS1 protein has minimal effects on nuclear localization but alters virus replication through disrupting protein dimerization. To explore how the NS1 R35A and D39X mutations were affecting NS1 expression and function, the proteins were expressed from cDNA expression vectors. 2014 Virology Result IV R35A;D39X 23;32 27;36 NS1;NS1 19;62 22;65 24928037 The R35 residue of the influenza A virus NS1 protein has minimal effects on nuclear localization but alters virus replication through disrupting protein dimerization. Viruses with NS1 R35A D39X mutations have altered NS1 subcellular localization patterns. 2014 Virology Result IV R35A;D39X 17;22 21;26 NS1;NS1 13;50 16;53 24928037 The R35 residue of the influenza A virus NS1 protein has minimal effects on nuclear localization but alters virus replication through disrupting protein dimerization. When NS1 wild type was expressed with NS1 R35A, YFP MFI levels were higher than that seen with NS1 R35A, but not as high as NS1 wild type. 2014 Virology Result IV R35A;R35A 42;99 46;103 NS1;NS1;NS1;NS1 5;38;95;124 8;41;98;127 24928037 The R35 residue of the influenza A virus NS1 protein has minimal effects on nuclear localization but alters virus replication through disrupting protein dimerization. When plaque diameters were measured, only the rWSN NS1 R35A D39Y virus had significantly smaller plaque diameters when compared to rWSN. 2014 Virology Result IV R35A;D39Y 55;60 59;64 NS1 51 54 24928037 The R35 residue of the influenza A virus NS1 protein has minimal effects on nuclear localization but alters virus replication through disrupting protein dimerization. While the rWSN R38A virus had smaller plaque diameter than rWSN, the rWSN R37A and rWSN K41A viruses had plaque diameters similar to rWSN. 2014 Virology Result IV R38A;R37A;K41A 15;74;88 19;78;92 24928037 The R35 residue of the influenza A virus NS1 protein has minimal effects on nuclear localization but alters virus replication through disrupting protein dimerization. YFP expression in cells expressing NS1 R35A fusion proteins was significantly lower than that observed in cells expressing NS1 wild type fusion proteins. 2014 Virology Result IV R35A 39 43 NS1;NS1 35;123 38;126 24940441 Analysis of the full-length genome of a novel strain of the H7N9 avian influenza virus. G228S and G186V mutations were also revealed to be present at the receptor binding site, with a mutation rate of 100%. 2014 Experimental and therapeutic medicine Result IV G228S;G186V 0;10 5;15 24940441 Analysis of the full-length genome of a novel strain of the H7N9 avian influenza virus. However, no A138S mutation was identified (Table II). 2014 Experimental and therapeutic medicine Result IV A138S 12 17 24940441 Analysis of the full-length genome of a novel strain of the H7N9 avian influenza virus. However, only one virus harbored the D701N mutation. 2014 Experimental and therapeutic medicine Result IV D701N 37 42 24940441 Analysis of the full-length genome of a novel strain of the H7N9 avian influenza virus. No E627K and D701N mutations were detected in the A/Changsha/2/2013 PB2 protein (Table II). 2014 Experimental and therapeutic medicine Result IV E627K;D701N 3;13 8;18 PB2 68 71 24940441 Analysis of the full-length genome of a novel strain of the H7N9 avian influenza virus. Other mutations in the new H7N9 virus isolated in 2013 included: P42S in the NS1 protein encoded by the NS gene; N30D and T215A in the M1 protein encoded by MP gene; and L89V in the PB2 protein (Table II). 2014 Experimental and therapeutic medicine Result IV P42S;N30D;T215A;L89V 65;113;122;170 69;117;127;174 M1;NS;NS1;PB2 135;104;77;182 137;106;80;185 24940441 Analysis of the full-length genome of a novel strain of the H7N9 avian influenza virus. Resistance gene loci analysis showed that the R294K mutation did not occur in the NA coding protein of the A/Changsha/2/2013 virus and other 50 H7N9 virus strains. 2014 Experimental and therapeutic medicine Result IV R294K 46 51 82 84 24940441 Analysis of the full-length genome of a novel strain of the H7N9 avian influenza virus. The PB2 gene of eight viruses among 51 new H7N9 viruses harbored the E627K mutation. 2014 Experimental and therapeutic medicine Result IV E627K 69 74 PB2 4 7 24940441 Analysis of the full-length genome of a novel strain of the H7N9 avian influenza virus. The Q226L amino acid mutation (the amino acid site encoded by the H3 type influenza virus corresponded to amino acid 235 in the present study) occurred in the HA protein of the new H7N9 viruses of human, avian and environmental origin. 2014 Experimental and therapeutic medicine Result IV Q226L 4 9 HA 159 161 24940441 Analysis of the full-length genome of a novel strain of the H7N9 avian influenza virus. The S31N mutation of the M2 protein encoded by the MP gene was identified in the 52 new H7N9 virus strains. 2014 Experimental and therapeutic medicine Result IV S31N 4 8 M2 25 27 25066276 Development and clinical testing of a simple, low-density gel element array for influenza identification, subtyping, and H275Y detection. 4.5 Influenza typing, subtyping and H275Y variant detection: clinical samples. 2014 Journal of virological methods Result IV H275Y 36 41 25066276 Development and clinical testing of a simple, low-density gel element array for influenza identification, subtyping, and H275Y detection. An important aspect of this study was to measure the performance of the pandemic N1/H275 probes on clinical samples that contained pandemic influenza A virus, given the observed cross-reactivity of pandemic N1 H275Y probe with the pandemic N1 WT amplicon (Table 2). 2014 Journal of virological methods Result IV H275Y 210 215 25066276 Development and clinical testing of a simple, low-density gel element array for influenza identification, subtyping, and H275Y detection. As expected from the analytical data, there was detectable signal on the pandemic N1 H275Y probe in 44 of 56 (78.6%) hybridizations that contained WT virus. 2014 Journal of virological methods Result IV H275Y 85 90 25066276 Development and clinical testing of a simple, low-density gel element array for influenza identification, subtyping, and H275Y detection. Both the seasonal WT and H275Y N1 variants were detectable in a mixture when present at >= 5% (Table 2). 2014 Journal of virological methods Result IV H275Y 25 30 25066276 Development and clinical testing of a simple, low-density gel element array for influenza identification, subtyping, and H275Y detection. Cross-reactivity between targets and probes that differ by only a single nucleotide is not uncommon, but the positive signal on the pandemic H275Y probe in a 100% WT population revealed the need to analyze and take into account the ratio of WT and H275Y SNR values when reporting on the detection of N1 variants. 2014 Journal of virological methods Result IV H275Y;H275Y 141;248 146;253 25066276 Development and clinical testing of a simple, low-density gel element array for influenza identification, subtyping, and H275Y detection. Data in Table 2 show that the microarray test is able to detect H275Y N1 variants in mixed populations of both seasonal and pandemic H1N1 RNA containing >=5% H275Y variant (10% mixtures were not tested). 2014 Journal of virological methods Result IV H275Y;H275Y 64;158 69;163 25066276 Development and clinical testing of a simple, low-density gel element array for influenza identification, subtyping, and H275Y detection. Despite the cross-hybridization, the calculated ratios of WT:H275Y N1 probe ratios ranged from 5.15 to 35.22 in 100% WT samples, and 0.008 to 2.76 in those containing the H275Y variant. 2014 Journal of virological methods Result IV H275Y;H275Y 61;171 66;176 25066276 Development and clinical testing of a simple, low-density gel element array for influenza identification, subtyping, and H275Y detection. Even with the slight cross-reactivity of the WT and H275Y probes observed in the clinical nasopharyngeal swab samples, the average H275Y probe signals from specific H275Y amplicons were significantly higher than H275Y signals obtained from non-specific hybridization (p = 4.82x10-16 for pandemic H1N1; p <0.00005 for seasonal H1N1, Student's t-test), data which can now be used to generate an automated decision rule for routine diagnostic use. 2014 Journal of virological methods Result IV H275Y;H275Y;H275Y;H275Y 52;131;165;212 57;136;170;217 25066276 Development and clinical testing of a simple, low-density gel element array for influenza identification, subtyping, and H275Y detection. Figure 1 shows the average N1 WT and H275Y probe SNR values for pandemic and seasonal viruses, with and without the presence of the H275Y variant. 2014 Journal of virological methods Result IV H275Y;H275Y 37;132 42;137 25066276 Development and clinical testing of a simple, low-density gel element array for influenza identification, subtyping, and H275Y detection. For the purpose of reporting the presence of an H275Y variant in clinical samples (below), however, we used a conservative SNR ratio of <= 1 for positively identifying an H275Y variant in the clinical samples, which implies that the sample would need >25% variant in order to report a positive detection of a seasonal or pandemic H275Y N1 variant. 2014 Journal of virological methods Result IV H275Y;H275Y;H275Y 48;171;330 53;176;335 25066276 Development and clinical testing of a simple, low-density gel element array for influenza identification, subtyping, and H275Y detection. Given the slight cross-reactivity of the pH275Y probe to the WT N1 amplicon, however, the pandemic H275Y signal (SNR = 91.03 at 1% H275Y variant) could in part be due to hybridization of the WT amplicon instead of the H275Y amplicon. 2014 Journal of virological methods Result IV H275Y;H275Y;H275Y 99;131;218 104;136;223 25066276 Development and clinical testing of a simple, low-density gel element array for influenza identification, subtyping, and H275Y detection. H275Y variant detection sensitivity and specificity. 2014 Journal of virological methods Result IV H275Y 0 5 25066276 Development and clinical testing of a simple, low-density gel element array for influenza identification, subtyping, and H275Y detection. However, the pandemic N1 H275Y probe was weakly cross-reactive with the pandemic N1 WT amplicon (SNR=9.37 at 100% WT). 2014 Journal of virological methods Result IV H275Y 25 30 25066276 Development and clinical testing of a simple, low-density gel element array for influenza identification, subtyping, and H275Y detection. In addition, the pandemic N1 WT probe was specific to the WT amplicon, with no observable cross-reactivity to the pandemic H275Y amplicon. 2014 Journal of virological methods Result IV H275Y 123 128 25066276 Development and clinical testing of a simple, low-density gel element array for influenza identification, subtyping, and H275Y detection. Influenza RNA titers were at or below the LoDs of the seasonal H275Y sub-typing probes (Table 1) for three discordant sH275Y tests. 2014 Journal of virological methods Result IV H275Y 63 68 25066276 Development and clinical testing of a simple, low-density gel element array for influenza identification, subtyping, and H275Y detection. Interestingly, 28 of 55 (50.9%) tests containing 100% WT virus displayed slight cross-reactivity with the seasonal N1 H275Y probe (SNR ratio = 9.09), a result that was not observed in analytical experiments. 2014 Journal of virological methods Result IV H275Y 118 123 25066276 Development and clinical testing of a simple, low-density gel element array for influenza identification, subtyping, and H275Y detection. No cross-reactive signals were observed between the WT probe and the seasonal H275Y samples. 2014 Journal of virological methods Result IV H275Y 78 83 25066276 Development and clinical testing of a simple, low-density gel element array for influenza identification, subtyping, and H275Y detection. No evidence of the H275Y variant was found. 2014 Journal of virological methods Result IV H275Y 19 24 25066276 Development and clinical testing of a simple, low-density gel element array for influenza identification, subtyping, and H275Y detection. Perfectly matched pandemic N1 microarray probes were positive for pandemic N1 amplicons in 56/58 (96.6%), 22/22 (100%), and 40/40 (100%) of hybridizations with 100% WT, mixed genotype, and 100% H275Y viruses, respectively. 2014 Journal of virological methods Result IV H275Y 194 199 25066276 Development and clinical testing of a simple, low-density gel element array for influenza identification, subtyping, and H275Y detection. Table 2 shows that microarray test specificity for the seasonal N1 probes (H275 WT and H275Y variant) were 100% specific for their intended N1 amplicons. 2014 Journal of virological methods Result IV H275Y 87 92 25066276 Development and clinical testing of a simple, low-density gel element array for influenza identification, subtyping, and H275Y detection. The pandemic WT and H275Y N1 variants were detected at concentrations as low as 1% of the total mixed population and at approximately 1000 RNA gc per reaction. 2014 Journal of virological methods Result IV H275Y 20 25 25066276 Development and clinical testing of a simple, low-density gel element array for influenza identification, subtyping, and H275Y detection. The seasonal N1 microarray probes were specific for the seasonal H1N1 viruses, consistent with the analytical data: 55 of 60 (91.7%) WT and 57 of 60 (95.0%) H275Y virus-positive samples generated positive results with the corresponding probes, consistent with prior DNA sequencing data. 2014 Journal of virological methods Result IV H275Y 157 162 25066276 Development and clinical testing of a simple, low-density gel element array for influenza identification, subtyping, and H275Y detection. There were no false positive probe responses beyond the H275Y target cross-reactivity described above. 2014 Journal of virological methods Result IV H275Y 56 61 25066276 Development and clinical testing of a simple, low-density gel element array for influenza identification, subtyping, and H275Y detection. These results again demonstrate the importance and value of using SNR ratios for H275Y detection, rather than the SNR values from individual probes, since analytical test behavior estimated from analytical experiments does not always translate directly to clinical samples or the actual use environment. 2014 Journal of virological methods Result IV H275Y 81 86 25066276 Development and clinical testing of a simple, low-density gel element array for influenza identification, subtyping, and H275Y detection. These results indicate that a threshold of N1 WT:H275Y probe ratios can detect the presence of pandemic H275Y variants that differ by a single nucleotide with high confidence, even when microarray hybridization is not 100% specific. 2014 Journal of virological methods Result IV H275Y;H275Y 49;104 54;109 25066276 Development and clinical testing of a simple, low-density gel element array for influenza identification, subtyping, and H275Y detection. To verify that these samples were indeed 100% WT, RNA was re-tested with an in-house, real-time RT-PCR H275Y TaqMan assay that is specific for the seasonal influenza A N1 gene. 2014 Journal of virological methods Result IV H275Y 103 108 25119465 Functional balance between the hemagglutinin and neuraminidase of influenza A(H1N1)pdm09 HA D222 variants. All seven isolates harbored P83S and I321V substitutions in the HA. 2014 PloS one Result IV P83S;I321V 28;37 32;42 HA 64 66 25119465 Functional balance between the hemagglutinin and neuraminidase of influenza A(H1N1)pdm09 HA D222 variants. All viruses except for Ste09G harbored the NA substitution V106I. 2014 PloS one Result IV V106I 59 64 43 45 25119465 Functional balance between the hemagglutinin and neuraminidase of influenza A(H1N1)pdm09 HA D222 variants. Altogether, these results indicate that the HA D222G substitution induced a shift in the binding profile by increasing the affinity for SAalpha-2,3 and decreasing the affinity for SAalpha-2,6, while the presence of N or E at position 222 increased the binding affinity for both SAalpha-2,3 and SAalpha-2,6 substrates. 2014 PloS one Result IV D222G 47 52 HA 44 46 25119465 Functional balance between the hemagglutinin and neuraminidase of influenza A(H1N1)pdm09 HA D222 variants. Despite differing from the Lyon09D and Ste09G NA only by the M15I substitution, Ste10D NA activity was two to ten-fold higher (Table 5). 2014 PloS one Result IV M15I 61 65 NA;NA 46;87 48;89 25119465 Functional balance between the hemagglutinin and neuraminidase of influenza A(H1N1)pdm09 HA D222 variants. In contrast, the matrix protein (M) had one substitution (V80I or N133I). 2014 PloS one Result IV V80I;N133I 58;66 62;71 M;M 33;17 34;23 25119465 Functional balance between the hemagglutinin and neuraminidase of influenza A(H1N1)pdm09 HA D222 variants. Lyon09D, Reu10G and Ste10D also harbored the NA N248D substitution. 2014 PloS one Result IV N248D 48 53 45 47 25119465 Functional balance between the hemagglutinin and neuraminidase of influenza A(H1N1)pdm09 HA D222 variants. Lyon11E and Reu10G were phylogenetically related to genetic group 6, characterized by the mutations D97N and S185T in HA. 2014 PloS one Result IV D97N;S185T 100;109 104;114 HA 118 120 25119465 Functional balance between the hemagglutinin and neuraminidase of influenza A(H1N1)pdm09 HA D222 variants. The HA sequences of Lyon09D and Ste09G differed by D222G and L32I, while those of Ste10D, Lim10G and Lyon10N were strictly identical except for the 222 polymorphism. 2014 PloS one Result IV D222G;L32I 51;61 56;65 HA 4 6 25119465 Functional balance between the hemagglutinin and neuraminidase of influenza A(H1N1)pdm09 HA D222 variants. The NA protein sequences of Lyon09D and Ste09G were identical and apart from M15I, so too were those of Ste10D, Lim10G and Lyon10N. 2014 PloS one Result IV M15I 77 81 4 6 25119465 Functional balance between the hemagglutinin and neuraminidase of influenza A(H1N1)pdm09 HA D222 variants. Those isolated in 2010, (Ste10D, Lim10G, Lyon10N) were phylogenetically related to the genetic group 3, characterized by the mutations A134T and S183P in HA. 2014 PloS one Result IV A134T;S183P 135;145 140;150 HA 154 156 25124927 Characterization of drug-resistant influenza A(H7N9) variants isolated from an oseltamivir-treated patient in Taiwan. Applying the WHO Antiviral Working Group criteria, NA-R292K virus was characterized as exhibiting highly reduced inhibition by oseltamivir and peramivir and reduced inhibition by zanamivir, laninamivir, and A-315675. 2015 The Journal of infectious diseases Result IV R292K 54 59 51 53 25124927 Characterization of drug-resistant influenza A(H7N9) variants isolated from an oseltamivir-treated patient in Taiwan. In all instances, substitutions occurred at the second nucleotide in the respective triplet: for R292K, AGG AAG; for E119V, GAA GTA; for I222R, ATA AGA; and for I222K, ATA AAA. 2015 The Journal of infectious diseases Result IV R292K;E119V;I222R;I222K 97;117;137;161 102;122;142;166 25124927 Characterization of drug-resistant influenza A(H7N9) variants isolated from an oseltamivir-treated patient in Taiwan. In contrast, NA-R292K virus exhibited delayed growth, with infectious titers 2-3 logs lower than those of the other viruses and the highest titer 48 hours after infection. 2015 The Journal of infectious diseases Result IV R292K 16 21 13 15 25124927 Characterization of drug-resistant influenza A(H7N9) variants isolated from an oseltamivir-treated patient in Taiwan. In MDCK-SIAT1 cells, NA-WT, NA-E119V, NA-I222K, and NA-I222R viruses replicated as efficiently as in MDCK cells, with titers peaking 24 hours after infection (Figure 1B). 2015 The Journal of infectious diseases Result IV E119V;I222K;I222R 31;41;55 36;46;60 NA;NA;NA;NA 21;28;38;52 23;30;40;54 25124927 Characterization of drug-resistant influenza A(H7N9) variants isolated from an oseltamivir-treated patient in Taiwan. Inflammatory cell counts (Figure 3B) and total protein concentrations (Figure 3C) in nasal wash specimens peaked on days 5 and 7 after inoculation with all 5 viruses; values for both parameters were lower (P < .05) in NA-R292K virus-infected animals during days 5-9 after inoculation. 2015 The Journal of infectious diseases Result IV R292K 221 226 218 220 25124927 Characterization of drug-resistant influenza A(H7N9) variants isolated from an oseltamivir-treated patient in Taiwan. Intermittent pyrexia (>=1.5 C above baseline) was detected early and late after inoculation in 1 animal infected with NA-I222R virus early and late after inoculation. 2015 The Journal of infectious diseases Result IV I222R 121 126 118 120 25124927 Characterization of drug-resistant influenza A(H7N9) variants isolated from an oseltamivir-treated patient in Taiwan. NA-E119V and NA-I222R viruses showed intermediate virulence. 2015 The Journal of infectious diseases Result IV E119V;I222R 3;16 8;21 NA;NA 0;13 2;15 25124927 Characterization of drug-resistant influenza A(H7N9) variants isolated from an oseltamivir-treated patient in Taiwan. NA-E119V virus caused 100% lethality in animals infected with 104 TCID50 (Figure 2H). 2015 The Journal of infectious diseases Result IV E119V 3 8 0 2 25124927 Characterization of drug-resistant influenza A(H7N9) variants isolated from an oseltamivir-treated patient in Taiwan. NA-E119V virus exhibited reduced inhibition by oseltamivir only. 2015 The Journal of infectious diseases Result IV E119V 3 8 0 2 25124927 Characterization of drug-resistant influenza A(H7N9) variants isolated from an oseltamivir-treated patient in Taiwan. NA-E119V virus had the second highest oseltamivir IC50 (an 84-fold increase), together with a 9-fold increase in the zanamivir IC50, with no effect on inhibition by peramivir, laninamivir, or A-315675. 2015 The Journal of infectious diseases Result IV E119V 3 8 0 2 25124927 Characterization of drug-resistant influenza A(H7N9) variants isolated from an oseltamivir-treated patient in Taiwan. NA-I222K and NA-I222R viruses shared a similar resistance profile; oseltamivir IC50 values were elevated by 32-37-fold, while 6-14-fold increases were detected for the remaining 4 NAIs. 2015 The Journal of infectious diseases Result IV I222K;I222R 3;16 8;21 NA;NA;NAI 0;13;180 2;15;184 25124927 Characterization of drug-resistant influenza A(H7N9) variants isolated from an oseltamivir-treated patient in Taiwan. NA-I222K virus was the most virulent (101.5 TCID50), while NA-WT and NA-R292K viruses exhibited 1000-fold lower virulence (104.5 TCID50). 2015 The Journal of infectious diseases Result IV I222K;R292K 3;72 8;77 NA;NA;NA 0;59;69 2;61;71 25124927 Characterization of drug-resistant influenza A(H7N9) variants isolated from an oseltamivir-treated patient in Taiwan. NA-R292K virus had the highest median inhibitory concentration (IC50) values (Table 2), with the >1000-fold increase in oseltamivir and peramivir IC50 values consistent with previous reports. 2015 The Journal of infectious diseases Result IV R292K 3 8 0 2 25124927 Characterization of drug-resistant influenza A(H7N9) variants isolated from an oseltamivir-treated patient in Taiwan. NA-R292K virus titers were approximately 1-2 logs lower than that of NA-WT virus on days 1, 2 (P = .004), and 3 (P = .003) after inoculation. 2015 The Journal of infectious diseases Result IV R292K 3 8 NA;NA 0;69 2;71 25124927 Characterization of drug-resistant influenza A(H7N9) variants isolated from an oseltamivir-treated patient in Taiwan. NA-WT sequence differed from the E1 consensus by 4 amino acid changes: PB2-V227M, PA-V554I, HA-N281S, and NS1-K126R. 2015 The Journal of infectious diseases Result IV V227M;V554I;N281S;K126R 75;85;95;110 80;90;100;115 HA;NA;NS1;PA;PB2 92;0;106;82;71 94;2;109;84;74 25124927 Characterization of drug-resistant influenza A(H7N9) variants isolated from an oseltamivir-treated patient in Taiwan. Notably, ferrets infected with NA-R292K virus did not experience weight loss and gained body weight at a faster rate than those infected with the other influenza A(H7N9) viruses tested. 2015 The Journal of infectious diseases Result IV R292K 34 39 31 33 25124927 Characterization of drug-resistant influenza A(H7N9) variants isolated from an oseltamivir-treated patient in Taiwan. Notably, replication of NA-R292K virus was delayed; no virus was detected in 2 of 4 animals on day 1 after inoculation, yet these 2 ferrets shed virus on day 7 after inoculation. 2015 The Journal of infectious diseases Result IV R292K 27 32 24 26 25124927 Characterization of drug-resistant influenza A(H7N9) variants isolated from an oseltamivir-treated patient in Taiwan. NS1-K126R was rare, with a K/R mixture detected in the NS of NA-R292K only. 2015 The Journal of infectious diseases Result IV K126R;R292K 4;64 9;69 NA;NS;NS1 61;55;0 63;57;3 25124927 Characterization of drug-resistant influenza A(H7N9) variants isolated from an oseltamivir-treated patient in Taiwan. One substitution, PB2-V227M, was unique to this virus and not found in other influenza A(H7N9) sequences available in GISAID. 2015 The Journal of infectious diseases Result IV V227M 22 27 PB2 18 21 25124927 Characterization of drug-resistant influenza A(H7N9) variants isolated from an oseltamivir-treated patient in Taiwan. Quantitative virus shedding, defined as the area under the curve (AUC) during days 1-6 (days 1-7 for NA-R292K virus), was measured and expressed as log10 TCID50/mL. 2015 The Journal of infectious diseases Result IV R292K 104 109 101 103 25124927 Characterization of drug-resistant influenza A(H7N9) variants isolated from an oseltamivir-treated patient in Taiwan. The acquisition of NA-I222R or NA-I222K resulted in reduced inhibition by oseltamivir and laninamivir, while NA-I222R also conferred reduced inhibition by zanamivir. 2015 The Journal of infectious diseases Result IV I222R;I222K;I222R 22;34;112 27;39;117 NA;NA;NA 19;31;109 21;33;111 25124927 Characterization of drug-resistant influenza A(H7N9) variants isolated from an oseltamivir-treated patient in Taiwan. The AUCs were 29.3 for NA-WT, 29.0 for NA-E119V, 26.6 for NA-I222K, 25.9 for NA-I222R, and 26.6 for NA-R292K viruses, indicating a trend toward lower replication rates of NA variants in the ferret's upper respiratory tract, with the exception of NA-E119V virus. 2015 The Journal of infectious diseases Result IV E119V;I222K;I222R;R292K;E119V 42;61;80;103;249 47;66;85;108;254 NA;NA;NA;NA;NA;NA;NA 23;39;58;77;100;171;246 25;41;60;79;102;173;248 25124927 Characterization of drug-resistant influenza A(H7N9) variants isolated from an oseltamivir-treated patient in Taiwan. The emergence of virus with R292K was detected in samples collected on 22 April and 25 April; a 292R/K mixture was reported in the sample collected on 24 April. 2015 The Journal of infectious diseases Result IV R292K 28 33 25124927 Characterization of drug-resistant influenza A(H7N9) variants isolated from an oseltamivir-treated patient in Taiwan. The HAs of 4 plaque-purified viruses differed from the E1 consensus sequence by a single amino acid (N281S), whereas NA-R292K contained D340G (Table 1). 2015 The Journal of infectious diseases Result IV N281S;R292K;D340G 101;120;136 106;125;141 117 119 25124927 Characterization of drug-resistant influenza A(H7N9) variants isolated from an oseltamivir-treated patient in Taiwan. The most abundant plaque-purified NA variant was I222R (49%), followed by R292K (23%), E119V (22%), I222K (4%), and wild type (WT; 1%). 2015 The Journal of infectious diseases Result IV I222R;R292K;E119V;I222K 49;74;87;100 54;79;92;105 34 36 25124927 Characterization of drug-resistant influenza A(H7N9) variants isolated from an oseltamivir-treated patient in Taiwan. The NA-E119V virus had arginine (R) at PA-556, while the other viruses had the glutamine (Q) consensus sequence at this position. 2015 The Journal of infectious diseases Result IV E119V 7 12 NA;PA 4;39 6;41 25124927 Characterization of drug-resistant influenza A(H7N9) variants isolated from an oseltamivir-treated patient in Taiwan. The NA-I222K virus possessed asparagine (N) in PB2-714; other viruses contained serine (S). 2015 The Journal of infectious diseases Result IV I222K 7 12 NA;PB2 4;47 6;50 25124927 Characterization of drug-resistant influenza A(H7N9) variants isolated from an oseltamivir-treated patient in Taiwan. The NA-R292K virus titer was significantly lower than that for WT 24 (P < .0001) and 72 (P = .0175) hours after infection (Figure 1C). 2015 The Journal of infectious diseases Result IV R292K 7 12 4 6 25124927 Characterization of drug-resistant influenza A(H7N9) variants isolated from an oseltamivir-treated patient in Taiwan. The Taiwan/1 viruses contained M2-S31N, a marker of resistance to M2 blockers found in all 2013-2014 influenza A(H7N9) viruses. 2015 The Journal of infectious diseases Result IV S31N 34 38 M2;M2 31;66 33;68 25124927 Characterization of drug-resistant influenza A(H7N9) variants isolated from an oseltamivir-treated patient in Taiwan. Therefore, replication of NA-R292K virus was notably attenuated in MDCK-SIAT1 cells but not in MDCK cells. 2015 The Journal of infectious diseases Result IV R292K 29 34 26 28 25124927 Characterization of drug-resistant influenza A(H7N9) variants isolated from an oseltamivir-treated patient in Taiwan. Unexpectedly, <10 TCID50 were required to infect 50% of animals with the 4 NA variant viruses, including NA-R292K virus (Table 1). 2015 The Journal of infectious diseases Result IV R292K 108 113 NA;NA 75;105 77;107 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. 3b), suggesting that the wild-type and the PB1-V43I viruses possess comparable viral fitness in vitro under minimal selection pressure. 2014 Nature communications Result IV V43I 47 51 PB1 43 46 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. A similar trend was observed when we calculated the mutational frequency in the NA gene of the H3N2 wild-type and the PB1-V43I viruses; the wild-type H3N2 virus (7.06 mutations per 104 nucleotides) showed 1.49-fold higher mutational frequency than that of the PB1-V43I virus (4.75 mutations per 104 nucleotides) (Supplementary Table 6). 2014 Nature communications Result IV V43I;V43I 122;264 126;268 NA;PB1;PB1 80;118;260 82;121;263 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. All mice (10 out of 10) in the wild-type group died within 14 days post-inoculation while only 4 of 10 mice died in the PB1-V43I virus group at 20 days post-inoculation. 2014 Nature communications Result IV V43I 124 128 PB1 120 123 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. Although there is a reduction in favipiravir sensitivity observed for the VN04 PB1-V43I polymerase complex by the mini-genome assay, the recombinant H5N1 VN04 virus carrying the PB1-V43I mutation (EC50=17.85; 95% CI 11.69-27.27 muM) did not show significant resistance to favipiravir while compared to its wild-type counterpart (EC50=18.97; 95% CI 12.26 to 29.38 muM) at MOI of 0.001. 2014 Nature communications Result IV V43I;V43I 83;182 87;186 PB1;PB1 79;178 82;181 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. Applying clonal sequencing, the mutational frequency in the HA gene of the recombinant H5N1 virus carrying the PB1-V43I mutation was lower compared to that of its wild-type counterpart by a factor of 1.39-1.55 (Figure 5d, Supplementary Table 9). 2014 Nature communications Result IV V43I 115 119 HA;PB1 60;111 62;114 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. Applying the mini-genome assay, the calculated EC50 as determined of the PB1-V43I H3N2 and PB1-V43I H5N1 viruses were shown to be 49.11 muM (95% CI 41.05 to 58.76 muM) and 59.66 muM (95% CI 41.00 to 86.81 muM), respectively; while those of the H3N2 and H5N1 wild-type polymerases were determined to be only 27.88 muM (95% CI 22.28 to 34.88 muM) and 40.08 muM (95% CI 33.84 to 47.47 muM), respectively. 2014 Nature communications Result IV V43I;V43I 77;95 81;99 PB1;PB1 73;91 76;94 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. As observed previously, the V43I mutation alone reduced polymerase activity by approximately 40% when compared to that of the wild-type virus; however, the combination of V43I and the A370V mutations increased the polymerase activity by 160% when compared to that of the wild-type virus (Supplementary Table 4). 2014 Nature communications Result IV V43I;V43I;A370V 28;171;184 32;175;189 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. As ribavirin is a purine analog, it is possible that the PB1-V43I mutant which exhibited altered selectivity to ribavirin would possess altered binding affinity for guanosine triphosphate (GTP) or adenosine triphosphate (ATP). 2014 Nature communications Result IV V43I 61 65 PB1 57 60 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. At an inoculation dose of 100 pfu, all mice in the wild-type group had died by day 11 post-inoculation compared with 5 out of 9 mice in the PB1-V43I virus group; three out of 9 mice with PB1-V43I survived at the end point of the experiment (20 days post-inoculation). 2014 Nature communications Result IV V43I;V43I 144;191 148;195 PB1;PB1 140;187 143;190 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. At day 3, the mutational frequencies in the HA gene of the wild-type H5N1 virus (8.2 mutations per 104 nucleotides) was higher than that of the PB1-V43I mutant virus (4.4 mutations per 104 nucleotides) by a factor of 1.86 (Fisher's exact test, P=0.0143). 2014 Nature communications Result IV V43I 148 152 HA;PB1 44;144 46;147 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. At day 6 and 8, the viral titre in the brain was observed to be higher for the wild-type group compared with the PB1-V43I mutant group (t test, P=0.0267). 2014 Nature communications Result IV V43I 117 121 PB1 113 116 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. Comparable virus replication efficiency was observed for the Wuhan wild-type and PB1-V43I mutant viruses at 37 C. 2014 Nature communications Result IV V43I 85 89 PB1 81 84 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. Compared to its wild-type counterpart, recombinant H5N1 virus with the PB1-V43I mutation showed reduced sensitivity to increasing concentrations of ribavirin in MDCK cells. 2014 Nature communications Result IV V43I 75 79 PB1 71 74 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. Comparing to the VN04 polymerase complex containing the PB1-M40L mutation, the combination of the M40L and V43I PB1 mutations retains resistance to ribavirin. 2014 Nature communications Result IV M40L;M40L;V43I 60;98;107 64;102;111 PB1;PB1 56;112 59;115 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. First, we identified that the mutations conferring the ribavirin-resistance phenotype resided in PB1, as co-transfecting the PB1 plasmid harboring the four mutations (V43I, V191I, A661T, S741F) identified from the clones derived from the N4 replicate with the PB2, PA, or NP plasmids derived from the wild-type virus, exhibited reduced sensitivity to ribavirin. 2014 Nature communications Result IV V43I;V191I;A661T;S741F 167;173;180;187 171;178;185;192 NP;PA;PB1;PB1;PB2 272;265;97;125;260 274;267;100;128;263 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. Fitness of the PB1-V43I recombinant virus in vitro. 2014 Nature communications Result IV V43I 19 23 PB1 15 18 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. For the H3N2 recombinant viruses, the PB1-V43I virus replicated to half a log lower titre than that of the wild-type virus at 6 hours post-infection; however, both viruses reached comparable titers after 8 hours post-infection. 2014 Nature communications Result IV V43I 42 46 PB1 38 41 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. For the H5N1 recombinant viruses, both the wild-type and the PB1-V43I viruses replicated to comparable titers. 2014 Nature communications Result IV V43I 65 69 PB1 61 64 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. Importantly, the PB1-V43I mutation did not significantly reduce the polymerase activity of the H5N1 polymerase complex [wild-type polymerase activity is 12.64+-0.5366 (mean firefly/renilla luciferase ratio+-standard deviation), whereas for V43I mutant is 12.98+-0.3647]. 2014 Nature communications Result IV V43I;V43I 21;240 25;244 PB1 17 20 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. In addition to applying clonal sequencing, we also directly sequenced the HA gene of plaques formed by the Wuhan wild-type and PB1-V43I viruses in MDCK cells by Sanger sequencing. 2014 Nature communications Result IV V43I 131 135 HA;PB1 74;127 76;130 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. In addition, we determined the viral replication kinetics with an MOI of 0.01 of the Wuhan wild-type and V43I mutant viruses at 33 C, 37 C, and 39 C in MDCK cells. 2014 Nature communications Result IV V43I 105 109 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. In contrast, increased guanosine (<= 40 muM) did not reverse the inhibitory effects of ribavirin on PB1-V43I as efficiently as that on the wild-type PB1 protein, suggesting that the PB1-V43I protein may possess a reduced affinity to GTP at low concentrations of guanosine. 2014 Nature communications Result IV V43I;V43I 104;186 108;190 PB1;PB1;PB1 100;149;182 103;152;185 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. In summary, we identified a single V43I mutation in PB1 protein that confers resistance to ribavirin in both the human-origin Wuhan95 and the avian-origin VN04 polymerase complexes. 2014 Nature communications Result IV V43I 35 39 PB1 52 55 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. Interestingly, we observed that the PB1-V43I protein exhibited more significant reduction of polymerase activity under increasing concentration of guanosine. 2014 Nature communications Result IV V43I 40 44 PB1 36 39 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. MDCK cells were infected at MOI 0.1 by a mixture of the H3N2 wild-type and the PB1-V43I variant at three different ratios. 2014 Nature communications Result IV V43I 83 87 PB1 79 82 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. No additional mutation was noted in the other seven segments of the PB1-V43I virus after 5 passages in MDCK cells by Sanger sequencing. 2014 Nature communications Result IV V43I 72 76 PB1 68 71 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. Overall, our results showed that a single V43I mutation in PB1 protein confers reduced genetic diversity of the H5N1 VN04 virus at an early time point (day 3) but not at later time point (day 8) post-inoculation in vivo. 2014 Nature communications Result IV V43I 42 46 PB1 59 62 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. Overall, the results suggest that the V43I mutation increased the nucleoside selectivity of the PB1 protein. 2014 Nature communications Result IV V43I 38 42 PB1 96 99 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. Overall, we identified the V43I mutation confers reduced sensitivity to both ribavirin. 2014 Nature communications Result IV V43I 27 31 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. PB1-V43I confers increased guanosine selectivity. 2014 Nature communications Result IV V43I 4 8 PB1 0 3 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. PB1-V43I confers reduced favipiravir sensitivity. 2014 Nature communications Result IV V43I 4 8 PB1 0 3 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. PB1-V43I confers ribavirin resistance to H3N2 and H5N1 IAVs. 2014 Nature communications Result IV V43I 4 8 PB1 0 3 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. PB1-V43I H5N1 IAV exhibited reduced pathogenicity in mice. 2014 Nature communications Result IV V43I 4 8 PB1 0 3 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. PB1-V43I mutation in the polymerase complex of either Wuhan95 (H3N2) or VN04 (H5N1) exhibited decreased sensitivity to favipiravir compared to that of the wild-type polymerase complexes, although the difference is not as significant as observed for ribavirin. 2014 Nature communications Result IV V43I 4 8 PB1 0 3 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. PB1-V43I reduces H3N2 and H5N1 mutational frequencies. 2014 Nature communications Result IV V43I 4 8 PB1 0 3 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. S741F mutation was found to confer minimal resistance to ribavirin. 2014 Nature communications Result IV S741F 0 5 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. Similar to the previous observation, the ratio of wild-type and V43I mutant remain comparable before and after one passage in MDCK cells (Figure 3c), suggesting that the PB1-V43I mutation did not compromise viral fitness under direct competition assay with the wild-type virus. 2014 Nature communications Result IV V43I;V43I 64;174 68;178 PB1 170 173 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. Since ribavirin may act as a mutagen for IAV RdRP, a reduced mutation frequency would be expected for the PB1-V43I virus after passaging in the presence of ribavirin. 2014 Nature communications Result IV V43I 110 114 PB1 106 109 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. suggesting that the PB1-V43I showed increased selectivity for nucleosides over the wild-type PB1 protein under the biased intracellular NTP concentrations. 2014 Nature communications Result IV V43I 24 28 PB1;PB1 20;93 23;96 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. The comparable mutational frequency between the wild-type and PB1-V43I mutant viruses in the mouse lungs at day 8 post-inoculation could be a result of strong selection pressure posed by host immune response. 2014 Nature communications Result IV V43I 66 70 PB1 62 65 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. The difference in lethality between wild-type and PB1-V43I is more pronounced when a lower inoculation dose of 10 pfu was used. 2014 Nature communications Result IV V43I 54 58 PB1 50 53 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. The difference in replication efficiency between the wild-type and PB1-V43I viruses was most noticeable at 39 C as the V43I mutant virus replicated to lower viral titers while compared to its wild-type counterpart at all six time-points examined. 2014 Nature communications Result IV V43I;V43I 71;119 75;123 PB1 67 70 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. The EC50 value of Wuhan95 recombinant PB1-V43I virus at an MOI of 0.1 was 73.49 muM (95% CI, 60.67 to 89.03 muM), which is higher than that of the recombinant wild-type virus, with an EC50 value of 39.49 muM (95% CI, 35.65 to 43.74 muM). 2014 Nature communications Result IV V43I 42 46 PB1 38 41 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. The effect of the A370V mutation was assessed using the mini-genome assay. 2014 Nature communications Result IV A370V 18 23 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. The HA gene of the recombinant Wuhan95 (H3N2) or VN04 (H5N1) wild-type and PB1-V43I viruses passaged twice in MDCK cells were analyzed. 2014 Nature communications Result IV V43I 79 83 HA;PB1 4;75 6;78 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. The introduction of the M40L mutation in the absence or presence of the PB1-V43I mutation was observed to reduce the polymerase activity to 80.21% and 64.19%, respectively (Supplementary Table 3). 2014 Nature communications Result IV M40L;V43I 24;76 28;80 PB1 72 75 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. The mutation frequency of the H3N2 wild-type virus was calculated to be higher compared with that of the PB1-V43I virus by a factor ranging from 0.98-3.12 in three independent experiments. 2014 Nature communications Result IV V43I 109 113 PB1 105 108 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. The mutational frequencies and genetic diversity of wild-type and PB1-V43I viruses in the mouse lungs were assessed by clonal sequencing at day 3 and day 8 post-inoculation. 2014 Nature communications Result IV V43I 70 74 PB1 66 69 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. The observed greater reduction of the polymerase activity (as reflected by expressed firefly luciferase activity) by the PB1-V43I protein under high guanosine concentrations (leading to biased intracellular NTP concentration) can be due to direct inhibition of RdRP as a result of increased nucleoside selectivity, or due to mutagenesis effect under the biased intracellular NTP concentration, leading to increased deleterious mutations in the luciferase mRNA and the synthesis of nonfunctional luciferase proteins. 2014 Nature communications Result IV V43I 125 129 PB1 121 124 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. The PB1- S678N mutation found in the N2 replicate was tested separately. 2014 Nature communications Result IV S678N 9 14 PB1 4 7 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. The PB1-V43I mutation in PB1 protein would lead to an amino acid change (V3I) in the N40 protein but not in the PB1-F2 protein, as CAG in PB1 and CAU in PB1-F2 both encode glutamine. 2014 Nature communications Result IV V3I;V43I 73;8 76;12 PB1;PB1;PB1;PB1F2;PB1F2 4;25;138;112;153 7;28;141;118;159 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. The PB1-V43I mutation introduced in recombinant Wuhan95 or VN04 viruses similarly confer to reduced sensitivity to ribavirin. 2014 Nature communications Result IV V43I 8 12 PB1 4 7 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. The PB1-V43I mutation was observed to reduce the polymerase activity of the Wuhan95 virus by 50% by the polymerase-based mini-genome assay (Table 1). 2014 Nature communications Result IV V43I 8 12 PB1 4 7 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. The PB1-V43I variant was 10-fold less lethal than wild-type virus with the MLD50 at 31.6 and 3.4 pfu, respectively. 2014 Nature communications Result IV V43I 8 12 PB1 4 7 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. The post-infection ratio between the Wuhan wild-type and PB1-V43I mutant viruses were determined by RT-PCR and sequencing of the PB1 gene flanking the V43I region with 32 picked plaques per reaction. 2014 Nature communications Result IV V43I;V43I 61;151 65;155 PB1;PB1 57;129 60;132 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. The ratios between the wild-type and the PB1-V43I variant in the viral progenies at 48 h post-infection, as determined by TOPO cloning of the RT-PCR product of viral RNA extracted from the virus supernatant, were comparable to that of the inoculums. 2014 Nature communications Result IV V43I 45 49 PB1 41 44 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. The reduced polymerase activity (as reflected by reduced firefly luciferase activity) was correlated with lower firefly luciferase mRNA levels from cells co-transfected with the PB1 plasmid carrying the V43I mutation. 2014 Nature communications Result IV V43I 203 207 PB1 178 181 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. The result suggests that the wild-type virus may possess a replicative advantage over the PB1-V43I virus under the suboptimal condition of higher temperature. 2014 Nature communications Result IV V43I 94 98 PB1 90 93 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. The S741F mutation was excluded because it conferred minimal resistance to ribavirin and reduced polymerase activity by mini-genome assay (Table 1). 2014 Nature communications Result IV S741F 4 9 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. The stability of the PB1-V43I mutation in the H3N2 virus after five passages in MDCK cells was confirmed by Sanger sequencing. 2014 Nature communications Result IV V43I 25 29 PB1 21 24 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. The three ratios between the wild-type and V43I mutant viruses were intended to be at 25%:75%, 50%:50%, and 75%:25%; however, the exact ratios were confirmed by clonal sequencing of the inoculum to be at 2.4%: 97.6%, 40%: 60%, and 56.3%: 43.8%. 2014 Nature communications Result IV V43I 43 47 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. The two viruses formed comparable sizes of plaques at 33 C or 37 C but the wild-type virus formed significantly larger plaques than that of the PB1-V43I virus at 39 C. 2014 Nature communications Result IV V43I 148 152 PB1 144 147 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. The VN04 polymerase complex was used for the assay as the V43I mutation does not significantly decrease its activity. 2014 Nature communications Result IV V43I 58 62 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. The wild-type H3N2 virus has an EC50 value of 10.98 muM (95% CI 6.93 to 17.41 muM), compared with a 2.24-fold increase in EC50 to 24.61 muM (95% CI 17.65 to 34.32 muM) in the PB1-V43I mutant when infected at a MOI of 0.1. 2014 Nature communications Result IV V43I 179 183 PB1 175 178 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. The wild-type virus (1.67 mutations per 104 nucleotides) has 4.76-fold higher mutational frequencies when compared to that of the PB1-V43I mutant (0.35 mutations per 104 nucleotides) (Supplementary Table 8). 2014 Nature communications Result IV V43I 134 138 PB1 130 133 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. Therefore, the A370V mutation may play a compensatory role to rescue the decreased polymerase activity caused by the V43I mutation in the Wuhan95 polymerase complex. 2014 Nature communications Result IV A370V;V43I 15;117 20;121 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. Therefore, we determined the mutational frequencies of the wild-type and the PB1-V43I viruses after 1 passage in the presence of 66.6muM ribavirin in MDCK cells. 2014 Nature communications Result IV V43I 81 85 PB1 77 80 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. This approach allows direct assessing of the effect of the PB1-V43I mutation in the PB1 protein without being confounded by the V3I mutation in the N40 protein. 2014 Nature communications Result IV V43I;V3I 63;128 67;131 PB1;PB1 59;84 62;87 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. Through testing each of the PB1 mutations with the mini-genome assay, we identified the PB1-V43I mutation that exhibited most significant resistance to ribavirin. 2014 Nature communications Result IV V43I 92 96 PB1;PB1 28;88 31;91 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. To assess if the wild-type and PB1-V43I viruses exhibited similar viral fitness at suboptimal conditions, we determined the plaque sizes of the wild-type and the PB1-V43I viruses at 33 C, 37 C, and 39 C. 2014 Nature communications Result IV V43I;V43I 35;166 39;170 PB1;PB1 31;162 34;165 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. To assess the stability of PB1-V43I in viruses in vivo, sequences of the PB1 segment of viruses collected at day 8 post-inoculation were examined by Sanger sequencing and no reversion to wild-type was observed, with no additional mutation was found in PB1. 2014 Nature communications Result IV V43I 31 35 PB1;PB1;PB1 27;73;252 30;76;255 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. To clarify the potential mechanism, we quantified the firefly luciferase mRNA copy numbers from cells co-transfected with the PB1 plasmid carrying the V43I mutation under high guanosine concentrations. 2014 Nature communications Result IV V43I 151 155 PB1 126 129 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. To compare the viral fitness of the PB1-V43I variant to its wild-type counterpart in vitro, we determined the single-cycle replication kinetics of the H3N2 and the H5N1 recombinant wild-type and PB1-V43I viruses in MDCK cells. 2014 Nature communications Result IV V43I;V43I 40;199 44;203 PB1;PB1 36;195 39;198 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. To confirm that the PB1-V43I mutation conferring ribavirin resistance would also affect IAV polymerase fidelity, clonal sequencing was performed to calculate the mutational frequency between the wild-type and the PB1-V43I viruses. 2014 Nature communications Result IV V43I;V43I 24;217 28;221 PB1;PB1 20;213 23;216 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. To confirm the results derived from the mini-genome assay, we generated recombinant H3N2 viruses harboring each of the 4 mutations in PB1 (S678N from replicate N2 and V43I, V191I, A661T from replicate N4). 2014 Nature communications Result IV S678N;V43I;V191I;A661T 139;167;173;180 144;171;178;185 PB1 134 137 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. To ensure that the phenotype we observed was purely derived from the PB1-V43I mutation but not due to the V3I mutation in the N40 protein, we eliminated the expression of N40 protein by introducing a PB1-M40L mutation to remove the start codon of PB1-N40 of the VN04 polymerase complex. 2014 Nature communications Result IV V43I;V3I;M40L 73;106;204 77;109;208 PB1;PB1;PB1 69;200;247 72;203;250 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. To evaluate if the PB1-V43I mutation would confer resistance to ribavirin in a different IAV polymerase complex, we introduced the V43I mutation into the H5N1 highly pathogenic VN04 virus. 2014 Nature communications Result IV V43I;V43I 23;131 27;135 PB1 19 22 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. To further examine the mechanism of the observed difference in lethality between the wild-type and PB1-V43I mutant, the viral titres in the brain were determined to assess the neurotropism of the wild-type and PB1-V43I viruses. 2014 Nature communications Result IV V43I;V43I 103;214 107;218 PB1;PB1 99;210 102;213 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. To further investigate the molecular mechanism for the increased resistance to ribavirin displayed by the PB1-V43I mutation, we applied the polymerase-based mini-genome assay to assess if the mutation would similarly confer reduced sensitivity to another purine analog, favipiravir, for which no IAV resistant variants has been reported. 2014 Nature communications Result IV V43I 110 114 PB1 106 109 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. To further verify the competitive fitness between the Wuhan wild-type and the PB1-V43I mutant viruses, MDCK cells were infected at MOI=0.1 with mixtures of the two viruses 41.9%:58.1%, 64.5%:35.5%, and 83.9%:16.1% (verified by RT-PCR and sequencing of the PB1 gene flanking the V43I region from plaques formed by the inoculums). 2014 Nature communications Result IV V43I;V43I 82;278 86;282 PB1;PB1 78;256 81;259 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. Under higher guanosine concentrations, at which a biased intracellular NTP concentration is likely present, the PB1-V43I protein exhibited further reduced polymerase activity than that of the wild-type PB1 protein. 2014 Nature communications Result IV V43I 116 120 PB1;PB1 112;202 115;205 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. Under increasing concentration of ribavirin, the recombinant Wuhan95 virus carrying the PB1-V43I mutation showed the most pronounced ribavirin resistance with a 10.8-fold higher virus titre at 60 muM ribavirin compared to that of the wild-type recombinant Wuhan95 virus. 2014 Nature communications Result IV V43I 92 96 PB1 88 91 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. VN04 polymerase complex was selected over the Wuhan95 polymerase complex to study the effect of PB1-N40 as the V43I mutation did not cause significant reduction in VN04 polymerase activity. 2014 Nature communications Result IV V43I 111 115 PB1 96 99 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. We evaluated the effect of guanosine treatment on the polymerase activity of both wild-type PB1 and PB-V43I proteins in IAV mini-genome assay. 2014 Nature communications Result IV V43I 103 107 PB1 92 95 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. We evaluated the effect of mutation frequency on viral fitness in vivo using the recombinant H5N1 viruses with or without the PB1-V43I mutation at a challenge dose of 100 pfu. 2014 Nature communications Result IV V43I 130 134 PB1 126 129 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. We further conducted a direct competition assay between the PB1-V43I variant to its wild-type counterpart in vitro. 2014 Nature communications Result IV V43I 64 68 PB1 60 63 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. We introduced 10 mutations found in the clones derived from the N4 replicates (Supplementary Table 2) into the PB2 (PB2-D309N, PB2-R702K), PB1 (PB1-V43I, PB1-V191I, PB1-A661T, PB1-S741F), PA (PA-L54F), and NP (NP-D101N, NP-S287N, NP-M371I) proteins as RNPrib-resist. 2014 Nature communications Result IV D309N;R702K;V43I;V191I;A661T;S741F;L54F;D101N;S287N;M371I 120;131;148;158;169;180;195;213;223;233 125;136;152;163;174;185;199;218;228;238 NP;NP;NP;NP;PA;PA;PB1;PB1;PB1;PB1;PB1;PB2;PB2;PB2 206;210;220;230;188;192;139;144;154;165;176;111;116;127 208;212;222;232;190;194;142;147;157;168;179;114;119;130 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. We observed that an increasing concentration of guanosine leads to reduced polymerase activity (as reflected by the expressed firefly luciferase activity) for both the wild-type as well as PB1-V43I polymerase complexes. 2014 Nature communications Result IV V43I 193 197 PB1 189 192 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. We observed that in the presence of ribavirin, the wild-type virus (5.53 mutations per 104 nucleotides) exhibited a 1.36-fold higher mutational frequency than that of the PB1-V43I virus (4.08 mutations per 104 nucleotides). 2014 Nature communications Result IV V43I 175 179 PB1 171 174 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. We observed that the V43I mutation similarly confers resistance to ribavirin in a mini-genome assay, with an EC50 value of 29.00 muM (95% CI, 23.46 to 35.86 muM), which is higher than that of the wild-type virus, with an EC50 value of 15.74 muM (95% CI, 11.82 to 20.96 muM). 2014 Nature communications Result IV V43I 21 25 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. We observed that the V43I mutation was stably maintained; however, a sub-population of A370V PB1 mutation was noted at passage 5 by Sanger sequencing and was further confirmed by clonal sequencing (46.2%). 2014 Nature communications Result IV V43I;A370V 21;87 25;92 PB1 93 96 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. We then evaluated the effect of guanosine for both the wild-type PB1 and PB1-V43I proteins in the presence of ribavirin. 2014 Nature communications Result IV V43I 77 81 PB1;PB1 65;73 68;76 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. We then examined if the PB1-V43I mutation affects the sensitivity of recombinant H3N2 or H5N1 viruses to favipiravir in MDCK cells. 2014 Nature communications Result IV V43I 28 32 PB1 24 27 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. We then individually evaluated the effect of all the mutations identified in the PB1 of the N2 (S678N) and N4 (V43I, V191I, A661T, S741F) replicates by the mini-genome assay. 2014 Nature communications Result IV S678N;V43I;V191I;A661T;S741F 96;111;117;124;131 101;115;122;129;136 PB1 81 84 25191344 Prevalence of Oseltamivir-Resistant 2009 H1N1 Influenza Virus among Patients with Pandemic 2009 H1N1 Influenza infection in NRITLD, Tehran, Iran. Drug resistance genotyping test was conducted retrospectively and the H275Y substitution was detected in both clinical specimens. 2011 Tanaffos Result IV H275Y 70 75 25191344 Prevalence of Oseltamivir-Resistant 2009 H1N1 Influenza Virus among Patients with Pandemic 2009 H1N1 Influenza infection in NRITLD, Tehran, Iran. Drug resistance genotyping test was conducted retrospectively and the H275Y substitution was detected in the second specimen. 2011 Tanaffos Result IV H275Y 70 75 25191344 Prevalence of Oseltamivir-Resistant 2009 H1N1 Influenza Virus among Patients with Pandemic 2009 H1N1 Influenza infection in NRITLD, Tehran, Iran. Further studies revealed the sample had H275Y mutation and contained the mutant subtype of the virus. 2011 Tanaffos Result IV H275Y 40 45 25191344 Prevalence of Oseltamivir-Resistant 2009 H1N1 Influenza Virus among Patients with Pandemic 2009 H1N1 Influenza infection in NRITLD, Tehran, Iran. Subsequent studies revealed that only the second sample had H275Y mutation and contained the oseltamivir resistant virus, as it was positive for seasonal influenza A virus. 2011 Tanaffos Result IV H275Y 60 65 25191344 Prevalence of Oseltamivir-Resistant 2009 H1N1 Influenza Virus among Patients with Pandemic 2009 H1N1 Influenza infection in NRITLD, Tehran, Iran. The H275Y substitution was detected in 4 patients as a result of drug resistance genotyping test (Figure 1). 2011 Tanaffos Result IV H275Y 4 9 25210166 Accumulation of human-adapting mutations during circulation of A(H1N1)pdm09 influenza virus in humans in the United Kingdom. For the A/195 constellation, we used a PA plasmid with the glycine 3 mutated to aspartic acid, since this difference was atypical among first-wave viruses. 2014 Journal of virology Result IV G3D 59 93 PA 39 41 25210166 Accumulation of human-adapting mutations during circulation of A(H1N1)pdm09 influenza virus in humans in the United Kingdom. Sequence analysis showed third-wave viruses possessed a cluster of amino acid changes in the NS1 protein in various combinations at positions E55Q, P114T, I123V, and G189D (Table 1). 2014 Journal of virology Result IV E55Q;P114T;I123V;G189D 142;148;155;166 146;153;160;171 NS1 93 96 25210166 Accumulation of human-adapting mutations during circulation of A(H1N1)pdm09 influenza virus in humans in the United Kingdom. The G189D variation also changed the coding sequence of the NEP protein (V32I), because the NS1 and NEP open reading frames overlap at this region. 2014 Journal of virology Result IV G189D;V32I 4;73 9;77 NEP;NEP;NS1 60;100;92 63;103;95 25210166 Accumulation of human-adapting mutations during circulation of A(H1N1)pdm09 influenza virus in humans in the United Kingdom. The mutation in PA N321K of third-wave viruses conferred enhanced replication in a minireplicon assay and in viral competition assays. 2014 Journal of virology Result IV N321K 19 24 PA 16 18 25210166 Accumulation of human-adapting mutations during circulation of A(H1N1)pdm09 influenza virus in humans in the United Kingdom. The only exception was A/675, which has an M227I (230 in H3 numbering) amino acid variation near the receptor binding pocket and retained strong binding to chicken erythrocytes. 2014 Journal of virology Result IV M227I 43 48 25210166 Accumulation of human-adapting mutations during circulation of A(H1N1)pdm09 influenza virus in humans in the United Kingdom. There are only four coding genetic differences between these two third-wave viruses: HA L176I, NS1 I123V, PB1 I12T, and PB2 N556S. 2014 Journal of virology Result IV L176I;I123V;I12T;N556S 88;99;110;124 93;104;114;129 HA;NS1;PB1;PB2 85;95;106;120 87;98;109;123 25210166 Accumulation of human-adapting mutations during circulation of A(H1N1)pdm09 influenza virus in humans in the United Kingdom. These changes also accumulated in second- and third-wave virus isolates from other regions of the United Kingdom and from the rest of the world (Table 2), except for G189D in NS1. 2014 Journal of virology Result IV G189D 166 171 NS1 175 178 25210166 Accumulation of human-adapting mutations during circulation of A(H1N1)pdm09 influenza virus in humans in the United Kingdom. These three changes were at PB2 V344M, I354L, and PA N321K (Table 1). 2014 Journal of virology Result IV V344M;I354L;N321K 32;39;53 37;44;58 PA;PB2 50;28 52;31 25210166 Accumulation of human-adapting mutations during circulation of A(H1N1)pdm09 influenza virus in humans in the United Kingdom. To assess whether the PA N321K mutation led to an enhancement of replication in the context of whole virus, we generated a 7:1 (PA) RG virus in which every genomic segment except for the A/687 PA segment was derived from A/195. 2014 Journal of virology Result IV N321K 25 30 PA;PA;PA 22;128;193 24;130;195 25409547 The K526R substitution in viral protein PB2 enhances the effects of E627K on influenza virus replication. As described above, the H3N2 virus obtained K526R around 1970 and the PB2-526R genotype immediately became the dominant circulating H3N2 in humans, persisting to the current day. 2014 Nature communications Result IV K526R 44 49 PB2 70 73 25409547 The K526R substitution in viral protein PB2 enhances the effects of E627K on influenza virus replication. Besides the previously described 627K, 701N and 591K loci, we found a K526R genotype associated with either 627E/627K or 701D/701N. 2014 Nature communications Result IV K526R 70 75 25409547 The K526R substitution in viral protein PB2 enhances the effects of E627K on influenza virus replication. Furthermore, sequence analysis found that the H3N2 virus obtained K526R around 1970 and that the PB2-526R genotype immediately became the dominant circulating H3N2 in humans. 2014 Nature communications Result IV K526R 66 71 PB2 97 100 25409547 The K526R substitution in viral protein PB2 enhances the effects of E627K on influenza virus replication. However, screening of sequences in the GenBank influenza database revealed that K526R is present in some H5N1 human isolates, particularly those from human cases in Indonesia (Table 1). 2014 Nature communications Result IV K526R 80 85 25409547 The K526R substitution in viral protein PB2 enhances the effects of E627K on influenza virus replication. In contrast to the effect on H3N2 virus, introduction of K526R into PR8 (H1N1) virus compromised virus replication in a similar assay. 2014 Nature communications Result IV K526R 57 62 25409547 The K526R substitution in viral protein PB2 enhances the effects of E627K on influenza virus replication. Our results showed that inclusion of K526R, alone or coupled with 627K or 701N, increased mortality in the infected mice. 2014 Nature communications Result IV K526R 37 42 25409547 The K526R substitution in viral protein PB2 enhances the effects of E627K on influenza virus replication. PB2-K526R is present in three influenza virus subtypes. 2014 Nature communications Result IV K526R 4 9 PB2 0 3 25409547 The K526R substitution in viral protein PB2 enhances the effects of E627K on influenza virus replication. This evidence supports our observations from H7N9 and H5N1-Indonesia viruses and indicates that the K526R substitution in the PB2 polymerase subunit provides a growth advantage to H3N2 influenza A virus, which may further enhance replication in humans. 2014 Nature communications Result IV K526R 100 105 PB2 126 129 25409547 The K526R substitution in viral protein PB2 enhances the effects of E627K on influenza virus replication. To confirm that the K526R substitution caused increased virus replication in vivo, mice were infected with a sub-lethal (2.25 x 104 plaque-forming units (PFU), based on pre-experimental data obtained using either 627K or 701N PB2 genotype viruses) dose of one of the different versions of H7N9 virus and were observed, and changes in body weight recorded over the following 14 days. 2014 Nature communications Result IV K526R 20 25 PB2 226 229 25409547 The K526R substitution in viral protein PB2 enhances the effects of E627K on influenza virus replication. We postulated that K526R may have provided additional optimization for the replication of the H3N2 virus following the incorporation of an avian PB1 into H2N2 in 1968 (ref.). 2014 Nature communications Result IV K526R 19 24 PB1 145 148 25409547 The K526R substitution in viral protein PB2 enhances the effects of E627K on influenza virus replication. While further studies are needed to reveal the molecular details of how PB2 and NEP interact with each other and host factors, it seems possible that the K526R-adaptive substitution enhances the interaction between PB2, the other RNP subunits and NEP during virus replication. 2014 Nature communications Result IV K526R 154 159 NEP;NEP;PB2;PB2;RNP 80;247;72;215;230 83;250;75;218;233 25470189 Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel. A cross-peak between I33 methyl groups and the thiophene ring (11 H1 to I33 gamma2 and delta1), together with the lack of NOEs to Val27 methyl groups (as were the case for S31N), place the aromatic group pointing down into the channel. 2014 Journal of the American Chemical Society Result IV S31N 172 176 25470189 Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel. As shown in Table 3, removal of the bromo substitution resulted in drastic decrease of S31N inhibition (11 versus 25), presumably due to the lack of favorable hydrophobic interactions with the V27 side chains. 2014 Journal of the American Chemical Society Result IV S31N 87 91 25470189 Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel. Because the bromo-substituted thiophene 11 had the highest dual inhibition against both WT and S31N, we decided to further explore the SAR. 2014 Journal of the American Chemical Society Result IV S31N 95 99 25470189 Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel. Chloro-substituted thiazole (6) had moderate activities against both WT and S31N. 2014 Journal of the American Chemical Society Result IV S31N 76 80 25470189 Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel. Compounds with ethyl (30) and cyclopropyl (31) substitutions showed drastic decrease in WT inhibition, while having little or no effect on their S31N inhibition. 2014 Journal of the American Chemical Society Result IV S31N 145 149 25470189 Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel. Compounds with hydrophilic amine substitution (16) and bulky tert-butyl substitution (24) were inactive against both WT and S31N. 2014 Journal of the American Chemical Society Result IV S31N 124 128 25470189 Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel. For the S31N (19-49) VANIG peptide, residues at V27, A30, N31, I33, and G34 are uniformly 15N-13C-labeled. 2014 Journal of the American Chemical Society Result IV S31N 8 12 25470189 Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel. However, the lack of systematic NOEs between the thiophene protons (H1 and H2) and V27 as were seen in the complex with S31N (19-49) VANIG (Figure 2A) together with the presence of NOEs locating the thiophene ring in the channel near Ala30 indicate that 11 is primarily bound with the heteroaryl group pointing down. 2014 Journal of the American Chemical Society Result IV S31N 120 124 25470189 Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel. In the S31N mutant, we initialized 11 with the bromo-thiophene moiety facing toward V27, and the ammonium aligned with the side chain of N31, as in the S31N-M2WJ332 (2) structure (PDB: 2LY0). 2014 Journal of the American Chemical Society Result IV S31N;S31N 7;152 11;156 25470189 Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel. Interestingly, the chloro-substituted 1,2,4-thiadiazole analogue (7) showed improved potency against S31N, and retained its WT inhibition in comparison to 6. 2014 Journal of the American Chemical Society Result IV S31N 101 105 25470189 Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel. It is also known that a variety of hydrophobic scaffolds are tolerated for WT inhibition, while adamantane is the preferred moiety for S31N inhibition. 2014 Journal of the American Chemical Society Result IV S31N 135 139 25470189 Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel. MD Simulations of the Dual Inhibitor 11 Binding to WT and S31N. 2014 Journal of the American Chemical Society Result IV S31N 58 62 25470189 Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel. Methyl substitution slightly increased S31N inhibition, but decreased WT inhibition in the case of 1,2,4-isoxazole (21 versus 12). 2014 Journal of the American Chemical Society Result IV S31N 39 43 25470189 Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel. Methyl-substituted thiophene (28) was 2-fold less active than its bromo analogue (11) in inhibiting both WT and S31N. 2014 Journal of the American Chemical Society Result IV S31N 112 116 25470189 Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel. Moving the substitutions from the 5-position of the thiophene to the 4-position (32) or the 3-position (33) led to the loss of activity against both WT and S31N, suggesting the binding geometry of the drug is important. 2014 Journal of the American Chemical Society Result IV S31N 156 160 25470189 Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel. NMR structural studies of a high-affinity inhibitor of S31N revealed that this inhibitor bound to S31N in a different orientation than previously characterized inhibitors of the WT protein: drugs like amantadine (1) and rimantadine bind to WT M2 channel with their positively charged ammonium facing downward toward H37; while M2WJ332 (2) bound to the S31N mutant in the opposite orientation with its ammonium facing upward V27. 2014 Journal of the American Chemical Society Result IV S31N;S31N;S31N 55;98;352 59;102;356 M2 243 245 25470189 Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel. NMR Studies of the Dual Inhibitor 11 Binding to WT and S31N M2. 2014 Journal of the American Chemical Society Result IV S31N 55 59 M2 60 62 25470189 Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel. On the basis of the binding mode of M2WJ332 (2) in S31N mutant as shown in Figure 1, the R group was expected to form hydrophobic interactions with the V27 side chain methyls. 2014 Journal of the American Chemical Society Result IV S31N 51 55 25470189 Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel. Other halides such as chloro and iodo were similarly tolerated in the same position, and the resulting compounds retained potent inhibition against both WT and S31N (11 versus 26 and 27). 2014 Journal of the American Chemical Society Result IV S31N 160 164 25470189 Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel. Our design was based on the idea that dual inhibitors bind to WT and S31N in opposite orientations. 2014 Journal of the American Chemical Society Result IV S31N 69 73 25470189 Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel. Previous SAR, structural studies, and MD simulations of drug-M2 interactions revealed a common mechanism of drug action: potent M2 inhibitors, regardless of whether they target WT, S31N, V27A, or L26F, all contain a positively charged ammonium, which presumably serves as a mimic of the conducting hydronium ion that forms water-mediated hydrogen bonds with backbone carbonyls of M2. 2014 Journal of the American Chemical Society Result IV S31N;V27A;L26F 181;187;196 185;191;200 M2;M2;M2 61;128;380 63;130;382 25470189 Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel. Rational Design of Dual Inhibitors Targeting WT and S31N. 2014 Journal of the American Chemical Society Result IV S31N 52 56 25470189 Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel. The assignment of the complex of S31N (19-49) VANIG in complex with 11 (Figure 2A) is similar to that used previously to solve the corresponding complex with M2WJ332 (2). 2014 Journal of the American Chemical Society Result IV S31N 33 37 25470189 Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel. The chemical shifts for the complexes of WT VASIGH and S31N VANIG in the presence of 11 were very similar to those observed for the amantadine-bound WT M2 TM and the M2WJ332 (2)-bound S31N, respectively. 2014 Journal of the American Chemical Society Result IV S31N;S31N 55;184 59;188 M2 152 154 25470189 Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel. The linker between adamantane and the heterocycle was kept constant as an ammonium methylene, as it has been shown to be critical for S31N inhibition. 2014 Journal of the American Chemical Society Result IV S31N 134 138 25470189 Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel. The most potent compound from the five-membered heterocyclic series was N-[(5-bromothiophen-2-yl)methyl]adamantan-1-amine (11), which showed 76% and 77% inhibition against S31N and WT M2, respectively. 2014 Journal of the American Chemical Society Result IV S31N 172 176 M2 184 186 25470189 Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel. The observed drug-flipping phenomenon provides a rationale for design of dual inhibitors that target both WT and S31N in opposite orientations. 2014 Journal of the American Chemical Society Result IV S31N 113 117 25470189 Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel. The orientations of amantadine (1) and rimantadine in WT, and M2WJ332 (2) in M2-S31N, were modeled by MD simulations, and the orientations were confirmed by solution and solid-state NMR spectroscopies, and further corroborated by SAR studies. 2014 Journal of the American Chemical Society Result IV S31N 80 84 M2 77 79 25470189 Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel. These NOEs unambiguously demonstrate the drug is up in the S31N channel. 2014 Journal of the American Chemical Society Result IV S31N 59 63 25470189 Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel. These peptide-drug NOEs, along with the distance constraints and backbone dihedral angle constraints for defining the peptide's tetrameric structure obtained for the S31N-M2WJ332 (2) structure, were used to build the models using XPLOR-NIH as shown in Figure 2D. 2014 Journal of the American Chemical Society Result IV S31N 166 170 25470189 Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel. Thus, we chose adamantane as the hydrophobic scaffold in order to retain S31N activity. 2014 Journal of the American Chemical Society Result IV S31N 73 77 25470189 Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel. To design such dual inhibitors, we started with our earlier reported inhibitors that had moderate inhibition against both WT and S31N (Table 1). 2014 Journal of the American Chemical Society Result IV S31N 129 133 25470189 Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel. Two-dimensional 13C-edited NOESY experiments with 150 ms mixing time were used to identify peptide-drug NOEs for S31N (19-49) VANIG peptide (Figure 2A) and the WT (19-49) VASIGH peptide (Figure 2B). 2014 Journal of the American Chemical Society Result IV S31N 113 117 25470189 Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel. Water molecules that are initially positioned around 11 leave the region between V27 and G34, with the exception of two water molecules coordinating the ammonium group, also seen in the previous S31N-M2WJ332 (2) simulations. 2014 Journal of the American Chemical Society Result IV S31N 195 199 25470189 Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel. We used MD simulations of M2-TM in a phospholipid bilayer to investigate the dual inhibitory behavior adopted by compound 11 against the M2 proton channels (both WT and S31N mutant) (Figure 3). 2014 Journal of the American Chemical Society Result IV S31N 169 173 M2;M2 26;137 28;139 25505461 D701N mutation in the PB2 protein contributes to the pathogenicity of H5N1 avian influenza viruses but not transmissibility in guinea pigs. In total, the following five amino acid changes between DK/357 and DK/357-L were identified: V96I, F135I, S688F, and D701N in the polymerase PB2 protein and N417S in the NP protein (Table 2). 2014 Frontiers in microbiology Result IV V96I;F135I;S688F;D701N;N417S 93;99;106;117;157 97;104;111;122;162 NP;PB2 170;141 172;144 25505461 D701N mutation in the PB2 protein contributes to the pathogenicity of H5N1 avian influenza viruses but not transmissibility in guinea pigs. When comparing DK/357 to the DK/357-T, three amino acids substitutions were found, i.e., V96I and D701N in the polymerase PB2 protein and N417S in the nucleoprotein (NP) protein (Table 2). 2014 Frontiers in microbiology Result IV V96I;D701N;N417S 89;98;138 93;103;143 NP;NP;PB2 166;151;122 168;164;125 25589893 Identification of novel compounds against an R294K substitution of influenza A (H7N9) virus using ensemble based drug virtual screening. R294K substitution has rarely occurred and to date has only been reported from the patients treated with Oseltamivir. 2015 International journal of medical sciences Result IV R294K 0 5 25589893 Identification of novel compounds against an R294K substitution of influenza A (H7N9) virus using ensemble based drug virtual screening. The docking results of H7N9 NA agreed well with the experiential results in which NA R292K substitution was highly resistant to Oseltamivir and Peramivir and partially resistant to Zanamivir. 2015 International journal of medical sciences Result IV R292K 85 90 NA;NA 28;82 30;84 25589893 Identification of novel compounds against an R294K substitution of influenza A (H7N9) virus using ensemble based drug virtual screening. These results explain experimental data that R294K substitution led to extreme resistance of NA to Oseltamivir and conferred less resistance to Peramivir, Zanamivir and Laninarmivir. 2015 International journal of medical sciences Result IV R294K 45 50 93 95 25659818 Assessment of transmission, pathogenesis and adaptation of H2 subtype influenza viruses in ferrets. Additional amino acid changes at positions Glu190Val, Gly205Val, and Met/Arg212Arg or Met in different combinations were also found depending on the ferret pair of both RD and DC transmission experiments (Table 5). 2015 Virology Result IV E190V;G205V;R212R;M212R 43;54;73;73 52;63;82;82 25659818 Assessment of transmission, pathogenesis and adaptation of H2 subtype influenza viruses in ferrets. Amino acids mutations that were consistently observed were Glu190Val, Gly205Val, Met/Arg212Arg or Met, Gln226Leu, and 228 (silent mutation). 2015 Virology Result IV E190V;G205V;R212R;Q226L;M212R 59;70;85;103;85 68;79;94;112;94 25659818 Assessment of transmission, pathogenesis and adaptation of H2 subtype influenza viruses in ferrets. and progressed to up to 3 mutations containing the substitutions, Gly205Val or Val/Gly, Met/Arg212Arg, Gln226Leu, including the silent mutation at position 228. 2015 Virology Result IV G205V;R212R;Q226L;M212R 66;92;103;92 75;101;112;101 25659818 Assessment of transmission, pathogenesis and adaptation of H2 subtype influenza viruses in ferrets. but contained only one mutation at position Glu190Val. 2015 Virology Result IV E190V 44 53 25659818 Assessment of transmission, pathogenesis and adaptation of H2 subtype influenza viruses in ferrets. For inoculated ferret #2 that did not transmit ckPA virus to its cage mate, changes were not present at those positions but only at amino acid 206 (Thr/Pro206). 2015 Virology Result IV T206P 148 158 25659818 Assessment of transmission, pathogenesis and adaptation of H2 subtype influenza viruses in ferrets. For the swMO transmission experiments, one HA1 amino acid change (Leu226Gln) was observed from nasal washes, and that occurred in only 1 of 6 ferrets used in DC or RD transmission experiments (Table 5). 2015 Virology Result IV L226Q 66 75 HA1 43 46 25659818 Assessment of transmission, pathogenesis and adaptation of H2 subtype influenza viruses in ferrets. However interestingly, no evidence of viruses containing the Gln226Leu amino acid substitutions was present. 2015 Virology Result IV Q226L 61 70 25659818 Assessment of transmission, pathogenesis and adaptation of H2 subtype influenza viruses in ferrets. In comparison to the avian H2 HAs, the swine (swMO) virus possesses a mutation, Gln226Leu, which correlates with increased binding affinity to alpha2-6 SA; swMO HA has Leu226/Gly228 at the RBS and was found to agglutinate both alpha2-6 and alpha2-3 sialylated RBCs (Table 1). 2015 Virology Result IV Q226L 80 89 HA 161 163 25659818 Assessment of transmission, pathogenesis and adaptation of H2 subtype influenza viruses in ferrets. In ferret pair #3, amino acid changes occurred in the inoculated ferret starting with one HA mutation (Met/Arg212Arg) on day 1 p.i. 2015 Virology Result IV R212R;M212R 107;107 116;116 HA 90 92 25659818 Assessment of transmission, pathogenesis and adaptation of H2 subtype influenza viruses in ferrets. In swMO virus infected tissues, the amino acid switch Leu226Gln crucial for change of receptor binding preference from alpha2-6 to alpha2-3 SA was observed in the tracheas of 2/3 ferrets but not in nasal turbinates, lung tissues or stock virus. 2015 Virology Result IV L226Q 54 63 25659818 Assessment of transmission, pathogenesis and adaptation of H2 subtype influenza viruses in ferrets. Interestingly, the mallMD virus from one inoculated and one unrelated DC contact ferrets had subpopulations with the key RBS amino acid substitution at position 226 (Gln226Leu). 2015 Virology Result IV Q226L 166 175 25659818 Assessment of transmission, pathogenesis and adaptation of H2 subtype influenza viruses in ferrets. Previously, mutations in the HA RBS of H1N1 (Glu190Asp/Gly225Asp) and H2N2/H3N2 (Gln226Leu and Gly228Ser) subtypes were found to be responsible for adaptation of these viruses from avian strain to human strain. 2015 Virology Result IV G225D;E190D;Q226L;G228S;E190G 55;45;81;95;45 64;54;90;104;54 HA 29 31 25659818 Assessment of transmission, pathogenesis and adaptation of H2 subtype influenza viruses in ferrets. Taken together, these findings identify significant amino acid mutations that occurred during H2 virus transmission, including Gln226Leu substitution that has been associated with alpha2,6 sialic acid (human-like) binding preference. 2015 Virology Result IV Q226L 127 136 25659818 Assessment of transmission, pathogenesis and adaptation of H2 subtype influenza viruses in ferrets. The HA1 sequences of ckPA viruses that were collected during the DC transmission experiment revealed that the virus in both inoculated and contact ferrets (pairs #1 and #3) underwent two amino acid changes at positions 190 (Glu190Gly pair #1 and Glu190Asp pair #3) and 216 (Glu216Asp) in both ferret pairs. 2015 Virology Result IV E190G;E190D;E216D 224;246;274 233;255;283 25659818 Assessment of transmission, pathogenesis and adaptation of H2 subtype influenza viruses in ferrets. The most consistent mutations that were present in the viruses collected from both ferrets were the Met/Arg212Met or Arg substitutions. 2015 Virology Result IV R212M;M212M 104;104 113;113 25659818 Assessment of transmission, pathogenesis and adaptation of H2 subtype influenza viruses in ferrets. The sequencing results revealed that mutations in HA1 were confined to the same positions and amino acids that were found in the nasal washes of the DC transmission experiment; Gly205Val, Met/Arg212Arg, 228 silent mutation (data not shown). 2015 Virology Result IV G205V;R212R;M212R 177;192;188 186;201;201 HA1 50 53 25659818 Assessment of transmission, pathogenesis and adaptation of H2 subtype influenza viruses in ferrets. Viruses containing Leu226 were not detected in the nasal washes of the ferret pair#1, but mutant viruses containing Gly205Val and Met/Arg212Met or Arg substitutions were present, appearing in inoculated ferrets on day 5 p.i. 2015 Virology Result IV G205V;R212M;M212M 116;134;134 125;143;143 25659818 Assessment of transmission, pathogenesis and adaptation of H2 subtype influenza viruses in ferrets. With respect to other key residues in the PB2 subunit, avian influenza viruses normally contain Gly590/Gln591 sequences in the PB2 gene; however mallMD has a Ser rather than a Gly at position 590, the same amino acid found in swine origin viruses. 2015 Virology Result IV G590S 158 195 PB2;PB2 42;127 45;130 25701593 Influenza A viruses of swine circulating in the United States during 2009-2014 are susceptible to neuraminidase inhibitors but show lineage-dependent resistance to adamantanes. (1930-2014) revealed a single N1 sequence that contained the clinically relevant H274Y-NA (Table 3). 2015 Antiviral research Result IV H274Y 81 86 87 89 25701593 Influenza A viruses of swine circulating in the United States during 2009-2014 are susceptible to neuraminidase inhibitors but show lineage-dependent resistance to adamantanes. (1930-2014), more than 99% possessed permissive NA substitutions that abolish the deleterious effect of H274Y; 37% to 46% of N1 sequences of the H1N1pdm09 in swine harbored substitutions that confer robust fitness on recent human H1N1pdm09 viruses (Table 4). 2015 Antiviral research Result IV H274Y 104 109 48 50 25701593 Influenza A viruses of swine circulating in the United States during 2009-2014 are susceptible to neuraminidase inhibitors but show lineage-dependent resistance to adamantanes. Although I27T-M2 emerged independently at least four times, it was fixed only three times in the classic swine lineage. 2015 Antiviral research Result IV I27T 9 13 M2 14 16 25701593 Influenza A viruses of swine circulating in the United States during 2009-2014 are susceptible to neuraminidase inhibitors but show lineage-dependent resistance to adamantanes. Because the EC50 values of the viruses with I27T-M2 were higher than the susceptible ones (<1 muM) but lower than the resistant ones (>100 muM), we propose that the I27T-M2 confers intermediate resistance to amantadine. 2015 Antiviral research Result IV I27T;I27T 44;165 48;169 M2;M2 49;170 51;172 25701593 Influenza A viruses of swine circulating in the United States during 2009-2014 are susceptible to neuraminidase inhibitors but show lineage-dependent resistance to adamantanes. By tracing the history of this particular position, we found that the S31N-M2 represents 83% of all changes that occur at this position across the phylogeny, suggesting that this mutation has a high probability of emerging randomly. 2015 Antiviral research Result IV S31N 70 74 M2 75 77 25701593 Influenza A viruses of swine circulating in the United States during 2009-2014 are susceptible to neuraminidase inhibitors but show lineage-dependent resistance to adamantanes. Culhane, personal communications), and thus IAV-S sequences with the I27T-M2 from the U.S. 2015 Antiviral research Result IV I27T 69 73 M2 74 76 25701593 Influenza A viruses of swine circulating in the United States during 2009-2014 are susceptible to neuraminidase inhibitors but show lineage-dependent resistance to adamantanes. Despite the epidemiological data on the presence of the I27T-M2 in IAV-S and human influenza viruses, the role of this substitution on the susceptibility to amantadine is not well defined. 2015 Antiviral research Result IV I27T 56 60 M2 61 63 25701593 Influenza A viruses of swine circulating in the United States during 2009-2014 are susceptible to neuraminidase inhibitors but show lineage-dependent resistance to adamantanes. H274Y-NA in human H1N1 influenza viruses is known to decrease the number of the NA expressed on the cell surface and attenuate virus replication in vitro and in vivo, as well as restrict airborne transmission between ferrets . 2015 Antiviral research Result IV H274Y 0 5 NA;NA 6;80 8;82 25701593 Influenza A viruses of swine circulating in the United States during 2009-2014 are susceptible to neuraminidase inhibitors but show lineage-dependent resistance to adamantanes. I27T-M2 in the classic swine lineage occurred in the A, B, and C sublineages in 2002.7, 2008.2, and 2003.7, respectively. 2015 Antiviral research Result IV I27T 0 4 M2 5 7 25701593 Influenza A viruses of swine circulating in the United States during 2009-2014 are susceptible to neuraminidase inhibitors but show lineage-dependent resistance to adamantanes. occurred after the S31N-M2 IAV-S became established in the swine population. 2015 Antiviral research Result IV S31N 19 23 M2 24 26 25701593 Influenza A viruses of swine circulating in the United States during 2009-2014 are susceptible to neuraminidase inhibitors but show lineage-dependent resistance to adamantanes. Of interest, IC50 values of 3 H1N1 IAV-S with the I117V-NA were on average 7.3-fold higher for oseltamivir than those of the susceptible control (individual IC50 values are shown in Table 2). 2015 Antiviral research Result IV I117V 50 55 56 58 25701593 Influenza A viruses of swine circulating in the United States during 2009-2014 are susceptible to neuraminidase inhibitors but show lineage-dependent resistance to adamantanes. Our analysis suggested that the fixation of the S31N mutation in the IAV-S population occurred as early as 1998.8, but it was not detected in the IAV-S population until 2009. 2015 Antiviral research Result IV S31N 48 52 25701593 Influenza A viruses of swine circulating in the United States during 2009-2014 are susceptible to neuraminidase inhibitors but show lineage-dependent resistance to adamantanes. Regardless, our results show that the emergence and rapid spread of the S31N-M2 amantadine-resistant IAV-S in the U.S. 2015 Antiviral research Result IV S31N 72 76 M2 77 79 25701593 Influenza A viruses of swine circulating in the United States during 2009-2014 are susceptible to neuraminidase inhibitors but show lineage-dependent resistance to adamantanes. S31N-M2 occurred sporadically in the IAV-S of the classic swine lineage, suggesting that this mutation emerged randomly. 2015 Antiviral research Result IV S31N 0 4 M2 5 7 25701593 Influenza A viruses of swine circulating in the United States during 2009-2014 are susceptible to neuraminidase inhibitors but show lineage-dependent resistance to adamantanes. Screening for markers of NAI resistance reported in surveillance or experimental studies revealed 0.38% (13/3396) sequences with the I117V-NA (including 3 IAV-S from this study), 0.24% (8/3396) with the Y155H-NA, and 0.09% (3/3396) with the E119K-NA among N1; 0.24% (8/3396) sequences with the V149A-NA, 0.15% (5/3396) with the I222V-NA, and 0.06% (2/3396) with the Y155H-NA among the N2 IAV-S (Table 3). 2015 Antiviral research Result IV I117V;Y155H;E119K;V149A;I222V;Y155H 133;203;241;294;328;366 138;208;246;299;333;371 NA;NA;NA;NA;NA;NA;NAI 139;209;247;300;334;372;25 141;211;249;302;336;374;28 25701593 Influenza A viruses of swine circulating in the United States during 2009-2014 are susceptible to neuraminidase inhibitors but show lineage-dependent resistance to adamantanes. The frequency of the I27T-M2 was 49% (486/993) in the classic swine lineage. 2015 Antiviral research Result IV I27T 21 25 M2 26 28 25701593 Influenza A viruses of swine circulating in the United States during 2009-2014 are susceptible to neuraminidase inhibitors but show lineage-dependent resistance to adamantanes. The mean EC50 values for viruses with the I27T-M2 were 50 muM (range 34.5-62.6 muM); these values were 7.6-fold and 1.3-fold higher than the average (6.6 muM) and maximum (39.7 muM) plasma concentrations of amantadine in humans, respectively. 2015 Antiviral research Result IV I27T 42 46 M2 47 49 25701593 Influenza A viruses of swine circulating in the United States during 2009-2014 are susceptible to neuraminidase inhibitors but show lineage-dependent resistance to adamantanes. The S31N-M2 accounted for 78% (585/747) of resistant sequences alone and 22% (162/747) in combination with the V27A-M2 in the Eurasian avian lineage. 2015 Antiviral research Result IV S31N;V27A 4;111 8;115 M2;M2 9;116 11;118 25701593 Influenza A viruses of swine circulating in the United States during 2009-2014 are susceptible to neuraminidase inhibitors but show lineage-dependent resistance to adamantanes. The V27A-M2 occurred independently at least twice in 2009 [2009.9 (BCI 2010.20-2009.9) lineage D and 2009.50 (BCI 2010.0-2009.1) lineage E]. 2015 Antiviral research Result IV V27A 4 8 M2 9 11 25701593 Influenza A viruses of swine circulating in the United States during 2009-2014 are susceptible to neuraminidase inhibitors but show lineage-dependent resistance to adamantanes. This finding and the observation that V27A-M2 is present only in combination with S31N-M2 suggests that the emergence of the amantadine-resistant double mutant (S31N-M2 + V27A-M2) in the Eurasian avian lineage of IAV-S in the U.S. 2015 Antiviral research Result IV V27A;S31N;S31N;V27A 38;82;161;171 42;86;165;175 M2;M2;M2;M2 43;87;166;176 45;89;168;178 25701593 Influenza A viruses of swine circulating in the United States during 2009-2014 are susceptible to neuraminidase inhibitors but show lineage-dependent resistance to adamantanes. To evaluate the role of swine as the host for influenza A viruses harboring the I27T-M2, we analyzed sequences with this substitution that were available in the IRD: 96.7% (589/609) genes were of swine origin, and 97.3% (573/609) were reported from the U.S., suggesting that viruses with the I27T-M2 were predominantly circulating in swine populations (data not shown). 2015 Antiviral research Result IV I27T;I27T 80;292 84;296 M2;M2 85;297 87;299 25701593 Influenza A viruses of swine circulating in the United States during 2009-2014 are susceptible to neuraminidase inhibitors but show lineage-dependent resistance to adamantanes. To evaluate the role of the I27T-M2 on the phenotypic susceptibility of IAV-S to amantadine, we tested representative isolates harboring this substitution (Table 5). 2015 Antiviral research Result IV I27T 28 32 M2 33 35 25701593 Influenza A viruses of swine circulating in the United States during 2009-2014 are susceptible to neuraminidase inhibitors but show lineage-dependent resistance to adamantanes. Two amino acid substitutions (I27V and I27T) were present in the IAV-S of classic swine lineage, and four were identified in the viruses of Eurasian avian lineage (V27I, V27A, V27S, and V27F). 2015 Antiviral research Result IV I27V;I27T;V27I;V27A;V27S;V27F 30;39;164;170;176;186 34;43;168;174;180;190 25701593 Influenza A viruses of swine circulating in the United States during 2009-2014 are susceptible to neuraminidase inhibitors but show lineage-dependent resistance to adamantanes. We observed six substitutions at position 27 of M2 protein (V27I, I27V, I27T, V27S, V27F, and V27A) among IAV-S isolated in the U.S. 2015 Antiviral research Result IV V27I;I27V;I27T;V27S;V27F;V27A 60;66;72;78;84;94 64;70;76;82;88;98 M2 48 50 25713566 PB2 segment promotes high-pathogenicity of H5N1 avian influenza viruses in mice. 90-Ala684Thr could replicate in the spleen and kidneys, but the other three mutants only replicated in the lungs with a titer of 3.58-5.75 log10EID50, at a dose of 106 EID50. 2015 Frontiers in microbiology Result IV A684T 3 12 25713566 PB2 segment promotes high-pathogenicity of H5N1 avian influenza viruses in mice. Notably, the Ser715Asn mutation sharply decreased the virulence of rgDK212 in mice (2710.19-fold) (Figures 3A,B, Tables 2, 3). 2015 Frontiers in microbiology Result IV S715N 13 22 25713566 PB2 segment promotes high-pathogenicity of H5N1 avian influenza viruses in mice. The 212-Gln39Lys, 212-Ile649Val, 212-Thr684Ala, and 212-Ser715Asn viruses caused 25.57-29.24% body weight loss, and killed all the mice at 6-9 DPI. 2015 Frontiers in microbiology Result IV Q39K;I649V;T684A;S715N 8;22;37;56 16;31;46;65 25713566 PB2 segment promotes high-pathogenicity of H5N1 avian influenza viruses in mice. The 90-Lys39Gln, 90-Val649Ile, 90-Ala684Thr and 90-Asn715Ser caused 2.12%-29.48% body weight loss, and killed 40-100% of mice. 2015 Frontiers in microbiology Result IV K39Q;V649I;A684T;N715S 7;20;34;51 15;29;43;60 25713566 PB2 segment promotes high-pathogenicity of H5N1 avian influenza viruses in mice. The titer of 212-Thr684Ala in the kidneys was lower than that of rgDK212 (p < 0.05). 2015 Frontiers in microbiology Result IV T684A 17 26 25742269 Oseltamivir-resistant influenza A(H1N1)pdm2009 strains found in Brazil are endowed with permissive mutations, which compensate the loss of fitness imposed by antiviral resistance. 1) (H275Y viruses in red). 2015 Memorias do Instituto Oswaldo Cruz Result IV H275Y 4 9 25742269 Oseltamivir-resistant influenza A(H1N1)pdm2009 strains found in Brazil are endowed with permissive mutations, which compensate the loss of fitness imposed by antiviral resistance. 1) and are predicted to compensate for the negative effects of H275Y change (Hurt et al. 2015 Memorias do Instituto Oswaldo Cruz Result IV H275Y 63 68 25742269 Oseltamivir-resistant influenza A(H1N1)pdm2009 strains found in Brazil are endowed with permissive mutations, which compensate the loss of fitness imposed by antiviral resistance. 2009, 2012); such as S79P, I188T and N225D. 2015 Memorias do Instituto Oswaldo Cruz Result IV S79P;I188T;N225D 21;27;37 25;32;42 25742269 Oseltamivir-resistant influenza A(H1N1)pdm2009 strains found in Brazil are endowed with permissive mutations, which compensate the loss of fitness imposed by antiviral resistance. Although low prevalence of H275Y viruses with permissive mutations in the NA is comparable to what is found in other countries, this information is critical for further drug stockpiling and pandemic preparedness. 2015 Memorias do Instituto Oswaldo Cruz Result IV H275Y 27 32 74 76 25742269 Oseltamivir-resistant influenza A(H1N1)pdm2009 strains found in Brazil are endowed with permissive mutations, which compensate the loss of fitness imposed by antiviral resistance. Among all confirmed cases of A(H1N1)pdm09, 208 samples presented reliable pyrograms, with respect to screening for the H275Y mutation. 2015 Memorias do Instituto Oswaldo Cruz Result IV H275Y 119 124 25742269 Oseltamivir-resistant influenza A(H1N1)pdm2009 strains found in Brazil are endowed with permissive mutations, which compensate the loss of fitness imposed by antiviral resistance. Differently than Australian samples, Japanese, North American and Brazilian samples from 2013 had the change N200S (Storms et al. 2015 Memorias do Instituto Oswaldo Cruz Result IV N200S 109 114 25742269 Oseltamivir-resistant influenza A(H1N1)pdm2009 strains found in Brazil are endowed with permissive mutations, which compensate the loss of fitness imposed by antiviral resistance. For example, the mutations N42S (2012) and N44S (2013) may create new glycosylation sites (Hurt et al. 2015 Memorias do Instituto Oswaldo Cruz Result IV N42S;N44S 27;43 31;47 25742269 Oseltamivir-resistant influenza A(H1N1)pdm2009 strains found in Brazil are endowed with permissive mutations, which compensate the loss of fitness imposed by antiviral resistance. For public health concerns, H275Y viruses from 2012 were found in the cities of Foz do Iguacu (state of Parana) and Florianopolis (state of Santa Catarina), whereas the two samples from 2013 were collected in Nova Iguacu (NIG) (state of Rio de Janeiro) and Porto Alegre (POA) (state of Rio Grande do Sul). 2015 Memorias do Instituto Oswaldo Cruz Result IV H275Y 28 33 25742269 Oseltamivir-resistant influenza A(H1N1)pdm2009 strains found in Brazil are endowed with permissive mutations, which compensate the loss of fitness imposed by antiviral resistance. Our data not only suggests that OST-resistant strains may be present in an even broader area of Brazil or South America, than previously thought, but also draws special attention to the community detection of influenza A(H1N1)pdm09 H275Y in highly populous developing countries in which antiviral resistance surveillance may be neglected. 2015 Memorias do Instituto Oswaldo Cruz Result IV H275Y 232 237 25742269 Oseltamivir-resistant influenza A(H1N1)pdm2009 strains found in Brazil are endowed with permissive mutations, which compensate the loss of fitness imposed by antiviral resistance. Remarkably, one Brazilian sample from 2013 had the change D344N, which is predicted to occur in A(H1N1)pdm09 NA by in silico data and capable of compensating for the reduction in NA activity by H275Y. 2015 Memorias do Instituto Oswaldo Cruz Result IV D344N;H275Y 58;194 63;199 NA;NA 109;179 111;181 25742269 Oseltamivir-resistant influenza A(H1N1)pdm2009 strains found in Brazil are endowed with permissive mutations, which compensate the loss of fitness imposed by antiviral resistance. The NA from Brazilian strains from 2012 and 2013 had the changes V241I and N369K in common. 2015 Memorias do Instituto Oswaldo Cruz Result IV V241I;N369K 65;75 70;80 4 6 25742269 Oseltamivir-resistant influenza A(H1N1)pdm2009 strains found in Brazil are endowed with permissive mutations, which compensate the loss of fitness imposed by antiviral resistance. The permissive mutation N386K, on the other hand, was found in Australia and Japan (Hurt et al. 2015 Memorias do Instituto Oswaldo Cruz Result IV N386K 24 29 25742269 Oseltamivir-resistant influenza A(H1N1)pdm2009 strains found in Brazil are endowed with permissive mutations, which compensate the loss of fitness imposed by antiviral resistance. The V241I and N369K enhance NA expression and activity in in vitro studies and this effect improve A(H1N1)pdm09 fitness. 2015 Memorias do Instituto Oswaldo Cruz Result IV V241I;N369K 4;14 9;19 28 30 25742269 Oseltamivir-resistant influenza A(H1N1)pdm2009 strains found in Brazil are endowed with permissive mutations, which compensate the loss of fitness imposed by antiviral resistance. Two specimens contained A(H1N1)pdm09 virus with the H275Y amino acid substitution indicative for OST resistance were found (Table). 2015 Memorias do Instituto Oswaldo Cruz Result IV H275Y 52 57 25766295 Structure and receptor binding of the hemagglutinin from a human H6N1 influenza virus. For ferret-transmissible H5 and human H7N9 isolates, the cis conformation is stabilized by hydrogen bonding of the Gal-2 6-hydroxyl to the Gly225 main chain and by hydrophobic interaction between Gal-2 C3 and Leu226 (except for the A/Shanghai/1/2013 H7N9 HA L226Q mutant in complex with 3'-SLNLN where the hydrophobic face of Gal-2 makes hydrophobic interactions with other hydrophobic residues of the RBS (PDB entry 4LKG)). 2015 Cell host & microbe Result IV L226Q 258 263 HA 255 257 25766295 Structure and receptor binding of the hemagglutinin from a human H6N1 influenza virus. Furthermore, mutation of Leu226 to Gln results in changes in the phi and psi angles of the Sia-Gal linkage compared to the AH-H7N9 wild type. 2015 Cell host & microbe Result IV L226Q 25 38 25766295 Structure and receptor binding of the hemagglutinin from a human H6N1 influenza virus. Furthermore, the Glu190Val substitution removes a conserved polar interaction of avian receptor analogs with the 190-helix between Sia-1 and the Glu190 carboxyl. 2015 Cell host & microbe Result IV E190V 17 26 25766295 Structure and receptor binding of the hemagglutinin from a human H6N1 influenza virus. In addition, the H6 RBS contains substitutions at two residues that normally contribute to Sia-1 binding in avian HA subtypes, E190V and G228S. 2015 Cell host & microbe Result IV E190V;G228S 127;137 132;142 HA 114 116 25766295 Structure and receptor binding of the hemagglutinin from a human H6N1 influenza virus. In the 220-loop, H6 HA contains the G228S substitution that is associated with the receptor specificity switch of the H2 and H3 human pandemic viruses. 2015 Cell host & microbe Result IV G228S 36 41 HA 20 22 25766295 Structure and receptor binding of the hemagglutinin from a human H6N1 influenza virus. Similar interactions with a human receptor analog were observed in an avian AH-H7N9 L226Q mutant with 6'-SLNLN (PDB entry 4LKK). 2015 Cell host & microbe Result IV L226Q 84 89 25766295 Structure and receptor binding of the hemagglutinin from a human H6N1 influenza virus. Taiwan/2/2013 H6 HA also contains Leu at position 186 instead of Pro, as in A/Chicken/Taiwan/A2837/2013 (Figure S1B). 2015 Cell host & microbe Result IV L186P 34 68 HA 17 19 25766295 Structure and receptor binding of the hemagglutinin from a human H6N1 influenza virus. The Gly228Ser substitution, which is also found in human H2 and H3 isolates, eliminates a conserved hydrogen bond between the Sia-1 9-hydroxyl group and the Gly228 main-chain carbonyl. 2015 Cell host & microbe Result IV G228S 4 13 25768797 Adamantane-resistant influenza a viruses in the world (1902-2013): frequency and distribution of M2 gene mutations. Adamantane-resistant mutations (L26F, V27A, A30T, S31N) were found at positions 26, 27, 30, and 31 in avian and swine influenza viruses. 2015 PloS one Result IV L26F;V27A;A30T;S31N 32;38;44;50 36;42;48;54 25768797 Adamantane-resistant influenza a viruses in the world (1902-2013): frequency and distribution of M2 gene mutations. Adamantane-resistant mutations known as L26F, V27A, A30T, S31N, G34E, and L38F were detected at all six sites (positions 26, 27, 30, 31, 34, and 38) of M2 protein in human influenza viruses (Table 4). 2015 PloS one Result IV L26F;V27A;A30T;S31N;G34E;L38F 40;46;52;58;64;74 44;50;56;62;68;78 M2 152 154 25768797 Adamantane-resistant influenza a viruses in the world (1902-2013): frequency and distribution of M2 gene mutations. Among these resistant viruses, 96.7% (8490/8777) of the H1, 93.6% (3844/4107) of the H3, 66.7% (2/3) of the H4, 83.3% (670/804) of the H5, 92% (23/25) of the H6, 86.1% (124/144) of the H7, 87.5% (232/265) of the H9, 100% (1/1) of the H10, 50% (1/2) of the H11, and 100% (3/3) of the H17 strains demonstrated the S31N substitution (Table 2). 2015 PloS one Result IV S31N 312 316 25768797 Adamantane-resistant influenza a viruses in the world (1902-2013): frequency and distribution of M2 gene mutations. Double resistance mutations at positions 26 and 31 (L26F/S31N), 27 and 31 (V27A/S31N) were also found in these hosts (Table 4). 2015 PloS one Result IV L26F;S31N;V27A;S31N 52;57;75;80 56;61;79;84 25768797 Adamantane-resistant influenza a viruses in the world (1902-2013): frequency and distribution of M2 gene mutations. For double adamantane resistance mutations, the L26F/S31N mutations distributed mainly in Thailand, United Kingdom, and United States. 2015 PloS one Result IV S31N;L26F 53;48 57;52 25768797 Adamantane-resistant influenza a viruses in the world (1902-2013): frequency and distribution of M2 gene mutations. Furthermore, influenza H1, H3 and H5 variants contained the L26F, V27A, A30T, L26F/S31N, and V27A/S31N adamantane resistant mutations (Table 2). 2015 PloS one Result IV L26F;V27A;A30T;L26F;S31N;V27A;S31N 60;66;72;78;83;93;98 64;70;76;82;87;97;102 25768797 Adamantane-resistant influenza a viruses in the world (1902-2013): frequency and distribution of M2 gene mutations. However, No G34E resistant mutation at position 34 was detected in avian influenza viruses. 2015 PloS one Result IV G34E 12 16 25768797 Adamantane-resistant influenza a viruses in the world (1902-2013): frequency and distribution of M2 gene mutations. However, the majority of drug-resistant influenza variants contained point mutations resulting in a serine to-asparagine change at amino acid 31 (S31N) of the M2 protein that conferred adamantane resistance. 2015 PloS one Result IV S31N 146 150 M2 159 161 25768797 Adamantane-resistant influenza a viruses in the world (1902-2013): frequency and distribution of M2 gene mutations. In addition, a small number of S31N adamantane resistance mutations were also detected in canine, cheetah, ferret, mink, cat, equine, bat, and environment influenza viruses (Table 4). 2015 PloS one Result IV S31N 31 35 25768797 Adamantane-resistant influenza a viruses in the world (1902-2013): frequency and distribution of M2 gene mutations. In addition, the L38F/S31N and A30V/S31N mutations were only found in influenza A H3 viruses. 2015 PloS one Result IV L38F;S31N;S31N;A30V 17;22;36;31 21;26;40;35 25768797 Adamantane-resistant influenza a viruses in the world (1902-2013): frequency and distribution of M2 gene mutations. In contrast, the G34E and L38F mutations only distributed in United States and South Korea, respectively. 2015 PloS one Result IV G34E;L38F 17;26 21;30 25768797 Adamantane-resistant influenza a viruses in the world (1902-2013): frequency and distribution of M2 gene mutations. In S1-S6 Tables we show more adamantane resistant variants carrying the S31N resistance mutation at position 31 in H3N2 and H1N1 human influenza viruses after 2003. 2015 PloS one Result IV S31N 72 76 25768797 Adamantane-resistant influenza a viruses in the world (1902-2013): frequency and distribution of M2 gene mutations. Notably, adamantane resistance mutations in all hosts were detected most frequently at position 31 (S31N), followed by position 27 (V27A). 2015 PloS one Result IV S31N;V27A 100;132 104;136 25768797 Adamantane-resistant influenza a viruses in the world (1902-2013): frequency and distribution of M2 gene mutations. Results from our analyses indicated that the viruses with L26F, V27A, A30T, G34E, and L38F mutations were found sporadically. 2015 PloS one Result IV L26F;V27A;A30T;G34E;L38F 58;64;70;76;86 62;68;74;80;90 25768797 Adamantane-resistant influenza a viruses in the world (1902-2013): frequency and distribution of M2 gene mutations. Similarly, Avian and swine influenza viruses also had no L38F adamantane resistant mutation at position 38. 2015 PloS one Result IV L38F 57 61 25768797 Adamantane-resistant influenza a viruses in the world (1902-2013): frequency and distribution of M2 gene mutations. The A30T/S31N mutations were found in Nicaragua and Australia, and the G34E/S31N mutations occured in United Kingdom and Canada. 2015 PloS one Result IV A30T;S31N;G34E;S31N 4;9;71;76 8;13;75;80 25768797 Adamantane-resistant influenza a viruses in the world (1902-2013): frequency and distribution of M2 gene mutations. The G34E and G34E/S31N mutations emerged only in influenza A H1 viruses, whereas the L38F mutation only occurred in the influenza A H2 virus. 2015 PloS one Result IV G34E;G34E;S31N;L38F 4;13;18;85 8;17;22;89 25768797 Adamantane-resistant influenza a viruses in the world (1902-2013): frequency and distribution of M2 gene mutations. The known mutations that confer adamantane resistance are L26F, V27A, A30T, A30V, S31N, G34E and L38F. 2015 PloS one Result IV L26F;V27A;A30T;A30V;S31N;G34E;L38F 58;64;70;76;82;88;97 62;68;74;80;86;92;101 25768797 Adamantane-resistant influenza a viruses in the world (1902-2013): frequency and distribution of M2 gene mutations. The L26F mutation distributed primarily in Hong Kong and New Zealand, the V27A mutation mainly distributed in China and Indonesia, and the A30T mutation distributed primarily in China. 2015 PloS one Result IV L26F;V27A;A30T 4;74;139 8;78;143 25768797 Adamantane-resistant influenza a viruses in the world (1902-2013): frequency and distribution of M2 gene mutations. The L38F/S31N and A30V/S31N mutations distributed only in Taiwan and United States, respectively. 2015 PloS one Result IV L38F;S31N;S31N;A30V 4;9;23;18 8;13;27;22 25768797 Adamantane-resistant influenza a viruses in the world (1902-2013): frequency and distribution of M2 gene mutations. The majority of the V27A/S31N mutations emerged in United States, Spain, South Korea, and Indonesia (Table 6). 2015 PloS one Result IV V27A;S31N 20;25 24;29 25768797 Adamantane-resistant influenza a viruses in the world (1902-2013): frequency and distribution of M2 gene mutations. The most common drug resistance mutation was S31N in human, avian, and swine influenza viruses with the frequencies of 98.7% (10813/10954), 88.1% (909/1032), and 77.4% (1595/2062), respectively. 2015 PloS one Result IV S31N 45 49 25768797 Adamantane-resistant influenza a viruses in the world (1902-2013): frequency and distribution of M2 gene mutations. The S31N mutation distributed across the world (Table 6). 2015 PloS one Result IV S31N 4 8 25768797 Adamantane-resistant influenza a viruses in the world (1902-2013): frequency and distribution of M2 gene mutations. These resistant strains possessed amino acid substitutions in the M2 protein at three positions-L26F, V27A, and S31N. 2015 PloS one Result IV L26F;V27A;S31N 96;102;112 100;106;116 M2 66 68 25768797 Adamantane-resistant influenza a viruses in the world (1902-2013): frequency and distribution of M2 gene mutations. We also found influenza strains with double adamantane resistance mutations (L26F/S31N, V27A/S31N, A30T/S31N, A30V/S31N, G34E/S31N, and L38F/S31N) at positions 26 and 31, 27 and 31, 30 and 31, 31 and 34 or 31 and 38 in the human population. 2015 PloS one Result IV L26F;S31N;V27A;S31N;A30T;S31N;A30V;S31N;G34E;S31N;L38F;S31N 77;82;88;93;99;104;110;115;121;126;136;141 81;86;92;97;103;108;114;119;125;130;140;145 25793397 Characterization of a novel mutation in NS1 protein of influenza A virus induced by a chemical substance for the attenuation of pathogenicity. According to the sequencing of mutant virus genome (clone 1), 2 mutations, C490U in ns gene (P164S in NS1) and G2044U in pb2 (G682C), were detected by comparing them to that of the parent virus (S1. 2015 PloS one Result IV P164S;G682C 93;126 98;131 NS1;PB2 102;121 105;124 25793397 Characterization of a novel mutation in NS1 protein of influenza A virus induced by a chemical substance for the attenuation of pathogenicity. Although we cannot completely deny the influence on attenuation of MFPTr virus to depend on G682C in PB2, it cannot be certain that the degree of influence could be small based on the present result. 2015 PloS one Result IV G682C 92 97 PB2 101 104 25793397 Characterization of a novel mutation in NS1 protein of influenza A virus induced by a chemical substance for the attenuation of pathogenicity. and other researchers reported that IAV which had mutated NS1, NS1P162A, P164A, P167A, showed suppression of activation of the PI3K/Akt signaling pathway, low virus titer and premature apoptosis in infected cells. 2015 PloS one Result IV P164A;P167A 73;80 78;85 NS1;NS1 58;63 61;66 25793397 Characterization of a novel mutation in NS1 protein of influenza A virus induced by a chemical substance for the attenuation of pathogenicity. In addition, no back mutation (S164P in NS1) was detected after an additional 10 passages in the absence of MFPT (data not shown). 2015 PloS one Result IV S164P 31 36 NS1 40 43 25793397 Characterization of a novel mutation in NS1 protein of influenza A virus induced by a chemical substance for the attenuation of pathogenicity. Therefore, it was suggested that NS1 might be a main target protein of MFPT and the P164S mutation might be speculated to contribute to the attenuated pathogenicity of MFPTr viruses. 2015 PloS one Result IV P164S 84 89 NS1 33 36 25793397 Characterization of a novel mutation in NS1 protein of influenza A virus induced by a chemical substance for the attenuation of pathogenicity. Therefore, it was suggested that the introduced mutation (P164S) in NS1 protein could suppress the progression of apoptosis induced by IAV replication. 2015 PloS one Result IV P164S 58 63 NS1 68 71 25793397 Characterization of a novel mutation in NS1 protein of influenza A virus induced by a chemical substance for the attenuation of pathogenicity. This also suggested that the polymerase activity of MFPTr virus might not be affected by another mutation, G682C in PB2. 2015 PloS one Result IV G682C 107 112 PB2 116 119 25861376 Molecular docking of potential inhibitors for influenza H7N9. These results indicated that the oseltamivir resistance caused by R294K mutation for neuraminidase in A/Shanghai/1/2013 might be generated from the H-bond loss, while other molecules might overcome the resistance. 2015 Computational and mathematical methods in medicine Result IV R294K 66 71 85 98 25876137 SNPer: an R library for quantitative variant analysis on single nucleotide polymorphisms among influenza virus populations. The position and call (e.g., A405G) illustrates the universal SNPs from the three subpopulations. 2015 PloS one Result IV A405G 29 34 25928577 Amino acid substitutions in the neuraminidase protein of an H9N2 avian influenza virus affect its airborne transmission in chickens. Mutations D368E, S370L, E313K and G381D in NA of SD01 virus abolished airborne transmission in chickens. 2015 Veterinary research Result IV D368E;S370L;E313K;G381D 10;17;24;34 15;22;29;39 43 45 25928577 Amino acid substitutions in the neuraminidase protein of an H9N2 avian influenza virus affect its airborne transmission in chickens. Mutations E368D, L370S, K313E and D381G in NA of r01/NASS confer virus airborne transmissibility in chickens. 2015 Veterinary research Result IV E368D;L370S;K313E;D381G 10;17;24;34 15;22;29;39 43 45 25928577 Amino acid substitutions in the neuraminidase protein of an H9N2 avian influenza virus affect its airborne transmission in chickens. r01/NASS-381 virus with mutations E368D, L370S, K313E and D381G in NA was generated on the backbone of the r01/NASS virus which had lost airborne transmissibility in chickens. 2015 Veterinary research Result IV E368D;L370S;K313E;D381G 34;41;48;58 39;46;53;63 67 69 25928577 Amino acid substitutions in the neuraminidase protein of an H9N2 avian influenza virus affect its airborne transmission in chickens. Recombinant virus r01/NA381 (which derives from r01/NAHB by two further substitutions: E313K + G381D) was not detected in the air and was not aerially transmitted, which demonstrates the importance of the amino-acid pair 313-381 in aerial transmission. 2015 Veterinary research Result IV E313K;G381D 87;95 92;100 22 24 25928577 Amino acid substitutions in the neuraminidase protein of an H9N2 avian influenza virus affect its airborne transmission in chickens. Recombinant virus r01/NAHB (which derives from rSD01 by the two substitutions D368E + S370L in the HB site) was detected in the air and was aerially transmitted, which demonstrates that the HB site has a modest impact on aerial transmission. 2015 Veterinary research Result IV D368E;S370L 78;86 83;91 25928577 Amino acid substitutions in the neuraminidase protein of an H9N2 avian influenza virus affect its airborne transmission in chickens. The G381D mutation was in a random coil region, and the conversion from a non-polar to polar amino acid may result in changes to protein hydrophilicity. 2015 Veterinary research Result IV G381D 4 9 25928577 Amino acid substitutions in the neuraminidase protein of an H9N2 avian influenza virus affect its airborne transmission in chickens. These results demonstrate that amino acid mutations E368D, L370S, K313E and D381G in the NA protein of r01/NASS enhanced viral NA activity and viral shedding from chickens, and restored airborne transmissibility in chickens, and the HB site had a minor impact on these characteristics, while the amino-acid pair 313-381 had a major effect. 2015 Veterinary research Result IV E368D;L370S;K313E;D381G 52;59;66;76 57;64;71;81 NA;NA 89;127 91;129 25928577 Amino acid substitutions in the neuraminidase protein of an H9N2 avian influenza virus affect its airborne transmission in chickens. To evaluate whether these amino acid mutations were related to H9N2 virus transmission in chickens, we tested two mutants, r01/NAHB (D368E and S370L) which derives from rSD01 by the two substitutions D368E + S370L in the hemadsorption site, and r01/NA381 (D368E, S370L, E313K and G381D) which derives from r01/NAHB by two further substitutions: E313K + G381D (Figure 1A). 2015 Veterinary research Result IV D368E;S370L;D368E;S370L;D368E;S370L;E313K;G381D;E313K;G381D 133;143;200;208;256;263;270;280;345;353 138;148;205;213;261;268;275;285;350;358 249 251 25928577 Amino acid substitutions in the neuraminidase protein of an H9N2 avian influenza virus affect its airborne transmission in chickens. When a G381D mutation occurred simultaneously with an E313K mutation in the beta-fold region, the protein structure was changed significantly, with the distance between the two reduced amino acids (Figure 1B). 2015 Veterinary research Result IV G381D;E313K 7;54 12;59 25939747 Two polar residues within C-terminal domain of M1 are critical for the formation of influenza A Virions. 2C), the results showed that there were two types of oligomerization pattern found in M1-S183A and M1-T185A oligomers. 2015 Cellular microbiology Result IV S183A;T185A 89;102 94;107 M1;M1 86;99 88;101 25939747 Two polar residues within C-terminal domain of M1 are critical for the formation of influenza A Virions. A total of 50% of the M1-S183A particles displayed fourfold symmetry, the other half displayed fivefold symmetry. 2015 Cellular microbiology Result IV S183A 25 30 M1 22 24 25939747 Two polar residues within C-terminal domain of M1 are critical for the formation of influenza A Virions. A total of 67% of the M1-T185A particles displayed fourfold symmetry, while 33% of other particles. 2015 Cellular microbiology Result IV T185A 25 30 M1 22 24 25939747 Two polar residues within C-terminal domain of M1 are critical for the formation of influenza A Virions. Because both M1-S183A and M1-T185A mutants could form 15.8 and 17.2 ml fractions. 2015 Cellular microbiology Result IV S183A;T185A 16;29 21;34 M1;M1 13;26 15;28 25939747 Two polar residues within C-terminal domain of M1 are critical for the formation of influenza A Virions. But the largest elution volumes of mutant proteins, which lack residues with hydroxyl side chains: M1-S183A and M1-T185A, were shifted to 17.2 ml. 2015 Cellular microbiology Result IV S183A;T185A 102;115 107;120 M1;M1 99;112 101;114 25939747 Two polar residues within C-terminal domain of M1 are critical for the formation of influenza A Virions. In cells infected with either WSN-M1-S183A or WSN-M1-T185A, both spherical and filamentous particles were produced. 2015 Cellular microbiology Result IV S183A;T185A 37;53 42;58 M1;M1 34;50 36;52 25939747 Two polar residues within C-terminal domain of M1 are critical for the formation of influenza A Virions. In contrast, 100% of the M1-S183A/T185A particles displayed fivefold symmetry. 2015 Cellular microbiology Result IV S183A;T185A 28;34 33;39 M1 25 27 25939747 Two polar residues within C-terminal domain of M1 are critical for the formation of influenza A Virions. The average width of M1-T185A mutant filamentous virus particles was about 80 nm. 2015 Cellular microbiology Result IV T185A 24 29 M1 21 23 25939747 Two polar residues within C-terminal domain of M1 are critical for the formation of influenza A Virions. The filamentous virus particles produced by WSN-M1-T185A mutant virus only occupied 8% in the total amount of generated virus. 2015 Cellular microbiology Result IV T185A 51 56 M1 48 50 25939747 Two polar residues within C-terminal domain of M1 are critical for the formation of influenza A Virions. The result showed that the ratio of filamentous particles in WSN-M1-S183A was 19%. 2015 Cellular microbiology Result IV S183A 68 73 M1 65 67 25939747 Two polar residues within C-terminal domain of M1 are critical for the formation of influenza A Virions. The single alanine substitution mutation of either of these positions (WSN-M1-S183A and WSN-M1-T185A) did not affect virus generation. 2015 Cellular microbiology Result IV S183A;T185A 78;95 83;100 M1;M1 75;92 77;94 25939747 Two polar residues within C-terminal domain of M1 are critical for the formation of influenza A Virions. The smallest oligomerization unit of the double-point mutant M1-S183A/T185A was also eluted at 17.2 ml. 2015 Cellular microbiology Result IV S183A;T185A 64;70 69;75 M1 61 63 25939747 Two polar residues within C-terminal domain of M1 are critical for the formation of influenza A Virions. The smallest oligomerization units of M1-L181A, M1-T184A, M1-K187A, M1-189A, M1-E190A, M1-Q191A, M1-M192A were also eluted at 15.8 ml, remaining the same as wild-type M1 proteins. 2015 Cellular microbiology Result IV L181A;T184A;K187A;E190A;Q191A;M192A 41;51;61;80;90;100 46;56;66;85;95;105 M1;M1;M1;M1;M1;M1;M1;M1 38;48;58;68;77;87;97;167 40;50;60;70;79;89;99;169 25939747 Two polar residues within C-terminal domain of M1 are critical for the formation of influenza A Virions. There was no obvious difference between wild-type virus and WSN-M1-S183A or WSN-M1-T185A mutant virus in the growth curves. 2015 Cellular microbiology Result IV S183A;T185A 67;83 72;88 M1;M1 64;80 66;82 25939747 Two polar residues within C-terminal domain of M1 are critical for the formation of influenza A Virions. These results demonstrated that the S183A and T185A mutations altered the smallest oligomerization state of M1, resulting in elution volume shift in gel filtration column and production of monomeric proteins. 2015 Cellular microbiology Result IV S183A;T185A 36;46 41;51 M1 108 110 25939747 Two polar residues within C-terminal domain of M1 are critical for the formation of influenza A Virions. Two hundred oligomeric particles from M1-S183A, or M1-T185A or M1-S183A/T185A were obtained, boxed out and processed by following the same procedure as the full-length protein. 2015 Cellular microbiology Result IV S183A;T185A;S183A;T185A 41;54;66;72 46;59;71;77 M1;M1;M1 38;51;63 40;53;65 25966032 Virological characterization of influenza H1N1pdm09 in Vietnam, 2010-2013. A deduced aspartic acid to asparagine substitution observed at position 222 (D222N) of the HA1 protein was detected in a virus isolated from a 45-year-old male patient in November 2013. 2015 Influenza and other respiratory viruses Result IV D222N 77 82 HA1 91 94 25966032 Virological characterization of influenza H1N1pdm09 in Vietnam, 2010-2013. A significant mutation at H275Y related to reduced susceptibility to oseltamivir was found in two isolates in 2011 and 2013 located in groups 7A and 5 (Figure4). 2015 Influenza and other respiratory viruses Result IV H275Y 26 31 25966032 Virological characterization of influenza H1N1pdm09 in Vietnam, 2010-2013. Additional significant changes found in Vietnamese isolates in group 6C included D222N (1 isolate) and G155E and N156K (5 isolates); notably, these mutations have previously been associated with increased virulence or severe and fatal disease (D222G/N) or reduced HI titers when using ferret antiserum raised against A/California/7/2009 (G155E and N156K) (Figure3, Table2). 2015 Influenza and other respiratory viruses Result IV D222N;G155E;N156K;D222G;D222N;G155E;N156K 81;103;113;244;244;338;348 86;108;118;251;251;343;353 25966032 Virological characterization of influenza H1N1pdm09 in Vietnam, 2010-2013. Beside common amino acid changes of group 6 (D97N, S185T, S203T, E374K, and S541N), study viruses in subgroup 6C also showed substitutions at I216M, V234I, T241I, K283E, and E499K compared to the reference virus A/California/7/09. 2015 Influenza and other respiratory viruses Result IV D97N;S185T;S203T;E374K;S541N;I216M;V234I;T241I;K283E;E499K 45;51;58;65;76;142;149;156;163;174 49;56;63;70;81;147;154;161;168;179 25966032 Virological characterization of influenza H1N1pdm09 in Vietnam, 2010-2013. Group 3 was divided by a substitution of K84R (Figure4, Table1). 2015 Influenza and other respiratory viruses Result IV K84R 41 45 25966032 Virological characterization of influenza H1N1pdm09 in Vietnam, 2010-2013. Group 7 (7A and 7B) contains viruses collected during the years 2011, 2012, and 2013 that diverged by the changes of G41R and Q313R, and which were close with viruses from Thailand, USA, and China in the same period compared to group 6 (Figure4, Table1). 2015 Influenza and other respiratory viruses Result IV G41R;Q313R 117;126 121;131 25966032 Virological characterization of influenza H1N1pdm09 in Vietnam, 2010-2013. Group 7 comprised eleven isolates and shared three additional amino acid changes at S143G, A197T, and N260D in comparison with group 6; the amino acid substitution E449K located at the root of clade 7 was first identified in 2011 and was also found in clade 6C. 2015 Influenza and other respiratory viruses Result IV S143G;A197T;N260D;E449K 84;91;102;164 89;96;107;169 25966032 Virological characterization of influenza H1N1pdm09 in Vietnam, 2010-2013. However, a small proportion (8 2%) of viruses showed reduced reactivity by HI (titer of 320); each of these five viruses had amino acid substitutions G155E and N156K in the HA (four isolates from 2013 and one isolate from 2011). 2015 Influenza and other respiratory viruses Result IV G155E;N156K 150;160 155;165 HA 173 175 25966032 Virological characterization of influenza H1N1pdm09 in Vietnam, 2010-2013. Most isolates from 2010 diverged into group 3 (9 isolates) and group 4 (9 isolates) and clustered with isolates from Thailand and China; at the same time, they all shared amino acid changes P83S, S203T, R223Q, and I321V compared with A/California/7/2009 strain (Figure3, Table1). 2015 Influenza and other respiratory viruses Result IV P83S;S203T;R223Q;I321V 190;196;203;214 194;201;208;219 25966032 Virological characterization of influenza H1N1pdm09 in Vietnam, 2010-2013. Subsequently, the substitutions P83S, S203T, R223Q, and I321V were found in all Vietnamese viruses (Table1). 2015 Influenza and other respiratory viruses Result IV P83S;S203T;R223Q;I321V 32;38;45;56 36;43;50;61 25966032 Virological characterization of influenza H1N1pdm09 in Vietnam, 2010-2013. The D222N mutation in relation to disease severity. 2015 Influenza and other respiratory viruses Result IV D222N 4 9 25966032 Virological characterization of influenza H1N1pdm09 in Vietnam, 2010-2013. The isolates collected in 2013 are predominant in this study (24/46) and concentrated in three groups/subgroups (5; and 6B, 6C) with common changes of N44S, V106I, and N248D, and more frequent in group 6 compared to A/California/07/2009 strain. 2015 Influenza and other respiratory viruses Result IV N44S;V106I;N248D 151;157;168 155;162;173 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. Although the MUT-I223V is capable of attaining high viral loads, its longer eclipse delay and shorter infectious lifespan relative to its wild-type counterpart in the H1N1pdm09 background puts it at a slight fitness disadvantage over the wild-type in the absence of pressure by oseltamivir therapy. 2015 PloS one Result IV I223V 17 22 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. As previously determined, the H275Y mutation is associated with a significant, disadvantageous reduction in total (RNA) and infectious (PFU) virus production rates (p < 0.001 and p = 0.01 respectively) which are over-compensated by an advantageous increase in the infectivity of the virus (beta, 500%, p = 0.005). 2015 PloS one Result IV H275Y 30 35 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. Comparing the H275Y and I223V oseltamivir-resistant mutations. 2015 PloS one Result IV H275Y;I223V 14;24 19;29 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. Comparing the MUT-H275Y with the MUT-I223V reveals that in the absence of oseltamivir (Fig 4C) the MUT-H275Y does produce more infectious virus (p = 0.04) and infects more cells (p < 0.001), but produces a similar amount of total virus compared with the MUT-I223V. 2015 PloS one Result IV H275Y;I223V;H275Y;I223V 18;37;103;258 23;42;108;263 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. Effect of the I223V mutation in the H1N1pdm09 background. 2015 PloS one Result IV I223V 14 19 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. Even with the relatively poor level of resistance offered by the I223V mutation, the presence of oseltamivir greatly reduces the fitness of the WT-I223 compared to that of the resistant MUT-I223V resulting in a lower peak of total virus (1.3 x 107 to 1.9 x 109 RNA copies/mL, p < 0.001), infectious virus (4.5 x 104 to 1.3 x 107 PFU/mL, p < 0.001), and a significant difference in the total fraction of cells infected (0.03 to 0.84, p < 0.001). 2015 PloS one Result IV I223V;I223V 65;190 70;195 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. Fig 2B presents a much more conservative scenario, with the inclusion of a simulated, oseltamivir concentration of 15nM, which corresponds to an efficacy of 97% and 85% against the WT-I223 and MUT-I223V strains, respectively (see Methods). 2015 PloS one Result IV I223V 197 202 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. Fig 2B presents a second simulated competition experiment between WT-I223 and MUT-I223V, but this time in the presence of oseltamivir. 2015 PloS one Result IV I223V;I223V 83;82 88;87 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. For the simulated competition between the WT-H275 vs MUT-H275Y (Fig 4A), the wild-type produces significantly more total virus (RNA copies, p = 0.04), but comparable concentrations infectious virus, infecting an equivalent fraction of the cells. 2015 PloS one Result IV H275Y 57 62 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. Having two sets of assays, each with the wild-type and a single mutant, enables us to compare side-by-side the effects of the I223V mutation to those of the H275Y mutation in the same H1N1pdm09 background. 2015 PloS one Result IV I223V;H275Y 126;157 131;162 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. Here we are evaluating a different aliquot of this same A/Quebec/144147/09 H1N1pdm09 wild-type strain sample (WT-I223) against another oseltamivir-resistant variant containing, instead, the single mutation I223V in its NA (MUT-I223V). 2015 PloS one Result IV I223V;I223V 206;227 211;232 219 221 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. Here, both MUT-H275Y and MUT-I223V strains have similar eclipse phase lengths, but the MUT-H275Y has a significantly increased viral infectiousness beta, relative to the MUT-I223V strain. 2015 PloS one Result IV H275Y;I223V;H275Y;I223V 15;29;91;174 20;34;96;179 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. If a higher dose of oseltamivir was administered, the relative fitness advantage of the MUT-I223V over the WT-I223 would be even more significant. 2015 PloS one Result IV I223V 92 97 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. In contrast, the I223V mutation appears to cause only disadvantageous changes (increase in the eclipse phase length and a decrease in the infectious cell lifespan or duration of virus production) with no significant compensatory advantages, suggesting it is likely overall less fit than its wild-type counterpart. 2015 PloS one Result IV I223V 17 22 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. In contrast, the I223V mutation causes no such changes in virus production rates or virus infectivity. 2015 PloS one Result IV I223V 17 22 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. In Fig 1A and 1B, the total viral load (RNA/mL) plateau in both the MC and SC assays are equivalent for WT-I223 and MUT-I223V. 2015 PloS one Result IV I223V 120 125 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. In previous work we determined the viral replication parameters characterizing the fitness of the wild-type A/Quebec/144147/09 H1N1pdm09 strain (WT-H275) and compared them against those of its oseltamivir-resistant variant containing the single mutation H275Y in its NA (MUT-H275Y). 2015 PloS one Result IV H275Y;H275Y 254;275 259;280 267 269 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. In previous work we explored the effect of another N1 NA mutation conferring oseltamivir resistance, the H275Y mutation, using a different aliquot of the same A/Quebec/144147/09 H1N1pdm09 strain sample. 2015 PloS one Result IV H275Y 105 110 54 56 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. In previous work, we estimated parameter values using our model, and then used these estimates to simulate and successfully predict the course and outcome of a true competition experiment conducted experimentally between the WT-H275 and MUT-H275Y strains. 2015 PloS one Result IV H275Y 241 246 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. In the presence of a NA inhibitor such as oseltamivir, the H1N1pdm09 MUT-I223V can overtake its oseltamivir-sensitive wild-type counterpart and become the dominant strain. 2015 PloS one Result IV I223V 73 78 21 23 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. In the presence of oseltamivir (Fig 4B), the wild-type's virus production rates are highly-suppressed, and MUT-H275Y gains a significant competitive advantage producing more total and infectious virus and infecting the most cells. 2015 PloS one Result IV H275Y 111 116 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. In the presence of oseltamivir (Fig 4D), the fitness advantage of the MUT-H275Y is emphasized, dominating the MUT-I223V strain significantly on all fronts, owing to its higher resistance to oseltamivir compared to the MUT-I223V strain. 2015 PloS one Result IV H275Y;I223V;I223V 74;114;222 79;119;227 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. Indeed, we computed a viral burst size of 6.5103RNA/cell for WT-I223 and 5.7103RNA/cell for MUT-I223V, a difference that is not statistically significant (p = 0.76). 2015 PloS one Result IV I223V 96 101 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. Observing the same plateau for both viruses indicates that the WT-I223 and MUT-I223V have the same virus burst size (p RNA tau I). 2015 PloS one Result IV I223V 79 84 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. Overall, the H275Y mutation causes a mixture of disadvantageous (increase in eclipse phase length and a decrease in virus production) and advantageous (increase in virus infectivity, beta) changes in viral replication parameters, leading to an overall fitness similar to that of its WT counterpart, as reported previously. 2015 PloS one Result IV H275Y 13 18 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. Specifically, since WT-I223 (current study) and WT-H275 (previous work) are different aliquots of the same strain sample, we express parameters for the MUT-I223V (or MUT-H275Y) in terms of fold-change from WT-I223 (or WT-H275). 2015 PloS one Result IV I223V;H275Y 156;170 161;175 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. The MUT-I223V has an eclipse period (tau E) which is 3.6 h longer (10.5 h vs 6.9 h, p < 0.001), and an infectious lifespan (tau I) 17 h shorter (11 h vs 28 h, p = 0.04) than that of its H1N1pdm09 WT-I223 counterpart. 2015 PloS one Result IV I223V 8 13 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. The parameter distributions extracted from the MCMC analysis (see Methods) for the H1N1pdm09 strain A/Quebec/144147/09 (WT-I223) and its mutant counterpart (MUT-I223V) are presented in Table 1, and the fit of the model to the data is presented in Fig 1. 2015 PloS one Result IV I223V 161 166 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. The two mutations are similar in the fact that both cause a significant (p < 0.001) increase in the length of the eclipse phase (tau E, 35% and 51% for H275Y and I223V, respectively), conferring a fitness disadvantage. 2015 PloS one Result IV H275Y;I223V 152;162 157;167 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. They also cause a disadvantageous reduction in the length of the infectious lifespan (tau I), and an advantageous reduction in the time required for one infectious cell to infect one other (t infect), but only the reduction in tau I for the I223V mutation was statistically significant (p = 0.04). 2015 PloS one Result IV I223V 241 246 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. They reveal that in the absence of NA inhibitors, WT-I223 has a definite replicative advantage over MUT-I223V in terms of the peak total viral load (1.5 x 1010 to 5.2 x 108 RNA copies/mL, p = 0.002), infectious virus titer (5.4 x 107 to 3.9 x 106 PFU/mL, p < 0.001), and fraction of cells infected (0.96 to 0.04, p < 0.001). 2015 PloS one Result IV I223V 104 109 35 37 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. This is in accordance with the frequency of emergence of MUT-H275Y in patients undergoing oseltamivir therapy, as ~ 350nM oseltamivir corresponds to an efficacy of 99.9% for the wild-type, 99.3% for the MUT-I223V but only 44% for the MUT-H275Y. 2015 PloS one Result IV H275Y;I223V;H275Y 61;207;238 66;212;243 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. This is primarily caused by the increase in the eclipse phase (tau E) for the MUT-I223V which creates a significant delay in its viral replication cycle, enabling the WT-I223 to take the lead early and retain it; a clear fitness advantage. 2015 PloS one Result IV I223V 82 87 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. We also directly compare the fitness of the wild-type and single-mutant MUT-I223V strains by performing a simulated competition experiment based on the results of the MCMC analysis. 2015 PloS one Result IV I223V 76 81 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. We find that the MUT-I223V single mutant in the H1N1pdm09 background has no statistically significant effect on most viral replication parameters, with two exceptions. 2015 PloS one Result IV I223V 21 26 25999284 Egg-adaptive mutations in H3N2v vaccine virus enhance egg-based production without loss of antigenicity or immunogenicity. CVV RG269, which carried the G1861V + N2461K HA substitutions, grew best(TRBC hemagglutination titer = 2048, log10 PFU/ml = 9.4); RG277, containing the N1651K + D902N HA substitutions, grew least readily (TRBC hemagglutination titer = 256, log10 PFU/ml = 7.9) and was excluded from further study. 2015 Vaccine Result IV G1861V;N2461K;N1651K;D902N 29;38;152;161 35;44;158;166 HA;HA 45;167 47;169 25999284 Egg-adaptive mutations in H3N2v vaccine virus enhance egg-based production without loss of antigenicity or immunogenicity. CVV RG275, containing HA mutation H1831L, grew very poorly in MDCK cells and moderately in eggs. 2015 Vaccine Result IV H1831L 34 40 HA 22 24 25999284 Egg-adaptive mutations in H3N2v vaccine virus enhance egg-based production without loss of antigenicity or immunogenicity. CVVs RG277 and RG281, containing the HA amino acid substitutions N1651K + D902N (the subscript two indicates HA2) and HA-N1651K + I102M, respectively, yielded titers similar to those of RG267 (Table 2). 2015 Vaccine Result IV N1651K;D902N;N1651K;I102M 65;74;121;130 71;79;127;135 HA;HA;HA 37;109;118 39;111;120 25999284 Egg-adaptive mutations in H3N2v vaccine virus enhance egg-based production without loss of antigenicity or immunogenicity. RG267, containing HA-G1861V, grew well in eggs (hemagglutination titer: 512, log10 pfu/ml = 8.6), and replication was enhanced by the additional mutation N2461K. 2015 Vaccine Result IV G1861V;N2461K 21;154 27;160 HA 18 20 25999284 Egg-adaptive mutations in H3N2v vaccine virus enhance egg-based production without loss of antigenicity or immunogenicity. The WT HA of RG265 acquired mutations similar to those of RG271 (L1941I + Y2331H) and displayed significant variation in antigenicity (Table 2). 2015 Vaccine Result IV L1941I;Y2331H 65;74 71;80 HA 7 9 25999284 Egg-adaptive mutations in H3N2v vaccine virus enhance egg-based production without loss of antigenicity or immunogenicity. Therefore, the egg-adaptive HA mutations G1861V + N2461K, N1651K + G1861V, T1281N + N1651K + R762G, and T1281N + N1651K + I102M did not significantly alter viral immunogenicity. 2015 Vaccine Result IV G1861V;N2461K;N1651K;G1861V;T1281N;N1651K;R762G;T1281N;N1651K;I102M 41;50;58;67;75;84;93;104;113;122 47;56;64;73;81;90;98;110;119;127 HA 28 30 25999284 Egg-adaptive mutations in H3N2v vaccine virus enhance egg-based production without loss of antigenicity or immunogenicity. This reference antiserum inhibited hemagglutination for the egg-passaged (E1) CVVs RG271 (HA L1941I/Y2331H) and RG275 (HA H1831L) more weakly than did homologous virus, RG265-C1, indicating that antigenicity varied in the HAs of RG271-E1 and RG275-E1. 2015 Vaccine Result IV Y2331H;H1831L;L1941I 100;122;93 106;128;99 HA;HA 90;119 92;121 25999284 Egg-adaptive mutations in H3N2v vaccine virus enhance egg-based production without loss of antigenicity or immunogenicity. To understand the effect of additional mutations acquired by RG279 and RG281 during six passages in eggs, we rescued two additional CVVs, designated RG314 (HA-T1281N + N1651K + R762G) and RG316 (HA-T1281N + N1651K + I102M). 2015 Vaccine Result IV T1281N;N1651K;R762G;T1281N;N1651K;I102M 159;168;177;198;207;216 165;174;182;204;213;221 HA;HA 156;195 158;197 25999284 Egg-adaptive mutations in H3N2v vaccine virus enhance egg-based production without loss of antigenicity or immunogenicity. We found that the NA amino acid change I71 T (with WT or mutant HA) did not affect virus growth (in MDCK cells or eggs) orantigenicity (data not shown); therefore, I71 NA was selected for further study. 2015 Vaccine Result IV I71T 39 44 HA;NA;NA 64;18;168 66;20;170 26038410 Adaptive mutation in influenza A virus non-structural gene is linked to host switching and induces a novel protein by alternative splicing. Cell free transcription/translation of radioactively labeled NS1-wt and NS1 D125G(GAT GGT) resulted in indistinguishable 26-kDa NS1 protein bands without the 20-kDa NS3 protein that was, however, synthesized from the synthetic NS3 cDNA construct (Figure 5A), confirming that the NS3 protein band was the product of this novel transcript. 2012 Emerging microbes & infections Result IV D125G 76 81 NS;NS;NS;NS1;NS1;NS1 165;227;279;61;72;128 167;229;281;64;75;131 26038410 Adaptive mutation in influenza A virus non-structural gene is linked to host switching and induces a novel protein by alternative splicing. Expression of the synthetic NS3 cDNA in transfected 293T cells also resulted in the production of the 20-kDa NS3 protein band detectable by anti-NS1 immunoblotting that was also synthesized from the NS1 D125G(GAT GGT) construct but not from the NS1 D125G(GAT-GGC) mutant (with the same NS1 coding sequence but with a defective splice donor site) (Figure 5B), indicating that NS3 protein production is dependent on splicing and furthermore is not the product of post-translational modification of the NS1 D125G mutant protein. 2012 Emerging microbes & infections Result IV D125G;D125G;D125G 203;249;504 208;254;509 NS;NS;NS;NS1;NS1;NS1;NS1;NS1 28;109;375;145;199;245;286;500 30;111;377;148;202;248;289;503 26038410 Adaptive mutation in influenza A virus non-structural gene is linked to host switching and induces a novel protein by alternative splicing. In contrast, growth in mouse cells showed a significant (P<0.05) increase in viral growth compared to wt (Figure 1C), where mutation D125G enhanced growth 102-fold, followed by the double and M124I mutants, with 41- and 2-fold increased yields respectively. 2012 Emerging microbes & infections Result IV D125G;M124I 133;192 138;197 26038410 Adaptive mutation in influenza A virus non-structural gene is linked to host switching and induces a novel protein by alternative splicing. Likewise, in vivo viral growth in mouse lungs showed increased growth for D125G and the double-mutant 1 day post-infection, with 20- and 16-fold increases relative to wt, respectively (Figure 1D). 2012 Emerging microbes & infections Result IV D125G 74 79 26038410 Adaptive mutation in influenza A virus non-structural gene is linked to host switching and induces a novel protein by alternative splicing. The A to G mutation at position 374 forms a requisite GU donor splice site at the 5' end of the intron (Figure 4C and 4D), thus producing NS3 via the novel donor splice site at position 373 and the NEP's acceptor splice site at position 503. 2012 Emerging microbes & infections Result IV A374G;A374C;A374G 3;3;4 190;190;35 NEP;NS 198;138 201;140 26038410 Adaptive mutation in influenza A virus non-structural gene is linked to host switching and induces a novel protein by alternative splicing. The addition of the 124I to the A374G(125G) mutation increased the likelihood score for the NS3 donor splice site (Figure 4D), since the 124I mutation further increased complementarity with the spliceosomal U1 snRNA binding sequence, ACUUACCU (identical in human and mouse), which initiates splicing. 2012 Emerging microbes & infections Result IV A374G 32 37 NS 92 94 26038410 Adaptive mutation in influenza A virus non-structural gene is linked to host switching and induces a novel protein by alternative splicing. The level of NS3 mRNA was undetectable for wt and 124I NS, and detectable in the A374G(125G) mutant with a 10-fold higher level in the double-mutant (Figure 4F and Supplementary Figure S4). 2012 Emerging microbes & infections Result IV A374G 81 86 NS;NS 13;55 15;57 26038410 Adaptive mutation in influenza A virus non-structural gene is linked to host switching and induces a novel protein by alternative splicing. The NS1 D125G and NS3 proteins are both stable in infected cells as previously shown in pulse labeling experiments (where the NS3 protein was initially identified as NS*). 2012 Emerging microbes & infections Result IV D125G 8 13 NS;NS;NS;NS1 18;126;166;4 20;128;168;7 26038410 Adaptive mutation in influenza A virus non-structural gene is linked to host switching and induces a novel protein by alternative splicing. The NS3 protein is a product of alternative splicing due to the A374G(125G) mutation. 2012 Emerging microbes & infections Result IV A374G 64 69 NS 4 6 26038410 Adaptive mutation in influenza A virus non-structural gene is linked to host switching and induces a novel protein by alternative splicing. The wt and M124I mutant sequences showed one putative donor and acceptor splice site at position 30 and 503 (Figure 4C) corresponding to the NEP splice sites. 2012 Emerging microbes & infections Result IV M124I 11 16 NEP 141 144 26038410 Adaptive mutation in influenza A virus non-structural gene is linked to host switching and induces a novel protein by alternative splicing. These natural observations are all in addition to the A374G (D125G) mutation which was also independently selected upon mouse adaptation of the human IAV (A/Aichi/2/68(H3N2)). 2012 Emerging microbes & infections Result IV A374G;D125G 54;61 59;66 26038410 Adaptive mutation in influenza A virus non-structural gene is linked to host switching and induces a novel protein by alternative splicing. This was in contrast to the phenotype seen on infection of mice with NS1 D125G(GAT GGT) where IFN-beta induction was significantly reduced relative to HK-wt indicating that IFN antagonism is a complex biological trait that differs for infections performed in vivo versus in vitro. 2012 Emerging microbes & infections Result IV D125G 73 78 NS1 69 72 26038410 Adaptive mutation in influenza A virus non-structural gene is linked to host switching and induces a novel protein by alternative splicing. Thus, the D125G NS mutation in human IAV showed a gain of function for viral replication in mouse tissues. 2012 Emerging microbes & infections Result IV D125G 10 15 NS 16 18 26038410 Adaptive mutation in influenza A virus non-structural gene is linked to host switching and induces a novel protein by alternative splicing. Thus, the gain of function shown for viral replication in mouse tissues due to the D125G(GAT GGT) NS mutation in human IAV was not due to the NS1 amino acid substitution at position 125 from aspartic acid to glycine, but was rather due to the novel splicing of the NS gene to produce NS3. 2012 Emerging microbes & infections Result IV D125G;D125G 83;182 88;215 NS;NS;NS;NS1 98;265;284;142 100;267;286;145 26038410 Adaptive mutation in influenza A virus non-structural gene is linked to host switching and induces a novel protein by alternative splicing. Thus, the increased replication due to the NS1 D125G(GAT GGT) in M1 cells cannot be explained by effects on inhibition of IFN-beta induction. 2012 Emerging microbes & infections Result IV D125G 47 52 M1;NS1 65;43 67;46 26038410 Adaptive mutation in influenza A virus non-structural gene is linked to host switching and induces a novel protein by alternative splicing. To assess the effect of the A374G(125G) mutation on RNA expression levels, RNA from infected M1 cells was quantified by quantitative RT-PCR for NS1, NEP, NS3, as well as a late (M1) and early gene transcript (NP). 2012 Emerging microbes & infections Result IV A374G 28 33 M1;M1;NEP;NP;NS;NS1 93;178;149;209;154;144 95;180;152;211;156;147 26038410 Adaptive mutation in influenza A virus non-structural gene is linked to host switching and induces a novel protein by alternative splicing. To determine how the M124I and D125G NS1 mutations affect viral replication, we measured viral growth in different hosts; in vitro, in MDCK canine kidney epithelial cells, M1 mouse kidney epithelial cells, A549 human lung epithelial cells, and in vivo, in CD-1 mouse lungs (Figure 1). 2012 Emerging microbes & infections Result IV M124I;D125G 21;31 26;36 M1;NS1 172;37 174;40 26038410 Adaptive mutation in influenza A virus non-structural gene is linked to host switching and induces a novel protein by alternative splicing. To determine whether the initial observation of increased growth observed in mouse lungs and cells was due to the D125G(A374G) mutation in the NS1 protein or due to NS3, the novel splice product of the NS gene, we generated recombinant HK (A/HK/1/68) viruses with a glycine at position 125 of the NS1 protein, but lacking the novel NS3 donor splice site (Figure 6A). 2012 Emerging microbes & infections Result IV A374G;D125G 120;114 125;119 NS;NS;NS;NS1;NS1 165;202;332;143;297 167;204;334;146;300 26038410 Adaptive mutation in influenza A virus non-structural gene is linked to host switching and induces a novel protein by alternative splicing. To further test the hypothesis that the novel 20-kDa NS3 band was the product of translation of a novel splice product of the NS gene, we expressed the NS1 D125G(GAT GGT) mutant NS gene, as well as a synthetic cDNA construct of NS3 in splicing competent 293T cells and the splicing incompetent coupled prokaryotic T7 transcription/reticulocyte translation systems. 2012 Emerging microbes & infections Result IV D125G 156 161 NS;NS;NS;NS;NS1 53;126;178;228;152 55;128;180;230;155 26038410 Adaptive mutation in influenza A virus non-structural gene is linked to host switching and induces a novel protein by alternative splicing. To identify the specific effects of the M124I(A372G) and D125G(A374G) mutations on virus biology, we generated recombinant IAV containing the wt NS, M124I, D125G or the double-mutant (M124I+D125G) genes in the A/Hong Kong/1/1968 (H3N2) genetic background. 2012 Emerging microbes & infections Result IV A372G;M124I;A374G;D125G;M124I;D125G;M124I;D125G 46;40;63;57;149;156;184;190 51;45;68;62;154;161;189;195 NS 145 147 26038410 Adaptive mutation in influenza A virus non-structural gene is linked to host switching and induces a novel protein by alternative splicing. We measured growth, as performed in Figure 1, in MDCK and M1 cells at 48 hpi and 1 day post-infection in CD-1 mice relative to wt and D125G(A374G) (Figure 4C). 2012 Emerging microbes & infections Result IV A374G;D125G 140;134 145;139 M1 58 60 26038410 Adaptive mutation in influenza A virus non-structural gene is linked to host switching and induces a novel protein by alternative splicing. Whereas HK-wt and NS1 M124I induced minimally detectable levels of IFN-beta, the HK NS1 D125G(GAT GGT) mutant produced significantly more IFN-beta that was however reduced in combination with the M124I mutation (Supplementary Figure S6). 2012 Emerging microbes & infections Result IV M124I;D125G;M124I 22;88;196 27;93;201 NS1;NS1 18;84 21;87 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. Among them, clone 27 had no additional mutations other than NA R292K and HA R220G (H3 numbering) (data not shown). 2014 Emerging microbes & infections Result IV R292K;R220G 63;76 68;81 HA;NA 73;60 75;62 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. As expected, oseltamivir carboxylate exhibited a poor inhibitory effect against SH5190 R292K (IC50>1000 microM, Figure 4 and Table 2). 2014 Emerging microbes & infections Result IV R292K 87 92 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. As shown in Figure 1, SH5190 R292K replicated to comparable titers as the wild-type counterpart in multicycle replication conditions in MDCK cells. 2014 Emerging microbes & infections Result IV R292K 29 34 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. As shown in Figure 5A, SH5190 R292K-infected mice exhibited a significant delay in weight loss compared to mice infected with the wild-type strain (Figure 5A). 2014 Emerging microbes & infections Result IV R292K 30 35 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. Considering the adverse clinical outcome associated with the emergence of the NA R292K mutation after receiving NAI treatment, there is a pressing need to evaluate alternative therapeutic options to control this mutant virus. 2014 Emerging microbes & infections Result IV R292K 81 86 NA;NAI 78;112 80;115 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. Evaluation of drug combinations on the R292K mutant virus. 2014 Emerging microbes & infections Result IV R292K 39 44 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. For the R292K mutant, however, all combinations among NAIs and non-NAIs exhibited antagonism largely or merely additive effects at IC50 (Table 3), which may be because the mutant virus is partially resistant to both zanamivir and peramivir. 2014 Emerging microbes & infections Result IV R292K 8 13 NAI;NAI 54;67 58;71 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. For this consideration, we further investigated if the combinations of non-NAIs (T705, ribavirin or NT-300) with zanamivir or peramivir, which retained partial inhibitory activity against the R292K mutant virus, and combination between non-NAIs, may act synergistically to suppress growth of the R292K variant. 2014 Emerging microbes & infections Result IV R292K;R292K 192;296 197;301 NAI;NAI 75;240 79;244 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. However, a greater than one log increase of IC50 in SH5190 R292K was observed for NT-300 (IC50 values of 1.60 microM). 2014 Emerging microbes & infections Result IV R292K 59 64 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. However, SH5190 R292K exhibited a highly reduced susceptibility to oseltamivir carboxylate (IC50>1000 nM), which was out of the range of drug concentrations used for the assay. 2014 Emerging microbes & infections Result IV R292K 16 21 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. However, the wild-type and the R292K variant showed an apparent difference in virus induced morbidity. 2014 Emerging microbes & infections Result IV R292K 31 36 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. In contrast, the plaque size of SH5190 R292K was not significantly affected in the presence (mean diameter=1.8 mm) or absence (mean diameter=1.8 mm) of 10microM oseltamivir carboxylate. 2014 Emerging microbes & infections Result IV R292K 39 44 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. In SH5190 R292K-infected lungs, the alveolar septum was slightly thickened with the infiltration of inflammatory cells. 2014 Emerging microbes & infections Result IV R292K 10 15 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. Mice inoculated with a high dose of the wild-type virus resulted in a 45.5% (5/11) survival, whereas 90.9% (10/11) of the mice survived after infection with the same dose of the R292K variant after 15 days of observation (P=0.018) (Figure 5C). 2014 Emerging microbes & infections Result IV R292K 178 183 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. Moreover, we did not observe any reversion of the R292K mutation to wild-type 292R in the absence of oseltamivir or exogenous NA during subsequent experiments, as evidenced by both Sanger sequencing and Taqman SNP qPCR assay. 2014 Emerging microbes & infections Result IV R292K 50 55 126 128 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. Next, we analyzed the sensitivity of SH5190 and SH5190 R292K against available NAIs and non-NAIs in a cell-based virus yield reduction assay. 2014 Emerging microbes & infections Result IV R292K 55 60 NAI;NAI 79;92 83;96 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. Of note, we did not detect a reversion of the R292K mutation back to the wild-type in the lungs of mice inoculated with SH5190 R292K during the observation period; in parallel, no R292K mutation was found in mice inoculated with the wild-type virus, as evidenced by the SNP qPCR assay (data not shown). 2014 Emerging microbes & infections Result IV R292K;R292K;R292K 46;127;180 51;132;185 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. Only at 100 microM (mean diameter=1.0 mm) or 1000 microM (mean diameter=0.8 mm) of oseltamivir carboxylate was there notable plaque size reduction for SH5190 R292K, which indicated the highly resistant phenotype to oseltamivir. 2014 Emerging microbes & infections Result IV R292K 158 163 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. Pathogenesisof R292K mutant virus in experimentally infected mice. 2014 Emerging microbes & infections Result IV R292K 15 20 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. Sensitivity of SH5190 and SH5190 R292K to NAIs and non-NAIs in virus yield reduction assay. 2014 Emerging microbes & infections Result IV R292K 33 38 NAI;NAI 42;55 46;59 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. Sensitivity of SH5190 and SH5190 R292K to NAIs in enzyme inhibition assay. 2014 Emerging microbes & infections Result IV R292K 33 38 NAI 42 46 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. Sensitivity of SH5190 and SH5190 R292K to oseltamivir carboxylate in plaque reduction assay. 2014 Emerging microbes & infections Result IV R292K 33 38 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. Sustained viral shedding was accompanied by the rapid emergence of the NA R292K quasispecies. 2014 Emerging microbes & infections Result IV R292K 74 79 71 73 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. The difference between SH5190 and SH5190 R292K in mouse lung titers is consistent with the trend in weight loss (Figure 5A) and the lethality of the viruses in mice (Figure 5C). 2014 Emerging microbes & infections Result IV R292K 41 46 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. The difference between the wild-type and the R292K mutant was best exemplified at day 5 after infection in the high (P<0.0001, Mann-Whitney U test) dose group. 2014 Emerging microbes & infections Result IV R292K 45 50 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. The NA-Star assay was applied to determine the IC50 of NA enzymatic activity of SH5190 and SH5190 R292K in the presence of three clinically available NAIs: oseltamivir carboxylate, zanamivir and peramivir. 2014 Emerging microbes & infections Result IV R292K 98 103 NA;NA;NAI 4;55;150 6;57;154 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. The presence of the R292K mutant was identified in the mixed population at a proportion of 77%, by Taqman SNP assay (data not shown). 2014 Emerging microbes & infections Result IV R292K 20 25 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. The R292K variant was observed to replicate less efficiently than the wild-type at day 3 post inoculation (2.32 versus 3.49 log10copy/mug RNA, P=0.05, Mann-Whitney U test). 2014 Emerging microbes & infections Result IV R292K 4 9 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. The R292K variant was successfully isolated under these conditions. 2014 Emerging microbes & infections Result IV R292K 4 9 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. The sensitivity of the SH5190 and SH5190 R292K to NAIs was further confirmed using enzymatic methods. 2014 Emerging microbes & infections Result IV R292K 41 46 NAI 50 54 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. The significant difference in oseltamivir sensitivity between SH5190 and SH5190 R292K was first confirmed by a plaque reduction assay under increasing concentration of oseltamivir carboxylate. 2014 Emerging microbes & infections Result IV R292K 80 85 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. The titers of the SH5190 R292K were even higher than those of the wild-type SH5190 at 12 h (P<0.05). 2014 Emerging microbes & infections Result IV R292K 25 30 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. This result suggested that the R292K mutation can be stably maintained in cell culture. 2014 Emerging microbes & infections Result IV R292K 31 36 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. Thus, clone 27 (named SH5190 R292K) exhibited minimum adaptive mutation and was chosen in conjunction with SH5190 for further study. 2014 Emerging microbes & infections Result IV R292K 29 34 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. To gain a better understanding of the pathogenesis of the wild-type and mutant H7N9 virus in vivo, C57BL/6 mice were intranasally inoculated with either SH5190 or SH5190 R292K at 105 PFU (high dose group) or 103 PFU (low dose group) and were monitored for 15 days. 2014 Emerging microbes & infections Result IV R292K 170 175 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. To isolate the R292K variant, limited serial passages in the presence of an ascending concentration of oseltamivir carboxylate (from 10 microM to 500 microM) and exogenous neuraminidase (2 mU/mL) were performed. 2014 Emerging microbes & infections Result IV R292K 15 20 172 185 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. To this end, we performed a cell-based assay to evaluate the inhibition of virus replication by three non-NAIs, T-705 (favipiravir), ribavirin and NT-300 (nitazoxanide), on the wild-type and the R292K mutant. 2014 Emerging microbes & infections Result IV R292K 195 200 NAI 106 110 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. We first compared the proliferative property of SH5190 and the R292K variant in cell culture. 2014 Emerging microbes & infections Result IV R292K 63 68 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. We hypothesized that the low NA activity possessed by the R292K variant might render the mutant strain less competent at competing with the wild-type virus. 2014 Emerging microbes & infections Result IV R292K 58 63 29 31 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. We observed that SH5190 and the R292K mutant exhibited comparable sensitivity to T-705 (IC50 values of 3.10 microM and 6.26 microM, respectively) and ribavirin (IC50 values of 3.32 microM and 7.43 microM, respectively). 2014 Emerging microbes & infections Result IV R292K 32 37 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. We thus concluded that the R292K mutant virus can propagate efficiently in cell culture. 2014 Emerging microbes & infections Result IV R292K 27 32 26056814 Molecular Characterisation of the Haemagglutinin Glycan-Binding Specificity of Egg-Adapted Vaccine Strains of the Pandemic 2009 H1N1 Swine Influenza A Virus. A dual alpha2,3/alpha2,6 glycan receptor specificity was reported for the A/California/04/09 D225G recombinant virus using a haemagglutination assay with turkey red blood cells. 2015 Molecules (Basel, Switzerland) Result IV D225G 93 98 26056814 Molecular Characterisation of the Haemagglutinin Glycan-Binding Specificity of Egg-Adapted Vaccine Strains of the Pandemic 2009 H1N1 Swine Influenza A Virus. alpha2,3 glycan affinity for the D225G mutants. 2015 Molecules (Basel, Switzerland) Result IV D225G 33 38 26056814 Molecular Characterisation of the Haemagglutinin Glycan-Binding Specificity of Egg-Adapted Vaccine Strains of the Pandemic 2009 H1N1 Swine Influenza A Virus. Belser et al., also reported a modest reduction in alpha2,6 glycan affinity of A/California/04/09 D225G recombinant virus with a concomitant increase in alpha2,3 glycan affinity. 2015 Molecules (Basel, Switzerland) Result IV D225G 98 103 26056814 Molecular Characterisation of the Haemagglutinin Glycan-Binding Specificity of Egg-Adapted Vaccine Strains of the Pandemic 2009 H1N1 Swine Influenza A Virus. Both the X181 and X179 (Q226R) viruses displayed comparable LSTc (alpha2,6) binding whereas the X121xp (K123N, Q226R) virus displayed relatively low binding affinity for both LSTa and LSTc. 2015 Molecules (Basel, Switzerland) Result IV Q226R;K123N;Q226R 24;104;111 29;109;116 26056814 Molecular Characterisation of the Haemagglutinin Glycan-Binding Specificity of Egg-Adapted Vaccine Strains of the Pandemic 2009 H1N1 Swine Influenza A Virus. Considering that the X121xp virus also harbors the Q226R mutation, it is possible that the introduction of a glycosylation site through a K123N mutation proximal to the RBS interferes with receptor binding. 2015 Molecules (Basel, Switzerland) Result IV Q226R;K123N 51;138 56;143 26056814 Molecular Characterisation of the Haemagglutinin Glycan-Binding Specificity of Egg-Adapted Vaccine Strains of the Pandemic 2009 H1N1 Swine Influenza A Virus. Glycan array results reported by Lui et al., revealed that an egg-passaged isolate of A/Hamburg/5/09 harboring the D225G HA mutation displayed an enhanced alpha2,3-glycan affinity and a largely unchanged alpha2,6-glycan affinity compared to the wild-type virus A/Moldova/G186/09. 2015 Molecules (Basel, Switzerland) Result IV D225G 115 120 HA 121 123 26056814 Molecular Characterisation of the Haemagglutinin Glycan-Binding Specificity of Egg-Adapted Vaccine Strains of the Pandemic 2009 H1N1 Swine Influenza A Virus. Glycan Binding Specificity of Pandemic 2009 H1N1 K123N, D225G and Q226R HA Mutants. 2015 Molecules (Basel, Switzerland) Result IV K123N;D225G;Q226R 49;56;66 54;61;71 HA 72 74 26056814 Molecular Characterisation of the Haemagglutinin Glycan-Binding Specificity of Egg-Adapted Vaccine Strains of the Pandemic 2009 H1N1 Swine Influenza A Virus. Glycan Structure-Recognition Characteristics of Pandemic 2009 H1N1 D225G, Q226R and D225G/Q226R HA Mutants Examined through in Silico Docking and Modeling. 2015 Molecules (Basel, Switzerland) Result IV D225G;Q226R;D225G;Q226R 67;74;84;90 72;79;89;95 HA 96 98 26056814 Molecular Characterisation of the Haemagglutinin Glycan-Binding Specificity of Egg-Adapted Vaccine Strains of the Pandemic 2009 H1N1 Swine Influenza A Virus. High-throughput sequencing studies of specimens from infected individuals during the second wave of the 2009 H1N1 pandemic in Japan revealed that the K123N, D225G (substitution rate 0.01%-0.11%) and Q226R (substitution rate 0.1%-0.41%) mutations exist as a very minor population in humans. 2015 Molecules (Basel, Switzerland) Result IV K123N;D225G;Q226R 150;157;199 155;162;204 26056814 Molecular Characterisation of the Haemagglutinin Glycan-Binding Specificity of Egg-Adapted Vaccine Strains of the Pandemic 2009 H1N1 Swine Influenza A Virus. Hydrogen bond interactions within the LSTc (alpha2,6)-D225G/Q226R double mutant complex of note include K133 (NZ) and the hydroxyl group on the terminal Gal moiety (3.0 A), D190 side chain (OD1) and GlcNac3 (3.0 A), K145 (NZ) and the hydroxyl present on sialic acid (3.2 A), the hydroxyls of Gal2 with the side chain amines of K222 (NZ; 3.0 A), R226 (NH1; 3.2 A) and the carbonyl of G225 (O; 3.1 A) (Figure 2D). 2015 Molecules (Basel, Switzerland) Result IV D225G;Q226R 54;60 59;65 26056814 Molecular Characterisation of the Haemagglutinin Glycan-Binding Specificity of Egg-Adapted Vaccine Strains of the Pandemic 2009 H1N1 Swine Influenza A Virus. In contrast, glycan array analysis using the recombinant HA of the pandemic H1N1 A/Texas/5/09 isolate revealed that the D225G mutation results in a strong alpha2,6-linked sialyl preference with a weak alpha2,3-linked sialyl affinity. 2015 Molecules (Basel, Switzerland) Result IV D225G 120 125 HA 57 59 26056814 Molecular Characterisation of the Haemagglutinin Glycan-Binding Specificity of Egg-Adapted Vaccine Strains of the Pandemic 2009 H1N1 Swine Influenza A Virus. In line with the glycan binding data for the Q226R egg adapted viruses, the recombinant A/California/07/09 Q226R single mutant HA displayed a complete loss of alpha2,6-linked sialyl-glycan affinity with a switch to an alpha2,3-linked sialyl-glycan preference. 2015 Molecules (Basel, Switzerland) Result IV Q226R;Q226R 45;107 50;112 HA 127 129 26056814 Molecular Characterisation of the Haemagglutinin Glycan-Binding Specificity of Egg-Adapted Vaccine Strains of the Pandemic 2009 H1N1 Swine Influenza A Virus. In our hands, the recombinant A/California/07/2009 D225G single mutant HA displayed enhanced binding affinity for both alpha2,6- and alpha2,3-linked sialyl-glycans in the array, although its alpha2,6-glycan affinity was generally higher compared to its alpha2,3-glycan affinity. 2015 Molecules (Basel, Switzerland) Result IV D225G 51 56 HA 71 73 26056814 Molecular Characterisation of the Haemagglutinin Glycan-Binding Specificity of Egg-Adapted Vaccine Strains of the Pandemic 2009 H1N1 Swine Influenza A Virus. In the Q226R model we observe far fewer hydrogen bond contacts with the 220-loop and the 190-helix and D225 scoring suggest a potential clash with Gal2. 2015 Molecules (Basel, Switzerland) Result IV Q226R 7 12 26056814 Molecular Characterisation of the Haemagglutinin Glycan-Binding Specificity of Egg-Adapted Vaccine Strains of the Pandemic 2009 H1N1 Swine Influenza A Virus. In the second wave of the 2009 H1N1 pandemic, D225G variants were frequently identified in specimens from the lower respiratory tract, and has been associated with a higher mortality and increased severity of pulmonary infection. 2015 Molecules (Basel, Switzerland) Result IV D225G 46 51 26056814 Molecular Characterisation of the Haemagglutinin Glycan-Binding Specificity of Egg-Adapted Vaccine Strains of the Pandemic 2009 H1N1 Swine Influenza A Virus. Interestingly, Chen et al., reported that egg-adapted strains of A/California/04/09 with Q226R residue and A/California/07/09 with D225G and Q226R HA substitutions reacted similarly to ferret reference sera from animals immunised with the corresponding wild-type strains. 2015 Molecules (Basel, Switzerland) Result IV Q226R;D225G;Q226R 89;131;141 94;136;146 HA 147 149 26056814 Molecular Characterisation of the Haemagglutinin Glycan-Binding Specificity of Egg-Adapted Vaccine Strains of the Pandemic 2009 H1N1 Swine Influenza A Virus. LSTc (alpha2,6) binding, however, is rescued in the D225G/Q226R double mutant HA model, where we notice positive residue scoring at those positions. 2015 Molecules (Basel, Switzerland) Result IV D225G;Q226R 52;58 57;63 HA 78 80 26056814 Molecular Characterisation of the Haemagglutinin Glycan-Binding Specificity of Egg-Adapted Vaccine Strains of the Pandemic 2009 H1N1 Swine Influenza A Virus. More specifically their data showed that these D225G mutants displayed an enhanced affinity for alpha2,3-linked glycans, whereas the binding to alpha2,6-linked glycans was comparable to the D225 wild type viruses, A/Ohio/07/09 and A/New York/18/09. 2015 Molecules (Basel, Switzerland) Result IV D225G 47 52 26056814 Molecular Characterisation of the Haemagglutinin Glycan-Binding Specificity of Egg-Adapted Vaccine Strains of the Pandemic 2009 H1N1 Swine Influenza A Virus. Notably, enhanced alpha2,3-linked glycan affinity of D225G viruses has been correlated with increased capacity to infect ciliated epithelial cells, alveolar type II pneumocytes, bronchial submucosal glands and Calu-3 bronchial epithelial cells which are prevalent along the entire airway epithelium and perform an important mucociliary clearance functions. 2015 Molecules (Basel, Switzerland) Result IV D225G 53 58 26056814 Molecular Characterisation of the Haemagglutinin Glycan-Binding Specificity of Egg-Adapted Vaccine Strains of the Pandemic 2009 H1N1 Swine Influenza A Virus. Notably, the alpha2,6 alpha2,3 switch seen with the Q226R HA single mutant was more pronounced compared to the viruses, as the latter retained some ability to bind to the alpha2,6-linked biantennary glycans MSLNH and SLNFPI. 2015 Molecules (Basel, Switzerland) Result IV Q226R 52 57 HA 58 60 26056814 Molecular Characterisation of the Haemagglutinin Glycan-Binding Specificity of Egg-Adapted Vaccine Strains of the Pandemic 2009 H1N1 Swine Influenza A Virus. On this note, the discrepancies in the literature noted above for the D225G variants may also be a result of the type of glycan binding platform employed and again the use of whole virus particles versus purified HA protein. 2015 Molecules (Basel, Switzerland) Result IV D225G 70 75 HA 213 215 26056814 Molecular Characterisation of the Haemagglutinin Glycan-Binding Specificity of Egg-Adapted Vaccine Strains of the Pandemic 2009 H1N1 Swine Influenza A Virus. Paradoxically, Chen et al., reported a reduced alpha2,6 binding affinity for egg adapted A/California/04/09 D225G HA mutants using a haemagglutination assay with chicken red blood cells. 2015 Molecules (Basel, Switzerland) Result IV D225G 108 113 HA 114 116 26056814 Molecular Characterisation of the Haemagglutinin Glycan-Binding Specificity of Egg-Adapted Vaccine Strains of the Pandemic 2009 H1N1 Swine Influenza A Virus. Results revealed that all three viruses display a strong LSTa (alpha2,3) binding preference with the X181 (N133D, Q226R) virus displaying highest binding affinity which is consistent with its ability to replicate more efficiently in eggs than the other two strains. 2015 Molecules (Basel, Switzerland) Result IV N133D;Q226R 107;114 112;119 26056814 Molecular Characterisation of the Haemagglutinin Glycan-Binding Specificity of Egg-Adapted Vaccine Strains of the Pandemic 2009 H1N1 Swine Influenza A Virus. Similar findings were reported by Takemae et al., who showed egg-adapted D225G mutants of A/Sw/Ratchaburi/NIAH101942/08 and A/Sw/Tochigi/1/08 had an increased haemagglutinating activity for mouse and sheep erythrocytes, that predominantly express alpha2,3 glycans. 2015 Molecules (Basel, Switzerland) Result IV D225G 73 78 26056814 Molecular Characterisation of the Haemagglutinin Glycan-Binding Specificity of Egg-Adapted Vaccine Strains of the Pandemic 2009 H1N1 Swine Influenza A Virus. Similar to our findings, this group also noted the receptor affinities of the D225G mutant HA were higher than that of the wild type A/California/04/09 HA. 2015 Molecules (Basel, Switzerland) Result IV D225G 78 83 HA;HA 91;152 93;154 26056814 Molecular Characterisation of the Haemagglutinin Glycan-Binding Specificity of Egg-Adapted Vaccine Strains of the Pandemic 2009 H1N1 Swine Influenza A Virus. Similarly, Chen et al., reported a dual alpha2,3 and alpha2,6 binding specificity for the egg adapted 2009 pandemic H1N1 viruses A/Mexico/Indre/4114/09, and A/New York/04/09 harbouring the D225G HA mutation. 2015 Molecules (Basel, Switzerland) Result IV D225G 189 194 HA 195 197 26056814 Molecular Characterisation of the Haemagglutinin Glycan-Binding Specificity of Egg-Adapted Vaccine Strains of the Pandemic 2009 H1N1 Swine Influenza A Virus. The D225G mutant produced interesting results, with an increase in binding values for both LSTc and LSTa (Figure 2B). 2015 Molecules (Basel, Switzerland) Result IV D225G 4 9 26056814 Molecular Characterisation of the Haemagglutinin Glycan-Binding Specificity of Egg-Adapted Vaccine Strains of the Pandemic 2009 H1N1 Swine Influenza A Virus. The docking model for the Q226R mutant depicts a near halving of the affinity of LSTc (alpha2,6) receptor suggesting that the molecule does not bind efficiently, if at all (Figure 2C and Table A2). 2015 Molecules (Basel, Switzerland) Result IV Q226R 26 31 26056814 Molecular Characterisation of the Haemagglutinin Glycan-Binding Specificity of Egg-Adapted Vaccine Strains of the Pandemic 2009 H1N1 Swine Influenza A Virus. The ELISA competition data revealed that the X179 (Q226R) and X181 (N136D, Q226R) viruses displayed a comparable pattern of highly specific binding to alpha2,3-linked sialyl-glycans, with a negligible affinity for most of the alpha2,6-linked sialyl-glycans. 2015 Molecules (Basel, Switzerland) Result IV Q226R;N136D;Q226R 51;68;75 56;73;80 26056814 Molecular Characterisation of the Haemagglutinin Glycan-Binding Specificity of Egg-Adapted Vaccine Strains of the Pandemic 2009 H1N1 Swine Influenza A Virus. The glycan binding specificity of the virus particles and purified recombinant A/California/07/09 HAs harboring the RBS mutations D225G, Q226R, D225G/Q226R and Q226R/K123N was also examined using an expanded glycan array solid phase assays ELISA assay. 2015 Molecules (Basel, Switzerland) Result IV D225G;Q226R;D225G;Q226R;Q226R;K123N 130;137;144;150;160;166 135;142;149;155;165;171 26056814 Molecular Characterisation of the Haemagglutinin Glycan-Binding Specificity of Egg-Adapted Vaccine Strains of the Pandemic 2009 H1N1 Swine Influenza A Virus. The preference for the lower respiratory tract may also account for the lower frequency at which the D225G variant is transmitted. 2015 Molecules (Basel, Switzerland) Result IV D225G 101 106 26056814 Molecular Characterisation of the Haemagglutinin Glycan-Binding Specificity of Egg-Adapted Vaccine Strains of the Pandemic 2009 H1N1 Swine Influenza A Virus. The Q226R substitution, however, makes the right corner trough of the binding pocket narrower compared to the binding pocket of wild-type A/California/07/09 HA (Figure 2E). 2015 Molecules (Basel, Switzerland) Result IV Q226R 4 9 HA 157 159 26056814 Molecular Characterisation of the Haemagglutinin Glycan-Binding Specificity of Egg-Adapted Vaccine Strains of the Pandemic 2009 H1N1 Swine Influenza A Virus. The recombinant A/California/07/09 K123N/Q226R double mutant HA displayed a pattern of highly specific binding to alpha2,3-linked sialyl-glycans comparable to the X121xp virus which harbours the same HA mutations, moreover, its ability to bind all of the glycans in the array was ~2-3-fold lower compared to the Q226R and D225G/Q226R recombinant HAs. 2015 Molecules (Basel, Switzerland) Result IV Q226R;K123N;Q226R;Q226R;D225G 41;35;312;328;322 46;40;317;333;327 HA;HA 61;200 63;202 26056814 Molecular Characterisation of the Haemagglutinin Glycan-Binding Specificity of Egg-Adapted Vaccine Strains of the Pandemic 2009 H1N1 Swine Influenza A Virus. The World Health Organisation (WHO) reported that the overall prevalence of the D222G was <1.8% and ~7.1% in fatal cases of H1N1. 2015 Molecules (Basel, Switzerland) Result IV D222G 80 85 26056814 Molecular Characterisation of the Haemagglutinin Glycan-Binding Specificity of Egg-Adapted Vaccine Strains of the Pandemic 2009 H1N1 Swine Influenza A Virus. The X121xp (K123N, Q226R,) virus displayed a comparable glycan binding profile, however, its ability to bind all glycan types was ~5-fold lower than the X179 and X181 viruses. 2015 Molecules (Basel, Switzerland) Result IV K123N;Q226R 12;19 17;24 26056814 Molecular Characterisation of the Haemagglutinin Glycan-Binding Specificity of Egg-Adapted Vaccine Strains of the Pandemic 2009 H1N1 Swine Influenza A Virus. These factors may contribute to the selection of the D225G mutation and to the severity of disease associated with D225G influenza virus pulmonary infections. 2015 Molecules (Basel, Switzerland) Result IV D225G;D225G 53;115 58;120 IV infections;IV infections 115;121 157;157 26056814 Molecular Characterisation of the Haemagglutinin Glycan-Binding Specificity of Egg-Adapted Vaccine Strains of the Pandemic 2009 H1N1 Swine Influenza A Virus. This drastic loss of alpha2,6 binding capacity has also been reported for the egg passaged virus A/New York/18/09 harbouring the Q226R HA mutation. 2015 Molecules (Basel, Switzerland) Result IV Q226R 129 134 HA 135 137 26056814 Molecular Characterisation of the Haemagglutinin Glycan-Binding Specificity of Egg-Adapted Vaccine Strains of the Pandemic 2009 H1N1 Swine Influenza A Virus. This suggests that the latter mutation dominates over the D225G mutation. 2015 Molecules (Basel, Switzerland) Result IV D225G 58 63 26056814 Molecular Characterisation of the Haemagglutinin Glycan-Binding Specificity of Egg-Adapted Vaccine Strains of the Pandemic 2009 H1N1 Swine Influenza A Virus. This was rectified through the rescue of viruses with the egg-adaption mutations K123N, D225G and Q226R in the viral HA during reassortment. 2015 Molecules (Basel, Switzerland) Result IV K123N;D225G;Q226R 81;88;98 86;93;103 HA 117 119 26056814 Molecular Characterisation of the Haemagglutinin Glycan-Binding Specificity of Egg-Adapted Vaccine Strains of the Pandemic 2009 H1N1 Swine Influenza A Virus. Thus the dual receptor specificity of D225G variants may facilitate entry into the lower respiratory tract where alpha2,3 glycans are more prevalently expressed. 2015 Molecules (Basel, Switzerland) Result IV D225G 38 43 26056814 Molecular Characterisation of the Haemagglutinin Glycan-Binding Specificity of Egg-Adapted Vaccine Strains of the Pandemic 2009 H1N1 Swine Influenza A Virus. Unlike the Q226R single mutation which abolished alpha2,6 binding, the recombinant A/California/07/09 D225G/Q226R double mutant exhibited a restored capacity to bind alpha2,6-linked sialyl-glycans, albeit, it still retained the strong alpha2,3-linked sialyl-glycan preference seen with the Q226R single mutant. 2015 Molecules (Basel, Switzerland) Result IV Q226R;Q226R;D225G;Q226R 11;108;102;290 16;113;107;295 26056814 Molecular Characterisation of the Haemagglutinin Glycan-Binding Specificity of Egg-Adapted Vaccine Strains of the Pandemic 2009 H1N1 Swine Influenza A Virus. Zhang et al., also demonstrated dual alpha2,3 and alpha2,6 binding specificity for D225G recombinant A/California/04/09 HA using a surface Plasmon resonance glycan binding platform to measure the affinity for two biotinylated receptor analogues. 2015 Molecules (Basel, Switzerland) Result IV D225G 83 88 HA 120 122 26056814 Molecular Characterisation of the Haemagglutinin Glycan-Binding Specificity of Egg-Adapted Vaccine Strains of the Pandemic 2009 H1N1 Swine Influenza A Virus. Zhang et al., have previously established that the D225G single mutation switches binding specificity to a dual receptor specificity, and Pan et al., demonstrated a free energy gain for the alpha2,3- glycans in a D225G mutant of H1N1 brought about by an increase in energy contribution by Q226. 2015 Molecules (Basel, Switzerland) Result IV D225G;D225G 51;213 56;218 26077257 Influenza A(H7N9) virus acquires resistance-related neuraminidase I222T substitution when infected mallards are exposed to low levels of oseltamivir in water. NA inhibition by OC and ZA, tested on 10 NA I222T samples and 3 wild-type samples, showed increased IC50s of the NA I222T variant compared to those of the wild-type virus for both OC (P = 0.000011; 95% CI for difference in means, 2.5 to 4.6 nM) and ZA (P = 0.016; 95% CI for difference in means, 0.16 to 1.28 nM) (Table 1). 2015 Antimicrobial agents and chemotherapy Result IV I222T;I222T 44;116 49;121 NA;NA;NA 0;41;113 2;43;115 26077257 Influenza A(H7N9) virus acquires resistance-related neuraminidase I222T substitution when infected mallards are exposed to low levels of oseltamivir in water. Sequencing of NA demonstrated the amino acid substitution I222T (ATA for isoleucine changed to ACA for threonine) in a small proportion of virus from one mallard in generation one 2 days postinoculation, while OC exposure was 2.5 mug/liter. 2015 Antimicrobial agents and chemotherapy Result IV I222T 58 63 14 16 26077257 Influenza A(H7N9) virus acquires resistance-related neuraminidase I222T substitution when infected mallards are exposed to low levels of oseltamivir in water. The proportion of the I222T variant increased over 3 days, and from day 5 all subsequently sequenced viruses had the I222T variant until the end of IAV transmission. 2015 Antimicrobial agents and chemotherapy Result IV I222T;I222T 22;117 27;122 26263554 Phenotypic and Genetic Characterization of Avian Influenza H5N2 Viruses with Intra- and Inter-Duck Variations in Taiwan. All these results suggest that the substitution of N170D in HA may have the potential to modulate viral binding to MDCK cells, contributing to the better growth of DV518 and its derived two plaque-purified strains in mammalian cells. 2015 PloS one Result IV N170D 51 56 HA 60 62 26263554 Phenotypic and Genetic Characterization of Avian Influenza H5N2 Viruses with Intra- and Inter-Duck Variations in Taiwan. It is possible that the substitution of N170D in HA has the potential to modulate viral binding to the cells. 2015 PloS one Result IV N170D 40 45 HA 49 51 26345289 Influenza virus surveillance in Argentina during the 2012 season: antigenic characterization, genetic analysis and antiviral susceptibility. NA gene sequencing of this isolate and the original clinical specimen showed both carried the amino acid substitution N295S, known to reduce the inhibitory effects of the NAIs studied. 2016 Epidemiology and infection Result IV N295S 118 123 NA;NAI 0;171 2;175 26345289 Influenza virus surveillance in Argentina during the 2012 season: antigenic characterization, genetic analysis and antiviral susceptibility. The genetic group 6 viruses clearly split into two subgroups with four viruses from Salta being defined by amino acid substitutions K283R (HA1) and I510T (HA2) and the larger group being defined by N260T (HA1) substitution and showing further subdivision based on HA1 substitutions N38D with V173I, and R45G with V321I. 2016 Epidemiology and infection Result IV K283R;I510T;N260T;N38D;V173I;R45G;V321I 132;148;198;282;292;303;313 137;153;203;286;297;307;318 HA;HA1;HA1;HA1 155;139;205;264 157;142;208;267 26345289 Influenza virus surveillance in Argentina during the 2012 season: antigenic characterization, genetic analysis and antiviral susceptibility. The reactivity pattern of A/Salta/1122/2012, which carries the D156D/N polymorphism in HA1, more closely resembled those of the reference viruses A/Bayern/69/2009 and A/Lviv/N6/2009 which carry the G155E substitution and G155E/G polymorphism, respectively, in their HA1 component. 2016 Epidemiology and infection Result IV G155E;G155G;D156D;D156N;G155E 198;221;63;63;221 203;228;70;70;228 HA1;HA1 87;266 90;269 26391278 Dual E627K and D701N mutations in the PB2 protein of A(H7N9) influenza virus increased its virulence in mammalian models. All ferrets that shed virus after exposure to the wild type AH1 virus retained the 627K residue in the PB2 gene but two of the three physical contact animals carried a mixed population at the 701 position, with the D701N mutation occurring at a frequency of 94.2% and 86.8% respectively on their peak shedding day (3 and 4 dpe respectively, Table 1). 2015 Scientific reports Result IV D701N 215 220 PB2 103 106 26391278 Dual E627K and D701N mutations in the PB2 protein of A(H7N9) influenza virus increased its virulence in mammalian models. Neither of the two AH1 airborne exposed ferrets that shed virus possessed the D701N mutation even though they were paired with the contact exposed animals that did. 2015 Scientific reports Result IV D701N 78 83 26422258 Oseltamivir Resistance in Influenza A(H6N2) Caused by an R292K Substitution in Neuraminidase Is Not Maintained in Mallards without Drug Pressure. Mean IC50 values are displayed in Table 3 and correspond to 15,000 fold and 10 fold increased IC50s for the R292K mutant by OC and zanamivir respectively. 2015 PloS one Result IV R292K 108 113 26422258 Oseltamivir Resistance in Influenza A(H6N2) Caused by an R292K Substitution in Neuraminidase Is Not Maintained in Mallards without Drug Pressure. Median IC50s by OC and ZA differed between wild type and R292K mutated virus (P = 0.008 for both). 2015 PloS one Result IV R292K 57 62 26422258 Oseltamivir Resistance in Influenza A(H6N2) Caused by an R292K Substitution in Neuraminidase Is Not Maintained in Mallards without Drug Pressure. Presence of D113N or D141N did not influence the results. 2015 PloS one Result IV D113N;D141N 12;21 17;26 26422258 Oseltamivir Resistance in Influenza A(H6N2) Caused by an R292K Substitution in Neuraminidase Is Not Maintained in Mallards without Drug Pressure. The NA substitutions D113N and D141N persisted through the experiments and the ECE propagation process. 2015 PloS one Result IV D113N;D141N 21;31 26;36 4 6 26422258 Oseltamivir Resistance in Influenza A(H6N2) Caused by an R292K Substitution in Neuraminidase Is Not Maintained in Mallards without Drug Pressure. The resistant viral variant with only R292K was transmitted to one naive Mallard after removal of OC, but was not detected the following day (Table 2). 2015 PloS one Result IV R292K 38 43 26609523 Phylogenetic Analysis of Hemagglutinin Genes of H9N2 Avian Influenza Viruses Isolated from Chickens in Shandong, China, between 1998 and 2013. 29 out of 35 H9N2 AIVs had leucine (L) at position 226, including all of the isolates between 2005 and 2013 (Table 3). 2015 BioMed research international Result IV L226L 26 55 IAV infections 18 22 26609523 Phylogenetic Analysis of Hemagglutinin Genes of H9N2 Avian Influenza Viruses Isolated from Chickens in Shandong, China, between 1998 and 2013. AA residues on the left edge of receptor-binding pocket had a substitution Q227L (M), and most isolates (4 out of 6) between 2012 and 2013 had M at position 227. 2015 BioMed research international Result IV Q227L 75 80 26609523 Phylogenetic Analysis of Hemagglutinin Genes of H9N2 Avian Influenza Viruses Isolated from Chickens in Shandong, China, between 1998 and 2013. Only one substitution was found in the position A190V(T) (H3 numbering is used throughout the paper) (Table 3). 2015 BioMed research international Result IV A190V 48 53 26754751 Coupling high-throughput genetics with phylogenetic information reveals an epistatic interaction on the influenza A virus M segment. A209T is a compensatory substitution for Q214H. 2016 BMC genomics Result IV A209T;Q214H 0;41 5;46 26754751 Coupling high-throughput genetics with phylogenetic information reveals an epistatic interaction on the influenza A virus M segment. Consequently, M2 C50S was ignored in the downstream analysis. 2016 BMC genomics Result IV C50S 17 21 M2 14 16 26754751 Coupling high-throughput genetics with phylogenetic information reveals an epistatic interaction on the influenza A virus M segment. However, A209T alone did not improve the replication kinetics above the wild type. 2016 BMC genomics Result IV A209T 9 14 26754751 Coupling high-throughput genetics with phylogenetic information reveals an epistatic interaction on the influenza A virus M segment. However, M2 C50S, which was shown to be a non-essential palmitoylation site, had no fitness cost in the virus rescue experiment. 2016 BMC genomics Result IV C50S 12 16 M2 9 11 26754751 Coupling high-throughput genetics with phylogenetic information reveals an epistatic interaction on the influenza A virus M segment. In fact, A209T and Q214H were both located at a putative alpha-helix, helix 12 (amino acid residues 197-218), of the M1 C-terminal domain. 2016 BMC genomics Result IV A209T;Q214H 9;19 14;24 M1 117 119 26754751 Coupling high-throughput genetics with phylogenetic information reveals an epistatic interaction on the influenza A virus M segment. In fact, the deleterious effect of M1 D231N was also previously demonstrated in another genetic background. 2016 BMC genomics Result IV D231N 38 43 M1 35 37 26754751 Coupling high-throughput genetics with phylogenetic information reveals an epistatic interaction on the influenza A virus M segment. It suggests that, at least in natural evolution, mutation at residue 198 was unlikely to impose a significant compensatory effect on the fitness cost Q214H. 2016 BMC genomics Result IV Q214H 150 155 26754751 Coupling high-throughput genetics with phylogenetic information reveals an epistatic interaction on the influenza A virus M segment. Seven substitutions (K21Q, R78P, A186P, G136R, K47T, I107M, and D30G) had undetectable viral titer, three substitutions (V219L, R49K, and P50S) had two-log drop in viral titer as compared to wild-type (WT), two substitutions (T169P and T139S) had one-log drop in viral titer as compared to WT, and only one substitution (S70T) had WT-like viral titer. 2016 BMC genomics Result IV K21Q;R78P;A186P;G136R;K47T;I107M;D30G;V219L;R49K;P50S;T169P;T139S;S70T 21;27;33;40;47;53;64;121;128;138;226;236;321 25;31;38;45;51;58;68;126;132;142;231;241;325 26754751 Coupling high-throughput genetics with phylogenetic information reveals an epistatic interaction on the influenza A virus M segment. The deleterious effects of M1 Q214H and M1 D231N were validated by virus rescue experiment. 2016 BMC genomics Result IV Q214H;D231N 30;43 35;48 M1;M1 27;40 29;42 26754751 Coupling high-throughput genetics with phylogenetic information reveals an epistatic interaction on the influenza A virus M segment. The interaction between A209T and Q214H in M1 demonstrates the feasibility of identifying epistatic residues through an integration of high-throughput genetics and phylogenetic information. 2016 BMC genomics Result IV A209T;Q214H 24;34 29;39 M1 43 45 26754751 Coupling high-throughput genetics with phylogenetic information reveals an epistatic interaction on the influenza A virus M segment. The viral titer of Q214H was ~100-fold lower than WT across different time points. 2016 BMC genomics Result IV Q214H 19 24 26754751 Coupling high-throughput genetics with phylogenetic information reveals an epistatic interaction on the influenza A virus M segment. Therefore, we hypothesized that the replication defect of Q214H could be compensated by either S207N or A209T, or both of them. 2016 BMC genomics Result IV Q214H;S207N;A209T 58;95;104 63;100;109 26754751 Coupling high-throughput genetics with phylogenetic information reveals an epistatic interaction on the influenza A virus M segment. These three substitutions were C50S on M2 (RF index max=0.05), D231N on M1 (RF index max=0.15), and Q214H on M1 (RF index max=0.16). 2016 BMC genomics Result IV C50S;D231N;Q214H 31;63;100 35;68;105 M1;M1;M2 72;109;39 74;111;41 26754751 Coupling high-throughput genetics with phylogenetic information reveals an epistatic interaction on the influenza A virus M segment. This defect was rescued with the addition of A209T. 2016 BMC genomics Result IV A209T 45 50 26754751 Coupling high-throughput genetics with phylogenetic information reveals an epistatic interaction on the influenza A virus M segment. To test our hypothesis, the fitness effects of S207N and A209T on Q214H were tested by virus rescue experiment. 2016 BMC genomics Result IV S207N;A209T;Q214H 47;57;66 52;62;71 26754751 Coupling high-throughput genetics with phylogenetic information reveals an epistatic interaction on the influenza A virus M segment. Together, these results showed that A209T could act as a compensatory substitution for Q214H. 2016 BMC genomics Result IV A209T;Q214H 36;87 41;92 26754751 Coupling high-throughput genetics with phylogenetic information reveals an epistatic interaction on the influenza A virus M segment. We postulated that either C50S was a false positive from the identification of deleterious mutations or with a fitness cost that could only be detectable under a competitive growth environment which resembled that of the high-throughput genetics experiment. 2016 BMC genomics Result IV C50S 26 30 26754751 Coupling high-throughput genetics with phylogenetic information reveals an epistatic interaction on the influenza A virus M segment. While the addition of S207N further decreased the viral titer, addition of A209T fully restored the viral titer to WT level. 2016 BMC genomics Result IV S207N;A209T 22;75 27;80 26782141 PB2-588 V promotes the mammalian adaptation of H10N8, H7N9 and H9N2 avian influenza viruses. although it did not result in a markedly increased virulence when compared to introduction of substitution E627K or A588V/E627K into the PB2. 2016 Scientific reports Result IV E627K;A588V;E627K 107;116;122 112;121;127 PB2 137 140 26782141 PB2-588 V promotes the mammalian adaptation of H10N8, H7N9 and H9N2 avian influenza viruses. By contrast, the PB2 substitution V588A markedly decreased virus replication of JX436 although it was not significant when compared to the substitution K627E and V588A/K627E in both MDCK and HEK293T cells. 2016 Scientific reports Result IV V588A;K627E;V588A;K627E 34;152;162;168 39;157;167;173 PB2 17 20 26782141 PB2-588 V promotes the mammalian adaptation of H10N8, H7N9 and H9N2 avian influenza viruses. By contrast, the single substitution V588A, similar to K627E in PB2 for the human-origin JX346, had a slight effect on the MLD50 value, virulence, and virus replication in lungs of infected mice (Table 3), but the substitution V588A coupled with K627E in PB2 attenuated the parental JX346 virus, evidenced by a significantly enhanced MLD50 value and no case fatality rate in infected mice (Table 3 and. 2016 Scientific reports Result IV V588A;K627E;V588A;K627E 37;55;227;246 42;60;232;251 PB2;PB2 64;255 67;258 26782141 PB2-588 V promotes the mammalian adaptation of H10N8, H7N9 and H9N2 avian influenza viruses. Consistent with the results of polymerase activity, both G1-PB2 588V and G1-PB2 627K mutant viruses replicated more efficiently than the wild type parental G1 virus in both MDCK and HEK293T cells, but did not grow to the same high titers as the double mutant G1-PB2 A588V/E627K virus. 2016 Scientific reports Result IV A588V;E627K 266;272 271;277 PB2;PB2;PB2 60;76;262 63;79;265 26782141 PB2-588 V promotes the mammalian adaptation of H10N8, H7N9 and H9N2 avian influenza viruses. In both MDCK and HEK293T cells, the substitution A588V markedly enhanced virus replication of JX102 and A588V/E627K slightly increased virus replication when compared to the E627K substitution. 2016 Scientific reports Result IV A588V;A588V;E627K;E627K 49;104;110;174 54;109;115;179 26782141 PB2-588 V promotes the mammalian adaptation of H10N8, H7N9 and H9N2 avian influenza viruses. In DF1 cells, both G1-PB2 A588V and G1-PB2 E627K substitutions exhibited a same level of polymerase activity that was significantly higher than that of the parental G1-PB2. 2016 Scientific reports Result IV A588V;E627K 26;43 31;48 PB2;PB2;PB2 22;39;168 25;42;171 26782141 PB2-588 V promotes the mammalian adaptation of H10N8, H7N9 and H9N2 avian influenza viruses. Moreover, the results of mini-genome assays in HEK293T cells and DF1 cells showed that the polymerase activity was significantly enhanced due to introduction of PB2 A588V substitution into the JX102 PB2 when compared to the parental JX102-PB2. 2016 Scientific reports Result IV A588V 165 170 PB2;PB2;PB2 161;199;239 164;202;242 26782141 PB2-588 V promotes the mammalian adaptation of H10N8, H7N9 and H9N2 avian influenza viruses. Mutation of A588V in PB2 enhances polymerase activity, virus replication, and virulence of avian-origin H7N9 and H9N2 viruses. 2016 Scientific reports Result IV A588V 12 17 PB2 21 24 26782141 PB2-588 V promotes the mammalian adaptation of H10N8, H7N9 and H9N2 avian influenza viruses. Since JX346-PB2 627E still exhibited a high pathogenicity in mice and in order to demine the influence of the other 10 amino acids besides 627K differing between JX346 and JX102 on polymerase activity, we performed a mini-genome assay using different genotypes of JX346 PB2 containing single substitutions (87E D, 195G D, 292V I, 340K R, 389K R, 411V I, 588V A, 598V T, 648V L, 676M T) combined with the K627E mutation in human 293T and avian DF-1 cells. 2016 Scientific reports Result IV K627E 424 429 PB2;PB2 12;270 15;273 26782141 PB2-588 V promotes the mammalian adaptation of H10N8, H7N9 and H9N2 avian influenza viruses. Taken together, the substitution A588V in PB2 also enhanced the polymerase activity in both human and avian cells and the virulence of avian-origin H7N9 and H9N2 viruses. 2016 Scientific reports Result IV A588V 33 38 PB2 42 45 26782141 PB2-588 V promotes the mammalian adaptation of H10N8, H7N9 and H9N2 avian influenza viruses. The results of mini-genome assays in HEK293T cells showed that the polymerase activity was significantly enhanced due to the introduction of PB2 A588V substitution into the G1 PB2 at both 33 C and 37 C, as compared with the parental G1-PB2, although it did not result in a similar level of polymerase activity induced by the substitution of E627K or A588V/E627K. 2016 Scientific reports Result IV A588V;E627K;A588V;E627K 145;343;352;358 150;348;357;363 PB2;PB2;PB2 141;176;238 144;179;241 26782141 PB2-588 V promotes the mammalian adaptation of H10N8, H7N9 and H9N2 avian influenza viruses. The single substitution A588V in PB2 enhanced the virulence of the avian-origin JX102 virus, evidenced by a reduced the dose of MLD50 and the efficient virus lung replication in infected mice when compared to the parental JX102 virus (Table 3 and. 2016 Scientific reports Result IV A588V 24 29 PB2 33 36 26782141 PB2-588 V promotes the mammalian adaptation of H10N8, H7N9 and H9N2 avian influenza viruses. The substitution A588V in PB2 significantly increased the polymerase activity in both HEK293T and DF1 cells. 2016 Scientific reports Result IV A588V 17 22 PB2 26 29 26782141 PB2-588 V promotes the mammalian adaptation of H10N8, H7N9 and H9N2 avian influenza viruses. To investigate the effects of PB2 A588V on the virulence of the H10N8 viruses, we determined the 50% mouse lethal dose (MLD50) and virus replication in mice using mutant viruses. 2016 Scientific reports Result IV A588V 34 39 PB2 30 33 26782141 PB2-588 V promotes the mammalian adaptation of H10N8, H7N9 and H9N2 avian influenza viruses. To investigate whether the effects of mutation A588V on virulence and virus replication also apply for the emerging zoonotic H7N9 virus, the mutant viruses with single (A588V or E627K) or double (A588V/E627K) substitutions in PB2 were generated in the genetic background of the H7N9 avian-origin G1 virus. 2016 Scientific reports Result IV A588V;A588V;E627K;A588V;E627K 47;169;178;196;202 52;174;183;201;207 PB2 226 229 26782141 PB2-588 V promotes the mammalian adaptation of H10N8, H7N9 and H9N2 avian influenza viruses. We generated a mutant V-PB2 A588V/K627E virus in the genetic background of the V-PB2 627E virus to investigate the effects of the PB2 A588V substitution on virulence. 2016 Scientific reports Result IV K627E;A588V;A588V 34;28;134 39;33;139 PB2;PB2;PB2 24;81;130 27;84;133 26782141 PB2-588 V promotes the mammalian adaptation of H10N8, H7N9 and H9N2 avian influenza viruses. While 87E, 292V, 340K, 588V, 627K, 648V, and 676M in PB2 play a critical role in the virulence the H10N8 JX346 virus, only the V588A substitution in PB2 resulted in a significantly lower polymerase activity in both human 293T and avian DF-1 cells. 2016 Scientific reports Result IV V588A 127 132 PB2;PB2 53;149 56;152 26845764 Genomic Signatures for Avian H7N9 Viruses Adapting to Humans. {K191E, N559T, M570I} is a most appearing combination in 50 or more sequences in Table 3. 2016 PloS one Result IV K191E;N559T;M570I 0;8;15 6;13;20 26845764 Genomic Signatures for Avian H7N9 Viruses Adapting to Humans. A CAT reporter RNP activity assay was performed to evaluate the effects of the PB2 K627E covariations. 2016 PloS one Result IV K627E 83 88 PB2;RNP 79;15 82;18 26845764 Genomic Signatures for Avian H7N9 Viruses Adapting to Humans. Along with PB2 K627E, four strains isolated early in season I exhibited Q591K. 2016 PloS one Result IV K627E;Q591K 15;72 20;77 PB2 11 14 26845764 Genomic Signatures for Avian H7N9 Viruses Adapting to Humans. Although no cooccurrence of Q591K, K627E, and D701N was observed, other amino acid changes coemerged with K627E at various degrees. 2016 PloS one Result IV Q591K;K627E;D701N;K627E 28;35;46;106 33;40;51;111 26845764 Genomic Signatures for Avian H7N9 Viruses Adapting to Humans. Although S286G, R340K, M473V, K526R, T569A, and A588V were observed (Table 3), their association with K627E was seen in four or fewer instances. 2016 PloS one Result IV S286G;R340K;M473V;K526R;T569A;A588V;K627E 9;16;23;30;37;48;102 14;21;28;35;42;53;107 26845764 Genomic Signatures for Avian H7N9 Viruses Adapting to Humans. Another example is the combination {M473V, V511I, M535L, I647V} appearing in 12 different strains:five in season II including A/Taiwan/3/2013 and A/Taiwan/1/2014, and seven in season III. 2016 PloS one Result IV M473V;V511I;M535L;I647V 35;43;50;57 41;48;55;62 26845764 Genomic Signatures for Avian H7N9 Viruses Adapting to Humans. For example, V139I, K191E, V511I, M535L, N559T, M570I, I647V, and M676V each had cosubstitutions ranging from 8 to 21 instances with respect to K627E. 2016 PloS one Result IV V139I;K191E;V511I;M535L;N559T;M570I;I647V;M676V;K627E 13;20;27;34;41;48;55;66;144 18;25;32;39;46;53;60;71;149 26845764 Genomic Signatures for Avian H7N9 Viruses Adapting to Humans. HA Q226L (Q235L in H7 numbering) was seen in the 2nd through the 4th Taiwanese patients. 2016 PloS one Result IV Q226L;Q235L 3;10 8;15 HA 0 2 26845764 Genomic Signatures for Avian H7N9 Viruses Adapting to Humans. However, the other seven amino acid substitutions that covaried with K627E exhibited no such effect. 2016 PloS one Result IV K627E 69 74 26845764 Genomic Signatures for Avian H7N9 Viruses Adapting to Humans. In particular, amino acid substitutions cooccurring with K627E were bolded, and their counts were summarized (Table 3). 2016 PloS one Result IV K627E 57 62 26845764 Genomic Signatures for Avian H7N9 Viruses Adapting to Humans. In particular, both PB2 K627E and D701N were observed only in TW2/2014 and the two CGMH genomes, in which 627E is characteristic of the avian species. 2016 PloS one Result IV K627E;D701N 24;34 29;39 PB2 20 23 26845764 Genomic Signatures for Avian H7N9 Viruses Adapting to Humans. It was mentioned that two PB2 mutations Q591K and D701N could enhance polymerase activity of avian viruses in human 293T cells. 2016 PloS one Result IV Q591K;D701N 40;50 45;55 PB2 26 29 26845764 Genomic Signatures for Avian H7N9 Viruses Adapting to Humans. M535L is another mutation exhibiting the compensatory effect with 627E (17.7%, P < 0.05). 2016 PloS one Result IV M535L 0 5 26845764 Genomic Signatures for Avian H7N9 Viruses Adapting to Humans. Moreover, 14 viruses exhibited another covarying position D701N with K627E observed in seasons I and II but missing in season III. 2016 PloS one Result IV D701N;K627E 58;69 63;74 26845764 Genomic Signatures for Avian H7N9 Viruses Adapting to Humans. On the contrary, there was only one displaying D701N among the avian H7N9 viruses. 2016 PloS one Result IV D701N 47 52 26845764 Genomic Signatures for Avian H7N9 Viruses Adapting to Humans. One example is the combination {V139I, S286G, T569A, M676V}, observed only in season II (November 2013-January 2014) in 12 strains from Shenzhen and Hong Kong; among them, three carried 627E and nine carried 627K. 2016 PloS one Result IV V139I;S286G;T569A;M676V 31;39;46;53 37;44;51;58 26845764 Genomic Signatures for Avian H7N9 Viruses Adapting to Humans. Only 10 mutations (amino acid positions with asterisks in Table 3) displaying at least six cosubstitutions with the 36 strains having K627E were tested. 2016 PloS one Result IV K627E 134 139 26845764 Genomic Signatures for Avian H7N9 Viruses Adapting to Humans. The Q591K and D701N residues accompanying K627E considerably restored the RNP activity back to 65.9% and 70.2%, respectively (both with P < 0.001). 2016 PloS one Result IV Q591K;D701N;K627E 4;14;42 9;19;47 RNP 74 77 26845764 Genomic Signatures for Avian H7N9 Viruses Adapting to Humans. The trio emerged in April 2013 in early stage of the outbreak and stayed in the H7N9 population in almost the entire seasons II and III, except that M570I seemed to fade out in half of the strains collected in season III. 2016 PloS one Result IV M570I 149 154 26845764 Genomic Signatures for Avian H7N9 Viruses Adapting to Humans. This suggests the existence of other mutations, which would possibly compensate for the K627E change, enabling this avian virus to infect humans. 2016 PloS one Result IV K627E 88 93 26847414 Amino acid changes in PB2 and HA affect the growth of a recombinant influenza virus expressing a fluorescent reporter protein. 1A), suggesting a contribution of the HA-T380A mutation to, at least, virus replication in cultured cells. 2016 Scientific reports Result IV T380A 41 46 HA 38 40 26847414 Amino acid changes in PB2 and HA affect the growth of a recombinant influenza virus expressing a fluorescent reporter protein. Although the mechanism is not currently understood, PB2-E712D and HA-T380A (in this study), as well as other mutations found in the MA-Venus-H5N1 virus, are useful for generating recombinant fluorescent influenza viruses that replicate efficiently in cultured cells and mice. 2016 Scientific reports Result IV E712D;T380A 56;69 61;74 HA;PB2 66;52 68;55 26847414 Amino acid changes in PB2 and HA affect the growth of a recombinant influenza virus expressing a fluorescent reporter protein. Because the HA-T380A substitution is located on an alpha-helix in the HA2 subunit. 2016 Scientific reports Result IV T380A 15 20 HA;HA 12;70 14;72 26847414 Amino acid changes in PB2 and HA affect the growth of a recombinant influenza virus expressing a fluorescent reporter protein. Collectively, our data indicate that the PB2-E712D substitution is primarily responsible for the increased replicative ability, Venus expression, and virulence in mice of MA-Venus-PR8 virus. 2016 Scientific reports Result IV E712D 45 50 PB2 41 44 26847414 Amino acid changes in PB2 and HA affect the growth of a recombinant influenza virus expressing a fluorescent reporter protein. Hence, the PB2-E712D substitution is primarily responsible for the increased virulence of MA-Venus-PR8 relative to WT-Venus-PR8 in mice. 2016 Scientific reports Result IV E712D 15 20 PB2 11 14 26847414 Amino acid changes in PB2 and HA affect the growth of a recombinant influenza virus expressing a fluorescent reporter protein. In conclusion, the increased replicative ability, Venus expression, and virulence in mice of MA-Venus-PR8 are primarily brought about by the PB2-E712D mutation, with a minor additional contribution by HA-T380A. 2016 Scientific reports Result IV E712D;T380A 145;204 150;209 HA;PB2 201;141 203;144 26847414 Amino acid changes in PB2 and HA affect the growth of a recombinant influenza virus expressing a fluorescent reporter protein. In fact, the PB2-D701N and PB2-S714R mutations facilitate adaptation of avian influenza viruses to mammals by affecting the PB2 interaction with importin, resulting in better exposure of the PB2 nuclear localization signal. 2016 Scientific reports Result IV D701N;S714R 17;31 22;36 PB2;PB2;PB2;PB2 13;27;124;191 16;30;127;194 26847414 Amino acid changes in PB2 and HA affect the growth of a recombinant influenza virus expressing a fluorescent reporter protein. In the context of a minireplicon that measures viral replication and transcription, the PB2-E712D mutation is thus attenuating; in contrast, this mutation enhances viral growth in the context of replicating virus. 2016 Scientific reports Result IV E712D 92 97 PB2 88 91 26847414 Amino acid changes in PB2 and HA affect the growth of a recombinant influenza virus expressing a fluorescent reporter protein. Interestingly, the PB2-E712D mutation does not increase viral replication and transcription in minireplicon assays perhaps because it affects PB2 binding to importins, which are essential for protein import into the nucleus. 2016 Scientific reports Result IV E712D 23 28 PB2;PB2 19;142 22;145 26847414 Amino acid changes in PB2 and HA affect the growth of a recombinant influenza virus expressing a fluorescent reporter protein. The wild-type HA had a threshold for membrane fusion of pH 5.5, whereas the threshold for HA-T380A was pH 5.8. 2016 Scientific reports Result IV T380A 93 98 HA;HA 14;90 16;92 26847414 Amino acid changes in PB2 and HA affect the growth of a recombinant influenza virus expressing a fluorescent reporter protein. These data indicate that the PB2-E712D and HA-T380A mutations both contributed to increased virus replication in MDCK cells. 2016 Scientific reports Result IV E712D;T380A 33;46 38;51 HA;PB2 43;29 45;32 26847414 Amino acid changes in PB2 and HA affect the growth of a recombinant influenza virus expressing a fluorescent reporter protein. To assess the contributions of PB2-E712D and HA-T380A to the increased replicative ability of MA-Venus-PR8, we used reverse genetics to generate two single-gene reassortants that possessed the PB2 or HA viral RNA (vRNA) of MA-Venus-PR8 and the remaining vRNA segments from WT-Venus-PR8 (referred to as PB2-Venus-PR8 and HA-Venus-PR8, respectively). 2016 Scientific reports Result IV E712D;T380A 35;48 40;53 HA;HA;HA;PB2;PB2;PB2 45;200;320;31;193;302 47;202;322;34;196;305 26847414 Amino acid changes in PB2 and HA affect the growth of a recombinant influenza virus expressing a fluorescent reporter protein. To assess whether the PB2-E712D mutation directly affects the viral polymerase activity, we performed a minireplicon assay in human HEK293 cells. 2016 Scientific reports Result IV E712D 26 31 PB2 22 25 26847414 Amino acid changes in PB2 and HA affect the growth of a recombinant influenza virus expressing a fluorescent reporter protein. To demonstrate that the PB2-E712D mutation increased the Venus expression levels, we infected MDCK cells with the indicated viruses at an MOI of 1 and performed confocal microscopy 12 h later. 2016 Scientific reports Result IV E712D 28 33 PB2 24 27 26847414 Amino acid changes in PB2 and HA affect the growth of a recombinant influenza virus expressing a fluorescent reporter protein. Unexpectedly, the polymerase activity of PB2-E712D was lower than that of the parental PB2. 2016 Scientific reports Result IV E712D 45 50 PB2;PB2 41;87 44;90 26847414 Amino acid changes in PB2 and HA affect the growth of a recombinant influenza virus expressing a fluorescent reporter protein. We speculate that the PB2-E712D mutation may affect these steps, resulting in the higher virulence of the PB2-E712D mutant virus in vivo. 2016 Scientific reports Result IV E712D;E712D 26;110 31;115 PB2;PB2 22;106 25;109 26974849 Effects of egg-adaptation on receptor-binding and antigenic properties of recent influenza A (H3N2) vaccine viruses. AA substitution D225N, occurring between 2004 and 2005, was demonstrated to be the major cause of a structural conformation change. 2016 The Journal of general virology Result IV D225N 16 21 26974849 Effects of egg-adaptation on receptor-binding and antigenic properties of recent influenza A (H3N2) vaccine viruses. Although RG/Vic361e D190E and CVV NIB-79 reacted poorly in HI assays, there were no dramatic alterations in binding profile using BLI or RBC agglutination. 2016 The Journal of general virology Result IV D190E 20 25 26974849 Effects of egg-adaptation on receptor-binding and antigenic properties of recent influenza A (H3N2) vaccine viruses. Antisera raised against either IVR-165 or X-217 recognised NIB-79 and RG/Vic361e D190E at titres of 320, 4-fold reduced compared to the homologous titre. 2016 The Journal of general virology Result IV D190E 81 86 26974849 Effects of egg-adaptation on receptor-binding and antigenic properties of recent influenza A (H3N2) vaccine viruses. Both IVR-165 and X-217 carry substitutions R156Q and S219Y, which are not seen in Vic361e or NIB-79. 2016 The Journal of general virology Result IV R156Q;S219Y 43;53 48;58 26974849 Effects of egg-adaptation on receptor-binding and antigenic properties of recent influenza A (H3N2) vaccine viruses. Both the exclusively cell culture-propagated cultivar of Switz13 (Switz13c) and the RG/Vic361c H156R virus bound with high avidity to 6-SLN. 2016 The Journal of general virology Result IV H156R 95 100 26974849 Effects of egg-adaptation on receptor-binding and antigenic properties of recent influenza A (H3N2) vaccine viruses. CVV NIB-79 encoded a D190E substitution in HA1. 2016 The Journal of general virology Result IV D190E 21 26 HA1 43 46 26974849 Effects of egg-adaptation on receptor-binding and antigenic properties of recent influenza A (H3N2) vaccine viruses. CVV X-223, derived from Tex50e and carrying a substitution at residue 226 of HA1 (I226N), also failed to bind to 6-SLN (data not shown) but bound with high avidity to 3-SLN. 2016 The Journal of general virology Result IV I226N 82 87 HA1 77 80 26974849 Effects of egg-adaptation on receptor-binding and antigenic properties of recent influenza A (H3N2) vaccine viruses. D190E is a common egg-adaptive substitution and the AA at this position has been shown to be involved in the receptor-binding specificity of both H3 and H1 subtypes. 2016 The Journal of general virology Result IV D190E 0 5 26974849 Effects of egg-adaptation on receptor-binding and antigenic properties of recent influenza A (H3N2) vaccine viruses. Due to the overlapping nature of the antibody and receptor-binding regions of the HA molecule, studies such as these are required to indicate which substitutions mainly affect antigenicity (D190E) or receptor-binding properties (V186G and G186V) or both, as seen in viruses with HA1 position 156 substitutions. 2016 The Journal of general virology Result IV D190E;V186G;G186V 190;229;239 195;234;244 HA;HA1 82;279 84;282 26974849 Effects of egg-adaptation on receptor-binding and antigenic properties of recent influenza A (H3N2) vaccine viruses. For example, this has been reported previously for H3N2 IAV circulating during the 2003-2004 season whereby introduction of HA1 substitution G186V improved virus replication in eggs but showed no altered antigenic properties and G186V in combination with N246K has been shown to significantly enhance virus propagation in eggs without changing virus antigenicity or immunogenicity of zoonotic H3N2 variant IAV CVV A/Indiana/08/2011. 2016 The Journal of general virology Result IV G186V;G186V;N246K 141;229;255 146;234;260 HA1 124 127 26974849 Effects of egg-adaptation on receptor-binding and antigenic properties of recent influenza A (H3N2) vaccine viruses. From this we can deduce that the D190E substitution mainly affects antigenicity with only little effect on receptor-binding. 2016 The Journal of general virology Result IV D190E 33 38 26974849 Effects of egg-adaptation on receptor-binding and antigenic properties of recent influenza A (H3N2) vaccine viruses. Furthermore, G186V in combination with L194P demonstrated increased immunogenicity in ferrets and higher homologous HI titres with H3N2 viruses from 2005 and 2007. 2016 The Journal of general virology Result IV G186V;L194P 13;39 18;44 26974849 Effects of egg-adaptation on receptor-binding and antigenic properties of recent influenza A (H3N2) vaccine viruses. G186V is one of the most commonly identified egg-adaptations in H3N2 viruses and our data complement other studies that have also demonstrated that G186V substitution does not affect virus antigenicity. 2016 The Journal of general virology Result IV G186V;G186V 0;148 5;153 26974849 Effects of egg-adaptation on receptor-binding and antigenic properties of recent influenza A (H3N2) vaccine viruses. However, introduction of substitution H156R into cell-propagated Vic361 (Vic361c) to produce RG/Vic361c H156R, also resulted in this virus binding with high avidity to 6-SLN. 2016 The Journal of general virology Result IV H156R;H156R 38;104 43;109 26974849 Effects of egg-adaptation on receptor-binding and antigenic properties of recent influenza A (H3N2) vaccine viruses. I226N substitution establishes a new potential glycosylation motif. 2016 The Journal of general virology Result IV I226N 0 5 26974849 Effects of egg-adaptation on receptor-binding and antigenic properties of recent influenza A (H3N2) vaccine viruses. In contrast, viruses carrying substitutions at HA1 position 186, notably RG/Vic361e V186G and RG/Vic361c G186V, showed significant alterations in BLI receptor-analogue and RBC binding with no major changes in antigenic properties. 2016 The Journal of general virology Result IV V186G;G186V 84;105 89;110 HA1 47 50 26974849 Effects of egg-adaptation on receptor-binding and antigenic properties of recent influenza A (H3N2) vaccine viruses. In support of this, introduction of I226N into Vic361e HA to produce RG/Vic361e I226N resulted in increased binding avidity for 3-SLN. 2016 The Journal of general virology Result IV I226N;I226N 36;80 41;85 HA 55 57 26974849 Effects of egg-adaptation on receptor-binding and antigenic properties of recent influenza A (H3N2) vaccine viruses. In the set of 2015 and 2015-2016 CVVs derived from Switz13e, X-247 and NIB-88, both carried AA substitutions at residue 219, S219F and S219Y respectively, compared to the egg-propagated prototype Switz13e. 2016 The Journal of general virology Result IV S219F;S219Y 125;135 130;140 26974849 Effects of egg-adaptation on receptor-binding and antigenic properties of recent influenza A (H3N2) vaccine viruses. Introducing the R156Q+S219Y combination into Vic361e resulted in no detectable binding of the virus to either 3-SLN. 2016 The Journal of general virology Result IV R156Q;S219Y 16;22 21;27 26974849 Effects of egg-adaptation on receptor-binding and antigenic properties of recent influenza A (H3N2) vaccine viruses. Introduction of substitutions R156Q and S219Y independently into Vic361e HA resulted in some increased binding to 3-SLN. 2016 The Journal of general virology Result IV R156Q;S219Y 30;40 35;45 HA 73 75 26974849 Effects of egg-adaptation on receptor-binding and antigenic properties of recent influenza A (H3N2) vaccine viruses. It is also possible that the phenotype of strong binding avidity to 3-SLN of viruses RG/Vic361e S219Y and RG/Vic361 S219F may be attributed to various potential combinations of AA residues at positions 219, 156 and/or 225, or additional substitutions located in regions other than those listed in Table 1 which may be compensating for the 219Y and 219F residue changes. 2016 The Journal of general virology Result IV S219Y;S219F 96;116 101;121 26974849 Effects of egg-adaptation on receptor-binding and antigenic properties of recent influenza A (H3N2) vaccine viruses. It is worth noting that the effect of the I226N substitution has the potential to differ between RG/Vic361e HA and X-223 HA, as a single substitution in one virus background will not necessarily confer the same effect when introduced into another background, even if the differences between the two backgrounds are minimal. 2016 The Journal of general virology Result IV I226N 42 47 HA;HA 108;121 110;123 26974849 Effects of egg-adaptation on receptor-binding and antigenic properties of recent influenza A (H3N2) vaccine viruses. Moreover, egg-propagated RG virus RG/Vic361e R156Q+S219Y and cell culture-propagated RG viruses RG/Vic361c H156Q, S219F, S219Y, and H156Q+S219Y have significantly lower HI titres of 320 when tested against NIB-79 antiserum. 2016 The Journal of general virology Result IV R156Q;S219Y;H156Q;S219F;S219Y;S219Y;H156Q 45;51;107;114;121;138;132 50;56;112;119;126;143;137 26974849 Effects of egg-adaptation on receptor-binding and antigenic properties of recent influenza A (H3N2) vaccine viruses. NIB-79 contains a D190E substitution, also shared with RG/Vic361e D190E, but not present in any of the other viruses tested. 2016 The Journal of general virology Result IV D190E;D190E 18;66 23;71 26974849 Effects of egg-adaptation on receptor-binding and antigenic properties of recent influenza A (H3N2) vaccine viruses. No cell culture-propagated viruses or the egg-propagated RG/Vic361e R156H were able to agglutinate chicken RBC, consistent with previous reports. 2016 The Journal of general virology Result IV R156H 68 73 26974849 Effects of egg-adaptation on receptor-binding and antigenic properties of recent influenza A (H3N2) vaccine viruses. None of the cell culture-propagated viruses, with the exceptions of RG/Vic361c H156R and RG/Vic361c H156Q, which contain 'egg-like' residues at position 156, were able to agglutinate turkey RBC. 2016 The Journal of general virology Result IV H156R;H156Q 79;100 84;105 26974849 Effects of egg-adaptation on receptor-binding and antigenic properties of recent influenza A (H3N2) vaccine viruses. Results for cell culture-propagated cultivars of Tex50, RG/Vic361c D190E and RG/Vic361c I226N could not be generated as they propagated to very low yield, making subsequent analyses impossible. 2016 The Journal of general virology Result IV D190E;I226N 67;88 72;93 26974849 Effects of egg-adaptation on receptor-binding and antigenic properties of recent influenza A (H3N2) vaccine viruses. RG viruses were produced with either one or both of the R156Q and S219Y AA substitutions to define which was responsible for the lack of measurable binding to the receptor-analogues. 2016 The Journal of general virology Result IV R156Q;S219Y 56;66 61;71 26974849 Effects of egg-adaptation on receptor-binding and antigenic properties of recent influenza A (H3N2) vaccine viruses. RG/Vic361e D190E showed reduced recognition by the antiserum (4-fold reduced over the homologous titre) indicating that it may be responsible for the change in antigenicity. 2016 The Journal of general virology Result IV D190E 11 16 26974849 Effects of egg-adaptation on receptor-binding and antigenic properties of recent influenza A (H3N2) vaccine viruses. RG/Vic361e D190E, constructed to correspond to NIB-79, showed a similar binding profile to 3-SLN. 2016 The Journal of general virology Result IV D190E 11 16 26974849 Effects of egg-adaptation on receptor-binding and antigenic properties of recent influenza A (H3N2) vaccine viruses. RG/Vic361e I226N reacted well (HI titre 1280) with antiserum raised against Vic361e (homologous titre 2560), indicating that the CVV X-223 is antigenically similar to the Tex50 virus (Table S1) from which it was derived. 2016 The Journal of general virology Result IV I226N 11 16 26974849 Effects of egg-adaptation on receptor-binding and antigenic properties of recent influenza A (H3N2) vaccine viruses. Similarly, the I226N substitution has previously been reported to improve virus replication in eggs of a cold-adapted H3N2 IAV A/Brisbane/10/07 without affecting virus antigenicity. 2016 The Journal of general virology Result IV I226N 15 20 26974849 Effects of egg-adaptation on receptor-binding and antigenic properties of recent influenza A (H3N2) vaccine viruses. The AA substitution I226N carried by X-223 is probably responsible for the strong virus binding avidity for 3-SLN and AA substitution at position 226 of HA1 is a frequently documented host-receptor adaptation, with Q226L substitution causing altered binding preferences from avian to human receptors. 2016 The Journal of general virology Result IV I226N;Q226L 20;215 25;220 HA1 153 156 26974849 Effects of egg-adaptation on receptor-binding and antigenic properties of recent influenza A (H3N2) vaccine viruses. The cell-propagated viruses, RG/Vic361c S219F and S219Y, reacted less well in HI assays and carried 186G while the egg-propagated-viruses, RG/Vic361e S219F and S219Y, reacted well in HI assays and carried 186V. 2016 The Journal of general virology Result IV S219F;S219Y;S219F;S219Y 40;50;150;160 45;55;155;165 26974849 Effects of egg-adaptation on receptor-binding and antigenic properties of recent influenza A (H3N2) vaccine viruses. The effects of substitutions at residue 219 are perplexing: cell-propagated viruses RG/Vic361c S219F and S219Y reacted less well in HI assays with 4-fold decreases in titre; however, egg-propagated viruses with the same substitutions, RG/Vic361e S219F and S219Y reacted well, and it is noteworthy that RG/Vic361e S219Y had an increased binding avidity for 3-SLN. 2016 The Journal of general virology Result IV S219F;S219Y;S219F;S219Y;S219Y 95;105;246;256;313 100;110;251;261;318 26974849 Effects of egg-adaptation on receptor-binding and antigenic properties of recent influenza A (H3N2) vaccine viruses. The introduction of H156R substitution into Vic361c made the RG virus more like the egg-propagated virus, which was found to bind with high avidity to 6-SLN. 2016 The Journal of general virology Result IV H156R 20 25 26974849 Effects of egg-adaptation on receptor-binding and antigenic properties of recent influenza A (H3N2) vaccine viruses. The lack of binding to 6-SLN may be due to the maintained 156H in HA1, making the virus more 'cell-like' as described above for egg-propagated RG/Vic361e R156H. 2016 The Journal of general virology Result IV R156H 154 159 HA1 66 69 26974849 Effects of egg-adaptation on receptor-binding and antigenic properties of recent influenza A (H3N2) vaccine viruses. The observation that NIB-88 and X-247 failed to bind 3-SLN was surprising in light of the ability of both RG/Vic361e S219Y and RG/Vic361e S219F. 2016 The Journal of general virology Result IV S219Y;S219F 117;138 122;143 26974849 Effects of egg-adaptation on receptor-binding and antigenic properties of recent influenza A (H3N2) vaccine viruses. These viruses included Vic361c and RG viruses with AA substitutions at HA positions 156 and 219, RG/Vic361e R156Q, R156Q+S219Y, RG/Vic361c H156Q, S219Y, S219F, H156Q+S219Y. 2016 The Journal of general virology Result IV R156Q;R156Q;S219Y;H156Q;S219Y;S219F;S219Y;H156Q 108;115;121;139;146;153;166;160 113;120;126;144;151;158;171;165 HA 71 73 26974849 Effects of egg-adaptation on receptor-binding and antigenic properties of recent influenza A (H3N2) vaccine viruses. This includes the egg-propagated viruses RG/Vic361e R156Q, R156Q+S219Y, and cell-propagated viruses RG/Vic361c H156Q, and H156Q+S219Y which were all engineered to be partial analogues of CVVs IVR-165 and X-217. 2016 The Journal of general virology Result IV R156Q;R156Q;S219Y;H156Q;H156Q;S219Y 52;59;65;111;122;128 57;64;70;116;127;133 26974849 Effects of egg-adaptation on receptor-binding and antigenic properties of recent influenza A (H3N2) vaccine viruses. Two RG viruses RG/Vic361e R156H and RG/Vic361e V186G were constructed to represent viruses with single substitutions. 2016 The Journal of general virology Result IV R156H;V186G 26;47 31;52 27089319 The Molecular Epidemiology and Evolutionary Dynamics of Influenza B Virus in Two Italian Regions during 2010-2015: The Experience of Sicily and Liguria. Among tested Ligurian isolates belonging to B/Yamagata clade 3, B/Genoa/0112/1213 and B/Genoa/0613/1213 presented a close relationship with the reference strain B/Phuket/3073/2013 at HI assay, with which they shared the same amino-acid substitutions K116N in the 120-loop and T199I in the 190-helix. 2016 International journal of molecular sciences Result IV K116N;T199I 250;276 255;281 27089319 The Molecular Epidemiology and Evolutionary Dynamics of Influenza B Virus in Two Italian Regions during 2010-2015: The Experience of Sicily and Liguria. As for B/Victoria isolates (Table 2), B/Genoa/22/2011 showed the closest relationship with the vaccine strain B/Brisbane/60/2008 in terms of hemagglutination inhibition (HI) titer, although the predicted amino-acid sequences of the HA1 domains of the strains showed two differences in the sequenced region (I37V and G80R). 2016 International journal of molecular sciences Result IV I37V;G80R 307;316 311;320 HA1 232 235 27089319 The Molecular Epidemiology and Evolutionary Dynamics of Influenza B Virus in Two Italian Regions during 2010-2015: The Experience of Sicily and Liguria. B/Genoa/04/2010 had only one amino-acid substitution with respect to B/Brisbane/60/2008 (V146I), but this is located in the 150-loop, one of the most important antibody-binding sites on influenza B virus HA protein: this single mutation affected the HI titration, showing a quite different antigenic profile between the clinical isolate and the vaccine strain, although they belonged to the same phylogenetic clade (1A). 2016 International journal of molecular sciences Result IV V146I 89 94 HA 204 206 27089319 The Molecular Epidemiology and Evolutionary Dynamics of Influenza B Virus in Two Italian Regions during 2010-2015: The Experience of Sicily and Liguria. B/Genoa/0413/1213 and B/Genoa/0713/1213 phylogenetically belonged to B/Yamagata clade 2, the same clade of the reference strain B/Massachusetts/02/2012, and they showed the same amino-acid substitutions, in particular a lysine (K) residue at position 48, a serine (S) at position 150, a threonine (T) at position 199, and an asparagine (N) at positions 166 and 203. 2016 International journal of molecular sciences Result IV K48K;S150S;N166N 219;256;324 254;284;357 27089319 The Molecular Epidemiology and Evolutionary Dynamics of Influenza B Virus in Two Italian Regions during 2010-2015: The Experience of Sicily and Liguria. B/Genoa/11/2015 presented the highest HI titers towards all three reference vaccine strains and only two amino-acid substitutions in the four major epitopes with respect to B/Wisconsin/01/2010, namely K116N in the 120-loop and T199I in the 190-helix. 2016 International journal of molecular sciences Result IV K116N;T199I 201;227 206;232 27089319 The Molecular Epidemiology and Evolutionary Dynamics of Influenza B Virus in Two Italian Regions during 2010-2015: The Experience of Sicily and Liguria. Conversely, B/Genoa/09/2015 showed reduced HI titers when tested with B/Wisconsin/01/2010 and B/Massachusetts/02/2012 antisera, although it presented only two differences with B/Genoa/11/2015 in the entire sequenced region: noteworthy, B/Genoa/09/2015 presented an aspartic acid (D) at position 197, a key residue at the glycosylation site. 2016 International journal of molecular sciences Result IV D197D 264 299 27089319 The Molecular Epidemiology and Evolutionary Dynamics of Influenza B Virus in Two Italian Regions during 2010-2015: The Experience of Sicily and Liguria. D197N and D196N in 190-helix (based on Victoria clade 1 and Yamagata clade 2/Yamagata clade 3 vaccine strains numbering, respectively), which represent key residues at the glycosylation site, were found in almost all viruses collected in the two Italian regions during the study period (100%, n = 29/29; 100%, n = 112/112; 96.4%, n = 54/56, for B/Victoria clade 1, B/Yamagata clade 2 and B/Yamagata clade 3, respectively). 2016 International journal of molecular sciences Result IV D197N;D196N 0;10 5;15 27089319 The Molecular Epidemiology and Evolutionary Dynamics of Influenza B Virus in Two Italian Regions during 2010-2015: The Experience of Sicily and Liguria. In details, the most represented substitutions were N116K in the 120-loop, shared by 83.9% (n = 47/56) of B/Yamagata clade 3 strains and I146V in the 150-loop, which was detected in 89.6% (n = 26/29) of B/Victoria clade 1 strains. 2016 International journal of molecular sciences Result IV N116K;I146V 52;137 57;142 27089319 The Molecular Epidemiology and Evolutionary Dynamics of Influenza B Virus in Two Italian Regions during 2010-2015: The Experience of Sicily and Liguria. Interestingly, substitutions H122Q and N126D for B/Victoria viruses, and K197R and S202N for B/Yamagata clade 3 viruses were exclusively observed in a few Sicilian strains, while substitution N126S in the 120-loop was recorded in only one isolate from Liguria. 2016 International journal of molecular sciences Result IV H122Q;N126D;K197R;S202N;N126S 29;39;73;83;192 34;44;78;88;197 27089319 The Molecular Epidemiology and Evolutionary Dynamics of Influenza B Virus in Two Italian Regions during 2010-2015: The Experience of Sicily and Liguria. The same mutation was observed in B/Genoa/08/2010 and B/Genoa/12/2011 viruses, phylogenetically belonging to B/Victoria clade 1B: together with P58L substitution, that fell within 120-loop, these two mutations heavily affected the antigenic pattern of the Ligurian viruses, as also shown by the low HI titer. 2016 International journal of molecular sciences Result IV P58L 144 148 27097026 Novel Polymerase Gene Mutations for Human Adaptation in Clinical Isolates of Avian H5N1 Influenza Viruses. A similar effect was observed for virus strains with some of the mutations selected in patients (e.g., PB1-P756S/P627L/E618D/K386R, PA-E327K, Inter-5 and Inter-8), despite their impact on polymerase activity in minigenome assays. 2016 PLoS pathogens Result IV P756S;P627L;E618D;K386R;E327K 107;113;119;125;135 112;118;124;130;140 PA;PB1 132;103 134;106 27097026 Novel Polymerase Gene Mutations for Human Adaptation in Clinical Isolates of Avian H5N1 Influenza Viruses. An unusually long beta-ribbon, where PB1-D175N, T182I, K198R and K214R were located, contacts the 3'-end of vRNA and the beta-hairpin, where PB1-L384S was located, forming a 5' vRNA binding site together with a PA-arch domain. 2016 PLoS pathogens Result IV D175N;T182I;K198R;K214R;L384S 41;48;55;65;145 46;53;60;70;150 PA;PB1;PB1 211;37;141 213;40;144 27097026 Novel Polymerase Gene Mutations for Human Adaptation in Clinical Isolates of Avian H5N1 Influenza Viruses. As shown in S6 Fig, PB2-K627E produced less vRNA than EG/D1 (wt), indicating that PB2-E627K increased the replication activity of EG/D1 (wt) polymerase. 2016 PLoS pathogens Result IV K627E;E627K 24;86 29;91 PB2;PB2 20;82 23;85 27097026 Novel Polymerase Gene Mutations for Human Adaptation in Clinical Isolates of Avian H5N1 Influenza Viruses. At 37 C, the PB2-M473V/D195N, PB1-K198R, PB1-K198R/D175N, PB1-T182I/K214R/L384S, Inter-1, Inter-2 and Inter-4 mutants and EG/D1 (wt) produced similar amounts of progeny vRNA at 24 and 48 h post-infection, and up to 11.0-fold more progeny vRNA than EG/D1 (wt) virus at 72 h post-infection (Fig 4A and 4B). 2016 PLoS pathogens Result IV M473V;D195N;K198R;K198R;D175N;T182I;K214R;L384S 17;23;34;45;51;62;68;74 22;28;39;50;56;67;73;79 PB1;PB1;PB1;PB2 30;41;58;13 33;44;61;16 27097026 Novel Polymerase Gene Mutations for Human Adaptation in Clinical Isolates of Avian H5N1 Influenza Viruses. For PB1 mutations, D175N, T182I, K198R and K214R were in the beta-ribbon domain (residues 177-214) that interacts with vRNA, L384S was in the beta-hairpin that binds to vRNA and P627L was in the thumb domain. 2016 PLoS pathogens Result IV D175N;T182I;K198R;K214R;L384S;P627L 19;26;33;43;125;178 24;31;38;48;130;183 PB1 4 7 27097026 Novel Polymerase Gene Mutations for Human Adaptation in Clinical Isolates of Avian H5N1 Influenza Viruses. For PB2 mutations, K80R was in the N1-subdomain (residues 55-103) that interacts with the PB1-thumb domain, D195N was in the helical-lid domain (residues 160-212), M473V was in the Cap-binding domain (residues 318-483) and M570I was in the 627 domain (residues 538-676). 2016 PLoS pathogens Result IV K80R;D195N;M473V;M570I 19;108;164;223 23;113;169;228 PB1;PB2 90;4 93;7 27097026 Novel Polymerase Gene Mutations for Human Adaptation in Clinical Isolates of Avian H5N1 Influenza Viruses. In addition, a database search of virus gene sequences found that PB1-K198R, PB1-T182I, PB1-K214R and PB1-L384S were present in some Asian H5N1 human isolates as well as in H3N2 and H1N1 human isolates (Table 1), which also suggested a human adaptation function for these residues. 2016 PLoS pathogens Result IV K198R;T182I;K214R;L384S 70;81;92;106 75;86;97;111 PB1;PB1;PB1;PB1 66;77;88;102 69;80;91;105 27097026 Novel Polymerase Gene Mutations for Human Adaptation in Clinical Isolates of Avian H5N1 Influenza Viruses. In addition, at 33 C, the PB1-K198R/D175N double mutation had a synergistic effect and induced up to 5-fold greater polymerase activity in cRNA-oriented minigenome assays than wild-type; i.e., PB1-K198R < PB1-K198R/D175N, P <0.01 by ANOVA with Tukey's multiple comparison test. 2016 PLoS pathogens Result IV D175N;K198R;K198R;K198R;D175N 36;30;197;209;215 41;35;202;214;220 PB1;PB1;PB1 26;193;205 29;196;208 27097026 Novel Polymerase Gene Mutations for Human Adaptation in Clinical Isolates of Avian H5N1 Influenza Viruses. In addition, in cRNA-oriented minigenome assays, PB1-T182I and PB1-K198R increased polymerase activity 3.7-fold and 6.0-fold, respectively, at 37 C and PB1-K198R also increased polymerase activity 2.9-fold at 33 C (Fig 2B). 2016 PLoS pathogens Result IV T182I;K198R;K198R 53;67;156 58;72;161 PB1;PB1;PB1 49;63;152 52;66;155 27097026 Novel Polymerase Gene Mutations for Human Adaptation in Clinical Isolates of Avian H5N1 Influenza Viruses. In contrast, strains with the PB1-K198R and PB1-P627L mutations were scattered or clustered in branches of human isolates and were not found in any closely related avian viruses, indicating that avian clade 2.2.1.2 viruses, some of which also carried PB1-T182I and K214R, might acquire PB1-K198R or PB1-P627L during viral growth in humans. 2016 PLoS pathogens Result IV K198R;P627L;T182I;K214R;K198R;P627L 34;48;255;265;290;303 39;53;260;270;295;308 PB1;PB1;PB1;PB1;PB1 30;44;251;286;299 33;47;254;289;302 27097026 Novel Polymerase Gene Mutations for Human Adaptation in Clinical Isolates of Avian H5N1 Influenza Viruses. In our simulations, a plausible model showed that mutations in the PB1 beta-ribbon and beta-hairpin backbone modified the topology of these two structures (S10B-S10E Fig) and changed the interaction energies between the vRNA promoter region and the known vRNA contact residues (residues 188 and 203 in the beta-ribbon) and between the vRNA promoter region and the trimeric polymerase complex (S4 Table). 2016 PLoS pathogens Result IV S10E 161 165 PB1 67 70 27097026 Novel Polymerase Gene Mutations for Human Adaptation in Clinical Isolates of Avian H5N1 Influenza Viruses. In particular, at 33 C, PB1-P627L and PA-E327K increased polymerase activity 6.3-fold and 2.5-fold, respectively, in vRNA-oriented minigenome assays (Fig 2A) and 5.0-fold and 3.4-fold, respectively, in cRNA-oriented minigenome assays (Fig 2B). 2016 PLoS pathogens Result IV P627L;E327K 28;41 33;46 PA;PB1 38;24 40;27 27097026 Novel Polymerase Gene Mutations for Human Adaptation in Clinical Isolates of Avian H5N1 Influenza Viruses. In particular, in cRNA-oriented minigenome assays, the PB1-T182I/K214R/L384S triple mutation induced up to 5-fold and 2.4-fold greater polymerase activity than wild-type in an additive manner at 37 C and 33 C, respectively; i.e., PB1-T182I < PB1-T182I/K214R/L384S, P <0.05 by ANOVA with Tukey's multiple comparison test (Fig 3B). 2016 PLoS pathogens Result IV T182I;K214R;L384S;T182I;T182I;K214R;L384S 59;65;71;234;246;252;258 64;70;76;239;251;257;263 PB1;PB1;PB1 55;230;242 58;233;245 27097026 Novel Polymerase Gene Mutations for Human Adaptation in Clinical Isolates of Avian H5N1 Influenza Viruses. In particular, the PB1-T182I and PB1-K214R mutations reduced the interaction energies between the vRNA promoter and PB1 vRNA contact residues 188 and 203, but increased the interaction energies between the vRNA promoter and the trimeric polymerase complex. 2016 PLoS pathogens Result IV T182I;K214R 23;37 28;42 PB1;PB1;PB1 19;33;116 22;36;119 27097026 Novel Polymerase Gene Mutations for Human Adaptation in Clinical Isolates of Avian H5N1 Influenza Viruses. In this study, 293T cells were co-transfected with plasmids expressing EG/D1 PB2, PB1, PA or NP, each carrying the indicated mutations that had a significant effect on progeny vRNA production in human airway cells, including PB2-E627K, with the PB2-K627E back mutation, and a plasmid expressing cRNA as a template for replication (cRNA to vRNA synthesis). 2016 PLoS pathogens Result IV E627K;K627E 229;249 234;254 NP;PA;PB1;PB2;PB2;PB2 93;87;82;77;225;245 95;89;85;80;228;248 27097026 Novel Polymerase Gene Mutations for Human Adaptation in Clinical Isolates of Avian H5N1 Influenza Viruses. In this study, PB2-D701N was included as a reference mutation, although this human adaptation mutation has not yet been detected in H5N1 viruses isolated from Egyptian patients, because the known human adaptation polymerase mutations, except PB2-E627K, had not been detected in H5N1 viruses isolated from patients in Egypt at the time of this study. 2016 PLoS pathogens Result IV D701N;E627K 19;246 24;251 PB2;PB2 15;242 18;245 27097026 Novel Polymerase Gene Mutations for Human Adaptation in Clinical Isolates of Avian H5N1 Influenza Viruses. Interestingly, the PB2-D701N human adaptation mutation decreased progeny vRNA production in SAE cells (S4 Fig). 2016 PLoS pathogens Result IV D701N 23 28 PB2 19 22 27097026 Novel Polymerase Gene Mutations for Human Adaptation in Clinical Isolates of Avian H5N1 Influenza Viruses. Of the PB1 mutations, PB1-T182I, PB1-K214R and PB1-L384S were present in both avian and human isolates, and strains with these mutations formed two subclades distinguishable from ancestral clade 2.2.1 strains: these subclades have been designated clade 2.2.1-B and/or clade 2.2.1.2 (clade 2.2.1-C): the latter is now dominant in Egypt. 2016 PLoS pathogens Result IV T182I;K214R;L384S 26;37;51 31;42;56 PB1;PB1;PB1;PB1 7;22;33;47 10;25;36;50 27097026 Novel Polymerase Gene Mutations for Human Adaptation in Clinical Isolates of Avian H5N1 Influenza Viruses. Preliminary experiments showed that EG/D1 polymerase had substantially higher polymerase activity than a strain with the PB2-K627E back mutation. 2016 PLoS pathogens Result IV K627E 125 130 PB2 121 124 27097026 Novel Polymerase Gene Mutations for Human Adaptation in Clinical Isolates of Avian H5N1 Influenza Viruses. The Asian human isolates carry either PB2-627E or PB2-627K, suggesting that PB1-K198R, PB1-T182I, PB1-K214R and PB1-L384S may increase Asian H5N1 virus growth by themselves and/or in combination with PB2-627K. 2016 PLoS pathogens Result IV K198R;T182I;K214R;L384S 80;91;102;116 85;96;107;121 PB1;PB1;PB1;PB1;PB2;PB2;PB2 76;87;98;112;38;50;200 79;90;101;115;41;53;203 27097026 Novel Polymerase Gene Mutations for Human Adaptation in Clinical Isolates of Avian H5N1 Influenza Viruses. The effects of these single/multiple mutations in increasing polymerase activity were comparable to that of PB2-D701N in each of the conditions studied (Figs 2 and 3). 2016 PLoS pathogens Result IV D701N 112 117 PB2 108 111 27097026 Novel Polymerase Gene Mutations for Human Adaptation in Clinical Isolates of Avian H5N1 Influenza Viruses. The PB1-P627L and Inter-3 mutants only produced more progeny vRNA than EG/D1 (wt) at 33 C, indicating a lower temperature-specific increase in virus replication. 2016 PLoS pathogens Result IV P627L 8 13 PB1 4 7 27097026 Novel Polymerase Gene Mutations for Human Adaptation in Clinical Isolates of Avian H5N1 Influenza Viruses. This was in agreement with previous studies of other H5N1 clade viruses, in which the polymerase activity of H5N1 viruses with a single PB2-E627K mutation was lower than that of seasonal human influenza viruses. 2016 PLoS pathogens Result IV E627K 140 145 PB2 136 139 27097026 Novel Polymerase Gene Mutations for Human Adaptation in Clinical Isolates of Avian H5N1 Influenza Viruses. To investigate the effect(s) of the mutations on viral polymerase activity, we carried out minigenome assays of the polymerases with these mutations in the genetic background of influenza virus A/duck/Egypt/D1Br/2007 (EG/D1), since EG/D1 is a representative H5N1 clade 2.2.1 strain carrying PB2-E627K. 2016 PLoS pathogens Result IV E627K 295 300 PB2 291 294 27105450 Residues in the PB2 and PA genes contribute to the pathogenicity of avian H7N3 influenza A virus in DBA/2 mice. Analysis of the cytokine and chemokine concentration in lung homogenates of H7N3 and H7N3-PAP190S inoculated mice, we found significantly less CCL2, CCL3, KC, and GM-CSF at 3 dpi (P<0.01) and 6 dpi (P<0.05, Figure 7). 2016 Virology Result IV P190S 91 97 PA 90 92 27105450 Residues in the PB2 and PA genes contribute to the pathogenicity of avian H7N3 influenza A virus in DBA/2 mice. Animals infected with the P190S mutant or the Q400P mutant lost significantly (P<0.01) less weight and fewer animals succumbed to infection (Figure 6 and Table 1). 2016 Virology Result IV P190S;Q400P 26;46 31;51 27105450 Residues in the PB2 and PA genes contribute to the pathogenicity of avian H7N3 influenza A virus in DBA/2 mice. Compared to H7N9 virus, inoculation with H7N9-PB2V358E resulted in an increase in weight-loss on day 8 (7% versus 15%, P<0.01, Table 1) and mortality (15% versus 33%, P = 0.25, Table 1). 2016 Virology Result IV V358E 49 54 PB2 46 49 27105450 Residues in the PB2 and PA genes contribute to the pathogenicity of avian H7N3 influenza A virus in DBA/2 mice. Compared to the wild type H7N3, position G62R, and E681G had no effect on morbidity and mortality (Figure 5 and Table 1). 2016 Virology Result IV G62R;E681G 41;51 45;56 27105450 Residues in the PB2 and PA genes contribute to the pathogenicity of avian H7N3 influenza A virus in DBA/2 mice. Finally, the E358V change in the PB2N3 gene resulted in significantly reduced weight loss and increased survival (P<0.001). 2016 Virology Result IV E358V 13 18 PB2 33 36 27105450 Residues in the PB2 and PA genes contribute to the pathogenicity of avian H7N3 influenza A virus in DBA/2 mice. Finally, the glutamic acid to valine change at position 358 of the PB2 of H7N3 virus significantly reduced the polymerase activity (P<0.001, Figure 2C). 2016 Virology Result IV E358V 13 59 PB2 67 70 27105450 Residues in the PB2 and PA genes contribute to the pathogenicity of avian H7N3 influenza A virus in DBA/2 mice. Finally, we measured the impact of N184S, P190S and Q400P substitutions on the polymerase activity of H7N3 virus (Figure 2C). 2016 Virology Result IV N184S;P190S;Q400P 35;42;52 40;47;57 27105450 Residues in the PB2 and PA genes contribute to the pathogenicity of avian H7N3 influenza A virus in DBA/2 mice. Four positions were selected (G62R, E358V, A471T, and E681G) based on the difference in chemical properties of the amino-acids involved. 2016 Virology Result IV E358V;G62R;A471T;E681G 36;30;43;54 41;34;48;59 27105450 Residues in the PB2 and PA genes contribute to the pathogenicity of avian H7N3 influenza A virus in DBA/2 mice. Inoculation of DBA/2J mice with the H7N3-PB2E358V virus induced a maximum weight loss of 15.3% on day 8 and only 20% of the inoculated animals succumbed to infection. 2016 Virology Result IV E358V 44 49 PB2 41 44 27105450 Residues in the PB2 and PA genes contribute to the pathogenicity of avian H7N3 influenza A virus in DBA/2 mice. The A471T substitution significantly increased morbidity (P<0.01 on 6 dpi) and mortality (P<0.05) of the mutant virus compared to wild type H7N3. 2016 Virology Result IV A471T 4 9 27105450 Residues in the PB2 and PA genes contribute to the pathogenicity of avian H7N3 influenza A virus in DBA/2 mice. The N184S substitution had no effect on weight loss or survival after intranasal infection in DBA/2J mice. 2016 Virology Result IV N184S 4 9 27105450 Residues in the PB2 and PA genes contribute to the pathogenicity of avian H7N3 influenza A virus in DBA/2 mice. Three positions in the PA gene were selected (N184S, P190S, and Q400P) based on the difference in chemical properties of the amino-acids involved. 2016 Virology Result IV P190S;N184S;Q400P 53;46;64 58;51;69 PA 23 25 27105450 Residues in the PB2 and PA genes contribute to the pathogenicity of avian H7N3 influenza A virus in DBA/2 mice. To determine if the P190S substitution reduced virus replication we analyzed viral loads at day 2, 3 and 6 post inoculation. 2016 Virology Result IV P190S 20 25 27105450 Residues in the PB2 and PA genes contribute to the pathogenicity of avian H7N3 influenza A virus in DBA/2 mice. To evaluate the importance of PB2358 in the context of the H7N9 virus, we introduced a glutamic acid (V358E) at this position and evaluated pathogenesis. 2016 Virology Result IV V358E 102 107 27186639 In-Depth Analysis of HA and NS1 Genes in A(H1N1)pdm09 Infected Patients. Concerning NS1, M106I (1.59% in pt1) and S195T (0.52% in pt8) are suggested to be related to increased virulence of H5N1. 2016 PloS one Result IV M106I;S195T 16;41 21;46 NS1 11 14 27186639 In-Depth Analysis of HA and NS1 Genes in A(H1N1)pdm09 Infected Patients. In addition, HA N276S (only observed in pt2, 0.53%), removes a potential N-glycosylation site, which may also affect antigenic and other properties of HA. 2016 PloS one Result IV N276S 16 21 HA;HA 13;151 15;153 27186639 In-Depth Analysis of HA and NS1 Genes in A(H1N1)pdm09 Infected Patients. Known polymorphisms, namely S203T (HA) and I123V (NS1), were observed as dominant variants (>98%) in all but one (pt2) patients; five further non polymorphic variants were detected at frequency >40%, namely three within HA, P271S (43.16%) in pt7; D222E (97.45%) in pt 8; E258D (98.54%) in pt9, and two within NS1, N133D (97.64%) in pt8; D173N (98.38%) in pt7. 2016 PloS one Result IV S203T;I123V;P271S;D222E;E258D;N133D;D173N 28;43;224;247;271;314;337 33;48;229;252;276;319;342 HA;HA;NS1;NS1 35;220;50;309 37;222;53;312 27186639 In-Depth Analysis of HA and NS1 Genes in A(H1N1)pdm09 Infected Patients. This analysis showed that seven HA minority variants (Q188R/N194S/N194D/D222E/Q223R/E224G/T245N) may play a role in the host specificity shift and that two (S190G/Q223R) are related to antigenic drift and/or escape mutant. 2016 PloS one Result IV Q188R;N194S;N194D;D222E;E224G;T245N;Q223R;Q223R;S190G 54;60;66;72;84;90;78;163;157 59;65;71;77;89;95;83;168;162 HA 32 34 27186639 In-Depth Analysis of HA and NS1 Genes in A(H1N1)pdm09 Infected Patients. Three HA (D196G/N247I/T277I) and four NS1 minority variants (L130Q/L141S/S165P/I198T) were novel. 2016 PloS one Result IV D196G;N247I;T277I;L130Q;L141S;S165P;I198T 10;16;22;61;67;73;79 15;21;27;66;72;78;84 HA;NS1 6;38 8;41 27268229 Detection of reassortant avian influenza A (H11N9) virus in environmental samples from live poultry markets in China. The N30D and T215A substitutions in the M1 protein, which have been associated with increased H5N1 pathogenicity in mice, were found in JX/26/2009 and JX/28/2009. 2016 Infectious diseases of poverty Result IV N30D;T215A 4;13 8;18 M1 40 42 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. After 8 rounds of passage, no resistant virus emerged from A/California/7/2009 in the presence of 39.29; by contrast, resistant viruses were readily selected in the presence of a neutralizing antibody against the head group of A/California/7/2009 HA, with a dominant mutation (Gly172Glu) in HA head, consistent with the common view that broadly neutralizing stalk-binding antibodies are less permissive for mutational escape. 2016 PLoS pathogens Result IV G172E 277 286 HA;HA 247;291 249;293 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. Among these, only the N228I mutation in PA has been reported, and it has no effect on viral fitness. 2016 PLoS pathogens Result IV N228I 22 27 PA 40 42 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. As expected, 39.29 still did not bind the Q387K mutant HA at lower pH. 2016 PLoS pathogens Result IV Q387K 42 47 HA 55 57 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. As expected, flow cytometry revealed a total loss of binding of the Q387K mutant to 39.29. 2016 PLoS pathogens Result IV Q387K 68 73 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. As shown in Fig 5, 39.29 did not bind Q387K HA0 whereas it bound D391Y, F175Y/D391G and WT HA0s well (Stage 1). 2016 PLoS pathogens Result IV Q387K;D391Y;F175Y;D391G 38;65;72;78 43;70;77;83 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. At pH 4.8, Q386K and D390G showed reduced binding compared to WT; however, they still bound 39.29 significantly (Fig 6A). 2016 PLoS pathogens Result IV Q386K;D390G 11;21 16;26 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. At pH 5.8, D391Y and F175Y/D391G HAs were still able to form large syncytia whereas the syncytia formed by WT HA were much smaller in size. 2016 PLoS pathogens Result IV D391Y;F175Y;D391G 11;21;27 16;26;32 HA 110 112 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. At pH 5.9, D391Y and F175Y/D391G still induced syncytium formation while WT did not. 2016 PLoS pathogens Result IV D391Y;F175Y;D391G 11;21;27 16;26;32 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. By contrast, consistent with its inability to bind the Q387K HA, 39.29 did not block membrane fusion induced by the Q387K mutant (Fig 4B). 2016 PLoS pathogens Result IV Q387K;Q387K 55;116 60;121 HA 61 63 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. By contrast, syncytium formation by Q387K HA was similar to that mediated by WT HA across the range of pHs tested, with the exception of pH 5.8, where the syncytia formed by Q387K HA appeared to be smaller than those induced by WT (Fig 3A). 2016 PLoS pathogens Result IV Q387K;Q387K 36;174 41;179 HA;HA;HA 42;80;180 44;82;182 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. By contrast, the D391Y and F175Y/D391G mutants bound 39.29 as well as the WT at pH 7 (Fig 2A, middle panel). 2016 PLoS pathogens Result IV D391Y;F175Y;D391G 17;27;33 22;32;38 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. By contrast, the D391Y and F175Y/D391G mutations allowed viruses to escape 39.29-mediated neutralization despite being bound by the antibody even at low pH. 2016 PLoS pathogens Result IV D391Y;F175Y;D391G 17;27;33 22;32;38 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. Consequently, 39.29 completely blocked the fusion mediated by G234E HA (Fig 7B) despite its enhanced fusion ability. 2016 PLoS pathogens Result IV G234E 62 67 HA 68 70 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. Differences in the rate of fusion became apparent at 40 and 20 second exposures, with the efficiency of fusion: D391Y = F175Y/D391G > WT > Q387K. 2016 PLoS pathogens Result IV D391Y;F175Y;D391G;Q387K 112;120;126;139 117;125;131;144 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. First, we performed large multiple sequence alignments to examine whether the Q387K, D391Y and D391G mutations are pre-existing within field isolates of the influenza A virus. 2016 PLoS pathogens Result IV Q387K;D391Y;D391G 78;85;95 83;90;100 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. Flow cytometry showed that, unlike the corresponding mutant HAs of the H3 subtype, all three mutant H1 HAs, including Q386K, bound 39.29 as well as the WT at pH 7 (Fig 6A). 2016 PLoS pathogens Result IV Q386K 118 123 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. For example, the pH to achieve 90% fusion was 5.69 for WT, 5.79 for D391Y and 5.82 for F175Y/D391G. 2016 PLoS pathogens Result IV D391Y;F175Y;D391G 68;87;93 73;92;98 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. For other viral proteins, two unique single amino acid polymorphisms were identified for the WT virus, one in NA (T148K) and the other in NP (G384R). 2016 PLoS pathogens Result IV T148K;G384R 114;142 119;147 NA;NP 110;138 112;140 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. However, a 2-minute pH drop abolished D391Y and F175Y/D391G binding even with pre-bound 39.29 (Fig 5 Stage 3), indicating that the D391 mutations could overcome the block of HA conformational change by 39.29, possibly due to the enhanced fusion ability of the mutant HAs. 2016 PLoS pathogens Result IV D391Y;F175Y;D391G 38;48;54 43;53;59 HA 174 176 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. However, at pHs 6.0 and 6.2 when WT HA did not cause any fusion, G234E was still able to induce syncytia. 2016 PLoS pathogens Result IV G234E 65 70 HA 36 38 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. Interestingly, 39.29 completely blocked the fusion mediated by both the WT and the mutant HAs (Fig 6C), including Q386K and D390G that showed significantly reduced binding to 39.29 at pH4.8 (Fig 6A). 2016 PLoS pathogens Result IV Q386K;D390G 114;124 119;129 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. Interestingly, the D390Y or D390G mutations did not enhance fusion at any pH tested (Fig 6B), indicating that structural and functional differences exist in the stalk regions of H1 and H3 HAs despite their highly conserved sequences. 2016 PLoS pathogens Result IV D390Y;D390G 19;28 24;33 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. Interestingly, the D391Y and F175Y/D391G mutants were able to induce giant syncytia in the presence of 39.29 as well as a negative control antibody (Fig 4B). 2016 PLoS pathogens Result IV D391Y;F175Y;D391G 19;29;35 24;34;40 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. Maximal fusion was achieved at pH 5.4 for both WT and G234E HAs. 2016 PLoS pathogens Result IV G234E 54 59 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. One possible scenario for the observed resistance of the D391Y and F175Y/D391G mutants is that although 39.29 binds these mutants at neutral pH, it falls off at low pH in the endosome. 2016 PLoS pathogens Result IV D391Y;F175Y;D391G 57;67;73 62;72;78 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. Phe175 is located in the HA1 head region distant from the Helix A and F175Y is likely an inconsequential random mutation as results obtained with the F175Y/D391G double mutant HA are very similar to those with the D391G single mutant HA, and F175Y single mutant HA behaves like the WT HA (S1 Fig). 2016 PLoS pathogens Result IV F175Y;F175Y;D391G;D391G;F175Y 70;150;156;214;242 75;155;161;219;247 HA;HA;HA;HA;HA1 176;234;262;285;25 178;236;264;287;28 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. Results from the binding studies suggested that the Q387K mutant escapes 39.29 neutralization by abolishing antibody binding. 2016 PLoS pathogens Result IV Q387K 52 57 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. Scatchard analysis confirmed that the Q387K mutation abolished binding of the HA by 39.29 at pH 4.8, whereas HAs harboring the D391Y and F175Y/D391G mutations showed only 2-3 fold reduced affinities to 39.29 compared to WT at this pH (Table 1). 2016 PLoS pathogens Result IV Q387K;D391Y;F175Y;D391G 38;127;137;143 43;132;142;148 HA 78 80 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. Sequence analysis revealed individual mutations in the HA gene: (Mutant 1) Gln387Lys (Q387K); (Mutant 2) Asp391Tyr (D391Y); (Mutant 3) Phe175Tyr/Asp391Gly (F175Y/D391G). 2016 PLoS pathogens Result IV D391G;Q387K;Q387K;D391Y;D391Y;F175Y;F175Y;D391G;F175D;F175G 145;75;86;105;116;135;156;162;135;135 154;84;91;114;121;144;161;167;144;144 HA 55 57 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. Since the Q386K, D390Y and D390G mutant H1 HAs showed different levels of 39.29 binding at low pH, we tested whether they could escape the fusion block by 39.29 in a fusion assay performed at pH4.8 to ensure maximal fusion in the absence of the antibody. 2016 PLoS pathogens Result IV Q386K;D390Y;D390G 10;17;27 15;22;32 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. Statistically, significant difference was observed between WT and each of the three mutant HAs at 20 second, and between WT and D391Y or F175Y/D391G at 40 second. 2016 PLoS pathogens Result IV D391Y;F175Y;D391G 128;137;143 133;142;148 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. Taken together, our results from the binding and fusion assays suggested the existence of two different virus escape mechanisms to broadly neutralizing stalk-binding antibody: (a) abolishing antibody binding, as exemplified by the Q387K mutant; (b) enhancing the membrane fusion ability of the HA protein, possibly in conjunction with reduced antibody binding at low pH, as exemplified by the D391Y and the F175Y/D391G mutants. 2016 PLoS pathogens Result IV Q387K;D391Y;F175Y;D391G 231;393;407;413 236;398;412;418 HA 294 296 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. The curves for D391Y and F175Y/D391G HAs were right-shifted compared to WT HA, quantitatively demonstrating the ability of the D391 mutants to caused membrane fusion at higher pH compared to WT. 2016 PLoS pathogens Result IV D391Y;F175Y;D391G 15;25;31 20;30;36 HA 75 77 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. The D391Y and F175Y/D391G mutant HAs showed reduced binding compared to WT, but were still clearly bound by 39.29 as compared to the mock- and Q387K-transfected cells (Fig 2A, right panel). 2016 PLoS pathogens Result IV D391Y;F175Y;D391G;Q387K 4;14;20;143 9;19;25;148 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. The Q386K mutant yielded slightly smaller syncytia compared to the WT HA at all pHs tested, which is consistent with the slightly lower fusion efficiency observed for the Q387K H3 HA mutant. 2016 PLoS pathogens Result IV Q386K;Q387K 4;171 9;176 HA;HA 70;180 72;182 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. The R384G substitution has been found in influenza A viruses isolated from 1993 onwards and allows escape from CTL recognition. 2016 PLoS pathogens Result IV R384G 4 9 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. The T148K substitution in NA has been found in recent H3N2 influenza A isolates and influenza B isolates. 2016 PLoS pathogens Result IV T148K 4 9 26 28 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. The three corresponding mutations in H1 HA are Q386K, D390Y and D390G; there is no phenylalanine corresponding to Phe175 in H1 HA. 2016 PLoS pathogens Result IV Q386K;D390Y;D390G 47;54;64 52;59;69 HA;HA 40;127 42;129 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. The WT, D391Y and F175Y/D391G virus particles were bound by 39.29, whereas the Q387K virus particle showed no binding (Fig 2B, middle and bottom panels). 2016 PLoS pathogens Result IV D391Y;F175Y;D391G;Q387K 8;18;24;79 13;23;29;84 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. Therefore, the R384G substitution in all three 39.29-resistant A/Perth/16/2009 viruses possibly contributes to their reduced fitness. 2016 PLoS pathogens Result IV R384G 15 20 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. These results are in line with recent studies that the time required to achieve hemifusion of an H3N2 virus is 30-40 seconds and demonstrate that D391Y and F175Y/D391G mutants mediate fusion faster than WT, while Q387K is slower. 2016 PLoS pathogens Result IV D391Y;F175Y;D391G;Q387K 146;156;162;213 151;161;167;218 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. To test this, we introduced into the A/Perth/16/2009 HA a previously reported fusion-enhancing mutation, G234E, which is distant from the 39.29 epitope. 2016 PLoS pathogens Result IV G234E 105 110 HA 53 55 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. We first confirmed that the G234E mutation indeed enhanced fusion significantly (S4 Fig). 2016 PLoS pathogens Result IV G234E 28 33 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. We next showed that G234E HA bound 39.29 as well as the WT at both neutral and low pHs (Fig 7A). 2016 PLoS pathogens Result IV G234E 20 25 HA 26 28 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. WT and the D391Y and F175Y/D391G mutant HAs had similar binding affinity (Kd) to 39.29 while the Q387K mutant did not bind at all (Table 1). 2016 PLoS pathogens Result IV D391Y;F175Y;D391G;Q387K 11;21;27;97 16;26;32;102 27405392 G45R mutation in the nonstructural protein 1 of A/Puerto Rico/8/1934 (H1N1) enhances viral replication independent of dsRNA-binding activity and type I interferon biology. A single amino acid substitution, G45R, in PR8 NS1 contributed to enhanced viral replication. 2016 Virology journal Result IV G45R 34 38 NS1 47 50 27405392 G45R mutation in the nonstructural protein 1 of A/Puerto Rico/8/1934 (H1N1) enhances viral replication independent of dsRNA-binding activity and type I interferon biology. As shown earlier, the G45R/NS1 virus replicated more efficiently than the WT virus, which is particularly apparent early in infection. 2016 Virology journal Result IV G45R 22 26 NS1 27 30 27405392 G45R mutation in the nonstructural protein 1 of A/Puerto Rico/8/1934 (H1N1) enhances viral replication independent of dsRNA-binding activity and type I interferon biology. As such, G45R/NS1 did not suppress type I IFN expression to facilitate virus replication. 2016 Virology journal Result IV G45R 9 13 NS1 14 17 27405392 G45R mutation in the nonstructural protein 1 of A/Puerto Rico/8/1934 (H1N1) enhances viral replication independent of dsRNA-binding activity and type I interferon biology. As the G45R/NS1 virus replicated to the highest titer, it was selected for further studies. 2016 Virology journal Result IV G45R 7 11 NS1 12 15 27405392 G45R mutation in the nonstructural protein 1 of A/Puerto Rico/8/1934 (H1N1) enhances viral replication independent of dsRNA-binding activity and type I interferon biology. As viruses containing G45R/NS1 replicated at the highest rate, we sought to elucidate its impact on RNA binding activity in vitro. 2016 Virology journal Result IV G45R 22 26 NS1 27 30 27405392 G45R mutation in the nonstructural protein 1 of A/Puerto Rico/8/1934 (H1N1) enhances viral replication independent of dsRNA-binding activity and type I interferon biology. Based on these observations we concluded that G45R/NS1 does not possess type I IFN suppressive activity and hence is not responsible for the increased G45R/NS1 virus replication. 2016 Virology journal Result IV G45R;G45R 46;151 50;155 NS1;NS1 51;156 54;159 27405392 G45R mutation in the nonstructural protein 1 of A/Puerto Rico/8/1934 (H1N1) enhances viral replication independent of dsRNA-binding activity and type I interferon biology. G45R/NS1 did not increase binding to dsRNA in vitro. 2016 Virology journal Result IV G45R 0 4 NS1 5 8 27405392 G45R mutation in the nonstructural protein 1 of A/Puerto Rico/8/1934 (H1N1) enhances viral replication independent of dsRNA-binding activity and type I interferon biology. G45R/NS1 did not increase inhibition of RIG-I mediated IFNbeta-promoter activation. 2016 Virology journal Result IV G45R 0 4 NS1 5 8 27405392 G45R mutation in the nonstructural protein 1 of A/Puerto Rico/8/1934 (H1N1) enhances viral replication independent of dsRNA-binding activity and type I interferon biology. G45R/NS1 increased virus replication independent of type I IFN induction. 2016 Virology journal Result IV G45R 0 4 NS1 5 8 27405392 G45R mutation in the nonstructural protein 1 of A/Puerto Rico/8/1934 (H1N1) enhances viral replication independent of dsRNA-binding activity and type I interferon biology. However, G45R/NS1 did not increase the binding ability of NS1 compared to WT/NS1. 2016 Virology journal Result IV G45R 9 13 NS1;NS1;NS1 14;58;77 17;61;80 27405392 G45R mutation in the nonstructural protein 1 of A/Puerto Rico/8/1934 (H1N1) enhances viral replication independent of dsRNA-binding activity and type I interferon biology. If type I IFNs were involved in the difference between the replication kinetics of WT and G45R/NS1 viruses, replication of the G45R/NS1 virus should be greater than the WT/NS1 virus in WT Let1 cells yet similar in IFNARnull Let1 cells. 2016 Virology journal Result IV G45R;G45R 90;127 94;131 NS1;NS1;NS1 95;132;172 98;135;175 27405392 G45R mutation in the nonstructural protein 1 of A/Puerto Rico/8/1934 (H1N1) enhances viral replication independent of dsRNA-binding activity and type I interferon biology. Interestingly, the G45R/NS1 virus induced greater expression of IFNalpha/beta mRNA compared to the WT/NS1. 2016 Virology journal Result IV G45R 19 23 NS1;NS1 24;102 27;105 27405392 G45R mutation in the nonstructural protein 1 of A/Puerto Rico/8/1934 (H1N1) enhances viral replication independent of dsRNA-binding activity and type I interferon biology. Our data suggested that the anti-RIG-I activity of the G45R/NS1 variant was similar to WT NS1. 2016 Virology journal Result IV G45R 55 59 NS1;NS1 60;90 63;93 27405392 G45R mutation in the nonstructural protein 1 of A/Puerto Rico/8/1934 (H1N1) enhances viral replication independent of dsRNA-binding activity and type I interferon biology. the G45R/NS1 virus replicated to higher titers compared to the WT/NS1 virus in both WT and IFNARnull Let1 cells at every time point investigated, further supporting our conclusion that modulation of type I interferon biology, at the level of RIG-I-induced IFN activation or at later levels of type I interferon activity, is not the reason for the increased replicative capacity of the G45R/NS1 virus observed. 2016 Virology journal Result IV G45R;G45R 4;385 8;389 NS1;NS1;NS1 9;66;390 12;69;393 27405392 G45R mutation in the nonstructural protein 1 of A/Puerto Rico/8/1934 (H1N1) enhances viral replication independent of dsRNA-binding activity and type I interferon biology. The G45R/NS1 virus replicated to the highest titer (P <= 0.001) at 48 to 96 hpi while the replication rates of I68V and K70E/NS1s mutants were similar to the WT/NS1 virus. 2016 Virology journal Result IV G45R;I68V;K70E 4;111;120 8;115;124 NS1;NS1;NS1 9;161;125 12;164;129 27405392 G45R mutation in the nonstructural protein 1 of A/Puerto Rico/8/1934 (H1N1) enhances viral replication independent of dsRNA-binding activity and type I interferon biology. The increased virus replication with K55E substitution in PR8 NS1 has been addressed previously for cell-based vaccine production. 2016 Virology journal Result IV K55E 37 41 NS1 62 65 27405392 G45R mutation in the nonstructural protein 1 of A/Puerto Rico/8/1934 (H1N1) enhances viral replication independent of dsRNA-binding activity and type I interferon biology. The inhibition of RIG-I mediated IFNbeta-promoter activity by WT and G45R/NS1 proteins were similar while the NS1 expressions by each virus in the transfected cells were not different (Additional file 2. 2016 Virology journal Result IV G45R 69 73 27405392 G45R mutation in the nonstructural protein 1 of A/Puerto Rico/8/1934 (H1N1) enhances viral replication independent of dsRNA-binding activity and type I interferon biology. Therefore, G45R/NS1 does not play a significant role in the dsRNA-NS1 interaction in vitro. 2016 Virology journal Result IV G45R 11 15 NS1;NS1 16;66 19;69 27405392 G45R mutation in the nonstructural protein 1 of A/Puerto Rico/8/1934 (H1N1) enhances viral replication independent of dsRNA-binding activity and type I interferon biology. Therefore, the increased replication of G45R/NS1 virus was not due to NS1-mediated alterations of RIG-I mediated IFNbeta-promoter activation. 2016 Virology journal Result IV G45R 40 44 NS1;NS1 45;70 48;73 27405392 G45R mutation in the nonstructural protein 1 of A/Puerto Rico/8/1934 (H1N1) enhances viral replication independent of dsRNA-binding activity and type I interferon biology. To assess the dsRNA binding ability of the G45R/NS1 protein, the RBD of PR8 NS1 [WT, G45R and the dsRNA binding deficient mutant R38AK41A (AA)] were expressed in E. 2016 Virology journal Result IV G45R;G45R 43;85 47;89 NS1;NS1 48;76 51;79 27405392 G45R mutation in the nonstructural protein 1 of A/Puerto Rico/8/1934 (H1N1) enhances viral replication independent of dsRNA-binding activity and type I interferon biology. To further evaluate the relevance of type I IFNs for virus replication, we conducted growth kinetics experiments using WT, G45R and AA/NS1s viruses in WT and type I interferon receptor null (IFNARnull) murine lung epithelial type I (Let1) cells. 2016 Virology journal Result IV G45R 123 127 NS1 135 139 27405392 G45R mutation in the nonstructural protein 1 of A/Puerto Rico/8/1934 (H1N1) enhances viral replication independent of dsRNA-binding activity and type I interferon biology. To test this hypothesis, we infected A549 cells with WT and G45R/NS1 viruses at an MOI of 1 to measure type I IFN mRNA expression and single step growth kinetics. 2016 Virology journal Result IV G45R 60 64 NS1 65 68 27405392 G45R mutation in the nonstructural protein 1 of A/Puerto Rico/8/1934 (H1N1) enhances viral replication independent of dsRNA-binding activity and type I interferon biology. Viruses with NS1 mutations at G45R and K55E (G45R and K55E/NS1s) grew to higher titers compared to the wild type (WT), I68V and K70E/NS1s viruses. 2016 Virology journal Result IV G45R;K55E;G45R;K55E;I68V;K70E 30;39;45;54;119;128 34;43;49;58;123;132 NS1;NS1;NS1 13;59;133 16;63;137 27405392 G45R mutation in the nonstructural protein 1 of A/Puerto Rico/8/1934 (H1N1) enhances viral replication independent of dsRNA-binding activity and type I interferon biology. We assessed whether G45R/NS1 was able to inhibit RIG-I mediated IFN synthesis in 293 T cells co-transfected with plasmids including pCAGGS_PR8NS1 (WT, G45R or AA) or empty pCAGGS as a control, pRIG-I and pfirefly luciferase driven by the IFNbeta promoter and pRenilla Luciferase. 2016 Virology journal Result IV G45R;G45R 20;151 24;155 NS1 25 28 27405392 G45R mutation in the nonstructural protein 1 of A/Puerto Rico/8/1934 (H1N1) enhances viral replication independent of dsRNA-binding activity and type I interferon biology. We selected four point mutations at positions 45, 55, 68 and 70, which did not affect NS2 expression, to introduce into the RBD coding region of PR8 NS1 to generate viruses containing PR8 NS1 with G45R, K55E, I68V or K70E mutations via reverse genetics. 2016 Virology journal Result IV G45R;K55E;I68V;K70E 197;203;209;217 201;207;213;221 NS1;NS1;NS2 149;188;86 152;191;89 27413002 Pulmonary changes in Norwegian fatal cases of pandemic influenza H1N1 (2009) infection: a morphologic and molecular genetic study. A Haemagglutinin viral mutation (HA D222G) in A(H1N1)pdm09 is associated with severe disease outcome. 2016 Influenza and other respiratory viruses Result IV D222G 36 41 HA;HA 33;2 35;16 27413002 Pulmonary changes in Norwegian fatal cases of pandemic influenza H1N1 (2009) infection: a morphologic and molecular genetic study. No apparent association between swab location and detection of the HA D222G mutation was observed in these subjects (Table 2). 2016 Influenza and other respiratory viruses Result IV D222G 70 75 HA 67 69 27413002 Pulmonary changes in Norwegian fatal cases of pandemic influenza H1N1 (2009) infection: a morphologic and molecular genetic study. The HA substitution D222G was detected in six cases (four males and two females, aged 25-59 years), while the other nine patients possessed the wild-type D222D. 2016 Influenza and other respiratory viruses Result IV D222G;D222D 20;154 25;159 HA 4 6 27535054 NS1 Protein Mutation I64T Affects Interferon Responses and Virulence of Circulating H3N2 Human Influenza A Viruses. Altogether, these data indicate that substitution I64T also affects the ability of 1918 NS1 to inhibit host protein expression and demonstrate the key role of this amino acid residue located in the dsRNA-binding domain of IAV NS1 in regulating general gene expression. 2016 Journal of virology Result IV I64T 50 54 NS1;NS1 88;226 91;229 27535054 NS1 Protein Mutation I64T Affects Interferon Responses and Virulence of Circulating H3N2 Human Influenza A Viruses. Altogether, these results indicate that I64T substitution decreases IAV NS1 binding to CPSF30 and provides a mechanism for the impairment of T64-NS1-mediated inhibition of general gene expression. 2016 Journal of virology Result IV I64T 40 44 NS1;NS1 72;145 75;148 27535054 NS1 Protein Mutation I64T Affects Interferon Responses and Virulence of Circulating H3N2 Human Influenza A Viruses. As expected, 1918 NS1 variants that efficiently blocked GFP and Gluc expression levels (E26K and R224K) were barely detected by Western blotting, similar to WT 1918 NS1. 2016 Journal of virology Result IV E26K;R224K 88;97 92;102 NS1;NS1 18;165 21;168 27535054 NS1 Protein Mutation I64T Affects Interferon Responses and Virulence of Circulating H3N2 Human Influenza A Viruses. consistent with previous results showing that the mutation I64T impairs the function of NS1 to counteract host defenses. 2016 Journal of virology Result IV I64T 59 63 NS1 88 91 27535054 NS1 Protein Mutation I64T Affects Interferon Responses and Virulence of Circulating H3N2 Human Influenza A Viruses. Data correlated with the GFP levels observed previously, indicating that virus with the mutation I64T presented defects in counteracting host defenses. 2016 Journal of virology Result IV I64T 97 101 27535054 NS1 Protein Mutation I64T Affects Interferon Responses and Virulence of Circulating H3N2 Human Influenza A Viruses. Effect of I64T mutation on the binding of NS1 to CPSF30. 2016 Journal of virology Result IV I64T 10 14 NS1 42 45 27535054 NS1 Protein Mutation I64T Affects Interferon Responses and Virulence of Circulating H3N2 Human Influenza A Viruses. Effect of I64T mutation on the binding of NS1 to dsRNA. 2016 Journal of virology Result IV I64T 10 14 NS1 42 45 27535054 NS1 Protein Mutation I64T Affects Interferon Responses and Virulence of Circulating H3N2 Human Influenza A Viruses. Effect of I64T mutation on virulence, virus growth, and IFN-beta induction in vivo. 2016 Journal of virology Result IV I64T 10 14 27535054 NS1 Protein Mutation I64T Affects Interferon Responses and Virulence of Circulating H3N2 Human Influenza A Viruses. Finally, the virus from patient 85 presented E26K, I64T, and R224K changes (Table 4). 2016 Journal of virology Result IV E26K;I64T;R224K 45;51;61 49;55;66 27535054 NS1 Protein Mutation I64T Affects Interferon Responses and Virulence of Circulating H3N2 Human Influenza A Viruses. However, IAV infecting patient 55 presented an E26K change, while the virus infecting patient 87 presented E26K and R224K changes. 2016 Journal of virology Result IV E26K;E26K;R224K 47;107;116 51;111;121 27535054 NS1 Protein Mutation I64T Affects Interferon Responses and Virulence of Circulating H3N2 Human Influenza A Viruses. However, substitutions E26K and R224K did not have a significant effect on the ability of 1918 NS1 to inhibit host protein expression. 2016 Journal of virology Result IV E26K;R224K 23;32 27;37 NS1 95 98 27535054 NS1 Protein Mutation I64T Affects Interferon Responses and Virulence of Circulating H3N2 Human Influenza A Viruses. I64T substitution in 1918 NS1 significantly affected the ability of 1918 NS1 to inhibit host gene expression as evaluated by GFP. 2016 Journal of virology Result IV I64T 0 4 NS1;NS1 26;73 29;76 27535054 NS1 Protein Mutation I64T Affects Interferon Responses and Virulence of Circulating H3N2 Human Influenza A Viruses. mutation I64T does not significantly impair the binding of NS1 to dsRNA. 2016 Journal of virology Result IV I64T 9 13 NS1 59 62 27535054 NS1 Protein Mutation I64T Affects Interferon Responses and Virulence of Circulating H3N2 Human Influenza A Viruses. Mutation I64T in the NS1 protein is found very rarely in circulating human, swine, and avian influenza A viruses. 2016 Journal of virology Result IV I64T 9 13 NS1 21 24 27535054 NS1 Protein Mutation I64T Affects Interferon Responses and Virulence of Circulating H3N2 Human Influenza A Viruses. Notably, NS1 protein mutations E26K and R224K had no significant effects on VSV-GFP growth. 2016 Journal of virology Result IV E26K;R224K 31;40 35;45 NS1 9 12 27535054 NS1 Protein Mutation I64T Affects Interferon Responses and Virulence of Circulating H3N2 Human Influenza A Viruses. On the other hand, 1918 NS1 I64T was detected by Western blotting, as expected, based on the results obtained with GFP and Gluc reporter assays. 2016 Journal of virology Result IV I64T 28 32 NS1 24 27 27535054 NS1 Protein Mutation I64T Affects Interferon Responses and Virulence of Circulating H3N2 Human Influenza A Viruses. the mutation I64T decreases the ability of the NS1 protein to inhibit general gene expression. 2016 Journal of virology Result IV I64T 13 17 NS1 47 50 27535054 NS1 Protein Mutation I64T Affects Interferon Responses and Virulence of Circulating H3N2 Human Influenza A Viruses. These data further confirmed that the mutation I64T diminished the capability of NS1 to antagonize cellular antiviral responses. 2016 Journal of virology Result IV I64T 47 51 NS1 81 84 27535054 NS1 Protein Mutation I64T Affects Interferon Responses and Virulence of Circulating H3N2 Human Influenza A Viruses. These data showed that the mutation I64T diminished the capability of NS1 to antagonize cellular antiviral responses, whereas the mutations at positions 26 and 224 did not show a significant effect. 2016 Journal of virology Result IV I64T 36 40 NS1 70 73 27535054 NS1 Protein Mutation I64T Affects Interferon Responses and Virulence of Circulating H3N2 Human Influenza A Viruses. These results indicated that I64T substitution affected the ability of NS1 to inhibit SeV-mediated activation of both promoters, the induction of secreted IFN, and the induction of IFN-stimulated genes, such as ISG15, possibly because of a defect in inhibiting general host expression. 2016 Journal of virology Result IV I64T 29 33 NS1 71 74 27535054 NS1 Protein Mutation I64T Affects Interferon Responses and Virulence of Circulating H3N2 Human Influenza A Viruses. These results suggested that NS1 I64T mutation generates a virus with an attenuated phenotype in vivo that correlates with the inability of NS1 to inhibit host gene expression and therefore to counteract the antiviral state induced by type I IFN responses. 2016 Journal of virology Result IV I64T 33 37 NS1;NS1 29;140 32;143 27535054 NS1 Protein Mutation I64T Affects Interferon Responses and Virulence of Circulating H3N2 Human Influenza A Viruses. To analyze the frequency of I64T mutation in IAV infecting subjects worldwide, the sequences from H3N2 NS1 proteins from human viruses circulating since 1968 (from the Influenza Research Database [IRD]) were analyzed. 2016 Journal of virology Result IV I64T 28 32 NS1 103 106 27535054 NS1 Protein Mutation I64T Affects Interferon Responses and Virulence of Circulating H3N2 Human Influenza A Viruses. To analyze whether I64T mutation leads to virus attenuation, recombinant viruses encoding the NS1 proteins from patients 85 and 87 (differing only in the amino acid at position 64) were generated (r85 and r87, respectively). 2016 Journal of virology Result IV I64T 19 23 NS1 94 97 27535054 NS1 Protein Mutation I64T Affects Interferon Responses and Virulence of Circulating H3N2 Human Influenza A Viruses. To analyze whether I64T substitution could also impair the binding of NS1 to dsRNA, agarose beads conjugated to poly(I C) were incubated with the in vitro-transcribed and -translated NS1 from patients 85 and 87 (differing only in the I64T position) or with PR8 NS1 as a control. 2016 Journal of virology Result IV I64T;I64T 19;234 23;238 NS1;NS1;NS1 70;183;261 73;186;264 27535054 NS1 Protein Mutation I64T Affects Interferon Responses and Virulence of Circulating H3N2 Human Influenza A Viruses. To analyze whether the low frequency of the I64T mutation also applies to other influenza subtypes, such as human H1N1, human 2009 pandemic H1N1, human H5, human H7, avian H1N1, avian H3N2, swine H1N1, swine 2009 pandemic H1N1, and swine H3N2, NS1 protein sequences from the Influenza Research Database were further analyzed (see Table S6 in the supplemental material). 2016 Journal of virology Result IV I64T 44 48 NS1 244 247 27535054 NS1 Protein Mutation I64T Affects Interferon Responses and Virulence of Circulating H3N2 Human Influenza A Viruses. To assess whether I64T mutation plays a role in the binding of NS1 to CPSF30, cell extracts from human 293T cells transfected with a plasmid encoding FLAG-tagged CPSF30 were incubated with in vitro-transcribed and -translated NS1 proteins from patients 85 and 87 (differing only at I64T position), or with PR8 NS1 as control, and with agarose beads conjugated with an anti-FLAG antibody. 2016 Journal of virology Result IV I64T;I64T 18;282 22;286 NS1;NS1;NS1 63;226;310 66;229;313 27535054 NS1 Protein Mutation I64T Affects Interferon Responses and Virulence of Circulating H3N2 Human Influenza A Viruses. To determine whether incorporating the mutation I64T in the NS1 protein induces higher IFN-beta responses in vivo, the levels of IFN-beta mRNA were evaluated in lungs from mice infected with virus r85 and r87 at 1, 3, and 5 dpi. 2016 Journal of virology Result IV I64T 48 52 NS1 60 63 27535054 NS1 Protein Mutation I64T Affects Interferon Responses and Virulence of Circulating H3N2 Human Influenza A Viruses. To further analyze the effect of NS1 I64T mutation on the antagonism of innate immune responses, human A549 cells were transiently transfected with plasmids expressing 1918-NS1-I64 (WT protein), 1918-NS1-T64, and PR8 NS1. 2016 Journal of virology Result IV I64T 37 41 NS1;NS1;NS1;NS1 33;173;200;217 36;176;203;220 27535054 NS1 Protein Mutation I64T Affects Interferon Responses and Virulence of Circulating H3N2 Human Influenza A Viruses. To further evaluate the effect of mutations E26K, I64T, and R224K on the ability of NS1 to inhibit host innate immune responses and gene expression, these mutations were introduced in the 1918 NS1 background. 2016 Journal of virology Result IV E26K;I64T;R224K 44;50;60 48;54;65 NS1;NS1 84;193 87;196 27535054 NS1 Protein Mutation I64T Affects Interferon Responses and Virulence of Circulating H3N2 Human Influenza A Viruses. To test whether I64T mutation diminishes the NS1 protein's ability to counteract host innate immune responses in the context of virus infection, MDCK cells constitutively expressing GFP and Fluc reporter genes under the control of the IFN-beta promoter (MDCK IFN-beta GFP-CAT/IFN-beta Fluc) were mock infected or infected (MOI, 4) with either r85 or r87 virus. 2016 Journal of virology Result IV I64T 16 20 NS1 45 48 27535054 NS1 Protein Mutation I64T Affects Interferon Responses and Virulence of Circulating H3N2 Human Influenza A Viruses. We next evaluated the effect of NS1 protein I64T mutation in virus growth and virulence in vivo. 2016 Journal of virology Result IV I64T 44 48 NS1 32 35 27630240 Human Monoclonal Antibody 81.39a Effectively Neutralizes Emerging Influenza A Viruses of Group 1 and 2 Hemagglutinins. An A(H7N9) virus, A/Taiwan/1/2013 (clone S2), possessed HA2-Asp19Gly (Table 1). 2016 Journal of virology Result IV D19G 60 68 HA 56 58 27630240 Human Monoclonal Antibody 81.39a Effectively Neutralizes Emerging Influenza A Viruses of Group 1 and 2 Hemagglutinins. In mice inoculated with the HA2-Asp19Gly virus, the higher dose of antibody resulted in protection of 16 of 18 (~90%, P < 0.0001) mice and the lower dose protected 11 of 18 (~60%; P = 0.013). 2016 Journal of virology Result IV D19G 32 40 HA 28 30 27630240 Human Monoclonal Antibody 81.39a Effectively Neutralizes Emerging Influenza A Viruses of Group 1 and 2 Hemagglutinins. Specifically, HA2-Asp19Asn was found in H11, H13, and H16 subtype viruses; these three subtypes form cluster H1b of group 1. 2016 Journal of virology Result IV D19N 18 26 HA 14 16 27630240 Human Monoclonal Antibody 81.39a Effectively Neutralizes Emerging Influenza A Viruses of Group 1 and 2 Hemagglutinins. The 50 mug/ml concentration of MAb failed to reach the 50% (32% reduction in focus number; range, 19 to 44%) infectivity inhibition for the HA2-Asp19Gly clone compared to that of the control (infected, untreated cells). 2016 Journal of virology Result IV D19G 144 152 HA 140 142 27630240 Human Monoclonal Antibody 81.39a Effectively Neutralizes Emerging Influenza A Viruses of Group 1 and 2 Hemagglutinins. The dose-dependent effect of treatment was not apparent, particularly in mice infected with the HA2-Asp19Gly virus. 2016 Journal of virology Result IV D19G 100 108 HA 96 98 27630240 Human Monoclonal Antibody 81.39a Effectively Neutralizes Emerging Influenza A Viruses of Group 1 and 2 Hemagglutinins. The inhibitory effect of 81.39a on virus replication was also observed in lungs of mice inoculated with the HA2-Asp19Gly A(H7N9) virus. 2016 Journal of virology Result IV D19G 112 120 HA 108 110 27630240 Human Monoclonal Antibody 81.39a Effectively Neutralizes Emerging Influenza A Viruses of Group 1 and 2 Hemagglutinins. The majority (~99%) of H7N9 viruses recovered from humans (n = 231) maintained HA2-Asp19; only two viruses, A/Jiangsu/02/2013 and A/Wuxi/1/2013, contained Asp19Asn, and a single virus, A/Shenzhen/SP39/2014, had Asp19Gly. 2016 Journal of virology Result IV D19N;D19G 155;211 163;219 HA 79 81 27630240 Human Monoclonal Antibody 81.39a Effectively Neutralizes Emerging Influenza A Viruses of Group 1 and 2 Hemagglutinins. The results confirmed that the HA2-Asp19Gly substitution reduced the ability of the MAb to neutralize virus infectivity in vitro. 2016 Journal of virology Result IV D19G 35 43 HA 31 33 27630240 Human Monoclonal Antibody 81.39a Effectively Neutralizes Emerging Influenza A Viruses of Group 1 and 2 Hemagglutinins. Therefore, the diminishing effect of the HA2-Asp19Gly substitution on survival was only observed at the lower dose of treatment. 2016 Journal of virology Result IV D19G 45 53 HA 41 43 27630240 Human Monoclonal Antibody 81.39a Effectively Neutralizes Emerging Influenza A Viruses of Group 1 and 2 Hemagglutinins. To maximize the translational relevance, we used both HA2-Asp19 (wild type) and HA2-Asp19Gly A(H7N9) (A/Taiwan/1/2013) influenza viruses in our experiments. 2016 Journal of virology Result IV D19G 84 92 HA;HA 54;80 56;82 27630240 Human Monoclonal Antibody 81.39a Effectively Neutralizes Emerging Influenza A Viruses of Group 1 and 2 Hemagglutinins. Two H12 subtype viruses tested had HA2-Asp19Ala; this subtype belongs to cluster H9 of group 1 HA. 2016 Journal of virology Result IV D19A 39 47 HA;HA 35;95 37;97 27630240 Human Monoclonal Antibody 81.39a Effectively Neutralizes Emerging Influenza A Viruses of Group 1 and 2 Hemagglutinins. We found that the number of foci produced by the HA2-Asp19Gly clone in cells treated with 300 mug/ml of 81.39a was much lower. 2016 Journal of virology Result IV D19G 53 61 HA 49 51 27630240 Human Monoclonal Antibody 81.39a Effectively Neutralizes Emerging Influenza A Viruses of Group 1 and 2 Hemagglutinins. While clone C7 possessed HA2-Asp19 (wild type), clone S2 possessed HA2-Asp19Gly. 2016 Journal of virology Result IV D19G 71 79 HA;HA 25;67 27;69 27657178 Discovery of Potent Antivirals against Amantadine-Resistant Influenza A Viruses by Targeting the M2-S31N Proton Channel. Both of these strains are the predominant strains circulating among humans in North America in recent years, and both of them are amantadine-resistant and contain the M2-S31N mutant. 2016 ACS infectious diseases Result IV S31N 170 174 M2 167 169 27657178 Discovery of Potent Antivirals against Amantadine-Resistant Influenza A Viruses by Targeting the M2-S31N Proton Channel. Compounds 10c and 16f, which had less than 70% M2-S31N channel inhibition at 100 muM, were also chosen in order to determine a correlation between the channel blockage activity and the antiviral activity. 2016 ACS infectious diseases Result IV S31N 50 54 M2 47 49 27657178 Discovery of Potent Antivirals against Amantadine-Resistant Influenza A Viruses by Targeting the M2-S31N Proton Channel. Compounds 10f, 16d, and 20c all had more than 80% M2-S31N channel inhibition at 100 muM. 2016 ACS infectious diseases Result IV S31N 53 57 M2 50 52 27657178 Discovery of Potent Antivirals against Amantadine-Resistant Influenza A Viruses by Targeting the M2-S31N Proton Channel. For the pyrimidine series of compounds, the intermediate compound 9, which lacks a hydrophobic substitution, had minimal M2-S31N channel inhibition (8.8 +- 1.9%) at 100 muM (Table 1). 2016 ACS infectious diseases Result IV S31N 124 128 M2 121 123 27657178 Discovery of Potent Antivirals against Amantadine-Resistant Influenza A Viruses by Targeting the M2-S31N Proton Channel. In summary, compounds 10c and 16d were found to have consistently low micromolar antiviral efficacy against several M2-S31N-containing influenza A viruses. 2016 ACS infectious diseases Result IV S31N 119 123 M2 116 118 27657178 Discovery of Potent Antivirals against Amantadine-Resistant Influenza A Viruses by Targeting the M2-S31N Proton Channel. In the present study, the goal is to optimize the channel blockage potency of M2-S31N inhibitors by diversifying the aromatic head groups and the hydrophobic substitutions. 2016 ACS infectious diseases Result IV S31N 81 85 M2 78 80 27657178 Discovery of Potent Antivirals against Amantadine-Resistant Influenza A Viruses by Targeting the M2-S31N Proton Channel. In this assay, the M2-S31N channel was expressed in the oocyte cell membrane and was activated by acidic pH (pH = 5.5). 2016 ACS infectious diseases Result IV S31N 22 26 M2 19 21 27657178 Discovery of Potent Antivirals against Amantadine-Resistant Influenza A Viruses by Targeting the M2-S31N Proton Channel. Moreover, there is a positive correlation between M2-S31N channel blockage activity and antiviral activity: compounds 10b, 10f, 16d, and 20c, which had more potent channel blockage activity in electrophysiological assays than compounds 10c and 16f, were also more active in the antiviral CPE assays than compounds 10c and 16f. 2016 ACS infectious diseases Result IV S31N 53 57 M2 50 52 27657178 Discovery of Potent Antivirals against Amantadine-Resistant Influenza A Viruses by Targeting the M2-S31N Proton Channel. Overall, these results indicate that a hydrophobic substitution on the aromatic head group is required for M2-S31N inhibition. 2016 ACS infectious diseases Result IV S31N 110 114 M2 107 109 27657178 Discovery of Potent Antivirals against Amantadine-Resistant Influenza A Viruses by Targeting the M2-S31N Proton Channel. Similar results were found for other precursors, such as compounds 12, 15, and 19, and all of them had weak M2-S31N channel inhibition (Table 1). 2016 ACS infectious diseases Result IV S31N 111 115 M2 108 110 27657178 Discovery of Potent Antivirals against Amantadine-Resistant Influenza A Viruses by Targeting the M2-S31N Proton Channel. Synthesized compounds were tested for their channel blockage against the M2-S31N proton channel using the two-electrode voltage clamp (TEVC) assay. 2016 ACS infectious diseases Result IV S31N 76 80 M2 73 75 27657178 Discovery of Potent Antivirals against Amantadine-Resistant Influenza A Viruses by Targeting the M2-S31N Proton Channel. The antiviral activity was tested against the amantadine-resistant A/WSN/33 (H1N1) virus, which contains the M2-S31N mutant, using the cytopathic effect (CPE) assay. 2016 ACS infectious diseases Result IV S31N 112 116 M2 109 111 27657178 Discovery of Potent Antivirals against Amantadine-Resistant Influenza A Viruses by Targeting the M2-S31N Proton Channel. To further prove the antiviral efficacy of M2-S31N inhibitors against M2-S31N-containing influenza A viruses, we tested two inhibitors, the pyrimidine 10c and 3-substitued pyridine 16d, against two clinically relevant human influenza A strains, A/Switzerland/9715293/2013 (H1N1) and A/California/07/2009 (H1N1). 2016 ACS infectious diseases Result IV S31N;S31N 46;73 50;77 M2;M2 43;70 45;72 27657178 Discovery of Potent Antivirals against Amantadine-Resistant Influenza A Viruses by Targeting the M2-S31N Proton Channel. When a pyrrolidine substitution was introduced to the pyrimidine aromatic head group, compound 10a showed increased M2-S31N channel inhibition (47.8 +- 2.8 %). 2016 ACS infectious diseases Result IV S31N 119 123 M2 116 118 27663652 Amino acid substitutions involved in the adaptation of a novel highly pathogenic H5N2 avian influenza virus in mice. In this study, amino acid substitutions, in the PB2 (E627K), PB1 (I181T), HA (A150S), NS1 (WRNKVAD was extended at the C-terminal of the protein), and NS2 (E69G) proteins were identified in a MA-6DK19. 2016 Virology journal Result IV E627K;I181T;A150S;E69G 53;66;78;156 58;71;83;160 HA;NS1;NS2;PB1;PB2 74;86;151;61;48 76;89;154;64;51 27663652 Amino acid substitutions involved in the adaptation of a novel highly pathogenic H5N2 avian influenza virus in mice. Several amino acid substitutions including PB2 (Q591K and D701N), polymerase acidic protein (PA) (I554V), HA (S227N), and NP (R351K) have been described in mouse adapted H5N2 AIVs that have increased virulence and enhanced replication kinetics in mice and cell lines. 2016 Virology journal Result IV Q591K;D701N;I554V;S227N;R351K 48;58;98;110;126 53;63;103;115;131 HA;NP;PA;PB2;PA 106;122;93;43;66 108;124;95;46;83 27663652 Amino acid substitutions involved in the adaptation of a novel highly pathogenic H5N2 avian influenza virus in mice. The E627K substitution in the PB2 protein has been reported to influence host range and to confer increased virulence in models of H3, H5, H6, and H9 infection. 2016 Virology journal Result IV E627K 4 9 PB2 30 33 27713074 An influenza A virus (H7N9) anti-neuraminidase monoclonal antibody with prophylactic and therapeutic activity in vivo. The NA of A/Shanghai/1/2013(H7N9) has been shown to be resistant to the NA inhibitor, oseltamivir, due to a R289K substitution in the enzyme active site. 2016 Antiviral research Result IV R289K 108 113 NA;NA 4;72 6;74 27713074 An influenza A virus (H7N9) anti-neuraminidase monoclonal antibody with prophylactic and therapeutic activity in vivo. To determine if 3c10-3 maintains the ability to bind NA carrying the R289K substitution, recNA encoding this mutation was constructed and binding kinetics were determined using BLI. 2016 Antiviral research Result IV R289K 69 74 53 55 27741319 Cross-Neutralising Nanobodies Bind to a Conserved Pocket in the Hemagglutinin Stem Region Identified Using Yeast Display and Deep Mutational Scanning. Additionally, the adjacent mutations V18A and D19V/G/E were predicted by mutational scanning to uniquely affect R2a-G8 binding however these mutations were not experimentally confirmed (Fig 4A, S2 Table). 2016 PloS one Result IV D19G;D19E;V18A;D19V 46;46;37;46 54;54;41;54 27741319 Cross-Neutralising Nanobodies Bind to a Conserved Pocket in the Hemagglutinin Stem Region Identified Using Yeast Display and Deep Mutational Scanning. Antibody R2a-G8 was uniquely affected by the M17K mutation whereas other antibodies remained tolerant of this change. 2016 PloS one Result IV M17K 45 49 27741319 Cross-Neutralising Nanobodies Bind to a Conserved Pocket in the Hemagglutinin Stem Region Identified Using Yeast Display and Deep Mutational Scanning. Binding specificity to D46N in the context of the entire HA sequence from different H1N1 and H5N1 viral strains was subsequently tested using surface plasmon resonance (SPR) (Table 2, S4 Fig). 2016 PloS one Result IV D46N 23 27 HA 57 59 27741319 Cross-Neutralising Nanobodies Bind to a Conserved Pocket in the Hemagglutinin Stem Region Identified Using Yeast Display and Deep Mutational Scanning. Both N53K and V52E mutations were shown to uniquely affect antibodies R1a-A5 and R2b-E8 whereas the binding of other antibodies were tolerant of these mutations (Fig 4C). 2016 PloS one Result IV N53K;V52E 5;14 9;18 27741319 Cross-Neutralising Nanobodies Bind to a Conserved Pocket in the Hemagglutinin Stem Region Identified Using Yeast Display and Deep Mutational Scanning. For example the I45F mutation correlates with H2 viral subtypes (S3 Table) and this was shown to eliminate binding of all stem binding sdAbs except R2b-D9 (Fig 6). 2016 PloS one Result IV I45F 16 20 27741319 Cross-Neutralising Nanobodies Bind to a Conserved Pocket in the Hemagglutinin Stem Region Identified Using Yeast Display and Deep Mutational Scanning. M17V/M17R/M17K, I45F/I45A/I45N/I45S/I45T, I48T/I48N/I48S, G20R/G20E, W21R/W21G, N53I/N53K/N53S/N53T) (S2 Table) reflecting the particular importance of these residues for each sdAbs. 2016 PloS one Result IV M17R;M17V;M17K;I45S;I45N;I45T;I45F;I45A;I48T;I48N;I48S;G20R;G20E;W21R;W21G;N53I;N53K;N53S;N53T 5;0;10;31;26;36;16;21;42;47;52;58;63;69;74;80;85;90;95 9;4;14;35;30;40;20;25;46;51;56;62;67;73;78;84;89;94;99 27741319 Cross-Neutralising Nanobodies Bind to a Conserved Pocket in the Hemagglutinin Stem Region Identified Using Yeast Display and Deep Mutational Scanning. The 2009 H1N1 virus continues to evolve and a new prominent substitution in the HA2 domain, E47K, has emerged in 2010 which is located behind D46N in the HA structure (Fig 5B). 2016 PloS one Result IV E47K;D46N 92;142 96;146 HA;HA 80;154 82;156 27741319 Cross-Neutralising Nanobodies Bind to a Conserved Pocket in the Hemagglutinin Stem Region Identified Using Yeast Display and Deep Mutational Scanning. The D46N mutation was shown to uniquely interfere with R2b-E8 binding whereas all other stem binding antibodies were unaffected (Fig 6A). 2016 PloS one Result IV D46N 4 8 27741319 Cross-Neutralising Nanobodies Bind to a Conserved Pocket in the Hemagglutinin Stem Region Identified Using Yeast Display and Deep Mutational Scanning. The HA2-E47K substitution has been shown to correlate with a lower threshold pH for viral membrane fusion which enhances viral infectivity and stability. 2016 PloS one Result IV E47K 8 12 HA 4 6 27741319 Cross-Neutralising Nanobodies Bind to a Conserved Pocket in the Hemagglutinin Stem Region Identified Using Yeast Display and Deep Mutational Scanning. This confirms D46N as a key determinant of R2b-E8 specificity and demonstrates its potential utility in differentiating strains derived from A(H1N1)pdm09 from other circulating seasonal H1N1 strains (S3 Fig, Table 2). 2016 PloS one Result IV D46N 14 18 27849220 Surveillance of antiviral resistance markers in Argentina: detection of E119V neuraminidase mutation in a post-treatment immunocompromised patient. Out of 888 A(H3N2) samples received at the NIC, 842 were tested for the E119V substitution: 836 samples were collected from untreated patients and six samples were obtained from six patients (four of them immunocompromised) after treatment. 2016 Memorias do Instituto Oswaldo Cruz Result IV E119V 72 77 27849220 Surveillance of antiviral resistance markers in Argentina: detection of E119V neuraminidase mutation in a post-treatment immunocompromised patient. Sanger sequencing of both pre- and post-treatment samples confirmed the results obtained by E119V SNP screening and further quantitative assays will be necessary to confirm this finding. 2016 Memorias do Instituto Oswaldo Cruz Result IV E119V 92 97 27869615 Highly Pathogenic Influenza A(H5Nx) Viruses with Altered H5 Receptor-Binding Specificity. At 2 positions that differ between H5N12.3.4 and H5N8 HAs (S137A and S185P), we observed changes in the potential to form hydrogen bonds between major elements of the receptor-binding site (Figure 8). 2017 Emerging infectious diseases Result IV S137A;S185P 59;69 64;74 27869615 Highly Pathogenic Influenza A(H5Nx) Viruses with Altered H5 Receptor-Binding Specificity. However, substitution S227R (Figure 7, panel B) had a more specific negative effect. 2017 Emerging infectious diseases Result IV S227R 22 27 27869615 Highly Pathogenic Influenza A(H5Nx) Viruses with Altered H5 Receptor-Binding Specificity. In comparison with wild-type H5N12.3.4 HA (Figure 2, panel A), substitution K222Q (Figure 7, panel A) strongly decreased binding. 2017 Emerging infectious diseases Result IV K222Q 76 81 HA 39 41 27869615 Highly Pathogenic Influenza A(H5Nx) Viruses with Altered H5 Receptor-Binding Specificity. In contrast, combined substitutions K222Q and S227R (Figure 7, panel C) enhanced binding to the glycans bound by the wild-type H5N12.3.4 HA (Figure 2, panel A) and resulted in additional binding of fucosylated glycans that are also bound by H5N8 HA (Figure 2, panel B). 2017 Emerging infectious diseases Result IV K222Q;S227R 36;46 41;51 HA;HA 137;246 139;248 27869615 Highly Pathogenic Influenza A(H5Nx) Viruses with Altered H5 Receptor-Binding Specificity. In the course of further evolution, a glycosylation site at the head domain at position 160 is lost, and there are 2 other unique substitutions (K193N, T193D) in the vicinity of the receptor-binding site. 2017 Emerging infectious diseases Result IV K193N;T193D 145;152 150;157 27869615 Highly Pathogenic Influenza A(H5Nx) Viruses with Altered H5 Receptor-Binding Specificity. In the glycan array, the R227S substitution did not affect binding of H5N8 HA to fucosylated sialosides (Figure 7, panel E), but the Q222K substitution, alone or in combination with the R227S substitution, inhibited binding of fucosylated receptors (Figure 7, panels D, F). 2017 Emerging infectious diseases Result IV R227S;Q222K;R227S 25;133;186 30;138;191 HA 75 77 27869615 Highly Pathogenic Influenza A(H5Nx) Viruses with Altered H5 Receptor-Binding Specificity. Reduction of binding was not observed when substitution K222Q was combined with S227R. 2017 Emerging infectious diseases Result IV K222Q;S227R 56;80 61;85 27869615 Highly Pathogenic Influenza A(H5Nx) Viruses with Altered H5 Receptor-Binding Specificity. Substitution T160A did not change receptor fine specificity (Technical Appendix Figure). 2017 Emerging infectious diseases Result IV T160A 13 18 27869615 Highly Pathogenic Influenza A(H5Nx) Viruses with Altered H5 Receptor-Binding Specificity. Substitutions K222Q and S227R (H3 numbering used here, corresponding to K218Q and S223R in H5 numbering), which have rarely occurred (0.08% and 0.9%, respectively), were found in the receptor-binding site. 2017 Emerging infectious diseases Result IV K222Q;S227R;K218Q;S223R 14;24;72;82 19;29;77;87 27869615 Highly Pathogenic Influenza A(H5Nx) Viruses with Altered H5 Receptor-Binding Specificity. Substitutions R227S or Q222K hardly affected fetuin binding (Figure 6, panel B). 2017 Emerging infectious diseases Result IV R227S;Q222K 14;23 19;28 27869615 Highly Pathogenic Influenza A(H5Nx) Viruses with Altered H5 Receptor-Binding Specificity. Substitutions T160A or S227R did not affect fetuin binding (Figure 6, panel A), but K222Q reduced binding 2-fold. 2017 Emerging infectious diseases Result IV T160A;S227R;K222Q 14;23;84 19;28;89 27869615 Highly Pathogenic Influenza A(H5Nx) Viruses with Altered H5 Receptor-Binding Specificity. The branch of clade 2.3.4.4 H5 proteins that contains viruses from Taiwan and North America contains reverse substitution R227S (Figure 5). 2017 Emerging infectious diseases Result IV R227S 122 127 27869615 Highly Pathogenic Influenza A(H5Nx) Viruses with Altered H5 Receptor-Binding Specificity. This steric hindrance is maintained in H5N12.3.4 HA but is lost after the K222Q substitution in H5N8 HA (Figure 8, panels B, C). 2017 Emerging infectious diseases Result IV K222Q 74 79 HA;HA 49;101 51;103 27869615 Highly Pathogenic Influenza A(H5Nx) Viruses with Altered H5 Receptor-Binding Specificity. We conclude that the combination of substitutions K222Q and S227R, already present in the earliest clade 2.3.4.4 H5Nx viruses (Figure 5), is largely responsible for the different receptor-binding properties of the H5N12.3.4 and the H5N8 HAs. 2017 Emerging infectious diseases Result IV K222Q;S227R 50;60 55;65 27933797 Nuclear Magnetic Resonance and Molecular Dynamics Simulation of the Interaction between Recognition Protein H7 of the Novel Influenza Virus H7N9 and Glycan Cell Surface Receptors. Comparing the estimated slopes and values of the RMSD functions for LSTc and LSTa in the bound state with H7 or H7sm explained how the G228S mutation reduces the mobility for both glycans, even though it was slightly more evident for LSTa. 2016 Biochemistry Result IV G228S 135 140 27933797 Nuclear Magnetic Resonance and Molecular Dynamics Simulation of the Interaction between Recognition Protein H7 of the Novel Influenza Virus H7N9 and Glycan Cell Surface Receptors. MD simulations of the LSTa:H7sm and LSTc:H7sm complexes were compared to those of the previously discussed LSTa:H7 and LSTc:H7 complexes to observe binding epitope and dynamic changes upon H7 mutation (G228S), possibly indicating changes to H7 specificity. 2016 Biochemistry Result IV G228S 202 207 27933797 Nuclear Magnetic Resonance and Molecular Dynamics Simulation of the Interaction between Recognition Protein H7 of the Novel Influenza Virus H7N9 and Glycan Cell Surface Receptors. The kinetic, glycan microarray, and solid surface binding assays support an improvement in the affinity of H7 for both human and avian receptor mimetics upon G228S mutation, even though a weak preference for the avian form could be deduced in glycan microarray and kinetic tests. 2016 Biochemistry Result IV G228S 158 163 27933797 Nuclear Magnetic Resonance and Molecular Dynamics Simulation of the Interaction between Recognition Protein H7 of the Novel Influenza Virus H7N9 and Glycan Cell Surface Receptors. The LSTa:H7 and LSTc:H7 model complexes allowed analysis of the H7 RBS at atomic precision, visualizing the way in which the G228S mutation potentially introduces an additional hydrogen bond between H7 RBS and the sialyl tail, C7-C8-C9 of Neu5Ac in both glycans (Figure S4a). 2016 Biochemistry Result IV G228S 125 130 28084423 Single PA mutation as a high yield determinant of avian influenza vaccines. Application of PA E31K to other avian CVVs. 2017 Scientific reports Result IV E31K 18 22 PA 15 17 28084423 Single PA mutation as a high yield determinant of avian influenza vaccines. By the PA E31K mutation, however, E31-mediated negative force disappears, and K31-mediated attractive force may catalyze efficient PA-RNA binding. 2017 Scientific reports Result IV E31K 10 14 PA;PA 7;131 9;133 28084423 Single PA mutation as a high yield determinant of avian influenza vaccines. Combined, our results demonstrate that the PA E31K mutation can be a single molecular determinant to increase virus yields and HA contents of avian influenza CVVs. 2017 Scientific reports Result IV E31K 46 50 HA;PA 127;43 129;45 28084423 Single PA mutation as a high yield determinant of avian influenza vaccines. Considered all together, our results suggest the feasibility of the PA E31K mutation as a high yield, molecular determinant of avian influenza CVVs. 2017 Scientific reports Result IV E31K 71 75 PA 68 70 28084423 Single PA mutation as a high yield determinant of avian influenza vaccines. Considered together, our results indicate that the PA E31K mutation may confer replication enhancement to influenza vaccine viruses by increasing viral polymerase activity through an efficient interaction between PA protein and viral RNA, which may, in turn, contribute to the higher expression of viral RNAs and proteins. 2017 Scientific reports Result IV E31K 54 58 PA;PA 51;213 53;215 28084423 Single PA mutation as a high yield determinant of avian influenza vaccines. Consistent with our observation, in the Vero cells transfected with the four plasmids of viral polymerase complex (PB2, PB1, PA, and NP) and a luciferase reporter plasmid, the PA E31K mutation increased luciferase expression in a dose-dependent manner. 2017 Scientific reports Result IV E31K 179 183 NP;PA;PA;PB1;PB2 133;125;176;120;115 135;127;178;123;118 28084423 Single PA mutation as a high yield determinant of avian influenza vaccines. Contribution of the PA E31K mutation to viral polymerase complex activity. 2017 Scientific reports Result IV E31K 23 27 PA 20 22 28084423 Single PA mutation as a high yield determinant of avian influenza vaccines. Even though combination of the four mutations had the highest impact, the PA E31K mutation appeared to make a major contribution to the replication of rIETR15 in the Vero cells. 2017 Scientific reports Result IV E31K 77 81 PA 74 76 28084423 Single PA mutation as a high yield determinant of avian influenza vaccines. Even though the HA titers of the H7N9 and H9N2 CVVs were below the detection limit (data not shown), the PA E31K mutation demonstrated its beneficial effects on replication properties of H7N9 and H9N2 subtype CVVs. 2017 Scientific reports Result IV E31K 108 112 HA;PA 16;105 18;107 28084423 Single PA mutation as a high yield determinant of avian influenza vaccines. In the subsequent results of quantitative real-time PCR (qRT-PCR) and western blotting assay in the Vero cells, the PA E31K mutation also consistently increased mRNA and protein expression levels of viral NP protein, respectively. 2017 Scientific reports Result IV E31K 119 123 NP;PA 205;116 207;118 28084423 Single PA mutation as a high yield determinant of avian influenza vaccines. Intriguingly, rIETR/PA:E31K exhibited the highest increase of replication property among the single mutant viruses. 2017 Scientific reports Result IV E31K 23 27 PA 20 22 28084423 Single PA mutation as a high yield determinant of avian influenza vaccines. Of the four single mutant viruses, rIETR/M2:R80Q (maximum titer, 106.06 PFU/ml) exhibited a similar replication rate to rIETR, and rIETR/PB2:R136K and rIETR/HA:A172T appeared to have slightly increased replication properties. 2017 Scientific reports Result IV R80Q;R136K;A172T 44;141;160 48;146;165 HA;M2;PB2 157;41;137 159;43;140 28084423 Single PA mutation as a high yield determinant of avian influenza vaccines. The E31K mutation in the PA protein, which is one of the four subunits of influenza virus polymerase complex, is a novel molecular alteration rIETR15 because almost all the PA proteins of influenza H1N1 viruses appear to possess a glutamic acid at this residue rather than lysine (Table S2). 2017 Scientific reports Result IV E31K 4 8 PA;PA 25;173 27;175 28084423 Single PA mutation as a high yield determinant of avian influenza vaccines. The effects of the PA E31K mutation on viral replication in the Vero cells were also evaluated on the other subtype CVVs. 2017 Scientific reports Result IV E31K 22 26 PA 19 21 28084423 Single PA mutation as a high yield determinant of avian influenza vaccines. These mutations included R136K in the PB2, E31K in the PA, A172T in the HA, and R80Q in the M2 protein (Table 1). 2017 Scientific reports Result IV R136K;E31K;A172T;R80Q 25;43;59;80 30;47;64;84 HA;M2;PA;PB2 72;92;55;38 74;94;57;41 28084423 Single PA mutation as a high yield determinant of avian influenza vaccines. These results confirm the effects of the PA E31K mutation on viral replication capacity presented in Figs 1 and 2. 2017 Scientific reports Result IV E31K 44 48 PA 41 43 28084423 Single PA mutation as a high yield determinant of avian influenza vaccines. To address how these mutations affected the growth characteristics of rIETR15, we generated the five mutant viruses harboring each mutation (rIETR/PB2:R136K, rIETR/PA:E31K, rIETR/HA:A172T, and rIETR/M2:R80Q) and all of the four mutations (rIETR/4Mut) (Table 1) and evaluated their replication properties. 2017 Scientific reports Result IV R136K;E31K;A172T;R80Q 151;167;182;202 156;171;187;206 HA;M2;PA;PB2 179;199;164;147 181;201;166;150 28084423 Single PA mutation as a high yield determinant of avian influenza vaccines. We observed the beneficial effects of the PA E31K mutation on the viral replication property of the H5N1 CVV (Figs 1 and 2). 2017 Scientific reports Result IV E31K 45 49 PA 42 44 28087313 An M2-V27A channel blocker demonstrates potent in vitro and in vivo antiviral activities against amantadine-sensitive and -resistant influenza A viruses. Amantadine (1) was not effective in preventing death, as A/WSN/33 (M2-N31S + V27A) (H1N1) was amantadine-resistant in vitro. 2017 Antiviral research Result IV N31S;V27A 70;77 74;81 M2 67 69 28087313 An M2-V27A channel blocker demonstrates potent in vitro and in vivo antiviral activities against amantadine-sensitive and -resistant influenza A viruses. As compound 3 was confirmed already to be a potent blocker of both M2-WT and M2-V27A proton channels (Table 1), we then wanted to confirm its antiviral efficacy against both M2-WT- and M2-V27A-containing influenza A viruses. 2017 Antiviral research Result IV V27A;V27A 80;188 84;192 M2;M2;M2;M2 67;77;174;185 69;79;176;187 28087313 An M2-V27A channel blocker demonstrates potent in vitro and in vivo antiviral activities against amantadine-sensitive and -resistant influenza A viruses. Collectively, the two analogs, 7 and 16, had confirmed channel blockage activity against both M2-WT and M2-V27A mutant channels. 2017 Antiviral research Result IV V27A 107 111 M2;M2 94;104 96;106 28087313 An M2-V27A channel blocker demonstrates potent in vitro and in vivo antiviral activities against amantadine-sensitive and -resistant influenza A viruses. Compound 7 had no effect on the replication of the M2-V27A-containing A/WSN/33 (M2-N31S + V27A) (H1N1) virus up to 30 muM, despite its potent channel blockage, as confirmed by the TEVC assay (Table 4). 2017 Antiviral research Result IV V27A;N31S;V27A 54;83;90 58;87;94 M2;M2 51;80 53;82 28087313 An M2-V27A channel blocker demonstrates potent in vitro and in vivo antiviral activities against amantadine-sensitive and -resistant influenza A viruses. For M2-V27A channel inhibition, all compounds nearly completely inhibited the current conductance at 100 muM, and the IC50 values for compounds 3, 7, and 16 in inhibiting the A/Udorn/72 (M2-V27A) were 0.3 +- 0.1 muM, 0.5 +- 0.2 muM, and 0.4 +- 0.1 muM, respectively (Table 4). 2017 Antiviral research Result IV V27A;V27A 7;190 11;194 M2;M2 4;187 6;189 28087313 An M2-V27A channel blocker demonstrates potent in vitro and in vivo antiviral activities against amantadine-sensitive and -resistant influenza A viruses. Further increasing the concentration of amantadine (1) to 50 muM also failed to significantly inhibit the replication of the A/WSN/33 (M2-N31S + V27A) (H1N1) virus (plaque reduction less than 10 %). 2017 Antiviral research Result IV N31S;V27A 138;145 142;149 M2 135 137 28087313 An M2-V27A channel blocker demonstrates potent in vitro and in vivo antiviral activities against amantadine-sensitive and -resistant influenza A viruses. Gratifyingly, compound 3 showed dose-dependent inhibition of the M2-V27A mutant-containing A/WSN/33 (M2-N31S + V27A) (H1N1) virus with an EC50 of 1.8 +- 0.2 muM. 2017 Antiviral research Result IV V27A;N31S;V27A 68;104;111 72;108;115 M2;M2 65;101 67;103 28087313 An M2-V27A channel blocker demonstrates potent in vitro and in vivo antiviral activities against amantadine-sensitive and -resistant influenza A viruses. In addition, valine in position 27 was mutated to alanine. 2017 Antiviral research Result IV V27A 13 57 28087313 An M2-V27A channel blocker demonstrates potent in vitro and in vivo antiviral activities against amantadine-sensitive and -resistant influenza A viruses. In contrast, amantadine (1) showed minimum effectiveness at 100 mg/kg/day in treating the M2-V27A virus infection. 2017 Antiviral research Result IV V27A 93 97 M2 90 92 28087313 An M2-V27A channel blocker demonstrates potent in vitro and in vivo antiviral activities against amantadine-sensitive and -resistant influenza A viruses. In contrast, only compound 16 had potent antiviral activity against the M2-V27A-containing A/WSN/33 (M2-N31S + V27A) (H1N1) virus, with an EC50 value of 1.0 +- 0.1 muM. 2017 Antiviral research Result IV V27A;N31S;V27A 75;104;111 79;108;115 M2;M2 72;101 74;103 28087313 An M2-V27A channel blocker demonstrates potent in vitro and in vivo antiviral activities against amantadine-sensitive and -resistant influenza A viruses. In contrast, the A/WSN/33 (M2-N31S + V27A) (H1N1) virus was nearly completely resistant to amantadine (1). 2017 Antiviral research Result IV N31S;V27A 30;37 34;41 M2 27 29 28087313 An M2-V27A channel blocker demonstrates potent in vitro and in vivo antiviral activities against amantadine-sensitive and -resistant influenza A viruses. In contrast, the M2-V27A channel inhibition by compound 7 was nearly completely reversible. 2017 Antiviral research Result IV V27A 20 24 M2 17 19 28087313 An M2-V27A channel blocker demonstrates potent in vitro and in vivo antiviral activities against amantadine-sensitive and -resistant influenza A viruses. In summary, compound 3 not only had potent channel blockage activity against the A/Udorn/72 M2-WT and M2-V27A channels with IC50 values of 18.7 +- 1.4 muM and 0.3 +- 0.1 muM, respectively, it also had potent antiviral activity against both M2-WT and M2-V27A mutant-containing influenza A viruses. 2017 Antiviral research Result IV V27A;V27A 105;253 109;257 M2;M2;M2;M2 92;102;240;250 94;104;242;252 28087313 An M2-V27A channel blocker demonstrates potent in vitro and in vivo antiviral activities against amantadine-sensitive and -resistant influenza A viruses. In vivo antiviral efficacy of compound 3 in treatment of a M2-V27A-containing influenza A/WSN/33 (M2-N31S + V27A) (H1N1) virus infection in mice. 2017 Antiviral research Result IV V27A;N31S;V27A 62;101;108 66;105;112 M2;M2 59;98 61;100 Influenza A virus H1N1 infection 115 136 28087313 An M2-V27A channel blocker demonstrates potent in vitro and in vivo antiviral activities against amantadine-sensitive and -resistant influenza A viruses. Similarly, compound 7 had very poor antiviral (EC50 > 30 muM) potency against M2-V27A-containing A/WSN/33 (M2-N31S + V27A) (H1N1) virus despite its potent channel blockage (93.3 +- 1.3 % at 100 muM). 2017 Antiviral research Result IV V27A;N31S;V27A 81;110;117 85;114;121 M2;M2 78;107 80;109 28087313 An M2-V27A channel blocker demonstrates potent in vitro and in vivo antiviral activities against amantadine-sensitive and -resistant influenza A viruses. The A/Udorn/72 (H3N2) virus and the A/WSN/33 (M2-N31S + V27A) (H1N1) virus, which contain M2-WT and M2-V27A, respectively, were chosen to assess the drug sensitivity of compound 3. 2017 Antiviral research Result IV N31S;V27A;V27A 49;56;103 53;60;107 M2;M2;M2 46;90;100 48;92;102 28087313 An M2-V27A channel blocker demonstrates potent in vitro and in vivo antiviral activities against amantadine-sensitive and -resistant influenza A viruses. The A/WSN/33 (M2-N31S + V27A) (H1N1) virus was generated by reverse genetics. 2017 Antiviral research Result IV N31S;V27A 17;24 21;28 M2 14 16 28087313 An M2-V27A channel blocker demonstrates potent in vitro and in vivo antiviral activities against amantadine-sensitive and -resistant influenza A viruses. The asparagine residue in position 31 was mutated to serine, and the A/WSN/33-N31S (H1N1) was amantadine-sensitive, similar to the M2-WT. 2017 Antiviral research Result IV N31S;N31S 78;4 82;59 M2 131 133 28087313 An M2-V27A channel blocker demonstrates potent in vitro and in vivo antiviral activities against amantadine-sensitive and -resistant influenza A viruses. The channel blockage activity of the newly synthesized compounds 7 and 16 was assayed against both M2-WT and M2-V27A proton channels using the two-electrode voltage clamp (TEVC) assays (Table 4). 2017 Antiviral research Result IV V27A 112 116 M2;M2 99;109 101;111 28087313 An M2-V27A channel blocker demonstrates potent in vitro and in vivo antiviral activities against amantadine-sensitive and -resistant influenza A viruses. The dithiane compound 16, on the other hand, showed essentially irreversible inhibition of the M2-V27A channel on this time scale, and only 12.2 +- 1.3 % current was recovered at the second activation event. 2017 Antiviral research Result IV V27A 98 102 M2 95 97 28087313 An M2-V27A channel blocker demonstrates potent in vitro and in vivo antiviral activities against amantadine-sensitive and -resistant influenza A viruses. the M2-V27A channel remained partially occluded even with perfusion with compound-free solution (pH = 8.5). 2017 Antiviral research Result IV V27A 7 11 M2 4 6 28087313 An M2-V27A channel blocker demonstrates potent in vitro and in vivo antiviral activities against amantadine-sensitive and -resistant influenza A viruses. These results were expected since compounds 3, 7, and 16 were designed to target the M2-V27A mutant, not the M2-S31N mutant. 2017 Antiviral research Result IV V27A;S31N 88;112 92;116 M2;M2 85;109 87;111 28087313 An M2-V27A channel blocker demonstrates potent in vitro and in vivo antiviral activities against amantadine-sensitive and -resistant influenza A viruses. We then tested the antiviral activity of compounds 7 and 16 against both M2-WT-containing A/Udorn/72 (M2-WT) (H3N2) virus and the M2-V27A-containing A/WSN/33 (M2-N31S + V27A) (H1N1) virus in plaque assays. 2017 Antiviral research Result IV V27A;N31S;V27A 133;162;169 137;166;173 M2;M2;M2;M2 73;102;130;159 75;104;132;161 28087313 An M2-V27A channel blocker demonstrates potent in vitro and in vivo antiviral activities against amantadine-sensitive and -resistant influenza A viruses. When tested against another M2-WT-containing virus A/WSN/33 (M2-N31S) (H1N1) virus, both amantadine (1) and compound 3 showed potent antiviral activity with EC50 values of 0.2 +- 0.01 muM, and 0.1 +- 0.01 muM, respectively (Table S1). 2017 Antiviral research Result IV N31S 64 68 M2;M2 28;61 30;63 28087313 An M2-V27A channel blocker demonstrates potent in vitro and in vivo antiviral activities against amantadine-sensitive and -resistant influenza A viruses. When tested against the M2-S31N channel, none of the compounds (3, 7, and 16) showed more than 12 % channel inhibition at 100 muM. 2017 Antiviral research Result IV S31N 27 31 M2 24 26 28102191 A broadly protective therapeutic antibody against influenza B virus with two mechanisms of action. 46B8 N297G fully protected mice against the WT virus but completely lost efficacy against the A4 mutant, supporting an important role of Fc functions in in vivo protection. 2017 Nature communications Result IV N297G 5 10 28102191 A broadly protective therapeutic antibody against influenza B virus with two mechanisms of action. A 46B8 variant with an N297G mutation in Fc (46B8 N297G) that abolishes FcgammaR binding was not able to induce ADCC, validating the involvement of Fc-FcgammaR interaction in 46B8-mediated ADCC. 2017 Nature communications Result IV N297G;N297G 23;50 28;55 28102191 A broadly protective therapeutic antibody against influenza B virus with two mechanisms of action. As summarized in Supplementary Table 1, three most dominant (>99%) mutations unique to A4 (R185K) or B1 and C2 (I303M and E582G) were identified in the PB2 protein. 2017 Nature communications Result IV R185K;I303M;E582G 91;112;122 96;117;127 PB2 152 155 28102191 A broadly protective therapeutic antibody against influenza B virus with two mechanisms of action. At pH 4.8, both WT and K401E HAs bound 46B8 significantly, whereas S301F and the double mutant completely lost binding. 2017 Nature communications Result IV K401E;S301F 23;67 28;72 28102191 A broadly protective therapeutic antibody against influenza B virus with two mechanisms of action. At pH 7.0, three HA mutants, P302A, S300F and E306K, showed reduced binding to 46B8 whereas the remaining mutants bound 46B8 similarly to the WT HA. 2017 Nature communications Result IV P302A;S300F;E306K 29;36;46 34;41;51 HA;HA 17;145 19;147 28102191 A broadly protective therapeutic antibody against influenza B virus with two mechanisms of action. B1 and C2 contain an additional mutation in HA, Lys401Glu (K401E). 2017 Nature communications Result IV K401E;K401E 48;59 57;64 HA 44 46 28102191 A broadly protective therapeutic antibody against influenza B virus with two mechanisms of action. E306K and T52A reduced binding moderately, whereas L73F and N74A bound 46B8 similarly to the WT HA. 2017 Nature communications Result IV E306K;T52A;L73F;N74A 0;10;51;60 5;14;55;64 HA 96 98 28102191 A broadly protective therapeutic antibody against influenza B virus with two mechanisms of action. however, retained the ability to bind mutant HAs at pH 7.0, as evidenced by immunogold-EM studies: 34B5, 46B8 and 46B8 N297G all bound efficiently to both the WT and mutant viruses, whereas a control IgG did not bind. 2017 Nature communications Result IV N297G 119 124 28102191 A broadly protective therapeutic antibody against influenza B virus with two mechanisms of action. Interestingly, 60% of the mice infected with the B1 or C2 mutant were protected by 46B8 N297G, possibly due to the partial sensitivity of these two viruses to the mAb. 2017 Nature communications Result IV N297G 88 93 28102191 A broadly protective therapeutic antibody against influenza B virus with two mechanisms of action. Interestingly, A4 appeared to be more resistant to 46B8 or 46B8 N297G than B1 and C2 in a neutralization assay that detects the expression of viral nucleoprotein at 16 h post infection. 2017 Nature communications Result IV N297G 64 69 NP 148 161 28102191 A broadly protective therapeutic antibody against influenza B virus with two mechanisms of action. Mice were infected with the minimum lethal dose of the WT or mutant viruses and treated with 15 mg kg-1 of 46B8, 46B8 N297G or a control IgG at 72 h post infection. 2017 Nature communications Result IV N297G 118 123 28102191 A broadly protective therapeutic antibody against influenza B virus with two mechanisms of action. S300F and P302A completely abolished binding whereas K53E, H55E and V105F decreased binding by more than 10-fold. 2017 Nature communications Result IV S300F;P302A;K53E;H55E;V105F 0;10;53;59;68 5;15;57;63;73 28102191 A broadly protective therapeutic antibody against influenza B virus with two mechanisms of action. Sequence analysis revealed a common mutation, Ser301Phe (S301F, numbering includes the signal sequence), in the HA proteins of all three viruses. 2017 Nature communications Result IV S301F;S301F 46;57 55;62 HA 112 114 28102191 A broadly protective therapeutic antibody against influenza B virus with two mechanisms of action. The almost identical binding profiles between WT and K401E and between S301F and S301F/K401E suggest that K401E is likely an inconsequential random mutation. 2017 Nature communications Result IV K401E;S301F;S301F;K401E;K401E 53;71;81;87;106 58;76;86;92;111 28102191 A broadly protective therapeutic antibody against influenza B virus with two mechanisms of action. The K401E mutant bound 46B8 as well as the WT HA, whereas S301F and S301F/K401E showed slightly reduced binding at pH 7.0 (middle panel). 2017 Nature communications Result IV K401E;S301F;S301F;K401E 4;58;68;74 9;63;73;79 HA 46 48 28102191 A broadly protective therapeutic antibody against influenza B virus with two mechanisms of action. To study the effect of the mutations on 46B8 binding, we expressed single (S301F or K401E) or double (S301F/K401E) mutant HAs on cell surface and tested 46B8 binding by flow cytometry. 2017 Nature communications Result IV S301F;K401E;S301F;K401E 75;84;102;108 80;89;107;113 28102191 A broadly protective therapeutic antibody against influenza B virus with two mechanisms of action. Two other highly dominant mutations (K338R and V625A) were identified in the PA protein. 2017 Nature communications Result IV K338R;V625A 37;47 42;52 PA 77 79 28102191 A broadly protective therapeutic antibody against influenza B virus with two mechanisms of action. When an I196T substitution in the 190-helix of RBP (numbering excludes the signal sequence) was introduced into the B/Wisconsin/1/2010 HA, it conferred susceptibility to 34B5 binding and sensitivity to 34B5 neutralisation of pseudotype virus. 2017 Nature communications Result IV I196T 8 13 HA 135 137 28128091 Development of oseltamivir and zanamivir resistance in influenza A(H1N1)pdm09 virus, Denmark, 2014. Against zanamivir there was normal inhibition of the virus isolates carrying the H275Y only. 2017 Euro surveillance Result IV H275Y 81 86 28128091 Development of oseltamivir and zanamivir resistance in influenza A(H1N1)pdm09 virus, Denmark, 2014. At this time point the H275Y mutation was still recognised, however, a mixed population with the I223R/I mutation was also observed by Sanger sequencing. 2017 Euro surveillance Result IV H275Y;I223R;I223I 23;97;97 28;104;104 28128091 Development of oseltamivir and zanamivir resistance in influenza A(H1N1)pdm09 virus, Denmark, 2014. Both contained virus with the H275Y mutation at a frequency of 60.3% (day 20) and > 99% (day 27). 2017 Euro surveillance Result IV H275Y 30 35 28128091 Development of oseltamivir and zanamivir resistance in influenza A(H1N1)pdm09 virus, Denmark, 2014. During propagation it was observed by sequencing that the antiviral resistance mutation I223R found in the original sample materials was lost after cell propagation, while new mutations indicative of cell adaptation occurred at positions A86T, R173K, and Q313K (Table 1 and 2). 2017 Euro surveillance Result IV I223R;A86T;R173K;Q313K 88;238;244;255 93;242;249;260 28128091 Development of oseltamivir and zanamivir resistance in influenza A(H1N1)pdm09 virus, Denmark, 2014. For two virus isolates propagated with antivirals in the growth medium it was possible to rescue viruses with the I223R mutation (Table 1). 2017 Euro surveillance Result IV I223R 114 119 28128091 Development of oseltamivir and zanamivir resistance in influenza A(H1N1)pdm09 virus, Denmark, 2014. In a sample obtained as BAL there was a higher frequency of the major resistance-inducing mutations (E119G: 35.9%, I223R: 51.8%, and H275Y: 88.2%) compared with a sample obtained as nasopharyngeal swab (E119G: 7.3%, I223R: 34.2% and H275Y:74.9%). 2017 Euro surveillance Result IV E119G;I223R;H275Y;E119G;I223R;H275Y 101;115;133;203;216;233 106;120;138;208;221;238 28128091 Development of oseltamivir and zanamivir resistance in influenza A(H1N1)pdm09 virus, Denmark, 2014. The I223R substitution was later confirmed by NGS with a frequency of 53.4% (Figure, Table 1). 2017 Euro surveillance Result IV I223R 4 9 28128091 Development of oseltamivir and zanamivir resistance in influenza A(H1N1)pdm09 virus, Denmark, 2014. The nasopharyngeal swab on the other hand showed three additional mutations related to antiviral resistance, however, at a low frequency (R118M: 1.1%, Q136K: 2.5%, and S247N: 6.2%). 2017 Euro surveillance Result IV R118M;Q136K;S247N 138;151;168 143;156;173 28128091 Development of oseltamivir and zanamivir resistance in influenza A(H1N1)pdm09 virus, Denmark, 2014. The sample contained influenza A(H1N1)pdm09 virus with the H275Y mutation and Sanger sequencing revealed an additional S247N mutation(Figure, Table 1). 2017 Euro surveillance Result IV H275Y;S247N 59;119 64;124 28128091 Development of oseltamivir and zanamivir resistance in influenza A(H1N1)pdm09 virus, Denmark, 2014. Three virus isolates carrying only the H275Y mutation had mean IC50s against oseltamivir, which were ca 500-900 fold higher than the wild type H275 strain A/California/07/2009(H1N1pdm09) virus, thereby showing highly reduced inhibition (Table 3). 2017 Euro surveillance Result IV H275Y 39 44 28128091 Development of oseltamivir and zanamivir resistance in influenza A(H1N1)pdm09 virus, Denmark, 2014. Unfortunately the virus isolates carrying both the I223R/I and H275Y mutations did not display NA activity and the phenotypic NA inhibition by oseltamivir and zanamivir could not be determined for these isolates. 2017 Euro surveillance Result IV I223R;I223I;H275Y 51;51;63 58;58;68 NA;NA 95;126 97;128 28128091 Development of oseltamivir and zanamivir resistance in influenza A(H1N1)pdm09 virus, Denmark, 2014. zanamivir treatment, respectively, revealed a mixed population of virus with wild type and resistant-conferring residues at position 275 (H275Y/H) as well as at position 223 (I223R/I) using Sanger sequencing (Figure, Table 1). 2017 Euro surveillance Result IV H275Y;H275H;I223R;I223I 138;138;175;175 145;145;182;182 28132927 Antigenic and genetic characterization of influenza viruses circulating in Bulgaria during the 2015/2016 season. All 20 Bulgarian B/Victoria-lineage viruses belonged to clade 1A with signature HA1 substitutions, N75K, N165K and S172P, compared to a previous vaccine virus, B/Malaysia/2506/2004. 2017 Infection, genetics and evolution Result IV N75K;N165K;S172P 99;105;115 103;110;120 HA1 80 83 28132927 Antigenic and genetic characterization of influenza viruses circulating in Bulgaria during the 2015/2016 season. All 57 A(H1N1)pdm09 HA sequences contained 11 amino acid changes in HA1 polypeptide and three in HA2: HA1 substitutions P83S, S203T and I321V that were fixed and present in viruses from all genetic groups; substitutions D97N and S185T in HA1 with E47K and S124N in HA2 defining group 6 (A/St. 2017 Infection, genetics and evolution Result IV P83S;S203T;I321V;D97N;S185T;E47K;S124N 120;126;136;220;229;247;256 124;131;141;224;234;251;261 HA;HA;HA;HA1;HA1;HA1 20;97;265;68;102;238 22;99;267;71;105;241 28132927 Antigenic and genetic characterization of influenza viruses circulating in Bulgaria during the 2015/2016 season. All three Bulgarian strains (subclade 3C.2a) showed variations at eight HA1 positions and three HA2 positions compared to the vaccine virus: HA1 : L3I, A128T (resulting in the gain of a N-glycosylation motif), N144S (resulting in the loss of N-glycosylation motif), F159Y, K160T (resulting in the gain of a N-glycosylation motif), N171K, Q311H, S312R, I406V (corresponding to HA2-subunit position 77), G484E (G155E in HA2), D489N (D160N in HA2). 2017 Infection, genetics and evolution Result IV L3I;A128T;N144S;F159Y;K160T;N171K;Q311H;S312R;I406V;G484E;G155E;D489N;D160N 147;152;210;266;273;331;338;345;352;402;409;424;431 150;157;215;271;278;336;343;350;357;407;414;429;436 HA;HA;HA;HA;HA1;HA1 96;376;418;440;72;141 98;378;420;442;75;144 28132927 Antigenic and genetic characterization of influenza viruses circulating in Bulgaria during the 2015/2016 season. Among the specified amino acid substitutions, five were located in antigenic sites: S203T in site Ca1; A141T in Ca2; S162N and K163Q in Sa and S185T in Sb. 2017 Infection, genetics and evolution Result IV S203T;A141T;S162N;K163Q;S185T 84;103;117;127;143 89;108;122;132;148 28132927 Antigenic and genetic characterization of influenza viruses circulating in Bulgaria during the 2015/2016 season. As with the vast majority of A(H1N1)pdm09 viruses, M2 proteins carried S31N substitution associated with resistance to M2-channel blockers (amantadine and rimantadine). 2017 Infection, genetics and evolution Result IV S31N 71 75 M2;M2 51;119 53;121 28132927 Antigenic and genetic characterization of influenza viruses circulating in Bulgaria during the 2015/2016 season. Compared to A/Switzerland/9715293/2013, loss and gain of potential N-glycosylation motifs were observed at HA1 positions144 and 128, respectively, while the HA2 G155E substitution was within a N-glycosylation motif (NGT NET). 2017 Infection, genetics and evolution Result IV G155E 161 166 HA;HA1 157;107 159;110 28132927 Antigenic and genetic characterization of influenza viruses circulating in Bulgaria during the 2015/2016 season. Four putative N-glycosylation motifs were identified, at positions 56, 64, 144 and 284, all of which were conserved except in B/Bulgaria/790/2016 which carried N144D substitution. 2017 Infection, genetics and evolution Result IV N144D 160 165 28132927 Antigenic and genetic characterization of influenza viruses circulating in Bulgaria during the 2015/2016 season. In addition, sixteen (28%) viruses carried HA1 A141T substitution and nine (16%) viruses had HA2 I91V substitution. 2017 Infection, genetics and evolution Result IV A141T;I91V 47;97 52;101 HA;HA1 93;43 95;46 28132927 Antigenic and genetic characterization of influenza viruses circulating in Bulgaria during the 2015/2016 season. In common with other subclade 6B.1 viruses, Bulgarian isolates contained amino acid substitutions in all proteins: Q208K and Y280H in M1; A22T and M105T in NP; D2E, E125D, R224G, A225T, A241T and T268A in NS1; R299K and S453T in PB2. 2017 Infection, genetics and evolution Result IV D2E;Q208K;Y280H;A22T;M105T;E125D;R224G;A225T;A241T;T268A;R299K;S453T 160;115;125;138;147;165;172;179;186;196;210;220 163;120;130;142;152;170;177;184;191;201;215;225 M1;NP;NS1;PB2 134;156;205;229 136;158;208;232 28132927 Antigenic and genetic characterization of influenza viruses circulating in Bulgaria during the 2015/2016 season. In the National Laboratory "Influenza and ARD", all 210 detected A(H1N1)pdm09 viruses were analyzed by real-time RT-PCR with respect to the H275Y oseltamivir resistance substitution : all viruses carried 275H indicative of retained susceptibility. 2017 Infection, genetics and evolution Result IV H275Y 140 145 28132927 Antigenic and genetic characterization of influenza viruses circulating in Bulgaria during the 2015/2016 season. NA sequences of the same 57 A(H1N1)pdm09 viruses differed from that of A/California/7/2009 by 15 substitutions: N248D and Y351K in viruses of all genetic groups; N44S, N200S, V241I and N369K in genetic group 6 viruses; I34V, L40I, I321V, N386K and K432E in genetic group 6B viruses; V13I, K264I, N270K and I314M in genetic group 6B.1 viruses. 2017 Infection, genetics and evolution Result IV N248D;Y351K;N44S;N200S;V241I;N369K;I34V;L40I;I321V;N386K;K432E;V13I;K264I;N270K;I314M 112;122;162;168;175;185;219;225;231;238;248;283;289;296;306 117;127;166;173;180;190;223;229;236;243;253;287;294;301;311 0 2 28132927 Antigenic and genetic characterization of influenza viruses circulating in Bulgaria during the 2015/2016 season. Only the S185T substitution falls within a domain defining the receptor binding site (RBS): 190-helix (residues 184-191); 220-loop (218-225); 130-loop (131-135), and in highly conserved residues (Y91, W150, H180 and Y192). 2017 Infection, genetics and evolution Result IV S185T 9 14 28132927 Antigenic and genetic characterization of influenza viruses circulating in Bulgaria during the 2015/2016 season. Petersburg/27/2011); HA1 substitutions K163Q, A256T and K283E with E172K in HA2 defining group 6B (A/South Africa/3626/2013) and HA1 substitutions S84N, S162N and I216T defining subclade 6B.1 (exemplified by the reference virus A/Slovenia/2903/2015). 2017 Infection, genetics and evolution Result IV K163Q;A256T;K283E;E172K;S84N;S162N;I216T 39;46;56;67;147;153;163 44;51;61;72;151;158;168 HA;HA1;HA1 76;21;129 78;24;132 28132927 Antigenic and genetic characterization of influenza viruses circulating in Bulgaria during the 2015/2016 season. S162N substitution, specific to subclade 6B.1 viruses, generated a new potential N-glycosylation motif within the Sa antigenic site. 2017 Infection, genetics and evolution Result IV S162N 0 5 28132927 Antigenic and genetic characterization of influenza viruses circulating in Bulgaria during the 2015/2016 season. Substitutions A128T and N144S are located in antigenic site A while S159Y and K160T are in antigenic site B. 2017 Infection, genetics and evolution Result IV A128T;N144S;S159Y;K160T 14;24;68;78 19;29;73;83 28132927 Antigenic and genetic characterization of influenza viruses circulating in Bulgaria during the 2015/2016 season. T48A substitution was detected in 7 (12%) Bulgarian viruses and 16 viruses harboured additional NA single amino acid changes. 2017 Infection, genetics and evolution Result IV T48A 0 4 96 98 28132927 Antigenic and genetic characterization of influenza viruses circulating in Bulgaria during the 2015/2016 season. The NA of Bulgarian viruses differed from the NA of A/Switzerland/9715293/2013 by 6 amino acid substitutions: S245N (resulting in gain of a N-glycosylation motif), S247T, T267K, P339N, I380V and P468H. 2017 Infection, genetics and evolution Result IV S245N;S247T;T267K;P339N;I380V;P468H 110;164;171;178;185;195 115;169;176;183;190;200 NA;NA 4;46 6;48 28132927 Antigenic and genetic characterization of influenza viruses circulating in Bulgaria during the 2015/2016 season. The substitutions N144S, F159Y, K160T, N225D and Q311H in HA1, compared to a previous vaccine virus, A/Texas/50/2012, define subclade 3C.2a; Bulgarian viruses fell into a cluster having HA proteins with HA1 N171K and S312R, and HA2 I77V and G155E substitutions. 2017 Infection, genetics and evolution Result IV N144S;F159Y;K160T;N225D;Q311H;N171K;S312R;I77V;G155E 18;25;32;39;49;207;217;232;241 23;30;37;44;54;212;222;236;246 HA;HA;HA1;HA1 186;228;58;203 188;230;61;206 28132927 Antigenic and genetic characterization of influenza viruses circulating in Bulgaria during the 2015/2016 season. Two amino acid substitutions were identified in HA, both (I117V and N129D) in the 120-loop (positions 116-137) antigenic site; no amino acid substitutions occurred in the remaining antigenic sites : 150-loop (positions 141-150), 160-loop (positions 162-167) and 190-helix (positions 194-202). 2017 Infection, genetics and evolution Result IV I117V;N129D 58;68 63;73 HA 48 50 28182419 Expeditious Lead Optimization of Isoxazole-Containing Influenza A Virus M2-S31N Inhibitors Using the Suzuki-Miyaura Cross-Coupling Reaction. All of these compounds (9a, 9d, 9f, 9h, 9q, 9r, 9s, 9t, 9u, and 9v) also had potent channel blockage against the AM2-S31N channel (> 70% at 100 muM), which is consistent with their potent antiviral activity. 2017 Journal of medicinal chemistry Result IV S31N 117 121 28182419 Expeditious Lead Optimization of Isoxazole-Containing Influenza A Virus M2-S31N Inhibitors Using the Suzuki-Miyaura Cross-Coupling Reaction. All synthesized compounds were tested for channel blockage against the AM2-S31N proton channel and antiviral activity against the A/California/07/2009 (H1N1) virus using the two-electrode voltage clamp (TEVC) assay and plaque assay, respectively. 2017 Journal of medicinal chemistry Result IV S31N 75 79 28182419 Expeditious Lead Optimization of Isoxazole-Containing Influenza A Virus M2-S31N Inhibitors Using the Suzuki-Miyaura Cross-Coupling Reaction. Briefly, the AM2-S31N channel was expressed in the oocyte cell membrane and was activated by acidic pH (pH = 5.5), compound was added at 100 muM concentration and the channel conductance current at the two-minute time point was recorded. 2017 Journal of medicinal chemistry Result IV S31N 17 21 28182419 Expeditious Lead Optimization of Isoxazole-Containing Influenza A Virus M2-S31N Inhibitors Using the Suzuki-Miyaura Cross-Coupling Reaction. CHANNEL INHIBITION, ANTIVIRAL ACTIVITY, AND CYTOTOXICITY OF ISOXAZOLE-CONTAINING AM2-S31N INHIBITORS. 2017 Journal of medicinal chemistry Result IV S31N 85 89 28182419 Expeditious Lead Optimization of Isoxazole-Containing Influenza A Virus M2-S31N Inhibitors Using the Suzuki-Miyaura Cross-Coupling Reaction. Compounds with substitutions at the meta position of benzene (9i and 9j) were also less potent in blocking the AM2-S31N channel than 9a, suggesting substitution at the meta position is not tolerated. 2017 Journal of medicinal chemistry Result IV S31N 115 119 28182419 Expeditious Lead Optimization of Isoxazole-Containing Influenza A Virus M2-S31N Inhibitors Using the Suzuki-Miyaura Cross-Coupling Reaction. For AM2-S31N proton channel inhibition, it was found that benzene and thiophene are the preferred aryl substitutions at the 5-position of isoxazole (Table 2), while pyridines (9b and 9c) were not tolerated. 2017 Journal of medicinal chemistry Result IV S31N 8 12 28182419 Expeditious Lead Optimization of Isoxazole-Containing Influenza A Virus M2-S31N Inhibitors Using the Suzuki-Miyaura Cross-Coupling Reaction. For this reason, the Openout-Closedin conformation of the AM2-S31N channel (PDB: 2LY0) was chosen for the docking of the most potent compound 9q. 2017 Journal of medicinal chemistry Result IV S31N 62 66 28182419 Expeditious Lead Optimization of Isoxazole-Containing Influenza A Virus M2-S31N Inhibitors Using the Suzuki-Miyaura Cross-Coupling Reaction. Four compounds (9b, 9i, 9j, and 9k) fell to the northeast side of the curve (above the curve), meaning that their actual antiviral activity was less potent than that predicted by their AM2-S31N channel blockage efficacy. 2017 Journal of medicinal chemistry Result IV S31N 189 193 28182419 Expeditious Lead Optimization of Isoxazole-Containing Influenza A Virus M2-S31N Inhibitors Using the Suzuki-Miyaura Cross-Coupling Reaction. In contrast, when AM2-S31N inhibitors such as M2WJ332 binds to the AM2-S31N channel, the channel adapts the Openout-Closedin conformation as shown by the solution NMR structure (PDB: 2LY0). 2017 Journal of medicinal chemistry Result IV S31N;S31N 22;71 26;75 28182419 Expeditious Lead Optimization of Isoxazole-Containing Influenza A Virus M2-S31N Inhibitors Using the Suzuki-Miyaura Cross-Coupling Reaction. In summary, the docking model shows that compound 9q binds to the Openout-Closedin conformation of the AM2-S31N channel, which is consistent with previously solved solution NMR structure (PDB: 2LY0). 2017 Journal of medicinal chemistry Result IV S31N 107 111 28182419 Expeditious Lead Optimization of Isoxazole-Containing Influenza A Virus M2-S31N Inhibitors Using the Suzuki-Miyaura Cross-Coupling Reaction. In the drug-free form, AM2-S31N adapts the Closedout-Openin conformation as shown by the X-ray crystal structure (PDB: 3C02) in Figure 4A. 2017 Journal of medicinal chemistry Result IV S31N 27 31 28182419 Expeditious Lead Optimization of Isoxazole-Containing Influenza A Virus M2-S31N Inhibitors Using the Suzuki-Miyaura Cross-Coupling Reaction. In the next step, all compounds were tested for their antiviral activity in plaque assays at 10 muM against the amantadine-resistant influenza A virus A/California/07/2009 (H1N1), which contains the AM2-S31N mutation. 2017 Journal of medicinal chemistry Result IV S31N 203 207 28182419 Expeditious Lead Optimization of Isoxazole-Containing Influenza A Virus M2-S31N Inhibitors Using the Suzuki-Miyaura Cross-Coupling Reaction. It can be seen clearly from the overlay structures of the docking model and the drug-free AM2-S31N structure (Figure 4D) that when compound 9q binds to the AM2-S31N channel, the channel undergoes a conformation change, leading to the opening of the N-terminus of the channel to accommodate the bulky drug 9q. 2017 Journal of medicinal chemistry Result IV S31N;S31N 94;160 98;164 28182419 Expeditious Lead Optimization of Isoxazole-Containing Influenza A Virus M2-S31N Inhibitors Using the Suzuki-Miyaura Cross-Coupling Reaction. It was found that compound 9q binds to the AM2-S31N channel with its aryl group facing towards the N-terminus of the channel (Figure 4C). 2017 Journal of medicinal chemistry Result IV S31N 47 51 28182419 Expeditious Lead Optimization of Isoxazole-Containing Influenza A Virus M2-S31N Inhibitors Using the Suzuki-Miyaura Cross-Coupling Reaction. Likewise, six compounds (9c, 9h, 9o, 9p, 9q, and 9s) fell to the southwest side of the curve (below the curve), meaning that their actual antiviral activity was more potent than that predicted by their AM2-S31N channel blockage efficacy. 2017 Journal of medicinal chemistry Result IV S31N 206 210 28182419 Expeditious Lead Optimization of Isoxazole-Containing Influenza A Virus M2-S31N Inhibitors Using the Suzuki-Miyaura Cross-Coupling Reaction. Overall, these results suggest that AM2-S31N inhibitors are potent antivirals against influenza A viruses with diverse genetic backgrounds. 2017 Journal of medicinal chemistry Result IV S31N 40 44 28182419 Expeditious Lead Optimization of Isoxazole-Containing Influenza A Virus M2-S31N Inhibitors Using the Suzuki-Miyaura Cross-Coupling Reaction. Previous synthesis of isoxazole-containing AM2-S31N inhibitors involved a five-step synthesis procedure. 2017 Journal of medicinal chemistry Result IV S31N 47 51 28182419 Expeditious Lead Optimization of Isoxazole-Containing Influenza A Virus M2-S31N Inhibitors Using the Suzuki-Miyaura Cross-Coupling Reaction. The A/Washington/29/2009 (H1N1) and A/Denmark/528/2009 (H1N1) viruses were chosen because they are representative examples of multidrug-resistant influenza A viruses and these two strains are resistant to both amantadine and oseltamivir due to AM2-S31N and H275Y mutations in their AM2 and neuraminidase genes, respectively. 2017 Journal of medicinal chemistry Result IV S31N;H275Y 248;257 252;262 290 303 28182419 Expeditious Lead Optimization of Isoxazole-Containing Influenza A Virus M2-S31N Inhibitors Using the Suzuki-Miyaura Cross-Coupling Reaction. The last step alkylation of bromide 7 with the amantadine analog 8 furnished the isoxazole-containing AM2-S31N inhibitor 9. 2017 Journal of medicinal chemistry Result IV S31N 106 110 28182419 Expeditious Lead Optimization of Isoxazole-Containing Influenza A Virus M2-S31N Inhibitors Using the Suzuki-Miyaura Cross-Coupling Reaction. The overlay of the drug-free AM2-S31N structure (PDB: 3C02) with the amantadine-bound AM2-WT structure (PDB: 3C9J) was shown in Figure 4B. 2017 Journal of medicinal chemistry Result IV S31N 33 37 28182419 Expeditious Lead Optimization of Isoxazole-Containing Influenza A Virus M2-S31N Inhibitors Using the Suzuki-Miyaura Cross-Coupling Reaction. This result was not a surprising finding as this class of compounds were designed to specifically target the amantadine-resistant AM2-S31N mutant channel. 2017 Journal of medicinal chemistry Result IV S31N 134 138 28182419 Expeditious Lead Optimization of Isoxazole-Containing Influenza A Virus M2-S31N Inhibitors Using the Suzuki-Miyaura Cross-Coupling Reaction. This strain is resistant to amantadine due to AM2-S31N mutation but is sensitive to oseltamivir. 2017 Journal of medicinal chemistry Result IV S31N 50 54 28182419 Expeditious Lead Optimization of Isoxazole-Containing Influenza A Virus M2-S31N Inhibitors Using the Suzuki-Miyaura Cross-Coupling Reaction. To further dissect the correlation between channel blockage efficacy and antiviral activity of all the synthesized AM2-S31N inhibitors, we plotted the percentage of channel blockage against the percentage of plaque formation and calculated the correlation coefficient (r). 2017 Journal of medicinal chemistry Result IV S31N 119 123 28182419 Expeditious Lead Optimization of Isoxazole-Containing Influenza A Virus M2-S31N Inhibitors Using the Suzuki-Miyaura Cross-Coupling Reaction. To gain further insights how the most potent compound 9q binds to the AM2-S31N channel, molecular docking was performed (Figure. 2017 Journal of medicinal chemistry Result IV S31N 74 78 28251891 Mid-season real-time estimates of seasonal influenza vaccine effectiveness in persons 65 years and older in register-based surveillance, Stockholm County, Sweden, and Finland, January 2017. In addition, the amino acid substitutions T135K and G479E in the HA1 and HA2 part of the haemagglutinin were determined in 58 of the 95 subclade 3C.2a1 viruses (Figure 4). 2017 Euro surveillance Result IV T135K;G479E 42;52 47;57 HA;HA1;HA 73;65;89 75;68;103 28251891 Mid-season real-time estimates of seasonal influenza vaccine effectiveness in persons 65 years and older in register-based surveillance, Stockholm County, Sweden, and Finland, January 2017. Nine of these 12 samples had the additional amino acid substitutions T131K, R142K and R261Q in HA1. 2017 Euro surveillance Result IV T131K;R142K;R261Q 69;76;86 74;81;91 HA1 95 98 28251891 Mid-season real-time estimates of seasonal influenza vaccine effectiveness in persons 65 years and older in register-based surveillance, Stockholm County, Sweden, and Finland, January 2017. Twenty-five of the 95 3C.2a1 viruses and 16 of the 58 viruses with the T135K and G479E substitutions were from vaccinated patients. 2017 Euro surveillance Result IV T135K;G479E 71;81 76;86 28252002 NEDDylation of PB2 Reduces Its Stability and Blocks the Replication of Influenza A Virus. Also, WSN-PB2 K699R caused 30% mortality as early as at 5 day post-infection (dpi), and 67% mortality at 6 dpi, which were higher than that caused by WSN. 2017 Scientific reports Result IV K699R 14 19 PB2 10 13 28252002 NEDDylation of PB2 Reduces Its Stability and Blocks the Replication of Influenza A Virus. At 12 h, 24 h and 36 h post infection, the titers of WSN-PB2 K699R were significantly higher than that of WSN. 2017 Scientific reports Result IV K699R 61 66 PB2 57 60 28252002 NEDDylation of PB2 Reduces Its Stability and Blocks the Replication of Influenza A Virus. Consistently, immunoblotting data indicated that the protein levels of M1, NP and PB2 of WSN but not WSN-PB2 K699R in NEDD8- overexpressing cells were greatly decreased compared to that in control cells. 2017 Scientific reports Result IV K699R 109 114 M1;NP;PB2;PB2 71;75;82;105 73;77;85;108 28252002 NEDDylation of PB2 Reduces Its Stability and Blocks the Replication of Influenza A Virus. Consistently, viral titers in lungs of mice infected with WSN-PB2 K699R were higher than that of WSN infected mice at both time points. 2017 Scientific reports Result IV K699R 66 71 PB2 62 65 28252002 NEDDylation of PB2 Reduces Its Stability and Blocks the Replication of Influenza A Virus. Furthermore, we examined the replication of wild type WSN virus and WSN-PB2 K699R mutant in A549 cells transfected with NEDD8 expressing plasmid or control plasmid. 2017 Scientific reports Result IV K699R 76 81 PB2 72 75 28252002 NEDDylation of PB2 Reduces Its Stability and Blocks the Replication of Influenza A Virus. However, the alveolar damage and interstitial inflammatory infiltration in WSN-PB2 K699R mice were much more severe than that of WSN infected mice. 2017 Scientific reports Result IV K699R 83 88 PB2 79 82 28252002 NEDDylation of PB2 Reduces Its Stability and Blocks the Replication of Influenza A Virus. Mice infected with WSN-PB2 K699R exhibited more severe weight loss compared to those infected with WSN. 2017 Scientific reports Result IV K699R 27 32 PB2 23 26 28252002 NEDDylation of PB2 Reduces Its Stability and Blocks the Replication of Influenza A Virus. More importantly, we found that the titers of WSN were significantly reduced in the NEDD8-overexpressing cells while the titers of WSN-PB2 K699R were comparable between control and NEDD8-overexpressing cells. 2017 Scientific reports Result IV K699R 139 144 PB2 135 138 28252002 NEDDylation of PB2 Reduces Its Stability and Blocks the Replication of Influenza A Virus. Moreover, necrosis was observed in the lung tissues of mice infected with WSN-PB2 K699R. 2017 Scientific reports Result IV K699R 82 87 PB2 78 81 28252002 NEDDylation of PB2 Reduces Its Stability and Blocks the Replication of Influenza A Virus. Since PB2 can also be modified by ubiquitin, we compared the level of ubiquitination of wild-type PB2 (PB2-WT) and mutant PB2 K699R (PB2-K699R). 2017 Scientific reports Result IV K699R;K699R 126;137 131;142 PB2;PB2;PB2;PB2;PB2 6;98;103;122;133 9;101;106;125;136 28252002 NEDDylation of PB2 Reduces Its Stability and Blocks the Replication of Influenza A Virus. The data indicated that HDM2 C464A can no longer promote the NEDDylation of PB2. 2017 Scientific reports Result IV C464A 29 34 PB2 76 79 28252002 NEDDylation of PB2 Reduces Its Stability and Blocks the Replication of Influenza A Virus. The data indicated that the level of PB2-WT was decreased in cells treated with CHX and reduced more dramatically in NEDD8 overexpressed cells, whereas the level of PB2-K699R did not decrease even in cells overexpressing His-NEDD8. 2017 Scientific reports Result IV K699R 169 174 PB2;PB2 37;165 40;168 28252002 NEDDylation of PB2 Reduces Its Stability and Blocks the Replication of Influenza A Virus. The data showed that luciferase activity in WSN infected cells were much lower than that in WSN-PB2 K699R infected cells. 2017 Scientific reports Result IV K699R 100 105 PB2 96 99 28252002 NEDDylation of PB2 Reduces Its Stability and Blocks the Replication of Influenza A Virus. The data showed that the titers of WSN were lower than that of WSN-PB2 K699R. 2017 Scientific reports Result IV K699R 71 76 PB2 67 70 28252002 NEDDylation of PB2 Reduces Its Stability and Blocks the Replication of Influenza A Virus. The level of NEDDylation in the K699R mutant was dramatically reduced compared to that of wild type and other PB2 mutants. 2017 Scientific reports Result IV K699R 32 37 PB2 110 113 28252002 NEDDylation of PB2 Reduces Its Stability and Blocks the Replication of Influenza A Virus. the level of ubiquitination of PB2-WT and PB2-K699R are comparable, suggesting that K699 is not a ubiquitination site. 2017 Scientific reports Result IV K699R 46 51 PB2;PB2 31;42 34;45 28252002 NEDDylation of PB2 Reduces Its Stability and Blocks the Replication of Influenza A Virus. The relative levels of FLAG-PB2 and FLAG-PB2 K699R from 2 independent experiments were quantified. 2017 Scientific reports Result IV K699R 45 50 PB2;PB2 28;41 31;44 28252002 NEDDylation of PB2 Reduces Its Stability and Blocks the Replication of Influenza A Virus. The total cell lysates were harvested for immunoblotting to determine the amount of FLAG-PB2 and FLAG-PB2 K699R. 2017 Scientific reports Result IV K699R 106 111 PB2;PB2 89;102 92;105 28252002 NEDDylation of PB2 Reduces Its Stability and Blocks the Replication of Influenza A Virus. Then we compared the proliferation kinetics of WSN with WSN-PB2 K699R. 2017 Scientific reports Result IV K699R 64 69 PB2 60 63 28252002 NEDDylation of PB2 Reduces Its Stability and Blocks the Replication of Influenza A Virus. These results illustrate that WSN-PB2 K699R causes more severe pathogenicity in mice than that of WSN, suggesting that preventing NEDDylation of PB2 promotes virus propagation and enhances virulence. 2017 Scientific reports Result IV K699R 38 43 PB2;PB2 34;145 37;148 28252002 NEDDylation of PB2 Reduces Its Stability and Blocks the Replication of Influenza A Virus. To examine whether NEDDylation of PB2 influences its stability, we compared the half-life of PB2-WT and PB2-K699R. 2017 Scientific reports Result IV K699R 108 113 PB2;PB2;PB2 34;93;104 37;96;107 28252002 NEDDylation of PB2 Reduces Its Stability and Blocks the Replication of Influenza A Virus. To understand the biological significance of NEDDylation of PB2 K699 in the propagation of IAV, we generated an IAV mutant in which PB2 was mutated to PB2 K699R (WSN-PB2 K699R) by taking the approach of reverse genetics. 2017 Scientific reports Result IV K699R;K699R 155;170 160;175 PB2;PB2;PB2;PB2 60;132;151;166 63;135;154;169 28252002 NEDDylation of PB2 Reduces Its Stability and Blocks the Replication of Influenza A Virus. We infected BALB/c mice intranasally with WSN or WSN-PB2 K699R at a dose of 10000 PFU, measuring the body weights and monitoring for survival daily after challenge. 2017 Scientific reports Result IV K699R 57 62 PB2 53 56 28252002 NEDDylation of PB2 Reduces Its Stability and Blocks the Replication of Influenza A Virus. We infected MDCK cells with WSN or WSN-PB2 K699R and harvested the supernatants at different time points (6, 12, 24, and 36 h post-infection) for plaque assay. 2017 Scientific reports Result IV K699R 43 48 PB2 39 42 28252002 NEDDylation of PB2 Reduces Its Stability and Blocks the Replication of Influenza A Virus. We infected the 293T-IAV-Luc cells with WSN or WSN-PB2 K699R and harvested the cell lysates for luciferase assay. 2017 Scientific reports Result IV K699R 55 60 PB2 51 54 28252002 NEDDylation of PB2 Reduces Its Stability and Blocks the Replication of Influenza A Virus. We then generated a HDM2 C464A mutant, which lacks E3 ligase activity, and repeated the experiment. 2017 Scientific reports Result IV C464A 25 30 28252002 NEDDylation of PB2 Reduces Its Stability and Blocks the Replication of Influenza A Virus. We transfected HEK293T cells with pCMV-FLAG-PB2 or pCMV-FLAG-PB2 K699R with or without pEF-His-NEDD8, and then treated the cells with cycloheximide (CHX) for 1 and 2 h. 2017 Scientific reports Result IV K699R 65 70 PB2;PB2 44;61 47;64 28252002 NEDDylation of PB2 Reduces Its Stability and Blocks the Replication of Influenza A Virus. WSN-PB2 K699R replicated much more efficiently than WSN in MDCK cells, resulting in higher virus titers. 2017 Scientific reports Result IV K699R 8 13 PB2 4 7 28252002 NEDDylation of PB2 Reduces Its Stability and Blocks the Replication of Influenza A Virus. WSN-PB2 K699R virus possesses higher virulence than WSN. 2017 Scientific reports Result IV K699R 8 13 PB2 4 7 28282440 H1N1 influenza viruses varying widely in hemagglutinin stability transmit efficiently from swine to swine and to ferrets. A K153E mutation reduced the HA activation pH by approximately 0.2 units on the backgrounds of WT pH1N1, Y17H, and Y17H/R106K (Fig 7). 2017 PLoS pathogens Result IV K153E;Y17H;Y17H;R106K 2;105;115;120 7;109;119;125 HA 29 31 28282440 H1N1 influenza viruses varying widely in hemagglutinin stability transmit efficiently from swine to swine and to ferrets. Accordingly, the R106K groups exhibited relatively little sequence variation (Fig 5). 2017 PLoS pathogens Result IV R106K 17 22 28282440 H1N1 influenza viruses varying widely in hemagglutinin stability transmit efficiently from swine to swine and to ferrets. As the input HA activation pH for Y17H was 6.0, average decreases of 0.2 and 0.5 pH units were associated with adaptation and transmission in swine and ferrets, respectively. 2017 PLoS pathogens Result IV Y17H 34 38 HA 13 15 28282440 H1N1 influenza viruses varying widely in hemagglutinin stability transmit efficiently from swine to swine and to ferrets. Cellular infiltration and transcription of inflammatory genes in the lungs of pigs inoculated with Y17H virus were minimal. 2017 PLoS pathogens Result IV Y17H 99 103 28282440 H1N1 influenza viruses varying widely in hemagglutinin stability transmit efficiently from swine to swine and to ferrets. Compared to the Y17H- or PBS-inoculated groups, WT- and R106K-infected pigs had more infiltrating cells in their TBAL fluid (S3A Fig), as well as increased levels of mRNAs encoding proinflammatory cytokines (i.e., IL-1beta and IL-6) and chemokines (i.e., MIP2alpha and MCP1) (S3B Fig). 2017 PLoS pathogens Result IV Y17H;R106K 16;56 20;61 28282440 H1N1 influenza viruses varying widely in hemagglutinin stability transmit efficiently from swine to swine and to ferrets. Compared to WT and R106K, Y17H with a destabilized HA protein (pH 6.0) had reduced replication and was a loss-of-function mutant for airborne transmission in ferrets. 2017 PLoS pathogens Result IV R106K;Y17H 19;26 24;30 HA 51 53 28282440 H1N1 influenza viruses varying widely in hemagglutinin stability transmit efficiently from swine to swine and to ferrets. Compared to WT virus, the destabilized Y17H mutant yielded peak nasal swab titers that were delayed by 3 days and reduced 30-fold (P < 0.05); Y17H viral loads were also significantly reduced in TBAL fluid and lung homogenates (Fig 2). 2017 PLoS pathogens Result IV Y17H;Y17H 39;142 43;146 28282440 H1N1 influenza viruses varying widely in hemagglutinin stability transmit efficiently from swine to swine and to ferrets. Compared to WT virus, the stabilized R106K mutant displayed no statistically significant differences with respect to the viral load in nasal swabs, tracheal homogenates, or tracheobronchoalveolar lavage (TBAL) fluid (Fig 2). 2017 PLoS pathogens Result IV R106K 37 42 28282440 H1N1 influenza viruses varying widely in hemagglutinin stability transmit efficiently from swine to swine and to ferrets. For pigs infected with any of the 3 viruses, we found no notable lesions in the lungs or trachea, except in 1 animal infected with R106K (Table 1 and S2 Fig). 2017 PLoS pathogens Result IV R106K 131 136 28282440 H1N1 influenza viruses varying widely in hemagglutinin stability transmit efficiently from swine to swine and to ferrets. For swine-to-ferret transmission of Y17H, the measured HA activation pH values for ferret recipients were initially 5.5, 5.6, and 5.9 (Fig 4C). 2017 PLoS pathogens Result IV Y17H 36 40 HA 55 57 28282440 H1N1 influenza viruses varying widely in hemagglutinin stability transmit efficiently from swine to swine and to ferrets. Histopathologic analyses also showed similar spread by WT and R106K viruses in the nasal turbinates and trachea (Table 1). 2017 PLoS pathogens Result IV R106K 62 67 28282440 H1N1 influenza viruses varying widely in hemagglutinin stability transmit efficiently from swine to swine and to ferrets. In 2 separate experiments, we intranasally inoculated a total of 8 pigs with pH1N1 WT, Y17H, or R106K viruses: 5 to be used for daily measurements of the viral load in nasal swabs and 3 in which to examine the tissue titers, histopathology, and inflammatory responses at 3 days post-inoculation (dpi). 2017 PLoS pathogens Result IV Y17H;R106K 87;96 91;101 28282440 H1N1 influenza viruses varying widely in hemagglutinin stability transmit efficiently from swine to swine and to ferrets. In both experiments, a proportion of the HA1-H17Y reversion mutation was detected in pigs (donor and contact) and ferrets. 2017 PLoS pathogens Result IV H17Y 45 49 HA1 41 44 28282440 H1N1 influenza viruses varying widely in hemagglutinin stability transmit efficiently from swine to swine and to ferrets. In contrast, similar observations were made in only a third of pigs infected with R106K or Y17H. 2017 PLoS pathogens Result IV R106K;Y17H 82;91 87;95 28282440 H1N1 influenza viruses varying widely in hemagglutinin stability transmit efficiently from swine to swine and to ferrets. In contrast, the R106K mutant showed greater spread in the lungs by immunohistochemistry, perhaps explaining in part why lung viral loads in the R106K group were an average of 30-fold higher (P < 0.05) than in the WT group (Fig 2D). 2017 PLoS pathogens Result IV R106K;R106K 17;145 22;150 28282440 H1N1 influenza viruses varying widely in hemagglutinin stability transmit efficiently from swine to swine and to ferrets. In contrast, the R106K virus, which had an HA stabilized at pH 5.3, retained a stable genotype and phenotype, along with wild-type-like replication and transmissibility in pigs and ferrets by contact and airborne routes, respectively. 2017 PLoS pathogens Result IV R106K 17 22 HA 43 45 28282440 H1N1 influenza viruses varying widely in hemagglutinin stability transmit efficiently from swine to swine and to ferrets. In contrast, the transmission of the destabilized Y17H virus was significantly delayed (P < 0.04), with the first detection and peak of infection occurring at averages of 5.0 and 7.3 days after donor inoculation, respectively, in pigs and 6.3 and 9.0 days after donor inoculation, respectively, in ferrets (Table 2). 2017 PLoS pathogens Result IV Y17H 50 54 28282440 H1N1 influenza viruses varying widely in hemagglutinin stability transmit efficiently from swine to swine and to ferrets. In experiment 1, HA2-K153E emerged in each of the 3 donor pigs and in 1 of the contact pigs (S6 Fig). 2017 PLoS pathogens Result IV K153E 21 26 HA 17 19 28282440 H1N1 influenza viruses varying widely in hemagglutinin stability transmit efficiently from swine to swine and to ferrets. In experiment 2, HA2-V55I was a minor population in 1 of the 2 donor pigs, was more than 90% abundant in the contact pig, and reached more than 99% abundance in each of the 3 ferrets (S6 Fig). 2017 PLoS pathogens Result IV V55I 21 25 HA 17 19 28282440 H1N1 influenza viruses varying widely in hemagglutinin stability transmit efficiently from swine to swine and to ferrets. In the R106K-infected/exposed groups, the HA activation pH averaged 5.4 (range, 5.30-5.55) in pigs and 5.3 (range, 5.20-5.40) in ferrets (Fig 4B and 4E). 2017 PLoS pathogens Result IV R106K 7 12 HA 42 44 28282440 H1N1 influenza viruses varying widely in hemagglutinin stability transmit efficiently from swine to swine and to ferrets. In the Y17H groups, the HA activation pH ranged from 5.55 to 6.00 in donor pigs (average, 5.83), from 5.55 to 5.93 in contact pigs (mean, 5.77), and from 5.47 to 5.63 in ferrets (mean, 5.52) (Fig 4C and 4F). 2017 PLoS pathogens Result IV Y17H 7 11 HA 24 26 28282440 H1N1 influenza viruses varying widely in hemagglutinin stability transmit efficiently from swine to swine and to ferrets. Minor populations of HA2-R106K were also detected in both experiments. 2017 PLoS pathogens Result IV R106K 25 30 HA 21 23 28282440 H1N1 influenza viruses varying widely in hemagglutinin stability transmit efficiently from swine to swine and to ferrets. Minor populations of the NA mutations V46A and K253R were detected in 1 donor pig and 1 contact pig, respectively, but were not associated with transmission. 2017 PLoS pathogens Result IV V46A;K253R 38;47 42;52 25 27 28282440 H1N1 influenza viruses varying widely in hemagglutinin stability transmit efficiently from swine to swine and to ferrets. No variant with a K253R mutation in the NA protein was found in pigs, whereas the mutation had an abundance of 95% in one R106K-group ferret on day 3, although this decreased to 68% of the virus population within 2 days, suggesting that it is not a preferred mutation. 2017 PLoS pathogens Result IV K253R;R106K 18;122 23;127 40 42 28282440 H1N1 influenza viruses varying widely in hemagglutinin stability transmit efficiently from swine to swine and to ferrets. Overall, mutations associated with Y17H adaptation in pigs and ferrets were found to stabilize the HA protein, consistent with the average HA activation pH for this group shifting from 6.0 to 5.8 in pigs and 5.5 in ferrets (Fig 4). 2017 PLoS pathogens Result IV Y17H 35 39 HA;HA 99;139 101;141 28282440 H1N1 influenza viruses varying widely in hemagglutinin stability transmit efficiently from swine to swine and to ferrets. Overall, the HA-stabilizing mutation R106K (pH 5.3) supported pH1N1 growth, spread, and pathogenicity comparable to those observed with WT virus (pH 5.5), whereas the HA-destabilizing Y17H mutation (pH 6.0) resulted in delayed or reduced virus growth, spread, and pathogenicity. 2017 PLoS pathogens Result IV R106K;Y17H 37;184 42;188 HA;HA 13;167 15;169 28282440 H1N1 influenza viruses varying widely in hemagglutinin stability transmit efficiently from swine to swine and to ferrets. Some isolates contained HA2-V192A substitutions, but their proportions remained below 30%, suggesting that these substitutions did not improve fitness. 2017 PLoS pathogens Result IV V192A 28 33 HA 24 26 28282440 H1N1 influenza viruses varying widely in hemagglutinin stability transmit efficiently from swine to swine and to ferrets. The activation pH values for the R106K groups in pigs increased by an average of 0.1 pH units and remained at an average of 5.3 in ferrets (Fig 4E). 2017 PLoS pathogens Result IV R106K 33 38 28282440 H1N1 influenza viruses varying widely in hemagglutinin stability transmit efficiently from swine to swine and to ferrets. The following five HA mutations located in the stalk region were transmitted to or emerged in contact pigs and/or ferrets: HA1-H17Y (reversion), HA2-V55I, HA2-R106K, HA2-K153E, and HA2-V192A (Fig 6). 2017 PLoS pathogens Result IV H17Y;V55I;R106K;K153E;V192A 127;149;159;170;185 131;153;164;175;190 HA;HA;HA;HA;HA;HA1 19;145;155;166;181;123 21;147;157;168;183;126 28282440 H1N1 influenza viruses varying widely in hemagglutinin stability transmit efficiently from swine to swine and to ferrets. The HA sequence variation averaged approximately 2% in the Y17H groups (Fig 5), and subpopulations of viruses containing HA protein mutations emerged (S6 Fig). 2017 PLoS pathogens Result IV Y17H 59 63 HA;HA 4;121 6;123 28282440 H1N1 influenza viruses varying widely in hemagglutinin stability transmit efficiently from swine to swine and to ferrets. The packing of residue 55 into its pocket may be stabilized by a V55I mutation, which reduced the HA activation pH by approximately 0.2 to 0.3 units (Fig 7). 2017 PLoS pathogens Result IV V55I 65 69 HA 98 100 28282440 H1N1 influenza viruses varying widely in hemagglutinin stability transmit efficiently from swine to swine and to ferrets. The R106K mutation stabilizes the HA protein by 0.2 to 0.3 pH units, perhaps by reducing electrostatic repulsions at the core of the central triple-stranded coiled-coil at the hinge between helices C and D (Figs 6D and 7). 2017 PLoS pathogens Result IV R106K 4 9 HA 34 36 28282440 H1N1 influenza viruses varying widely in hemagglutinin stability transmit efficiently from swine to swine and to ferrets. The transmission timing of the stabilized R106K virus was similar to that of WT virus (P > 0.2). 2017 PLoS pathogens Result IV R106K 42 47 28282440 H1N1 influenza viruses varying widely in hemagglutinin stability transmit efficiently from swine to swine and to ferrets. Thus, HA stability phenotypes were maintained in pigs and ferrets infected with WT and R106K viruses. 2017 PLoS pathogens Result IV R106K 87 92 HA 6 8 28282440 H1N1 influenza viruses varying widely in hemagglutinin stability transmit efficiently from swine to swine and to ferrets. To determine experimentally the permissible range of HA activation pH for IAV replication and transmission in swine, we selected 3 previously characterized pH1N1 viruses that have a common A/TN/1-560/2009 (pH1N1) backbone: WT (pH 5.5), HA2-R106K (5.3), and HA1-Y17H (6.0). 2017 PLoS pathogens Result IV R106K;Y17H 240;261 245;265 HA;HA;HA1 53;236;257 55;238;260 28282440 H1N1 influenza viruses varying widely in hemagglutinin stability transmit efficiently from swine to swine and to ferrets. Two of the three Y17H-infected pigs were negative for NP by immunohistochemical staining (IHC) in their nasal turbinates, tracheae, and lungs. 2017 PLoS pathogens Result IV Y17H 17 21 NP 54 56 28282440 H1N1 influenza viruses varying widely in hemagglutinin stability transmit efficiently from swine to swine and to ferrets. We generated reverse-genetics viruses containing mutations associated with transmission in the Y17H groups. 2017 PLoS pathogens Result IV Y17H 95 99 28323816 An NS-segment exonic splicing enhancer regulates influenza A virus replication in mammalian cells. Although no significant difference in NP protein level was observed between WT virus and the A540G mutant, NEP and NS1 protein levels were significantly affected in the early hours of A540G mutant virus infection, up until 12 h post infection, with NS1 being downregulated and NEP upregulated. 2017 Nature communications Result IV A540G;A540G 93;184 98;189 NEP;NEP;NP;NS1;NS1 107;277;38;115;249 110;280;40;118;252 28323816 An NS-segment exonic splicing enhancer regulates influenza A virus replication in mammalian cells. Although positions 38 and 41 are both important for NS1 RNA binding, our result showed that only R38A/K41A double mutations abolished interaction between NS1 and SF2. 2017 Nature communications Result IV K41A;R38A 102;97 106;101 NS1;NS1 52;154 55;157 28323816 An NS-segment exonic splicing enhancer regulates influenza A virus replication in mammalian cells. An A540G mutation within the identified NEP-ESE site affects H7N9 virus replication in mammalian cells, but not in those of avian origin. 2017 Nature communications Result IV A540G 3 8 NEP 40 43 28323816 An NS-segment exonic splicing enhancer regulates influenza A virus replication in mammalian cells. and it is therefore possible that avian cells are less sensitive to splicing changes caused by A540G substitution in the NS RNA. 2017 Nature communications Result IV A540G 95 100 NS 121 123 28323816 An NS-segment exonic splicing enhancer regulates influenza A virus replication in mammalian cells. As cell culture experiments showed that A540G substitution has a more significant effect on virus protein expression during the early stage of virus infection. 2017 Nature communications Result IV A540G 40 45 28323816 An NS-segment exonic splicing enhancer regulates influenza A virus replication in mammalian cells. As expected from the higher ESE score, A540G increased the proportion of the spliced form of NS mRNA, NEP mRNA, in infected cells, starting from 6 h post infection. 2017 Nature communications Result IV A540G 39 44 NEP;NS 102;93 105;95 28323816 An NS-segment exonic splicing enhancer regulates influenza A virus replication in mammalian cells. As H7N9 virus acquired internal genes from avian H9N2 virus, we surveyed H9N2 NS sequences in the public database and discovered that G540A, as well as an adjacent nucleotide mutation, U539C, emerged in early 2000; since 2009-2011, U539C/G540A became increasingly prevalent, being the predominant variant from 2012 onwards. 2017 Nature communications Result IV G540A;G540A 134;238 139;243 NS 78 80 28323816 An NS-segment exonic splicing enhancer regulates influenza A virus replication in mammalian cells. As sequence surveillance found another substitution, C539U, which emerged alongside G540A in H9N2 viruses since 2000 and is present in all H7N9 viruses. 2017 Nature communications Result IV G540A 84 89 28323816 An NS-segment exonic splicing enhancer regulates influenza A virus replication in mammalian cells. As the G540A substitution caused an amino acid change, E172K, in the NS1 protein but was a silent mutation in the NEP. 2017 Nature communications Result IV G540A;E172K 7;55 12;60 NEP;NS1 114;69 117;72 28323816 An NS-segment exonic splicing enhancer regulates influenza A virus replication in mammalian cells. As the H7N9 virus acquired internal genes from H9N2, we similarly constructed two additional pairs of wild type (WT) and A540G mutant viruses; one set with a complete H9N2 virus genome (H9N2), the other with internal genes from H7N9 virus and surface genes derived from H9N2 (rH9N2). 2017 Nature communications Result IV A540G 121 126 28323816 An NS-segment exonic splicing enhancer regulates influenza A virus replication in mammalian cells. At higher infectious doses (4.75 x 104 and 4.75 x 105 plaque-forming units), both strains caused severe body weight loss in mice, but the A540G-NS mutant was still less pathogenic than the WT virus. 2017 Nature communications Result IV A540G 138 143 NS 144 146 28323816 An NS-segment exonic splicing enhancer regulates influenza A virus replication in mammalian cells. Consistent with that observed with the H7N9 backbone, introduction of the A540G substitution caused attenuation of both rH9N2 and H9N2 virus replication in A549 cells, but not in DF-1 cells. 2017 Nature communications Result IV A540G 74 79 28323816 An NS-segment exonic splicing enhancer regulates influenza A virus replication in mammalian cells. Consistent with the SF2 interaction result, we found that the NS1 mutant, which is unable to interact with SF2 (R38A/K41A), is also attenuated in its ability to inhibit NEP mRNA splicing even though it is localized in the nucleus. 2017 Nature communications Result IV R38A;K41A 112;117 116;121 NEP;NS1 169;62 172;65 28323816 An NS-segment exonic splicing enhancer regulates influenza A virus replication in mammalian cells. Consistent with the virus infection result, comparison of splicing ratios for NS mRNAs transcribed from transfected NS plasmids encoding WT or truncated NS1 proteins showed that A540G substitution increased the splicing ratio of NS mRNAs. 2017 Nature communications Result IV A540G 178 183 NS;NS;NS;NS1 78;116;229;153 80;118;231;156 28323816 An NS-segment exonic splicing enhancer regulates influenza A virus replication in mammalian cells. Consistent with the western blot result, quantitative reverse-transcription-PCR (RT-qPCR) showed that in comparison with WT virus-infected cells, unspliced NS mRNA (NS1) is decreased in A540G mutant infections, whereas spliced NS mRNA (NEP) is increased. 2017 Nature communications Result IV A540G 186 191 NEP;NS;NS;NS1 236;156;227;165 239;158;229;168 28323816 An NS-segment exonic splicing enhancer regulates influenza A virus replication in mammalian cells. Consistent with this report, phylogenetic analysis showed that all H9N2 G57 genotype viruses have the NS G540A substitution and form a distinct group. 2017 Nature communications Result IV G540A 105 110 NS 102 104 28323816 An NS-segment exonic splicing enhancer regulates influenza A virus replication in mammalian cells. EMSA showed that SF2 has higher affinity for the NEP A540G mutant than WT (540A) in both direct and competition binding assays. 2017 Nature communications Result IV A540G 53 58 NEP 49 52 28323816 An NS-segment exonic splicing enhancer regulates influenza A virus replication in mammalian cells. G540A caused an E172K amino acid change in the NS1 protein, but not in NEP. 2017 Nature communications Result IV G540A;E172K 0;16 5;21 NEP;NS1 71;47 74;50 28323816 An NS-segment exonic splicing enhancer regulates influenza A virus replication in mammalian cells. G540A substitution enhances virus virulence in mice. 2017 Nature communications Result IV G540A 0 5 28323816 An NS-segment exonic splicing enhancer regulates influenza A virus replication in mammalian cells. G540A substitution modulates NEP expression. 2017 Nature communications Result IV G540A 0 5 NEP 29 32 28323816 An NS-segment exonic splicing enhancer regulates influenza A virus replication in mammalian cells. Growth kinetics analysis showed that A540G mutation caused attenuation of H7N9 virus replication in A549 human lung cancer cells, but not in DF-1 chicken fibroblasts. 2017 Nature communications Result IV A540G 37 42 28323816 An NS-segment exonic splicing enhancer regulates influenza A virus replication in mammalian cells. However, there was no significant difference between the WT and A540G groups when virus titres in lung tissues collected 3 days after infection were measured, implying that 540A may associate with virulence properties other than virus replication ability in vivo. 2017 Nature communications Result IV A540G 64 69 28323816 An NS-segment exonic splicing enhancer regulates influenza A virus replication in mammalian cells. Interestingly, M1 protein expression was also affected by NS-A540G mutation, presumably due to the altered level of NS1 as reported in other studies, including one in which NS1 protein was found to promote M1 to M2 splicing in nuclear speckles. 2017 Nature communications Result IV A540G 61 66 M1;M1;M2;NS;NS1;NS1 15;206;212;58;116;173 17;208;214;60;119;176 28323816 An NS-segment exonic splicing enhancer regulates influenza A virus replication in mammalian cells. It is noted that the F162S/V163R mutant, which reduces SF2 RNA binding ability, did not affect SF2 interaction with NS1. 2017 Nature communications Result IV F162S;V163R 21;27 26;32 NS1 116 119 28323816 An NS-segment exonic splicing enhancer regulates influenza A virus replication in mammalian cells. Notably, the effect of A540G back mutation on NEP/NS1 mRNA ratios is not apparent in avian DF-1 cells infected with rH9N2 virus. 2017 Nature communications Result IV A540G 23 28 NEP;NS1 46;50 49;53 28323816 An NS-segment exonic splicing enhancer regulates influenza A virus replication in mammalian cells. Notably, WT H7N9 NS (540A) has a score of 2.64, whereas the A540G mutant showed a much higher score of 5.22, indicating that the mutant is more efficiently spliced. 2017 Nature communications Result IV A540G 60 65 NS 17 19 28323816 An NS-segment exonic splicing enhancer regulates influenza A virus replication in mammalian cells. RNA stability testing showed no differences between WT and A540G mutant mRNAs. 2017 Nature communications Result IV A540G 59 64 28323816 An NS-segment exonic splicing enhancer regulates influenza A virus replication in mammalian cells. Similarly, unspliced M1 mRNA levels are downregulated when NS1 expression is decreased in A540G mutant virus infected cells. 2017 Nature communications Result IV A540G 90 95 M1;NS1 21;59 23;62 28323816 An NS-segment exonic splicing enhancer regulates influenza A virus replication in mammalian cells. substitution of A540G significantly attenuated virus pathogenicity, as shown by the body weight curve. 2017 Nature communications Result IV A540G 16 21 28323816 An NS-segment exonic splicing enhancer regulates influenza A virus replication in mammalian cells. Taken together, these results clearly characterize a new ESE located in the 535-541 region of exon 2 of NEP pre-mRNA and demonstrate that an A to G substitution at position 540 significantly affects the ability of this ESE to splice NEP mRNA. 2017 Nature communications Result IV A540G 141 176 NEP;NEP 104;233 107;236 28323816 An NS-segment exonic splicing enhancer regulates influenza A virus replication in mammalian cells. The 2013 H7N9 virus contains a unique NS-G540A substitution. 2017 Nature communications Result IV G540A 41 46 NS 38 40 28323816 An NS-segment exonic splicing enhancer regulates influenza A virus replication in mammalian cells. The data suggest that G540A substitution in the NS segment provides H7N9 and H9N2 viruses with enhanced ability to replicate in mammalian cells, without reducing fitness in avian cells. 2017 Nature communications Result IV G540A 22 27 NS 48 50 28323816 An NS-segment exonic splicing enhancer regulates influenza A virus replication in mammalian cells. The EMSA and RNA IP/RT-qPCR assays clearly demonstrate that the NEP-ESE site is directly bound by the splicing regulator SF2, and that A/G substitution at position 540 of the NS segment alters SF2-binding affinity for this ESE site, leading to different splicing efficiency. 2017 Nature communications Result IV A540G 137 167 NEP;NS 64;175 67;177 28323816 An NS-segment exonic splicing enhancer regulates influenza A virus replication in mammalian cells. The following experiments are therefore focused on characterizing the biological significance of the G540A mutation. 2017 Nature communications Result IV G540A 101 106 28323816 An NS-segment exonic splicing enhancer regulates influenza A virus replication in mammalian cells. The mutant virus contained an NS A540G (K172E) mutation, reversed from the prevailing NS genotype at this position, with a view to disrupting any function specifically associated with G540A. 2017 Nature communications Result IV A540G;K172E;G540A 33;40;184 38;45;189 NS;NS 30;86 32;88 28323816 An NS-segment exonic splicing enhancer regulates influenza A virus replication in mammalian cells. The NEP-ESE motif was able to function, as indicated by exon 7 inclusion in SMN1 mini gene mRNA splicing, and furthermore the A540G substitution also enhances the efficiency of exon-7 inclusion. 2017 Nature communications Result IV A540G 126 131 NEP 4 7 28323816 An NS-segment exonic splicing enhancer regulates influenza A virus replication in mammalian cells. The results showed that naturally acquired (H7N9) or artificially introduced (H9N2-E172K) G540A substitution in the NS segment significantly enhances virus replication in A549 cells. 2017 Nature communications Result IV E172K;G540A 83;90 88;95 NS 116 118 28323816 An NS-segment exonic splicing enhancer regulates influenza A virus replication in mammalian cells. These binding experiments clearly demonstrated that the NEP-ESE site (nucleotides 529-548) is recognized by the SF2 splicing regulator, and that A540G substitution increases SF2 binding in in vitro assays. 2017 Nature communications Result IV A540G 145 150 NEP 56 59 28323816 An NS-segment exonic splicing enhancer regulates influenza A virus replication in mammalian cells. These results further demonstrate that the NEP ESE is associated with splicing of NS mRNAs, and that the G540A substitution in this ESE affects the ratio of NS1 to NEP mRNAs, leading to more NEP protein being expressed in the early hours of infection. 2017 Nature communications Result IV G540A 105 110 NEP;NEP;NEP;NS;NS1 43;164;191;82;157 46;167;194;84;160 28323816 An NS-segment exonic splicing enhancer regulates influenza A virus replication in mammalian cells. These results suggest that the biological impact of G540A substitution in the NS segment may not lie in the amino acid change at position 172 of the NS1 protein. 2017 Nature communications Result IV G540A 52 57 NS;NS1 78;149 80;152 28323816 An NS-segment exonic splicing enhancer regulates influenza A virus replication in mammalian cells. To characterize the effect of NS G540A (NS1 E172K) on virus replication, we first tested one pair of H7N9 viruses constructed from the backbone of the 2013 H7N9 virus strain. 2017 Nature communications Result IV G540A;E172K 33;44 38;49 NS;NS1 30;40 32;43 28323816 An NS-segment exonic splicing enhancer regulates influenza A virus replication in mammalian cells. To characterize the effect of WT and A540G mutant viruses in vivo, we compared the pathogenic properties of H7N9 viruses containing either 540 A-NS (WT) or 540G-NS (mutant) in a mouse model. 2017 Nature communications Result IV A540G 37 42 NS;NS 145;161 147;163 28323816 An NS-segment exonic splicing enhancer regulates influenza A virus replication in mammalian cells. To exclude the effect of other viral proteins on regulation of NS mRNA splicing, transfection experiments with WT and mutated NS segments were performed and the result showed that A540G back mutation significantly increases the NEP/NS1 mRNA ratio in HEK293T cells. 2017 Nature communications Result IV A540G 180 185 NEP;NS;NS;NS1 228;63;126;232 231;65;128;235 28323816 An NS-segment exonic splicing enhancer regulates influenza A virus replication in mammalian cells. To exclude the possible influence of other cellular proteins present in the NEs prepared from SF2-transfected cells, we confirmed that antibody purified SF2 is able to bind to the NEP-ESE site, and that A540G mutant appears to have higher affinity for SF2. 2017 Nature communications Result IV A540G 203 208 NEP 180 183 28323816 An NS-segment exonic splicing enhancer regulates influenza A virus replication in mammalian cells. To further confirm the notion that the NEP ESE modulates NEP and NS1 expression during virus infection, we examined levels of viral mRNAs in A549 cells infected with either WT or A540G-NS rH9N2 virus. 2017 Nature communications Result IV A540G 179 184 NEP;NEP;NS;NS1 39;57;185;65 42;60;187;68 28323816 An NS-segment exonic splicing enhancer regulates influenza A virus replication in mammalian cells. To further demonstrate the general effect of gaining G540A substitution on virus replication in mammalian cells, we tested growth kinetics using recombinant virus containing either the NS segment from a H7N9 (540A), H9N2 (540G) or mutated H9N2-NS (540A) virus with the rest of the segments from the A/WSN/33 (H1N1) backbone. 2017 Nature communications Result IV G540A 53 58 NS;NS 185;244 187;246 28323816 An NS-segment exonic splicing enhancer regulates influenza A virus replication in mammalian cells. To investigate adaptations in the H7N9 virus genome, we compared available sequences and found a unique substitution, G540A, in the NS segment of H7N9 virus. 2017 Nature communications Result IV G540A 118 123 NS 132 134 28323816 An NS-segment exonic splicing enhancer regulates influenza A virus replication in mammalian cells. To verify that the G540A substitution affects ESE function in NEP mRNA splicing regulation, we compared NEP/NS1 mRNA ratios in WT and A540G mutant virus-infected cells using primer sets to specifically amplify NEP and NS1 mRNAs. 2017 Nature communications Result IV G540A;A540G 19;134 24;139 NEP;NEP;NEP;NS1;NS1 62;104;210;108;218 65;107;213;111;221 28323816 An NS-segment exonic splicing enhancer regulates influenza A virus replication in mammalian cells. To verify the contention that the effect of G540A is due to the nucleotide substitution, rather than the change of amino acid at position 172, stop codons were introduced at different positions within the NS1 open reading frame to interrupt protein translation from the plasmid. 2017 Nature communications Result IV G540A 44 49 NS1 205 208 28323816 An NS-segment exonic splicing enhancer regulates influenza A virus replication in mammalian cells. we also tested a mutant H7N9 virus containing a C539U back mutation in the NS segment, both alone and in combination with A540G, and found that back mutation at position 539 did not affect virus replication in A549 cells. 2017 Nature communications Result IV A540G 122 127 NS 75 77 28323816 An NS-segment exonic splicing enhancer regulates influenza A virus replication in mammalian cells. We then analysed mRNA levels of cytokines in the lungs of these mice, but found no significant difference between WT and A540G virus-infected mice. 2017 Nature communications Result IV A540G 121 126 28402848 The 150-Loop Restricts the Host Specificity of Human H10N8 Influenza Virus. As a consequence of the Q226L mutation, hydrophobic interaction between Leu226 and Gal-2 C6 stabilizes binding of the human analog. 2017 Cell reports Result IV Q226L 24 29 28402848 The 150-Loop Restricts the Host Specificity of Human H10N8 Influenza Virus. As we have previously shown, introducing Q226L, G228S or Q226L-G228S (H10LS) mutations in WT H10 HA results in loss of binding to alpha2-3 sialosides with no gain in binding to human-type alpha2-6 receptors (Figure 1C4; Figure S1D3-4). 2017 Cell reports Result IV Q226L;G228S;Q226L;G228S 41;48;57;63 46;53;62;68 HA 97 99 28402848 The 150-Loop Restricts the Host Specificity of Human H10N8 Influenza Virus. D193T on wt H10 reduced binding to avian-type receptors (Figure S1D6) and on H10LS resulted in gain of binding to human-type receptors with only weak residual binding to avian-type receptors (Figure S1D7). 2017 Cell reports Result IV D193T 0 5 28402848 The 150-Loop Restricts the Host Specificity of Human H10N8 Influenza Virus. Deletion of either K158a (H10DeltaK158a), or K158a and G158b (H10DeltaK158a-DeltaG158b), resulted in similar binding to avian analogs as for wt H10 HA (Figure S3A), whereas these deletions on H10LS and H10LS-D193T resulted in gain of binding to human analogs with minimal binding to avian analogs (Figures 3A and S3A3). 2017 Cell reports Result IV D193T 208 213 HA 148 150 28402848 The 150-Loop Restricts the Host Specificity of Human H10N8 Influenza Virus. For H10LS-K158aA and H10LS-D193T, electron density was observed for three sugars of 6'-SLNLN (Figure S2B). 2017 Cell reports Result IV D193T 27 32 28402848 The 150-Loop Restricts the Host Specificity of Human H10N8 Influenza Virus. For H10LS-K158aA-D193T, a significant increase in binding to alpha2-6 sialosides was detected (Kd 24.8-0.49 mug/ml), with slight reduction to alpha2-3 sialosides (Kd 1.55-0.84 mug/ml). 2017 Cell reports Result IV D193T 17 22 28402848 The 150-Loop Restricts the Host Specificity of Human H10N8 Influenza Virus. Further introduction of D193T (H10LS-K158aA-D193T) strongly increased binding to human trachea epithelium (Figure 4B4). 2017 Cell reports Result IV D193T;D193T 24;44 29;49 28402848 The 150-Loop Restricts the Host Specificity of Human H10N8 Influenza Virus. However, Sia-1 interactions with the 220-loop differ from wt H10 HA due to the Q226L and G228S mutations that result in loss of two hydrogen bonds to Sia-1. 2017 Cell reports Result IV Q226L;G228S 79;89 84;94 HA 65 67 28402848 The 150-Loop Restricts the Host Specificity of Human H10N8 Influenza Virus. In addition, the G228S mutation displaces Sia-1 ~1 A from the 220-loop towards the 130-loop (Figure 2C) and loss of interaction with His183 (Figure S2C). 2017 Cell reports Result IV G228S 17 22 28402848 The 150-Loop Restricts the Host Specificity of Human H10N8 Influenza Virus. In contrast to its binding to human trachea, the H10LS-K158aA-D193T mutant exhibited markedly reduced binding to chicken trachea epithelium relative to H10 wt HA (Figure S4 D1 vs D2), although staining with higher concentrations of HA exhibited clear binding to chicken trachea epithelium (Figure S4E2), consistent with weak binding in glycan arrays and strong binding in the glycan ELISA (Figure 1D). 2017 Cell reports Result IV D193T 62 67 HA;HA 159;232 161;234 28402848 The 150-Loop Restricts the Host Specificity of Human H10N8 Influenza Virus. Sh2H7 HA already contains Leu at position 226, but mutation of Gly226 to Ser still maintains avian specificity (; de Vries et al., submitted). 2017 Cell reports Result IV G226S 63 76 HA 6 8 28402848 The 150-Loop Restricts the Host Specificity of Human H10N8 Influenza Virus. Sia-1 makes a hydrophobic interaction with Trp153 and hydrogen bonds with Tyr98, 130-loop and 190-helix, but not with the 220-loop, due to the Q226L and G228S mutations. 2017 Cell reports Result IV Q226L;G228S 143;153 148;158 28402848 The 150-Loop Restricts the Host Specificity of Human H10N8 Influenza Virus. Significantly, D193T on H10LS-K158aA (H10LS-K158aA-D193T) produced strong binding to human-type receptors (Figure 1C6) represented by long, branched, N-linked glycans (#121-131) (Table S1) similar to A/Cal/04/09 pandemic H1N1 and A/Beijing/353/1989 H3N2 HAs (Figure S1D2). 2017 Cell reports Result IV D193T;D193T 15;51 20;56 28402848 The 150-Loop Restricts the Host Specificity of Human H10N8 Influenza Virus. Similar results were obtained by introducing D193T onto H10LS-K158aG where binding was also observed to long, branched, O-linked human-type receptors (# 107-111) (Figure S1D8). 2017 Cell reports Result IV D193T 45 50 28402848 The 150-Loop Restricts the Host Specificity of Human H10N8 Influenza Virus. Superposition of the H10LS-K158aA-D193T mutant with H10 wt reveals differences in the human analog conformation mainly arising from changes in the phi (from ~35 in wt to ~76 in the mutant) and psi (from ~173 to ~155 ) angles of the Sia-Gal bond (Figure 2C). 2017 Cell reports Result IV D193T 34 39 28402848 The 150-Loop Restricts the Host Specificity of Human H10N8 Influenza Virus. The crystal structure of H10LS-K158aA-D193T HA with human receptor analogue 6'-SLNLN (NeuAcalpha2-6Galbeta1-4GlcNAcbeta1-3Galbeta1-4GlcNA) (Figure 2A; Table S3) exhibited electron density for three of the five sugars in the RBS of protomers A and C (Figure S2B), but only Sia-1 in protomer B. 2017 Cell reports Result IV D193T 38 43 HA 44 46 28402848 The 150-Loop Restricts the Host Specificity of Human H10N8 Influenza Virus. The human analog conformation in H10LS-K158aA resembles that in H10LS-K158aA-D193T but, in H10LS-D193T, the electron density is weaker and the Sia-Gal phi angle differs slightly (from ~76 to ~67 ) indicating that this change only slightly reduces the steric clash between Lys158a and 6'-SLNLN (Figures S2E and S2F). 2017 Cell reports Result IV D193T;D193T 97;77 102;82 28402848 The 150-Loop Restricts the Host Specificity of Human H10N8 Influenza Virus. To establish that binding to human trachea is sialic acid dependent, binding of H10wt and H10LS-K158aA-D193T was assessed after treatment with sialidase (Figures 4C3 and 4C4), which abolished binding to epithelial cells. 2017 Cell reports Result IV D193T 103 108 28402848 The 150-Loop Restricts the Host Specificity of Human H10N8 Influenza Virus. To evaluate the reduced binding of the H10 mutants to avian analogs, we determined the crystal structure of H10LS-K158aA-D193T with 3'-SLN (NeuAcalpha2-3Galbeta1-4GlcNAc); electron density was observed for all three sugars (Figure S2B; Table S3). 2017 Cell reports Result IV D193T 121 126 28402848 The 150-Loop Restricts the Host Specificity of Human H10N8 Influenza Virus. To examine the 150-loop in H7, we mutated Asp158a to Ala on the background of G228S, which resulted in gain of binding to human receptor analogs, although binding to avian analogs was maintained (Figure 3B). 2017 Cell reports Result IV G228S 78 83 28402848 The 150-Loop Restricts the Host Specificity of Human H10N8 Influenza Virus. To investigate the structural basis for change in receptor specificity, crystal structures of H10LS-K158aA-D193T, H10LS-K158aA and H10LS-D193T mutants were determined (Table S3) and were very similar to H10 wt (Ca RMSD of 0.38 A), but with the RBS being more accessible to human-type receptors, especially for the K158aA mutants (Figure S2A). 2017 Cell reports Result IV D193T;D193T 137;107 142;112 28402848 The 150-Loop Restricts the Host Specificity of Human H10N8 Influenza Virus. To quantify the change in the avidity of the H10 mutants, we used a glycan ELISA-type assay to assess binding of H10 wt and H10LS-K158aA-D193T to biantennary, N-linked sialosides with one to four LN repeats (LN1-4) (Figure 1D). 2017 Cell reports Result IV D193T 137 142 28410396 Evolution of the neuraminidase gene of seasonal influenza A and B viruses in Thailand between 2010 and 2015. Between 2009 and 2015, 6.4% of viruses circulating in Thailand of A(H1N1)pdm09 were H275Y strains, whereas, 1.4% had an S247N mutation. 2017 PloS one Result IV H275Y;S247N 84;120 89;125 28410396 Evolution of the neuraminidase gene of seasonal influenza A and B viruses in Thailand between 2010 and 2015. For A(H1N1)pdm09, strains with mutation S247N circulated in 2010 belonged to clade 2 (Fig 2). 2017 PloS one Result IV S247N 40 45 28410396 Evolution of the neuraminidase gene of seasonal influenza A and B viruses in Thailand between 2010 and 2015. For NA sequences of influenza B virus, the A395E NAI-resistant strains belonged to Victoria lineage (clade 1) (Fig 4). 2017 PloS one Result IV A395E 43 48 NA;NAI 4;49 6;52 28410396 Evolution of the neuraminidase gene of seasonal influenza A and B viruses in Thailand between 2010 and 2015. In addition, we found that the NA protein in influenza B was mutated at positions A245S (0.4%), K360R (0.9%), and A395V/T/D/S (12.5%). 2017 PloS one Result IV A245S;K360R;A395V;A395T;A395D;A395S 82;96;114;114;114;114 87;101;125;125;125;125 31 33 28410396 Evolution of the neuraminidase gene of seasonal influenza A and B viruses in Thailand between 2010 and 2015. In contrast, the H275Y oseltamivir-resistant strains that were circulated in other years were clustered separately: clade 1 (2009 season), clades 2, 5, and 7 (2010 season), clade 6A (2012 season), and clade 6B (2014 season). 2017 PloS one Result IV H275Y 17 22 28410396 Evolution of the neuraminidase gene of seasonal influenza A and B viruses in Thailand between 2010 and 2015. In the years after the influenza A virus pandemic of 2010, 485 samples tested positive for A(H1N1)pdm09 of which 4 (0.82%) were oseltamivir-resistant (H275Y) strains (S1 Fig and S2 Table). 2017 PloS one Result IV H275Y 151 156 28410396 Evolution of the neuraminidase gene of seasonal influenza A and B viruses in Thailand between 2010 and 2015. Most of the H275Y oseltamivir-resistant strains had the additional NA mutations at positions V106I, V241I, N248D, and N369K. 2017 PloS one Result IV H275Y;V106I;V241I;N248D;N369K 12;93;100;107;118 17;98;105;112;123 67 69 28410396 Evolution of the neuraminidase gene of seasonal influenza A and B viruses in Thailand between 2010 and 2015. Most of the strains with A395V/T/D substitutions were found in the Victoria lineages. 2017 PloS one Result IV A395V;A395T;A395D 25;25;25 34;34;34 28410396 Evolution of the neuraminidase gene of seasonal influenza A and B viruses in Thailand between 2010 and 2015. Most of these oseltamivir-resistant viruses (95%, 19/20) from 2007 to 2009 had a D354G mutation in the coding region when compared with the reference strain (A/Brisbane/59/2007). 2017 PloS one Result IV D354G 81 86 28410396 Evolution of the neuraminidase gene of seasonal influenza A and B viruses in Thailand between 2010 and 2015. Most of these strains (83.3%) had amino acid mutations at positions L81P, D93G, S367N, K369T, N402D, and I464L. 2017 PloS one Result IV L81P;D93G;S367N;K369T;N402D;I464L 68;74;80;87;94;105 72;78;85;92;99;110 28410396 Evolution of the neuraminidase gene of seasonal influenza A and B viruses in Thailand between 2010 and 2015. Only one D197N NAI-resistant isolate was classified in Yamagata lineage (clade 2). 2017 PloS one Result IV D197N 9 14 NAI 15 18 28410396 Evolution of the neuraminidase gene of seasonal influenza A and B viruses in Thailand between 2010 and 2015. The A(H3N2) viruses circulating in Thailand had amino acid substitutions at positions D151N/G (1.7%) and I222T/V (1.2%), which are in the active site of the NA protein and may affect enzyme activity. 2017 PloS one Result IV D151G;D151N;I222T;I222V 86;86;105;105 93;93;112;112 157 159 28410396 Evolution of the neuraminidase gene of seasonal influenza A and B viruses in Thailand between 2010 and 2015. The NB sequences of influenza B virus circulated in Thailand between 1990 and 2015 had an amino acid mutation at position D197N (0.4%), and an amino acid substitution at position A395E (1.7%) was also found. 2017 PloS one Result IV D197N;A395E 122;179 127;184 NB 4 6 28410396 Evolution of the neuraminidase gene of seasonal influenza A and B viruses in Thailand between 2010 and 2015. The strains with a D151N/G mutation were clustered separately in clades 3C.2 and 3C.3. 2017 PloS one Result IV D151N;D151G 19;19 26;26 28410396 Evolution of the neuraminidase gene of seasonal influenza A and B viruses in Thailand between 2010 and 2015. The strains with a I222T/V mutation were grouped into clade 3C.2; these two strains maintained the NA gene signature amino acid substitutions L81P, D93G, S367N, K369T, N402D, and I464L. 2017 PloS one Result IV I222T;I222V;L81P;D93G;S367N;K369T;N402D;I464L 19;19;142;148;154;161;168;179 26;26;146;152;159;166;173;184 99 101 28410396 Evolution of the neuraminidase gene of seasonal influenza A and B viruses in Thailand between 2010 and 2015. They possessed amino acid mutations at positions N248D, I389V, and V394I compared with the reference (strain A/California/07/2009) (Table 2). 2017 PloS one Result IV N248D;I389V;V394I 49;56;67 54;61;72 28418242 Slow but Steady Wins the Race: Dissimilarities among New Dual Inhibitors of the Wild-Type and the V27A Mutant M2 Channels of Influenza A Virus. As reference, Amt inhibited the wt A/M2 channel with an IC50 of 16.0 muM, while displaying much lower activity against the S31N mutant channel (IC50 of 200 muM), and being totally inactive against the V27A mutant. 2017 Journal of medicinal chemistry Result IV S31N;V27A 123;201 127;205 M2 37 39 28418242 Slow but Steady Wins the Race: Dissimilarities among New Dual Inhibitors of the Wild-Type and the V27A Mutant M2 Channels of Influenza A Virus. Compound 8, that did not inhibit the V27A channel (Table 1 and Figure 2H) but showed antiviral activity against the A/HK/7/87, was also assayed. 2017 Journal of medicinal chemistry Result IV V27A 37 41 28418242 Slow but Steady Wins the Race: Dissimilarities among New Dual Inhibitors of the Wild-Type and the V27A Mutant M2 Channels of Influenza A Virus. Hence, although compounds 2 and 7 can bind the V27A channel (Table 1), i. 2017 Journal of medicinal chemistry Result IV V27A 47 51 28418242 Slow but Steady Wins the Race: Dissimilarities among New Dual Inhibitors of the Wild-Type and the V27A Mutant M2 Channels of Influenza A Virus. In contrast, the inhibition of the V27A M2 mutant channel with 8 was already at steady-state after just 1 min (Figure 2H). 2017 Journal of medicinal chemistry Result IV V27A 35 39 M2 40 42 28418242 Slow but Steady Wins the Race: Dissimilarities among New Dual Inhibitors of the Wild-Type and the V27A Mutant M2 Channels of Influenza A Virus. In the case of the V27A mutant channel (right panels in Figure 2), compounds 2 and 7 had higher affinity (IC50 of 3.6 +- 0.6 and 16.2 +- 1.7 muM, respectively) compared with Amt (IC50 > 500 muM) and compound 8 (IC50 > 500 muM) (Table 1). 2017 Journal of medicinal chemistry Result IV V27A 19 23 28418242 Slow but Steady Wins the Race: Dissimilarities among New Dual Inhibitors of the Wild-Type and the V27A Mutant M2 Channels of Influenza A Virus. In the next step, the IC50 values for the compounds that inhibited the V27A channel by more than 60% were obtained using an isochronic (2 min) inhibition assay. 2017 Journal of medicinal chemistry Result IV V27A 71 75 28418242 Slow but Steady Wins the Race: Dissimilarities among New Dual Inhibitors of the Wild-Type and the V27A Mutant M2 Channels of Influenza A Virus. Indeed, the inhibitory effect increases from 48.1 (8) to 92% (2) in the wt M2 channel, and from 10.1 (8) to 85.7% (2) in the V27A mutant M2 channel. 2017 Journal of medicinal chemistry Result IV V27A 125 129 M2;M2 75;137 77;139 28418242 Slow but Steady Wins the Race: Dissimilarities among New Dual Inhibitors of the Wild-Type and the V27A Mutant M2 Channels of Influenza A Virus. Interestingly, the case of compound 2 clearly exemplifies the different outcomes in the wt and V27A channels: although this compound has similar IC50 values (4.1 and 3.6 muM, respectively, Table 1), the faster koff in the mutated channel, probably reflecting a worse fitting to the wider pore, allows the compound to be washed away, revoking the channel blockade. 2017 Journal of medicinal chemistry Result IV V27A 95 99 28418242 Slow but Steady Wins the Race: Dissimilarities among New Dual Inhibitors of the Wild-Type and the V27A Mutant M2 Channels of Influenza A Virus. Moving the adamantane ring from position 2, as found in 8 and in the family of compounds reported by Kolocouris et al., to position 4 of the piperidine, as in the rest of our new inhibitors, had a clear incremental effect on the inhibitory activity for both wt and V27A channels. 2017 Journal of medicinal chemistry Result IV V27A 265 269 28418242 Slow but Steady Wins the Race: Dissimilarities among New Dual Inhibitors of the Wild-Type and the V27A Mutant M2 Channels of Influenza A Virus. On the other hand, since the lumen of the V27A M2 protein is wider than that of the wt channel, size-expanded Amt derivatives may lead to better inhibition of the V27A mutant channel. 2017 Journal of medicinal chemistry Result IV V27A;V27A 42;163 46;167 M2 47 49 28418242 Slow but Steady Wins the Race: Dissimilarities among New Dual Inhibitors of the Wild-Type and the V27A Mutant M2 Channels of Influenza A Virus. Only the 1-adamantyl substituted derivative 2 showed minimal antiviral activity against a virus carrying the V27A A/M2 mutant channel, despite its potent channel blockage. 2017 Journal of medicinal chemistry Result IV V27A 109 113 M2 116 118 28418242 Slow but Steady Wins the Race: Dissimilarities among New Dual Inhibitors of the Wild-Type and the V27A Mutant M2 Channels of Influenza A Virus. Overall, these findings add valuable insights into the drug-resistance mechanism postulated for the V27A mutation. 2017 Journal of medicinal chemistry Result IV V27A 100 104 28418242 Slow but Steady Wins the Race: Dissimilarities among New Dual Inhibitors of the Wild-Type and the V27A Mutant M2 Channels of Influenza A Virus. Several novel compounds were low micromolar blockers of the wt A/M2 channel and/or the V27A A/M2 variant. 2017 Journal of medicinal chemistry Result IV V27A 87 91 M2;M2 65;94 67;96 28418242 Slow but Steady Wins the Race: Dissimilarities among New Dual Inhibitors of the Wild-Type and the V27A Mutant M2 Channels of Influenza A Virus. Similar trends were also observed from the inhibitory data determined against the V27A mutant. 2017 Journal of medicinal chemistry Result IV V27A 82 86 28418242 Slow but Steady Wins the Race: Dissimilarities among New Dual Inhibitors of the Wild-Type and the V27A Mutant M2 Channels of Influenza A Virus. Surprisingly, while their blocking abilities in the wt M2 channel nicely correlated with their antiviral activity in a wt-containing influenza A virus, there was a lack of correlation between their V27A channel blockage and antiviral activity of a V27A-containing influenza A virus. 2017 Journal of medicinal chemistry Result IV V27A;V27A 198;248 202;252 M2 55 57 28418242 Slow but Steady Wins the Race: Dissimilarities among New Dual Inhibitors of the Wild-Type and the V27A Mutant M2 Channels of Influenza A Virus. The activity of the compounds has been tested against the wt M2 channel as well as the V27A and S31N mutant forms in the two-electrode voltage clamp (TEVC) assay. 2017 Journal of medicinal chemistry Result IV V27A;S31N 87;96 91;100 M2 61 63 28418242 Slow but Steady Wins the Race: Dissimilarities among New Dual Inhibitors of the Wild-Type and the V27A Mutant M2 Channels of Influenza A Virus. The anti-influenza virus activity of compounds 2, 3, 7 and 19, that inhibited the V27A channel (Table 1), was also determined in MDCK cells using a 46-h virus PRA with the A/WSN/33 virus (H1N1 subtype), which carries a N31S/V27A M2 protein. 2017 Journal of medicinal chemistry Result IV V27A;V27A;N31S 82;224;219 86;228;223 M2 229 231 28418242 Slow but Steady Wins the Race: Dissimilarities among New Dual Inhibitors of the Wild-Type and the V27A Mutant M2 Channels of Influenza A Virus. This behavior agrees with the resistance mechanism proposed for Amt in the V27A mutant. 2017 Journal of medicinal chemistry Result IV V27A 75 79 28418242 Slow but Steady Wins the Race: Dissimilarities among New Dual Inhibitors of the Wild-Type and the V27A Mutant M2 Channels of Influenza A Virus. This change triggered a substantial increase of the inhibitory activity against both wt and V27A channels, as noted in the 11- and 17-fold reduction of the IC50 observed between compounds 3 and 2. 2017 Journal of medicinal chemistry Result IV V27A 92 96 28418242 Slow but Steady Wins the Race: Dissimilarities among New Dual Inhibitors of the Wild-Type and the V27A Mutant M2 Channels of Influenza A Virus. This fact correlates with the antiviral activity assays (see above), justifying that some compounds with promising V27A mutant M2 channel blockade activities fail to behave as good antivirals likely due to fast dissociation (fast koff rate). 2017 Journal of medicinal chemistry Result IV V27A 115 119 M2 127 129 28418242 Slow but Steady Wins the Race: Dissimilarities among New Dual Inhibitors of the Wild-Type and the V27A Mutant M2 Channels of Influenza A Virus. To further characterize the inhibitory effects on wt and V27A channels and rationalize the antiviral results, the current kinetics of the most potent channel blockers 2, 7, 8, 19 and 20 were determined and compared with the profile obtained for Amt (Figure 2 and Table 3; see also results for 19 and 20 in SI). 2017 Journal of medicinal chemistry Result IV V27A 57 61 28418242 Slow but Steady Wins the Race: Dissimilarities among New Dual Inhibitors of the Wild-Type and the V27A Mutant M2 Channels of Influenza A Virus. Unluckily, none of the tested molecules had activity against the S31N channel (<10%) (data not shown). 2017 Journal of medicinal chemistry Result IV S31N 65 69 28433777 Design and expeditious synthesis of organosilanes as potent antivirals targeting multidrug-resistant influenza A viruses. Channel blockage, antiviral efficacy, and cytotoxicity of organosilane-based AM2-S31N inhibitors. 2017 European journal of medicinal chemistry Result IV S31N 81 85 28433777 Design and expeditious synthesis of organosilanes as potent antivirals targeting multidrug-resistant influenza A viruses. Compounds 5d and 5e both had slightly reduced percentage channel blockage against the AM2-S31N channel when compared with compound 5b, and both were also less potent than 5b in terms of their antiviral activity. 2017 European journal of medicinal chemistry Result IV S31N 90 94 28433777 Design and expeditious synthesis of organosilanes as potent antivirals targeting multidrug-resistant influenza A viruses. However, the difference between compounds 5b and 10 was more obvious, with the organosilane 5b being more potent than its carbon analogue 10 in blocking the AM2-S31N channel (86.7 +- 0.7% versus 75.4 +- 2.3%). 2017 European journal of medicinal chemistry Result IV S31N 161 165 28433777 Design and expeditious synthesis of organosilanes as potent antivirals targeting multidrug-resistant influenza A viruses. Molecular docking of organosilane 5b in the AM2-S31N channel. 2017 European journal of medicinal chemistry Result IV S31N 48 52 28433777 Design and expeditious synthesis of organosilanes as potent antivirals targeting multidrug-resistant influenza A viruses. None of the compounds showed significant inhibition (>35%) against the AM2-WT channel, which was expected since these compounds were designed to target the drug-resistant AM2-S31N channel, not the WT-AM2. 2017 European journal of medicinal chemistry Result IV S31N 175 179 28433777 Design and expeditious synthesis of organosilanes as potent antivirals targeting multidrug-resistant influenza A viruses. organosilane 5b binds to the AM2-S31N channel with its trimethylsilyl-substituted benzene ring facing towards the N-terminus of the channel. 2017 European journal of medicinal chemistry Result IV S31N 33 37 28433777 Design and expeditious synthesis of organosilanes as potent antivirals targeting multidrug-resistant influenza A viruses. Substituting benzene with pyridine led to a slight increase in AM2-S31N channel inhibition (5c vs 5a). 2017 European journal of medicinal chemistry Result IV S31N 67 71 28433777 Design and expeditious synthesis of organosilanes as potent antivirals targeting multidrug-resistant influenza A viruses. The common feature among these influenza A strains is that they all contain the AM2-S31N mutation in their M2 genes, which explains their drug sensitivity to organosilane 5b. 2017 European journal of medicinal chemistry Result IV S31N 84 88 M2 107 109 28433777 Design and expeditious synthesis of organosilanes as potent antivirals targeting multidrug-resistant influenza A viruses. The increased potency might be a result of the favorable hydrophobic interaction between the hydrophobic trimethylsilyl group from 5b and the valine side chain methyls located at the N-terminus of the AM2-S31N channel. 2017 European journal of medicinal chemistry Result IV S31N 205 209 28433777 Design and expeditious synthesis of organosilanes as potent antivirals targeting multidrug-resistant influenza A viruses. The solution NMR structure of AM2-S31N channel (PDB: 2LY0) was used for the docking. 2017 European journal of medicinal chemistry Result IV S31N 34 38 28433777 Design and expeditious synthesis of organosilanes as potent antivirals targeting multidrug-resistant influenza A viruses. The viruses tested include multidrug-resistant strains such as the A/Denmark/528/2009 (H1N1), A/Washington/29/2009 (H1N1), and A/Texas/04/2009 (H1N1), all of which are resistant to both amantadine and oseltamivir due to AM2-S31N and H275Y mutations in their M2 and neuraminidase genes, respectively. 2017 European journal of medicinal chemistry Result IV S31N;H275Y 224;233 228;238 M2;NA 258;265 260;278 28433777 Design and expeditious synthesis of organosilanes as potent antivirals targeting multidrug-resistant influenza A viruses. This prediction is validated by the antiviral assay result which showed that compound 5f was not active in inhibiting the AM2-S31N-containing A/WSN/33 (H1N1) virus (EC50 > 10 muM, Table 1). 2017 European journal of medicinal chemistry Result IV S31N 126 130 28433777 Design and expeditious synthesis of organosilanes as potent antivirals targeting multidrug-resistant influenza A viruses. To gain further insights how organosilane 5b binds to the AM2-S31N channel, molecular docking was performed. 2017 European journal of medicinal chemistry Result IV S31N 62 66 28433777 Design and expeditious synthesis of organosilanes as potent antivirals targeting multidrug-resistant influenza A viruses. To validate the design hypothesis, the synthesized organosilanes were tested for their AM2-S31N channel blockage, antiviral activity, and cellular cytotoxicity by electrophysiological two-electrode voltage clamp (TEVC) assay, plaque assay, and neutral red assay, respectively (Table 1). 2017 European journal of medicinal chemistry Result IV S31N 91 95 28465552 A reassortant H9N2 influenza virus containing 2009 pandemic H1N1 internal-protein genes acquired enhanced pig-to-pig transmission after serial passages in swine. the substitution of aspartic acid by glycine at position 225 of the HA RBS (HA-D225G). 2017 Scientific reports Result IV D225G;D225G 79;20 84;60 HA;HA 68;76 70;78 28465552 A reassortant H9N2 influenza virus containing 2009 pandemic H1N1 internal-protein genes acquired enhanced pig-to-pig transmission after serial passages in swine. Two other mutations appeared de novo after transmission at a frequency >15%: a substitution of alanine to valine at position 115 of the NS1 and a substitution of threonine to alanine at position 58 of the PB2. 2017 Scientific reports Result IV A115V;T58A 95;162 128;197 NS1;PB2 136;205 139;208 28477572 Host dihydrofolate reductase (DHFR)-directed cycloguanil analogues endowed with activity against influenza virus and respiratory syncytial virus. At 100 muM, neither of the three compounds significantly inhibited the wild type or S31N mutant M2 channel, thus excluding M2 inhibition as the antiviral mechanism of action in virus-infected MDCK cells (data not shown). 2017 European journal of medicinal chemistry Result IV S31N 84 88 M2;M2 96;123 98;125 28477572 Host dihydrofolate reductase (DHFR)-directed cycloguanil analogues endowed with activity against influenza virus and respiratory syncytial virus. The A/Virginia/ATCC3/2009 strain, which has an S31N mutant M2 protein alike most currently circulating influenza A strains, had marginal to no sensitivity to the adamantane-based M2-blockers. 2017 European journal of medicinal chemistry Result IV S31N 47 51 M2;M2 59;179 61;181 28498306 A Conserved Residue, Tyrosine (Y) 84, in H5N1 Influenza A Virus NS1 Regulates IFN Signaling Responses to Enhance Viral Infection. A Y84F Mutation Abrogates NS1-Mediated Inhibition of Type I IFN Signaling. 2017 Viruses Result IV Y84F 2 6 NS1 26 29 28498306 A Conserved Residue, Tyrosine (Y) 84, in H5N1 Influenza A Virus NS1 Regulates IFN Signaling Responses to Enhance Viral Infection. A Y84F Mutation in the H5N1 NS1 Conserved Putative SH2-Binding Domain Affects the Ability for NS1 to Upregulate AKT Phosphorylation. 2017 Viruses Result IV Y84F 2 6 NS1;NS1 28;94 31;97 28498306 A Conserved Residue, Tyrosine (Y) 84, in H5N1 Influenza A Virus NS1 Regulates IFN Signaling Responses to Enhance Viral Infection. Accordingly, we used site-directed mutagenesis to introduce the Y84F mutation within the conserved H5N1 NS1 putative SH2-binding domain, to examine its contribution to NS1-mediated down-regulation of IFN-inducible STAT phosphorylation and IAV virulence. 2017 Viruses Result IV Y84F 64 68 NS1;NS1 104;168 107;171 28498306 A Conserved Residue, Tyrosine (Y) 84, in H5N1 Influenza A Virus NS1 Regulates IFN Signaling Responses to Enhance Viral Infection. Additionally, we observed increases in the expression of EIF2AK2 (24-fold), OAS1 (10-fold), IFNA4 (10-fold) and IFNB1 (10-fold) in the lungs of rWSN-GH-NS1-Y84F infected mice treated with IFN-beta on day 1 post-infection compared with the lungs of infected, but untreated mice (Figure 11B). 2017 Viruses Result IV Y84F 156 160 NS1 152 155 28498306 A Conserved Residue, Tyrosine (Y) 84, in H5N1 Influenza A Virus NS1 Regulates IFN Signaling Responses to Enhance Viral Infection. As anticipated, the results in Figure 2 reveal that 24 h post-transfection, cells expressing NS1-wt exhibit a 1.5-fold increase (significant p < 0.01) in AKT phosphorylation compared with cells expressing NS1-Y84F. 2017 Viruses Result IV Y84F 209 213 NS1;NS1 93;205 96;208 28498306 A Conserved Residue, Tyrosine (Y) 84, in H5N1 Influenza A Virus NS1 Regulates IFN Signaling Responses to Enhance Viral Infection. At 12 h post-IFN-beta-treatment, EIF2AK2 (Figure 6A) and MxA (Figure 6B) were induced in cells infected with rWSN-GH-NS1-Y84F, whereas cells infected with rWSN-GH-NS1-wt exhibited no ISG induction. 2017 Viruses Result IV Y84F 121 125 NS1;NS1 117;163 120;166 28498306 A Conserved Residue, Tyrosine (Y) 84, in H5N1 Influenza A Virus NS1 Regulates IFN Signaling Responses to Enhance Viral Infection. C57BL/6 mice received an intranasal inoculation of 1 x 105 PFU of either the rIAV expressing the NS1-wt or the rIAV expressing the NS1-Y84F. 2017 Viruses Result IV Y84F 135 139 NS1;NS1 97;131 100;134 28498306 A Conserved Residue, Tyrosine (Y) 84, in H5N1 Influenza A Virus NS1 Regulates IFN Signaling Responses to Enhance Viral Infection. Consistent with greater neutrophil numbers, mice infected with virus expressing NS1-wt exhibited 7.5-fold and 15-fold greater CXCL1 and CXCL2 gene expression, respectively, in their lungs compared with mice infected with virus expressing NS1-Y84F on day 1 post-infection (Figure 10C). 2017 Viruses Result IV Y84F 242 246 NS1;NS1 80;238 83;241 28498306 A Conserved Residue, Tyrosine (Y) 84, in H5N1 Influenza A Virus NS1 Regulates IFN Signaling Responses to Enhance Viral Infection. Flow cytometry analysis of lung infiltrates on day 1 post-infection showed that there were of the order of 1-log fold more neutrophils (CD45+, CD11b+, Ly6G+) in the lungs of rWSN-GH-NS1-wt infected mice compared with the lungs from mice infected with rWSN-GH-NS1-Y84F (Figure 10B). 2017 Viruses Result IV Y84F 263 267 NS1;NS1 182;259 185;262 28498306 A Conserved Residue, Tyrosine (Y) 84, in H5N1 Influenza A Virus NS1 Regulates IFN Signaling Responses to Enhance Viral Infection. Following IFN-beta treatment, we observed a greater reduction in M gene expression in A549 cells infected with rWSN-GH-NS1-Y84F, compared to cells infected with rWSN-GH-NS1-wt (Figure 6C). 2017 Viruses Result IV Y84F 123 127 M;NS1;NS1 65;119;169 66;122;172 28498306 A Conserved Residue, Tyrosine (Y) 84, in H5N1 Influenza A Virus NS1 Regulates IFN Signaling Responses to Enhance Viral Infection. Furthermore, mice infected with virus expressing NS1-wt had higher lung viral titers than mice infected with virus expressing NS1-Y84F on days 1 and 3 post-infection (Figure 9B). 2017 Viruses Result IV Y84F 130 134 NS1;NS1 49;126 52;129 28498306 A Conserved Residue, Tyrosine (Y) 84, in H5N1 Influenza A Virus NS1 Regulates IFN Signaling Responses to Enhance Viral Infection. Having demonstrated that expression of NS1-wt reduces cell surface IFNAR1 expression, we likewise examined whether the NS1-Y84F mutant would affect IFNAR1 cell surface expression. 2017 Viruses Result IV Y84F 123 127 NS1;NS1 39;119 42;122 28498306 A Conserved Residue, Tyrosine (Y) 84, in H5N1 Influenza A Virus NS1 Regulates IFN Signaling Responses to Enhance Viral Infection. Here, we show that the levels of IFN-inducible STAT1 and STAT2 phosphorylation are unaffected in cells expressing the mutant NS1-Y84F, compared with a reduction in cells expressing NS1-wt (Figure 3). 2017 Viruses Result IV Y84F 129 133 NS1;NS1 125;181 128;184 28498306 A Conserved Residue, Tyrosine (Y) 84, in H5N1 Influenza A Virus NS1 Regulates IFN Signaling Responses to Enhance Viral Infection. In a first series of experiments, we examined the effects of expression of the wildtype NS1 (NS1-wt) or Y84F mutation (NS1-Y84F) in HeLa cells on AKT phosphorylation, a signaling effector downstream of PI3K. 2017 Viruses Result IV Y84F;Y84F 104;123 108;127 NS1;NS1;NS1 88;93;119 91;96;122 28498306 A Conserved Residue, Tyrosine (Y) 84, in H5N1 Influenza A Virus NS1 Regulates IFN Signaling Responses to Enhance Viral Infection. In addition, A549 cells infected with rWSN-GH-NS1-Y84F produced approximately 1.7-fold and 2.6-fold more IFN-beta than cells infected with rWSN-GH-NS1-wt. 2017 Viruses Result IV Y84F 50 54 NS1;NS1 46;147 49;150 28498306 A Conserved Residue, Tyrosine (Y) 84, in H5N1 Influenza A Virus NS1 Regulates IFN Signaling Responses to Enhance Viral Infection. In comparison to rWSN-GH-NS1-wt infected mice, we show that IFN-beta production is elevated in the lungs of rWSN-GH-NS1-Y84F infected mice on both days 1 and 3 post-infection (Figure 9C). 2017 Viruses Result IV Y84F 120 124 NS1;NS1 25;116 28;119 28498306 A Conserved Residue, Tyrosine (Y) 84, in H5N1 Influenza A Virus NS1 Regulates IFN Signaling Responses to Enhance Viral Infection. In contrast, both rIAVs replicated in STAT1-/- MEFs with rWSN-GH-NS1-wt and rWSN-GH-NS1-Y84F viral titers increasing by approximately 7.6- and 10.9-fold, respectively (Figure 8). 2017 Viruses Result IV Y84F 88 92 NS1;NS1 65;84 68;87 28498306 A Conserved Residue, Tyrosine (Y) 84, in H5N1 Influenza A Virus NS1 Regulates IFN Signaling Responses to Enhance Viral Infection. In STAT1+/+ MEFs, viral titers increased by approximately 2.6-fold for rWSN-GH-NS1-wt between 6 and 36 h post-infection, whereas a marginal 1.5-fold increase in viral titers was observed for rWSN-GH-NS1-Y84F. 2017 Viruses Result IV Y84F 203 207 NS1;NS1 79;199 82;202 28498306 A Conserved Residue, Tyrosine (Y) 84, in H5N1 Influenza A Virus NS1 Regulates IFN Signaling Responses to Enhance Viral Infection. In subsequent experiments, we infected STAT1+/+ and STAT1-/- MEFs with the rIAVs to further determine whether the differences in viral replication that we observed between rWSN-GH-NS1-wt and rWSN-GH-NS1-Y84F were due primarily to effects of NS1 on the IFN-alpha/beta response. 2017 Viruses Result IV Y84F 203 207 NS1;NS1;NS1 180;199;241 183;202;244 28498306 A Conserved Residue, Tyrosine (Y) 84, in H5N1 Influenza A Virus NS1 Regulates IFN Signaling Responses to Enhance Viral Infection. Lung histology and H&E staining revealed more cell infiltrates in the lungs of rWSN-GH-NS1-wt infected mice compared with mice infected with rWSN-GH-NS1-Y84F (Figure 10A). 2017 Viruses Result IV Y84F 153 157 NS1;NS1 87;149 90;152 28498306 A Conserved Residue, Tyrosine (Y) 84, in H5N1 Influenza A Virus NS1 Regulates IFN Signaling Responses to Enhance Viral Infection. Mice infected with virus expressing the mutant NS1-Y84F lost less than 5% of their starting body weight by day 3 post-infection, whereas mice infected with virus expressing the NS1-wt lost greater than 10% of their starting body weight over the same time period (Figure 9A). 2017 Viruses Result IV Y84F 51 55 NS1;NS1 47;177 50;180 28498306 A Conserved Residue, Tyrosine (Y) 84, in H5N1 Influenza A Virus NS1 Regulates IFN Signaling Responses to Enhance Viral Infection. Next, we conducted a series of experiments to investigate whether, as we had observed for HeLa cells expressing NS1-wt or NS1-Y84F, an intact putative SH2-binding domain influences the response to IFN-beta treatment. 2017 Viruses Result IV Y84F 126 130 NS1;NS1 112;122 115;125 28498306 A Conserved Residue, Tyrosine (Y) 84, in H5N1 Influenza A Virus NS1 Regulates IFN Signaling Responses to Enhance Viral Infection. Next, we performed a series of experiments to examine the effects of the Y84F mutation on the ability of NS1 to regulate the type I IFN signaling response. 2017 Viruses Result IV Y84F 73 77 NS1 105 108 28498306 A Conserved Residue, Tyrosine (Y) 84, in H5N1 Influenza A Virus NS1 Regulates IFN Signaling Responses to Enhance Viral Infection. Notably, IFN-beta doses of 100 and 1000 U/mL reduced viral titers in rWSN-GH-NS1-Y84F infected A549s to <10 PFU/mL. 2017 Viruses Result IV Y84F 81 85 NS1 77 80 28498306 A Conserved Residue, Tyrosine (Y) 84, in H5N1 Influenza A Virus NS1 Regulates IFN Signaling Responses to Enhance Viral Infection. Our measurements of virus in culture supernatants revealed that IFN-beta treatment for 36 h reduced viral titers in a dose-dependent manner, albeit to a greater extent in the cells infected with rWSN-GH-NS1-Y84F: 1000 U/mL of IFN-beta reduced the viral titer of rWSN-GH-NS1-wt by 1-log (17-fold), in comparison to 50 U/mL of IFN-beta that reduced the titer of rWSN-GH-NS1-Y84F by 1-log (40-fold; Figure 6D). 2017 Viruses Result IV Y84F;Y84F 207;372 211;376 NS1;NS1;NS1 203;270;368 206;273;371 28498306 A Conserved Residue, Tyrosine (Y) 84, in H5N1 Influenza A Virus NS1 Regulates IFN Signaling Responses to Enhance Viral Infection. Specifically, A549 cells were infected with rWSN-GH-NS1-wt or rWSN-GH-NS1-Y84F at a MOI of 0.01 for 12 h, and then treated with varying doses of IFN-beta. 2017 Viruses Result IV Y84F 74 78 NS1;NS1 52;70 55;73 28498306 A Conserved Residue, Tyrosine (Y) 84, in H5N1 Influenza A Virus NS1 Regulates IFN Signaling Responses to Enhance Viral Infection. Studies were conducted in C57BL/6 mice to compare the infectivity of rWSN-GH-NS1-wt with rWSN-GH-NS1-Y84F, following intranasal inoculation. 2017 Viruses Result IV Y84F 101 105 NS1;NS1 77;97 80;100 28498306 A Conserved Residue, Tyrosine (Y) 84, in H5N1 Influenza A Virus NS1 Regulates IFN Signaling Responses to Enhance Viral Infection. The data in Figure 4 reveal that in contrast to NS1-wt expression, which reduces IFNAR1 but not IFNAR2 expression, NS1-Y84F expression has no effect on IFNAR1 or IFNAR2 expression. 2017 Viruses Result IV Y84F 119 123 NS1;NS1 48;115 51;118 28498306 A Conserved Residue, Tyrosine (Y) 84, in H5N1 Influenza A Virus NS1 Regulates IFN Signaling Responses to Enhance Viral Infection. The objective was to demonstrate that, in contrast to NS1-wt, which is known to induce AKT phosphorylation, NS1-Y84F would fail to increase AKT phosphorylation. 2017 Viruses Result IV Y84F 112 116 NS1;NS1 54;108 57;111 28498306 A Conserved Residue, Tyrosine (Y) 84, in H5N1 Influenza A Virus NS1 Regulates IFN Signaling Responses to Enhance Viral Infection. This 12 h time point post-infection was selected to allow for NS1-wt or NS1-Y84F to be expressed in infected cells, yet early enough in the infection to preclude profound differences in viral titers. 2017 Viruses Result IV Y84F 76 80 NS1;NS1 62;72 65;75 28498306 A Conserved Residue, Tyrosine (Y) 84, in H5N1 Influenza A Virus NS1 Regulates IFN Signaling Responses to Enhance Viral Infection. This in silico model shows that residue Y84 in the H5N1 NS1 putative SH2-binding domain may interact via hydrogen bonding with residue D569 in the p85beta i-SH2 domain and that a Y84F substitution eliminates this interaction (Figure 1B). 2017 Viruses Result IV Y84F 179 183 NS1 56 59 28498306 A Conserved Residue, Tyrosine (Y) 84, in H5N1 Influenza A Virus NS1 Regulates IFN Signaling Responses to Enhance Viral Infection. This NS1-p85beta binding has been ascribed to an SH2-binding domain in NS1, since a tyrosine to phenylalanine mutation at residue 89 (Y89F), within this domain, abrogated NS1 binding to host cell p85beta and reduced IAV replication. 2017 Viruses Result IV Y89F;Y89F 134;84 138;132 NS1;NS1;NS1 5;71;171 8;74;174 28498306 A Conserved Residue, Tyrosine (Y) 84, in H5N1 Influenza A Virus NS1 Regulates IFN Signaling Responses to Enhance Viral Infection. Time course studies in A549 human lung epithelial cells revealed that rWSN-GH-NS1-wt grows to approximately 100-fold higher titers than rWSN-GH-NS1-Y84F (Figure 5A). 2017 Viruses Result IV Y84F 148 152 NS1;NS1 78;144 81;147 28498306 A Conserved Residue, Tyrosine (Y) 84, in H5N1 Influenza A Virus NS1 Regulates IFN Signaling Responses to Enhance Viral Infection. To examine the potential differential effects of IFN treatment on viral replication following infection with the different recombinant viruses, mice were infected with virus expressing the NS1-wt or virus expressing the NS1-Y84F mutant and at 8 h post-infection mice were treated with a single dose of 1 x 105 U of murine IFN-beta1. 2017 Viruses Result IV Y84F 224 228 NS1;NS1 189;220 192;223 28498306 A Conserved Residue, Tyrosine (Y) 84, in H5N1 Influenza A Virus NS1 Regulates IFN Signaling Responses to Enhance Viral Infection. To further examine the importance of this Y84 residue within the putative SH2-binding domain in H5N1 NS1, we generated rIAVs expressing either the H5N1 NS1-wt or NS1-Y84F: rWSN-GH-NS1-wt and rWSN-GH-NS1-Y84F, respectively. 2017 Viruses Result IV Y84F;Y84F 203;166 207;170 NS1;NS1;NS1;NS1;NS1 101;152;162;180;199 104;155;165;183;202 28498306 A Conserved Residue, Tyrosine (Y) 84, in H5N1 Influenza A Virus NS1 Regulates IFN Signaling Responses to Enhance Viral Infection. Viral titers increased for both rIAVs expressing NS1-wt and NS1-Y84F between days 1 and 3 post-infection. 2017 Viruses Result IV Y84F 64 68 NS1;NS1 49;60 52;63 28498306 A Conserved Residue, Tyrosine (Y) 84, in H5N1 Influenza A Virus NS1 Regulates IFN Signaling Responses to Enhance Viral Infection. We observed approximately 0.5 to 1-log fold greater expression of ISG15, EIF2AK2, OAS1, IFNA4, and IFNB1 in the lungs of rWSN-GH-NS1-Y84F infected mice on days 1 and 3 post-infection compared with the lungs of rWSN-GH-NS1-wt infected mice (Figure 9D). 2017 Viruses Result IV Y84F 133 137 NS1;NS1 129;218 132;221 28498306 A Conserved Residue, Tyrosine (Y) 84, in H5N1 Influenza A Virus NS1 Regulates IFN Signaling Responses to Enhance Viral Infection. While IFN-beta treatment did not alter the lung viral titers of mice infected with rWSN-GH-NS1-wt, we observed a marginal reduction in the lung viral titers of mice infected with rWSN-GH-NS1-Y84F on days 1 and 3 post-infection (Figure 11A). 2017 Viruses Result IV Y84F 191 195 NS1;NS1 91;187 94;190 28588133 Novel Nonreplicating Vaccinia Virus Vector Enhances Expression of Heterologous Genes and Suppresses Synthesis of Endogenous Viral Proteins. Although the two intermediate transcription factors A8 and A23 encoded by the A8R and A23R genes are each essential for virus replication, null mutants can be propagated in a cell line that constitutively expresses these proteins. 2017 mBio Result IV A8R;A23R 78;86 81;90 28588133 Novel Nonreplicating Vaccinia Virus Vector Enhances Expression of Heterologous Genes and Suppresses Synthesis of Endogenous Viral Proteins. Because MVA and the A23R deletion mutant are replication defective in mice, luminescence was largely restricted to the site of inoculation and was maximal on day 1 and gradually decreased thereafter. 2017 mBio Result IV A23R 20 24 28588133 Novel Nonreplicating Vaccinia Virus Vector Enhances Expression of Heterologous Genes and Suppresses Synthesis of Endogenous Viral Proteins. is based on a recombinant VACV in which the A23R open reading frame (ORF) was deleted and is therefore capable of expressing genes with only early promoters in noncomplementing cells. 2017 mBio Result IV A23R 44 48 28659482 Complete Genome Sequencing of Influenza A Viruses within Swine Farrow-to-Wean Farms Reveals the Emergence, Persistence, and Subsidence of Diverse Viral Genotypes. Additionally, annotation of the matrix genes (segment 7) using the NCBI Flu Annotation Web service (FLAN) identified a signature mutation (S31N) associated with resistance to the antiviral amantadine in 79% (n = 98) of the sequences, which was found in matrix genes with and without pandemic origins. 2017 Journal of virology Result IV S31N 139 143 M;M 32;253 38;259 28659482 Complete Genome Sequencing of Influenza A Viruses within Swine Farrow-to-Wean Farms Reveals the Emergence, Persistence, and Subsidence of Diverse Viral Genotypes. and a single polymorphic site had 3 polymorphic amino acids (VG7; I370L/S). 2017 Journal of virology Result IV I370L;I370S 66;66 73;73 28659482 Complete Genome Sequencing of Influenza A Viruses within Swine Farrow-to-Wean Farms Reveals the Emergence, Persistence, and Subsidence of Diverse Viral Genotypes. Only a single site in HA proteins had 3 polymorphic amino acids at this position (VG5; E503D/N), while all the other sites had only 2 polymorphic amino acids. 2017 Journal of virology Result IV E503D;E503N 87;87 94;94 HA 22 24 28744280 Amino Acid Substitution K470R in the Nucleoprotein Increases the Virulence of H5N1 Influenza A Virus in Mammals. Among these substitutions, K470R produced the highest levels of mRNA, cRNA, and vRNA, which were 10.8-fold, 2.6-fold, and 5.1-fold greater than those of rWT, respectively (Figure 5). 2017 Frontiers in microbiology Result IV K470R 27 32 28744280 Amino Acid Substitution K470R in the Nucleoprotein Increases the Virulence of H5N1 Influenza A Virus in Mammals. As shown in Figure 2, the K91R and K198R mutants displayed substantially lower luciferase activity than that of WT, while the K227R, K229R, and K470R mutants increased the polymerase activity by 1.4-, 1.5-, and 1.9-fold, respectively. 2017 Frontiers in microbiology Result IV K91R;K198R;K227R;K229R;K470R 26;35;126;133;144 30;40;131;138;149 28744280 Amino Acid Substitution K470R in the Nucleoprotein Increases the Virulence of H5N1 Influenza A Virus in Mammals. Effects of K227R, K229R, and K470R on the Synthesis of Viral mRNA, cRNA, and vRNA. 2017 Frontiers in microbiology Result IV K227R;K229R;K470R 11;18;29 16;23;34 28744280 Amino Acid Substitution K470R in the Nucleoprotein Increases the Virulence of H5N1 Influenza A Virus in Mammals. Effects of K227R, K229R, and K470R on Viral Pathogenicity in Mice. 2017 Frontiers in microbiology Result IV K227R;K229R;K470R 11;18;29 16;23;34 28744280 Amino Acid Substitution K470R in the Nucleoprotein Increases the Virulence of H5N1 Influenza A Virus in Mammals. Effects of K227R, K229R, and K470R on Virus Growth In Vitro. 2017 Frontiers in microbiology Result IV K227R;K229R;K470R 11;18;29 16;23;34 28744280 Amino Acid Substitution K470R in the Nucleoprotein Increases the Virulence of H5N1 Influenza A Virus in Mammals. Generation of NP K227R, K229R, and K470R Mutant Viruses. 2017 Frontiers in microbiology Result IV K227R;K229R;K470R 17;24;35 22;29;40 NP 14 16 28744280 Amino Acid Substitution K470R in the Nucleoprotein Increases the Virulence of H5N1 Influenza A Virus in Mammals. However, K91R and K198R mutants displayed cytoplasmic localization at 24 and 30 h p.t., respectively (Figures 3A,B). 2017 Frontiers in microbiology Result IV K91R;K198R 9;18 13;23 28744280 Amino Acid Substitution K470R in the Nucleoprotein Increases the Virulence of H5N1 Influenza A Virus in Mammals. In addition, the results of cytoplasmic and nuclear fractionation experiments also demonstrated that K91R and K198R mutations increased the cytoplasmic distribution of NP (Figure 3C). 2017 Frontiers in microbiology Result IV K91R;K198R 101;110 105;115 NP 168 170 28744280 Amino Acid Substitution K470R in the Nucleoprotein Increases the Virulence of H5N1 Influenza A Virus in Mammals. In contrast, four rK470R virus-infected mice died by day 8 (Figures 6A,B), consistent with the increased the virus growth of the K470R in mammalian cells. 2017 Frontiers in microbiology Result IV K470R 129 134 28744280 Amino Acid Substitution K470R in the Nucleoprotein Increases the Virulence of H5N1 Influenza A Virus in Mammals. In contrast, the K91R and K198R mutant viruses were not viable in three independent experiments, suggesting the two mutations in NP were critical for the viral life cycle. 2017 Frontiers in microbiology Result IV K91R;K198R 17;26 21;31 NP 129 131 28744280 Amino Acid Substitution K470R in the Nucleoprotein Increases the Virulence of H5N1 Influenza A Virus in Mammals. Minireplicon assays were performed to evaluate the impact of the NP substitutions K91R, K198R, K227R, K229R, and K470R on the polymerase activity in human embryonic kidney (293T) cells at 37 C. 2017 Frontiers in microbiology Result IV K91R;K198R;K227R;K229R;K470R 82;88;95;102;113 86;93;100;107;118 NP 65 67 28744280 Amino Acid Substitution K470R in the Nucleoprotein Increases the Virulence of H5N1 Influenza A Virus in Mammals. Mutations of several residues, such as the R8A and Y296F mutations, cause cytoplasmic accumulation of NP. 2017 Frontiers in microbiology Result IV R8A;Y296F 43;51 46;56 NP 102 104 28744280 Amino Acid Substitution K470R in the Nucleoprotein Increases the Virulence of H5N1 Influenza A Virus in Mammals. Our results indicated that K91R and K198R mutants likely lost the ability to support viral polymerase activity, resulting in the growth defects of the mutant viruses. 2017 Frontiers in microbiology Result IV K91R;K198R 27;36 31;41 28744280 Amino Acid Substitution K470R in the Nucleoprotein Increases the Virulence of H5N1 Influenza A Virus in Mammals. Plasmids encoding NP WT, K91R or K198R were transfected into 293T cells, and the transfected cells were fixed at 9, 24, and 30 h p.t. 2017 Frontiers in microbiology Result IV K91R;K198R 25;33 29;38 NP 18 20 28744280 Amino Acid Substitution K470R in the Nucleoprotein Increases the Virulence of H5N1 Influenza A Virus in Mammals. Taken together, these results indicated that K470R enhanced viral transcription and replication by increasing the synthesis of viral mRNA, cRNA, and vRNA in human cells. 2017 Frontiers in microbiology Result IV K470R 45 50 28744280 Amino Acid Substitution K470R in the Nucleoprotein Increases the Virulence of H5N1 Influenza A Virus in Mammals. The expression of viral protein (PB1, NA and PA) was almost similar in all of the wild-type (WT) and mutant NP-transfected cells, although the NP expression level in K91R, K198R and K227R was lower than that of wild-type (Figure 1A). 2017 Frontiers in microbiology Result IV K91R;K198R;K227R 166;172;182 170;177;187 NA;NP;NP;PA;PB1 38;108;143;45;33 40;110;145;47;36 28744280 Amino Acid Substitution K470R in the Nucleoprotein Increases the Virulence of H5N1 Influenza A Virus in Mammals. The lung index and the virus titer of rK470R-infected mice were higher than other groups (Figures 6C,D). 2017 Frontiers in microbiology Result IV K470R 39 44 28744280 Amino Acid Substitution K470R in the Nucleoprotein Increases the Virulence of H5N1 Influenza A Virus in Mammals. Therefore, the K470R mutants enhanced virus growth of H5N1 in mammalian cells in a single cycle growth curve. 2017 Frontiers in microbiology Result IV K470R 15 20 28744280 Amino Acid Substitution K470R in the Nucleoprotein Increases the Virulence of H5N1 Influenza A Virus in Mammals. To determine the function of five lysines (K91, K198, K227, K229, and K470) in NP, we performed site-directed mutagenesis to replace the lysine (K) residues with arginine (R) and generated the K91R, K198R, K227R, K229R, and K470R recombinant viruses using plasmid-driven reverse genetics. 2017 Frontiers in microbiology Result IV K470R;K91R;K198R;K227R;K229R 224;193;199;206;213 229;197;204;211;218 NP 79 81 28744280 Amino Acid Substitution K470R in the Nucleoprotein Increases the Virulence of H5N1 Influenza A Virus in Mammals. Together, our results indicated that the K470R mutant increased the virus growth in mammalian cells, while the K229R suppressed the virus growth and the K227R had no effect. 2017 Frontiers in microbiology Result IV K470R;K229R;K227R 41;111;153 46;116;158 28744280 Amino Acid Substitution K470R in the Nucleoprotein Increases the Virulence of H5N1 Influenza A Virus in Mammals. Together, our results showed that NP-K91R/K198R disrupted the cellular location of NP. 2017 Frontiers in microbiology Result IV K91R;K198R 37;42 41;47 NP;NP 34;83 36;85 28790432 Conformational modulation of influenza virus hemagglutinin: characterization and in vivo efficacy of monomeric form. F88E existed as monomers and trimers, whereas a trimer was dominant in V91W. 2017 Scientific reports Result IV F88E;V91W 0;71 4;75 28790432 Conformational modulation of influenza virus hemagglutinin: characterization and in vivo efficacy of monomeric form. Four mutants were trimers upon removal of the foldon, like the CU44 wild-type HA, whereas two mutants, F88E and V91W, were detected as monomers in solution. 2017 Scientific reports Result IV F88E;V91W 103;112 107;116 HA 78 80 28790432 Conformational modulation of influenza virus hemagglutinin: characterization and in vivo efficacy of monomeric form. In order to further destabilize the HA trimer, we produced the double mutant F88E/V91W. 2017 Scientific reports Result IV V91W;F88E 82;77 86;81 HA 36 38 28790432 Conformational modulation of influenza virus hemagglutinin: characterization and in vivo efficacy of monomeric form. It appears that F88E has a higher tendency to destabilize the trimer than V91W, revealing higher proportions of the loosely-assembled trimer and monomer simultaneously. 2017 Scientific reports Result IV F88E;V91W 16;74 20;78 28790432 Conformational modulation of influenza virus hemagglutinin: characterization and in vivo efficacy of monomeric form. Our results thus demonstrate that the two CU44 HA mutants, F88E and V91W, become monomers upon proteolytic cleavage of the foldon. 2017 Scientific reports Result IV F88E;V91W 59;68 63;72 HA 47 49 28790432 Conformational modulation of influenza virus hemagglutinin: characterization and in vivo efficacy of monomeric form. Starting from the wild-type HA trimer of CU44, six mutants were constructed: S199F of HA1 and G47E of HA2, according to the corresponding amino acid of KR01 HA, and R75L, F88E, V91W, and R106E of HA2 in the stem region, in an attempt to destabilize the trimer due to electrostatic or steric repulsion. 2017 Scientific reports Result IV S199F;G47E;R75L;F88E;V91W;R106E 77;94;165;171;177;187 82;98;169;175;181;192 HA;HA;HA;HA;HA1 28;102;157;196;86 30;104;159;198;89 28814518 A Single-Amino-Acid Substitution at Position 225 in Hemagglutinin Alters the Transmissibility of Eurasian Avian-Like H1N1 Swine Influenza Virus in Guinea Pigs. although the affinity of rHLJ/27 and rGX/18-HA1-E225G for the alpha2,3-glycopolymer was higher than that of rGX/18 and rHLJ/27-HA1-G225E. 2017 Journal of virology Result IV E225G;G225E 48;131 53;136 HA1;HA1 44;127 47;130 28814518 A Single-Amino-Acid Substitution at Position 225 in Hemagglutinin Alters the Transmissibility of Eurasian Avian-Like H1N1 Swine Influenza Virus in Guinea Pigs. Although the rGX/18-HA1-E225G variant did not transmit in guinea pigs, the rGX/18-HLJHA virus transmitted to one of the three exposed guinea pigs, and this finding was reproducible. 2017 Journal of virology Result IV E225G 24 29 HA1 20 23 28814518 A Single-Amino-Acid Substitution at Position 225 in Hemagglutinin Alters the Transmissibility of Eurasian Avian-Like H1N1 Swine Influenza Virus in Guinea Pigs. and Table 2), indicating that the E225G mutation of HA1 eliminated the transmission of the GX/18 virus in guinea pigs. 2017 Journal of virology Result IV E225G 34 39 HA1 52 55 28814518 A Single-Amino-Acid Substitution at Position 225 in Hemagglutinin Alters the Transmissibility of Eurasian Avian-Like H1N1 Swine Influenza Virus in Guinea Pigs. One virus, rGX/18-HA1-E225G, did not transmit to any of the exposed animals. 2017 Journal of virology Result IV E225G 22 27 HA1 18 21 28814518 A Single-Amino-Acid Substitution at Position 225 in Hemagglutinin Alters the Transmissibility of Eurasian Avian-Like H1N1 Swine Influenza Virus in Guinea Pigs. The amino acid glutamic acid (E) at position 225 of HA is critical for the transmissibility of the GX/18 virus in guinea pigs. 2017 Journal of virology Result IV E225E 14 49 HA 52 54 28814518 A Single-Amino-Acid Substitution at Position 225 in Hemagglutinin Alters the Transmissibility of Eurasian Avian-Like H1N1 Swine Influenza Virus in Guinea Pigs. The viruses recovered from the guinea pigs that were exposed to the rGX/18-HLJHA virus contained a D24N mutation in the HA1 gene. 2017 Journal of virology Result IV D24N 99 103 HA1 120 123 28814518 A Single-Amino-Acid Substitution at Position 225 in Hemagglutinin Alters the Transmissibility of Eurasian Avian-Like H1N1 Swine Influenza Virus in Guinea Pigs. These results suggest that the D24N mutation in HA may play a role in the transmission of the rGX/18-HLJHA virus. 2017 Journal of virology Result IV D24N 31 35 HA 48 50 28814518 A Single-Amino-Acid Substitution at Position 225 in Hemagglutinin Alters the Transmissibility of Eurasian Avian-Like H1N1 Swine Influenza Virus in Guinea Pigs. This result indicates that the E225G or G225E mutation in HA changes only the receptor-binding affinity and does not cause a switch in the receptor-binding preferences of the GX/18 and HLJ/27 viruses. 2017 Journal of virology Result IV E225G;G225E 31;40 36;45 HA 58 60 28814518 A Single-Amino-Acid Substitution at Position 225 in Hemagglutinin Alters the Transmissibility of Eurasian Avian-Like H1N1 Swine Influenza Virus in Guinea Pigs. Titers of rGX/18-HA1-E225G were significantly lower than those of rGX/18 at all four time points postinfection, whereas the replication level of rHLJ/27-HA1-G225E was significantly increased at 24, 36, and 48 h postinfection. 2017 Journal of virology Result IV E225G;G225E 21;157 26;162 HA1;HA1 17;153 20;156 28814518 A Single-Amino-Acid Substitution at Position 225 in Hemagglutinin Alters the Transmissibility of Eurasian Avian-Like H1N1 Swine Influenza Virus in Guinea Pigs. We also tested the replication of the rGX/18, rHLJ/27, rGX/18-HA1-E225G, and rHLJ/27-HA1-G225E viruses in guinea pigs. 2017 Journal of virology Result IV E225G;G225E 66;89 71;94 HA1;HA1 62;85 65;88 28814518 A Single-Amino-Acid Substitution at Position 225 in Hemagglutinin Alters the Transmissibility of Eurasian Avian-Like H1N1 Swine Influenza Virus in Guinea Pigs. We analyzed the HA levels of the four samples in the cell pellets by Western blotting and found that the levels of intracellular HA in GX/18 and rHLJ/27-HA1-G225E were considerably lower than those in HLJ/27 and rGX/18-HA1-E225G. 2017 Journal of virology Result IV G225E;E225G 157;223 162;228 HA;HA;HA1;HA1 16;129;153;219 18;131;156;222 28814518 A Single-Amino-Acid Substitution at Position 225 in Hemagglutinin Alters the Transmissibility of Eurasian Avian-Like H1N1 Swine Influenza Virus in Guinea Pigs. We detected the rHLJ/27-HA1-G225E virus in two of the three exposed animals. 2017 Journal of virology Result IV G225E 28 33 HA1 24 27 28814518 A Single-Amino-Acid Substitution at Position 225 in Hemagglutinin Alters the Transmissibility of Eurasian Avian-Like H1N1 Swine Influenza Virus in Guinea Pigs. We examined the effect of the amino acid at position 225 of HA on VLP formation by producing four different VLPs, designated rGX/18-VLP, rHLJ/27-VLP, rGX/18-HA1-E225G-VLP, and rHLJ/27-HA1-G225E-VLP, and comparing their productivities. 2017 Journal of virology Result IV E225G;G225E 161;188 166;193 HA;HA1;HA1 60;157;184 62;160;187 28814518 A Single-Amino-Acid Substitution at Position 225 in Hemagglutinin Alters the Transmissibility of Eurasian Avian-Like H1N1 Swine Influenza Virus in Guinea Pigs. We found that rGX/18-VLP and rHLJ/27-HA1-G225E-VLP produced significantly higher levels of hemagglutinin units in the cell supernatants than did rGX/18-HA1-E225G-VLP and rHLJ/27-VLP. 2017 Journal of virology Result IV G225E;E225G 41;156 46;161 HA1;HA1;HA 37;152;91 40;155;104 28814518 A Single-Amino-Acid Substitution at Position 225 in Hemagglutinin Alters the Transmissibility of Eurasian Avian-Like H1N1 Swine Influenza Virus in Guinea Pigs. We found that the cells adsorbed similar amounts of the rGX/18, rHLJ/27, rGX/18-HA1-E225G, and rHLJ/27-HA1-G225E viruses. 2017 Journal of virology Result IV E225G;G225E 84;107 89;112 HA1;HA1 80;103 83;106 28814518 A Single-Amino-Acid Substitution at Position 225 in Hemagglutinin Alters the Transmissibility of Eurasian Avian-Like H1N1 Swine Influenza Virus in Guinea Pigs. We then introduced the G225E mutation of HA1 into the HLJ/27 virus and tested the transmissibility of the mutant in guinea pigs. 2017 Journal of virology Result IV G225E 23 28 HA1 41 44 28814518 A Single-Amino-Acid Substitution at Position 225 in Hemagglutinin Alters the Transmissibility of Eurasian Avian-Like H1N1 Swine Influenza Virus in Guinea Pigs. We therefore evaluated the receptor-binding preferences of the rGX/18, rGX/18-HA1-E225G, rHLJ/27, and rHLJ/27-HA1-G225E viruses by using solid-phase binding assays, as described previously, with two different glycopolymers. 2017 Journal of virology Result IV E225G;G225E 82;114 87;119 HA1;HA1 78;110 81;113 28814518 A Single-Amino-Acid Substitution at Position 225 in Hemagglutinin Alters the Transmissibility of Eurasian Avian-Like H1N1 Swine Influenza Virus in Guinea Pigs. When we sequenced the whole genome of the rGX/18-HLJHA virus that was recovered from the animals in the transmission studies, we found that a D24N mutation consistently occurred in the HA1 gene of the rGX/18-HLJHA virus and that this mutation was not detected in any samples that we collected from rGX/18-HLJHA-infected animals. 2017 Journal of virology Result IV D24N 142 146 HA1 185 188 28814737 Susceptibility of influenza A(H1N1)/pdm2009, seasonal A(H3N2) and B viruses to Oseltamivir in Guangdong, China between 2009 and 2014. All of eight oseltamivir-resistant strains from Guangdong occurred N44S, N200S,V241I, H275Y and N369K mutations in common, among these, there are three strains possessing several other mutations like I321V,N386K and K432E. 2017 Scientific reports Result IV N44S;N200S;V241I;H275Y;N369K;N386K;I321V;K432E 67;73;79;86;96;206;200;216 71;78;84;91;101;211;205;221 28814737 Susceptibility of influenza A(H1N1)/pdm2009, seasonal A(H3N2) and B viruses to Oseltamivir in Guangdong, China between 2009 and 2014. Along with Arg368 and Lys432, the N369K mutation made the local electrical density of NA more positive. 2017 Scientific reports Result IV N369K 34 39 86 88 28814737 Susceptibility of influenza A(H1N1)/pdm2009, seasonal A(H3N2) and B viruses to Oseltamivir in Guangdong, China between 2009 and 2014. Another two important substitutions were N369K and K432E, as both single and double mutations. 2017 Scientific reports Result IV N369K;K432E 41;51 46;56 28814737 Susceptibility of influenza A(H1N1)/pdm2009, seasonal A(H3N2) and B viruses to Oseltamivir in Guangdong, China between 2009 and 2014. Apart from that, the NA gene mutation sites of Guangdong A(H1N1) pdm2009 resistant strains, circulating between the 2013-2014, were found to be consistent with that of the resistant strains from clusters cases reported in Sapporo of Japan, Louisiana and Washington of the United States, except few mutations like N44S and N386K. 2017 Scientific reports Result IV N44S;N386K 313;322 317;327 21 23 28814737 Susceptibility of influenza A(H1N1)/pdm2009, seasonal A(H3N2) and B viruses to Oseltamivir in Guangdong, China between 2009 and 2014. As mentioned above, V241I made the binding pocket longer along residues H275 to D151. 2017 Scientific reports Result IV V241I 20 25 28814737 Susceptibility of influenza A(H1N1)/pdm2009, seasonal A(H3N2) and B viruses to Oseltamivir in Guangdong, China between 2009 and 2014. Even the I321V mutations existed in NA variants, the little difference of side chain between I and V can be adapted by hydrophobicity, the mutation did not force this hydrophobic core to change its conformation. 2017 Scientific reports Result IV I321V 9 14 36 38 28814737 Susceptibility of influenza A(H1N1)/pdm2009, seasonal A(H3N2) and B viruses to Oseltamivir in Guangdong, China between 2009 and 2014. For mutation N386K, significant changes within the side chain electrical properties would lead to a series of conformational changes. 2017 Scientific reports Result IV N386K 13 18 28814737 Susceptibility of influenza A(H1N1)/pdm2009, seasonal A(H3N2) and B viruses to Oseltamivir in Guangdong, China between 2009 and 2014. For mutation V241I, sequence alignments analysis showed that V241I substitutions almost occurred in all resistant and sensitive strains circulating between the 2012-2014. 2017 Scientific reports Result IV V241I;V241I 13;61 18;66 28814737 Susceptibility of influenza A(H1N1)/pdm2009, seasonal A(H3N2) and B viruses to Oseltamivir in Guangdong, China between 2009 and 2014. If N369K and K432E both occurred in NA, this positive electrostatic field would be broken, and the mutated E432 would be able to form a salt bridge with K369. 2017 Scientific reports Result IV N369K;K432E 3;13 8;18 36 38 28814737 Susceptibility of influenza A(H1N1)/pdm2009, seasonal A(H3N2) and B viruses to Oseltamivir in Guangdong, China between 2009 and 2014. If V241I existed in conjunction with H275Y, the side-chains of these residues would shift more than V241I alone. 2017 Scientific reports Result IV V241I;H275Y;V241I 3;37;100 8;42;105 28814737 Susceptibility of influenza A(H1N1)/pdm2009, seasonal A(H3N2) and B viruses to Oseltamivir in Guangdong, China between 2009 and 2014. In addition, some amino acid substitutions at positions N44S, V106I,N200S,V241I,I321V,N369K,N386K and K432E were observed not only in 2013/2014 oseltamivir-resistant strains, but also in a few 2012/2013/2014 oseltamivir-sensitive strains. 2017 Scientific reports Result IV N44S;N386K;N200S;V241I;N369K;I321V;V106I;K432E 56;92;68;74;86;80;62;102 60;97;73;79;91;85;67;107 28814737 Susceptibility of influenza A(H1N1)/pdm2009, seasonal A(H3N2) and B viruses to Oseltamivir in Guangdong, China between 2009 and 2014. In addition, the double mutation (N369K and K432E) made the binding pocket contract slightly and the oseltamivir conformation rotate approximately 35.1 degrees. 2017 Scientific reports Result IV N369K;K432E 34;44 39;49 28814737 Susceptibility of influenza A(H1N1)/pdm2009, seasonal A(H3N2) and B viruses to Oseltamivir in Guangdong, China between 2009 and 2014. In addition, the V241I and N386K double mutation, which existed in most strains isolated from the Influenza Surveillance Network Platform of Guangdong Province, resulted in a synergistic effect within the binding pocket for oseltamivir. 2017 Scientific reports Result IV V241I;N386K 17;27 22;32 28814737 Susceptibility of influenza A(H1N1)/pdm2009, seasonal A(H3N2) and B viruses to Oseltamivir in Guangdong, China between 2009 and 2014. So in this study, the N-terminal peptide was not constructed into the stucture models, as well as N44S mutation. 2017 Scientific reports Result IV N44S 98 102 28814737 Susceptibility of influenza A(H1N1)/pdm2009, seasonal A(H3N2) and B viruses to Oseltamivir in Guangdong, China between 2009 and 2014. So in this study, we pay more discussion on NA-V241I, N369K, N386K and K432E substitutions due to their potential role on susceptibility. 2017 Scientific reports Result IV V241I;N369K;N386K;K432E 47;54;61;71 52;59;66;76 44 46 28814737 Susceptibility of influenza A(H1N1)/pdm2009, seasonal A(H3N2) and B viruses to Oseltamivir in Guangdong, China between 2009 and 2014. The strong salt bridge effect even shifted the side chain of Trp399 outward approximately 4.4 A, close to the K432E mutation. 2017 Scientific reports Result IV K432E 110 115 28814737 Susceptibility of influenza A(H1N1)/pdm2009, seasonal A(H3N2) and B viruses to Oseltamivir in Guangdong, China between 2009 and 2014. Thus, the N386K mutation, in combination with V241I, elongated the binding pocket while pushing several loops outward. 2017 Scientific reports Result IV N386K;V241I 10;46 15;51 28815216 Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity. As PB1 M645I, PB1 D27N, and the PB1 M645I PA T97I double mutant were not resistant to any of the nucleoside drugs, we did not analyze them further. 2017 mSphere Result IV M645I;D27N;M645I;T97I 7;18;36;45 12;22;41;49 PA;PB1;PB1;PB1 42;3;14;32 44;6;17;35 28815216 Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity. At 24 h postinfection, there was no significant difference in the number of genomes for PB1 T123A. 2017 mSphere Result IV T123A 92 97 PB1 88 91 28815216 Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity. Both PA T97I and the PB1 T123A PA T97I double mutant had mutation rates that were very similar to those of the WT. 2017 mSphere Result IV T97I;T123A;T97I 8;25;34 12;30;38 PA;PA;PB1 5;31;21 7;33;24 28815216 Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity. Both PB1 D27N (0.70 +- 0.09) and PB1 V43I (0.47 +- 0.08) had dramatically reduced fitness compared with WT. 2017 mSphere Result IV D27N;V43I 9;37 13;41 PB1;PB1 5;33 8;36 28815216 Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity. Both PB1 M645I and PA T97I were essentially neutral. 2017 mSphere Result IV M645I;T97I 9;22 14;26 PA;PB1 19;5 21;8 28815216 Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity. In contrast, the PB1 T123A mutant, which has an increased baseline rate of C-to-U and G-to-A mutations, selectively buffers against further drug-induced increases in the same classes. 2017 mSphere Result IV T123A 21 26 PB1 17 20 28815216 Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity. In contrast, we observed smaller decreases in genome production in drug for both PB1 T123A and PB1 T123A PA T97I, especially at later time points. 2017 mSphere Result IV T123A;T123A;T97I 85;99;108 90;104;112 PA;PB1;PB1 105;81;95 107;84;98 28815216 Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity. Interestingly, PA T97I, which was identified only in populations passaged in ribavirin, conferred resistance to 100 muM 5FU (5-fold sensitivity reduction; Dunnett's adjusted P value of 0.0048), but not to 20 muM ribavirin or 20 muM 5-azacytidine. 2017 mSphere Result IV T97I 18 22 PA 15 17 28815216 Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity. Of the five single mutants tested, only PB1 T123A and PA T97I exhibited reduced sensitivity to our panel of nucleoside analogs. 2017 mSphere Result IV T123A;T97I 44;57 49;61 PA;PB1 54;40 56;43 28815216 Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity. Surprisingly, the PB1 T123A PA T97I double mutant, which was not found in passaged populations, exhibited a 54-fold reduction in sensitivity to 100 muM 5FU (Dunnett's adjusted P value of <0.0001). 2017 mSphere Result IV T123A;T97I 22;31 27;35 PA;PB1 28;18 30;21 28815216 Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity. The decreased fitness of PB1 V43I is consistent with previous data on its growth kinetics. 2017 mSphere Result IV V43I 29 33 PB1 25 28 28815216 Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity. The increase in transition mutations in the PA T97I mutant with 5FU treatment was similar to that of the WT. 2017 mSphere Result IV T97I 47 51 PA 44 46 28815216 Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity. The other mutation enriched in ribavirin-passaged populations, PB1 M645I, did not alter sensitivity to any of the three nucleoside analogs. 2017 mSphere Result IV M645I 67 72 PB1 63 66 28815216 Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity. The PA T97I mutant exhibited a similar decrease in genome output in drug. 2017 mSphere Result IV T97I 7 11 PA 4 6 28815216 Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity. The PA T97I mutation was found in all three ribavirin-passaged populations at frequencies of 88, 55, and 11%. 2017 mSphere Result IV T97I 7 11 PA 4 6 28815216 Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity. The PB1 D27N mutant appeared to be more sensitive than WT PR8 to 5-azacytidine (18-fold increase; Dunnett's adjusted P value of 0.0089). 2017 mSphere Result IV D27N 8 12 PB1 4 7 28815216 Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity. The PB1 M645I PA T97I double mutant had higher fitness than the WT, which indicates that selection of PB1 M645I in ribavirin-passaged populations reflected culture adaptation rather than mutagen resistance. 2017 mSphere Result IV M645I;T97I;M645I 8;17;106 13;21;111 PA;PB1;PB1 14;4;102 16;7;105 28815216 Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity. The PB1 M645I PA T97I double mutant was identified in our ribavirin-passaged viral populations. 2017 mSphere Result IV M645I;T97I 8;17 13;21 PA;PB1 14;4 16;7 28815216 Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity. The PB1 M645I PA T97I double mutant, which was identified in ribavirin-passaged populations, exhibited a pattern of nucleoside analog sensitivity that was very similar to the PA T97I single mutant but which did not achieve statistical significance (3-fold reduction in sensitivity to 5FU; Dunnett's adjusted P value of 0.157). 2017 mSphere Result IV M645I;T97I;T97I 8;17;178 13;21;182 PA;PA;PB1 14;175;4 16;177;7 28815216 Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity. The PB1 T123A mutation was found in all three 5FU-passaged populations at frequencies of 34, 31, and 8%. 2017 mSphere Result IV T123A 8 13 PB1 4 7 28815216 Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity. The PB1 T123A mutation, which was identified in 5FU-passaged populations, conferred a 10-fold reduction in sensitivity to 100 muM 5FU (Dunnett's adjusted P value of <0.0001) but no change in sensitivity to 20 muM ribavirin or 20 muM 5-azacytidine. 2017 mSphere Result IV T123A 8 13 PB1 4 7 28815216 Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity. The PB1 T123A PA T97I double mutant also buffers against C-to-U mutations induced by 5FU, albeit not as dramatically as the PB1 T123A single mutant. 2017 mSphere Result IV T123A;T97I;T123A 8;17;128 13;21;133 PA;PB1;PB1 14;4;124 16;7;127 28815216 Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity. The PB1 T123A PA T97I double mutant maintained its generally lower level of genome production across multiple time points, consistent with epistatic interactions between these mutations and their impact on 5FU resistance. 2017 mSphere Result IV T123A;T97I 8;17 13;21 PA;PB1 14;4 16;7 28815216 Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity. The PB1 T123A PA T97I double mutant was not found naturally, but these mutations on distinct segments could plausibly interact genetically. 2017 mSphere Result IV T123A;T97I 8;17 13;21 PA;PB1 14;4 16;7 28815216 Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity. The PB1 T123A PA T97I double mutant, which was highly resistant to 5FU, exhibited reciprocal sign epistasis, as it had a marked decrease in fitness while each single mutant mutation was beneficial or neutral. 2017 mSphere Result IV T123A;T97I 8;17 13;21 PA;PB1 14;4 16;7 28815216 Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity. The PB1 T123A virus was more fit than the WT, even out of the drug, and released more genomes into the supernatant early in replication than either WT or the other mutants. 2017 mSphere Result IV T123A 8 13 PB1 4 7 28815216 Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity. The PB1 V43I mutant had no evident resistance to nucleoside analogs or altered mutation rate in the PR8 genetic background. 2017 mSphere Result IV V43I 8 12 PB1 4 7 28815216 Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity. The ribavirin-resistant mutation PB1 V43I was not found in any of the populations, and PB1 D27N was only found in one ribavirin-passaged population at a frequency of 3%. 2017 mSphere Result IV V43I;D27N 37;91 41;95 PB1;PB1 33;87 36;90 28815216 Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity. Therefore, the limited class-specific fidelity phenotype of PB1 T123A is unlikely to contribute significantly to the virus' mutagen resistance. 2017 mSphere Result IV T123A 64 69 PB1 60 63 28815216 Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity. These data indicate that the observed decrease in 5FU-induced C-to-U mutations in PB1 T123A virus is not sufficient to cause a corresponding change in specific infectivity. 2017 mSphere Result IV T123A 86 91 PB1 82 85 28815216 Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity. These data suggest that the resistance phenotypes of PB1 D27N and PB1 V43I are dependent on strain background. 2017 mSphere Result IV D27N;V43I 57;70 61;74 PB1;PB1 53;66 56;69 28815216 Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity. Together, these data show that PB1 T123A has an increased rate for two transition mutation types while also limiting further induction by 5FU treatment. 2017 mSphere Result IV T123A 35 40 PB1 31 34 28815216 Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity. Unexpectedly, PB1 T123A made significantly more C-to-U and G-to-A mutations than the WT. 2017 mSphere Result IV T123A 18 23 PB1 14 17 28815216 Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity. We also evaluated PB1 V43I, which has been reported to be a fidelity variant. 2017 mSphere Result IV V43I 22 26 PB1 18 21 28815216 Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity. We also generated the PB1 T123A PA T97I and PB1 M645I PA T97I double mutants. 2017 mSphere Result IV T123A;T97I;M645I;T97I 26;35;48;57 31;39;53;61 PA;PA;PB1;PB1 32;54;22;44 34;56;25;47 28815216 Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity. We also identified the PB1 M645I mutation at frequencies of 90, 14, and 1% in the same ribavirin-passaged populations. 2017 mSphere Result IV M645I 27 32 PB1 23 26 28815216 Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity. We found that the two previously identified ribavirin-resistant mutants, PB1 D27N and PB1 V43I, were just as sensitive as the wild-type PR8 strain to both ribavirin and 5FU. 2017 mSphere Result IV D27N;V43I 77;90 81;94 PB1;PB1 73;86 76;89 28815216 Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity. We measured the fitness of PB1 T123A, PA T97I, and the PB1 T123A PA T97I double mutant in the presence of 25 and 50 muM 5FU to better quantify their mutagen sensitivity. 2017 mSphere Result IV T123A;T97I;T123A;T97I 31;41;59;68 36;45;64;72 PA;PA;PB1;PB1 38;65;27;55 40;67;30;58 28815216 Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity. While 15 muM 5FU increased all transition mutations approximately 5-fold in PR8, we observed almost no change in C-to-U mutations in the PB1 T123A mutant. 2017 mSphere Result IV T123A 141 146 PB1 137 140 28837667 Influenza NS1 directly modulates Hedgehog signaling during infection. Both the PR8-WT and PR8-A122V viruses established comparable levels of infection as assessed by viral titers in lungs (Fig 7A) and the range of tissues infected in mice at either two, four, or seven days post infection (influenza was below the limit of detection in the brain, spleen, and liver)), and displayed similar temporal regulation of viral genes in cell culture (see S1 Text and S8A Fig). 2017 PLoS pathogens Result IV A122V 24 29 28837667 Influenza NS1 directly modulates Hedgehog signaling during infection. Commensurate with NS1 altering the activity of the transcriptional effector of the Hh signaling pathway, an interaction was also detected between NS1 and the transcriptional effector of the Notch (N) signaling pathway, N-ICD, which could also be relieved by the A122V mutation (S1 Text and S4 Fig). 2017 PLoS pathogens Result IV A122V 262 267 NS1;NS1 18;146 21;149 28837667 Influenza NS1 directly modulates Hedgehog signaling during infection. Despite the lower levels, and in contrast to the diminished activity of NS1-A122V when expressed in flies and in transfected cells, the mutated virus induced higher expression of the Hh target Ptch1 compared to PR8-WT (Fig 6A and 6F). 2017 PLoS pathogens Result IV A122V 76 81 NS1 72 75 28837667 Influenza NS1 directly modulates Hedgehog signaling during infection. Furthermore, expression of NS1(Vn)-A122V showed a significant reduction in this interaction, represented by lifetime values between 2.0 to 2.3 ns, resulting in 2-5% FRET efficiency and a 50% reversal in comparison to NS1(Vn)-WT expressing discs (Fig 4O vs. 2017 PLoS pathogens Result IV A122V 35 40 NS1;NS1 27;217 30;220 28837667 Influenza NS1 directly modulates Hedgehog signaling during infection. Furthermore, IL6 expression was higher in PR8-A122V infected cells compared to PR8-WT (Fig 7D and 7E). 2017 PLoS pathogens Result IV A122V 46 51 28837667 Influenza NS1 directly modulates Hedgehog signaling during infection. Futhermore, the A122V mutation eliminated this interaction such that NS1(Vn)-A122V could no longer prevent Gli1-mediated activation of dpp-lacZEP expression (Fig 3U vs. 2017 PLoS pathogens Result IV A122V;A122V 16;77 21;82 NS1 69 72 28837667 Influenza NS1 directly modulates Hedgehog signaling during infection. Having observed an effect of PR8-A122V in the context of in vivo infection in mice, we next examined its physiological effects. 2017 PLoS pathogens Result IV A122V 33 38 28837667 Influenza NS1 directly modulates Hedgehog signaling during infection. However, PR8-A122V did not discernibly alter the expression of BMP2 compared to PR8-WT. 2017 PLoS pathogens Result IV A122V 13 18 28837667 Influenza NS1 directly modulates Hedgehog signaling during infection. However, the PR8-A122V virus significantly hastened lethality of mice compared to the parental PR8 (PR8-WT) strain in three independent experiments (Fig 7B) and produced greater signs of morbidity by 3 days post-infection (e.g., reduced mobility, hunched posture, labored breathing, and pilo-erectus, although insignificant change in weight loss-S8B Fig), indicating that the mutant virus is considerably more pathogenic than the parental strain. 2017 PLoS pathogens Result IV A122V 17 22 28837667 Influenza NS1 directly modulates Hedgehog signaling during infection. However, this greater activity of NS1(PR8) was also reduced 3.53X (n = 6, p<, p<6.4x10-3) by the A122V mutation (Fig 2K and 2L). 2017 PLoS pathogens Result IV A122V 97 102 NS1 34 37 28837667 Influenza NS1 directly modulates Hedgehog signaling during infection. Indeed, levels of the proinflammatory cytokines IL6 (Fig 7C) and CXCL-10 (S9 Fig) were significantly higher in extracts (lavages) from lungs infected with PR8-A122V compared to PR8-WT viruses, while other factors such as TNF-alpha and IL-1alpha were not significantly altered (S9 Fig). 2017 PLoS pathogens Result IV A122V 159 164 28837667 Influenza NS1 directly modulates Hedgehog signaling during infection. Interestingly, in NL20 cells (Fig 5A and 5C) as well as in mouse lungs infected with the PR8 strain of influenza virus (Fig 5D), we observed a higher proportion of NS1(PR8)-A122V in the nucleus as compared to NS1(PR8)-WT. 2017 PLoS pathogens Result IV A122V 173 178 NS1;NS1 164;209 167;212 28837667 Influenza NS1 directly modulates Hedgehog signaling during infection. Nonetheless, when cells with the highest levels of NS1(PR8)-A122V (A122V-high in S6B Fig) were compared to those expressing NS1(PR8)-WT, a clear reduction in BMP2 induction was still observed in the mutant-expressing cells (Fig 5A and 5B). 2017 PLoS pathogens Result IV A122V;A122V 60;67 65;72 NS1;NS1 51;124 54;127 28837667 Influenza NS1 directly modulates Hedgehog signaling during infection. NS1(PR8)-A122V protein levels appeared generally lower than NS1-WT in NL20 cells (S6B Fig). 2017 PLoS pathogens Result IV A122V 9 14 NS1;NS1 0;60 3;63 28837667 Influenza NS1 directly modulates Hedgehog signaling during infection. Plasmids containing NS1(PR8)-WT-, NS1(PR8)-A122V-, or GFP-encoding sequences were transfected into the human lung epithelial cell line, NL20, and analyzed for expression of the Hh target gene BMP2, the mammalian homologue of Drosophila dpp. 2017 PLoS pathogens Result IV A122V 43 48 NS1;NS1 20;34 23;37 28837667 Influenza NS1 directly modulates Hedgehog signaling during infection. PR8-A122V is more pathogenic than PR8-WT. 2017 PLoS pathogens Result IV A122V 4 9 28837667 Influenza NS1 directly modulates Hedgehog signaling during infection. Sibling mice were infected with either the PR8-WT or PR8-A122V virus and lung airway epithelium were analyzed for Hh target gene expression 2 days post-infection. 2017 PLoS pathogens Result IV A122V 57 62 28837667 Influenza NS1 directly modulates Hedgehog signaling during infection. Similar to NL20 cells, NS1 expressed from the PR8-A122V mutant virus was found at slightly but statistically significantly lower levels compared to NS1 expressed from the WT virus (Fig 6E). 2017 PLoS pathogens Result IV A122V 50 55 NS1;NS1 23;148 26;151 28837667 Influenza NS1 directly modulates Hedgehog signaling during infection. Taken together, NS1-A122V has altered activity compared to NS1-WT in flies, human cells, and in vivo in mice. 2017 PLoS pathogens Result IV A122V 20 25 NS1;NS1 16;59 19;62 28837667 Influenza NS1 directly modulates Hedgehog signaling during infection. The differences in activity between NS1(PR8) and NS1(Vn) notwithstanding, incorporation of the A122V mutation into NS1(PR8) reversed its effects on all Hh target genes, indicating that this single amino acid is critical for both the positive and negative effects of NS1 across strains (Fig 2K and 2L and S1D, S1H and S1L Fig). 2017 PLoS pathogens Result IV A122V 95 100 NS1;NS1;NS1;NS1 36;49;115;266 39;52;118;269 28837667 Influenza NS1 directly modulates Hedgehog signaling during infection. This latter fact was important since the A122V mutation in NS1(Ud), presumably due to its proximity to the CPSF30 binding site at M106, reduced this binding interaction in vitro (S7 Fig). 2017 PLoS pathogens Result IV A122V 41 46 NS1 59 62 28837667 Influenza NS1 directly modulates Hedgehog signaling during infection. This NS1 mutant carried an alanine to valine substitution at position 122 (A122V):a highly conserved residue mapping to the surface of the ED (Fig 2N). 2017 PLoS pathogens Result IV A122V;A122V 75;27 80;73 NS1 5 8 28837667 Influenza NS1 directly modulates Hedgehog signaling during infection. This observation suggests that lower levels of Hh target gene induction by NS1-WT during infection in vivo may serve a protective function for the host whereas unrestrained signaling, as occurs during infection with PR8-A122V, may be more detrimental. 2017 PLoS pathogens Result IV A122V 220 225 NS1 75 78 28837667 Influenza NS1 directly modulates Hedgehog signaling during infection. This supports a model in which the A122V mutation alters the specific activity of NS1 and/or its distribution and proximity to host binding partners. 2017 PLoS pathogens Result IV A122V 35 40 NS1 82 85 28837667 Influenza NS1 directly modulates Hedgehog signaling during infection. We next tested whether Hh signaling was altered by influenza in a murine infection model, and whether the A122V mutation of NS1 had any effect on such activity. 2017 PLoS pathogens Result IV A122V 106 111 NS1 124 127 28860593 Prerequisites for the acquisition of mammalian pathogenicity by influenza A virus with a prototypic avian PB2 gene. Among the tested mutations, only I133V and E627K significantly increased polymerase activity; these increases were 4- and 80-fold, respectively. 2017 Scientific reports Result IV I133V;E627K 33;43 38;48 28860593 Prerequisites for the acquisition of mammalian pathogenicity by influenza A virus with a prototypic avian PB2 gene. Based on previously identified candidate amino acids, we generated mutant 01310 PB2 genes with single amino acid mutations [PB2(01310)-I66M, PB2(01310)-K88R, PB2(01310)-I109V, PB2(01310)-I133V, PB2(01310)-R157K, PB2(01310)-K340R, PB2(01310)-L373I, PB2(01310)-V575M, PB2(01310)-E627K, and PB2(01310)-A674T] and tested their polymerase activity using an in vitro mini-genome assay in the 293T human embryonic kidney cell line. 2017 Scientific reports Result IV I66M;K88R;I109V;I133V;R157K;K340R;L373I;V575M;E627K;A674T 135;152;169;187;205;223;241;259;277;299 139;156;174;192;210;228;246;264;282;304 PB2;PB2;PB2;PB2;PB2;PB2;PB2;PB2;PB2;PB2;PB2 80;124;141;158;176;194;212;230;248;266;288 83;127;144;161;179;197;215;233;251;269;291 28860593 Prerequisites for the acquisition of mammalian pathogenicity by influenza A virus with a prototypic avian PB2 gene. Based on the high frequencies of the MVV and MIV mutations among the examined AIVs, we introduced multiple mutations combined with E627K and A674T into 01310 PB2 (MIV, MVV, MVVT, MIVKT, MVVK, and MVVKT) and performed mini-genome assays. 2017 Scientific reports Result IV E627K;A674T 131;141 136;146 PB2 158 161 28860593 Prerequisites for the acquisition of mammalian pathogenicity by influenza A virus with a prototypic avian PB2 gene. Cloned amplicons encoding amino acid residues 590-701 were sequenced, and well-known mammalian pathogenic mutations such as Q591R/K, E627K, and D701N were identified in four out of five lungs. 2017 Scientific reports Result IV Q591R;Q591K;E627K;D701N 124;124;133;144 131;131;138;149 28860593 Prerequisites for the acquisition of mammalian pathogenicity by influenza A virus with a prototypic avian PB2 gene. During mouse infectivity screening, however, we observed detectable growth of mutant viruses containing the I66M, I109V, I133V, E627K, or A674T mutations (Table 1). 2017 Scientific reports Result IV I66M;I109V;I133V;E627K;A674T 108;114;121;128;138 112;119;126;133;143 28860593 Prerequisites for the acquisition of mammalian pathogenicity by influenza A virus with a prototypic avian PB2 gene. Furthermore, compared to rPB2(01310)-E627K and rPB2(01310)-MVV, rPB2(01310)-MVVK and rPB2(01310)-MVVKT efficiently replicated in the lungs (105.8 EID50 and 106.0 EID50, respectively, at 3 dpi; 104.1 EID50 and 104.4 EID50, respectively, at 6 dpi) and caused severe body weight loss and 100% mortality (Table 3 and. 2017 Scientific reports Result IV E627K 37 42 28860593 Prerequisites for the acquisition of mammalian pathogenicity by influenza A virus with a prototypic avian PB2 gene. Furthermore, rPB2(PR8)-IIIE and rPB2(PR8)-IIIEA replicated less efficiently than rPR8 and rPB2(PR8)-K627E. 2017 Scientific reports Result IV K627E 100 105 28860593 Prerequisites for the acquisition of mammalian pathogenicity by influenza A virus with a prototypic avian PB2 gene. Furthermore, the combination of III with 627E or 627E and 674A [PB2(PR8)-IIIE and PB2(PR8)-IIIEA] significantly decreased the polymerase activity compared to PB2(PR8)-III, PB2(PR8)-IIIA, and PB2(PR8)-K627E (P < 0.05). 2017 Scientific reports Result IV K627E 200 205 PB2;PB2;PB2;PB2;PB2 64;82;158;172;191 67;85;161;175;194 28860593 Prerequisites for the acquisition of mammalian pathogenicity by influenza A virus with a prototypic avian PB2 gene. In other words, the I66M, I109V, and I133V mutations may affect the structural integrity of the polymerase complex. 2017 Scientific reports Result IV I66M;I109V;I133V 20;26;37 24;31;42 28860593 Prerequisites for the acquisition of mammalian pathogenicity by influenza A virus with a prototypic avian PB2 gene. In the same experimental context, we mixed equal titres of rPB2(01310) and rPB2(01310)-E627K and inoculated MDCK cells, ECEs, and EDEs. 2017 Scientific reports Result IV E627K 87 92 28860593 Prerequisites for the acquisition of mammalian pathogenicity by influenza A virus with a prototypic avian PB2 gene. Moreover, the pathogenicity of rPB2(PR8)-IIIE was markedly attenuated; this variant caused no body weight loss and produced much lower virus titres in the lungs of infected mice than rPB2(PR8)-K627E and rPB2(PR8)-III (Table 3). 2017 Scientific reports Result IV K627E 193 198 28860593 Prerequisites for the acquisition of mammalian pathogenicity by influenza A virus with a prototypic avian PB2 gene. Next, we assessed the pathogenicity of rPB2(PR8)-IIIE, rPB2(PR8)-III, and rPB2(PR8)-K627E in mice. 2017 Scientific reports Result IV K627E 84 89 28860593 Prerequisites for the acquisition of mammalian pathogenicity by influenza A virus with a prototypic avian PB2 gene. Only rPB2(01310)-E627K caused slight body weight loss of up to 4% over 7-10 days post-infection (dpi) (P < 0.05). 2017 Scientific reports Result IV E627K 17 22 28860593 Prerequisites for the acquisition of mammalian pathogenicity by influenza A virus with a prototypic avian PB2 gene. Recombinant viruses with the I133V, L373I, or E627K mutations produced higher titres than the parent strain rPB2(01310) (P < 0.05). 2017 Scientific reports Result IV I133V;L373I;E627K 29;36;46 34;41;51 28860593 Prerequisites for the acquisition of mammalian pathogenicity by influenza A virus with a prototypic avian PB2 gene. rPB2(01310)-E627K outgrew rPB2(01310) in MDCK cells (4/4), but rPB2(01310) outgrew rPB2(01310)-E627K in ECEs and EDEs (5/5) after only one passage. 2017 Scientific reports Result IV E627K;E627K 12;95 17;100 28860593 Prerequisites for the acquisition of mammalian pathogenicity by influenza A virus with a prototypic avian PB2 gene. Surprisingly, at least half of the quasi-species of three mice possessed mammalian pathogenic mutations (Q591K, E627K, or D701N), and double mutations [E627K (10/10) and Q591R (1/10)] were observed in one mouse. 2017 Scientific reports Result IV Q591K;E627K;D701N;E627K;Q591R 105;112;122;152;170 110;117;127;157;175 28860593 Prerequisites for the acquisition of mammalian pathogenicity by influenza A virus with a prototypic avian PB2 gene. The combinations of 627K or 627K and 674T with MIV (MIVKT) or MVV (MVVK and MVVKT) significantly increased the replication efficiencies of the corresponding recombinant viruses [rPB2(01310)-MIVKT, rPB2(01310)-MVVK, and rPB2(01310)-MVVKT] in MDCK cells compared to the 627K mutation alone [rPB2(01310)-E627K]. 2017 Scientific reports Result IV E627K 301 306 28860593 Prerequisites for the acquisition of mammalian pathogenicity by influenza A virus with a prototypic avian PB2 gene. The E627K mutation has a well-characterized role related to mammalian pathogenicity, whereas the A674T mutation, which is conserved among most human influenza viruses, does not appear to be related to mammalian pathogenicity. 2017 Scientific reports Result IV E627K;A674T 4;97 9;102 28860593 Prerequisites for the acquisition of mammalian pathogenicity by influenza A virus with a prototypic avian PB2 gene. The histopathological pulmonary lesions of mice infected with rPB2(01310), rPB2(01310)-E627K, rPB2(01310)-MVV, rPB2(01310)-MVVK, rPB2(PR8)-III, rPB2(PR8)-IIIE, and rPR8 were compared, and the average lesion scores of 5 mice per virus type, except rPB2(PR8)-III (4 mice due to 1 mouse death) and rPR8 (2 mice due to 3 mouse deaths), were calculated. 2017 Scientific reports Result IV E627K 87 92 28860593 Prerequisites for the acquisition of mammalian pathogenicity by influenza A virus with a prototypic avian PB2 gene. The L373I mutation, which increases viral replication efficiency in MDCK cells, was excluded from further analysis because viruses carrying this mutation did not proliferate sufficiently in mouse lung. 2017 Scientific reports Result IV L373I 4 9 28860593 Prerequisites for the acquisition of mammalian pathogenicity by influenza A virus with a prototypic avian PB2 gene. The polymerase activities of the LOF mutants possessing the 66I-109I-133I [PB2(PR8)-III], 66I-109I-133I-674A [PB2(PR8)-IIIA], or 627E [PB2(PR8)-K627E] mutations were significantly lower than that of the PR8 PB2 gene [PB2(PR8)]. 2017 Scientific reports Result IV K627E 144 149 PB2;PB2;PB2;PB2;PB2 75;110;135;207;217 78;113;138;210;220 28860593 Prerequisites for the acquisition of mammalian pathogenicity by influenza A virus with a prototypic avian PB2 gene. The pulmonary lesions induced by rPB2(01310)-E627K and rPB2(01310)-MVVK were characterized by necrotizing bronchiolitis, severe peribronchiolitis and interstitial pneumonia (average lesion scores 3.5 and 4, respectively), but rPB2(01310)-MVVK induced more severe necrotizing bronchiolitis in infected mice. 2017 Scientific reports Result IV E627K 45 50 Lung lesions;Bronchiolitis;Peribronchiolitis;Pneumonia;Bronchiolitis 4;94;128;150;263 21;119;145;172;288 28860593 Prerequisites for the acquisition of mammalian pathogenicity by influenza A virus with a prototypic avian PB2 gene. The well-known mammalian pathogenic factor, D701N mutation, occurs less frequently than the E627K mutation in the PB2 genes of "human" and "bird to human" IAVs (Table 2). 2017 Scientific reports Result IV D701N;E627K 44;92 49;97 PB2 114 117 28860593 Prerequisites for the acquisition of mammalian pathogenicity by influenza A virus with a prototypic avian PB2 gene. Thus, we concentrated on the effect of E627K and its synergistic effects with the MVV mutations with regard to mammalian pathogenicity. 2017 Scientific reports Result IV E627K 39 44 28860593 Prerequisites for the acquisition of mammalian pathogenicity by influenza A virus with a prototypic avian PB2 gene. To predict the structure-function relationship of I66M, I109V, and I133V, we located each amino acid residue in a 3D structure of the PB1, PB2, and PA trimer from a bat IAV. 2017 Scientific reports Result IV I66M;I109V;I133V 50;56;67 54;61;72 PA;PB1;PB2 148;134;139 150;137;142 28860593 Prerequisites for the acquisition of mammalian pathogenicity by influenza A virus with a prototypic avian PB2 gene. To understand the frequency of each identified mutation (I66M, I109V, I133V, E627K, and A674T), we examined IAVs collected from birds, pigs and humans (Table 2). 2017 Scientific reports Result IV I66M;I109V;I133V;E627K;A674T 57;63;70;77;88 61;68;75;82;93 28860626 Topological N-glycosylation and site-specific N-glycan sulfation of influenza proteins in the highly expressed H1N1 candidate vaccines. Interestingly, those sulfated N-glycans were also observed to be highly fucosylated, which were localized at the unique site of Asn136 but absent from that of the influenza vaccine NYMC-X181A. 2017 Scientific reports Result IV X181A 186 191 28860626 Topological N-glycosylation and site-specific N-glycan sulfation of influenza proteins in the highly expressed H1N1 candidate vaccines. Mass spectrometric analyses revealed similar N-glycan compositions and profiles of HA and NA at the conserved sequence regions of the respective proteins in the vaccines of NIBRG-121xp and NYMC-X181A except at the specified mutation sites. 2017 Scientific reports Result IV X181A 194 199 HA;NA 83;90 85;92 28860626 Topological N-glycosylation and site-specific N-glycan sulfation of influenza proteins in the highly expressed H1N1 candidate vaccines. The structural pattern of sulfated N-glycans of NA in the influenza vaccine NYMC-X181A was identical to those in the influenza vaccine NIBRG-121xp at the highly conserved sequence region at residue Asn146. 2017 Scientific reports Result IV X181A 81 86 48 50 28860626 Topological N-glycosylation and site-specific N-glycan sulfation of influenza proteins in the highly expressed H1N1 candidate vaccines. The unique glycosylation site was located on either Lys136Asn of HA (NIBRG-121xp) or Asn88Gly of NA (NYMC-X181), which was demonstrated to have a significant effect on the growth yields of influenza viruses. 2017 Scientific reports Result IV K136N;N88G 52;85 61;93 HA;NA 65;97 67;99 28940727 Whole-genome sequencing and antigenic analysis of the first equine influenza virus identified in Turkey. A maximum-likelihood phylogenetic tree confirmed that A/equine Ankara/1/2013 is an FC2 strain as it clustered with other isolates in that clade that have the I179V substitution, that is the "179 group" (Figure 1). 2018 Influenza and other respiratory viruses Result IV I179V 158 163 28940727 Whole-genome sequencing and antigenic analysis of the first equine influenza virus identified in Turkey. A/equine/Ankara/1/2013 also has a substitution I214T which appears to be unique. 2018 Influenza and other respiratory viruses Result IV I214T 47 52 28940727 Whole-genome sequencing and antigenic analysis of the first equine influenza virus identified in Turkey. Comparison of HA amino acid sequences demonstrated that A/equine/Ankara/1/2013 HA has the fixed substitutions that emerged around 2007 (E291D) and 2010 (P103L and V112I).5, 30 In 2011, two subpopulations were identified with an additional change at either position 144 or at 179.30 A/equine/Ankara/1/2013 has the substitution I179V similar to A/equine/East Renfrewshire/2/2011, A/equine/Sweden/SVA111128SZ0073/VIR160172/2011, A/equine/Cambremer/1/2012 and A/equine/Saone et Loire/1/2015. 2018 Influenza and other respiratory viruses Result IV E291D;P103L;V112I;I179V 136;153;163;326 141;158;168;331 HA;HA 14;79 16;81 28940727 Whole-genome sequencing and antigenic analysis of the first equine influenza virus identified in Turkey. Four of the NA amino acid substitutions R109K, T381I, I410V, K415R and T434S are conserved in the majority of European FC2 viruses since 2009/2010. 2018 Influenza and other respiratory viruses Result IV R109K;T381I;I410V;K415R;T434S 40;47;54;61;71 45;52;59;66;76 12 14 28940727 Whole-genome sequencing and antigenic analysis of the first equine influenza virus identified in Turkey. However, the other non-structural protein PB1-F2 substitution D50V is highly conserved since 2010 and R75H is present in A/equine/Cambremer/1/2012 and A/equine/Saone et Loire/1/2015. 2018 Influenza and other respiratory viruses Result IV D50V;R75H 62;102 66;106 NS;PB1F2 19;42 33;48 28940727 Whole-genome sequencing and antigenic analysis of the first equine influenza virus identified in Turkey. Of the 13 amino acid substitutions in the polymerase complex, S107N (PB2), T221A (PB1), K158R and M210T (PA) are highly conserved in European FC2 viruses since 2009/2010, and D27N and A100T (PA) are present in A/equine/Perthshire/3/2009, A/equine/East Renfrewshire/2/2011, A/equine/Cambremer/1/2012 and A/equine/Saone et Loire/1/2015, but the other seven substitutions appear to be unique to A/equine/Ankara/1/2013. 2018 Influenza and other respiratory viruses Result IV S107N;T221A;K158R;M210T;D27N;A100T 62;75;88;98;175;184 67;80;93;103;179;189 PA;PA;PB1;PB2 105;191;82;69 107;193;85;72 28940727 Whole-genome sequencing and antigenic analysis of the first equine influenza virus identified in Turkey. The M2 ion channel protein has 2 amino acid changes (D21G and V68I). 2018 Influenza and other respiratory viruses Result IV D21G;V68I 53;62 57;66 M2 4 6 28940727 Whole-genome sequencing and antigenic analysis of the first equine influenza virus identified in Turkey. The non-structural proteins PB1-F2 and NS1 have 2 (D50V and R75H) and 5 (H17N, E26G, T80I, V111A and Y207H) amino acid changes, respectively. 2018 Influenza and other respiratory viruses Result IV D50V;R75H;H17N;E26G;T80I;V111A;Y207H 51;60;73;79;85;91;101 55;64;77;83;89;96;106 NS;NS1;PB1F2 4;39;28 18;42;34 28940727 Whole-genome sequencing and antigenic analysis of the first equine influenza virus identified in Turkey. The structural NP, M1 and NEP proteins have 2 (M239V and N473S), 1 (T168I)) and 1 (R86G) amino acid changes, respectively. 2018 Influenza and other respiratory viruses Result IV M239V;N473S;T168I;R86G 47;57;68;83 52;62;73;87 M1;NEP;NP 19;26;15 21;29;17 28940727 Whole-genome sequencing and antigenic analysis of the first equine influenza virus identified in Turkey. The surface glycoproteins HA and NA have 5 and 6 amino acid changes, respectively (HA: P103L, V112I, I179V, I214T, E291D, NA: G47R, R109K, T381I, I410V, K415R, T434S) (Table 2). 2018 Influenza and other respiratory viruses Result IV P103L;V112I;I179V;I214T;E291D;G47R;R109K;T381I;I410V;K415R;T434S 87;94;101;108;115;126;132;139;146;153;160 92;99;106;113;120;130;137;144;151;158;165 HA;HA;NA;NA 26;83;33;122 28;85;35;124 28940727 Whole-genome sequencing and antigenic analysis of the first equine influenza virus identified in Turkey. The T381I substitution is less common but present in A/equine/East Renfrewshire/2/2011 and A/equine/Saone et Loire/1/2015. 2018 Influenza and other respiratory viruses Result IV T381I 4 9 28940727 Whole-genome sequencing and antigenic analysis of the first equine influenza virus identified in Turkey. Within the RNA-dependent polymerase complex (PB2, PB1 and PA), a total of 3 (S107N, R389K and R586K), 3 (E75K, T221A and H456Y) and 7 (K22R, D27N, A100T, K158R, M210T, D394N and R531K) amino acid changes were observed, respectively. 2018 Influenza and other respiratory viruses Result IV S107N;R389K;R586K;E75K;T221A;H456Y;K22R;D27N;A100T;K158R;M210T;D394N;R531K 77;84;94;105;111;121;135;141;147;154;161;168;178 82;89;99;109;116;126;139;145;152;159;166;173;183 PA;PB1;PB2 58;50;45 60;53;48 28951584 Identification of neuraminidase inhibitors against dual H274Y/I222R mutant strains. Besides the H274Y/I222R mutant sites, the dual mutant and wild type structure do not significantly differ. 2017 Scientific reports Result IV H274Y;I222R 12;18 17;23 28951584 Identification of neuraminidase inhibitors against dual H274Y/I222R mutant strains. Finally, the identified compounds showed less than 10 microM inhibition for the H274Y and I222R mutant strains. 2017 Scientific reports Result IV H274Y;I222R 80;90 85;95 28951584 Identification of neuraminidase inhibitors against dual H274Y/I222R mutant strains. For instance, the H274Y mutation occurs in the sialic site and will also reduce the interaction energy between residues R224 and E276. 2017 Scientific reports Result IV H274Y 18 23 28951584 Identification of neuraminidase inhibitors against dual H274Y/I222R mutant strains. For the H274Y mutation, NSC162535 and NSC45609 contained showed better inhibition than GS4071 (oseltamivir carboxylate), though zanamivir continued to show a greater inhibition for this strain. 2017 Scientific reports Result IV H274Y 8 13 NS;NS 24;38 26;40 28951584 Identification of neuraminidase inhibitors against dual H274Y/I222R mutant strains. Furthermore, E119G mutation will reduce zanamivir susceptibility 1,400-fold, suggesting this anchor could play an important role in designing NA inhibitors for the sialic acid binding site. 2017 Scientific reports Result IV E119G 13 18 142 144 28951584 Identification of neuraminidase inhibitors against dual H274Y/I222R mutant strains. However, the H274Y mutation produces a strain resistant to oseltamivir. 2017 Scientific reports Result IV H274Y 13 18 28951584 Identification of neuraminidase inhibitors against dual H274Y/I222R mutant strains. However, the surface view of the dual mutant structure shows a change in volume and polarity within the binding site due to the H274Y/I222R residue mutation. 2017 Scientific reports Result IV H274Y;I222R 128;134 133;139 28951584 Identification of neuraminidase inhibitors against dual H274Y/I222R mutant strains. In addition, inhibitory activities of these inhibitors were tested on H1N1 and H5N1 NAs with H274Y (NAH274Y). 2017 Scientific reports Result IV H274Y 93 98 NA;NA 100;84 102;87 28951584 Identification of neuraminidase inhibitors against dual H274Y/I222R mutant strains. In addition, the dual mutation (H274Y and I222R) causes ~20, ~12,000, and ~7,500-fold reduction in NA inhibition for zanamivir, oseltamivir, and peramivir, respectively. 2017 Scientific reports Result IV H274Y;I222R 32;42 37;47 99 101 28951584 Identification of neuraminidase inhibitors against dual H274Y/I222R mutant strains. It should be noted that these three new 150-cavity inhibitors were not located within the V4 anchor, which contains residues I222 and H274, suggesting that these inhibitors may not be affected by the two drug-resistant mutations R292K, N294S and H274Y. 2017 Scientific reports Result IV R292K;N294S;H274Y 229;236;246 234;241;251 28951584 Identification of neuraminidase inhibitors against dual H274Y/I222R mutant strains. Meanwhile, H5N1 NAs with H274Y (NAH274Y) mutation did not show a strong inhibitory effect. 2017 Scientific reports Result IV H274Y 25 30 NA;NA 32;16 34;19 28951584 Identification of neuraminidase inhibitors against dual H274Y/I222R mutant strains. The fluorescent fold change of the identified compounds performed better for the I22R and the H274Y/I222R strains compared to zanamivir and GS4071. 2017 Scientific reports Result IV I22R;H274Y;I222R 81;94;100 85;99;105 28951584 Identification of neuraminidase inhibitors against dual H274Y/I222R mutant strains. The I222R mutation has been previously shown to reduce the volume of the binding site. 2017 Scientific reports Result IV I222R 4 9 28951584 Identification of neuraminidase inhibitors against dual H274Y/I222R mutant strains. The identified compounds showed comparable inhibition for the I222R mutant strains. 2017 Scientific reports Result IV I222R 62 67 28951584 Identification of neuraminidase inhibitors against dual H274Y/I222R mutant strains. The protein sequence of the strain NIBRG14 (H5N1) with the H274Y/I222R mutations was submitted for the server. 2017 Scientific reports Result IV I222R;H274Y 65;59 70;64 28951584 Identification of neuraminidase inhibitors against dual H274Y/I222R mutant strains. The substitution of tyrosine for the H274Y mutant may further reduce the size of the hydrophobic pocket of the binding site. 2017 Scientific reports Result IV H274Y 37 42 28951584 Identification of neuraminidase inhibitors against dual H274Y/I222R mutant strains. This includes the mutations R292K (E1 and V2) and E119V (H1) to name a few. 2017 Scientific reports Result IV R292K;E119V 28;50 33;55 28951584 Identification of neuraminidase inhibitors against dual H274Y/I222R mutant strains. We subsequently tested the inhibitory activities of the 150-cavity inhibitors on H1N1 and H5N1 wild-type and with H274Y (NAH274Y), I222R (NAI222R), and H274Y & I222R (NAH274Y&I222R) mutant strains. 2017 Scientific reports Result IV H274Y;I222R;I222R;H274Y;I222R 114;175;131;152;160 119;180;136;157;165 NA;NA;NAI 121;167;138 123;169;141 28966609 Amino Acid Substitutions Associated with Avian H5N6 Influenza A Virus Adaptation to Mice. A previous study demonstrated that the HA Q227P substitution increased the ability of guinea pig-adapted H9N2 to bind an avian alpha2,3 receptor and did not affect its binding ability to a human alpha2,6 receptor, and demonstrated the critical effects of this mutation for influenza virus transmission in guinea pigs by direct contact. 2017 Frontiers in microbiology Result IV Q227P 42 47 HA 39 41 28966609 Amino Acid Substitutions Associated with Avian H5N6 Influenza A Virus Adaptation to Mice. Additionally, the PB2 E627K mutation could increase the strength of polymerase nucleocapsid binding and modulate nucleocapsid inhibition via the pathogen sensor RIG-I. 2017 Frontiers in microbiology Result IV E627K 22 27 PB2 18 21 28966609 Amino Acid Substitutions Associated with Avian H5N6 Influenza A Virus Adaptation to Mice. Alone or in combination with PB2 E627K, PA T97I was shown to enhance the polymerase activity, replication efficiency, and pathogenicity of influenza A virus to aid the adaptation of virus to mice, and this was also true for H5N2 and H7N9. 2017 Frontiers in microbiology Result IV E627K;T97I 33;43 38;47 PA;PB2 40;29 42;32 28966609 Amino Acid Substitutions Associated with Avian H5N6 Influenza A Virus Adaptation to Mice. Eight amino acid substitutions were identified, two in the HA subunit (I67V, R239H), two in the polymerase basic protein 2 (PB2) subunit (T23I, E627K), two in the polymerase acidic (PA) subunit (T97I, S388C) and two in the nucleoprotein (NP) subunit (H52Y, A430T) (Table 1). 2017 Frontiers in microbiology Result IV I67V;R239H;T23I;E627K;T97I;S388C;H52Y;A430T 71;77;138;144;195;201;251;257 75;82;142;149;199;206;255;262 HA;NP;NP;PA;PB2;PA 59;238;223;182;124;163 61;240;236;184;127;180 28966609 Amino Acid Substitutions Associated with Avian H5N6 Influenza A Virus Adaptation to Mice. In the present work, the PB2 E627K mutation played important roles in the early adaptation of the H5N6 virus to mice. 2017 Frontiers in microbiology Result IV E627K 29 34 PB2 25 28 28966609 Amino Acid Substitutions Associated with Avian H5N6 Influenza A Virus Adaptation to Mice. In this study, PA T97I and PB2 E627K together aided the adaptation of WT H5N6 virus to mice and enhanced the pathogenicity of P10. 2017 Frontiers in microbiology Result IV T97I;E627K 18;31 22;36 PA;PB2 15;27 17;30 28966609 Amino Acid Substitutions Associated with Avian H5N6 Influenza A Virus Adaptation to Mice. Most (five of eight) amino acid changes, including HA I67V, PA S388C, PB2 E627K, NP H52Y, and NP A430T, first occurred in the P1 virus, indicating that the WT H5N6 virus rapidly adapted in the presence of selective pressure in mice. 2017 Frontiers in microbiology Result IV I67V;S388C;E627K;H52Y;A430T 54;63;74;84;97 58;68;79;88;102 HA;NP;NP;PA;PB2 51;81;94;60;70 53;83;96;62;73 28966609 Amino Acid Substitutions Associated with Avian H5N6 Influenza A Virus Adaptation to Mice. PB2 E627K can aid the adaptation of influenza A virus to mammals in two ways. 2017 Frontiers in microbiology Result IV E627K 4 9 PB2 0 3 28966609 Amino Acid Substitutions Associated with Avian H5N6 Influenza A Virus Adaptation to Mice. PB2 T23I was identified in P2, HA R239H was found in P6 and T97I was first observed in P7. 2017 Frontiers in microbiology Result IV T23I;R239H;T97I 4;34;60 8;39;64 HA;PB2 31;0 33;3 28966609 Amino Acid Substitutions Associated with Avian H5N6 Influenza A Virus Adaptation to Mice. R239H (227 in H3 numbering) found in P6 was located in the 220 loop of influenza virus receptor binding sites. 2017 Frontiers in microbiology Result IV R239H 0 5 28966609 Amino Acid Substitutions Associated with Avian H5N6 Influenza A Virus Adaptation to Mice. The PA T97I substitution observed in P7 has also been identified in many other mouse-adapted influenza A viruses, such as H5N2, H6N1, H7N9, and H10N7. 2017 Frontiers in microbiology Result IV T97I 7 11 PA 4 6 28966609 Amino Acid Substitutions Associated with Avian H5N6 Influenza A Virus Adaptation to Mice. The PB2 E627K substitution found in P1 has been identified in many other mouse-adapted influenza viruses, including H5N1, H7N9, and H9N2. 2017 Frontiers in microbiology Result IV E627K 8 13 PB2 4 7 28966609 Amino Acid Substitutions Associated with Avian H5N6 Influenza A Virus Adaptation to Mice. The PB2 E627K substitution is one of the most common amino acid substitutions in different influenza viruses subtypes adapted in mice and occurs at the early stage of influenza A virus mouse adaptation. 2017 Frontiers in microbiology Result IV E627K 8 13 PB2 4 7 28966609 Amino Acid Substitutions Associated with Avian H5N6 Influenza A Virus Adaptation to Mice. The PB2 T23I substitution, which was first identified in P2 in our work, is located in the N-terminal domain of PB2, and we speculated that it might also inhibit IFN-beta expression and the immune escape of IFN-beta antiviral effects. 2017 Frontiers in microbiology Result IV T23I 8 12 PB2;PB2 4;112 7;115 28966609 Amino Acid Substitutions Associated with Avian H5N6 Influenza A Virus Adaptation to Mice. This amino acid substitution was also found in another mouse-adapted H5N6 influenza virus of duck origin, whereas other mutations including PA A343T, NA R143K, and NA G147E described in Peng's work were not found in our study. 2017 Frontiers in microbiology Result IV A343T;R143K;G147E 143;153;167 148;158;172 NA;NA;PA 150;164;140 152;166;142 28966609 Amino Acid Substitutions Associated with Avian H5N6 Influenza A Virus Adaptation to Mice. Thus PB2 T97I plays important roles in the late adaptation of H5N6 to mice. 2017 Frontiers in microbiology Result IV T97I 9 13 PB2 5 8 28966609 Amino Acid Substitutions Associated with Avian H5N6 Influenza A Virus Adaptation to Mice. Thus, PB2 E627K enhanced the replication capacity and pathogenicity of P1 compared with WT H5N6 (Figures 1-3). 2017 Frontiers in microbiology Result IV E627K 10 15 PB2 6 9 28966609 Amino Acid Substitutions Associated with Avian H5N6 Influenza A Virus Adaptation to Mice. We speculated that HA R227H could also improve the ability of P10 to bind avian alpha2,3 receptors and may confer transmissibility to P10. 2017 Frontiers in microbiology Result IV R227H 22 27 HA 19 21 29023600 Reduced accumulation of defective viral genomes contributes to severe outcome in influenza virus infected patients. Altogether, these data demonstrate that a mutated PA D529N derived from a fatal-case IAV decreases DVGs generation and support the idea that reduced DG accumulation is a pathogenic determinant for influenza virus in mice. 2017 PLoS pathogens Result IV D529N 53 58 PA 50 52 29023600 Reduced accumulation of defective viral genomes contributes to severe outcome in influenza virus infected patients. As predicted, introduction of the PA D529N mutation on the M mut background decreased the DVGs proportion (4-fold; Fig 5C, compare M-PA mut vs M mut). 2017 PLoS pathogens Result IV D529N 37 42 M;M;M;PA;PA 59;131;143;34;133 60;132;144;36;135 29023600 Reduced accumulation of defective viral genomes contributes to severe outcome in influenza virus infected patients. Changes in the viral polymerase PA (D529N) and PB2 (A221T) subunits and the surface glycoprotein HA (S127L) found in <1% of viruses circulating during 2009 influenza season were considered specific and potentially responsible for the difference in virulence. 2017 PLoS pathogens Result IV D529N;A221T;S127L 36;52;101 41;57;106 HA;PA;PB2 97;32;47 99;34;50 29023600 Reduced accumulation of defective viral genomes contributes to severe outcome in influenza virus infected patients. DVGs distribution per viral segment for total DVGs found in each virus is shown for the entire severe/fatal (Fig 10A and S12A Fig) and mild-associated case virus collection (Fig 10B and S12B Fig). 2017 PLoS pathogens Result IV S12A 121 125 29023600 Reduced accumulation of defective viral genomes contributes to severe outcome in influenza virus infected patients. Recombinant viruses with PA D529N change (PA mut and PB2/PA mut) induced higher infiltration of neutrophils and significant depletion of alveolar macrophages than attenuated PB2 mut virus at 2dpi in the lungs of infected animals (Fig 8B and 8C). 2017 PLoS pathogens Result IV D529N 28 33 PA;PA;PA;PB2;PB2 25;42;57;53;174 27;44;59;56;177 29023600 Reduced accumulation of defective viral genomes contributes to severe outcome in influenza virus infected patients. Since DVGs are mainly produced by the viral polymerase, PA D529N and PB2 A 221T changes in the polymerase subunits were selected as putative responsible for low DVGs production and increased pathogenicity of F-IAV. 2017 PLoS pathogens Result IV D529N;A221T 59;73 64;79 PA;PB2 56;69 58;72 29023600 Reduced accumulation of defective viral genomes contributes to severe outcome in influenza virus infected patients. Thereby, PA D529N present in a fatal-case virus is able to decrease the amount of DVGs in two different genetic backgrounds (Fig 5D), reinforcing the notion that this mutation itself confers this ability. 2017 PLoS pathogens Result IV D529N 12 17 PA 9 11 29023600 Reduced accumulation of defective viral genomes contributes to severe outcome in influenza virus infected patients. These data confirmed that CAL virus is pathogenic in mice and indicated that the PA D529N mutation greatly increased pathogenicity, suggesting a decisive effect of this polymerase change on disease outcome. 2017 PLoS pathogens Result IV D529N 84 89 PA 81 83 29023600 Reduced accumulation of defective viral genomes contributes to severe outcome in influenza virus infected patients. These data indicated that the PB2 A221T mutation enabled high DVGs accumulation (Fig 5A; compare CAL vs PB2 mut), whereas PA D529N mutation restricted their accumulation (Fig 5A; compare PB2 mut vs PB2/PA mut). 2017 PLoS pathogens Result IV A221T;D529N 34;125 39;130 PA;PA;PB2;PB2;PB2;PB2 122;202;30;104;187;198 124;204;33;107;190;201 29023600 Reduced accumulation of defective viral genomes contributes to severe outcome in influenza virus infected patients. These two alterations in cellular immune response observed for viruses carrying PA D529N change have been described as essential factors for lethal influenza virus infections and agree with the role of PA D529N change in pathogenicity in vivo. 2017 PLoS pathogens Result IV D529N;D529N 83;205 88;210 PA;PA 80;202 82;204 IV infections 148 174 29023600 Reduced accumulation of defective viral genomes contributes to severe outcome in influenza virus infected patients. To confirm that the PA D529N mutation in F-IAV has a major effect on the ability to produce low DVGs numbers, we generated recombinant CAL viruses bearing mutations in genes other than polymerase subunits, such as matrix 1 (M1) and matrix 2 (M2) viral genes (M1 S30N + M2 V86S). 2017 PLoS pathogens Result IV D529N;S30N;V86S 23;262;272 28;266;276 M1;M1;M2;M2;M;M;PA 224;259;242;269;214;232;20 226;261;244;271;220;238;22 29023600 Reduced accumulation of defective viral genomes contributes to severe outcome in influenza virus infected patients. To further characterize the role of mutations in the F-IAV polymerase subunits as virulence determinants, we generated on the A/H1N1/California/04/09 virus backbone (CAL), recombinant influenza viruses bearing the combination of PA D529N and PB2 A221T mutations (PB2/PA mut; F-IAV-like polymerase), or viruses bearing single PA D529N (PA mut) or PB2 A221T (PB2 mut) mutations (Table 1). 2017 PLoS pathogens Result IV D529N;A221T;D529N;A221T 232;246;328;350 237;251;333;355 PA;PA;PA;PA;PB2;PB2;PB2;PB2 229;267;325;335;242;263;346;357 231;269;327;337;245;266;349;360 29023600 Reduced accumulation of defective viral genomes contributes to severe outcome in influenza virus infected patients. We deep-sequenced RNA from virions purified from recombinant viruses with these M1/M2 mutations, alone (M mut) or with these M1/M2 mutations and PA D529N mutation (M-PA mut). 2017 PLoS pathogens Result IV D529N 148 153 M;M;M1;M1;M2;M2;PA;PA 104;164;80;125;83;128;145;166 105;165;82;127;85;130;147;168 29097654 Role of influenza A virus NP acetylation on viral growth and replication. As expected, reconstitution of VLPs comprising NP-K229Q in the presence of eight genome segments was reduced compared to wt SC35M NP. 2017 Nature communications Result IV K229Q 50 55 NP;NP 47;130 49;132 29097654 Role of influenza A virus NP acetylation on viral growth and replication. As expected, we could generate recombinant SC35M mutant viruses encoding NP-K77R, NP-K113R or NP-K229R. 2017 Nature communications Result IV K77R;K113R;K229R 76;85;97 80;90;102 NP;NP;NP 73;82;94 75;84;96 29097654 Role of influenza A virus NP acetylation on viral growth and replication. Astonishingly, both mutant viruses could be generated by reverse genetics, although rK77Q,K229Q revealed a virus stock titer that was 2770 fold lower than r77R,K229R. 2017 Nature communications Result IV K229Q;K229R 90;160 95;165 29097654 Role of influenza A virus NP acetylation on viral growth and replication. both SC35M-NP-K77Q and SC35M-NP-K113Q supported polymerase activity to comparable levels as wt NP, whereas the polymerase activity in the presence of SC35M-NP-K229Q was reduced to 59%, despite comparable protein expression. 2017 Nature communications Result IV K77Q;K229Q;K113Q 14;159;32 18;164;37 NP;NP;NP;NP 11;29;95;156 13;31;97;158 29097654 Role of influenza A virus NP acetylation on viral growth and replication. Considering, that various NP lysine residues might be concurrently acetylated, we generated SC35M NP mutant proteins harboring either two K to R or K to Q substitutions at position 77 and 229 and tested these mutants upon polymerase reconstitution in HEK293T cells. 2017 Nature communications Result IV K77Q 148 183 NP;NP 26;98 28;100 29097654 Role of influenza A virus NP acetylation on viral growth and replication. Enhanced levels of viral transcripts were also obtained with NP-K77R,K229R. 2017 Nature communications Result IV K77R;K229R 64;69 68;74 NP 61 63 29097654 Role of influenza A virus NP acetylation on viral growth and replication. Hence, decreased polymerase activity in presence of NP-K77Q,K229Q is not due to impaired PB2 binding but a step in the viral replication. 2017 Nature communications Result IV K77Q;K229Q 55;60 59;65 NP;PB2 52;89 54;92 29097654 Role of influenza A virus NP acetylation on viral growth and replication. However, even though both WSN NP non-acetylation mutants NP-K77R and NP-K229R supported polymerase activity, we already failed to generate recombinant WSN viruses expressing NP-K229R. 2017 Nature communications Result IV K77R;K229R;K229R 60;72;177 64;77;182 NP;NP;NP;NP 30;57;69;174 32;59;71;176 29097654 Role of influenza A virus NP acetylation on viral growth and replication. However, reconstitution with NP-K229R resulted in fewer VLPs. 2017 Nature communications Result IV K229R 32 37 NP 29 31 29097654 Role of influenza A virus NP acetylation on viral growth and replication. However, similar nuclear accumulation of wt SC35M NP, NP-K77R,K229R and NP-K77Q,K229Q was observed after transient expression of these proteins in HEK293T cells. 2017 Nature communications Result IV K77R;K229R;K77Q;K229Q 57;62;75;80 61;67;79;85 NP;NP;NP 50;54;72 52;56;74 29097654 Role of influenza A virus NP acetylation on viral growth and replication. however, succeeded as expected with NP-K113R. 2017 Nature communications Result IV K113R 39 44 NP 36 38 29097654 Role of influenza A virus NP acetylation on viral growth and replication. However, we were able to rescue both NP-K77Q (rK77Q) and NP-K229Q (rK229Q) in the context of SC35M. 2017 Nature communications Result IV K77Q;K229Q 40;60 44;65 NP;NP 37;57 39;59 29097654 Role of influenza A virus NP acetylation on viral growth and replication. immunoprecipitation of wt SC35M NP or NP-K77R,K229R using NP-specific antibodies resulted in the co-immunoprecipitation of PB2, whereas only residual PB2 levels were observed after immunoprecipitation of NP-K77Q,K229Q. 2017 Nature communications Result IV K77R;K229R;K77Q;K229Q 41;46;207;212 45;51;211;217 NP;NP;NP;NP;PB2;PB2 32;38;58;204;123;150 34;40;60;206;126;153 29097654 Role of influenza A virus NP acetylation on viral growth and replication. In contrast, in the presence of NP-K77Q,K229Q fewer cRNA and vRNA levels were observed. 2017 Nature communications Result IV K77Q;K229Q 35;40 39;45 NP 32 34 29097654 Role of influenza A virus NP acetylation on viral growth and replication. In contrast, mimicking constant acetylation (NP-K77Q,K229Q) severely diminished polymerase activity to below 5%. 2017 Nature communications Result IV K77Q;K229Q 48;53 52;58 NP 45 47 29097654 Role of influenza A virus NP acetylation on viral growth and replication. In line with the results obtained for mutant virus rK229R, the double mutant rK77R,K229R showed impaired viral growth in MDCK II cells at early time points of infection. 2017 Nature communications Result IV K229R 83 88 29097654 Role of influenza A virus NP acetylation on viral growth and replication. Infection of MDCK II cells with VLPs reconstituted with wt SC35M NP or NP-K77R and subsequent superinfection with wt SC35M resulted in numerous eGFP-expressing cells, indicating successful incorporation of the reporter segment. 2017 Nature communications Result IV K77R 74 78 NP;NP 65;71 67;73 29097654 Role of influenza A virus NP acetylation on viral growth and replication. Interestingly, in a parallel polymerase reconstitution experiment in which the viral minigenome was excluded (no functional vRNP formation) lower levels of PB2 were co-immunoprecipitated with wt SC35M NP, NP-K77R,K229R and NP-K77Q,K229Q. 2017 Nature communications Result IV K77R;K229R;K77Q;K229Q 208;213;226;231 212;218;230;236 NP;NP;NP;PB2 201;205;223;156 203;207;225;159 29097654 Role of influenza A virus NP acetylation on viral growth and replication. Intriguingly, though we observed wt-like activity of NP-K113Q in the polymerase reconstitution assay, we could not generate SC35M virus encoding this mutant protein. 2017 Nature communications Result IV K113Q 56 61 NP 53 55 29097654 Role of influenza A virus NP acetylation on viral growth and replication. Next we tried to rescue SC35M mutant viruses encoding either NP-K77R,K229R (rK77R,K229R) or NP-K77Q,K229Q (rK77Q,K229Q). 2017 Nature communications Result IV K77R;K77Q;K229R;K229R;K229Q;K229Q 64;95;69;82;100;113 68;99;74;87;105;118 NP;NP 61;92 63;94 29097654 Role of influenza A virus NP acetylation on viral growth and replication. Polymerase reconstitution with the NP mutant NP-K77R,K229R mimicking constant non-acetylation resulted in 107% polymerase activity, compared to wt SC35M NP. 2017 Nature communications Result IV K77R;K229R 48;53 52;58 NP;NP;NP 35;45;153 37;47;155 29097654 Role of influenza A virus NP acetylation on viral growth and replication. revealed that the two arginine substitutions of rK77R,K229R were maintained, whereas in cells infected with rK77Q,K229Q, an escape mutation emerged, restoring a wt-like lysine residue at position 229. 2017 Nature communications Result IV K229R;K229Q;K77R;K77Q 54;114;49;109 59;119;53;113 29097654 Role of influenza A virus NP acetylation on viral growth and replication. Strikingly, no attenuation was observed with rK77Q,K229Q. 2017 Nature communications Result IV K229Q;K77Q 51;46 56;50 29097654 Role of influenza A virus NP acetylation on viral growth and replication. Taken together, these results indicate that the NP mutant protein NP-K229R causes a block in the efficient release of infectious virions. 2017 Nature communications Result IV K229R 69 74 NP;NP 48;66 50;68 29097654 Role of influenza A virus NP acetylation on viral growth and replication. the NP mutation K229Q might also diminish release of viral particles as the NP mutation K229R. 2017 Nature communications Result IV K229Q;K229R 16;88 21;93 NP;NP 4;76 6;78 29097654 Role of influenza A virus NP acetylation on viral growth and replication. The NP mutation K229R impairs viral particle release. 2017 Nature communications Result IV K229R 16 21 NP 4 6 29097654 Role of influenza A virus NP acetylation on viral growth and replication. To elucidate the influence of NP acetylation on viral polymerase activity, we generated NP mutant proteins of SC35M and WSN with individual K to arginine (R) mutations (NP-K77R, NP-K113R, NP-K229R) with the exception of WSN NP-K113R. 2017 Nature communications Result IV K77R;K113R;K229R;K113R 172;181;191;227 176;186;196;232 NP;NP;NP;NP;NP;NP 30;88;169;178;188;224 32;90;171;180;190;226 29097654 Role of influenza A virus NP acetylation on viral growth and replication. Together these results suggest that NP-K77Q,K229Q fails to efficiently stabilize cRNA, thereby abrogating the viral replication process. 2017 Nature communications Result IV K77Q;K229Q 39;44 43;49 NP 36 38 29097654 Role of influenza A virus NP acetylation on viral growth and replication. we could not reconstitute VLPs in the presence of NP-K113Q. 2017 Nature communications Result IV K113Q 53 58 NP 50 52 29097654 Role of influenza A virus NP acetylation on viral growth and replication. we detected robust eGFP expression in HEK293T cells for wt SC35M NP, NP-K77R and NP-K229R. 2017 Nature communications Result IV K77R;K229R 72;84 76;89 NP;NP;NP 65;69;81 67;71;83 29097654 Role of influenza A virus NP acetylation on viral growth and replication. We excluded K113 from this analysis, since the NP mutation K113Q abrogates viral growth, impeding potential further analysis in the context of infectious virus. 2017 Nature communications Result IV K113Q 59 64 NP 47 49 29097654 Role of influenza A virus NP acetylation on viral growth and replication. With the exception of the WSN NP mutant NP-K229R all other K to R mutant proteins resulted in similar or even enhanced polymerase activities compared to wildtype (wt) WSN or SC35M NP, respectively. 2017 Nature communications Result IV K229R 43 48 NP;NP;NP 30;40;180 32;42;182 29100932 Evolution of equine influenza viruses (H3N8) during a Brazilian outbreak, 2015. Five amino acid substitutions were found in SP-2015 NA but not in A/equine/Rio Grande do Sul/1/2012: L36P, R40G, R171K, E411G and H450Y. 2018 Brazilian journal of microbiology Result IV L36P;R40G;R171K;E411G;H450Y 101;107;113;120;130 105;111;118;125;135 52 54 29100932 Evolution of equine influenza viruses (H3N8) during a Brazilian outbreak, 2015. Four of these substitutions were not present in the Brazilian 2012 outbreak strain (N3S, T121S, G142R and K304E) (Table 1). 2018 Brazilian journal of microbiology Result IV N3S;T121S;G142R;K304E 84;89;96;106 87;94;101;111 29100932 Evolution of equine influenza viruses (H3N8) during a Brazilian outbreak, 2015. Sao Paulo/15 NA sequences had 39 nt changes and there were 11 aa changes in relation to A/equine/Ohio1/03 (FC1): one in the transmembrane helix (V35A) and ten in the head domain. 2018 Brazilian journal of microbiology Result IV V35A 145 149 13 15 29100932 Evolution of equine influenza viruses (H3N8) during a Brazilian outbreak, 2015. The 2012 and 2015 Brazilian strains shared the substitutions V35A, N205S, R260K, E271G, S337N and G416E. 2018 Brazilian journal of microbiology Result IV V35A;N205S;R260K;E271G;S337N;G416E 61;67;74;81;88;98 65;72;79;86;93;103 29145498 Antigenicity of the 2015-2016 seasonal H1N1 human influenza virus HA and NA proteins. Additionally, there were variations in the HA stalk domain between the viruses infecting the 9 patients, as only two viruses (infecting patients ACU004 and 017) encoded substitution T472N (Table 1). 2017 PloS one Result IV T472N 182 187 HA 43 45 29145498 Antigenicity of the 2015-2016 seasonal H1N1 human influenza virus HA and NA proteins. All isolated viruses encoded the same HA head domain except for virus ACU009, which lacked the S179N mutation. 2017 PloS one Result IV S179N 95 100 HA 38 40 29145498 Antigenicity of the 2015-2016 seasonal H1N1 human influenza virus HA and NA proteins. All isolates encoded the same NA sequence, with the exception of viruses infecting patients ACU008 and 022, which did not encode the mutation I34V. 2017 PloS one Result IV I34V 142 146 30 32 29145498 Antigenicity of the 2015-2016 seasonal H1N1 human influenza virus HA and NA proteins. As seen on a 3D model of the NA protein (RCSB PDB ID: 3NSS), 5 out of the 14 mutations (N200S, N248D, I321V, N369K, and K432E) were at previously characterized Ab-binding sites (Fig 1C). 2017 PloS one Result IV N200S;N248D;I321V;N369K;K432E 88;95;102;109;120 93;100;107;114;125 29 31 29145498 Antigenicity of the 2015-2016 seasonal H1N1 human influenza virus HA and NA proteins. As shown on a 3D model of the HA protein (RCSB PDB ID: 3LZG), 5 mutations were found in previously characterized Ab-binding sites: S179N and K180Q, in Sa; P200S and S202T, in Sb; and S220T, in Ca1 (Fig 1A and Table 1). 2017 PloS one Result IV S179N;K180Q;P200S;S202T;S220T 131;141;155;165;183 136;146;160;170;188 HA 30 32 29145498 Antigenicity of the 2015-2016 seasonal H1N1 human influenza virus HA and NA proteins. Notably, strains encoding an HA protein with five of the mutations (P100S, P200S, S220T, I338V, and T214A) became the dominant circulating strains early in 2009 following detection of the outbreak (Fig 3). 2017 PloS one Result IV P100S;P200S;S220T;I338V;T214A 68;75;82;89;100 73;80;87;94;105 HA 29 31 29145498 Antigenicity of the 2015-2016 seasonal H1N1 human influenza virus HA and NA proteins. The HA sequences of viruses grown in MDCK cells were the same as those of viruses present in the original nasal washes/swabs (data not shown), with the exception of viruses isolated from patients ACU007 and ACU017, that introduced an additional mutation S207R (Table 1). 2017 PloS one Result IV S207R 254 259 HA 4 6 29145498 Antigenicity of the 2015-2016 seasonal H1N1 human influenza virus HA and NA proteins. Three of the mutations (K432E along the 430 loop, V241I and N248D) were located near the catalytic site (Fig 1D). 2017 PloS one Result IV K432E;V241I;N248D 24;50;60 29;55;65 29145498 Antigenicity of the 2015-2016 seasonal H1N1 human influenza virus HA and NA proteins. Three of the mutations (P200S and S202T close to the 190 alpha helix, and I233T along the 220 loop) were in close proximity to the receptor-binding domain (Fig 1B). 2017 PloS one Result IV P200S;S202T;I233T 24;34;74 29;39;79 29145498 Antigenicity of the 2015-2016 seasonal H1N1 human influenza virus HA and NA proteins. With respect to the NA protein, only one mutation, N248D, appeared in the NA protein of circulating strains immediately following the outbreak in early 2009 (Fig 4). 2017 PloS one Result IV N248D 51 56 NA;NA 20;74 22;76 29299528 Human Clade 2.3.4.4 A/H5N6 Influenza Virus Lacks Mammalian Adaptation Markers and Does Not Transmit via the Airborne Route between Ferrets. A/H5N6 GZ/14 possesses a high polymerase activity, mediated by the E627K substitution in PB2. 2018 mSphere Result IV E627K 67 72 PB2 89 92 29299528 Human Clade 2.3.4.4 A/H5N6 Influenza Virus Lacks Mammalian Adaptation Markers and Does Not Transmit via the Airborne Route between Ferrets. Control HAs, the A/H5N1 IN/05 wild-type (WT) HA (unstable), the A/H5N1 IN/05 HA carrying airborne-transmission substitutions (H103Y, T156A, Q222L, and G224S [H5 numbering used throughout]) (stable), and the human A/H3N2 NL/03 HA (stable), were included. 2018 mSphere Result IV H103Y;T156A;Q222L;G224S 126;133;140;151 131;138;145;156 HA;HA;HA 45;77;226 47;79;228 29299528 Human Clade 2.3.4.4 A/H5N6 Influenza Virus Lacks Mammalian Adaptation Markers and Does Not Transmit via the Airborne Route between Ferrets. In order to understand whether the high polymerase activity of A/H5N6 GZ/14 was the result of the presence of PB2-627K, the PB2 gene of A/H5N6 GZ/14 was mutated to the avian genotype (K627E). 2018 mSphere Result IV K627E 184 189 PB2;PB2 110;124 113;127 29299528 Human Clade 2.3.4.4 A/H5N6 Influenza Virus Lacks Mammalian Adaptation Markers and Does Not Transmit via the Airborne Route between Ferrets. These observations demonstrated that the high polymerase activity of A/H5N6 GZ/14 was mediated by the E627K substitution in PB2. 2018 mSphere Result IV E627K 102 107 PB2 124 127 29299533 Cooperating H3N2 Influenza Virus Variants Are Not Detectable in Primary Clinical Samples. Therefore, we conclude that the D151G variant was not present at appreciable frequencies in the original clinical infections. 2018 mSphere Result IV D151G 32 37 29299533 Cooperating H3N2 Influenza Virus Variants Are Not Detectable in Primary Clinical Samples. To ensure that we were not missing extremely low-frequency variation, we calculated the frequency of D151G in each clinical sample on the basis of the frequency of G-to-A mutations at the second nucleotide position of NA site 151. 2018 mSphere Result IV D151G 101 106 218 220 29299533 Cooperating H3N2 Influenza Virus Variants Are Not Detectable in Primary Clinical Samples. We did not observe the D151G variant in any of the nine clinical samples under these variant-calling criteria. 2018 mSphere Result IV D151G 23 28 29308074 Neuraminidase Gene Variations in Influenza A(H1N1)pdm09 Virus among Patients Admitted to Refferal Pulmonary Hospital, Tehran, Iran in 2009-2013. Mutations, including V106I, R130T, N200S, G201E, and G414R, were detected in the studied isolates, compared to the corresponding vaccine (Table 5). 2017 Tanaffos Result IV V106I;R130T;N200S;G201E;G414R 21;28;35;42;53 26;33;40;47;58 29308074 Neuraminidase Gene Variations in Influenza A(H1N1)pdm09 Virus among Patients Admitted to Refferal Pulmonary Hospital, Tehran, Iran in 2009-2013. The substitutions were as follows: I17V, A20T, N28D, L40I, L40V, N44S, V62I, S79P, V83M, S95N, D103N, V106I, C124R, R130T, P154S, N200S, G201E, N222D, V241I, N248D, R257K, V264A, K265P, H275Y, D284N, S285C, G320V, S334R, N369K, G414R, and T466P (Table 3). 2017 Tanaffos Result IV I17V;A20T;N28D;L40I;L40V;N44S;V62I;S79P;V83M;S95N;D103N;V106I;C124R;R130T;P154S;N200S;G201E;N222D;V241I;N248D;R257K;V264A;K265P;H275Y;D284N;S285C;G320V;S334R;N369K;G414R;T466P 35;41;47;53;59;65;71;77;83;89;95;102;109;116;123;130;137;144;151;158;165;172;179;186;193;200;207;214;221;228;239 39;45;51;57;63;69;75;81;87;93;100;107;114;121;128;135;142;149;156;163;170;177;184;191;198;205;212;219;226;233;244 29312300 Histone Deacetylase 1 Plays an Acetylation-Independent Role in Influenza A Virus Replication. 24 h postinfection, vRNA levels of the NP-K103A and NP-K103R mutant viruses were 8-fold and 2.5-fold higher, respectively, than that of the WT virus (Figure 3D). 2017 Frontiers in immunology Result IV K103A;K103R 42;55 47;60 NP;NP 39;52 41;54 29312300 Histone Deacetylase 1 Plays an Acetylation-Independent Role in Influenza A Virus Replication. Collectively, these data suggest that K103 is a key acetylation site and that the K103A and K103R mutants show increased virus replication levels in vitro than that in rWT. 2017 Frontiers in immunology Result IV K103A;K103R 82;92 87;97 29312300 Histone Deacetylase 1 Plays an Acetylation-Independent Role in Influenza A Virus Replication. First, we tested the replication function of K103A and K103R by using a mini-replicon system (containing luciferase as a reporter) that assays vRNA replication activity. 2017 Frontiers in immunology Result IV K103A;K103R 45;55 50;60 29312300 Histone Deacetylase 1 Plays an Acetylation-Independent Role in Influenza A Virus Replication. Growth analysis suggested that the virus titer of NP-rK103A/R mutant virus was twofold at 12 h and NP-rK103A fourfold at 48 h postinfection, compared to the rWT virus (Figures 3E,F). 2017 Frontiers in immunology Result IV K103A 103 108 NP;NP 50;99 52;101 29312300 Histone Deacetylase 1 Plays an Acetylation-Independent Role in Influenza A Virus Replication. HEK293T cells were transfected with NP-WT and NP-K103R expression plasmids with or without HDAC1. 2017 Frontiers in immunology Result IV K103R 49 54 NP;NP 36;46 38;48 29312300 Histone Deacetylase 1 Plays an Acetylation-Independent Role in Influenza A Virus Replication. However, the acetylation of NP-K103R was not downregulated (Figure 2G). 2017 Frontiers in immunology Result IV K103R 31 36 NP 28 30 29312300 Histone Deacetylase 1 Plays an Acetylation-Independent Role in Influenza A Virus Replication. The results showed that K103R reduced the 30% level of NP acetylation compared with that of the WT protein (Figures 2D,E). 2017 Frontiers in immunology Result IV K103R 24 29 NP 55 57 29312300 Histone Deacetylase 1 Plays an Acetylation-Independent Role in Influenza A Virus Replication. To assess the roles of K103 in virus life cycle, we introduced K103A/R substitution to mimic the K103 deacetylation state of NP protein. 2017 Frontiers in immunology Result IV K103A;K103R 63;63 70;70 NP 125 127 29312300 Histone Deacetylase 1 Plays an Acetylation-Independent Role in Influenza A Virus Replication. Two K103 NP mutants, K103A and K103R, lacking of regulation of K103 acetylation by HDAC1, enhanced the RNPs activity and replication efficiency of the recombinant viruses in vitro. 2017 Frontiers in immunology Result IV K103A;K103R 21;31 26;36 NP;RNP 9;103 11;107 29312300 Histone Deacetylase 1 Plays an Acetylation-Independent Role in Influenza A Virus Replication. We transfected HEK293T cells with the NP mutants (K91R, K103R, K198R, K227R, K229R, and K470R) and purified them by using Myc-tagged antibody and detected the Ace-NP using the Ace-lysine antibody. 2017 Frontiers in immunology Result IV K91R;K103R;K198R;K227R;K229R;K470R 50;56;63;70;77;88 54;61;68;75;82;93 NP;NP 38;163 40;165 29324781 Neuraminidase inhibitor susceptibility and neuraminidase enzyme kinetics of human influenza A and B viruses circulating in Thailand in 2010-2015. At 6 and 12 h post-infection (hpi), the growth of A/PR8-I222V virus was similar to that of A/PR8-WT, but the A/PR8-S331G and A/PR8-S331R virus yields were significantly lower (P < 0.05) (Fig 2A). 2018 PloS one Result IV I222V;S331G;S331R 56;115;131 61;120;136 29324781 Neuraminidase inhibitor susceptibility and neuraminidase enzyme kinetics of human influenza A and B viruses circulating in Thailand in 2010-2015. For recombinant influenza A viruses, the NA activity of the A/PR8-I222V virus was stable at 33 C to 55 C, whereas the A/PR8-S331G and A/PR8-S331R viruses showed lower activity at 55 C (Fig 1A and 1B). 2018 PloS one Result IV I222V;S331G;S331R 66;124;140 71;129;145 41 43 29324781 Neuraminidase inhibitor susceptibility and neuraminidase enzyme kinetics of human influenza A and B viruses circulating in Thailand in 2010-2015. In contrast, the B/YAM-D342S and B/YAM-A395T viruses had significantly higher NA activity when compared to the reference B/BR/60/08 virus (P < 0.01). 2018 PloS one Result IV D342S;A395T 23;39 28;44 78 80 29324781 Neuraminidase inhibitor susceptibility and neuraminidase enzyme kinetics of human influenza A and B viruses circulating in Thailand in 2010-2015. In contrast, the NAs of B/YAM viruses carrying D342S or A395T NA substitutions had a reduced Vmax (P < 0.05). 2018 PloS one Result IV D342S;A395T 47;56 52;61 NA;NA 62;17 64;20 29324781 Neuraminidase inhibitor susceptibility and neuraminidase enzyme kinetics of human influenza A and B viruses circulating in Thailand in 2010-2015. In contrast, virus carrying the D342S NA substitution possessed high NA activity that was thermostable (Fig 1C and 1D). 2018 PloS one Result IV D342S 32 37 NA;NA 38;69 40;71 29324781 Neuraminidase inhibitor susceptibility and neuraminidase enzyme kinetics of human influenza A and B viruses circulating in Thailand in 2010-2015. The A395D substitution decreased the NA activity of recombinant B/YAM virus, whereas the A395V NA substitution increased the NA activity relative to that of the B/BR/60/08 virus (Table 3). 2018 PloS one Result IV A395D;A395V 4;89 9;94 NA;NA;NA 37;95;125 39;97;127 29324781 Neuraminidase inhibitor susceptibility and neuraminidase enzyme kinetics of human influenza A and B viruses circulating in Thailand in 2010-2015. The A395T and A395D substitutions were genetically stable and were maintained unchanged during three passages, whereas the D342S and A395V substitutions were unstable and the NAs reverted to WT after three passages (Table 4). 2018 PloS one Result IV D342S;A395T;A395D;A395V 123;4;14;133 128;9;19;138 175 178 29324781 Neuraminidase inhibitor susceptibility and neuraminidase enzyme kinetics of human influenza A and B viruses circulating in Thailand in 2010-2015. The higher Vmax of the influenza A virus NA may facilitate the release and spread of A/PR8-S331G and A/PR8-S331R viruses, but the higher Km indicates that the NA has a low affinity for its substrate. 2018 PloS one Result IV S331G;S331R 91;107 96;112 NA;NA 41;159 43;161 29324781 Neuraminidase inhibitor susceptibility and neuraminidase enzyme kinetics of human influenza A and B viruses circulating in Thailand in 2010-2015. The I222V, S331G, and S331R NA substitutions were genetically stable in NA proteins on the genetic background of the A/PR8 virus. 2018 PloS one Result IV I222V;S331G;S331R 4;11;22 9;16;27 NA;NA 28;72 30;74 29324781 Neuraminidase inhibitor susceptibility and neuraminidase enzyme kinetics of human influenza A and B viruses circulating in Thailand in 2010-2015. The Km of A/PR8 virus NAs carrying S331G and S331R NA substitutions was significantly increased relative to that of WT NA (P < 0.01), whereas the D342S and A395T NA substitutions decreased the Km of recombinant B/YAM viruses (P < 0.01 and P < 0.05, respectively). 2018 PloS one Result IV S331G;S331R;D342S;A395T 35;45;146;156 40;50;151;161 NA;NA;NA;NA 51;119;162;22 53;121;164;25 29324781 Neuraminidase inhibitor susceptibility and neuraminidase enzyme kinetics of human influenza A and B viruses circulating in Thailand in 2010-2015. The NA substitutions at residue 331 (S331G and S331R) significantly decreased the NA activity of recombinant A/PR8 viruses as compared to that of A/PR8-WT NA (P < 0.001 and P < 0.01, respectively), whereas the I222V NA substitution slightly increased the NA activity (Table 3). 2018 PloS one Result IV S331G;S331R;I222V 37;47;210 42;52;215 NA;NA;NA;NA;NA 4;82;155;216;255 6;84;157;218;257 29324781 Neuraminidase inhibitor susceptibility and neuraminidase enzyme kinetics of human influenza A and B viruses circulating in Thailand in 2010-2015. The S331G and S331R NA substitutions increased the Vmax of recombinant influenza A virus NAs (P < 0.001 and P < 0.01, respectively) (Table 3). 2018 PloS one Result IV S331G;S331R 4;14 9;19 NA;NA 20;89 22;92 29324781 Neuraminidase inhibitor susceptibility and neuraminidase enzyme kinetics of human influenza A and B viruses circulating in Thailand in 2010-2015. These findings indicate that genetically unstable D342S and A395V NA substitutions are unlikely to emerge at a high frequency in influenza B viruses. 2018 PloS one Result IV D342S;A395V 50;60 55;65 66 68 29324781 Neuraminidase inhibitor susceptibility and neuraminidase enzyme kinetics of human influenza A and B viruses circulating in Thailand in 2010-2015. These results demonstrated that A/PR8 viruses carrying NA from A(H3N2) virus with single I222V, S331R, or S331G NA substitutions were susceptible to NAIs. 2018 PloS one Result IV I222V;S331R;S331G 89;96;106 94;101;111 NA;NA;NAI 55;112;149 57;114;153 29324781 Neuraminidase inhibitor susceptibility and neuraminidase enzyme kinetics of human influenza A and B viruses circulating in Thailand in 2010-2015. These results demonstrated that the NA substitutions S331G and S331R (on an A/PR8 background) and D342S, A395T, A395V, and A395D (on a B/YAM background) reduced the enzyme activity and thermostability of the NA. 2018 PloS one Result IV S331G;S331R;D342S;A395T;A395V;A395D 53;63;98;105;112;123 58;68;103;110;117;128 NA;NA 36;208 38;210 29324781 Neuraminidase inhibitor susceptibility and neuraminidase enzyme kinetics of human influenza A and B viruses circulating in Thailand in 2010-2015. These results revealed that B/YAM viruses carrying NAs from currently circulating influenza B viruses with single D342S, A395T, A395V, or A395D NA substitutions were susceptible to NAIs. 2018 PloS one Result IV D342S;A395T;A395V;A395D 114;121;128;138 119;126;133;143 NA;NAI;NA 144;181;51 146;185;54 29324781 Neuraminidase inhibitor susceptibility and neuraminidase enzyme kinetics of human influenza A and B viruses circulating in Thailand in 2010-2015. Thus, the S331G substitution had the greatest impact on the NA activity of recombinant A/PR8 viruses, followed by the S331R substitution, and the D342S and A395T substitutions had the greatest effect on the NA activity of recombinant B/YAM viruses. 2018 PloS one Result IV S331G;S331R;D342S;A395T 10;118;146;156 15;123;151;161 NA;NA 60;207 62;209 29409570 Early season co-circulation of influenza A(H3N2) and B(Yamagata): interim estimates of 2017/18 vaccine effectiveness, Canada, January 2018. Most sequenced influenza A(H3N2) viruses belonged to genetic clade 3C.2a (213/229; 93%) and of these most (204/213; 96%) belonged to a single genetic subgroup of 3C.2a (denoted subgroup 3 by nextflu.org), bearing antigenic site A substitutions T131K and R142K and antigenic site E substitution R261Q (Table 1). 2018 Euro surveillance Result IV T131K;R142K;R261Q 244;254;294 249;259;299 29409570 Early season co-circulation of influenza A(H3N2) and B(Yamagata): interim estimates of 2017/18 vaccine effectiveness, Canada, January 2018. Virtually all sequenced influenza B viruses were B(Yamagata) clade 3 (227/233; 97%) and all but one had L172Q + M251V non-antigenic site substitutions, the dominant genetic variant circulating globally since 2015; one virus had M251V without L172Q. 2018 Euro surveillance Result IV L172Q;M251V;M251V;L172Q 104;112;228;242 109;117;233;247 29433792 Clinical characteristics of influenza virus-induced lower respiratory infection during the 2015 to 2016 season. The sequence data for the NA gene revealed that patient 2 was infected with the oseltamivir-resistant H275Y mutant virus from the specimen taken before the treatment of neuraminidase inhibitor. 2018 Journal of infection and chemotherapy Result IV H275Y 102 107 NA;NA 26;169 28;182 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. Although some substitutions (I39M of M2 and M481I of NP) showed a P value of .054, they were not significant in the correlation analysis of genetic substitution and mortality. 2018 Influenza and other respiratory viruses Result IV I39M;M481I 29;44 33;49 M2;NP 37;53 39;55 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. Based on the NA phylogenetic tree, viruses from the 2014-2015 season fell into two distinct clusters based on amino acid substitution I392T for clade 3C.3a and T267K and I380V for clade 3C.2a. 2018 Influenza and other respiratory viruses Result IV I392T;T267K;I380V 134;160;170 139;165;175 13 15 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. Compared with the NA gene of the vaccine strain, A/Cheongju/G792/2013(H1N1) carried L40V, N44S, S52N, N200S, V241I, N248D, T289I, Y351F, and N369K substitutions. 2018 Influenza and other respiratory viruses Result IV L40V;N44S;S52N;N200S;V241I;N248D;T289I;Y351F;N369K 84;90;96;102;109;116;123;130;141 88;94;100;107;114;121;128;135;146 18 20 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. Compared with vaccine strain, amino acid mutations were found in the A/Cheongju/G792/2013(H1N1) HA gene: the P83S, S84G, S143G, K163I, G170R, S185T, A197T, S203T, A261T, G262E, H273N, and I321V substitutions were located in the HA1 region, the E47K, S124N, I183V, and V193A substitutions were located in the HA2 region (Table 4). 2018 Influenza and other respiratory viruses Result IV P83S;S84G;S143G;K163I;G170R;S185T;A197T;S203T;A261T;G262E;H273N;I321V;E47K;S124N;I183V;V193A 109;115;121;128;135;142;149;156;163;170;177;188;244;250;257;268 113;119;126;133;140;147;154;161;168;175;182;193;248;255;262;273 HA;HA;HA1 96;308;228 98;310;231 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. In addition, the NA sequence of the 2011-2012 season (n = 2) carried an I222V substitution, an NA inhibitor resistance mutation.13, 14, 15, 16 The NA sequence of several samples carried substitutions: I20T in A/Ansan/D342/2013, D339N in A/Cheongju/G1629/2014, Y67F in A/Ansan/D765/2014, and D151N, W383C in A/Seoul/A1251/2015. 2018 Influenza and other respiratory viruses Result IV I222V;I20T;D339N;Y67F;D151N;W383C 72;201;228;260;291;298 77;205;233;264;296;303 NA;NA;NA 17;95;147 19;97;149 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. In the analysis of internal genes, the M sequence of all the isolates investigated harbored the S31N genetic marker for adamantine resistance in M2. 2018 Influenza and other respiratory viruses Result IV S31N 96 100 M;M2 39;145 40;147 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. Interestingly, the PA gene of A/Ansan/D765/2014, A/Cheongju/G1532/2014, A/Cheongju/G1629/2014, A/Cheongju/G2156/2015, and A/Switzerland/ 9715293/2013 carried 5 amino acid mutations: Q256K, I308V, I554V, K605R, and V669I. 2018 Influenza and other respiratory viruses Result IV Q256K;I308V;I554V;K605R;V669I 182;189;196;203;214 187;194;201;208;219 PA 19 21 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. The clade 6B was differentiated into two groups by the amino acid substitutions V152T and V173I in group 1 and S84N, S162N, and I216T in group 2. 2018 Influenza and other respiratory viruses Result IV V152T;V173I;S84N;S162N;I216T 80;90;111;117;128 85;95;115;122;133 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. The phylogenetic tree of A(H1N1)pdm09 NA genes has shown that the two groups varied in terms of amino acid substitutions V67I, T381I in group 1 and V13I, I34V in group 2. 2018 Influenza and other respiratory viruses Result IV V67I;T381I;V13I;I34V 121;127;148;154 125;132;152;158 38 40 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. Viruses from the 2014-2015 season could be split into two clades based on the amino acid substitutions A138S, F159S, and N225D for clade 3C.3a and L3I, N144S, F159Y, and N225D for clade 3C.2a. 2018 Influenza and other respiratory viruses Result IV L3I;A138S;F159S;N225D;N144S;F159Y;N225D 147;103;110;121;152;159;170 150;108;115;126;157;164;175 29489903 Design and synthesis of constrained bicyclic molecules as candidate inhibitors of influenza A neuraminidase. All new compounds (16 a-f and 19 a-e), were tested with N2, N1 and N1-H274Y and found to be inactive at 2 mM concentration. 2018 PloS one Result IV H274Y 70 75 29489903 Design and synthesis of constrained bicyclic molecules as candidate inhibitors of influenza A neuraminidase. Compound 4a which was already 4 orders of magnitude less active than oseltamivir free acid against both N1 and N2, was not active toward the H274Y mutant in the range of concentrations tested (up to 1 mM). 2018 PloS one Result IV H274Y 141 146 29489903 Design and synthesis of constrained bicyclic molecules as candidate inhibitors of influenza A neuraminidase. Initially, we measured Km values of the three NAs (A/Anhui/1/2005 H5N1 wild-type and H274Y mutant, and A/Chicken/HongKong/G9/1997 H9N2) for the MUNANA substrate in MES buffer (32.5 mM 2-(N-morpholino)ethanesulfonic acid, 4 mM CaCl2, pH 6.5). 2018 PloS one Result IV H274Y 85 90 46 49 29489903 Design and synthesis of constrained bicyclic molecules as candidate inhibitors of influenza A neuraminidase. The enzymatic activity of the N1 H274Y mutant appears to be comparable to that of wild type viruses with compromised ability to bind oseltamivir.- Indeed, before starting the evaluation of new compounds, we performed control experiments with oseltamivir free acid, MS-257 (Fig 11, a known nanomolar inhibitor of influenza A neuraminidase) and compound 4a (compound belonging to the first series of compounds and previously tested). 2018 PloS one Result IV H274Y 33 38 324 337 29489903 Design and synthesis of constrained bicyclic molecules as candidate inhibitors of influenza A neuraminidase. The inhibition constant (Ki) of oseltamivir free acid for the mutant N1 H274Y showed an increase of 580-fold, compared to the wild-type. 2018 PloS one Result IV H274Y 72 77 29489903 Design and synthesis of constrained bicyclic molecules as candidate inhibitors of influenza A neuraminidase. The Km values were 12.8 +- 1.9 muM for N1 (H5N1), 26.5 +- 1.7 muM for N1 H274Y mutant, and 70 +- 6.8 muM for N2 (H9N2). 2018 PloS one Result IV H274Y 73 78 29489903 Design and synthesis of constrained bicyclic molecules as candidate inhibitors of influenza A neuraminidase. This is consistent with previously reported data, which showed MS-257 to be more active against an Oseltamivir-resistant virus H1N1 with the H274Y mutation compared to oseltamivir free acid. 2018 PloS one Result IV H274Y 141 146 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. a mutation of the channel facing residue alanine 30 to threonine not only changes the channel pore size, but also the polarity of the channel, which may explain the complete resistance of the AM2-S31N/L26I/A30T to compounds 1 and 2. 2018 Antiviral research Result IV A30T;L26I;S31N;A30T 206;201;196;41 210;205;200;64 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. After drug withdrawal at 1P10 for three additional passages, the 1P13 viral population retained the AM2-S31N/V27I mutation. 2018 Antiviral research Result IV V27I;S31N 109;104 113;108 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. After the second passage, the population of AM2-S31N viruses eclipsed the AM2-S31N/L26I/A30T triple mutant. 2018 Antiviral research Result IV S31N;L26I;S31N;A30T 48;83;78;88 52;87;82;92 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. AM2-S31N inhibitors 1 and 2 have potent channel blockage and antiviral activity. 2018 Antiviral research Result IV S31N 4 8 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. AM2-S31N/L26I/A30T triple mutant channel had reduced specific proton conductance than AM2-S31N, AM2-S31N/V27I, and AM2-S31N/L26I mutant channels. 2018 Antiviral research Result IV S31N;L26I;A30T;S31N;S31N;V27I;S31N;L26I 4;9;14;90;100;105;119;124 8;13;18;94;104;109;123;128 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. AM2-S31N/L26I/A30T triple mutant-containing virus had compromised replication fitness compared with AM2-S31N, AM2-S31N/V27I, or AM2-S31N/L26I-containing viruses. 2018 Antiviral research Result IV S31N;L26I;A30T;S31N;S31N;V27I;S31N;L26I 4;9;14;104;114;119;132;137 8;13;18;108;118;123;136;141 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. At passage 03, the AM2-S31N/L26I/A30T triple mutant rH3N2 virus was approximately 11% of the total viral population based on the sequence analysis. 2018 Antiviral research Result IV L26I;S31N;A30T 28;23;33 32;27;37 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. Both compounds 1 and 2 partially inhibited AM2-S31N/V27I and AM2-S31N/L26I double mutant channels, but with reduced potency compared with AM2-S31N when tested at 100 muM after 2 minutes at pH 5.5. 2018 Antiviral research Result IV V27I;S31N;S31N;L26I;S31N 52;47;65;70;142 56;51;69;74;146 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. Both the conservative (V27I and L26I) and non-conservative (A30T) mutations were located around the N-terminal drug binding site of AM2-S31N. 2018 Antiviral research Result IV V27I;L26I;A30T;S31N 23;32;60;136 27;36;64;140 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. By the third passage, there was no detectable AM2-S31N/L26I/A30T triple mutant in the population. 2018 Antiviral research Result IV L26I;S31N;A30T 55;50;60 59;54;64 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. Collectively, the evolved conservative and non-conservative mutations are all located at the N-terminal drug-binding site of AM2-S31N and they have either a direct or indirect effect on the channel pore which leads to either reduced or completely loss of drug sensitivity. 2018 Antiviral research Result IV S31N 129 133 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. Compounds 1 and 2 are hydroxyl adamantane AM2-S31N inhibitors containing aryl substitutions at the 5-position of the isoxazole group. 2018 Antiviral research Result IV S31N 46 50 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. Drug-resistant mutants are located at the N-terminal drug-binding site of AM2-S31N. 2018 Antiviral research Result IV S31N 78 82 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. Following drug withdrawal, the A30T mutant disappeared, and only AM2-S31N/L26I double mutant was found at 2P13. 2018 Antiviral research Result IV A30T;L26I;S31N 31;74;69 35;78;73 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. For 18,686 AM2 protein sequences from avian influenza viruses, over 14% contained the AM2-S31N mutant, only 0.09% had the AM2-S31N/V27I double mutant, and around 2% had the AM2-S31N/L26I mutant. 2018 Antiviral research Result IV S31N;V27I;S31N;S31N;L26I 90;131;126;177;182 94;135;130;181;186 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. For 8,749 AM2 sequences from swine influenza viruses, over 76% contained the AM2-S31N mutant, around 1% contained the AM2-S31N/V27I double mutant, and around 3% contained the AM2-S31N/L26I double mutant. 2018 Antiviral research Result IV S31N;V27I;S31N;S31N;L26I 81;127;122;179;184 85;131;126;183;188 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. For each compound, the AM2-S31N EC50 value was chosen as the initial drug concentration, and the dosage was doubled following each passage. 2018 Antiviral research Result IV S31N 27 31 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. For the growth curve, AM2-S31N/V27I and AM2-S31N/L26I rH3N2 viruses had no difference in the growth rate compared to the AM2-S31N rH3N2 virus. 2018 Antiviral research Result IV V27I;S31N;L26I;S31N;S31N 31;26;49;44;125 35;30;53;48;129 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. Frequency of AM2-S31N, AM2-S31N/V27I, AM2-S31N/L26I, and AM2-S31N/L26I/A30T mutants among circulating influenza A viruses. 2018 Antiviral research Result IV S31N;S31N;V27I;S31N;L26I;S31N;L26I;A30T 17;27;32;42;47;61;66;71 21;31;36;46;51;65;70;75 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. From these results, it is likely that the AM2-S31N/L26I/A30T triple mutant has an effect on the replication of influenza viruses. 2018 Antiviral research Result IV L26I;A30T;S31N 51;56;46 55;60;50 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. In comparison, amantadine evolved resistance after a single passage of the AM2-N31S A/WSN/33 (H1N1) virus. 2018 Antiviral research Result IV N31S 79 83 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. In contrast, the growth kinetics for the AM2-S31N/L26I/A30T rH3N2 virus was significantly attenuated, having approximately 2-log units lower viral titers from 8 to 32 hpi. 2018 Antiviral research Result IV L26I;S31N;A30T 50;45;55 54;49;59 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. In contrast, the population of the AM2-S31N/L26I/A30T triple mutant began to decline after passage 01, meanwhile the relative population of AM2-S31N viruses increased. 2018 Antiviral research Result IV L26I;S31N;A30T;S31N 44;39;49;144 48;43;53;148 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. In contrast, the specific activity of AM2-S31N/L26I/A30T triple mutant channel was only about 12.5% of the AM2-S31N channel. 2018 Antiviral research Result IV A30T;S31N;L26I;S31N 52;42;47;111 56;46;51;115 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. In order to rule out the possibility that secondary mutations located in viral proteins other than AM2 might influence virus growth, we repeated the growth kinetics using recombinant A/Udorn/1972 (rH3N2) viruses containing AM2-S31N, AM2-S31N/V27I, AM2-S31N/L26I, and AM2-S31N/L26I/A30T mutant channels. 2018 Antiviral research Result IV S31N;V27I;S31N;L26I;S31N;L26I;S31N;A30T 227;242;237;257;252;276;271;281 231;246;241;261;256;280;275;285 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. In summary, both the AM2-S31N/V27I and AM2-S31N/L26I mutations we identified in serial viral passage experiments indeed displayed reduced drug sensitivity in its channel function, but retained a partial degree of channel blockage. 2018 Antiviral research Result IV V27I;S31N;L26I;S31N 30;25;48;43 34;29;52;47 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. In the docking model of compound 1 in complex with AM2-S31N. 2018 Antiviral research Result IV S31N 55 59 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. In the docking model of compound 2 in complex with AM2-S31N. 2018 Antiviral research Result IV S31N 55 59 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. In the docking models of compounds 1 and 2 in the AM2-S31N channel. 2018 Antiviral research Result IV S31N 54 58 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. In vitro serial viral passage experiments select both conservative and non-conservative drug-resistant mutations against AM2-S31N inhibitors 1 and 2. 2018 Antiviral research Result IV S31N 125 129 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. It was found that AM2-S31N/V27I mutation remained dominant after three passages, and no increase in the AM2-S31N population was detected. 2018 Antiviral research Result IV V27I;S31N;S31N 27;22;108 31;26;112 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. Neither compound 1 nor 2 showed inhibition against AM2-S31N/L26I/A30T triple mutant channel. 2018 Antiviral research Result IV A30T;L26I;S31N 65;60;55 69;64;59 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. Neither compound had inhibitory activity against the AM2-S31N/L26I/A30T triple mutant. 2018 Antiviral research Result IV S31N;L26I;A30T 57;62;67 61;66;71 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. Neither the AM2-L26I/A30T double mutant nor the AM2-S31N/L26I/A30T triple mutant was found in human, avian, or swine influenza strains in these analyses. 2018 Antiviral research Result IV L26I;A30T;L26I;S31N;A30T 16;21;57;52;62 20;25;61;56;66 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. No additional mutation was found in the AM2-S31N/V27I gene segment. 2018 Antiviral research Result IV V27I;S31N 49;44 53;48 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. Out of 29,312 AM2 protein sequences from human influenza viruses, nearly 80% contain the AM2-S31N mutation, while less than 0.5% contained the AM2-S31N/L26I double mutation and only 0.2% had the AM2-S31N/V27I double mutation. 2018 Antiviral research Result IV S31N;L26I;S31N;S31N;V27I 93;152;147;199;204 97;156;151;203;208 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. Out of the two double mutants, AM2-S31N/L26I double mutant is more frequently found in both avian and swine hosts, while the AM2-S31N/V27I double mutant is slightly higher for human isolated strains. 2018 Antiviral research Result IV S31N;L26I;V27I;S31N 35;40;134;129 39;44;138;133 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. Overall, compounds 1 and 2 were found to have potent antiviral activity with low cellular cytotoxicity, with a mechanism of action dependent upon AM2-S31N channel blockage. 2018 Antiviral research Result IV S31N 150 154 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. Overall, the absence of AM2-S31N/L26I/A30T triple mutant among circulating influenza A viruses suggest that this triple mutant might have deleterious effect on the fitness of viral replication. 2018 Antiviral research Result IV S31N;L26I;A30T 28;33;38 32;37;42 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. Overall, the triple mutant-harboring virus appears to be driven to extinction in the presence of AM2-S31N viruses, despite an initial bias in its favor. 2018 Antiviral research Result IV S31N 101 105 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. Overall, these results suggest that the triple mutant AM2-S31N/L26I/A30T identified in the drug passage has attenuated channel activity, while the double mutants AM2-S31N/V27I and AM2-S31N/L26I had similar channel activity as the AM2-S31N channel. 2018 Antiviral research Result IV A30T;L26I;S31N;S31N;V27I;L26I;S31N;S31N 68;63;58;166;171;189;184;234 72;67;62;170;175;193;188;238 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. Plaque-purified virus harboring the AM2-S31N/L26I/A30T triple mutant had significantly reduced growth at 8, 14, 20, 26, and 32 hpi compared to both AM2-S31N, -S31N/V27I, and -S31N/L26I-containing viruses. 2018 Antiviral research Result IV L26I;S31N;A30T;S31N;V27I;S31N;L26I;S31N 45;40;50;152;164;159;180;175 49;44;54;156;168;163;184;179 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. Plaque-purified virus harboring the AM2-S31N/V27I mutant had comparable growth to the AM2-S31N-containing A/California/07/2009 (H1N1) virus, while the plaque-purified virus harboring the AM2-S31N/L26I mutant had partially reduced growth. 2018 Antiviral research Result IV V27I;S31N;S31N;L26I;S31N 45;40;90;196;191 49;44;94;200;195 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. Previous solution NMR structure of AM2-S31N proton channel in complex with an isoxazole inhibitor WJ332 (PDB: 2LY0) showed that the channel blocker fits in the N-terminal channel pore and forms both hydrophobic and hydrogen bonds with the AM2-S31N channel. 2018 Antiviral research Result IV S31N;S31N 39;243 43;247 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. Similar to plaque-purified viruses, AM2-S31N/V27I and AM2-S31N/L26I rH3N2 viruses remained the dominant population after three passages. 2018 Antiviral research Result IV V27I;S31N;L26I;S31N 45;40;63;58 49;44;67;62 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. Similarly, compound 2 showed no inhibition against AM2-S31N/L26I/A30T rH3N2 virus up to 30 muM. 2018 Antiviral research Result IV L26I;S31N;A30T 60;55;65 64;59;69 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. Similarly, the population of the AM2-S31N/L26I did not change. 2018 Antiviral research Result IV S31N;L26I 37;42 41;46 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. Taken together, these results demonstrate that the AM2-S31N inhibitors have a higher genetic barrier to drug resistance than amantadine at least in cell culture. 2018 Antiviral research Result IV S31N 55 59 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. The calculated specific activities of AM2-S31N/V27I and AM2-S31N/L26I channels were about 77.6% and 93.7% of the AM2-S31N channel, respectively. 2018 Antiviral research Result IV V27I;S31N;S31N;L26I;S31N 47;42;60;65;117 51;46;64;69;121 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. The EC50 values of compounds 1 and 2 against AM2-S31N, AM2-S31N/V27I, and AM2-S31N/L26I rH3N2 viruses are shown in Table 2. 2018 Antiviral research Result IV S31N;V27I;S31N;L26I;S31N 49;64;59;83;78 53;68;63;87;82 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. The emergence of a triple mutation AM2-S31N/L26I/A30T was observed in 2P08, and its population continued to increase at 2P09 and 2P10. 2018 Antiviral research Result IV A30T;S31N;L26I 49;39;44 53;43;48 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. The growth curve for the AM2-S31N-containing A/California/07/2009 (H1N1) virus was included as a control for comparison. 2018 Antiviral research Result IV S31N 29 33 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. The introduction of V27I mutation into AM2-S31N protein increased Kd value of compound 1 from 12.8 +- 2.1 muM to 193.5 +- 39.9 muM; similarly, the introduction of L26I mutation into AM2-S31N protein increased Kd value of compound 2 from 7.3 +- 0.5 muM to 28.0 +- 5.0 muM. 2018 Antiviral research Result IV V27I;S31N;L26I;S31N 20;43;163;186 24;47;167;190 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. The other conservative mutation L26I occurs at a helix-interface facing residue, therefore it might have an indirect effect on the channel pore drug-binding site. 2018 Antiviral research Result IV L26I 32 36 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. This greatly biased the infection to favor growth of the mutant viruses over the AM2-S31N containing A/California/07/2009 (H1N1) virus. 2018 Antiviral research Result IV S31N 85 89 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. This is in agreement with previously reported TECV experiments using AM2-S31N under the A/Udorn/1972 background. 2018 Antiviral research Result IV S31N 73 77 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. To confirm whether the observed drug resistance in plaque assay was solely due to the corresponding AM2 mutations, we introduced each mutation into the AM2-S31N gene of the A/California/07/2009 (H1N1) virus and recorded the drug sensitivity in TEVC assays. 2018 Antiviral research Result IV S31N 156 160 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. To determine the AM2-S31N proton channel blockage by compounds 1 and 2, the AM2 channel from A/California/07/2009 (H1N1) virus was expressed in Xenopus oocytes for TECV measurements. 2018 Antiviral research Result IV S31N 21 25 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. To investigate the impact of the evolved AM2 mutations on viral replication, we performed multicycle growth curve measurements for plaque-purified viruses harboring either AM2-S31N/V27I, AM2-S31N/L26I, or AM2-S31N/L26I/A30T mutant channels. 2018 Antiviral research Result IV V27I;S31N;S31N;L26I;S31N;A30T;L26I 181;176;191;196;209;219;214 185;180;195;200;213;223;218 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. To quantitatively compare the binding affinity of compounds 1 and 2 towards AM2-S31N channel versus the evolved AM2-S31N/V27I, AM2-S31N/L26I, and AM2-S31N/L26I/A30T mutant channels, we next determined Kd values using electrophysiology. 2018 Antiviral research Result IV S31N;V27I;S31N;S31N;L26I;L26I;A30T;S31N 80;121;116;131;136;155;160;150 84;125;120;135;140;159;164;154 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. We did not observe significant reversal potential changes in AM2-S31N/V27I, AM2-S31N/L26I, or AM2-S31N/L26I/A30T (data not shown), indicating that these mutant AM2 channels have very similar proton selectivity as the AM2-S31N channel from the A/California/07/2009 (H1N1) virus. 2018 Antiviral research Result IV S31N;V27I;S31N;L26I;A30T;L26I;S31N;S31N 65;70;80;85;108;103;98;221 69;74;84;89;112;107;102;225 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. We previously tested the antiviral activity of AM2-S31N inhibitors 1 and 2 against the AM2-S31N-containing 2009 pandemic-like A/California/07/09 H1N1 (A/H1N1/pdm09) virus in plaque assay. 2018 Antiviral research Result IV S31N;S31N 51;91 55;95 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. When the M segment was sequenced and analyzed, we found the emergence of the conservative mutation V27I in 1P05 viruses and L26I in 2P04 viruses. 2018 Antiviral research Result IV V27I;L26I 99;124 103;128 M 9 10 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. When valine was mutated to isoleucine (V27I), it is likely that the channel pore became constricted and could not accommodate compound 1 as efficiently as the AM2-S31N channel. 2018 Antiviral research Result IV V27I;S31N 39;163 43;167 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. while the AM2-S31N/L26I/A30T triple mutant rH3N2 virus was eclipsed by AM2-S31N rH3N2 after 2 passages. 2018 Antiviral research Result IV L26I;S31N;A30T;S31N 19;14;24;75 23;18;28;79 29587786 Effects of the S42 residue of the H1N1 swine influenza virus NS1 protein on interferon responses and virus replication. A western blot assay showed that the molecular weight of the NS1 proteins from rSIV NS1 S42P, rSIV NS1 D92E and rSIV NS1 S42P/ D92E viruses were 26 kDa (as expected). 2018 Virology journal Result IV S42P;D92E;S42P;D92E 88;103;121;127 92;107;125;131 NS1;NS1;NS1;NS1 61;84;99;117 64;87;102;120 29587786 Effects of the S42 residue of the H1N1 swine influenza virus NS1 protein on interferon responses and virus replication. Additionally, rSIV NS1 S42P and rSIV NS1 D92E mutations were the result of single nucleotide changes from wild type TCC (S) to CCC (P) and GAC (D) to GAG (E), whereas the rSIV NS1 S42P/ D92E mutation was the result of double nucleotide changes from the wild type. 2018 Virology journal Result IV S42P;D92E;S42P;D92E 23;41;180;186 27;45;184;190 NS1;NS1;NS1 19;37;176 22;40;179 29587786 Effects of the S42 residue of the H1N1 swine influenza virus NS1 protein on interferon responses and virus replication. all mutated viruses declined in NS1 expression to a similar extent at 6 hpi, but at 24 hpi, there was a clear reduction of the NS1 level for S42P and S42P/ D92E mutant virus when compared to the wt virus, which revealed a nearly 40% (S42P) and 53% (S42P/ D92E) reduction, respectively, as the band intensities were analyzed with ImageJ software. 2018 Virology journal Result IV S42P;S42P;D92E;S42P;S42P;D92E 141;150;156;234;249;255 145;154;160;238;253;259 NS1;NS1 32;127 35;130 29587786 Effects of the S42 residue of the H1N1 swine influenza virus NS1 protein on interferon responses and virus replication. Collectively, the NS1 S42P, D92E and S42P/D92E mutant protein behaved very similarly to that of the wt NS1 protein, and thus, these point mutations had no effect on nuclear localization. 2018 Virology journal Result IV S42P;D92E;S42P;D92E 22;28;37;42 26;32;41;46 NS1;NS1 18;103 21;106 29587786 Effects of the S42 residue of the H1N1 swine influenza virus NS1 protein on interferon responses and virus replication. However, infection with rSIV NS1 D92E virus was very weak in its ability to induce IFN-alpha and IFN-beta production into the cell culture supernatant as no obvious difference was observed for the IFN-alpha and IFN-beta mRNA amount compared to wt virus infection. 2018 Virology journal Result IV D92E 33 37 NS1 29 32 29587786 Effects of the S42 residue of the H1N1 swine influenza virus NS1 protein on interferon responses and virus replication. However, no significant changes in the TNF-alpha mRNA level were observed in cells between the NS1 mutations (NS1 S42P, D92E and S42P/ D92E) and wt virus at 24 hpi. 2018 Virology journal Result IV S42P;D92E;S42P;D92E 114;120;129;135 118;124;133;139 NS1;NS1 95;110 98;113 29587786 Effects of the S42 residue of the H1N1 swine influenza virus NS1 protein on interferon responses and virus replication. However, the hydrogen bonds of NS1 S42P and NS1 D92E proteins between the 42 (or 92) and neighbor amino acids were changed. 2018 Virology journal Result IV S42P;D92E 35;48 39;52 NS1;NS1 31;44 34;47 29587786 Effects of the S42 residue of the H1N1 swine influenza virus NS1 protein on interferon responses and virus replication. However, the other mutant virus with NS1 D92E displayed almost equal titers with wt virus throughout the infection. 2018 Virology journal Result IV D92E 41 45 NS1 37 40 29587786 Effects of the S42 residue of the H1N1 swine influenza virus NS1 protein on interferon responses and virus replication. NF-kappaB-responsive promoter is not activated by NS1 S42P and D92E virus infection. 2018 Virology journal Result IV S42P;D92E 54;63 58;67 NS1 50 53 29587786 Effects of the S42 residue of the H1N1 swine influenza virus NS1 protein on interferon responses and virus replication. The grand average of hydropathicity (GRAVY) of NS1 S42P and NS1 S42P/D92E proteins was higher than NS1and the NS1 D92E protein. 2018 Virology journal Result IV S42P;D92E;S42P;D92E 51;69;64;114 55;73;68;118 NS;NS1;NS1;NS1 99;47;60;110 101;50;63;113 29587786 Effects of the S42 residue of the H1N1 swine influenza virus NS1 protein on interferon responses and virus replication. The instability index of NS1 S42P was the lowest among three mutant proteins. 2018 Virology journal Result IV S42P 29 33 NS1 25 28 29587786 Effects of the S42 residue of the H1N1 swine influenza virus NS1 protein on interferon responses and virus replication. The mutant of S42P and D92E did not change the structure of the NS1 protein. 2018 Virology journal Result IV S42P;D92E 14;23 18;27 NS1 64 67 29587786 Effects of the S42 residue of the H1N1 swine influenza virus NS1 protein on interferon responses and virus replication. The NS1 mutations S42P attenuated virus replication on MDCK cells. 2018 Virology journal Result IV S42P 18 22 NS1 4 7 29587786 Effects of the S42 residue of the H1N1 swine influenza virus NS1 protein on interferon responses and virus replication. The results indicated that infection with the rSIV NS1 S42P and S42P/ D92E virus readily induced relatively high levels of IFN-alpha and IFN-beta production compared to the wt virus, which was equivalent to a 2.04- and 3.19-fold increase after rSIV NS1 S42P infection, and a 2.21- and 3.62-fold increase, respectively, after rSIV NS1 S42P/ D92E infection. 2018 Virology journal Result IV S42P;S42P;D92E;S42P;S42P;D92E 55;64;70;253;334;340 59;68;74;257;338;344 NS1;NS1;NS1 51;249;330 54;252;333 29587786 Effects of the S42 residue of the H1N1 swine influenza virus NS1 protein on interferon responses and virus replication. The results showed that IRF3 was significantly phosphorylated in cells infected with rSIV NS1 S42P and S42P/ D92E virus, which is consistent with trends of IFN expression. 2018 Virology journal Result IV S42P;S42P;D92E 94;103;109 98;107;113 NS1 90 93 29587786 Effects of the S42 residue of the H1N1 swine influenza virus NS1 protein on interferon responses and virus replication. The S42P mutation weakened the effect of NS1 in suppressing IRF3 activation and IFN transcription. 2018 Virology journal Result IV S42P 4 8 NS1 41 44 29587786 Effects of the S42 residue of the H1N1 swine influenza virus NS1 protein on interferon responses and virus replication. the titers of rSIV NS1 S42P and rSIV NS1 S42P/ D92E virus were significantly lower than that of wt virus at 36 and 48 hpi., which presented approximately 100-fold lower titers. 2018 Virology journal Result IV S42P;S42P;D92E 23;41;47 27;45;51 NS1;NS1 19;37 22;40 29587786 Effects of the S42 residue of the H1N1 swine influenza virus NS1 protein on interferon responses and virus replication. These results indicated that rSIV NS1 S42P, rSIV NS1 D92E and rSIV NS1 S42P/ D92E viruses were successfully rescued. 2018 Virology journal Result IV S42P;D92E;S42P;D92E 38;53;71;77 42;57;75;81 NS1;NS1;NS1 34;49;67 37;52;70 29587786 Effects of the S42 residue of the H1N1 swine influenza virus NS1 protein on interferon responses and virus replication. To analyze whether the reduced replication of rSIV NS1 S42P, D92E and S42P/ D92E mutations is the result of an impaired ability of the NS1 protein to block host cell interferon production, the 293 T cells were infected with the 3 mutant viruses and the wt virus at an MOI of 1, and the production of IFN-alpha and IFN-beta of the supernatants was measured by real-time PCR at 24 h post infection. 2018 Virology journal Result IV S42P;D92E;S42P;D92E 55;61;70;76 59;65;74;80 NS1;NS1 51;135 54;138 29587786 Effects of the S42 residue of the H1N1 swine influenza virus NS1 protein on interferon responses and virus replication. To study the effects of the key amino acids on influenza virus replication, the basic amino acids at position 42 serine (S) and 92 aspartic acid (D) of NS1 were mutated to proline (P) and glutamic acid (E) and generated plasmids encoding NS1 S42P and D92E. 2018 Virology journal Result IV S42P;D92E 242;251 246;255 NS1;NS1 152;238 155;241 29587786 Effects of the S42 residue of the H1N1 swine influenza virus NS1 protein on interferon responses and virus replication. Viruses with NS1 S42P D92E mutations made no difference to the NS1 subcellular localization patterns. 2018 Virology journal Result IV S42P;D92E 17;22 21;26 NS1;NS1 13;63 16;66 29587786 Effects of the S42 residue of the H1N1 swine influenza virus NS1 protein on interferon responses and virus replication. We concluded that the S42P mutant reduced the protein hydropathicity and thus enhanced the stability of the NS1 mutant protein (Table 2). 2018 Virology journal Result IV S42P 22 26 NS1 108 111 29587792 Major contribution of the RNA-binding domain of NS1 in the pathogenicity and replication potential of an avian H7N1 influenza virus in chickens. (i) the wt-ED induced a ~twofold increase of the apparent polymerase activity, while the wt-RBD had a lesser impact (~ 38% increase); (ii) substitutions in either individually expressed domain (3841AA-RBD or A149V-ED) reduced or nearly abolished the positive effect observed with the wt-domain; (iii) the full-length NS1 induced a twofold increase of polymerase activity; (iv) the double substitution in the RBD, but not the A149V substitution in the ED, reduced the effect of the full-length protein. 2018 Virology journal Result IV A149V;A149V 208;425 213;430 NS1 317 320 29587792 Major contribution of the RNA-binding domain of NS1 in the pathogenicity and replication potential of an avian H7N1 influenza virus in chickens. A149V produced cytoplasmic aggregates that did not exhibit the crystal-like structures observed with the wt-NS1. 2018 Virology journal Result IV A149V 0 5 NS1 108 111 29587792 Major contribution of the RNA-binding domain of NS1 in the pathogenicity and replication potential of an avian H7N1 influenza virus in chickens. At day 2 p.i., M-vRNA loads in the lungs of A149V-inoculated chickens were about tenfold lower than those of wt-inoculated chickens. 2018 Virology journal Result IV A149V 44 49 M 15 16 29587792 Major contribution of the RNA-binding domain of NS1 in the pathogenicity and replication potential of an avian H7N1 influenza virus in chickens. Both the in vitro and in vivo data pointed to a dramatically reduced replicative efficiency of the 3841AA-virus, while the replication fitness of the A149V virus appeared to be moderately affected. 2018 Virology journal Result IV A149V 150 155 29587792 Major contribution of the RNA-binding domain of NS1 in the pathogenicity and replication potential of an avian H7N1 influenza virus in chickens. Histological examination of the lungs of wt- and A149V-inoculated chickens revealed severe lesions of peribronchiolar interstitial pneumonia, associated with intraluminal presence of a fibrinous exudate and some degenerating heterophils, typical of exudative bronchitis and parabronchitis. 2018 Virology journal Result IV A149V 49 54 Pneumonia 102 140 29587792 Major contribution of the RNA-binding domain of NS1 in the pathogenicity and replication potential of an avian H7N1 influenza virus in chickens. In addition, virus excretion in the upper respiratory tract was reduced by about tenfold in A149V-inoculated chickens, when compared to wt-inoculated animals. 2018 Virology journal Result IV A149V 92 97 29587792 Major contribution of the RNA-binding domain of NS1 in the pathogenicity and replication potential of an avian H7N1 influenza virus in chickens. In CLEC213 cells, a chicken lung epithelial cell line that we have previously described, the growth of the A149V virus was reduced by about tenfold as compared to its wt-counterpart, while no virus was found in the supernatant of the 3841AA-inoculated cells, in spite of repeated attempts. 2018 Virology journal Result IV A149V 107 112 29587792 Major contribution of the RNA-binding domain of NS1 in the pathogenicity and replication potential of an avian H7N1 influenza virus in chickens. In embryonated eggs, the A149V virus grew to HA titers that were slightly lower than those of the wt virus, while the 3841AA-mutant grew to dramatically reduced levels, about 5 log2 units lower than those of the wt virus. 2018 Virology journal Result IV A149V 25 30 HA 45 47 29587792 Major contribution of the RNA-binding domain of NS1 in the pathogenicity and replication potential of an avian H7N1 influenza virus in chickens. In multicycle growth assays in MDCK cells, the wt- and A149V-viruses showed virtually identical replication kinetics reaching 107 PFU/ml in the supernatant as early as 24 h post infection, while the growth of the 3841AA-virus was clearly delayed, with a maximum titer that remained at least tenfold lower than those of the two other viruses. 2018 Virology journal Result IV A149V 55 60 29587792 Major contribution of the RNA-binding domain of NS1 in the pathogenicity and replication potential of an avian H7N1 influenza virus in chickens. It is generally considered that the attenuated phenotype of viruses harboring the double substitution R38A-K41A results from the fact that the mutated RBD has lost its ability to bind double-stranded RNAs. 2018 Virology journal Result IV R38A;K41A 102;107 106;111 29587792 Major contribution of the RNA-binding domain of NS1 in the pathogenicity and replication potential of an avian H7N1 influenza virus in chickens. Macroscopic lesions were mainly observed at d2 and d3 in wt- and A149V-inoculated chickens, and were not recorded in 3841AA-inoculated birds. 2018 Virology journal Result IV A149V 65 70 29587792 Major contribution of the RNA-binding domain of NS1 in the pathogenicity and replication potential of an avian H7N1 influenza virus in chickens. NS1 expression was markedly reduced (by about 4 to 8-fold) in 3841AA-infected cells and slightly reduced in A149V-infected cells, compared to the levels observed in wt-infected cells. 2018 Virology journal Result IV A149V 108 113 NS1 0 3 29587792 Major contribution of the RNA-binding domain of NS1 in the pathogenicity and replication potential of an avian H7N1 influenza virus in chickens. Substitution A149V in the effector domain completely abolished this effect. 2018 Virology journal Result IV A149V 13 18 29587792 Major contribution of the RNA-binding domain of NS1 in the pathogenicity and replication potential of an avian H7N1 influenza virus in chickens. The clinical symptoms were much less severe in the A149V group, of which only one animal died at day 4. 2018 Virology journal Result IV A149V 51 56 29587792 Major contribution of the RNA-binding domain of NS1 in the pathogenicity and replication potential of an avian H7N1 influenza virus in chickens. The kinetics of viral replication in the lung was slightly delayed with the A149V virus, for which the highest loads were observed at days 2 and 3 p.i. 2018 Virology journal Result IV A149V 76 81 29587792 Major contribution of the RNA-binding domain of NS1 in the pathogenicity and replication potential of an avian H7N1 influenza virus in chickens. The latter observation could result from the fact that the effect of the A149V substitution was compensated for by the presence of the wt-RBD. 2018 Virology journal Result IV A149V 73 78 29587792 Major contribution of the RNA-binding domain of NS1 in the pathogenicity and replication potential of an avian H7N1 influenza virus in chickens. The wt-virus, and to a slightly lesser extent the A149V-virus, were found in the kidneys and brains, indicating limited systemic dissemination. 2018 Virology journal Result IV A149V 50 55 29587792 Major contribution of the RNA-binding domain of NS1 in the pathogenicity and replication potential of an avian H7N1 influenza virus in chickens. Transient expression of wt-NS1 diminished the L-poly(I:C)-induced Mx-promoter activation, while A149V-NS1 slightly increased the activation. 2018 Virology journal Result IV A149V 96 101 NS1;NS1 27;102 30;105 29587792 Major contribution of the RNA-binding domain of NS1 in the pathogenicity and replication potential of an avian H7N1 influenza virus in chickens. We genetically engineered three variants of this virus: the recombinant wild-type (wt) virus harboured a segment 8 identical to that of the parental isolate, the mutant virus dubbed 3841AA harboured a modified segment 8 encoding an RBD-mutated NS1 with the double substitution R38A-K41A; and the virus named A149V encoded an NS1 protein with a substitution in the ED that was shown to critically alter the IFN-antagonist activity of NS1. 2018 Virology journal Result IV R38A;K41A;A149V 277;282;308 281;286;313 NS1;NS1;NS1 244;325;433 247;328;436 29587792 Major contribution of the RNA-binding domain of NS1 in the pathogenicity and replication potential of an avian H7N1 influenza virus in chickens. we observed that most cells infected with the wt and A149V viruses exhibited a disfigured shape of nuclei, a feature that was much less pronounced with the 3841AA-virus. 2018 Virology journal Result IV A149V 53 58 29593694 Amino Acid Substitutions HA A150V, PA A343T, and PB2 E627K Increase the Virulence of H5N6 Influenza Virus in Mice. All virus containing PB2 E627K grew faster, yielding more than 1,000 folds virus titer than the wild-type virus (Table 1). 2018 Frontiers in microbiology Result IV E627K 25 30 PB2 21 24 29593694 Amino Acid Substitutions HA A150V, PA A343T, and PB2 E627K Increase the Virulence of H5N6 Influenza Virus in Mice. HA A150V alone caused a death rate of 60% (Figure 2B). 2018 Frontiers in microbiology Result IV A150V 3 8 HA 0 2 29593694 Amino Acid Substitutions HA A150V, PA A343T, and PB2 E627K Increase the Virulence of H5N6 Influenza Virus in Mice. HA A150V localizes near the 130 loop of the receptor domain, probably influencing receptor binding. 2018 Frontiers in microbiology Result IV A150V 3 8 HA 0 2 29593694 Amino Acid Substitutions HA A150V, PA A343T, and PB2 E627K Increase the Virulence of H5N6 Influenza Virus in Mice. HA A150V Plays a Key Role in Mammalian Receptor Affinity. 2018 Frontiers in microbiology Result IV A150V 3 8 HA 0 2 29593694 Amino Acid Substitutions HA A150V, PA A343T, and PB2 E627K Increase the Virulence of H5N6 Influenza Virus in Mice. However, HA A150V or PA A343T seems to attenuate PB2 E627K in vivo (Figure 2B). 2018 Frontiers in microbiology Result IV A150V;A343T;E627K 12;24;53 17;29;58 HA;PA;PB2 9;21;49 11;23;52 29593694 Amino Acid Substitutions HA A150V, PA A343T, and PB2 E627K Increase the Virulence of H5N6 Influenza Virus in Mice. In MDCK cells, the titer of virus containing PA A343T is ten times the wild-type virus (P > 0.05), but not in A549. 2018 Frontiers in microbiology Result IV A343T 48 53 PA 45 47 29593694 Amino Acid Substitutions HA A150V, PA A343T, and PB2 E627K Increase the Virulence of H5N6 Influenza Virus in Mice. PA A343T alone decreased the survival rate of mice compared with wild-type 6D2 (Figure 2B). 2018 Frontiers in microbiology Result IV A343T 3 8 PA 0 2 29593694 Amino Acid Substitutions HA A150V, PA A343T, and PB2 E627K Increase the Virulence of H5N6 Influenza Virus in Mice. r6D2-MA (HA) grew more efficiently than r6D2-WT in A549 cells at 48 h post infection (virus titers were 105.3 and 104.3 TCID50/100 mul, respectively, P < 0.05), demonstrating that HA A150V is responsible for the enhanced growth in human cells. 2018 Frontiers in microbiology Result IV A150V 183 188 HA;HA 9;180 11;182 29593694 Amino Acid Substitutions HA A150V, PA A343T, and PB2 E627K Increase the Virulence of H5N6 Influenza Virus in Mice. The 100% death rate demonstrates the pivotal role of PB2 E627K in H5N6. 2018 Frontiers in microbiology Result IV E627K 57 62 PB2 53 56 29593694 Amino Acid Substitutions HA A150V, PA A343T, and PB2 E627K Increase the Virulence of H5N6 Influenza Virus in Mice. The hemagglutination assay suggests that HA A150V completely abolishes the binding of HA with SAalpha2,3 receptors, but enhanced binding with SAalpha2,6 receptors (Table 2). 2018 Frontiers in microbiology Result IV A150V 44 49 HA;HA 41;86 43;88 29593694 Amino Acid Substitutions HA A150V, PA A343T, and PB2 E627K Increase the Virulence of H5N6 Influenza Virus in Mice. The virus titer of r6D2-MA (PB2) and r6D2-MA (HA/PA/PB2) grew similarly (viral titers were both 106 TCID50/100 mul) in A549 at 48 h post infection, 50 times higher than r6D2-WT (P < 0.01), indicating that PB2 E627K increased replication efficiency markedly. 2018 Frontiers in microbiology Result IV E627K 209 214 HA;PA;PB2;PB2;PB2 46;49;28;52;205 48;51;31;55;208 29593694 Amino Acid Substitutions HA A150V, PA A343T, and PB2 E627K Increase the Virulence of H5N6 Influenza Virus in Mice. Therefore, PA A343T alone is not sufficient to enhance replication ability substantially. 2018 Frontiers in microbiology Result IV A343T 14 19 PA 11 13 29593694 Amino Acid Substitutions HA A150V, PA A343T, and PB2 E627K Increase the Virulence of H5N6 Influenza Virus in Mice. This suggests that PA A343T alone is not sufficient to induce strong in vitro replication. 2018 Frontiers in microbiology Result IV A343T 22 27 PA 19 21 29593694 Amino Acid Substitutions HA A150V, PA A343T, and PB2 E627K Increase the Virulence of H5N6 Influenza Virus in Mice. Three amino acid substitutions (HA A150V, PA A343T, and PB2 E627K) discovered in a previous study were examined. 2018 Frontiers in microbiology Result IV A150V;A343T;E627K 35;45;60 40;50;65 HA;PA;PB2 32;42;56 34;44;59 29593694 Amino Acid Substitutions HA A150V, PA A343T, and PB2 E627K Increase the Virulence of H5N6 Influenza Virus in Mice. To determine the mechanism of HA A150V in the increased mouse death rate and virus titer in A549, we conducted homologous molecular modeling (Figure 5) using the Swiss-model. 2018 Frontiers in microbiology Result IV A150V 33 38 HA 30 32 29593694 Amino Acid Substitutions HA A150V, PA A343T, and PB2 E627K Increase the Virulence of H5N6 Influenza Virus in Mice. We hypothesized that PA A343T and PB2 E627K affect the polymerase activity of reconstituted ribonucleoprotein (RNP) complexes (Figure 6). 2018 Frontiers in microbiology Result IV A343T;E627K 24;38 29;43 PA;PB2;RNP 21;34;111 23;37;114 29630683 The use of plant lectins to regulate H1N1 influenza A virus receptor binding activity. In contrast, the number of human isolates expressing the S183P mutation was ~ 5.4% between 2009 and 2011, and rapidly increased in 2017 up to ~36.4% (S2 Fig). 2018 PloS one Result IV S183P 57 62 29630683 The use of plant lectins to regulate H1N1 influenza A virus receptor binding activity. Sequence analysis of the genome of the CA/04+SNA virus revealed three mutations in HA1 (N129D, G155E, and S183P). 2018 PloS one Result IV N129D;G155E;S183P 88;95;106 93;100;111 HA1 83 86 29630683 The use of plant lectins to regulate H1N1 influenza A virus receptor binding activity. The G201E NA mutation was found in ~0.1% of all H1N1 viruses examined. 2018 PloS one Result IV G201E 4 9 10 12 29630683 The use of plant lectins to regulate H1N1 influenza A virus receptor binding activity. The N129D or G155E HA1 amino acid substitutions were relatively infrequent and they were present in ~0.4% of the related H1N1 strains in the Influenza Research Database. 2018 PloS one Result IV N129D;G155E 4;13 9;18 HA1 19 22 29630683 The use of plant lectins to regulate H1N1 influenza A virus receptor binding activity. The S183P HA1 mutation was selected when CA/04 was passaged in the absence of lectins (Table 1). 2018 PloS one Result IV S183P 4 9 HA1 10 13 29630683 The use of plant lectins to regulate H1N1 influenza A virus receptor binding activity. Thus, our data indicate that the N1 NA carrying mutation, G201E, reduced NA ability to cleave 3'SLN glycan immobilized on the sensor surface, clearly suggesting that the catalysis of 3'SLN was diminished by the mutant N1 protein. 2018 PloS one Result IV G201E 58 63 NA;NA 36;73 38;75 29630683 The use of plant lectins to regulate H1N1 influenza A virus receptor binding activity. To evaluate the impact of the G201E mutation identified in the CA/04+MAA variant on NA enzyme activity, we determined the NA enzyme Km and Vmax values for the CA/04 and CA/04+MAA viruses using fluorogenic MUNANA as a substrate. 2018 PloS one Result IV G201E 30 35 NA;NA 84;122 86;124 29630683 The use of plant lectins to regulate H1N1 influenza A virus receptor binding activity. We found that passage of CA/04 in the presence of MAA resulted in development of two mutations in HA1 (G155E and S183P, H1 numbering used throughout the text) and one mutation in NA (G201E, N1 numbering used throughout the text). 2018 PloS one Result IV G155E;S183P;G201E 103;113;183 108;118;188 HA1;NA 98;179 101;181 29630683 The use of plant lectins to regulate H1N1 influenza A virus receptor binding activity. We observed that although the G201E mutation had no effect on the Km value, it decreased NA enzyme activity (Vmax ratio relative to the wild-type virus = 0.4; Fig 6 and Table 3). 2018 PloS one Result IV G201E 30 35 89 91 29643248 A Single Amino Acid in the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses. 3A and B and 4A and B), the MLD50 titers of rVc_BR60PA:K338R and rYm_WI01PA:K338R were determined to be 103.5 PFU and 105.6 PFU (Table 3), respectively, which were similar to those of the maVc_BR60 (103.5 PFU) and maYm_WI01 (105.5 PFU) viruses (Table 1). 2018 Journal of virology Result IV K338R;K338R 55;76 60;81 29643248 A Single Amino Acid in the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses. As seen in the viral pathogenicity analyses in mice, the viral polymerase complexes harboring the PA K338R mutation (pVc_BR60PA:K338R and pYm_WI01PA:K338R) enhanced luciferase expression of the respective WT polymerase complexes (pVc_BR60 and pYm_WI01) in human embryonic kidney (293T) and Madin-Darby kidney (MDCK) cells. 2018 Journal of virology Result IV K338R;K338R;K338R 101;128;149 106;133;154 PA 98 100 29643248 A Single Amino Acid in the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses. Because the PA protein consists of the viral polymerase complex of IBVs, we then investigated how the PA K338R mutation affects viral polymerase complex activities of IBVs. 2018 Journal of virology Result IV K338R 105 110 PA;PA 12;102 14;104 29643248 A Single Amino Acid in the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses. Considered together, these results indicate that the PA K338R mutation may contribute to the pathogenicity of both lineages of IBVs in mice. 2018 Journal of virology Result IV K338R 56 61 PA 53 55 29643248 A Single Amino Acid in the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses. Effects of the PA K338R mutation in ferrets. 2018 Journal of virology Result IV K338R 18 23 PA 15 17 29643248 A Single Amino Acid in the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses. Effects of the PA K338R mutation on viral polymerase complex activity. 2018 Journal of virology Result IV K338R 18 23 PA 15 17 29643248 A Single Amino Acid in the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses. Even though the pathogenicity of rVc_BR60 was higher than that of rYm_WI01 in mice, the PA of rVc_BR60 did not change the pathogenicity of rYm_WI01 at all, and the PA K338R mutation (rYm_WI01/BR60PA:K338R) did not increase viral pathogenicity, either. 2018 Journal of virology Result IV K338R;K338R 167;199 172;204 PA;PA 88;164 90;166 29643248 A Single Amino Acid in the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses. Genetic compatibility for the pathogenic effects of the PA K338R mutation. 2018 Journal of virology Result IV K338R 59 64 PA 56 58 29643248 A Single Amino Acid in the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses. Given these facts, we investigated whether the PA genes of both IBV lineage viruses could be interchangeable for the pathogenic effect of PA K338R. 2018 Journal of virology Result IV K338R 141 146 PA;PA 47;138 49;140 29643248 A Single Amino Acid in the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses. However, as demonstrated with the reduced pathogenicity of rYm_WI01/BR60PA and rYm_WI01/BR60PA:K338R, pYm_WI01/BR60PA and pYm_WI01/BR60PA:K338R showed much-reduced luciferase expression compared with pYm_WI01 and pYm_WI01PA:K338R. 2018 Journal of virology Result IV K338R;K338R;K338R 95;138;224 100;143;229 29643248 A Single Amino Acid in the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses. however, the PA K338R mutation of Vc_BR60 did not alter the pathogenicity of the rYm_WI01/BR60PA virus. 2018 Journal of virology Result IV K338R 16 21 PA 13 15 29643248 A Single Amino Acid in the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses. However, we focused on the concurrent PA K338R mutation of both the maVc_BR60 and maYm_WI01 viruses, and to investigate the pathogenic effects of this mutation, we generated mutant viruses harboring the PA K338R mutation in the genetic backbones of Vc_BR60 and Ym_WI01 (rVc_BR60PA:K338R and rYm_WI01PA:K338R, respectively) by reverse genetics and used them for subsequent analyses. 2018 Journal of virology Result IV K338R;K338R;K338R;K338R 41;206;281;302 46;211;286;307 PA;PA 38;203 40;205 29643248 A Single Amino Acid in the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses. In contrast to the results observed for the rVc_BR60/WI01PA and rVc_BR60/WI01PA:K338R viruses. 2018 Journal of virology Result IV K338R 80 85 29643248 A Single Amino Acid in the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses. In nasal washes, rVc_BR60 backbone viruses resulted in higher viral replication than rYm_WI01 backbone viruses, and rYm_WI01PA:K338R exhibited statistically significantly higher replication than rYm_WI01 (at 3 dpi, P < 0.01; at 5 dpi, P < 0.05), whereas these differences were barely observed for rVc_BR60 backbone viruses. 2018 Journal of virology Result IV K338R 127 132 29643248 A Single Amino Acid in the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses. Interestingly, both mouse-adapted viruses appeared to have the common amino acid mutation PA K338R. 2018 Journal of virology Result IV K338R 93 98 PA 90 92 29643248 A Single Amino Acid in the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses. Intriguingly, once again, the PA K338R mutation increased the pathogenicity of rVc_BR60/WI01PA. 2018 Journal of virology Result IV K338R 33 38 PA 30 32 29643248 A Single Amino Acid in the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses. Notably, the PA K338R mutant of Ym_WI01 (rYm_WI01PA:K338R) killed 80% of the infected mice at 6 dpi at the highest titer of 106 PFU, and the average body weight loss of these infected mice was approximately 24.9% at 5 dpi. 2018 Journal of virology Result IV K338R;K338R 16;52 21;57 PA 13 15 29643248 A Single Amino Acid in the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses. PA K338R mutation as a pathogenic determinant of IBVs in mice. 2018 Journal of virology Result IV K338R 3 8 PA 0 2 29643248 A Single Amino Acid in the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses. Specifically, maVc_BR60 appeared to harbor six amino acid mutations, in PB2 (Q78K), PB1 (A193T), PA (K338R and E550K), M2 (M21I), and NS1 (E162G), whereas three mutations were detected in maYm_WI01, in PB2 (P295T), PB1 (A541T), and PA (K338R). 2018 Journal of virology Result IV M21I;Q78K;A193T;K338R;E550K;E162G;P295T;A541T;K338R 123;77;89;101;111;139;207;220;236 127;81;94;106;116;144;212;225;241 M2;NS1;PA;PA;PB1;PB1;PB2;PB2 119;134;97;232;84;215;72;202 121;137;99;234;87;218;75;205 29643248 A Single Amino Acid in the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses. The mice infected with 103 PFU of rVc_BR60PA:K338R showed approximately 4% of maximal body weight loss at 8 dpi, and the mice infected with 104, 105, and 106 PFU of rVc_BR60PA:K338R showed more than 25% body weight losses before 9, 8, and 7 dpi, respectively. 2018 Journal of virology Result IV K338R;K338R 45;176 50;181 29643248 A Single Amino Acid in the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses. The mice infected with 104 PFU, 105 PFU, and 106 PFU of rVc_BR60PA:K338R were killed starting from 8, 7, and 6 dpi, respectively, and all the infected mice were dead before 10 dpi. 2018 Journal of virology Result IV K338R 67 72 29643248 A Single Amino Acid in the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses. The mice infected with 106 PFU of rVc_BR60/WI01PA:K338R experienced more than 25% body weight loss, and they all died before 9 dpi. 2018 Journal of virology Result IV K338R 50 55 29643248 A Single Amino Acid in the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses. The mice infected with rVc_BR60PA:K338R experienced more severe body weight losses than those infected with rVc_BR60. 2018 Journal of virology Result IV K338R 34 39 29643248 A Single Amino Acid in the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses. the PA K338R mutants also resulted in higher replication titers than their respective parental viruses. 2018 Journal of virology Result IV K338R 7 12 PA 4 6 29643248 A Single Amino Acid in the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses. These effects of PA K338R were similarly observed in the results of polymerase complex combinations with the different PA lineages (pVc_BR60/WI01PA:K338R and pYm_WI01/BR60PA:K338R). 2018 Journal of virology Result IV K338R;K338R;K338R 20;148;174 25;153;179 PA;PA 17;119 19;121 29643248 A Single Amino Acid in the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses. These results indicate that the PA K338R mutation upregulates the functional activity of the viral polymerase complex of IBVs, which may eventually affect viral pathogenicity, only within the compatible genetic background and constellation. 2018 Journal of virology Result IV K338R 35 40 PA 32 34 29643248 A Single Amino Acid in the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses. these results of ferret experiments may substantiate the effects of PA K338R on IBV pathogenicity. 2018 Journal of virology Result IV K338R 71 76 PA 68 70 29643248 A Single Amino Acid in the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses. These results suggest that the PA K338R mutation may be a pathogenic determinant exhibiting its effect across different IBV lineages. 2018 Journal of virology Result IV K338R 34 39 PA 31 33 29643248 A Single Amino Acid in the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses. To explore the effects of the PA K338R mutation on the increased pathogenicity of both mouse-adapted viruses, we infected BALB/c mice intranasally with rVc_BR60PA:K338R and rYm_WI01PA:K338R (103 to 106 PFU). 2018 Journal of virology Result IV K338R;K338R;K338R 33;163;184 38;168;189 PA 30 32 29643248 A Single Amino Acid in the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses. To further evaluate the effects of the PA K338R mutation, we determined the replication titers of rVc_BR60, rVc_BR60PA:K338R, rYm_WI01, and rYm_WI01PA:K338R in the upper and lower respiratory tracts of ferrets, which are the animal model often used for studies of influenza virus pathogenicity. 2018 Journal of virology Result IV K338R;K338R;K338R 42;119;151 47;124;156 PA 39 41 29643248 A Single Amino Acid in the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses. We generated the Vc_BR60 virus harboring the PA of Ym_WI01 (rVc_BR60/WI01PA), the Ym_WI01 virus harboring the PA of Vc_BR60 (rYm_WI01/BR60PA), and their respective PA K338R mutant viruses (rVc_BR60/WI01PA:K338R and rYm_WI01/BR60PA:K338R). 2018 Journal of virology Result IV K338R;K338R;K338R 167;205;231 172;210;236 PA;PA;PA 45;110;164 47;112;166 29688498 Dynamic Variation and Reversion in the Signature Amino Acids of H7N9 Virus During Human Infection. Among 10 other amino acids related to NAI resistance, only the H274Y mutation was detected in 1 sample from case 7; however, this resistant genotype reverted to the WT genotype 6 days later (Table 2). 2018 The Journal of infectious diseases Result IV H274Y 63 68 NAI 38 41 29688498 Dynamic Variation and Reversion in the Signature Amino Acids of H7N9 Virus During Human Infection. Among 3 other signature sites in NS1, which antagonizes type I interferon and tumor necrosis factor alpha, only N205S was detected, while D92E and G210R mutations were not detected (Supplementary Table 1). 2018 The Journal of infectious diseases Result IV N205S;D92E;G210R 112;138;147 117;142;152 NS1 33 36 29688498 Dynamic Variation and Reversion in the Signature Amino Acids of H7N9 Virus During Human Infection. Among other signature amino acids in the PB2 segment, the L89V and A588V mutations were detected in all the samples (Supplementary Table 1), while K526R substitutions occurred in 3 patients (Table 2). 2018 The Journal of infectious diseases Result IV L89V;A588V;K526R 58;67;147 62;72;152 PB2 41 44 29688498 Dynamic Variation and Reversion in the Signature Amino Acids of H7N9 Virus During Human Infection. Dual D701N and E627K mutations failed to achieve predominance in any sample. 2018 The Journal of infectious diseases Result IV D701N;E627K 5;15 10;20 29688498 Dynamic Variation and Reversion in the Signature Amino Acids of H7N9 Virus During Human Infection. For NS1, all the samples contained the P42S mutation (Supplementary Table 1), which enhances the pathogenicity of H5N1 avian influenza viruses in mice. 2018 The Journal of infectious diseases Result IV P42S 39 43 NS1 4 7 29688498 Dynamic Variation and Reversion in the Signature Amino Acids of H7N9 Virus During Human Infection. For PB1, viruses in all the samples maintained the WT 99H genotype, but the I368V mutation was present in 9 patients (Supplementary Table 1). 2018 The Journal of infectious diseases Result IV I368V 76 81 PB1 4 7 29688498 Dynamic Variation and Reversion in the Signature Amino Acids of H7N9 Virus During Human Infection. G228S mutation did not happen in any sample (Supplementary Table 1). 2018 The Journal of infectious diseases Result IV G228S 0 5 29688498 Dynamic Variation and Reversion in the Signature Amino Acids of H7N9 Virus During Human Infection. In case 2, the R292K mutation was detected in 183 reads (36%) 5 days after NAI treatment but was not detected 2 days later. 2018 The Journal of infectious diseases Result IV R292K 15 20 NAI 75 78 29688498 Dynamic Variation and Reversion in the Signature Amino Acids of H7N9 Virus During Human Infection. In case 7, 2107 reads (59.5%) acquired the R292K mutation 3 days after antiviral therapy, but the proportion of NAI-resistant genotypes only slightly increased to 67.3% with another 6 days of NAI treatment, and there was no significant difference (Figure 2A). 2018 The Journal of infectious diseases Result IV R292K 43 48 NAI;NAI 112;192 115;195 29688498 Dynamic Variation and Reversion in the Signature Amino Acids of H7N9 Virus During Human Infection. In case 9, 87.0% of the reads in the bronchoalveolar lavage fluid obtained on 5 June contained the R292K mutation; at this timepoint, the laboratory test for H7N9 was not complete, and antiviral treatment was not yet implemented. 2018 The Journal of infectious diseases Result IV R292K 99 104 29688498 Dynamic Variation and Reversion in the Signature Amino Acids of H7N9 Virus During Human Infection. In patients who were sampled at several timepoints, the R292K mutation expressed dynamic variation (Figure 2A). 2018 The Journal of infectious diseases Result IV R292K 56 61 29688498 Dynamic Variation and Reversion in the Signature Amino Acids of H7N9 Virus During Human Infection. In the PA segment, the mammalian-associated signature K356R and S409N mutations were detected in all available samples, whereas the V100A substitution was not detected (Supplementary Table 1). 2018 The Journal of infectious diseases Result IV K356R;S409N;V100A 54;64;132 59;69;137 PA 7 9 29688498 Dynamic Variation and Reversion in the Signature Amino Acids of H7N9 Virus During Human Infection. Moreover, we validated the R292K mutation in these samples with a SNP RT-PCR assay. 2018 The Journal of infectious diseases Result IV R292K 27 32 29688498 Dynamic Variation and Reversion in the Signature Amino Acids of H7N9 Virus During Human Infection. Q226L/I mutations occurred in all patients, and a few prolines (20.9%) were detected at this site in case 2. 2018 The Journal of infectious diseases Result IV Q226L;Q226I 0;0 7;7 29688498 Dynamic Variation and Reversion in the Signature Amino Acids of H7N9 Virus During Human Infection. R292K, the most prevalent mutation, was observed in 9 samples from 5 patients (Table 2). 2018 The Journal of infectious diseases Result IV R292K 0 5 29688498 Dynamic Variation and Reversion in the Signature Amino Acids of H7N9 Virus During Human Infection. Sustained dual R292K and H274Y mutations were not detected in any of the samples. 2018 The Journal of infectious diseases Result IV R292K;H274Y 15;25 20;30 29688498 Dynamic Variation and Reversion in the Signature Amino Acids of H7N9 Virus During Human Infection. The D256G, T271A, M535L, Q591K, and H357N mutations were not detected in these samples (Supplementary Table 1). 2018 The Journal of infectious diseases Result IV D256G;T271A;M535L;Q591K;H357N 4;11;18;25;36 9;16;23;30;41 29688498 Dynamic Variation and Reversion in the Signature Amino Acids of H7N9 Virus During Human Infection. The D701N substitution was identified in 8 samples from 4 patients, and this mutation coexisted with WT genotypes in all samples (Table 2). 2018 The Journal of infectious diseases Result IV D701N 4 9 29688498 Dynamic Variation and Reversion in the Signature Amino Acids of H7N9 Virus During Human Infection. The G186V mutation was detected in 9 patients, potentially favoring the mammalian adaption of avian influenza virus. 2018 The Journal of infectious diseases Result IV G186V 4 9 29688498 Dynamic Variation and Reversion in the Signature Amino Acids of H7N9 Virus During Human Infection. The PB2 E627K mutation was detected in 18 samples from 7 (77.78%) patients; among these samples, 12 from 5 patients demonstrated coexisting 627K/E (Table 2). 2018 The Journal of infectious diseases Result IV E627K 8 13 PB2 4 7 29688498 Dynamic Variation and Reversion in the Signature Amino Acids of H7N9 Virus During Human Infection. The T160A mutation occurred in all the samples, with 3 samples containing a mixed T/A population (Table 2). 2018 The Journal of infectious diseases Result IV T160A 4 9 29688498 Dynamic Variation and Reversion in the Signature Amino Acids of H7N9 Virus During Human Infection. Then, the R292K substitution was detected in 2.7% of 2459 total reads on 22 April but faded by the next day. 2018 The Journal of infectious diseases Result IV R292K 10 15 29688498 Dynamic Variation and Reversion in the Signature Amino Acids of H7N9 Virus During Human Infection. V473L and P598L substitutions were not detected in our study, but a sample from case 7 showed the minor occurrence (10.5%) of isoleucine in position 473 (Table 2; Supplementary Table 1). 2018 The Journal of infectious diseases Result IV V473L;P598L 0;10 5;15 29688498 Dynamic Variation and Reversion in the Signature Amino Acids of H7N9 Virus During Human Infection. We conducted nucleotide polymorphism analysis of the sites related to NAI resistance in the NA segment, including R118K, E119V, D151E, R152K, I222V, R224K, H274Y, E276D, R292K, N294S, and R371K (N2 numbering). 2018 The Journal of infectious diseases Result IV R118K;E119V;D151E;R152K;I222V;R224K;H274Y;E276D;R292K;N294S;R371K 114;121;128;135;142;149;156;163;170;177;188 119;126;133;140;147;154;161;168;175;182;193 NA;NAI 92;70 94;73 29743603 Unexpected infection outcomes of China-origin H7N9 low pathogenicity avian influenza virus in turkeys. Full-genome sequencing of the four R2 turkey and the one D0 chicken isolate all revealed the L235Q polymorphism to have occurred in the HA of all five (Table 2). 2018 Scientific reports Result IV L235Q 93 98 HA 136 138 29743603 Unexpected infection outcomes of China-origin H7N9 low pathogenicity avian influenza virus in turkeys. However, the PB2 Y360H and PA N10H polymorphisms appear to be unique to the viral progeny obtained in the current study. 2018 Scientific reports Result IV Y360H;N10H 17;30 22;34 PA;PB2 27;13 29;16 29743603 Unexpected infection outcomes of China-origin H7N9 low pathogenicity avian influenza virus in turkeys. L235Q polymorphisms in HA gene. 2018 Scientific reports Result IV L235Q 0 5 HA 23 25 29743603 Unexpected infection outcomes of China-origin H7N9 low pathogenicity avian influenza virus in turkeys. These polymorphisms were identified as changes relative to the H7N9 wt inoculum, with the PA R269K, NA T10I/S and PB1-F2 M1T (possible ablation of peptide) changes having also occurred in other sequenced China-origin H7N9 isolates (Supplementary Table S4). 2018 Scientific reports Result IV T10S;R269K;T10I 103;93;103 109;98;109 NA;PA;PB1F2 100;90;114 102;92;120 29750015 Symmetric dimeric adamantanes for exploring the structure of two viroporins: influenza virus M2 and hepatitis C virus p7. A previous solution NMR structure of the inhibitor-bound M2-S31N structure showed that the inhibitor binds to the S31N mutant in a flipped orientation relative to that in the M2-WT channel. 2018 Drug design, development and therapy Result IV S31N;S31N 60;114 64;118 M2;M2 57;175 59;177 29750015 Symmetric dimeric adamantanes for exploring the structure of two viroporins: influenza virus M2 and hepatitis C virus p7. In our dimeric compounds, this polar aryl group is missing, which explains their lack of efficacy in inhibiting the M2-S31N channel. 2018 Drug design, development and therapy Result IV S31N 119 123 M2 116 118 29750015 Symmetric dimeric adamantanes for exploring the structure of two viroporins: influenza virus M2 and hepatitis C virus p7. In summary, the lack of channel blockage of the dimeric amantadine and rimantadine analogs against M2-WT and M2-S31N mutant is consistent with previously proposed drug-binding mechanisms and further confirms that the pore-binding model is the pharmacologically relevant drug-binding model. 2018 Drug design, development and therapy Result IV S31N 112 116 M2;M2 99;109 101;111 29750015 Symmetric dimeric adamantanes for exploring the structure of two viroporins: influenza virus M2 and hepatitis C virus p7. Specifically, the amino group from the S31N mutant-bound inhibitor is oriented upward toward the N-terminal end. 2018 Drug design, development and therapy Result IV S31N 39 43 29750015 Symmetric dimeric adamantanes for exploring the structure of two viroporins: influenza virus M2 and hepatitis C virus p7. The inhibitory activity of these dimeric compounds was further evaluated against S31N M2 mutant form (Figure 3B). 2018 Drug design, development and therapy Result IV S31N 81 85 M2 86 88 29750015 Symmetric dimeric adamantanes for exploring the structure of two viroporins: influenza virus M2 and hepatitis C virus p7. The S31N represents the predominant amantadine-resistant M2 form. 2018 Drug design, development and therapy Result IV S31N 4 8 M2 57 59 29750015 Symmetric dimeric adamantanes for exploring the structure of two viroporins: influenza virus M2 and hepatitis C virus p7. This could be explained by the dimeric compounds lacking the adamantane-NH2+-CH2-aryl pharmacophore of M2-S31N inhibitors. 2018 Drug design, development and therapy Result IV S31N 106 110 M2 103 105 29750015 Symmetric dimeric adamantanes for exploring the structure of two viroporins: influenza virus M2 and hepatitis C virus p7. Up till now, compounds reported to possess inhibitory activity for M2-S31N mutant form share the general adamantane-NH2+-CH2-aryl pharmacophore (Figure 4B). 2018 Drug design, development and therapy Result IV S31N 70 74 M2 67 69 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. Additionally, the expression levels of NP and M1 in NS1 R38A/K41A virus-infected MDCK cells was much lower than those in NS1 R38A-, NS1 K41A-, and WT virus-infected cells (Figure 1B). 2018 Frontiers in cellular and infection microbiology Result IV R38A;K41A;R38A;K41A 56;61;125;136 60;65;129;140 M1;NP;NS1;NS1;NS1 46;39;52;121;132 48;41;55;124;135 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. Alanine (A) substitution at R38, K41, or both (R38A, K41A, and R38A/K41A) was introduced in the pPolI-NS plasmid of the 12-plasmid reverse genetics system. 2018 Frontiers in cellular and infection microbiology Result IV R38A;K41A;R38A;K41A 47;53;63;68 51;57;67;72 NS 102 104 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. Collectively, the NS1 R38A/K41A virus exerted full infectivity but was quickly cleared from the lung tissues due to robust innate immune responses. 2018 Frontiers in cellular and infection microbiology Result IV K41A;R38A 27;22 31;26 NS1 18 21 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. Consistently, the F2 titer of NS1 R38A/K41A virus was much lower than that of the WT virus and other NS1 mutant viruses and could not be detected in A549 cells after 3 passages by the plaque assay (Table 1 and Figure 3C). 2018 Frontiers in cellular and infection microbiology Result IV K41A;R38A 39;34 43;38 NS1;NS1 30;101 33;104 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. Finally, no virus could be detected in the lungs of NS1 R38A/K41A virus-infected mice at 7 d p.i. 2018 Frontiers in cellular and infection microbiology Result IV K41A;R38A 61;56 65;60 NS1 52 55 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. However, the weight of NS1 R38A/K41A virus pre-inoculated mice decreased to a maximum of about 10% at 7 d p.i. 2018 Frontiers in cellular and infection microbiology Result IV R38A;K41A 27;32 31;36 NS1 23 26 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. In addition, the WT virus could effectively replicate in Vero cells, while the NS1 R38A/K41A virus could no longer be detected in Vero cells after five passages (Figure 4A), indicating that the absence of IFN-alpha/beta was not enough to help the replication of the NS1 R38A/K41A virus. 2018 Frontiers in cellular and infection microbiology Result IV K41A;R38A;K41A;R38A 88;83;275;270 92;87;279;274 NS1;NS1 79;266 82;269 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. In contrast, there was no weight loss or death among the NS1 R38A/K41A- or PBS-treated mice (Figures 5A,B). 2018 Frontiers in cellular and infection microbiology Result IV R38A;K41A 61;66 65;70 NS1 57 60 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. It has been reported that recombinant IAV expressing the mutant NS1 R38A/K41A induces high levels of type I IFN, which will, in turn, inhibit viral replication. 2018 Frontiers in cellular and infection microbiology Result IV K41A;R38A 73;68 77;72 NS1 64 67 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. It was suggested that the NS1 R38A/K41A virus was able to steadily propagate in the IFN-deficient Tet-On 3G NS1 Vero cells for at least 20 passages. 2018 Frontiers in cellular and infection microbiology Result IV K41A;R38A 35;30 39;34 NS1;NS1 26;108 29;111 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. Moreover, we found that the NS1 R38A/K41A virus triggered robust IFN-alpha and IFN-beta production in mice, while the IFN production in WT virus-infected mice was severely restrained due to the IFN antagonist activity of NS1 (Figure 5E). 2018 Frontiers in cellular and infection microbiology Result IV K41A;R38A 37;32 41;36 NS1;NS1 28;221 31;224 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. Next, we further determined the replication ability of the NS1 R38A/K41A virus in A549 cells with the same initial infectious dose. 2018 Frontiers in cellular and infection microbiology Result IV R38A;K41A 63;68 67;72 NS1 59 62 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. NP and M1 expression levels of the NS1 R38A/K41A virus were much lower than those of the WT and other NS1 mutant viruses, and the viral proteins of the NS1 R38A/K41A virus were not detected after 4 passages (Figure 3A), indicating that the replication ability of NS1 R38A/K41A virus was limited in MDCK cells. 2018 Frontiers in cellular and infection microbiology Result IV R38A;K41A;R38A;K41A;R38A;K41A 39;44;156;161;267;272 43;48;160;165;271;276 M1;NP;NS1;NS1;NS1;NS1 7;0;35;102;152;263 9;2;38;105;155;266 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. NS1 R38A/K41A virus did not possess the ability to reproduce in IFN-competent A549 and MDCK cells after 3 or 4 passages. 2018 Frontiers in cellular and infection microbiology Result IV R38A;K41A 4;9 8;13 NS1 0 3 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. PBS or NS1 R38A/K41A virus-inoculated mice from the previous experiments were infected with WT WSN (103.88PFU) at day 17 after the first infection to test protective efficiency. 2018 Frontiers in cellular and infection microbiology Result IV R38A;K41A 11;16 15;20 NS1 7 10 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. Replication of NS1 R38A/K41A virus is limited in IFN-competent cells during successive passaging. 2018 Frontiers in cellular and infection microbiology Result IV R38A;K41A 19;24 23;28 NS1 15 18 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. Sera from the NS1 R38A/K41A virus-infected mice at 14 d p.i. 2018 Frontiers in cellular and infection microbiology Result IV K41A;R38A 23;18 27;22 NS1 14 17 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. The 293T cells were transfected with increasing amounts of WT NS1 and infected with NS1 R38A/K41A virus at 6 h p.t. 2018 Frontiers in cellular and infection microbiology Result IV K41A;R38A 93;88 97;92 NS1;NS1 62;84 65;87 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. The lung indices of the NS1 R38A/K41A virus-infected mice were much lower than those infected with the WT virus at 3, 5 and 7 d p.i. 2018 Frontiers in cellular and infection microbiology Result IV R38A;K41A 28;33 32;37 NS1 24 27 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. The NS1 R38A and NS1 R38A/K41A viruses could not be detected until 24 and 36 h post infection (p.i.) respectively. 2018 Frontiers in cellular and infection microbiology Result IV R38A;R38A;K41A 8;21;26 12;25;30 NS1;NS1 4;17 7;20 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. The NS1 R38A/K41A mutant displayed remarkably decreased binding to RIG-I compared to NS1 WT, NS1 R38A, and NS1 K41A (Figure 2C). 2018 Frontiers in cellular and infection microbiology Result IV K41A;R38A;R38A;K41A 13;8;97;111 17;12;101;115 NS1;NS1;NS1;NS1 4;85;93;107 7;88;96;110 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. The NS1 R38A/K41A virus infection led to a remarkable up-regulation of IFN-beta mRNA expression compared to the other viruses (Figure 2A). 2018 Frontiers in cellular and infection microbiology Result IV R38A;K41A 8;13 12;17 NS1 4 7 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. The NS1 R38A/K41A virus is immunogenic and protects mice from a lethal challenge. 2018 Frontiers in cellular and infection microbiology Result IV R38A;K41A 8;13 12;17 NS1 4 7 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. The NS1 R38A/K41A virus pre-inoculated mice all survived against a second infection with WT WSN. 2018 Frontiers in cellular and infection microbiology Result IV R38A;K41A 8;13 12;17 NS1 4 7 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. The NS1-expressing vero cell line facilitates the propagation of NS1 R38A/K41A virus. 2018 Frontiers in cellular and infection microbiology Result IV R38A;K41A 69;74 73;78 NS1;NS1 4;65 7;68 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. The replication of the NS1 R38A/K41A virus is limited in mice. 2018 Frontiers in cellular and infection microbiology Result IV R38A;K41A 27;32 31;36 NS1 23 26 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. The rescued WT and NS1 R38A/K41A virus of F1 were passaged blindly in Vero cells and subjected to plaque assays on MDCK cells to measure virus titers. 2018 Frontiers in cellular and infection microbiology Result IV K41A;R38A 28;23 32;27 NS1 19 22 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. The results showed that the exogenous supplementation of WT NS1 protein facilitated the replication of the NS1 R38A/K41A virus (Figure 4B). 2018 Frontiers in cellular and infection microbiology Result IV K41A;R38A 116;111 120;115 NS1;NS1 60;107 63;110 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. The results showed that the titers of the WT and NS1 R38A/K41A viruses in Vero cells (Figure 4A) were a bit little higher than those in A549 cells (Figure 3C). 2018 Frontiers in cellular and infection microbiology Result IV K41A;R38A 58;53 62;57 NS1 49 52 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. The virus titer of each passage of the NS1 R38A/K41A virus from MDCK cells was measured by plaque assays. 2018 Frontiers in cellular and infection microbiology Result IV K41A;R38A 48;43 52;47 NS1 39 42 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. the virus titers in lungs of the NS1 R38A/K41A virus-infected mice decreased more than 4 log10 PFU/mL compared with those of WT virus-infected mice at 3 and 5 d p.i. 2018 Frontiers in cellular and infection microbiology Result IV R38A;K41A 37;42 41;46 NS1 33 36 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. The virus titers of the NS1 R38A and NS1 R38A/K41A viruses at each time point were reduced >1,000-fold compared to those of the WT virus, while the NS1 K41A virus showed replication efficiency intermediate between that of the WT and NS1 R38A/K41A viruses (Figure 1C). 2018 Frontiers in cellular and infection microbiology Result IV R38A;R38A;K41A;K41A;K41A;R38A 28;41;46;152;242;237 32;45;50;156;246;241 NS1;NS1;NS1;NS1 24;37;148;233 27;40;151;236 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. These results indicated that the replication of the NS1 R38A/K41A virus was limited compared to that of the WT and other NS1 mutant viruses. 2018 Frontiers in cellular and infection microbiology Result IV R38A;K41A 56;61 60;65 NS1;NS1 52;121 55;124 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. Thus, the interaction between the R38A/K41A mutant and RIG-I was hindered, resulting in more IFN production. 2018 Frontiers in cellular and infection microbiology Result IV R38A;K41A 34;39 38;43 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. To evaluate the replication ability and pathogenicity of the NS1 R38A/K41A virus in vivo, 5-week-old female BALB/c mice were intranasally infected with the third passage the NS1 R38A/K41A virus from Tet-on NS1-expressing Vero cells (103 PFU), WT virus (103 PFU), or PBS as a control. 2018 Frontiers in cellular and infection microbiology Result IV R38A;K41A;R38A;K41A 65;70;178;183 69;74;182;187 NS1;NS1;NS1 61;174;206 64;177;209 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. To investigate the immunogenicity of the NS1 R38A/K41A virus, sera from the WT or NS1 R38A/K41A virus infected mice was collected at 3, 7, and 14 d p.i. 2018 Frontiers in cellular and infection microbiology Result IV R38A;K41A;K41A;R38A 45;50;91;86 49;54;95;90 NS1;NS1 41;82 44;85 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. We found that the NS1 R38A/K41A virus was able to effectively replicated, resulting in titers of 5-6 log10 PFU/mL in the NS1-expressing Vero cells after 3 passages, which was close to those of WT virus (Figure 4D), and the sequences of NS1 from different passages were not changed (data not shown). 2018 Frontiers in cellular and infection microbiology Result IV K41A;R38A 27;22 31;26 NS1;NS1;NS1 18;121;236 21;124;239 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. We found that the NS1 R38A/K41A virus was an IFN antagonist activity-defective and replication-limited strain that has the potential to become a vaccine candidate, while its replication was inhibited in IFN-competent cells. 2018 Frontiers in cellular and infection microbiology Result IV K41A;R38A 27;22 31;26 NS1 18 21 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. We next investigated the stability of the NS1 R38A/K41A virus in the Tet-On 3G NS1-expressing Vero cells during successive passaging. 2018 Frontiers in cellular and infection microbiology Result IV K41A;R38A 51;46 55;50 NS1;NS1 42;79 45;82 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. We observed that NS1 R38A/K41A recovered IFN production to the greatest extent compared to NS1 WT, NS1 R38A, and NS1 K41A (Figure 2B). 2018 Frontiers in cellular and infection microbiology Result IV R38A;K41A;R38A;K41A 21;26;103;117 25;30;107;121 NS1;NS1;NS1;NS1 17;91;99;113 20;94;102;116 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. We observed that the NP and M1 proteins of the NS1 R38A/K41A virus could not be detected after 3 passages by western blotting in A549 cells, while the NS1 K41A and R38A viruses showed protein expression levels intermediate between those of the WT and NS1 R38A/K41A viruses (Figure 3B). 2018 Frontiers in cellular and infection microbiology Result IV K41A;R38A;K41A;R38A;R38A;K41A 56;51;155;164;255;260 60;55;159;168;259;264 M1;NP;NS1;NS1;NS1 28;21;47;151;251 30;23;50;154;254 29783694 Adaptive Mutations in Influenza A/California/07/2009 Enhance Polymerase Activity and Infectious Virion Production. By contrast, the PA E349G substitution increased reporter activity by ~2-fold in 293T cells and by ~10-fold in mouse L cells. 2018 Viruses Result IV E349G 20 25 PA 17 19 29783694 Adaptive Mutations in Influenza A/California/07/2009 Enhance Polymerase Activity and Infectious Virion Production. CA/07 PB2, PB1, PA and NP genes of parental CA/07 virus were cloned into expression vectors, and the T156A and F740L substitutions in PB1 and the E349G substitution in PA were subsequently introduced by site-directed mutagenesis. 2018 Viruses Result IV T156A;F740L;E349G 101;111;146 106;116;151 NP;PA;PA;PB1;PB1;PB2 23;16;168;11;134;6 25;18;170;14;137;9 29783694 Adaptive Mutations in Influenza A/California/07/2009 Enhance Polymerase Activity and Infectious Virion Production. Compared to the reconstituted RNA polymerase complex from parental CA/07 virus, PB1 T156A and PB1 F740L substitutions had no effect on viral RNA polymerase activity when introduced alone or in combination (Figure 4A,B,D). 2018 Viruses Result IV T156A;F740L 84;98 89;103 PB1;PB1 80;94 83;97 29783694 Adaptive Mutations in Influenza A/California/07/2009 Enhance Polymerase Activity and Infectious Virion Production. For this reason, we do not know whether mutations present at <50% frequencies occur in the same molecule, including the F740L and T156A substitutions on PB1. 2018 Viruses Result IV F740L;T156A 120;130 125;135 PB1 153 156 29783694 Adaptive Mutations in Influenza A/California/07/2009 Enhance Polymerase Activity and Infectious Virion Production. In the PA segment, two mutations that resulted in E18G and E349G amino acid substitutions, respectively, reached over 99% in read frequency (Figure 2). 2018 Viruses Result IV E18G;E349G 50;59 54;64 PA 7 9 29783694 Adaptive Mutations in Influenza A/California/07/2009 Enhance Polymerase Activity and Infectious Virion Production. In the PB1 segment, two additional substitutions at 36% and 50% frequency resulted in T156A and F740L amino acid substitutions, respectively. 2018 Viruses Result IV T156A;F740L 86;96 91;101 PB1 7 10 29783694 Adaptive Mutations in Influenza A/California/07/2009 Enhance Polymerase Activity and Infectious Virion Production. Interestingly, the PA mutation E18G is located in the amino-terminal endonuclease domain of PA and resides close to PB1 T156A in the 3D structure. 2018 Viruses Result IV E18G;T156A 31;120 35;125 PA;PA;PB1 19;92;116 21;94;119 29783694 Adaptive Mutations in Influenza A/California/07/2009 Enhance Polymerase Activity and Infectious Virion Production. Of these substitutions, D222G has been found previously in the two CA/04 mouse adaptation studies and is believed to be responsible for increased binding to alpha 2,3-linked sialic acid. 2018 Viruses Result IV D222G 24 29 29783694 Adaptive Mutations in Influenza A/California/07/2009 Enhance Polymerase Activity and Infectious Virion Production. The effect of E349G substitution in PA was not due to higher expression levels of mutant PA compared to the wild-type PA in this assay (Figure 4C and Figure S2). 2018 Viruses Result IV E349G 14 19 PA;PA;PA 36;89;118 38;91;120 29783694 Adaptive Mutations in Influenza A/California/07/2009 Enhance Polymerase Activity and Infectious Virion Production. The F740L mutation lies within the C-terminal PB2-interacting region of PB1; in the crystal structure, this residue makes direct contact with the PA subunit. 2018 Viruses Result IV F740L 4 9 PA;PB1;PB2 146;72;46 148;75;49 29783694 Adaptive Mutations in Influenza A/California/07/2009 Enhance Polymerase Activity and Infectious Virion Production. The surface-exposed PA E349G substitution is located on the opposite side of the polymerase complex (Figure 3). 2018 Viruses Result IV E349G 23 28 PA 20 22 29783694 Adaptive Mutations in Influenza A/California/07/2009 Enhance Polymerase Activity and Infectious Virion Production. Thus, among the three adaptive mutations in PB1 and PA, the E349G substitution had the greatest impact on viral RNA polymerase activity, especially in mouse cells. 2018 Viruses Result IV E349G 60 65 PA;PB1 52;44 54;47 29783694 Adaptive Mutations in Influenza A/California/07/2009 Enhance Polymerase Activity and Infectious Virion Production. To determine whether the CA/07-MA amino acid substitutions that increased minireplicon activity (Figure 4) also affect IAV replication in mouse cells, we created and tested a recombinant CA/07-based virus with three amino acid substitutions: PA E349G and PB1 T156A,F740L (hereafter CA/07-PA,PB1-MA). 2018 Viruses Result IV E349G;T156A;F740L 245;259;265 250;264;270 PA;PA;PB1;PB1 242;288;255;291 244;290;258;294 29783694 Adaptive Mutations in Influenza A/California/07/2009 Enhance Polymerase Activity and Infectious Virion Production. We identified three amino acid substitutions in HA that reached >99% frequency in the CA/07-MA strain: N156D, S183P and D222G (Figure 2 and Table S2). 2018 Viruses Result IV N156D;S183P;D222G 103;110;120 108;115;125 HA 48 50 29882021 Lethal Influenza in Two Related Adults with Inherited GATA2 Deficiency. By Sanger method, we found a novel missense heterozygous R396L mutation in GATA2 in the three patients. 2018 Journal of clinical immunology Result IV R396L 57 62 29882021 Lethal Influenza in Two Related Adults with Inherited GATA2 Deficiency. Expression and function of R396L GATA2 allele in HEK 293T cells. 2018 Journal of clinical immunology Result IV R396L 27 32 29882021 Lethal Influenza in Two Related Adults with Inherited GATA2 Deficiency. However, the function of GATA2-R396L, GATA2-R396Q and GATA2-R398W mutants were severely impaired and did not increase with co-expression of PML (Figure 2B), suggesting that R396L is dysfunctional and hypomorphic. 2018 Journal of clinical immunology Result IV R396L;R396Q;R398W;R396L 31;44;60;173 36;49;65;178 29882021 Lethal Influenza in Two Related Adults with Inherited GATA2 Deficiency. In silico analyses performed by means of PolyPhen-2 and PROVEAN/SIFT showed that the damaging effect of the R396L mutation is highly probable. 2018 Journal of clinical immunology Result IV R396L 108 113 29882021 Lethal Influenza in Two Related Adults with Inherited GATA2 Deficiency. Interestingly, GATA-2-mediated decrease of relative luciferase activity was observed to decrease at higher concentrations of R396L vector, which could suggest promoter competition. 2018 Journal of clinical immunology Result IV R396L 125 130 29882021 Lethal Influenza in Two Related Adults with Inherited GATA2 Deficiency. Mutations in the zinc finger-2 domain, particularly R398W (one of most frequent mutations causing GATA-2 deficiency), R398Q, R396W and R396Q have been reported in several independent studies, underscoring the key role of these residues on GATA-2 function. 2018 Journal of clinical immunology Result IV R398W;R398Q;R396W;R396Q 52;118;125;135 57;123;130;140 29882021 Lethal Influenza in Two Related Adults with Inherited GATA2 Deficiency. Similar results were obtained with constant amounts of GATA2-WT vector and different amounts of GATA2 R396L, R396Q and R398W mutants (Figure 3B). 2018 Journal of clinical immunology Result IV R396L;R396Q;R398W 102;109;119 107;114;124 29882021 Lethal Influenza in Two Related Adults with Inherited GATA2 Deficiency. The novel R396L mutation suggests that the residue R396 at GATA2 may be a mutational hotspot. 2018 Journal of clinical immunology Result IV R396L 10 15 29882021 Lethal Influenza in Two Related Adults with Inherited GATA2 Deficiency. The protein expression of isoforms 1 and 2 of GATA-2 in HEK293T transfected cells was shown to be slightly reduced in the mutant GATA2 R396L, R396Q and R398W alleles compared to the WT (Figure 2A and Figure S1A-B). 2018 Journal of clinical immunology Result IV R396L;R396Q;R398W 135;142;152 140;147;157 29882021 Lethal Influenza in Two Related Adults with Inherited GATA2 Deficiency. These results suggest that haplo-insufficiency could be the mechanism of GATA-2 deficiency caused by the R396L, R398W and R396Q mutations. 2018 Journal of clinical immunology Result IV R396L;R398W;R396Q 105;112;122 110;117;127 29882021 Lethal Influenza in Two Related Adults with Inherited GATA2 Deficiency. We did not find the R396L mutation in public data-base (dbSNP, 1000 genome), in 55 healthy Caucasian individuals and in 1022 individuals from 52 ethnic groups from the HGDP-CEPH panel. 2018 Journal of clinical immunology Result IV R396L 20 25 29882021 Lethal Influenza in Two Related Adults with Inherited GATA2 Deficiency. We observed a non-significant decrease in GATA2-mediated relative luciferase activity with increasing levels of the GATA2-R396L, GATA2-R398W and GATA2-R396Q mutants. 2018 Journal of clinical immunology Result IV R396L;R398W;R396Q 122;135;151 127;140;156 29882021 Lethal Influenza in Two Related Adults with Inherited GATA2 Deficiency. We then performed luciferase assays in transient cotransfections with PML and combined vectors of GATA2-WT and GATA2-R396L, as well as vectors of GATA2-R398W and GATA2-R396Q as negative controls, in different amounts mimicking heterozygosity (Figure 3A). 2018 Journal of clinical immunology Result IV R396L;R398W;R396Q 117;152;168 122;157;173 29927982 Influenza D virus M2 protein exhibits ion channel activity in Xenopus laevis oocytes. Mutated DM2, namely Y72A and K76A, showed similar reversal potentials of -22 and -21 mV, respectively (Table 2). 2018 PloS one Result IV Y72A;K76A 20;29 24;33 29927982 Influenza D virus M2 protein exhibits ion channel activity in Xenopus laevis oocytes. The observed gating voltages represented by tail Vmid for Y72A- and K76A-mutated DM2 were -109 and -129 mV, respectively (Table 1; Fig 6A and 6E). 2018 PloS one Result IV Y72A;K76A 58;68 62;72 29927982 Influenza D virus M2 protein exhibits ion channel activity in Xenopus laevis oocytes. Y72A-DM2 showed activating Vmid values different from that of native DM2 (-127 mV). 2018 PloS one Result IV Y72A 0 4 29933553 Kinetic, Thermodynamic, and Structural Analysis of Drug Resistance Mutations in Neuraminidase from the 2009 Pandemic Influenza Virus. A similar effect on oseltamivir binding was previously observed for the H275Y substitution in H5N1 avian influenza neuraminidase. 2018 Viruses Result IV H275Y 72 77 115 128 29933553 Kinetic, Thermodynamic, and Structural Analysis of Drug Resistance Mutations in Neuraminidase from the 2009 Pandemic Influenza Virus. Analysis of the inhibition data (Table 2) revealed that while Ki values are increased only marginally for the I223V and S247N single mutants, H275Y substitution reduces susceptibility to oseltamivir by three orders of magnitude. 2018 Viruses Result IV I223V;S247N;H275Y 110;120;142 115;125;147 29933553 Kinetic, Thermodynamic, and Structural Analysis of Drug Resistance Mutations in Neuraminidase from the 2009 Pandemic Influenza Virus. As its side chain is exposed to the solvent, substitution of serine with the larger asparagine (S247N mutation) does not induce changes in the protein structure; the RMSD for superposition of 390 Calpha with the wt structure was 0.133 A. 2018 Viruses Result IV S247N 96 101 29933553 Kinetic, Thermodynamic, and Structural Analysis of Drug Resistance Mutations in Neuraminidase from the 2009 Pandemic Influenza Virus. Compared to wt, the I223V and S247N mutants had minor differences in the thermodynamic parameters of inhibitor binding. 2018 Viruses Result IV I223V;S247N 20;30 25;35 29933553 Kinetic, Thermodynamic, and Structural Analysis of Drug Resistance Mutations in Neuraminidase from the 2009 Pandemic Influenza Virus. Crystal structures of enzymes containing the H275Y substitution either alone or in combination with other mutations show that the bulkier tyrosine side chain pushes the side chain of the neighboring E277 into the binding site, affecting the binding pose of oseltamivir. 2018 Viruses Result IV H275Y 45 50 29933553 Kinetic, Thermodynamic, and Structural Analysis of Drug Resistance Mutations in Neuraminidase from the 2009 Pandemic Influenza Virus. For the H275Y single mutant, the enthalpy change for oseltamivir binding was substantially affected and was 8.7 kcal mol-1 less favorable than the wt value. 2018 Viruses Result IV H275Y 8 13 29933553 Kinetic, Thermodynamic, and Structural Analysis of Drug Resistance Mutations in Neuraminidase from the 2009 Pandemic Influenza Virus. In enzyme variants containing H275Y in combination with the I223V or S247N mutation, an oseltamivir pose similar to that found in H275Y was observed (Figure 2B,E,F). 2018 Viruses Result IV H275Y;I223V;S247N;H275Y 30;60;69;130 35;65;74;135 29933553 Kinetic, Thermodynamic, and Structural Analysis of Drug Resistance Mutations in Neuraminidase from the 2009 Pandemic Influenza Virus. In the H275Y/S247N variant, the water-mediated contact with the oxygen atom between the N247 side-chain and pentyloxy substituent of oseltamivir seen in S247N NA2009 does not form due to the change in position of the pentyloxy substituent caused by the H275Y substitution. 2018 Viruses Result IV H275Y;S247N;S247N;H275Y 7;13;153;253 12;18;158;258 159 161 29933553 Kinetic, Thermodynamic, and Structural Analysis of Drug Resistance Mutations in Neuraminidase from the 2009 Pandemic Influenza Virus. Ki values for the I223V/H275Y and S247N/H275Y double mutants were 3900- and 9000-fold higher than the wt NA2009 value, respectively. 2018 Viruses Result IV I223V;H275Y;S247N;H275Y 18;24;34;40 23;29;39;45 105 107 29933553 Kinetic, Thermodynamic, and Structural Analysis of Drug Resistance Mutations in Neuraminidase from the 2009 Pandemic Influenza Virus. Most of the mutated NAs retained Km values almost identical to that of wild-type, while the S247N/H275Y double mutation resulted in a three-fold decrease in substrate-binding ability. 2018 Viruses Result IV S247N;H275Y 92;98 97;103 20 23 29933553 Kinetic, Thermodynamic, and Structural Analysis of Drug Resistance Mutations in Neuraminidase from the 2009 Pandemic Influenza Virus. No change in oseltamivir pose was observed; the RMSD for superposition of oseltamivir atoms in the wt NA2009 structure (PDB code 3TI6), I223V variant, and S247N variant was 0.74 A. 2018 Viruses Result IV I223V;S247N 136;155 141;160 102 104 29933553 Kinetic, Thermodynamic, and Structural Analysis of Drug Resistance Mutations in Neuraminidase from the 2009 Pandemic Influenza Virus. On the other hand, the effects of the I223V and S247N substitutions are less dramatic on the structural level. 2018 Viruses Result IV I223V;S247N 38;48 43;53 29933553 Kinetic, Thermodynamic, and Structural Analysis of Drug Resistance Mutations in Neuraminidase from the 2009 Pandemic Influenza Virus. S247 forms hydrogen bonds with two water molecules present only in the wt enzyme and not in the S247N mutant. 2018 Viruses Result IV S247N 96 101 29933553 Kinetic, Thermodynamic, and Structural Analysis of Drug Resistance Mutations in Neuraminidase from the 2009 Pandemic Influenza Virus. The catalytic efficiencies of the H275Y, I223V/H275Y, and S247N/ H275Y variants were 4-6% of the wt value, illustrating the significant effect of the H275Y mutation on the enzyme's catalytic activity. 2018 Viruses Result IV H275Y;I223V;H275Y;S247N;H275Y;H275Y 34;41;47;58;65;150 39;46;52;63;70;155 29933553 Kinetic, Thermodynamic, and Structural Analysis of Drug Resistance Mutations in Neuraminidase from the 2009 Pandemic Influenza Virus. The crystal structure provides a direct explanation for the more than 1000-fold reduction in binding affinity for oseltamivir in variants containing the H275Y substitution. 2018 Viruses Result IV H275Y 153 158 29933553 Kinetic, Thermodynamic, and Structural Analysis of Drug Resistance Mutations in Neuraminidase from the 2009 Pandemic Influenza Virus. The dramatic effect of the H275Y/S247N double mutation on susceptibility to oseltamivir (8-fold and 500-fold increase in Ki compared to the H275Y and S247N single mutants, respectively) can thus be attributed to the combined influence of the change in oseltamivir pose and alterations in the hydration shell structure. 2018 Viruses Result IV S247N;H275Y;H275Y;S247N 33;27;140;150 38;32;145;155 29933553 Kinetic, Thermodynamic, and Structural Analysis of Drug Resistance Mutations in Neuraminidase from the 2009 Pandemic Influenza Virus. The enthalpy change in I223V NA2009 was partly compensated by a more favorable entropic contribution of 0.6 kcal mol-1. 2018 Viruses Result IV I223V 23 28 29 31 29933553 Kinetic, Thermodynamic, and Structural Analysis of Drug Resistance Mutations in Neuraminidase from the 2009 Pandemic Influenza Virus. The entropic contribution of oseltamivir binding to S247N NA2009 was almost unaffected; the value was within experimental error of the wt value. 2018 Viruses Result IV S247N 52 57 58 60 29933553 Kinetic, Thermodynamic, and Structural Analysis of Drug Resistance Mutations in Neuraminidase from the 2009 Pandemic Influenza Virus. The H275Y Mutation Impairs Neuraminidase Activity and Substantially Reduces Susceptibility to Oseltamivir. 2018 Viruses Result IV H275Y 4 9 27 40 29933553 Kinetic, Thermodynamic, and Structural Analysis of Drug Resistance Mutations in Neuraminidase from the 2009 Pandemic Influenza Virus. The I223V substitution did not induce any structural changes in the neighboring residues; however, the substitution for a smaller side chain results in enlargement of the volume of the enzyme active site pocket and loss of Van der Waals contacts with the pentyloxy substituent of oseltamivir. 2018 Viruses Result IV I223V 4 9 29933553 Kinetic, Thermodynamic, and Structural Analysis of Drug Resistance Mutations in Neuraminidase from the 2009 Pandemic Influenza Virus. The mutations in the resistant NAs decreased the binding affinity of oseltamivir by factors of 4 (I223V mutant), 3 (S247N mutant), and 95 (H275Y mutant). 2018 Viruses Result IV I223V;S247N;H275Y 98;116;139 103;121;144 31 34 29933553 Kinetic, Thermodynamic, and Structural Analysis of Drug Resistance Mutations in Neuraminidase from the 2009 Pandemic Influenza Virus. The resulting catalytic efficiencies (kcat/Km) of the single mutants I223V and S247N were only moderately decreased. 2018 Viruses Result IV I223V;S247N 69;79 74;84 29933553 Kinetic, Thermodynamic, and Structural Analysis of Drug Resistance Mutations in Neuraminidase from the 2009 Pandemic Influenza Virus. The RMSD for superposition of oseltamivir atoms in the H275Y, H275Y/I223V, and H275Y/S247N NA2009 variant was below 0.11 A. 2018 Viruses Result IV H275Y;H275Y;I223V;S247N;H275Y 55;62;68;85;79 60;67;73;90;84 91 93 29933553 Kinetic, Thermodynamic, and Structural Analysis of Drug Resistance Mutations in Neuraminidase from the 2009 Pandemic Influenza Virus. This interaction is not present in the I223V mutant, where the closest C-C distance between V223 and oseltamivir methyl groups is 5.0 A. 2018 Viruses Result IV I223V 39 44 29933553 Kinetic, Thermodynamic, and Structural Analysis of Drug Resistance Mutations in Neuraminidase from the 2009 Pandemic Influenza Virus. Three variants (H275Y, H275Y/I223V, and H275Y/S247N NA2009) crystallized in the monoclinic space group with four molecules in the asymmetric unit, representing the tetrameric biological unit. 2018 Viruses Result IV H275Y;H275Y;I223V;H275Y;S247N 16;23;29;40;46 21;28;34;45;51 52 54 29933553 Kinetic, Thermodynamic, and Structural Analysis of Drug Resistance Mutations in Neuraminidase from the 2009 Pandemic Influenza Virus. Two variants (I223V and S247N single mutants) crystallized in the centered orthorhombic space group with two molecules in the asymmetric unit; the tetrameric biological unit could be reconstructed from two symmetrically related dimers. 2018 Viruses Result IV I223V;S247N 14;24 19;29 29933553 Kinetic, Thermodynamic, and Structural Analysis of Drug Resistance Mutations in Neuraminidase from the 2009 Pandemic Influenza Virus. We conclude that structural changes caused by the individual mutations have a coacting effect on increase of oseltamivir resistance, reflected in the more than three-fold increase in Ki in H275Y/I223V NA2009 compared to H275Y NA2009. 2018 Viruses Result IV I223V;H275Y;H275Y 195;189;220 200;194;225 NA;NA 201;226 203;228 29933553 Kinetic, Thermodynamic, and Structural Analysis of Drug Resistance Mutations in Neuraminidase from the 2009 Pandemic Influenza Virus. We could not perform titrations against double-mutants since the expression yield of recombinant protein was not sufficient for proper estimation of Kd values that are expected to be higher than for H275Y mutant. 2018 Viruses Result IV H275Y 199 204 29933553 Kinetic, Thermodynamic, and Structural Analysis of Drug Resistance Mutations in Neuraminidase from the 2009 Pandemic Influenza Virus. We used a standard fluorometric in vitro activity assay to investigate the impact of the I223V, S247N, and H275Y single mutations and the I223V/H275Y and S247N/H275Y double mutations reported in patients on the catalytic activity of NA2009. 2018 Viruses Result IV I223V;S247N;H275Y;I223V;H275Y;S247N;H275Y 89;96;107;138;144;154;160 94;101;112;143;149;159;165 233 235 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. Apart from PA substitutions at position 38, A37T, E199G, N412D, V517A, and P632S were detected in one patient each. 2018 Scientific reports Result IV A37T;E199G;N412D;V517A;P632S 44;50;57;64;75 48;55;62;69;80 PA 11 13 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. By comparison, for rgB/Maryland/1/59, I38F conferred impaired replicative capacity, whereas I38T and I38M viruses were comparable to the wild-type. 2018 Scientific reports Result IV I38F;I38T;I38M 38;92;101 42;96;105 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. Collectively, I38T and I38M in A/H3N2 viruses were identified by the treatment-emergent monitoring of the pediatric study as conferring more than 10-fold reductions in BXA susceptibility, whereas A37T and E199G had lesser effects. 2018 Scientific reports Result IV I38T;I38M;A37T;E199G 14;23;196;205 18;27;200;210 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. Collectively, treatment-emergent monitoring in the phase 2 study identified I38T or I38F substitutions in A/H1N1 viruses as conferring more than 10-fold reductions in BXA susceptibility, whereas E23K had a significant but lesser impact. 2018 Scientific reports Result IV I38T;I38F;E23K 76;84;195 80;88;199 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. Drug testing demonstrated that introduction of A20S into rgA/WSN/33 (H1N1) did not affect BXA sensitivity, and the FCs of combinations of A20S + I38T and A20S + I38F were comparable levels to single I38T or F mutations (Table 1). 2018 Scientific reports Result IV A20S;A20S;I38T;A20S;I38F;I38T 47;138;145;154;161;199 51;142;149;158;165;203 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. Drug testing showed that the FCs of A/H3N2 with the single mutation of I38T or I38M were 56.59 and 13.77-fold, respectively (Table 1). 2018 Scientific reports Result IV I38T;I38M 71;79 75;83 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. E623K was detected along with I38T substitution in one patient. 2018 Scientific reports Result IV E623K;I38T 0;30 5;34 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. Extensive sequencing of the viral RNA from 25 patients who exhibited rebound in viral titre resulted in identification of the I38T change in A/H3N2 virus for three patients. 2018 Scientific reports Result IV I38T 126 130 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. For both FluA and FluB, the endonuclease activity of the I38T mutant was inhibited only at the highest BXA concentration (1:1 ratio), whereas WT forms showed reduced or no activity already at 0.5:1 BXA:protein ratio. 2018 Scientific reports Result IV I38T 57 61 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. For the FluB I38T mutant in the absence of ligand, the threonine side-chain changes rotamer. 2018 Scientific reports Result IV I38T 13 17 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. Given that I38 is highly conserved and that I38T and I38F were not detected in A/H1N1, A/H3N2 or type B viruses according to the NCBI database (Supp. 2018 Scientific reports Result IV I38T;I38F 44;53 48;57 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. In addition, a structure of the influenza B domain with the I38T mutation was determined without bound compound at 1.8 A resolution (Table 3). 2018 Scientific reports Result IV I38T 60 64 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. In MDCK cells, the viral titers of rgA/WSN/33 with I38T, I38F and I38M were lower than that of the wild-type (-2.78, -2.28 and -1.67 logTCID50/mL, respectively) at 24 hours post-infection, and similar results were obtained with rgA/Victoria/3/75 (H3N2) virus. 2018 Scientific reports Result IV I38F;I38T;I38M 57;51;66 61;55;70 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. In order to investigate the impact of the I38T, I38F, I38M mutations on virus growth, the replicative capacity of the corresponding recombinant viruses was evaluated by measuring the time-course of viral titers in the supernatant of infected cell cultures. 2018 Scientific reports Result IV I38T;I38F;I38M 42;48;54 46;52;58 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. In summary, I38T, I38F and I38M substitutions in A/H1N1 and A/H3N2 had impaired replicative capacity compared to the wild-type in canine MDCK and human RPMI2650 cells. 2018 Scientific reports Result IV I38T;I38F;I38M 12;18;27 16;22;31 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. In the case of rgB/Maryland/1/59, the viral titers of I38F were lower than that of the wild-type (-0.73 logTCID50/mL) at 24 hours post-infection, whereas those of I38T and I38M were comparable to the wild-type. 2018 Scientific reports Result IV I38F;I38T;I38M 54;163;172 58;167;176 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. In vitro endonuclease activity of wild-type and I38T endonuclease domain. 2018 Scientific reports Result IV I38T 48 52 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. It has been reported that PA E119D confers resistance to the compound L-742,001 that targets the CEN with a metal chelating mechanism similar to BXA. 2018 Scientific reports Result IV E119D 29 34 PA 26 28 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. Next, one of the NA inhibitor-resistant mutations, NA/H274Y, was introduced in A/H1N1 and the susceptibility to BXA was determined. 2018 Scientific reports Result IV H274Y 54 59 NA;NA 17;51 19;53 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. Of note, variants with E119D or E120D were not detected so far in the BXM clinical studies. 2018 Scientific reports Result IV E119D;E120D 23;32 28;37 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. Since I38M is rarely found in the NCBI database, with frequencies of 0.02% and 0.04% in A/H1N1 and A/H3N2, respectively (Supp. 2018 Scientific reports Result IV I38M 6 10 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. Since the viruses with I38F emerged during BXA treatment in one patient from a virus that originally possessed S20, the effects of A20S were assessed. 2018 Scientific reports Result IV I38F;A20S 23;131 27;135 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. Structural analysis of influenza A and B WT and I38T endonuclease with bound BXA. 2018 Scientific reports Result IV I38T 48 52 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. Susceptibility testing revealed that rgA/WSN/33 (H1N1) with the single substitution I38T, I38F or E23K showed FCs of 27.24, 10.61 and 4.74-fold, respectively, whereas the rgB/Maryland/1/59 with G548R mutation did not impact BXA sensitivity (Table 1). 2018 Scientific reports Result IV I38T;I38F;E23K;G548R 84;90;98;194 88;94;102;199 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. Table 2), I38M presumably emerged because of exposure to BXM. 2018 Scientific reports Result IV I38M 10 14 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. Table 2), it is suggested that the A/H1N1 I38T or I38F viruses emerged as a result of exposure to BXM. 2018 Scientific reports Result IV I38T;I38F 42;50 46;54 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. Taken together, these results are in line with the observed reduced replicative capacity and reduced sensitivity to BXA of mutant viruses bearing the AA change I38T (Table 1), with a more marked effect on FluA than on FluB. 2018 Scientific reports Result IV I38T 160 164 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. Testing demonstrated that A37T and E199G in A/H3N2 conferred slightly reduced susceptibility by 8.13 and 4.46-fold, respectively, whereas the mutations at positon 412, 517 and 632 did not impact on BXA susceptibility (Table 1). 2018 Scientific reports Result IV A37T;E199G 26;35 30;40 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. Testing with BXA yielded FC values for L28P, V63I and L28P + V63I in A/H3N2 of 2.58, 1.73 and 2.88-fold, respectively, and mutation at position 356 did not have impact on BXA sensitivity (Table 1). 2018 Scientific reports Result IV L28P;V63I;L28P;V63I 39;45;54;61 43;49;58;65 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. Testing with recombinant rgA/WSN/33 (H1N1) viruses with A36V and V545T mutations showed that FCs in EC50 were 3.59 and 0.73-fold, respectively (Table 1). 2018 Scientific reports Result IV A36V;V545T 56;65 60;70 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. The ~10 C less thermal stabilisation of the mutant compared to the wild-type endonuclease is consistent with BXA being less tightly bound by the I38T variant endonucleases. 2018 Scientific reports Result IV I38T 146 150 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. The effect of BXA binding on the thermal stability of wild-type and I38T endonuclease domains from both FluA and FluB was measured in solution using the Thermofluor assay. 2018 Scientific reports Result IV I38T 68 72 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. The results above suggest that substitution at I38 in PA protein is a major pathway for reduced susceptibility to BXA in the clinical setting, and I38T has the highest effect (30- to 50-fold). 2018 Scientific reports Result IV I38T 147 151 PA 54 56 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. The results show a 10-fold reduced activity of the I38T mutant endonuclease in vitro for both FluA and FluB. 2018 Scientific reports Result IV I38T 51 55 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. Therefore the impact of E623K and the combination of I38T + E623K on BXA susceptibility was evaluated with the conclusion that E623K had little impact. 2018 Scientific reports Result IV E623K;I38T;E623K;E623K 24;53;60;127 29;57;65;132 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. Therefore, the polymorphic S20 did not affect reduced sensitivity to BXA caused by I38T or I38F changes. 2018 Scientific reports Result IV I38T;I38F 83;91 87;95 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. Thermostabilisation of the wild-type and I38T endonuclease upon BXA binding. 2018 Scientific reports Result IV I38T 41 45 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. This extensive sequencing resulted in the detection of the E23K change in PA of A/H1N1pdm virus for one patient. 2018 Scientific reports Result IV E23K 59 63 PA 74 76 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. To give structural insight into the mechanism of reduced susceptibility of the I38T variant, we co-crystallised BXA with the PA endonuclease domain from influenza A and B virus polymerase with either I38 or T38. 2018 Scientific reports Result IV I38T 79 83 PA 125 127 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. To take account of the reduced activity of the mutant, for each strain we conducted two sets of experiments in which protein concentrations of WT or I38T were adjusted to allow an identical starting RNA degradation activity. 2018 Scientific reports Result IV I38T 149 153 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. To verify the reduced endonuclease activity of the I38T mutant, we purified the isolated endonuclease domain from influenza A and B virus polymerase with either Ile or Thr at position 38. 2018 Scientific reports Result IV I38T 51 55 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. Treatment-emergent I38 variants were detected with total 15 A/H3N2-infected subjects, including twelve I38T and three I38M changes. 2018 Scientific reports Result IV I38M;I38T 118;103 122;107 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. Treatment-emergent mutations in the PA region, which are defined as AA changes after a dose of BXM, were detected in five patients: I38T or I38F in two A/H1N1pdm-infected patients each and R548G in one type B-infected patient. 2018 Scientific reports Result IV I38T;I38F;R548G 132;140;189 136;144;194 PA 36 38 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. Using a FAM-labelled 42 nt ssRNA substrate we first compared the nuclease activity of FluA wild-type and I38T endonuclease domains under identical conditions. 2018 Scientific reports Result IV I38T 105 109 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. We also confirmed that A20S did not impact the replicative capacity of wild-type and I38F viruses (Supp. 2018 Scientific reports Result IV A20S;I38F 23;85 27;89 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. We also confirmed that polymorphic I38V, which occurs at a frequency of 0.06% in A/H1N1, did not affect BXA sensitivity (Table 1 and Supp. 2018 Scientific reports Result IV I38V 35 39 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. We also found that E623K did not affect the replicative capacity of wild-type and I38T viruses (Supp. 2018 Scientific reports Result IV E623K;I38T 19;82 24;86 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. We found that E119D conferred slightly reduced susceptibility to BXA by 6.46 and 4.51-fold in A/H1N1 and A/H3N2, respectively, while E120D in type B virus did not have a significant impact (Table 1). 2018 Scientific reports Result IV E119D;E120D 14;133 19;138 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. We then tested the effect of BXA binding on the endonuclease activity by incubating WT or I38T PA from FluA or FluB with increasing concentrations of inhibitor. 2018 Scientific reports Result IV I38T 90 94 PA 95 97 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. We therefore evaluated the antiviral effect of BXA to type A and B viruses with the PA mutations E119D and E120D, respectively. 2018 Scientific reports Result IV E119D;E120D 97;107 102;112 PA 84 86 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. When A36V was introduced into rgA/Victoria/3/75 (H3N2), a 6.09-fold reduced susceptibility to BXA was observed, but no significant fold changes were observed when the AA at position 36 was changed in type B virus (Table 1). 2018 Scientific reports Result IV A36V 5 9 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. Whilst NA/H274Y results in a more than 200-fold reduction in susceptibility to oseltamivir acid, BXA showed potent activity against these viruses. 2018 Scientific reports Result IV H274Y 10 15 7 9 29976861 Anti-Influenza A Viral Butenolide from Streptomyces sp. Smu03 Inhabiting the Intestine of Elephas maximus. The viral strains were influenza A/PR/8/34 (H1N1), A/Aichi/2/68 (H3N2), A/FM/1/47 (H1N1) mouse adapted strains, and oseltamivir-resistant influenza virus strains of A/PR/8/34 with NA-H274Y mutation. 2018 Viruses Result IV H274Y 183 188 180 182 29999583 A 627K variant in the PB2 protein of H9 subtype influenza virus in wild birds. An N66S substitution was found in the PB1-F2 protein of all the H9 strains in this study, which is associated with the increased virulence of the 1918 pandemic virus and the highly pathogenic AI H5N1 virus in mice and ferrets.21, 22 The mutations N30D and T215A in the M1 protein and some had P42S in the NS1 protein suggest the viruses would exhibit increased virulence in mammals. 2018 Influenza and other respiratory viruses Result IV N66S;N30D;T215A;P42S 3;247;256;293 7;251;261;297 M1;NS1;PB1F2 269;305;38 271;308;44 29999583 A 627K variant in the PB2 protein of H9 subtype influenza virus in wild birds. No amino acid substitutions were found in the M2 transmembrane domain, suggesting that this virus strain is sensitive to M2 ion channel inhibitors.23 The S31N amino acid substitution in the M2 protein was not present, indicating that these viral strains were sensitive to amantadine inhibitors.24 The virulence of influenza viruses in humans is related to their resistance to the antiviral effects of cytokines, such as interferon (IFN), and the D92E mutation in the NS1 protein increases resistance to IFN.25 However, no mutations at residue 92 of NS1 were observed in this study. 2018 Influenza and other respiratory viruses Result IV S31N;D92E 154;446 158;450 M2;M2;M2;NS1;NS1 46;121;190;467;549 48;123;192;470;552 29999583 A 627K variant in the PB2 protein of H9 subtype influenza virus in wild birds. None of the seven H9 viruses had a Y436H substitution in the PB1 protein or T515A substitution in the PA protein, which suggested low pathogenicity to mammalian and avian hosts. 2018 Influenza and other respiratory viruses Result IV Y436H;T515A 35;76 40;81 PA;PB1 102;61 104;64 29999583 A 627K variant in the PB2 protein of H9 subtype influenza virus in wild birds. The amino acid substitutions Q226L and G228S (H3 numbering, which is used throughout the manuscript) favor the affinity of influenza viruses for human-type receptors.13, 14 Necklace deletion in the NA gene confers enhanced virus lethality in mice.15 The aforementioned characteristic changes were detected here: two viruses, AH/BLH12 and AH/DGG4, not only showed Q226L receptor binding changes but also had NA gene necklace deletions at amino acids 63-65. 2018 Influenza and other respiratory viruses Result IV Q226L;G228S;Q226L 29;39;363 34;44;368 NA;NA 198;407 200;409 29999583 A 627K variant in the PB2 protein of H9 subtype influenza virus in wild birds. The influenza virus PB2 protein has several reported mutations that contribute to virulence and adaptation in mammalian hosts,16 including 89V,17 271A, 627K, and 701N.17, 18, 19 Two viruses, AH/BLH12 and AH/DGG4, showed the E627K mutation in their PB2 proteins, and the other five strains had 271T, 627E, or 701D mutations. 2018 Influenza and other respiratory viruses Result IV E627K 224 229 PB2;PB2 20;248 23;251 29999583 A 627K variant in the PB2 protein of H9 subtype influenza virus in wild birds. The substitution PB2-A588V may represent a new strategy for AIV adaptation to mammalian hosts.16 The seven H9 strains in this study all had no substitutions in PB2-A588V. 2018 Influenza and other respiratory viruses Result IV A588V;A588V 21;164 26;169 PB2;PB2 17;160 20;163 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. Examples of substitutions are NA-T242I (ferret 1 at 10 dpi) and HA-T151A (ferret 3 at 10 dpi) (Table 1). 2018 PloS one Result IV T242I;T151A 33;67 38;72 HA;NA 64;30 66;32 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. However, where viruses with the R292K substitution in NA generally increased in prevalence throughout the course of the experiment, to become dominant at the latest time points, none of the additional substitutions followed a similar trend. 2018 PloS one Result IV R292K 32 37 54 56 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. Illumina NGS revealed numerous mutations in HA and NA of the viruses beyond R292K, present in all Oseltamivir treated animals (Table 1, S1 Table). 2018 PloS one Result IV R292K 76 81 HA;NA 44;51 46;53 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. Illumina NGS was conducted to analyze the emergence of mutations beyond R292K that were potentially associated with Oseltamivir treatment in the HA and NA genes of influenza viruses in immunocompetent and immunocompromised ferrets at 2, 4, 6, 8 and 10 dpi. 2018 PloS one Result IV R292K 72 77 HA;NA 145;152 147;154 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. Like the msRT-PCR analysis, Illumina NGS allowed the detection of R292K in all immunocompromised and immunocompetent ferrets treated with Oseltamivir (Fig 3 and S6 Fig) (Table 1 and S1 Table). 2018 PloS one Result IV R292K 66 71 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. Mutation E119V was not detected in these samples, whereas the R292K resistance mutation was detected in the nose and throat swabs of all immunocompromised (Fig 2C) ferrets that were treated with Oseltamivir. 2018 PloS one Result IV E119V;R292K 9;62 14;67 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. Samples from all inoculated animals (Fig 2 and S3 Fig) were analyzed by mutation-specific RT-PCR to detect substitutions E119V and R292K in NA, the most common Oseltamivir associated resistance mutations in A/H3N2 influenza viruses. 2018 PloS one Result IV E119V;R292K 121;131 126;136 140 142 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. The R292K substitution first emerged in the throat at 5dpi in one animal (ferret 4) and at 6dpi and 7dpi in three (ferret 1, 2, 3) and two animals (ferret 5 and 6) respectively. 2018 PloS one Result IV R292K 4 9 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. There was good overall correspondence between the relative proportion of the R292K resistance substitution as determined by msRT-PCR and Illumina NGS (S5 Fig, R2 = 0.94, P<0.0001). 2018 PloS one Result IV R292K 77 82 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. Thus, under these experimental conditions, the emergence of viruses with the R292K substitution in NA was not accompanied by co-mutations in NA and HA that could act to compensate for potential fitness losses associated with Oseltamivir resistance. 2018 PloS one Result IV R292K 77 82 HA;NA;NA 148;99;141 150;101;143 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. To validate this approach, the frequency of the R292K resistance substitutions was first determined by Illumina NGS. 2018 PloS one Result IV R292K 48 53 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. When the R292K substitution occurred, it was initially present as a minor genotype in a mixed population of wild type and resistant viruses. 2018 PloS one Result IV R292K 9 14 30050898 Structurally Diverse Polyketides From the Mangrove-Derived Fungus Diaporthe sp. SCSIO 41011 With Their Anti-influenza A Virus Activities. Antiviral effect of the isolated compounds 1-28 and 5-chloroisorotiorin against different IAV subtypes, including A/Puerto Rico/8/34 H274Y (H1N1), A/FM-1/1/47 (H1N1), and A/Aichi/2/68 (H3N2), were then evaluated. 2018 Frontiers in chemistry Result IV H274Y 133 138 30050898 Structurally Diverse Polyketides From the Mangrove-Derived Fungus Diaporthe sp. SCSIO 41011 With Their Anti-influenza A Virus Activities. By the way, 5-chloroisorotiorin (Luo et al.,), a recently reported co-isolated chloroazaphilone derivative obtained with major amount, was also screened for anti-IAV activity, which presented selective inhibition activities against the two IAV subtypes of A/Puerto Rico/8/34 H274Y (H1N1) and A/Aichi/2/68 (H3N2) with the IC50 values of 2.52 +- 0.21 and 10.10 +- 1.84 muM, respectively. 2018 Frontiers in chemistry Result IV H274Y 275 280 30050898 Structurally Diverse Polyketides From the Mangrove-Derived Fungus Diaporthe sp. SCSIO 41011 With Their Anti-influenza A Virus Activities. Notably, among the three xanthones (25-27), only 3,8-dihydroxy-6-methyl-9-oxo-9H-xanthene-1-carboxylate (26) demonstrated remarkable inhibitory effects against A/FM-1/1/47 (H1N1), A/Puerto Rico/8/34 H274Y (H1N1), and A/Aichi/2/68 (H3N2) with IC50 values of 4.80 +- 1.28, 9.40 +- 1.96, and 5.12 +- 1.49 muM, respectively, which indicated the hydroxyl group at C-3 probably promote the anti-IAV activities toward the three subtypes. 2018 Frontiers in chemistry Result IV H274Y 199 204 30050898 Structurally Diverse Polyketides From the Mangrove-Derived Fungus Diaporthe sp. SCSIO 41011 With Their Anti-influenza A Virus Activities. The remaining ones (1-13, 16-26, 27-28) showed no obvious inhibition against A/FM-1/1/47 (H1N1), A/Puerto Rico/8/34 H274Y (H1N1), and A/Aichi/2/68 (H3N2). 2018 Frontiers in chemistry Result IV H274Y 116 121 30084768 Exchange of amino acids in the H1-haemagglutinin to H3 residues is required for efficient influenza A virus replication and pathology in Tmprss2 knock-out mice. In these viruses, referred to as PR8_HA(D) or PR8_HA(D-MVEKT), respectively, the glutamate at position 31 was replaced by aspartate from H3 (E31 to D31. 2018 The Journal of general virology Result IV E31D 81 131 30084768 Exchange of amino acids in the H1-haemagglutinin to H3 residues is required for efficient influenza A virus replication and pathology in Tmprss2 knock-out mice. Therefore, we also replaced this amino acid in H1 with the equivalent amino acid from the H3 sequence in addition to the HA-loop: aspartic acid at position 31 (mutant E31D). 2018 The Journal of general virology Result IV E31D 167 171 HA 121 123 30111290 Development of a quadruple qRT-PCR assay for simultaneous identification of highly and low pathogenic H7N9 avian influenza viruses and characterization against oseltamivir resistance. We then downloaded and compared the NA genes of the H7N9 viruses, selected the forward (N9-F), reverse (N9-R) primers covering the R292K mutation region, and designed a probe (N9-P-M) which can specifically recognize the R292K mutation. 2018 BMC infectious diseases Result IV R292K;R292K 131;221 136;226 N9;N9;N9;NA 88;104;176;36 90;106;178;38 30141905 The Stabilities of the Soluble Ectodomain and Fusion Peptide Hairpins of the Influenza Virus Hemagglutinin Subunit II Protein Are Positively Correlated with Membrane Fusion. 40 mL resulted in a ~0.3 mg/L greater purified yields of G1E- and I173E- HA2. 2018 Biochemistry Result IV G1E;I173E 57;66 60;71 HA 73 75 30141905 The Stabilities of the Soluble Ectodomain and Fusion Peptide Hairpins of the Influenza Virus Hemagglutinin Subunit II Protein Are Positively Correlated with Membrane Fusion. Both WT- and G1E- FHA2 proteins in DM have a dominant peak in the void volume corresponding to oligomers/aggregates with MW's > 1 MDa. 2018 Biochemistry Result IV G1E 13 16 30141905 The Stabilities of the Soluble Ectodomain and Fusion Peptide Hairpins of the Influenza Virus Hemagglutinin Subunit II Protein Are Positively Correlated with Membrane Fusion. For protocol B, there was complete solubilization in 40 mL buffer with SRC for the pellet from cells expressing WT-HA2, whereas 50 mL was required for the pellets from cells expressing G1E- or I173E- HA2. 2018 Biochemistry Result IV G1E;I173E 185;193 188;198 HA;HA 115;200 117;202 30141905 The Stabilities of the Soluble Ectodomain and Fusion Peptide Hairpins of the Influenza Virus Hemagglutinin Subunit II Protein Are Positively Correlated with Membrane Fusion. HA2 based on ~5x greater purified yields of WT-, G1E-, and I173E-FHA2 via protocol A vs. 2018 Biochemistry Result IV G1E;I173E 49;59 52;64 HA 0 2 30141905 The Stabilities of the Soluble Ectodomain and Fusion Peptide Hairpins of the Influenza Virus Hemagglutinin Subunit II Protein Are Positively Correlated with Membrane Fusion. HA2 is ~5 for the WT-, G1E-, and I173E- variants. 2018 Biochemistry Result IV G1E;I173E 23;33 26;38 HA 0 2 30141905 The Stabilities of the Soluble Ectodomain and Fusion Peptide Hairpins of the Influenza Virus Hemagglutinin Subunit II Protein Are Positively Correlated with Membrane Fusion. HA2, and for WT and G1E vs. 2018 Biochemistry Result IV G1E 20 23 HA 0 2 30141905 The Stabilities of the Soluble Ectodomain and Fusion Peptide Hairpins of the Influenza Virus Hemagglutinin Subunit II Protein Are Positively Correlated with Membrane Fusion. mutant- HA2's, with similar reduced fusion for both G1E and I173E. 2018 Biochemistry Result IV G1E;I173E 52;60 55;65 HA 8 10 30141905 The Stabilities of the Soluble Ectodomain and Fusion Peptide Hairpins of the Influenza Virus Hemagglutinin Subunit II Protein Are Positively Correlated with Membrane Fusion. S5 also presents spectra with [I173E-FHA2] = 1, 5, 10, and 20 muM, and all the theta222 values correlate to a significant fraction of alpha helical structure. 2018 Biochemistry Result IV I173E 31 36 30141905 The Stabilities of the Soluble Ectodomain and Fusion Peptide Hairpins of the Influenza Virus Hemagglutinin Subunit II Protein Are Positively Correlated with Membrane Fusion. S5 shows that for I173E-FHA2, similar spectra are obtained in the absence vs. 2018 Biochemistry Result IV I173E 18 23 30141905 The Stabilities of the Soluble Ectodomain and Fusion Peptide Hairpins of the Influenza Virus Hemagglutinin Subunit II Protein Are Positively Correlated with Membrane Fusion. The lower purified yields of G1E- and I173E- vs. 2018 Biochemistry Result IV G1E;I173E 29;38 32;43 30141905 The Stabilities of the Soluble Ectodomain and Fusion Peptide Hairpins of the Influenza Virus Hemagglutinin Subunit II Protein Are Positively Correlated with Membrane Fusion. The purified yields of WT-, G1E-, and I173E-FHA2 are ~10, 5, and 3 mg/L culture, whereas the yields of the corresponding HA2 variants are ~2, 1, and 0.7 mg/L culture. 2018 Biochemistry Result IV G1E;I173E 28;38 31;43 HA 121 123 30141905 The Stabilities of the Soluble Ectodomain and Fusion Peptide Hairpins of the Influenza Virus Hemagglutinin Subunit II Protein Are Positively Correlated with Membrane Fusion. The similar helicities of G1E and WT proteins are consistent with helical FP structure for G1E, whereas reduced helicity of I173E proteins supports some disruption of the SE structure in this mutant. 2018 Biochemistry Result IV G1E;G1E;I173E 26;91;124 29;94;129 30141905 The Stabilities of the Soluble Ectodomain and Fusion Peptide Hairpins of the Influenza Virus Hemagglutinin Subunit II Protein Are Positively Correlated with Membrane Fusion. The Tm values for G1E-FHA2 and I173E-FHA2 are near the middle of the 25-90 C experimental temperature range, and the ln Keq vs. 2018 Biochemistry Result IV G1E;I173E 18;31 21;36 30141905 The Stabilities of the Soluble Ectodomain and Fusion Peptide Hairpins of the Influenza Virus Hemagglutinin Subunit II Protein Are Positively Correlated with Membrane Fusion. Thermostability of constructs are qualitatively ordered WT-HA2 > WT-FHA2 > G1E-HA2, I173E-HA2 > G1E-FHA2 > I173E-FHA2. 2018 Biochemistry Result IV G1E;G1E;I173E;I173E 75;96;84;107 78;99;89;112 HA;HA;HA 59;79;90 61;81;92 30141905 The Stabilities of the Soluble Ectodomain and Fusion Peptide Hairpins of the Influenza Virus Hemagglutinin Subunit II Protein Are Positively Correlated with Membrane Fusion. This is a major peak for the I173E mutants in DM and a minor peak in other traces. 2018 Biochemistry Result IV I173E 29 34 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. All the mutations were exposed at the protein surface, except PA-M86V which was at the inter-subunit interface between the PA N-terminal region and the PB C-ext domain. 2018 Scientific reports Result IV M86V 65 69 PA;PA 62;123 64;125 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. Among the identified mutations, the PB2-D701N single mutation has been reported to increase the replication of avian H5N1 viruses in mammals and, therefore, was included in this study for comparison with other single and multiple mutations. 2018 Scientific reports Result IV D701N 40 45 PB2 36 39 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. At 37 C, the PB2-T81A/V344M/D701N, PB2-Y658H, PB2-Y658H/V344M and PA-M86V/A343T mutants produced progeny virus titers that were up to 4.0-fold higher in A549 cells and 8.3-fold higher in Calu-3 cells, compared to VN/HN (wt). 2018 Scientific reports Result IV V344M;D701N;T81A;Y658H;Y658H;V344M;M86V;A343T 23;29;18;40;51;57;70;75 28;34;22;45;56;62;74;80 PA;PB2;PB2;PB2 67;14;36;47 69;17;39;50 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. Based on their polymerase activity in human cells, we selected seven of the mutations that produced significant increases in polymerase activity (i.e., PB2-T81A/V344M/D701N, PB2-Y658H, PB2-Y658H/V344M, PB2-D701N, PA-A343T, PA-M86V/A343T and PA-M86V/A343T/E613V) for further study and rescued replicating viruses carrying these mutations. 2018 Scientific reports Result IV V344M;D701N;T81A;Y658H;V344M;Y658H;D701N;A343T;A343T;M86V;A343T;M86V;E613V 161;167;156;178;195;189;206;216;231;226;249;244;255 166;172;160;183;200;194;211;221;236;230;254;248;260 PA;PA;PA;PB2;PB2;PB2;PB2 213;223;241;152;174;185;202 215;225;243;155;177;188;205 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. For PA mutations, PA-M86V was in the PA-endonuclease domain, and A343T and E613V were in the PA-C terminal domain. 2018 Scientific reports Result IV M86V;A343T;E613V 21;65;75 25;70;80 PA;PA;PA;PA 4;18;37;93 6;20;39;95 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. In addition, viruses carrying either a putative negative control mutation (PB2-G685R) that had little effect on polymerase activity or a representative human adaptation mutation (PB2-E627K) were included in this study for comparison. 2018 Scientific reports Result IV G685R;E627K 79;183 84;188 PB2;PB2 75;179 78;182 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. In contrast, viral growth of the PB2-G685R putative negative control mutation was indistinguishable from that of VN/HN (wt), both at 33 and 37 C, although PB2-G685R is located in the PB2-627 domain. 2018 Scientific reports Result IV G685R;G685R 37;160 42;165 PB2;PB2;PB2 33;156;184 36;159;187 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. In each case, the effect of the multiple mutation in increasing polymerase activity was greater than the increase produced by the PB2-D701N single mutation. 2018 Scientific reports Result IV D701N 134 139 PB2 130 133 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. Minigenome assays showed that several single and multiple mutations in PB2 and PA increased H5N1 VN/HN polymerase activity in human 293T cells; e.g., PB2-T81A/V344M/D701N, PB2-Y658H, PB2-Y658H/V344M, PB2-D701N, PA-M86V/A343T, PA-M86V/A343T/E613V, PA-A343T and PA-A343T/E613V significantly increased polymerase activity at 37 C. 2018 Scientific reports Result IV V344M;D701N;T81A;Y658H;Y658H;V344M;D701N;A343T;M86V;M86V;E613V;A343T;A343T;E613V;A343T 159;165;154;176;187;193;204;219;214;229;240;234;250;269;263 164;170;158;181;192;198;209;224;218;233;245;239;255;274;268 PA;PA;PA;PA;PA;PB2;PB2;PB2;PB2;PB2 79;211;226;247;260;71;150;172;183;200 81;213;228;249;262;74;153;175;186;203 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. Of the PB2 mutations, T81A was in the N1-subdomain and close to the vRNA promoter, V344M was in the Cap-binding domain, Y658H was in the PB2-627 domain and D701N was in the PB2-NLS domain. 2018 Scientific reports Result IV T81A;V344M;Y658H;D701N 22;83;120;156 26;88;125;161 PB2;PB2;PB2 7;137;173 10;140;176 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. S3A-D, respectively): the maximum progeny virus titers were PB2-D701N < PB2-T81A/V344M/D701N (P < 0.01 by ANOVA with Tukey's multiple comparison test) and PA-A343T < PA-M86V/A343T (P < 0.01 by ANOVA with Tukey's multiple comparison test). 2018 Scientific reports Result IV D701N;V344M;D701N;T81A;A343T;M86V;A343T 64;81;87;76;158;169;174 69;86;92;80;163;173;179 PA;PA;PB2;PB2 155;166;60;72 157;168;63;75 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. The effects of these single and multiple mutations on viral replication in human cells were comparable to that produced by the PB2-D701N mutation and, in some conditions, comparable to that produced by the PB2-E627K mutation. 2018 Scientific reports Result IV D701N;E627K 131;210 136;215 PB2;PB2 127;206 130;209 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. The mutants were substantially more lethal than VN/HN (wt): the 50% mouse lethal dose (MLD50) was 1.47 FFU for the PB2-Y658H mutant, 2.05 FFU for the PB2-D701N mutant and 1.47 FFU for the PB2-T81A/V344M/D701N mutant, which were as much as 16.1-fold less than the MLD50 of 23.71 FFU for VN/HN (wt). 2018 Scientific reports Result IV Y658H;D701N;V344M;D701N;T81A 119;154;197;203;192 124;159;202;208;196 PB2;PB2;PB2 115;150;188 118;153;191 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. The PA-M86V/A343T double mutation also had a synergistic effect, with a 3.9-fold higher polymerase activity than wild-type PA and significantly higher polymerase activity than PA-A343T, which also increased polymerase activity. 2018 Scientific reports Result IV M86V;A343T;A343T 7;12;179 11;17;184 PA;PA;PA 4;123;176 6;125;178 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. The PB2-T81A/V344M/D701N and PA-M86V/A343T multiple mutations showed synergistic effects on viral replication compared with the corresponding single mutations both at 37 and 33 C. 2018 Scientific reports Result IV V344M;D701N;T81A;M86V;A343T 13;19;8;32;37 18;24;12;36;42 PA;PB2 29;4 31;7 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. the PB2-T81A/V344M/D701N triple mutation and PA-M86V/A343T double mutation had synergistic effects compared to the corresponding single mutations. 2018 Scientific reports Result IV V344M;D701N;T81A;A343T;M86V 13;19;8;53;48 18;24;12;58;52 PA;PB2 45;4 47;7 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. The PB2-T81A/V344M/D701N triple mutation produced up to 4.1-fold higher polymerase activity than wild-type PB2 and significantly higher polymerase activity than the known PB2-D701N human adaptation mutation. 2018 Scientific reports Result IV V344M;D701N;T81A;D701N 13;19;8;175 18;24;12;180 PB2;PB2;PB2 4;107;171 7;110;174 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. The progeny virus titers produced by the mutants were up to 31.2-fold higher in A549 cells and 298.4-fold higher in Calu-3 cells, with the highest increase produced by the PB2-T81A/V344M/D701N mutant. 2018 Scientific reports Result IV V344M;D701N;T81A 181;187;176 186;192;180 PB2 172 175 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. These results indicated that mutations that enhanced viral replication in human airway cells in vitro contributed to increased viral replication in mice in vivo and, of the mutations identified in this study, PB2-Y658H and PB2-T81A/V344M/D701N had the greatest effects on viral virulence in mammals. 2018 Scientific reports Result IV Y658H;D701N;V344M;T81A 213;238;232;227 218;243;237;231 PB2;PB2 209;223 212;226 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. VN/HN is a representative H5N1 clade 2.3.4 strain with no known human adaptation mutations (e.g., PB2-E627K and PB2-D701N) in its HA and polymerase genes. 2018 Scientific reports Result IV E627K;D701N 102;116 107;121 HA;PB2;PB2 130;98;112 132;101;115 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. with synergistic effects by the PB2-T81A/V344M/D701N triple mutation on viral replication (PB2-D701N < PB2-T81A/V344M/D701N, P < 0.01 by ANOVA with Tukey's multiple comparison test). 2018 Scientific reports Result IV V344M;D701N;T81A;D701N;D701N;V344M;T81A 41;47;36;95;118;112;107 46;52;40;100;123;117;111 PB2;PB2;PB2 32;91;103 35;94;106 30186261 Acquisition of Innate Inhibitor Resistance and Mammalian Pathogenicity During Egg Adaptation by the H9N2 Avian Influenza Virus. Considering the point mutations acquired in 01310- CE20 HA1 (T133N, V216G), these results are consistent with the presence of an additional N-glycosyl moiety at N133. 2018 Frontiers in microbiology Result IV T133N;V216G 61;68 66;73 HA1 56 59 30186261 Acquisition of Innate Inhibitor Resistance and Mammalian Pathogenicity During Egg Adaptation by the H9N2 Avian Influenza Virus. Furthermore, in comparison to rH20N20, rH20N20-N133T showed significantly decreased lung viral titers in mice (Figure 3C). 2018 Frontiers in microbiology Result IV N133T 47 52 30186261 Acquisition of Innate Inhibitor Resistance and Mammalian Pathogenicity During Egg Adaptation by the H9N2 Avian Influenza Virus. However, the HI titers from the mouse serum of rH20N20-N133T did not show any differences (Figure 6C). 2018 Frontiers in microbiology Result IV N133T 55 60 30186261 Acquisition of Innate Inhibitor Resistance and Mammalian Pathogenicity During Egg Adaptation by the H9N2 Avian Influenza Virus. Interestingly, rH20N20-N133T also showed significantly higher binding affinities to both avian-like (Figure 7A) and human-like (Figure 7B) receptors than rH20N20. 2018 Frontiers in microbiology Result IV N133T 23 28 30186261 Acquisition of Innate Inhibitor Resistance and Mammalian Pathogenicity During Egg Adaptation by the H9N2 Avian Influenza Virus. Loss-of-Function (LOF) Effects of N133T Mutation on Virus Replication, Mammalian Pathogenicity, and Resistance to Innate Inhibitors. 2018 Frontiers in microbiology Result IV N133T 34 39 30186261 Acquisition of Innate Inhibitor Resistance and Mammalian Pathogenicity During Egg Adaptation by the H9N2 Avian Influenza Virus. Of the HA mutations acquired by 01310-CE20, the T133N mutation occurred in the vicinity of the RBS and generated a new potential N-glycosylation site at position N133 (Figure 5A). 2018 Frontiers in microbiology Result IV T133N 48 53 HA 7 9 30186261 Acquisition of Innate Inhibitor Resistance and Mammalian Pathogenicity During Egg Adaptation by the H9N2 Avian Influenza Virus. rH20N20 caused significant body weight loss and mortality in inoculated mice, but rH20N20-N133T, similar to rH2N20, only caused body weight loss, with no mortality (Figures 3A,B). 2018 Frontiers in microbiology Result IV N133T 90 95 30186261 Acquisition of Innate Inhibitor Resistance and Mammalian Pathogenicity During Egg Adaptation by the H9N2 Avian Influenza Virus. The viral titer of rH20N20-N133T in MDCK cells was significantly lower than that of rH20N20 at 24 and 48 h post-inoculation (Figure 6A). 2018 Frontiers in microbiology Result IV N133T 27 32 30186261 Acquisition of Innate Inhibitor Resistance and Mammalian Pathogenicity During Egg Adaptation by the H9N2 Avian Influenza Virus. Thus, the LOF mutation (N133T) decreased viral replication efficiency in MDCK cells and mouse lungs and decreased in vivo pathogenicity and resistance to innate inhibitors. 2018 Frontiers in microbiology Result IV N133T 24 29 30186261 Acquisition of Innate Inhibitor Resistance and Mammalian Pathogenicity During Egg Adaptation by the H9N2 Avian Influenza Virus. To investigate the effects of T133N mutation on virus replication efficiency, mammalian pathogenicity, and innate inhibitor resistance, we generated a LOF mutant virus possessing an N133T mutation in HA, rH20N20-N133T, and compared its traits with those of rH20N20. 2018 Frontiers in microbiology Result IV T133N;N133T;N133T 30;182;212 35;187;217 HA 200 202 30201817 Characterization of Influenza B Virus Variants with Reduced Neuraminidase Inhibitor Susceptibility. In addition to a number of synonymous mutations found across the influenza genome, the MUT-Y273 virus from one recipient ferret also contained a M403V NA amino acid substitution, and the WT-D197 virus from all recipients contained an L274I amino acid substitution in the PA enzyme. 2018 Antimicrobial agents and chemotherapy Result IV M403V;L274I 145;234 150;239 NA;PA 151;271 153;273 30201817 Characterization of Influenza B Virus Variants with Reduced Neuraminidase Inhibitor Susceptibility. M403V in influenza B NA is distant from the enzyme active site and has only occurred on rare occasions in influenza B viruses (19 out of 5,556 sequences in the Global Initiative on Sharing All Influenza Data [GISAID]), while the PA substitution L274I has not been previously observed in any of the influenza B PA gene sequences on GISAID. 2018 Antimicrobial agents and chemotherapy Result IV M403V;L274I 0;245 5;250 NA;PA;PA 21;229;310 23;231;312 30201817 Characterization of Influenza B Virus Variants with Reduced Neuraminidase Inhibitor Susceptibility. Pyrosequencing analysis of relevant NA substitutions in nasal wash samples from all infected animals confirmed that neither the D197N nor the H273Y substitution was lost following replication within the airways of donor ferrets, or following transmission to recipient animals. 2018 Antimicrobial agents and chemotherapy Result IV D197N;H273Y 128;142 133;147 36 38 30201817 Characterization of Influenza B Virus Variants with Reduced Neuraminidase Inhibitor Susceptibility. The effects of the D197N and H273Y substitutions on NA enzyme function were assessed using four different assays. 2018 Antimicrobial agents and chemotherapy Result IV D197N;H273Y 19;29 24;34 52 54 30201817 Characterization of Influenza B Virus Variants with Reduced Neuraminidase Inhibitor Susceptibility. The MUT-Y273 virus in the recipient ferret had acquired a rare T90I HA substitution (contained in only 7 out of 7,373 strains in GISAID), as well as the NP, PA and PB1 genes from the WT-H273 virus, which differed by 4 amino acids compared to the MUT-Y273 virus. 2018 Antimicrobial agents and chemotherapy Result IV T90I 63 67 HA;NP;PA;PB1 68;153;157;164 70;155;159;167 30202644 Molecular identification of avian influenza virus subtypes H5N1 and H9N2 in birds from farms and live bird markets and in respiratory patients. and a comparison of HA sequences at the amino acid level showed 98.8-100% homology among the nine isolates, while they showed 94.1-96.1% identity with reference strains and the commonly used vaccine strain (A/chicken/Egypt/Q1995D/2010) in Egypt. 2018 PeerJ Result IV Q1995D 223 229 HA 20 22 30202644 Molecular identification of avian influenza virus subtypes H5N1 and H9N2 in birds from farms and live bird markets and in respiratory patients. In comparison with the reference (parent, classic and variant) strains in Egypt, all the isolates in the current study showed the R325K amino acid substitution, while the Q322K substitution was found in only four of our isolates compared to the reference and vaccine strains. 2018 PeerJ Result IV R325K;Q322K 130;171 135;176 30202644 Molecular identification of avian influenza virus subtypes H5N1 and H9N2 in birds from farms and live bird markets and in respiratory patients. The other four isolates showed an amino acid substitution (Q322K) at this cleavage site to make (321-P K GEKRRKKR/GLF-333). 2018 PeerJ Result IV Q322K 59 64 30245911 The 2015 Outbreak of Severe Influenza in Kashmir, North India: Emergence of a New Clade of A/H1n1 Influenza Virus. A rechecking of the analysis of the 285 Indian HA sequences of the period 2009-2015 was performed and it was found that K166Q mutation was established in Indian strains from 2013 (Table 2). 2018 PLoS currents Result IV K166Q 120 125 HA 47 49 30245911 The 2015 Outbreak of Severe Influenza in Kashmir, North India: Emergence of a New Clade of A/H1n1 Influenza Virus. HA sequencing and phylogenetic analysis of the A/H1N1 sequences depicted that 2015 isolates from Kashmir clustered with clade 6B.1 with clade specific S84N, S162N and I216T signature mutations (Figure 2). 2018 PLoS currents Result IV S84N;S162N;I216T 151;157;167 155;162;172 HA 0 2 30245911 The 2015 Outbreak of Severe Influenza in Kashmir, North India: Emergence of a New Clade of A/H1n1 Influenza Virus. HA-sequencing did not demonstrate any evidence of K166Q, D225 or T200A mutation, even in those who had a fatal outcome of their infection. 2018 PLoS currents Result IV K166Q;T200A 50;65 55;70 HA 0 2 30245911 The 2015 Outbreak of Severe Influenza in Kashmir, North India: Emergence of a New Clade of A/H1n1 Influenza Virus. In 2012 few Indian strains were observed with A200T mutation which did not get established and further it continued as A200 since 2013. 2018 PLoS currents Result IV A200T 46 51 30245911 The 2015 Outbreak of Severe Influenza in Kashmir, North India: Emergence of a New Clade of A/H1n1 Influenza Virus. No H275Y mutation on neuraminidase was reported from pandemic H1N1 positives, hence viruses remained susceptible to oseltamivir. 2018 PLoS currents Result IV H275Y 3 8 21 34 30282714 Amino Acid Residue 217 in the Hemagglutinin Glycoprotein Is a Key Mediator of Avian Influenza H7N9 Virus Antigenicity. All three serum escape mutations, A125T, A151T, and L217Q, were found in naturally occurring H7N9 isolates (Table 2). 2019 Journal of virology Result IV A125T;A151T;L217Q 34;41;52 39;46;57 30282714 Amino Acid Residue 217 in the Hemagglutinin Glycoprotein Is a Key Mediator of Avian Influenza H7N9 Virus Antigenicity. Among all of these substitutions, the prevalence of A125V in the HA of the mutant virus showed a sharp increase in epidemic wave 5 (Table 2) and has been shown to have a cumulative antigenic effect. 2019 Journal of virology Result IV A125V 52 57 HA 65 67 30282714 Amino Acid Residue 217 in the Hemagglutinin Glycoprotein Is a Key Mediator of Avian Influenza H7N9 Virus Antigenicity. As expected, compared with SF003-HA (Q217), the mutant SF003-HA with the Q217L substitution showed 8- and 3-fold increases in HI titers to ferret and chicken antisera, respectively. 2019 Journal of virology Result IV Q217L 73 78 HA;HA 33;61 35;63 30282714 Amino Acid Residue 217 in the Hemagglutinin Glycoprotein Is a Key Mediator of Avian Influenza H7N9 Virus Antigenicity. Both the A125T and A151T substitutions introduced N-linked glycosylation motif (N-X-T/S), and changes in the glycosylation pattern in the HA can interfere with antibody binding. 2019 Journal of virology Result IV A125T;A151T 9;19 14;24 HA 138 140 30282714 Amino Acid Residue 217 in the Hemagglutinin Glycoprotein Is a Key Mediator of Avian Influenza H7N9 Virus Antigenicity. Both the A125T and L217Q mutations are located within the receptor binding site (RBS). 2019 Journal of virology Result IV A125T;L217Q 9;19 14;24 30282714 Amino Acid Residue 217 in the Hemagglutinin Glycoprotein Is a Key Mediator of Avian Influenza H7N9 Virus Antigenicity. Compared with the Anhui/13 virus, the serum escape mutant (A125T+A151T+L217Q) showed an 11-fold reduction in hemagglutinin inhibition (HI) titer to the ferret homologous antiserum and a 7-fold reduction in HI titer to the chicken homologous antiserum. 2019 Journal of virology Result IV A125T;A151T;L217Q 59;65;71 64;70;76 HA 109 122 30282714 Amino Acid Residue 217 in the Hemagglutinin Glycoprotein Is a Key Mediator of Avian Influenza H7N9 Virus Antigenicity. Consistent with the observed results with SF003-HA, the A125V substitution did not affect the antigenicity of Anhui/13. 2019 Journal of virology Result IV A125V 56 61 HA 48 50 30282714 Amino Acid Residue 217 in the Hemagglutinin Glycoprotein Is a Key Mediator of Avian Influenza H7N9 Virus Antigenicity. Further comparison of HA sequences between Anhui/13 and SF003-HA revealed that in addition to the L217Q mutation, there are 6 other substitutions in the HA1 of SF003-HA: changes of isoleucine 38 to threonine (I38T), alanine 112 to proline (A112P), serine 118 to asparagine (S118N), alanine 125 to valine (A125V), lysine 164 to glutamate (K164E), and glycine 261 to arginine (G261R). 2019 Journal of virology Result IV L217Q;I38T;A112P;S118N;A125V;K164E;G261R;I38T;A112P;S118N;A125V;K164E;G261R 98;209;240;274;305;338;375;181;216;248;282;313;350 103;213;245;279;310;343;380;207;238;272;303;336;373 HA;HA;HA;HA1 22;62;166;153 24;64;168;156 30282714 Amino Acid Residue 217 in the Hemagglutinin Glycoprotein Is a Key Mediator of Avian Influenza H7N9 Virus Antigenicity. HA gene sequence analysis of the viruses passaged in eggs with PBS control revealed one clone with a change from glycine 209 to glutamate (G209E), two clones with the A180E change, four clones with the G189E change, two clones with the double mutation of asparagine 149 to aspartate (N149D) and valine 86 to A (V86A), and three clones with no identified mutations. 2019 Journal of virology Result IV G209E;A180E;G189E;N149D;V86A;G209E;N149D 139;167;202;284;311;113;255 144;172;207;289;315;137;282 HA 0 2 30282714 Amino Acid Residue 217 in the Hemagglutinin Glycoprotein Is a Key Mediator of Avian Influenza H7N9 Virus Antigenicity. However, in comparison to the LPAI Anhui/13, mutant SF003-HA/Q217L virus still displayed 3- and 2-fold lower HI titers to ferret and chicken antisera, respectively. 2019 Journal of virology Result IV Q217L 61 66 HA 58 60 30282714 Amino Acid Residue 217 in the Hemagglutinin Glycoprotein Is a Key Mediator of Avian Influenza H7N9 Virus Antigenicity. However, reconstitution of Anhui/13 virus that carried L217Q+A125V did not showed a marked difference in HI titers compared with those of virus that contained L217Q alone, indicating that the cumulative antigenic effect of L217Q+A125V might be linked to other amino acid differences between HA1 (I38T, A112P, S118N, K164E, and G261R) of the Anhui/13 and SH003-HA viruses. 2019 Journal of virology Result IV A125V;L217Q;L217Q;L217Q;A125V;I38T;A112P;S118N;K164E;G261R 61;55;159;223;229;296;302;309;316;327 66;60;164;228;234;300;307;314;321;332 HA;HA1 360;291 362;294 30282714 Amino Acid Residue 217 in the Hemagglutinin Glycoprotein Is a Key Mediator of Avian Influenza H7N9 Virus Antigenicity. However, the A125T+A151T double mutant virus displayed an 8-fold reduction in HI titer to ferret antiserum and a 4-fold reduction in HI titer to the chicken antiserum, indicating that these two substitutions had a cumulative antigenic effect. 2019 Journal of virology Result IV A125T;A151T 13;19 18;24 30282714 Amino Acid Residue 217 in the Hemagglutinin Glycoprotein Is a Key Mediator of Avian Influenza H7N9 Virus Antigenicity. However, the mutant L217Q virus containing the A151T mutation showed a compromise in the antigenic change caused by the L217Q substitution. 2019 Journal of virology Result IV L217Q;A151T;L217Q 20;47;120 25;52;125 30282714 Amino Acid Residue 217 in the Hemagglutinin Glycoprotein Is a Key Mediator of Avian Influenza H7N9 Virus Antigenicity. Incorporation of the additional mutation A125T along with L217Q did not dramatically affect the HI titers observed with L217Q mutation alone. 2019 Journal of virology Result IV A125T;L217Q;L217Q 41;58;120 46;63;125 30282714 Amino Acid Residue 217 in the Hemagglutinin Glycoprotein Is a Key Mediator of Avian Influenza H7N9 Virus Antigenicity. Notably, the A125V substitution first emerged in wave 2 and its detection among H7N9 isolates increased from 6.9% in wave 2 to 95% in wave 5. 2019 Journal of virology Result IV A125V 13 18 30282714 Amino Acid Residue 217 in the Hemagglutinin Glycoprotein Is a Key Mediator of Avian Influenza H7N9 Virus Antigenicity. Overall, these results indicated that the L217Q mutation is a key mediator of antigenic change in LPAI H7N9 viruses. 2019 Journal of virology Result IV L217Q 42 47 30282714 Amino Acid Residue 217 in the Hemagglutinin Glycoprotein Is a Key Mediator of Avian Influenza H7N9 Virus Antigenicity. Substitution L217Q was introduced into the HA of HK125/17 by site-directed mutagenesis. 2019 Journal of virology Result IV L217Q 13 18 HA 43 45 30282714 Amino Acid Residue 217 in the Hemagglutinin Glycoprotein Is a Key Mediator of Avian Influenza H7N9 Virus Antigenicity. Surprisingly, the L217Q mutation alone yielded a 23-fold reduction in HI titer to the ferret antiserum and an 8-fold reduction in HI titer to the chicken antiserum. 2019 Journal of virology Result IV L217Q 18 23 30282714 Amino Acid Residue 217 in the Hemagglutinin Glycoprotein Is a Key Mediator of Avian Influenza H7N9 Virus Antigenicity. Surprisingly, V125A alone did not affect the antigenicity of SF003-HA, indicating the cumulative antigenic effect of V125 and Q217 in SF003-HA. 2019 Journal of virology Result IV V125A 14 19 HA;HA 67;140 69;142 30282714 Amino Acid Residue 217 in the Hemagglutinin Glycoprotein Is a Key Mediator of Avian Influenza H7N9 Virus Antigenicity. The A125T substitution was found only in wave 2. 2019 Journal of virology Result IV A125T 4 9 30282714 Amino Acid Residue 217 in the Hemagglutinin Glycoprotein Is a Key Mediator of Avian Influenza H7N9 Virus Antigenicity. The comparative analysis of the HA genes of viruses passaged in the presence of ferret serum and the PBS control indicated that the A125T, A151T, and L217Q mutations arose only in viruses propagated with the immune antiserum and not through egg adaption. 2019 Journal of virology Result IV A125T;A151T;L217Q 132;139;150 137;144;155 HA 32 34 30282714 Amino Acid Residue 217 in the Hemagglutinin Glycoprotein Is a Key Mediator of Avian Influenza H7N9 Virus Antigenicity. The HK125/17 mutant virus with the L217Q substitution showed 23- and 16-fold reductions of HI titers with ferret and chicken antisera raised against Anhui/13, respectively. 2019 Journal of virology Result IV L217Q 35 40 30282714 Amino Acid Residue 217 in the Hemagglutinin Glycoprotein Is a Key Mediator of Avian Influenza H7N9 Virus Antigenicity. The L217Q mutation is a key mediator of antigenic change in LPAI H7N9 viruses. 2019 Journal of virology Result IV L217Q 4 9 30282714 Amino Acid Residue 217 in the Hemagglutinin Glycoprotein Is a Key Mediator of Avian Influenza H7N9 Virus Antigenicity. The L217Q mutation prevailed more often in the avian host (7.22%) than in the human host (3.98%) (Table 3). 2019 Journal of virology Result IV L217Q 4 9 30282714 Amino Acid Residue 217 in the Hemagglutinin Glycoprotein Is a Key Mediator of Avian Influenza H7N9 Virus Antigenicity. The progeny viruses showed amino acid mutations including changes from alanine 125 to threonine (A125T), alanine 151 to threonine (A151T), and leucine 217 to glutamine (L217Q) (the numbering for mature H7 HA is used throughout) in the HAs of all 12 selected cDNA clones analyzed as early as passage 5. 2019 Journal of virology Result IV A125T;A151T;L217Q;A125T;A151T;L217Q 97;131;169;71;105;143 102;136;174;95;129;167 HA 205 207 30282714 Amino Acid Residue 217 in the Hemagglutinin Glycoprotein Is a Key Mediator of Avian Influenza H7N9 Virus Antigenicity. The Q217L substitution was introduced into SF003-HA by site-directed mutagenesis. 2019 Journal of virology Result IV Q217L 4 9 HA 49 51 30282714 Amino Acid Residue 217 in the Hemagglutinin Glycoprotein Is a Key Mediator of Avian Influenza H7N9 Virus Antigenicity. The rates of both the A125T and A151T mutations appeared to be higher in human than in avian virus isolates, indicating that these two mutations that carry glycosylation motifs may play some adaptive role for humans, though the prevalence rates of both mutations are less than 1% (Table 3). 2019 Journal of virology Result IV A125T;A151T 22;32 27;37 30282714 Amino Acid Residue 217 in the Hemagglutinin Glycoprotein Is a Key Mediator of Avian Influenza H7N9 Virus Antigenicity. The single mutation A125T or A151T resulted in a <4-fold reduction in HI titer to ferret and chicken antisera, respectively (Table 1). 2019 Journal of virology Result IV A125T;A151T 20;29 25;34 30282714 Amino Acid Residue 217 in the Hemagglutinin Glycoprotein Is a Key Mediator of Avian Influenza H7N9 Virus Antigenicity. The V125A+Q217L double mutations in SF003-HA completely abolished the antigenic difference between the Anhui/13 and SF003-HA viruses (Table 4). 2019 Journal of virology Result IV Q217L;V125A 10;4 15;9 HA;HA 42;122 44;124 30282714 Amino Acid Residue 217 in the Hemagglutinin Glycoprotein Is a Key Mediator of Avian Influenza H7N9 Virus Antigenicity. These identified amino acid substitutions correspond to A135T, A160T, and L226Q by the H3 HA numbering. 2019 Journal of virology Result IV A135T;A160T;L226Q 56;63;74 61;68;79 HA 90 92 30282714 Amino Acid Residue 217 in the Hemagglutinin Glycoprotein Is a Key Mediator of Avian Influenza H7N9 Virus Antigenicity. This suggests that although substitution L217Q in the HA induces a large antigenic change, other amino acid differences in HA between HK125/17 and Anhui/13 (A112T, S118N, and A125V) may also to a minor extent contribute to antigenic variability among the different strains of H7N9 viruses. 2019 Journal of virology Result IV L217Q;A112T;S118N;A125V 41;157;164;175 46;162;169;180 HA;HA 54;123 56;125 30282714 Amino Acid Residue 217 in the Hemagglutinin Glycoprotein Is a Key Mediator of Avian Influenza H7N9 Virus Antigenicity. To further confirm the findings in the SF003-HA background, we introduced A125V and A125V+L217Q double mutations into Anhui/13. 2019 Journal of virology Result IV A125V;A125V;L217Q 74;84;90 79;89;95 HA 45 47 30282714 Amino Acid Residue 217 in the Hemagglutinin Glycoprotein Is a Key Mediator of Avian Influenza H7N9 Virus Antigenicity. To further confirm the impact of the leucine-to-glutamine change at residue 217 on the antigenicity of H7N9 viruses, we reconstituted another recombinant virus that contained the HA and neuraminidase (NA) genes from LPAI H7N9 virus (A/Hong Kong/125/2017, isolated during epidemic wave 5) and internal gene from PR8 virus (referred to as HK125/17). 2019 Journal of virology Result IV L217Q 37 79 HA;NA;NA 179;201;186 181;203;199 30282714 Amino Acid Residue 217 in the Hemagglutinin Glycoprotein Is a Key Mediator of Avian Influenza H7N9 Virus Antigenicity. To investigate the contribution of V125 in the antigenic cross-reactivity, V125A and V125A+Q217L substitutions were introduced into SF003-HA by site-directed mutagenesis. 2019 Journal of virology Result IV V125A;Q217L;V125A 75;91;85 80;96;90 HA 138 140 30282714 Amino Acid Residue 217 in the Hemagglutinin Glycoprotein Is a Key Mediator of Avian Influenza H7N9 Virus Antigenicity. We carried out the selection procedure for a further 5 passages; no further mutations in addition to A125T, A151T, and L217Q were detected. 2019 Journal of virology Result IV A125T;A151T;L217Q 101;108;119 106;113;124 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. 293T cells transfected with plasmids expressing NS1-WT or NS1-I178V were treated with CHX for the indicated times, and Western blot analysis was performed to measure the amount of NS1 protein remaining at various time points, and to calculate the rates of NS1 remaining in the cells as percentages of NS1 protein levels at the zero time point. 2018 Veterinary research Result IV I178V 62 67 NS1;NS1;NS1;NS1;NS1 48;58;180;256;301 51;61;183;259;304 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. Among the three most important pattern recognition receptors (PRRs) acting as sensors of influenza virus RNAs, only expression of RIG-I, but not MDA5 and TLR3, was influenced by the NS1-S212P mutant in cells infected with either WSN or PR8 delNS1 virus (Additional file 3). 2018 Veterinary research Result IV S212P 186 191 NS1 182 185 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. As shown in Figures 5C and D, the half-life of NS1-WT protein was more than 32 h, whereas I178V mutation dramatically shortened the half-life of NS1 to approximately 16 h, suggesting that I178V mutation promoted NS1 protein degradation in the cells. 2018 Veterinary research Result IV I178V;I178V 90;188 95;193 NS1;NS1;NS1 47;145;212 50;148;215 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. Consistent with these observations, the plaque assay showed that the viral titers in lung tissues of mice infected with PR8-S212 or PR8-I178 were significantly higher than those infected with PR8-WT (Figure 7C), suggesting that NS1-P212S or NS1-V178I mutation generates a virus with an increased virulence in vivo. 2018 Veterinary research Result IV P212S;V178I 232;245 237;250 NS1;NS1 228;241 231;244 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. However, in NS1-S212P transfected cells, the phosphorylation of STAT1 was comparable to that in EV transfected cells (Figures 3C and D), which indicated that S212P mutation disables the NS1 in preventing STAT1 activation. 2018 Veterinary research Result IV S212P;S212P 16;158 21;163 NS1;NS1 12;186 15;189 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. I178V mutation decreases the stability of H7N9 NS1 protein. 2018 Veterinary research Result IV I178V 0 5 NS1 47 50 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. I178V mutation induces NS1 protein degradation through proteasome pathway. 2018 Veterinary research Result IV I178V 0 5 NS1 23 26 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. In addition to IFN-beta, we observed that the expression of IFN-alpha, IL-28, MxA and OASL was also increased in NS1-S212P transfected cells comparing with that in NS1-WT transfected 293T cells after infection with WSN virus, while the expression of IL-29 and ISG15 was not influenced in these cells (Figures 2B-F, Additional file 2A). 2018 Veterinary research Result IV S212P 117 122 NS1;NS1 113;164 116;167 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. In contrast, no significant changes for NS1-I178V protein levels were observed in cells treated with either NH4Cl or chloroquine (Figures 6B and C). 2018 Veterinary research Result IV I178V 44 49 NS1 40 43 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. Interestingly, compared with the NS1 WT, NS1 S212P mutation caused the most significant increase in the IFN-beta expression (Figure 2A), suggesting that the S212P mutation weakened the inhibition of host antiviral response by H7N9 NS1. 2018 Veterinary research Result IV S212P;S212P 45;157 50;162 NS1;NS1;NS1 33;41;231 36;44;234 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. Moreover, levels of inflammatory factors, including IL-6 and IL-1beta, were also markedly affected by expression of NS1 S212P mutation (Figure 2G, Additional files 2E and F). 2018 Veterinary research Result IV S212P 120 125 NS1 116 119 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. P212S and V178I mutation in PR8 NS1 protein enhanced virulence and promoted virus replication in vivo. 2018 Veterinary research Result IV P212S;V178I 0;10 5;15 NS1 32 35 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. Previous study has shown that amino acid substitutions of NS1 protein would affect its steady-state level, we next estimated the relative half-lives of NS1-WT and NS1-I178V protein to examine whether NS1-I178V protein underwent degradation in the cell. 2018 Veterinary research Result IV I178V;I178V 167;204 172;209 NS1;NS1;NS1;NS1 58;152;163;200 61;155;166;203 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. S212P mutation in H7N9 NS1 protein reduces its ability to suppress IAV-induced RIG-I expression and STAT1 activation. 2018 Veterinary research Result IV S212P 0 5 NS1 23 26 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. S212P mutation of H7N9 NS1 protein results in a decrease in the viral replication. 2018 Veterinary research Result IV S212P 0 5 NS1 23 26 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. S212P substitution significantly impairs antagonistic effect of H7N9 NS1 protein on host innate immune response. 2018 Veterinary research Result IV S212P 0 5 NS1 69 72 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. Similarly, data showed that S212P mutation in H7N9 NS1 impaired its inhibitory effect on the expression of above antiviral factors (Figures 2B-F, Additional file 2D). 2018 Veterinary research Result IV S212P 28 33 NS1 51 54 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. Similarly, no matter infection with WSN virus or PR8 delNS1 virus, the virus titers in the supernatant derived from NS1-S212P transfected cells were decreased as compared with those derived from NS1-WT transfected cells (Figures 4E and F). 2018 Veterinary research Result IV S212P 120 125 NS1;NS1 116;195 119;198 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. Since JAK-STAT signaling pathway plays a key role in host innate immune response and STAT1 activation enhances the transcription of numerous IFN stimulatory genes, we further examined the effect of H7N9 NS1 S212P mutation on STAT1 activation. 2018 Veterinary research Result IV S212P 207 212 NS1 203 206 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. The results displayed that NP expression level of WSN virus or PR8 delNS1 virus was reduced to ~60% in cells expressing NS1-S212P mutant as compared to that in NS1-WT transfected cells (Figures 4A-D). 2018 Veterinary research Result IV S212P 124 129 NP;NS1;NS1 27;120;160 29;123;163 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. The substitutions were the following (avian_residue/Position/human_residue): R55E, H63Q, E70K, P87S, S114P, A143T, I178V, S212P (Additional file 1). 2018 Veterinary research Result IV R55E;H63Q;E70K;P87S;S114P;A143T;I178V;S212P 77;83;89;95;101;108;115;122 81;87;93;99;106;113;120;127 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. These data suggested that I178V mutation-induced NS1 degradation is by the proteasome pathway and not via the lysosome pathway. 2018 Veterinary research Result IV I178V 26 31 NS1 49 52 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. These results further indicate that P212S and V178I mutation in the NS1 protein enhanced PR8 virulence, and caused more severe organ damage. 2018 Veterinary research Result IV P212S;V178I 36;46 41;51 NS1 68 71 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. These results suggest that S212P mutation of H7N9 NS1 causes a significant reduction in the NP protein expression and the virus replication. 2018 Veterinary research Result IV S212P 27 32 NP;NS1 92;50 94;53 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. To analyze whether S212P mutation affects virus replication, plasmids expressing NS1-WT or NS1-S212P were transiently transfected into 293T cells. 2018 Veterinary research Result IV S212P;S212P 19;95 24;100 NS1;NS1 81;91 84;94 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. To determine whether the reduction of NS1-I178V protein level is the consequence of a decrease in its mRNA level, 293T cells transfected with NS1-WT or NS1-I178V were examined by RT-PCR. 2018 Veterinary research Result IV I178V;I178V 42;156 47;161 NS1;NS1;NS1 38;142;152 41;145;155 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. To further analyze whether S212P mutation in H7N9 NS1 protein affected its ability to counteract the innate immune responses, human 293T cells were transiently transfected with plasmids expressing WT NS1 or the NS1 mutant. 2018 Veterinary research Result IV S212P 27 32 NS1;NS1;NS1 50;200;211 53;203;214 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. To further evaluate the effect of amino acids mutation at 212 and 178 sites of NS1 protein on virus growth and virulence in vivo, we generated mutated PR8 virus harboring P212S or V178I mutation in the NS1 protein using reverse genetics approach. 2018 Veterinary research Result IV P212S;V178I 171;180 176;185 NS1;NS1 79;202 82;205 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. To investigate by which pathway the degradation of NS1-I178V protein is regulated, cells transfected with plasmids expressing NS1-WT or NS1-I178V were cotreated with CHX and distinct proteasome inhibitor MG132 or lysosome inhibitors NH4Cl and chloroquine. 2018 Veterinary research Result IV I178V;I178V 55;140 60;145 NS1;NS1;NS1 51;126;136 54;129;139 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. To verify whether these amino acid changes contributed to the high pathogenicity of H7N9 virus to human, site-directed mutagenesis was carried out to generate the eight H7N9 NS1 mutants, R55E, H63Q, E70K, P87S, S114P, A143T, I178V and S212P, and wild type (WT) NS1 and NS1 mutants were transfected into 293T cells, and the cells were then infected with WSN virus to examine the effect of NS1 mutation on its antagonism against host innate immunity during the IAV infection. 2018 Veterinary research Result IV R55E;H63Q;E70K;P87S;S114P;A143T;I178V;S212P 187;193;199;205;211;218;225;235 191;197;203;209;216;223;230;240 NS1;NS1;NS1;NS1 174;261;269;388 177;264;272;391 IAV infections 459 472 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. Together, these experiments demonstrated that S212P mutation in H7N9 NS1 protein impaired its ability to suppress RIG-I/STAT1-mediated host innate immunity. 2018 Veterinary research Result IV S212P 46 51 NS1 69 72 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. Unexpectedly, we found that protein expression of NS1 mutant I178V was less than that of the other seven mutants (Figure 5A). 2018 Veterinary research Result IV I178V 61 66 NS1 50 53 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. We found that treatment with MG132 reversed the effect of I178V mutation on NS1 protein stability and clearly increased NS1-I178V protein levels (Figure 6A). 2018 Veterinary research Result IV I178V;I178V 58;124 63;129 NS1;NS1 76;120 79;123 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. We observed that there were no statistically significant differences between NS1-WT and NS1-I178V mRNA levels (Figure 5B), indicating that the decrease in the amount of NS1-I178V protein may occur at the post-transcription, translation or protein degradation levels. 2018 Veterinary research Result IV I178V;I178V 92;173 97;178 NS1;NS1;NS1 77;88;169 80;91;172 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. We observed that WT NS1 of H7N9 significantly inhibited IAV-induced RIG-I expression, but S212P amino acid substitution impaired its ability to inhibit the RIG-I expression (Figures 3A, B and Additional file 3). 2018 Veterinary research Result IV S212P 90 95 NS1 20 23 30301950 Tree shrew as a new animal model to study the pathogenesis of avian influenza (H9N2) virus infection. Although there was no statistically significant difference between the two groups, some tree shrews infected with the Y280-PB2-E627K viruses showed an increase in body temperature and an increased loss of body weight at 1-day postinfection compared to the mean value of those infected with the Y280-wt virus. 2018 Emerging microbes & infections Result IV E627K 127 132 PB2 123 126 30301950 Tree shrew as a new animal model to study the pathogenesis of avian influenza (H9N2) virus infection. At this time point, we found that the mRNA levels of TNF-alpha, IFN-beta, IL-8, IL-13, and IL-6 in the upper respiratory tract (nasal turbinate or throat) and IL-8, RANTES, and IFN-beta in the lower respiratory tract (trachea or lung) were significantly higher in the tree shrews infected with Y280-PB2-E627K than in those infected with Y280-wt virus. 2018 Emerging microbes & infections Result IV E627K 303 308 PB2 299 302 30301950 Tree shrew as a new animal model to study the pathogenesis of avian influenza (H9N2) virus infection. Consistent with the results from the nasal wash, Y280-PB2-E627K virus showed higher viral replication than Y280-wt in nasal turbinate at 2 dpi, but neither viruses showed any replication at 4 or 6 dpi. 2018 Emerging microbes & infections Result IV E627K 58 63 PB2 54 57 30301950 Tree shrew as a new animal model to study the pathogenesis of avian influenza (H9N2) virus infection. Ferret infected with the wild-type virus regained weight more quickly than those infected with the PB2-E627K mutant. 2018 Emerging microbes & infections Result IV E627K 103 108 PB2 99 102 30301950 Tree shrew as a new animal model to study the pathogenesis of avian influenza (H9N2) virus infection. In contrast, higher levels of IL-8 (24 h), RANTES (24 h), IP-10 (24 h), and IL-10 (48 h) in the tracheas as well as IL-6 (24 h) and IP-10 (72 h) in the lungs were found in the Y280-w-infected group than in the Y280-PB2-E627K-infected group. 2018 Emerging microbes & infections Result IV E627K 219 224 PB2 215 218 30301950 Tree shrew as a new animal model to study the pathogenesis of avian influenza (H9N2) virus infection. In the ferret model, both the Y280-wt and Y280-PB2-E627K viruses brought an obvious increase in body temperature and weight loss during the first few days of infection. 2018 Emerging microbes & infections Result IV E627K 51 56 PB2 47 50 30301950 Tree shrew as a new animal model to study the pathogenesis of avian influenza (H9N2) virus infection. In tree shrews, the virus could be detected until day 6 in the group challenged by the PB2-E627K mutant, while the wild-type virus was not found in any of the tree shrews on day 4. 2018 Emerging microbes & infections Result IV E627K 91 96 PB2 87 90 30301950 Tree shrew as a new animal model to study the pathogenesis of avian influenza (H9N2) virus infection. Increased expression of viral antigens was detected in the epithelium of nasal turbinate tissues from the Y280-PB2-E627K-infected group compared to those infected with the Y280-wt virus. 2018 Emerging microbes & infections Result IV E627K 115 120 PB2 111 114 30301950 Tree shrew as a new animal model to study the pathogenesis of avian influenza (H9N2) virus infection. Interestingly, the lung tissues isolated from the Y280-PB2-E627K-infected group, including those with and those without positive detection of virus replication, all showed increased severity of lesions, including apparent necrotic and sloughed cells as well as inclusion bodies in the mucosal layer of bronchiolar epithelium, compared to the tree shrews infected with the Y280-wt virus. 2018 Emerging microbes & infections Result IV E627K 59 64 PB2 55 58 30301950 Tree shrew as a new animal model to study the pathogenesis of avian influenza (H9N2) virus infection. On the other hand, Y280-wt virus triggered significantly higher mRNA expression of MIG (2 dpi, trachea; 4 dpi, lung), IL-13 (2 dpi, trachea), MCP-1 (4 dpi, trachea), and IL-10 (6 dpi, nasal turbinate) than Y280-PB2-E627K virus. 2018 Emerging microbes & infections Result IV E627K 215 220 PB2 211 214 30301950 Tree shrew as a new animal model to study the pathogenesis of avian influenza (H9N2) virus infection. Replication in the throat and trachea could be found only in some tree shrews infected with either Y280-wt or Y280-PB2-E627K virus. 2018 Emerging microbes & infections Result IV E627K 119 124 PB2 115 118 30301950 Tree shrew as a new animal model to study the pathogenesis of avian influenza (H9N2) virus infection. The cytokine levels of TNF-alpha (24 h and 48 h), IFN-beta (24 h), IL-8 (48 h), IL-10 (72 h), IL-4 (24 h), and IL-13 (72 h) were significantly higher in the ex vivo lung tissues infected with the Y280-PB2-E627K virus than in those infected with Y280-wt virus. 2018 Emerging microbes & infections Result IV E627K 205 210 PB2 201 204 30301950 Tree shrew as a new animal model to study the pathogenesis of avian influenza (H9N2) virus infection. The PB2-E627K mutant replicated more quickly than the wild-type isotype on day 2 in both tree shrews and ferrets. 2018 Emerging microbes & infections Result IV E627K 8 13 PB2 4 7 30301950 Tree shrew as a new animal model to study the pathogenesis of avian influenza (H9N2) virus infection. The tissues isolated from the Y280-PB2-E627K-infected group showed an increased severity of lesions on the nasal turbinate, which were characterized by the identification of necrotic and sloughed epithelial cells, increased lymphocytic infiltration in the submucosal/intramucosal layers and vascular dilatation. 2018 Emerging microbes & infections Result IV E627K 39 44 PB2 35 38 30301950 Tree shrew as a new animal model to study the pathogenesis of avian influenza (H9N2) virus infection. To investigate the role of the mammalian adaptation mutation PB2-E627K, a Y280 virus (PB2-E627K) by reverse genetics and tested in parallel with the Y280-wt virus. 2018 Emerging microbes & infections Result IV E627K;E627K 65;90 70;95 PB2;PB2 61;86 64;89 30301950 Tree shrew as a new animal model to study the pathogenesis of avian influenza (H9N2) virus infection. Under comparable infection conditions, we found that the Y280-PB2-E627K virus replicated more efficiently in the nasal turbinate, trachea, and lung tissues than the Y280-wt virus did (p < 0.05). 2018 Emerging microbes & infections Result IV E627K 66 71 PB2 62 65 30301950 Tree shrew as a new animal model to study the pathogenesis of avian influenza (H9N2) virus infection. Virus replication in the lungs was found only at 2 and 4 dpi in the two tree shrews infected with Y280-PB2-E627K virus. 2018 Emerging microbes & infections Result IV E627K 107 112 PB2 103 106 30301950 Tree shrew as a new animal model to study the pathogenesis of avian influenza (H9N2) virus infection. Virus replication was found in the lung tissues of two tree shrews infected with the Y280-PB2-E627K virus, one at 2 dpi and one at 4 dpi. 2018 Emerging microbes & infections Result IV E627K 94 99 PB2 90 93 30301950 Tree shrew as a new animal model to study the pathogenesis of avian influenza (H9N2) virus infection. We established an ex vivo culture model (nasal turbinate, trachea and lung) to compare the replication of the H9N2 virus and its PB2-E627K mutant. 2018 Emerging microbes & infections Result IV E627K 133 138 PB2 129 132 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. Although intracellular expression levels of each IFNlambda4 variant were similar, (Fig 2B), wt PtIFNlambda4 was significantly more active than HsIFNlambda4 in each assay and had approximately equivalent activity to the HsIFNlambda4 K154E variant in signalling as well as antiviral assays (Fig 2C-2E). 2018 PLoS pathogens Result IV K154E 232 237 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. Although this was only statistically significant in the context of IAV, a similar trend was evident with ZIKV for the K154E variant compared to wt HsIFNlambda4. 2018 PLoS pathogens Result IV K154E 118 123 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. As controls, we also included the less active P70S and L79F HsIFNlambda4 variants alongside HsIFNlambda3op in these assays. 2018 PLoS pathogens Result IV P70S;L79F 46;55 50;59 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. By contrast, L79F and K154E are rare and, based on evidence in the 1000 Genomes Project Database, geographically restricted to West Africa/Americas, and central Africa, respectively (Fig 1A). 2018 PLoS pathogens Result IV L79F;K154E 13;22 17;27 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. By contrast, the K154E variant substantially enhanced antiviral activity and ISG induction. 2018 PLoS pathogens Result IV K154E 17 22 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. Comparing this set of genes to those from the RNA-Seq transcriptomic data obtained in vitro (Fig 4) showed that the majority (17/29 genes) of the chimpanzee-biased genes were induced by HsIFNlambda4 stimulation, with approximately half (8 genes) of those being significantly up-regulated to a great extent with K154E compared to wt, including MX1, IFITM1, IFIT1, IFIT3, TRIM22 and IFI44L (Fig 5C). 2018 PLoS pathogens Result IV K154E 311 316 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. Consistent with the hypothesis that additional genetic differences affect susceptibility to E154K, introducing a lysine into the equivalent position of HsIFNlambda3 had a much lesser effect on its activity compared to IFNlambda4 (Fig 2C-2E). 2018 PLoS pathogens Result IV E154K 92 97 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. Converting PtIFNlambda4 to encode the E154K variant significantly decreased activity to levels that were similar to those for wt HsIFNlambda4 (encoding lysine at position 154). 2018 PLoS pathogens Result IV E154K 38 43 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. Direct in vivo validation of our transcriptomic findings alone on the enhanced activity of the K154E variant would require liver biopsy samples from either HCV-infected Pygmies or chimpanzees combined with equivalent samples from infected humans encoding wt HsIFNlambda4. 2018 PLoS pathogens Result IV K154E 95 100 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. Each of the Baka and Bakola individuals also had additional non-synonymous HsIFNlambda4 variants (V158I and R151P, Baka and Bakola individuals respectively); these variants were included in our functional screen of HsIFNlambda4 variants but did not significantly alter activity (Fig 1C-1E and S2A-S2C Fig). 2018 PLoS pathogens Result IV V158I;R151P 98;108 103;113 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. For the HsIFNlambda4 K154E variant, each of the inhibitors blocked secretion by about 10-12-fold. 2018 PLoS pathogens Result IV K154E 21 26 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. From analysis of the Genome Aggregation Database (gnomAD), the SNP variant resulting in the K154E substitution was found in a further 29 out of a population of 8,655 African individuals. 2018 PLoS pathogens Result IV K154E 92 97 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. From further interrogation of the 1000 Genomes Database, the HsIFNlambda4 K154E variant was present in two individuals from different African rainforest 'Pygmy' hunter-gatherer populations (Baka and Bakola) in Cameroon (S4A Fig). 2018 PLoS pathogens Result IV K154E 74 79 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. From IPA pathway analysis, all HsIFNlambdas induced the same transcriptional programmes with differences in the overall significance of these pathways, most notably enhancement of the antigen presentation and protein ubiquitination pathways with the K154E variant (Fig 4D). 2018 PLoS pathogens Result IV K154E 250 255 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. From this screen, we concluded that three non-synonymous variants in HsIFNlambda4 (P70S, L79F and K154E), identified as either common or rare alleles in the human population, affect the antiviral activity of the protein. 2018 PLoS pathogens Result IV P70S;L79F;K154E 83;89;98 87;93;103 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. However, variants S56R and R60P (R60P is a common variant in Africa) did lead to marked reductions in the glycosylated form of HsIFNlambda4 as demonstrated by the mean ratio of glycosylated:non-glycosylated protein (S3 Fig) but did not greatly alter their antiviral activity in contrast with our findings with the N61A non-natural variant, which abolished both glycosylation and antiviral activity of conditioned media (S2A-S2C Fig and S3A and S3B Fig). 2018 PLoS pathogens Result IV S56R;R60P;R60P;N61A 18;27;33;314 22;31;37;318 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. HsIFNlambda4 and the P70S variant allowing genes to reach the significance threshold (Fig 4F). 2018 PLoS pathogens Result IV P70S 21 25 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. HsIFNlambda4 K154E also reduced titers of IAV and ZIKV to a greater extent than wt protein in A549 cells (~10-fold; Fig 3D and 3E). 2018 PLoS pathogens Result IV K154E 13 18 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. IFI27, MX1, ISG15; Fig 4E) although the magnitude of induction was consistently greatest for HsIFNlambda4 K154E (Fig 4F). 2018 PLoS pathogens Result IV K154E 106 111 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. In a final series of experiments aimed at giving further insight into the mechanism of action of IFNlambda4 K154E, we compared the relative activities and abundance of different IFNlambda4 variants in cell lysates. 2018 PLoS pathogens Result IV K154E 108 113 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. In addition, we constructed a series of negative controls (plasmids expressing EGFP and the frameshift TT variant of HsIFNlambda4), a positive control (HsIFNlambda3op) for comparative analysis to examine HsIFNlambda4 activity, and three HsIFNlambda4 variants, which do not occur naturally but were included as they could alter post-translational modification (N61A which ablates glycosylation) or potential receptor interactions (F159A and L162A located in helix F), respectively. 2018 PLoS pathogens Result IV N61A;F159A;L162A 360;430;440 364;435;445 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. In agreement with our data using FLAG-tagged HsIFNlambda4, the K154E variant of HsIFNlambda4 was secreted about 3 times more efficiently than the wt protein (Fig 6F and 6G). 2018 PLoS pathogens Result IV K154E 63 68 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. In signalling assays, the order of activity was E>Q/D>A>L>K>R (S9A Fig). 2018 PLoS pathogens Result IV S9A 63 66 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. In the case of wt HsIFNlambda4, BFA inhibited secretion to a greater extent (~20-fold) than for either HsIFNlambda3 or HsIFNlambda4 K154E whereas Monensin decreased secretion to a similar extent for all three proteins. 2018 PLoS pathogens Result IV K154E 132 137 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. Interestingly, three rare variants (A8S, S56R and L79F) were shared exclusively between African and American populations, which may have arisen due to relatively recent movements of people perhaps through the transatlantic slave trade. 2018 PLoS pathogens Result IV A8S;S56R;L79F 36;41;50 39;45;54 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. K154E was not found in other East or Southern African hunter-gatherer populations (such as Hadza and Sandawe) nor in the African San, who have the oldest genetic lineages among humans (S4B Fig); it was also not identified in Neanderthal and Denisovan lineages (denoted as 'archaic' in S4B Fig). 2018 PLoS pathogens Result IV K154E 0 5 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. Many of the differentially-expressed genes shared by HsIFNlambda4 wt, K154E and P70S included known restriction factors with antiviral activity (e.g. 2018 PLoS pathogens Result IV K154E;P70S 70;80 75;84 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. Moreover, HiBiT-tagged HsIFNlambda4 K154E was >10-fold more active than the wt form (S11C Fig). 2018 PLoS pathogens Result IV K154E 36 41 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. Notably, the human TT allele encodes a potential K154 codon suggesting that the E154K substitution arose in humans prior to IFNL4 pseudogenisation. 2018 PLoS pathogens Result IV E154K 80 85 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. Our analyses on the natural HsIFNlambda4 variants revealed that only three variants (P70S, L79F and K154E) consistently and substantially modulated antiviral activity and signalling compared to wt HsIFNlambda4 (Fig 1C-1E). 2018 PLoS pathogens Result IV P70S;L79F;K154E 85;91;100 89;95;105 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. Our results confirmed previous observations on the lower activity of the P70S variant and demonstrated that the rare L79F variant had a similar phenotype. 2018 PLoS pathogens Result IV P70S;L79F 73;117 77;121 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. Our results revealed a consistent decrease in HCV RNA levels over 8 passages spanning 25 days with the K154E variant exerting a greater inhibition on RNA replication compared to wt HsIFNlambda4; consistent with this conclusion, fewer sub-genomic replicon-bearing cells survived treatment with HsIFNlambda4 K154E than the wt protein (S6B and S6C Fig). 2018 PLoS pathogens Result IV K154E;K154E 103;306 108;311 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. P70S is a common variant that is found worldwide (in every population in the 1000 Genomes Database). 2018 PLoS pathogens Result IV P70S 0 4 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. Since a lysine residue encoded at positon 154 is unique to humans compared to other mammalian species (Fig 2A), we compared wt HsIFNlambda4 and its K154E variant to wt PtIFNlambda4 and an equivalent 'humanised' PtIFNlambda4 E154K mutant in both the EMCV and ISG induction assays as well as a CRISPR-Cas9 cell line in which the EGFP coding region had been introduced into the endogenous ISG15 gene upstream of and in-frame with the ISG15 open reading frame (ORF) (S5 Fig). 2018 PLoS pathogens Result IV K154E;E154K 148;224 153;229 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. The Baka subject was heterozygous at rs368234815 (DeltaG/TT) and thus only one allele (DeltaG) would produce full-length HsIFNlambda4, presumably K154E. 2018 PLoS pathogens Result IV K154E 146 151 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. The Bakola individual was homozygous for the DeltaG allele, indicating that the K154E variant would be encoded on one of the functional DeltaG HsIFNlambda4 alleles. 2018 PLoS pathogens Result IV K154E 80 85 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. The data revealed that K154E induced the broadest profile of significantly differentially-regulated genes (n = 273) compared with either the wt protein (n = 178) or the P70S variant (n = 115; Fig 4A-4C and S2 Data). 2018 PLoS pathogens Result IV K154E;P70S 23;169 28;173 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. The functional impact of variation on HsIFNlambda4 has only been assessed for the common P70S variant and so we sought to screen all other variants in activity assays. 2018 PLoS pathogens Result IV P70S 89 93 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. The non-natural N61A variant that is not glycosylated was secreted ~2-fold less efficiently than wt HsIFNlambda4. 2018 PLoS pathogens Result IV N61A 16 20 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. The non-natural variants N61A and F159A almost abolished activity compared to wt HsIFNlambda4 and HsIFNlambda3op while L162A gave slightly less activity in the ISG induction assay but activity was reduced to a greater extent in the EMCV assay. 2018 PLoS pathogens Result IV N61A;F159A;L162A 25;34;119 29;39;124 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. The pattern of genes induced by the positive control HsIFNlambda3op and HsIFNlambda4 K154E were very similar (Fig 4B and 4C). 2018 PLoS pathogens Result IV K154E 85 90 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. There were also several ISGs that only achieved significant induction by K154E and HsIFNlambda3op (e.g. 2018 PLoS pathogens Result IV K154E 73 78 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. These effects on activity for P70S, L79F and K154E did not arise from differences in the levels of HsIFNlambda4 intracellular production or changes to glycosylation (S3A and S3B Fig). 2018 PLoS pathogens Result IV P70S;L79F;K154E 30;36;45 34;40;50 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. Thus, both FLAG- and HiBiT-tagged forms of K154E gave higher antiviral activity and were secreted more efficiently than wt HsIFNlambda4. 2018 PLoS pathogens Result IV K154E 43 48 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. Thus, HsIFNlambda4 reduces HCV RNA replication and the K154E variant exerts greater potency against this stage in the virus life cycle. 2018 PLoS pathogens Result IV K154E 55 60 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. Thus, we could verify the occurrence of the L79F variant in Africa but not in the Americas. 2018 PLoS pathogens Result IV L79F 44 48 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. To examine further the inhibitory effect of wt HsIFNlambda4 and the K154E variant on viral RNA replication, Huh7 cells that constitutively expressed a HCV sub-genomic replicon [Tri-JFH1; ] were treated with both forms of the protein over several passages (S6A Fig). 2018 PLoS pathogens Result IV K154E 68 73 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. Together with the fact that nearly all humans encode K154, these data suggest that the less active E154K substitution emerged early during human evolution after the divergence of our last common ancestor with chimpanzees. 2018 PLoS pathogens Result IV E154K 99 104 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. Using the HCVcc infectious system in Huh7 cells, HsIFNlambda4 K154E significantly decreased both viral RNA abundance compared to wt protein and exhibited a trend towards a lower number of infected viral antigen (NS5A)-positive cells (Fig 3A, upper and lower panels respectively). 2018 PLoS pathogens Result IV K154E 62 67 NS 212 214 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. We expanded this predicted model based on both of the IFNlambda1 and IFNlambda3 crystal structures to explore the possible impact of K154E, P70S and L79F on IFNlambda4 function (Fig 6A and S8 Fig). 2018 PLoS pathogens Result IV K154E;P70S;L79F 133;140;149 138;144;153 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. We found that the P70S and L79F variants consistently reduced the ability of wt HsIFNlambda4 to protect against infection in most assays. 2018 PLoS pathogens Result IV P70S;L79F 18;27 22;31 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. We identified 15 non-synonymous HsIFNlambda4 variants in the 1000 Genomes Project Database (Fig 1A and S1 Data), including three previously described variants (C17Y, P60R and P70S; >1% global frequency, classified as 'common'). 2018 PLoS pathogens Result IV C17Y;P60R;P70S 160;166;175 164;170;179 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. We interpret these findings to conclude that E154 is biochemically the most favoured residue at this position with regards to antiviral potential, and that substitution of E154 to lysine results in the lowest potency for IFNlambda4 activity. 2018 PLoS pathogens Result IV E154K 172 186 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. We predict that the apparent selectivity by IFNlambda4 K154E results from the greater potency of this variant compared to wt. 2018 PLoS pathogens Result IV K154E 55 60 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. We were able to obtain DNA from lymphoblastoid cell lines developed from the 2 individuals encoding the L79F variant; our analysis revealed that the West African subject carried the SNP for this variant but not the individual from the Americas see Materials and Methods).). 2018 PLoS pathogens Result IV L79F 104 108 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. wt HsIFNlambda4 reduced HCV RNA replication compared to EGFP and introducing the K154E mutation into wt HsIFNlambda4 gave a further significant reduction in replication. 2018 PLoS pathogens Result IV K154E 81 86 30349332 Antiviral resistance markers in influenza virus sequences in Mexico, 2000-2017. All viruses carrying the marker H275Y had the codon UAC (12/12), while the other viruses had CAC (316/316). 2018 Infection and drug resistance Result IV H275Y 32 37 30349332 Antiviral resistance markers in influenza virus sequences in Mexico, 2000-2017. In all cases of N70S, the codon was AGC (6/6), and the other viruses presented AAC (12/12). 2018 Infection and drug resistance Result IV N70S 16 20 30349332 Antiviral resistance markers in influenza virus sequences in Mexico, 2000-2017. Only one of the resistance-associated genotypic markers (Q136K) was present in the 70 (1.5%) analyzed N2 sequences. 2018 Infection and drug resistance Result IV Q136K 57 62 30349332 Antiviral resistance markers in influenza virus sequences in Mexico, 2000-2017. Only two resistance markers were present, H275Y in 10/20 (50.0%) and N70S in 6/18 (33.3%) sequences. 2018 Infection and drug resistance Result IV H275Y;N70S 42;69 47;73 30349332 Antiviral resistance markers in influenza virus sequences in Mexico, 2000-2017. Seasonal H1N1 viruses had S31N in a much lower proportion: 5.8% (1/17) (Table 3). 2018 Infection and drug resistance Result IV S31N 26 30 30349332 Antiviral resistance markers in influenza virus sequences in Mexico, 2000-2017. The analyzed sequences showed a high frequency of the molecular marker S31N, which is associated with resistance to M2 blockers. 2018 Infection and drug resistance Result IV S31N 71 75 M2 116 118 30349332 Antiviral resistance markers in influenza virus sequences in Mexico, 2000-2017. The most frequent codon in H274Y change was UAU (9/10), while the other viruses had CAC (7/10) and CAU (3/10). 2018 Infection and drug resistance Result IV H274Y 27 32 30349332 Antiviral resistance markers in influenza virus sequences in Mexico, 2000-2017. The most frequent was H275Y, present in 12/328 (3.6%), while S247N was present in 1/329 (0.30%). 2018 Infection and drug resistance Result IV H275Y;S247N 22;61 27;66 30349332 Antiviral resistance markers in influenza virus sequences in Mexico, 2000-2017. The only one virus carrying the marker S247N presented the codon AAU, and the other viruses had AGU (328/328). 2018 Infection and drug resistance Result IV S247N 39 44 30349332 Antiviral resistance markers in influenza virus sequences in Mexico, 2000-2017. The S247N change is also associated with zanamivir resistance and was the only sequence detected for this drug. 2018 Infection and drug resistance Result IV S247N 4 9 30352857 The mechanism of resistance to favipiravir in influenza. At 24 h, the P653L virus titer was significantly greater than Eng195 (one-way ANOVA, P = 0.003). 2018 Proc Natl Acad Sci U S A Result IV P653L 13 18 30352857 The mechanism of resistance to favipiravir in influenza. By contrast, the polymerase containing the PA P653L mutation showed a 5-fold higher activity compared with the wild-type polymerase. 2018 Proc Natl Acad Sci U S A Result IV P653L 46 51 PA 43 45 30352857 The mechanism of resistance to favipiravir in influenza. By contrast, the polymerase containing the PB1 K229R mutation produced RNA that contained significantly fewer errors in the presence of favipiravir compared with the wild type (two-way ANOVA, P < 0.001), even at high drug concentrations. 2018 Proc Natl Acad Sci U S A Result IV K229R 47 52 PB1 43 46 30352857 The mechanism of resistance to favipiravir in influenza. Further inspection of the next-generation sequencing data of the F2 and F3 populations showed that the P653L mutation was present in both populations, albeit at a low level (6% in population F2 and 5% in F3). 2018 Proc Natl Acad Sci U S A Result IV P653L 103 108 30352857 The mechanism of resistance to favipiravir in influenza. However, similar to Eng195 RNA polymerase, the P653L mutation did not provide resistance to favipiravir in the H3N2 and H7N9 polymerases, but compensated for the small reduction in K229R polymerase activity entirely when combined with K229R in the H7N9 RNA polymerase. 2018 Proc Natl Acad Sci U S A Result IV P653L;K229R;K229R 47;181;235 52;186;240 30352857 The mechanism of resistance to favipiravir in influenza. However, the PB1 K229R mutant showed only a slight decrease in activity in the presence of the drug, implying that the K229R mutation rendered the polymerase resistant to favipiravir (79% activity at 100 microM) (two-way ANOVA, P < 0.001). 2018 Proc Natl Acad Sci U S A Result IV K229R;K229R 17;119 22;124 PB1 13 16 30352857 The mechanism of resistance to favipiravir in influenza. Importantly, minigenome assays of a mutant polymerase containing both PA P653L and PB1 K229R mutations showed a 4-fold higher level of polymerase activity compared with wild type, while the favipiravir resistance was similar to PB1 K229R (no loss of activity until >20 microM and 57% activity at 100 microM, two-way ANOVA, P = 0.53). 2018 Proc Natl Acad Sci U S A Result IV P653L;K229R;K229R 73;87;232 78;92;237 PA;PB1;PB1 70;83;228 72;86;231 30352857 The mechanism of resistance to favipiravir in influenza. In a transcription assay with labeled capped primer terminating in AG and 3' 4U template we noted significantly less G-product relative to C-product synthesis by the P653L-containing mutants (SI Appendix. 2018 Proc Natl Acad Sci U S A Result IV P653L 166 171 30352857 The mechanism of resistance to favipiravir in influenza. In a viral yield experiment in presence of different drug doses, the K229R + P653L double mutant virus was ~30-fold less susceptible to favipiravir than the wild-type virus (IC90 55 microM vs. 2018 Proc Natl Acad Sci U S A Result IV K229R;P653L 69;77 74;82 30352857 The mechanism of resistance to favipiravir in influenza. In contrast, in reactions with the K229R polymerase efficient GTP incorporation was observed even when F-RTP was present. 2018 Proc Natl Acad Sci U S A Result IV K229R 35 40 30352857 The mechanism of resistance to favipiravir in influenza. In the absence of favipiravir, the PB1 K229R mutant showed a 30-fold reduction in polymerase activity compared with the wild type. 2018 Proc Natl Acad Sci U S A Result IV K229R 39 44 PB1 35 38 30352857 The mechanism of resistance to favipiravir in influenza. Interestingly, the cost to polymerase activity of the K229R mutation in H7N9 and H3N2 was not as severe as for the Eng195 RNA polymerase. 2018 Proc Natl Acad Sci U S A Result IV K229R 54 59 30352857 The mechanism of resistance to favipiravir in influenza. K229R Confers Resistance to Favipiravir. 2018 Proc Natl Acad Sci U S A Result IV K229R 0 5 30352857 The mechanism of resistance to favipiravir in influenza. K229R Mutation in PB1 Confers Favipiravir Resistance to RdRP of Other Influenza A Virus Subtypes. 2018 Proc Natl Acad Sci U S A Result IV K229R 0 5 PB1 18 21 30352857 The mechanism of resistance to favipiravir in influenza. K229R Prevents Mutations in the Presence of Favipiravir. 2018 Proc Natl Acad Sci U S A Result IV K229R 0 5 30352857 The mechanism of resistance to favipiravir in influenza. Modeling of the K229R mutation into the bat influenza polymerase structure shows that it reduces the NTP binding space of the active site. 2018 Proc Natl Acad Sci U S A Result IV K229R 16 21 30352857 The mechanism of resistance to favipiravir in influenza. Moreover, by contrast to Eng195, introduction of the P653L mutation in the H3N2 and H7N9 RNA polymerases did not raise polymerase activity. 2018 Proc Natl Acad Sci U S A Result IV P653L 53 58 30352857 The mechanism of resistance to favipiravir in influenza. Multicycle growth curves performed in MDCK cells showed that, in comparison with the wild-type Eng195 virus, the K229R virus was attenuated (one-way ANOVA, P < 0.001 at 48 h), while there was no difference in growth for the P653L virus (one-way ANOVA, P = 0.052) or the virus containing both mutations (one-way ANOVA, P = 0.12). 2018 Proc Natl Acad Sci U S A Result IV K229R;P653L 113;224 118;229 30352857 The mechanism of resistance to favipiravir in influenza. Neither the K229R nor the P653L mutation was seen in F1 or any of the control populations. 2018 Proc Natl Acad Sci U S A Result IV K229R;P653L 12;26 17;31 30352857 The mechanism of resistance to favipiravir in influenza. Next-generation sequencing showed a fixed lysine 229 to arginine (K229R) mutation in PB1 in populations F2 and F3. 2018 Proc Natl Acad Sci U S A Result IV K229R;K229R 66;42 71;64 PB1 85 88 30352857 The mechanism of resistance to favipiravir in influenza. Next, we considered what effects the P653L mutation in PA might have on the polymerase. 2018 Proc Natl Acad Sci U S A Result IV P653L 37 42 PA 55 57 30352857 The mechanism of resistance to favipiravir in influenza. One possible mechanism by which the K229R mutation might confer resistance to favipiravir would be to increase the fidelity of the polymerase, as has been observed for ribavirin resistance in several viral systems. 2018 Proc Natl Acad Sci U S A Result IV K229R 36 41 30352857 The mechanism of resistance to favipiravir in influenza. PA P653L Preferentially Initiates Transcription from 3' U. 2018 Proc Natl Acad Sci U S A Result IV P653L 3 8 PA 0 2 30352857 The mechanism of resistance to favipiravir in influenza. Reconstituted polymerases harboring the K229R mutation displayed resistance to favipiravir to a similar degree as Eng195 polymerase in a minigenome assay. 2018 Proc Natl Acad Sci U S A Result IV K229R 40 45 30352857 The mechanism of resistance to favipiravir in influenza. Sanger sequencing of the PB1, PB2, and PA genes confirmed the presence of the K229R mutation in PB1 in all four clones and revealed the presence of an additional proline 653 to leucine mutation (P653L) in the PA subunit in all four clones. 2018 Proc Natl Acad Sci U S A Result IV K229R;P653L;P653L 78;195;162 83;200;184 PA;PA;PB1;PB1;PB2 39;209;25;96;30 41;211;28;99;33 30352857 The mechanism of resistance to favipiravir in influenza. Since both possible +2 products, whether a G product (Cap-AGCF) or, the much less likely, C product (CapAGFC) require F-RTP incorporation, this suggests that the K229R mutation prevented incorporation of F-RTP in vitro. 2018 Proc Natl Acad Sci U S A Result IV K229R 162 167 30352857 The mechanism of resistance to favipiravir in influenza. Taken together, these results suggest that K229R in PB1 confers resistance to favipiravir to the influenza virus polymerase in cell culture and that P653L in PA compensates for a fitness cost for resistance. 2018 Proc Natl Acad Sci U S A Result IV K229R;P653L 43;149 48;154 PA;PB1 158;52 160;55 30352857 The mechanism of resistance to favipiravir in influenza. The double mutant containing both PB1 K229R and PA P653L polymerase mutations displayed a similar relative mutation frequency as the PB1 K229R mutant (two-way ANOVA, P = 0.83). 2018 Proc Natl Acad Sci U S A Result IV K229R;P653L;K229R 38;51;137 43;56;142 PA;PB1;PB1 48;34;133 50;37;136 30352857 The mechanism of resistance to favipiravir in influenza. The favipiravir sensitivity of the P653L mutant was not significantly different from the wild-type polymerase (two-way ANOVA, P = 0.08). 2018 Proc Natl Acad Sci U S A Result IV P653L 35 40 30352857 The mechanism of resistance to favipiravir in influenza. The K229R Mutant Shows Reduced Favipiravir Incorporation During Replication in Vitro. 2018 Proc Natl Acad Sci U S A Result IV K229R 4 9 30352857 The mechanism of resistance to favipiravir in influenza. The K229R Mutant Shows Reduced Favipiravir Incorporation During Transcription in Vitro. 2018 Proc Natl Acad Sci U S A Result IV K229R 4 9 30352857 The mechanism of resistance to favipiravir in influenza. the K229R mutation reduces F-RTP incorporation in vitro. 2018 Proc Natl Acad Sci U S A Result IV K229R 4 9 30352857 The mechanism of resistance to favipiravir in influenza. The low level of the P653L mutation may have been caused by defective interfering particles that only contained the K229R mutation and not the P653L mutation. 2018 Proc Natl Acad Sci U S A Result IV P653L;K229R;P653L 21;116;143 26;121;148 30352857 The mechanism of resistance to favipiravir in influenza. The mutation frequency observed for the P653L mutant was higher compared with the wild-type polymerase at each drug concentration (two-way ANOVA, P < 0.001). 2018 Proc Natl Acad Sci U S A Result IV P653L 40 45 30352857 The mechanism of resistance to favipiravir in influenza. This implies that P653L can compensate for the loss of activity in the K229R mutant without affecting favipiravir resistance in cell culture. 2018 Proc Natl Acad Sci U S A Result IV P653L;K229R 18;71 23;76 30352857 The mechanism of resistance to favipiravir in influenza. This observation suggests that the K229R mutation confers specific resistance to favipiravir and likely does not confer favipiravir resistance by increasing polymerase fidelity. 2018 Proc Natl Acad Sci U S A Result IV K229R 35 40 30352857 The mechanism of resistance to favipiravir in influenza. This suggests that the P653L mutation had changed either how the template is positioned in the active site, how the primer is bound by the polymerase, how important Watson-Crick base pairing is for base pairing between the template and the incoming base, or a combination of these possibilities. 2018 Proc Natl Acad Sci U S A Result IV P653L 23 28 30352857 The mechanism of resistance to favipiravir in influenza. To confirm that the K229R mutant provides resistance to F-RTP in vitro, we performed a replication assay. 2018 Proc Natl Acad Sci U S A Result IV K229R 20 25 30352857 The mechanism of resistance to favipiravir in influenza. To demonstrate whether the PB1 K229R, the PA P653L, or a combination of both mutations was responsible for the favipiravir resistance observed in the F2 and F3 populations, we introduced the K229R and P653L mutations into PB1 and PA expression plasmids and tested the reconstituted polymerase activity of the mutant viral polymerases in presence or absence of favipiravir using a minigenome assay. 2018 Proc Natl Acad Sci U S A Result IV K229R;P653L;K229R;P653L 31;45;191;201 36;50;196;206 PA;PA;PB1;PB1 42;230;27;222 44;232;30;225 30352857 The mechanism of resistance to favipiravir in influenza. To investigate whether the K229R, the P653L, or the double mutant conferred resistance to other nucleoside analogs, such as ribavirin, we tested the susceptibility of the double mutant to ribavirin in a minigenome assay. 2018 Proc Natl Acad Sci U S A Result IV K229R;P653L 27;38 32;43 30352857 The mechanism of resistance to favipiravir in influenza. To rule out that the K229R mutation confers resistance to favipiravir by reducing the RdRP error rate, we used next-generation sequencing to quantify viral mutations. 2018 Proc Natl Acad Sci U S A Result IV K229R 21 26 30352857 The mechanism of resistance to favipiravir in influenza. To study the effect of the PB1 K229R and PA P653L mutations in more detail, we expressed recombinant polymerases harboring either of the single mutations or both mutations together and purified the recombinant polymerases using a Protein A tag on the C terminus of the PB2 subunit. 2018 Proc Natl Acad Sci U S A Result IV K229R;P653L 31;44 36;49 PA;PB1;PB2 41;27;269 43;30;272 30352857 The mechanism of resistance to favipiravir in influenza. To test if the resistance mutations identified above also conferred resistance to other influenza virus strains, we next engineered the K229R mutation into the PB1 subunit and the P653L mutation into the PA subunit of a historic H3N2 human influenza virus. 2018 Proc Natl Acad Sci U S A Result IV K229R;P653L 136;180 141;185 PA;PB1 204;160 206;163 30352857 The mechanism of resistance to favipiravir in influenza. To verify the above results, we next generated recombinant Eng195 viruses containing either the PA P653L or PB1 K229R mutation, or both mutations. 2018 Proc Natl Acad Sci U S A Result IV P653L;K229R 99;112 104;117 PA;PB1 96;108 98;111 30352857 The mechanism of resistance to favipiravir in influenza. When the same experiment was repeated with the polymerase with single P653L mutation or the double mutant, the polymerase with the K229R mutation in PB1 incorporated GTP in presence of F-RTP, but P653L alone did not. 2018 Proc Natl Acad Sci U S A Result IV P653L;K229R;P653L 70;131;196 75;136;201 PB1 149 152 30353004 Genome-wide characterization of the seasonal H3N2 virus in Shanghai reveals natural temperature-sensitive strains conferred by the I668V mutation in the PA subunit. Compared to the polymerase activity of SC/09, the isoleucine-to-valine substitution in the mutant PA I668V of the H1N1 subtype resulted in lower polymerase activity at 39 C, which was consistent with the PA mutant polymerase complex of the H3N2 subtype. 2018 Emerging microbes & infections Result IV I668V 101 106 PA;PA 98;205 100;207 30353004 Genome-wide characterization of the seasonal H3N2 virus in Shanghai reveals natural temperature-sensitive strains conferred by the I668V mutation in the PA subunit. Compared with the WHO-recommended vaccine strains for the 2016-2018 influenza seasons (A/Hong Kong/4801/ 2014), the 2017sum and 2016-2017win virus strains contained 11 amino acid substitutions (T114S, T131K, I140T, R142K, and R261Q in the 2016-2017win strains and K92R, T114S, N121K, T135K/N, N171K, D291E, and H311Q in the 2017sum strains). 2018 Emerging microbes & infections Result IV T114S;T131K;I140T;R142K;R261Q;K92R;T114S;N121K;T135K;T135N;N171K;D291E;H311Q 194;201;208;215;226;264;270;277;284;284;293;300;311 199;206;213;220;231;268;275;282;291;291;298;305;316 30353004 Genome-wide characterization of the seasonal H3N2 virus in Shanghai reveals natural temperature-sensitive strains conferred by the I668V mutation in the PA subunit. However, the polymerase reconstituted with the PA I668V mutant exhibited significantly reduced activity, a feature that was generally more pronounced at 39 C than at 33 C or 37 C. 2018 Emerging microbes & infections Result IV I668V 50 55 PA 47 49 30353004 Genome-wide characterization of the seasonal H3N2 virus in Shanghai reveals natural temperature-sensitive strains conferred by the I668V mutation in the PA subunit. The following amino acid mutations were associated with adamantane resistance: L26F, V27A/T, A30T/V, S31N/R, G34E, A30V, S193F, and R45H. 2018 Emerging microbes & infections Result IV L26F;V27A;V27T;A30T;A30V;S31N;S31R;G34E;A30V;S193F;R45H 79;85;85;93;93;101;101;109;115;121;132 83;91;91;99;99;107;107;113;119;126;136 30353004 Genome-wide characterization of the seasonal H3N2 virus in Shanghai reveals natural temperature-sensitive strains conferred by the I668V mutation in the PA subunit. These results suggested that the temperature sensitivity of the 2016-2017win viruses was associated with a defect in the replication activity of the polymerase and that the PA I668V mutant might potentially lead to reduced polymerase activity at high temperatures. 2018 Emerging microbes & infections Result IV I668V 176 181 PA 173 175 30353004 Genome-wide characterization of the seasonal H3N2 virus in Shanghai reveals natural temperature-sensitive strains conferred by the I668V mutation in the PA subunit. To understand the effects of the PB2 and PA mutations in the 2016-2017win and 2017sum virus strains, we introduced three individual mutations, as summarized in Table 2 (PB2 R299K, PB2 R340K, and PA I668V), into the reassortant polymerase complex from the 2017sum viruses. 2018 Emerging microbes & infections Result IV R299K;R340K;I668V 173;184;198 178;189;203 PA;PA;PB2;PB2;PB2 41;195;33;169;180 43;197;36;172;183 30353004 Genome-wide characterization of the seasonal H3N2 virus in Shanghai reveals natural temperature-sensitive strains conferred by the I668V mutation in the PA subunit. To verify the decrease in the activity of the PA I668V mutant at 39 C, an A/Sichuan/1/2009 virus polymerase complex containing the PA I668V mutation (SC/09 PA-I668V) was constructed, and the activity was measured in transfected cells. 2018 Emerging microbes & infections Result IV I668V;I668V;I668V 49;135;160 54;140;165 PA;PA;PA 46;132;157 48;134;159 30400276 Combination Therapy with Oseltamivir and Favipiravir Delays Mortality but Does Not Prevent Oseltamivir Resistance in Immunodeficient Mice Infected with Pandemic A(H1N1) Influenza Virus. and, on day 15 p.i., three mice out of four had 16.4, 6.5 and 1.7% of H275Y variant (Table 2). 2018 Viruses Result IV H275Y 70 75 30400276 Combination Therapy with Oseltamivir and Favipiravir Delays Mortality but Does Not Prevent Oseltamivir Resistance in Immunodeficient Mice Infected with Pandemic A(H1N1) Influenza Virus. but, on day 15 p.i., they showed higher proportion of H275Y variant with three mice having 19.1, 16.91 and 26.24% of H275Y variant (Table 1). 2018 Viruses Result IV H275Y;H275Y 54;117 59;122 30400276 Combination Therapy with Oseltamivir and Favipiravir Delays Mortality but Does Not Prevent Oseltamivir Resistance in Immunodeficient Mice Infected with Pandemic A(H1N1) Influenza Virus. did not show the presence of the H275Y in mice treated with oseltamivir. 2018 Viruses Result IV H275Y 33 38 30400276 Combination Therapy with Oseltamivir and Favipiravir Delays Mortality but Does Not Prevent Oseltamivir Resistance in Immunodeficient Mice Infected with Pandemic A(H1N1) Influenza Virus. However, the chromatogram of the NA genes from three mice treated with the combination and positive for H275Y by ddPCR showed a mixed population at this codon. 2018 Viruses Result IV H275Y 104 109 33 35 30400276 Combination Therapy with Oseltamivir and Favipiravir Delays Mortality but Does Not Prevent Oseltamivir Resistance in Immunodeficient Mice Infected with Pandemic A(H1N1) Influenza Virus. Interestingly, RT-ddPCR assay demonstrated that the group treated with oseltamivir-favipiravir combination had higher % of H275Y mutant population than that of mice treated with oseltamivir monotherapy on days 8 and 12 p.i. 2018 Viruses Result IV H275Y 123 128 30400276 Combination Therapy with Oseltamivir and Favipiravir Delays Mortality but Does Not Prevent Oseltamivir Resistance in Immunodeficient Mice Infected with Pandemic A(H1N1) Influenza Virus. Interestingly, RT-ddPCR assay designed for the detection and quantification of H275Y associated with oseltamivir-resistant variant demonstrated that two out of four mice treated with oseltamivir contained low or intermediate levels of mutant population on days 8 (2.26 and 1.92%) and 12 p.i. 2018 Viruses Result IV H275Y 79 84 30400276 Combination Therapy with Oseltamivir and Favipiravir Delays Mortality but Does Not Prevent Oseltamivir Resistance in Immunodeficient Mice Infected with Pandemic A(H1N1) Influenza Virus. The oseltamivir resistance phenotype associated with H275Y was not detected by NAI assay (Table 2). 2018 Viruses Result IV H275Y 53 58 NAI 79 82 30405591 Identification of Amino Acid Residues Responsible for Inhibition of Host Gene Expression by Influenza A H9N2 NS1 Targeting of CPSF30. Altogether, these results indicate that the combination of amino acid residues F103L/M106I/S114P/D125G/D139N in WI/66 NS1 protein is sufficient to loss its ability to inhibit host gene expression. 2018 Frontiers in microbiology Result IV M106I;F103L;S114P;D139N;D125G 85;79;91;103;97 90;84;96;108;102 NS1 118 121 30405591 Identification of Amino Acid Residues Responsible for Inhibition of Host Gene Expression by Influenza A H9N2 NS1 Targeting of CPSF30. Amino Acid Changes L103F/I106M/P114S/G125D/N139D Restore the Ability of HK/97 IAV NS1 to Bind to CPSF30. 2018 Frontiers in microbiology Result IV L103F;I106M;P114S;G125D;N139D 19;25;31;37;43 24;30;36;42;48 NS1 82 85 30405591 Identification of Amino Acid Residues Responsible for Inhibition of Host Gene Expression by Influenza A H9N2 NS1 Targeting of CPSF30. Amino acid changes MF103L/M106I (WI 9) had a minimal effect on inhibition of reporter gene expression as compared to WI/66 WT or M106I (WI 3) mutant (Figures 5B,C) indicating that amino acid substitutions F103L and M106I have a minimal effect on the ability of WI/66 NS1 protein to inhibit host gene expression (Figures 6B,C). 2018 Frontiers in microbiology Result IV M106I;M106I;F103L;M106I 26;129;205;215 31;134;210;220 NS1 267 270 30405591 Identification of Amino Acid Residues Responsible for Inhibition of Host Gene Expression by Influenza A H9N2 NS1 Targeting of CPSF30. As expected, none of the single HK/97 NS1 mutants completely restored the ability to inhibit host gene expression (Figures 7B,C) with mutant HK 3 (I106M) showing approximately 50% of inhibition in reporter gene expression as compared to HK/97 WT NS1. 2018 Frontiers in microbiology Result IV I106M 147 152 NS1;NS1 38;246 41;249 30405591 Identification of Amino Acid Residues Responsible for Inhibition of Host Gene Expression by Influenza A H9N2 NS1 Targeting of CPSF30. However, mutant HK 13 (L103F/I106M/P114S/G125D/N139D) and WI/66 NS1 were detected by Western blot in the co-immunoprecipitation, suggesting binding to CPSF30 (Figure 9A, IP alpha-HA). 2018 Frontiers in microbiology Result IV L103F;I106M;P114S;G125D;N139D 23;29;35;41;47 28;34;40;46;52 HA;NS1 179;64 181;67 30405591 Identification of Amino Acid Residues Responsible for Inhibition of Host Gene Expression by Influenza A H9N2 NS1 Targeting of CPSF30. In order to evaluate the ability of HK/97and WI/66 NS1 proteins and their respective HK 13 (L103F/I106M/P114S/G125D/N139D) and WI 13 (F103L/M106I/S114P/D125G/D139N) mutants to counteract IFN and ISG responses, HEK293T cells were co-transfected with pCAGGS plasmids expressing HK/97 WT, HK 13, WI/66 WT and WI 13 NS1 proteins together with reporter plasmids expressing Firefly luciferase (FFluc) under the control of the IFN-beta (Figure 10A) or ISRE (Figure 10C) promoters. 2018 Frontiers in microbiology Result IV L103F;I106M;P114S;G125D;N139D;F103L;M106I;S114P;D125G;D139N 92;98;104;110;116;134;140;146;152;158 97;103;109;115;121;139;145;151;157;163 NS1;NS1 51;312 54;315 30405591 Identification of Amino Acid Residues Responsible for Inhibition of Host Gene Expression by Influenza A H9N2 NS1 Targeting of CPSF30. In the case of PR8 NS1 protein, amino acid changes S103F and I106M restored the ability of PR8 NS1 binding to CPSF30 and concomitant inhibition of host gene expression. 2018 Frontiers in microbiology Result IV S103F;I106M 51;61 56;66 NS1;NS1 19;95 22;98 30405591 Identification of Amino Acid Residues Responsible for Inhibition of Host Gene Expression by Influenza A H9N2 NS1 Targeting of CPSF30. Likewise, expression levels of all NS1 HK/97 mutants was detected by Western blot (Figure 8D) with the exception of HK 11 (L103F/I106M/G125D), HK 13 (L103F/I106M/P114S/G125D/N139D) and HK 8 (E92D/L103F/I106M/T112A/P114S/G125D/N139D) (Figure 8D). 2018 Frontiers in microbiology Result IV I106M;L103F;G125D;I106M;L103F;P114S;G125D;N139D;I106M;E92D;L103F;T112A;P114S;G125D;N139D 129;123;135;156;150;162;168;174;202;191;196;208;214;220;226 134;128;140;161;155;167;173;179;207;195;201;213;219;225;231 NS1 35 38 30405591 Identification of Amino Acid Residues Responsible for Inhibition of Host Gene Expression by Influenza A H9N2 NS1 Targeting of CPSF30. Mutant HK 13 containing five amino acid (L103F/I106M/P114S/G125D/N139D) was able to inhibit reporter gene expression to the same level of WI/66 NS1 WT (Figures 8B,C). 2018 Frontiers in microbiology Result IV I106M;L103F;P114S;G125D;N139D 47;41;53;59;65 52;46;58;64;70 NS1 144 147 30405591 Identification of Amino Acid Residues Responsible for Inhibition of Host Gene Expression by Influenza A H9N2 NS1 Targeting of CPSF30. Mutant HK 8 containing the seven amino acid changes (E92D/L103F/I106M/T112A/P114S/G125D/N139D) inhibited reporter gene expression to levels comparable to WI/66 WT NS1 (Figures 7B,C), further demonstrating that a combination of more than one amino acid is involved in the ability to inhibit host gene expression. 2018 Frontiers in microbiology Result IV I106M;E92D;L103F;T112A;P114S;G125D;N139D 64;53;58;70;76;82;88 69;57;63;75;81;87;93 NS1 163 166 30405591 Identification of Amino Acid Residues Responsible for Inhibition of Host Gene Expression by Influenza A H9N2 NS1 Targeting of CPSF30. Notably, mutant WI 13 (F103L/M106I/S114P/D125G/D139N) was unable to inhibit reporter gene expression (Figures 6B,C), similar to WI 8, that contains the seven amino acid changes, and HK WT NS1 (Figures 6B,C). 2018 Frontiers in microbiology Result IV M106I;F103L;S114P;D125G;D139N 29;23;35;41;47 34;28;40;46;52 NS1 188 191 30405591 Identification of Amino Acid Residues Responsible for Inhibition of Host Gene Expression by Influenza A H9N2 NS1 Targeting of CPSF30. Only mutants WI 3 (F103L) and WI 6 (D125G) were less active than the WI/66 WT (Figures 5B,C). 2018 Frontiers in microbiology Result IV F103L;D125G 19;36 24;41 30405591 Identification of Amino Acid Residues Responsible for Inhibition of Host Gene Expression by Influenza A H9N2 NS1 Targeting of CPSF30. Substitutions L103F/I106M/P114S/G125D/N139D Restore the Ability to Inhibit Host Gene Expression in HK/97 IAV NS1 Protein. 2018 Frontiers in microbiology Result IV L103F;I106M;P114S;G125D;N139D 14;20;26;32;38 19;25;31;37;43 NS1 109 112 30405591 Identification of Amino Acid Residues Responsible for Inhibition of Host Gene Expression by Influenza A H9N2 NS1 Targeting of CPSF30. The amino acid change D125G was also included because when this single change was introduced (WI 6 mutant) we saw an effect on reporter gene expression (Figure 5). 2018 Frontiers in microbiology Result IV D125G 22 27 30405591 Identification of Amino Acid Residues Responsible for Inhibition of Host Gene Expression by Influenza A H9N2 NS1 Targeting of CPSF30. The amino acid substitutions S114P and D139N were also included since they are located in the region responsible for the loss/gain of inhibition of host gene expression (Figure 3) and are different between the NS1 protein from WI/66 and HK/97 NS1 (Figure 4). 2018 Frontiers in microbiology Result IV S114P;D139N 29;39 34;44 NS1;NS1 210;243 213;246 30405591 Identification of Amino Acid Residues Responsible for Inhibition of Host Gene Expression by Influenza A H9N2 NS1 Targeting of CPSF30. The other HK/97 NS1 mutants containing the same combination of amino acid changes than those previously described for WI/66 NS1 showed an intermediate phenotype between the double mutant HK 9 (L103F/I106M) and mutant HK 13 (Figures 8B,C), as previously described for WI/66NS1 (Figures 6B,C). 2018 Frontiers in microbiology Result IV I106M;L103F 199;193 204;198 NS1;NS1 16;124 19;127 30405591 Identification of Amino Acid Residues Responsible for Inhibition of Host Gene Expression by Influenza A H9N2 NS1 Targeting of CPSF30. The triple mutants WI 10 (F103L/M106I/S114P) and WI 12 (F103L/M106I/D139N) were slightly affected, as compared to WI/66 NS1 WT in inhibiting reporter gene expression (Figures 6B,C) while the triple mutant WI 11 (F103L/M106I/D125G) was severely affected in inhibiting host gene expression, and only differed in ~20% inhibition with HK WT NS1 (Figures 6B,C). 2018 Frontiers in microbiology Result IV M106I;F103L;S114P;M106I;F103L;D139N;M106I;F103L;D125G 32;26;38;62;56;68;218;212;224 37;31;43;67;61;73;223;217;229 NS1;NS1 120;337 123;340 30405591 Identification of Amino Acid Residues Responsible for Inhibition of Host Gene Expression by Influenza A H9N2 NS1 Targeting of CPSF30. These results demonstrate that amino acid substitutions L103F/I106M/P114S/G125D/N139D restored the ability of HK/97 NS1 protein to interact with CPFS30, providing a mechanism for inhibition of host gene expression. 2018 Frontiers in microbiology Result IV L103F;I106M;P114S;G125D;N139D 56;62;68;74;80 61;67;73;79;85 NS1 116 119 30405591 Identification of Amino Acid Residues Responsible for Inhibition of Host Gene Expression by Influenza A H9N2 NS1 Targeting of CPSF30. Thus, we produced the F103L and M106I WI/66 NS1 double mutant and use it as a template to make the rest of amino acid mutant combinations (Figure 6A). 2018 Frontiers in microbiology Result IV F103L;M106I 22;32 27;37 NS1 44 47 30405591 Identification of Amino Acid Residues Responsible for Inhibition of Host Gene Expression by Influenza A H9N2 NS1 Targeting of CPSF30. To evaluate if the five amino acid substitutions L103F/I106M/P114S/G125D/N139D in HK/97 NS1 restore its ability to bind to CPSF30, cell extracts from HEK293T transfected with a pCAGGS plasmid expressing a FLAG-tagged CPSF30 were incubated with in vitro transcribed and translated HK/97 NS1 WT, HK/97 NS1 13 (L103F/I106M/P114S/G125D/N139D) and WI/66 NS1 WT fused to an HA-tag (Figure 9A) and agarose beds conjugated with an anti-FLAG pAb. 2018 Frontiers in microbiology Result IV L103F;I106M;P114S;G125D;N139D;L103F;I106M;P114S;G125D;N139D 49;55;61;67;73;308;314;320;326;332 54;60;66;72;78;313;319;325;331;337 HA;NS1;NS1;NS1;NS1 368;88;286;300;349 370;91;289;303;352 30405591 Identification of Amino Acid Residues Responsible for Inhibition of Host Gene Expression by Influenza A H9N2 NS1 Targeting of CPSF30. To test the individual and combined contribution of these amino acid residues in the inhibition of host protein synthesis, we introduced the amino acid changes D92E, F103L, M106I, A112T, S114P, D125G, and D139N individually or together in WI/66 NS1 (Figure 5A). 2018 Frontiers in microbiology Result IV D92E;F103L;M106I;A112T;S114P;D125G;D139N 160;166;173;180;187;194;205 164;171;178;185;192;199;210 NS1 245 248 30405591 Identification of Amino Acid Residues Responsible for Inhibition of Host Gene Expression by Influenza A H9N2 NS1 Targeting of CPSF30. We identified seven amino acids changes between WI/66 and HK/97 (D92E, F103L, M106I, A112T, S114P, D125G, and D139N) that could be involved in the presence/lack of inhibition of host gene expression between the different H9N2 NS1 proteins (Figure 4, red). 2018 Frontiers in microbiology Result IV D92E;F103L;M106I;A112T;S114P;D125G;D139N 65;71;78;85;92;99;110 69;76;83;90;97;104;115 NS1 226 229 30428893 Analysis of influenza B virus lineages and the HA1 domain of its hemagglutinin gene in Guangzhou, southern China, during 2016. Four of these mutations : I132V, N144D, C196S, and E198D : were in antigenic epitopes. 2018 Virology journal Result IV I132V;N144D;C196S;E198D 26;33;40;51 31;38;45;56 30428893 Analysis of influenza B virus lineages and the HA1 domain of its hemagglutinin gene in Guangzhou, southern China, during 2016. Relative to B/Brisbane/60/2008, there were 12 mutation sites in the HA1 domain in our Victoria isolates: I112M (n = 3), I132V (n = 34), N144D (n = 34), A169T (n = 3), I190M (n = 3), C196S (n = 1), E198D (n = 1), A214T (n = 34), T236I (n = 6), I261L (n = 1), I261F (n = 1), and A291T (n = 2). 2018 Virology journal Result IV I112M;I132V;N144D;A169T;I190M;C196S;E198D;A214T;T236I;I261L;I261F;A291T 105;120;136;152;167;182;197;212;228;243;258;277 110;125;141;157;172;187;202;217;233;248;263;282 HA1 68 71 30428893 Analysis of influenza B virus lineages and the HA1 domain of its hemagglutinin gene in Guangzhou, southern China, during 2016. Relative to B/Phuket/3073/2013, there were 5 mutation sites in the HA1 domain of our Yamagata isolates: T12 M (n = 3), L1871Q (n = 9), K226R (n = 2), N232D (n = 1), and M266 V (n = 9). 2018 Virology journal Result IV T12M;L1871Q;K226R;N232D;M266V 104;119;135;150;169 109;125;140;155;175 HA1 67 70 30428893 Analysis of influenza B virus lineages and the HA1 domain of its hemagglutinin gene in Guangzhou, southern China, during 2016. We also analyzed the NA gene of 20 samples for 4 specific mutations known to confer resistance to NA inhibitors: G109E, R152K, D198N, and G402S (Additional file 4: Table S2). 2018 Virology journal Result IV G109E;R152K;D198N;G402S 113;120;127;138 118;125;132;143 NA;NA 21;98 23;100 30439983 Influenza B viruses circulated during last 5 years in Mongolia. As shown in Fig 5, I114T mutation was found in B/Ulaanbaatar/1113/2014 strain, which might cause reduced susceptibility to peramivir. 2018 PloS one Result IV I114T 19 24 30439983 Influenza B viruses circulated during last 5 years in Mongolia. B/Victoria isolates in 2014 had amino acid substitutions (I146V) in 150-loop whereas isolates in 2016 had double amino acid substitutions (I117V and N129D) in 120-loop as compared to B/Brisbane/60/2008. 2018 PloS one Result IV I146V;I117V;N129D 58;139;149 63;144;154 30439983 Influenza B viruses circulated during last 5 years in Mongolia. B/Yamagata isolates and B/Phuket/3073/2013 strain had same amino acid substitution (N116K) in 120 loop as, compared to B/Wisconsin/01/2010. 2018 PloS one Result IV N116K 84 89 30439983 Influenza B viruses circulated during last 5 years in Mongolia. Besides those, B/Ulaanbaatar/1495/2014 had E105K mutation and B/Ulaanbaatar/1708/2014 had G104R mutation, those also might cause reduced susceptibility to NA inhibitors. 2018 PloS one Result IV E105K;G104R 43;90 48;95 155 157 30439983 Influenza B viruses circulated during last 5 years in Mongolia. G140R mutation was found in B/Khentii/1137/2014 and H101N and E105K mutations were found in B/Darkhan/1484/2014 strain. 2018 PloS one Result IV G140R;H101N;E105K 0;52;62 5;57;67 30439983 Influenza B viruses circulated during last 5 years in Mongolia. The antigenic analysis showed that B/Ulaanbaatar/1913/2016 strain was closer relationship with B/Brisbane/60/2008 than other strains, which might be explained by the amino acid substitution (N197S) in HA protein. 2018 PloS one Result IV N197S 191 196 HA 201 203 30439983 Influenza B viruses circulated during last 5 years in Mongolia. The most represented substitutions were N116K in 120-loop, detected in all 10 B/Yamagata isolates (100%), and I146V in 150-loop was detected in 6 out of 15 (40%) B/Victoria isolates. 2018 PloS one Result IV N116K;I146V 40;110 45;115 30463209 A PB1-K577E Mutation in H9N2 Influenza Virus Increases Polymerase Activity and Pathogenicity in Mice. All mice inoculated with rWT or rHA-N132D survived, although significant body weight losses were observed in the rHA-N132D-inoculated mice compared to those in rWT-inoculated mice. 2018 Viruses Result IV N132D;N132D 36;117 41;122 30463209 A PB1-K577E Mutation in H9N2 Influenza Virus Increases Polymerase Activity and Pathogenicity in Mice. All rHA-N198S/PB1-K577E-inoculated mice died by day 5 post-infection, which is a shorter mean death time than that of rPB1-K577E-infected mice (Figure 1A), suggesting a possible synergic effect between these PB1 and HA mutations on pathogenicity. 2018 Viruses Result IV K577E;N198S;K577E 18;8;123 23;13;128 HA;PB1;PB1 216;14;208 218;17;211 30463209 A PB1-K577E Mutation in H9N2 Influenza Virus Increases Polymerase Activity and Pathogenicity in Mice. Although the virus titers in the lungs of rWT-, rPB1-K577E-, and rPB2-E627K-inoculated mice were similar, those in the nasal turbinates of mutant virus-inoculated mice were significantly higher than that of rWT-inoculated mice. 2018 Viruses Result IV K577E;E627K 53;70 58;75 30463209 A PB1-K577E Mutation in H9N2 Influenza Virus Increases Polymerase Activity and Pathogenicity in Mice. In contrast, half of the mice inoculated with rHA-N198S died by day 8 post-inoculation. 2018 Viruses Result IV N198S 50 55 30463209 A PB1-K577E Mutation in H9N2 Influenza Virus Increases Polymerase Activity and Pathogenicity in Mice. In contrast, the mobilities of untreated rHA-N132D and rHA-N198S HA were faster than that of wild-type HA, indicating that they were missing an oligosaccharide side chain. 2018 Viruses Result IV N132D;N198S 45;59 50;64 HA;HA 65;103 67;105 30463209 A PB1-K577E Mutation in H9N2 Influenza Virus Increases Polymerase Activity and Pathogenicity in Mice. In contrast, those inoculated with rPB1-K577E and rPB2-E627K showed 100% (p < 0.01 vs. 2018 Viruses Result IV K577E;E627K 40;55 45;60 30463209 A PB1-K577E Mutation in H9N2 Influenza Virus Increases Polymerase Activity and Pathogenicity in Mice. In human 293T cells at 37 C, viral polymerase harboring the PB1-K577E mutation showed one log higher activity than WT polymerase, as did the polymerase with the PB2-E627K mutation, which is known to enhance the polymerase activity of avian influenza virus in human cells (Figure 3A). 2018 Viruses Result IV K577E;E627K 65;166 70;171 PB1;PB2 61;162 64;165 30463209 A PB1-K577E Mutation in H9N2 Influenza Virus Increases Polymerase Activity and Pathogenicity in Mice. Interestingly, greater enhancement of polymerase activity was observed at 33 C than at 37 C; 30-times or 300-times higher activity was observed with PB1-K577E or PB2-E627K mutation, respectively, compared to that of the WT polymerase (Figure 3B). 2018 Viruses Result IV K577E;E627K 155;168 160;173 PB1;PB2 151;164 154;167 30463209 A PB1-K577E Mutation in H9N2 Influenza Virus Increases Polymerase Activity and Pathogenicity in Mice. Only one rPB2-E627K-infected mouse recovered after a 20% body weight loss. 2018 Viruses Result IV E627K 14 19 30463209 A PB1-K577E Mutation in H9N2 Influenza Virus Increases Polymerase Activity and Pathogenicity in Mice. Since the growth of the rHA-N132D and rHA-N198S viruses in cell culture was suboptimal, leading to unclear resolution of the assay, we generated viruses bearing HA-N132D or HA-N198S mutation together with the PB2-E627K mutation by reverse genetics (referred as rHA-N132D/PB2-E627K and rHA-N198S/PB2-E627K, respectively). 2018 Viruses Result IV N132D;N198S;N132D;N198S;E627K;E627K;N132D;E627K;N198S 28;42;164;176;213;275;265;299;289 33;47;169;181;218;280;270;304;294 HA;HA;PB2;PB2;PB2 161;173;209;271;295 163;175;212;274;298 30463209 A PB1-K577E Mutation in H9N2 Influenza Virus Increases Polymerase Activity and Pathogenicity in Mice. The HA-N132D and N198S/T mutations found in all MA viruses potentially abolished N-glycosylation sites. 2018 Viruses Result IV N198T;N132D;N198S 17;7;17 24;12;24 HA 4 6 30463209 A PB1-K577E Mutation in H9N2 Influenza Virus Increases Polymerase Activity and Pathogenicity in Mice. The PB2-E627K and PA-T97I mutations found in HK-MA1 and/or HK-MA2 were previously reported as important signatures for mammalian adaptation in other subtypes of avian influenza viruses, whereas the PB1-K577E mutation, which had not been previously reported, was only found in HK-MA3, and in the absence of the PB2-E627K mutation. 2018 Viruses Result IV E627K;T97I;K577E;E627K 8;21;202;314 13;25;207;319 PA;PB1;PB2;PB2 18;198;4;310 20;201;7;313 30463209 A PB1-K577E Mutation in H9N2 Influenza Virus Increases Polymerase Activity and Pathogenicity in Mice. Then, we inoculated these mutants as well as rPB2-E627K, which possesses wild-type HA, into MDCK cells. 2018 Viruses Result IV E627K 50 55 HA 83 85 30463209 A PB1-K577E Mutation in H9N2 Influenza Virus Increases Polymerase Activity and Pathogenicity in Mice. These data demonstrate that the PB1-K577E mutation was robustly responsible for the increased pathogenicity in mice, as was PB2-E627K mutation. 2018 Viruses Result IV K577E;E627K 36;128 41;133 PB1;PB2 32;124 35;127 30463209 A PB1-K577E Mutation in H9N2 Influenza Virus Increases Polymerase Activity and Pathogenicity in Mice. These data demonstrate that, although both HA-N132D and HA-N198S are involved in mouse pathogenicity, the latter had a stronger role than the former. 2018 Viruses Result IV N132D;N198S 46;59 51;64 HA;HA 43;56 45;58 30463209 A PB1-K577E Mutation in H9N2 Influenza Virus Increases Polymerase Activity and Pathogenicity in Mice. These data suggest that both the HA-N132D and HA-N198S mutations led to the loss of an N-glycosylation site. 2018 Viruses Result IV N132D;N198S 36;49 41;54 HA;HA 33;46 35;48 30463209 A PB1-K577E Mutation in H9N2 Influenza Virus Increases Polymerase Activity and Pathogenicity in Mice. These data suggest that the glutamate (E) at position 577 of PB1 is important for viral polymerase activity in mammalian cells, leading to the high growth property of the HK-MA3 virus in mouse. 2018 Viruses Result IV E577E 27 58 PB1 61 64 30463209 A PB1-K577E Mutation in H9N2 Influenza Virus Increases Polymerase Activity and Pathogenicity in Mice. To assess the role of the HA mutations in virus pathogenicity, we next generated two recombinant HK1703 viruses possessing either the HA-N132D or N198S mutation (referred as rHA-N132D or rHA-N198S, respectively). 2018 Viruses Result IV N132D;N198S;N132D;N198S 137;146;178;191 142;151;183;196 HA;HA 26;134 28;136 30463209 A PB1-K577E Mutation in H9N2 Influenza Virus Increases Polymerase Activity and Pathogenicity in Mice. To examine whether the PB1-K577E mutation affects the polymerase activity of the H9N2 virus, we performed a mini-replicon luciferase assay in mammalian and avian cells at 37 C and 33 C, which are the temperatures corresponding to the mammalian lower and upper respiratory tracts, respectively. 2018 Viruses Result IV K577E 27 32 PB1 23 26 30463209 A PB1-K577E Mutation in H9N2 Influenza Virus Increases Polymerase Activity and Pathogenicity in Mice. To identify the mutations responsible for H9N2 virus adaptation to mice, we first generated two recombinant HK1703 viruses, one possessing the PB1-K577E or PB2-E627K mutation, as well as a wild-type virus by reverse genetics (referred as rPB1-K577E, rPB2-E627K, and rWT, respectively). 2018 Viruses Result IV K577E;E627K;K577E;E627K 147;160;243;255 152;165;248;260 PB1;PB2 143;156 146;159 30463209 A PB1-K577E Mutation in H9N2 Influenza Virus Increases Polymerase Activity and Pathogenicity in Mice. We also generated a mutant virus containing both HA-N198S and PB1-K577E (referred as rHA-N198S/PB1-K577E), which has the same genotype as HK-MA3, and tested its pathogenicity (Figure 2A,B). 2018 Viruses Result IV N198S;K577E;K577E;N198S 52;66;99;89 57;71;104;94 HA;PB1;PB1 49;62;95 51;65;98 30463209 A PB1-K577E Mutation in H9N2 Influenza Virus Increases Polymerase Activity and Pathogenicity in Mice. We hypothesized that the HA-N132D and HA-N198S/T mutations found in the MA viruses abolished N-linked glycosylation sites. 2018 Viruses Result IV N198T;N132D;N198S 41;28;41 48;33;48 HA;HA 25;38 27;40 30509291 Conserved methionine 165 of matrix protein contributes to the nuclear import and is essential for influenza A virus replication. All viruses were rescued except M165A mutant, when the M2 protein was not detected in MDCK cells re-infected with medium from transfected cells. 2018 Virology journal Result IV M165A 32 37 M2 55 57 30509291 Conserved methionine 165 of matrix protein contributes to the nuclear import and is essential for influenza A virus replication. Although the co-localization of NP and both M1 and M165A proteins were not disrupted, the migration pattern of M165 and especially NP in the cells transfected with M165A was completely different. 2018 Virology journal Result IV M165A;M165A 51;164 56;169 M1;NP;NP 44;32;131 46;34;133 30509291 Conserved methionine 165 of matrix protein contributes to the nuclear import and is essential for influenza A virus replication. Association of M165A protein with CRM1 around the nucleus. 2018 Virology journal Result IV M165A 15 20 30509291 Conserved methionine 165 of matrix protein contributes to the nuclear import and is essential for influenza A virus replication. Compare to M1, the amount of M165A protein was significantly reduced in the nuclei (p < 0.05). 2018 Virology journal Result IV M165A 29 34 M1 11 13 30509291 Conserved methionine 165 of matrix protein contributes to the nuclear import and is essential for influenza A virus replication. In M165A transfected cells, transport into the nucleus was impaired and CLUH was co-localized with M165 in the cytoplasm and around the nucleus. 2018 Virology journal Result IV M165A 3 8 30509291 Conserved methionine 165 of matrix protein contributes to the nuclear import and is essential for influenza A virus replication. M1 and M165A were observed in the cytoplasm and nucleus. 2018 Virology journal Result IV M165A 7 12 M1 0 2 30509291 Conserved methionine 165 of matrix protein contributes to the nuclear import and is essential for influenza A virus replication. M165A blocked transport of NP into the nucleus. 2018 Virology journal Result IV M165A 0 5 NP 27 29 30509291 Conserved methionine 165 of matrix protein contributes to the nuclear import and is essential for influenza A virus replication. M165A influences CLUH translocation to the nucleoplasm. 2018 Virology journal Result IV M165A 0 5 30509291 Conserved methionine 165 of matrix protein contributes to the nuclear import and is essential for influenza A virus replication. M165A is associated with the plasma membrane. 2018 Virology journal Result IV M165A 0 5 30509291 Conserved methionine 165 of matrix protein contributes to the nuclear import and is essential for influenza A virus replication. M165A protein was broadly co-localized with plasma membrane. 2018 Virology journal Result IV M165A 0 5 30509291 Conserved methionine 165 of matrix protein contributes to the nuclear import and is essential for influenza A virus replication. Mutation M165A did not interrupt M1 association with the host cellular membrane. 2018 Virology journal Result IV M165A 9 14 M1 33 35 30509291 Conserved methionine 165 of matrix protein contributes to the nuclear import and is essential for influenza A virus replication. Mutation M165A resulted in blockage of NP and M1 transport into the nucleus. 2018 Virology journal Result IV M165A 9 14 M1;NP 46;39 48;41 30509291 Conserved methionine 165 of matrix protein contributes to the nuclear import and is essential for influenza A virus replication. On the other hand, NP expressed in the cells transfected with M165A was co-localized with M165A protein in the cytoplasm and around the nucleus. 2018 Virology journal Result IV M165A;M165A 62;90 67;95 NP 19 21 30509291 Conserved methionine 165 of matrix protein contributes to the nuclear import and is essential for influenza A virus replication. Since anti-M1 antibody did not work in western blot, we used anti-M2 polyclonal serum to compare expression of M2 protein after transfection with M1 (control virus - VC), R163A, Q164A, M165A, and V166A plasmids. 2018 Virology journal Result IV R163A;Q164A;M165A;V166A 171;178;185;196 176;183;190;201 M1;M1;M2;M2 11;146;66;111 13;148;68;113 30509291 Conserved methionine 165 of matrix protein contributes to the nuclear import and is essential for influenza A virus replication. Subcellular localization of NP protein was examined in the cells transfected with both M1 and M165A proteins. 2018 Virology journal Result IV M165A 94 99 M1;NP 87;28 89;30 30509291 Conserved methionine 165 of matrix protein contributes to the nuclear import and is essential for influenza A virus replication. The lack of M165A virus replication in re-infected MDCK cells was confirmed by RT-PCR. 2018 Virology journal Result IV M165A 12 17 30509291 Conserved methionine 165 of matrix protein contributes to the nuclear import and is essential for influenza A virus replication. The quantification analyses showed that the nuclear signal of NP protein in the cells transfected with M1 is significantly lower (p < 0.01) in comparison with NP in the cells transfected with M165A. 2018 Virology journal Result IV M165A 192 197 M1;NP;NP 103;62;159 105;64;161 30509291 Conserved methionine 165 of matrix protein contributes to the nuclear import and is essential for influenza A virus replication. The viral RNA was detected only in the MDCK cells re-infected with supernatant from VC, R163A, Q164A, and V166A mutants. 2018 Virology journal Result IV R163A;Q164A;V166A 88;95;106 93;100;111 30509291 Conserved methionine 165 of matrix protein contributes to the nuclear import and is essential for influenza A virus replication. There were differences in the proportion of M1 and M165A mutated protein in the nuclei of transfected cells. 2018 Virology journal Result IV M165A 51 56 M1 44 46 30509291 Conserved methionine 165 of matrix protein contributes to the nuclear import and is essential for influenza A virus replication. There were no obvious differences among control wild type virus (VC) prepared by reverse genetic system and R163A, Q164A and V166A mutant viruses in the growth curves. 2018 Virology journal Result IV R163A;Q164A;V166A 108;115;125 113;120;130 30509291 Conserved methionine 165 of matrix protein contributes to the nuclear import and is essential for influenza A virus replication. To determine co-localization M165A and CLUH, co-cultured 293 T and MDCK cells were transfected with eight plasmids for reverse genetic system where M1 was replaced by M165A mutant and CLUH localization was analysed. 2018 Virology journal Result IV M165A;M165A 29;167 34;172 M1 148 150 30509291 Conserved methionine 165 of matrix protein contributes to the nuclear import and is essential for influenza A virus replication. To determine whether M165A mutation change the M1 presence at the plasma membrane, the co-cultured 293 T and MDCK cells were transfected as described above and plasma membrane were labelled with the anti-sodium potassium ATPase antibody. 2018 Virology journal Result IV M165A 21 26 M1 47 49 30509291 Conserved methionine 165 of matrix protein contributes to the nuclear import and is essential for influenza A virus replication. To understand the role of M165 in virus replication, we examined the effect of M165A mutation on the transport of M1 and NP in transfected cells. 2018 Virology journal Result IV M165A 79 84 M1;NP 114;121 116;123 30509291 Conserved methionine 165 of matrix protein contributes to the nuclear import and is essential for influenza A virus replication. Transfection with M1 and M165A resulted in increased amount of the CRM1 protein in the nucleus. 2018 Virology journal Result IV M165A 25 30 M1 18 20 30509291 Conserved methionine 165 of matrix protein contributes to the nuclear import and is essential for influenza A virus replication. Unlike M1 protein co-localized with CRM1 protein in the nucleus, M165A protein was co-localized with CRM1 protein on the cytoplasmic face of the nuclear membrane. 2018 Virology journal Result IV M165A 65 70 M1 7 9 30518648 HDAC6 Restricts Influenza A Virus by Deacetylation of the RNA Polymerase PA Subunit. Based on the results, we generated PA mutants that carried one substitution with Arg at Lys(281), Lys(497), Lys(643), and Lys(664), along with a Flag tag. 2019 Journal of virology Result IV R281K 81 96 PA 35 37 30518648 HDAC6 Restricts Influenza A Virus by Deacetylation of the RNA Polymerase PA Subunit. In contrast, the level of acetylation of one PA mutant (K664R, referred to here as PA K664R) was dramatically decreased. 2019 Journal of virology Result IV K664R;K664R 56;86 61;91 PA;PA 45;83 47;85 30518648 HDAC6 Restricts Influenza A Virus by Deacetylation of the RNA Polymerase PA Subunit. Three PA mutants that carried Arg substitutions (K281R, K497R, and K643R) were found to still be acetylated. 2019 Journal of virology Result IV K281R;K497R;K643R 49;56;67 54;61;72 PA 6 8 30518648 HDAC6 Restricts Influenza A Virus by Deacetylation of the RNA Polymerase PA Subunit. To address this, Flag-PA (PA-WT [wild type]), an acetylation mimic PA mutant (PA K664Q), and an acetylation dead PA mutant (PA K664R) were expressed in 293T cells with or without tubacin treatment. 2019 Journal of virology Result IV K664Q;K664R 81;127 86;132 PA;PA;PA;PA;PA;PA 22;26;67;78;113;124 24;28;69;80;115;126 30533399 Potential Pandemic of H7N9 Avian Influenza A Virus in Human. A trend for fixation occurred in the 5th wave in 17 sites: A118T, S123N, R136K, A131V, L173I, and M232I in HA1 (H5 numbering); E383A, V426I, and S486R in HA2 (H5 numbering); I16T, S247P, and N327S in NA (N9 numbering); N394D in PA (N9 numbering); E24D in M2 (N9 numbering); and K191E, N559T and A588V in PB2 (N9 numbering) (Figure 3). 2018 Frontiers in cellular and infection microbiology Result IV A118T;S123N;R136K;A131V;L173I;M232I;E383A;V426I;S486R;I16T;S247P;N327S;N394D;E24D;K191E;N559T;A588V 59;66;73;80;87;98;127;134;145;174;180;191;219;247;278;285;295 64;71;78;85;92;103;132;139;150;178;185;196;224;251;283;290;300 HA;HA1;M2;N9;N9;N9;N9;NA;PA;PB2 154;107;255;204;232;259;309;200;228;304 156;110;257;206;234;261;311;202;230;307 30533399 Potential Pandemic of H7N9 Avian Influenza A Virus in Human. Amino acid change N327S was first identified in the 2nd wave at a proportion of 9.90%. 2018 Frontiers in cellular and infection microbiology Result IV N327S 18 23 30533399 Potential Pandemic of H7N9 Avian Influenza A Virus in Human. Amino acid changes R136K in HA1, V426I in HA2, N394D in PA, and A588V in PB2 showed much higher proportions in human-isolated than avian-isolated H7N9 in the 5th wave. 2018 Frontiers in cellular and infection microbiology Result IV R136K;V426I;N394D;A588V 19;33;47;64 24;38;52;69 HA;HA1;PA;PB2 42;28;56;73 44;31;58;76 30533399 Potential Pandemic of H7N9 Avian Influenza A Virus in Human. Amino acid changes S155N, T156A, G182V, S205Y, and Q222L (H5 numbering) in HA had very high proportions in both human- and avian-isolated H7N9 (Figure 1A). 2018 Frontiers in cellular and infection microbiology Result IV S155N;T156A;G182V;S205Y;Q222L 19;26;33;40;51 24;31;38;45;56 HA 75 77 30533399 Potential Pandemic of H7N9 Avian Influenza A Virus in Human. E/D627K/N and D701N in PB2 had much higher proportions in human-isolated than avian-isolated H7N9 in all 5 waves (Figure 2). 2018 Frontiers in cellular and infection microbiology Result IV E627K;E627N;D627K;D627N;D701N 0;0;0;0;14 9;9;9;9;19 PB2 23 26 30533399 Potential Pandemic of H7N9 Avian Influenza A Virus in Human. In comparison, one in three sequences (33.33%) of H9N2 has amino acid change E/D627K/N in wave 4, and one in four sequences (25%) have change D701N in wave 3. 2018 Frontiers in cellular and infection microbiology Result IV E627K;E627N;D627K;D627N;D701N 77;77;77;77;142 86;86;86;86;147 30533399 Potential Pandemic of H7N9 Avian Influenza A Virus in Human. In comparisons of H7N9 and H9N2, the former has high proportions of the amino acid changes V100A in PA and K526R, E/D627K/N, and D701N in PB2. 2018 Frontiers in cellular and infection microbiology Result IV V100A;K526R;E627K;E627N;D627K;D627N;D701N 91;107;114;114;114;114;129 96;112;123;123;123;123;134 PA;PB2 100;138 102;141 30533399 Potential Pandemic of H7N9 Avian Influenza A Virus in Human. In HA2, the proportions for the amino acid changes E383A and S486R rose from the 2nd wave to the 5th wave, and V426I started to increase starting with the 4th wave. 2018 Frontiers in cellular and infection microbiology Result IV E383A;S486R;V426I 51;61;111 56;66;116 HA 3 5 30533399 Potential Pandemic of H7N9 Avian Influenza A Virus in Human. In waves 1-4, Q222L in HA and K526R in PB2 had high proportions in both human- and avian-isolated H7N9. 2018 Frontiers in cellular and infection microbiology Result IV Q222L;K526R 14;30 19;35 HA;PB2 23;39 25;42 30533399 Potential Pandemic of H7N9 Avian Influenza A Virus in Human. Substitutions I16T and S247P in NA had very low proportions in the 1st wave with (6.54 and 0.38%, respectively), but then their proportions increased quickly reaching 100 and 97.43%, respectively, by the 5th wave. 2018 Frontiers in cellular and infection microbiology Result IV I16T;S247P 14;23 18;28 32 34 30533399 Potential Pandemic of H7N9 Avian Influenza A Virus in Human. Substitutions S123N and R136K began in the 2nd wave, and continued to increase in proportion in subsequent waves. 2018 Frontiers in cellular and infection microbiology Result IV S123N;R136K 14;24 19;29 30533399 Potential Pandemic of H7N9 Avian Influenza A Virus in Human. The substitution ratios of A118T and M232I increased from zero in the first three waves to 50% (A138T) and 67% (M232I) in the 4th wave and then 76% (A138T) and 85% (M232I) in the 5th wave. 2018 Frontiers in cellular and infection microbiology Result IV A118T;M232I;A138T;M232I;A138T;M232I 27;37;96;112;149;165 32;42;101;117;154;170 30533399 Potential Pandemic of H7N9 Avian Influenza A Virus in Human. These were also found to have very high proportions in both human- and avian-isolated H7N9 (Supplementary Table 2) as follows: three amino acids in HA (I116M, N154D, I198V, Figure 1A); four in NA (M26I, R143K, T223I, N390K, Figure 1B); 10 in PB2 (T63I, L89V, K251R, G309D, T339K, Q368R, H447Q, I471T, R477G, I495V, Figure 2); 11 in PB1 (A3V, L13P, R207K, K328N, I368V, S375N/T, H436Y, A469T, L473V, V652A, M677T, Supplementary Figure 1); nine in PA (V135A, H266R, F277S, C278Q, K356R, N383D, S409N, S/A515T, L653P, Supplementary Figure 2); five in MP (V15I/T, N30D, T215A, S31N, L55F, Supplementary Figure 3a); and six in NS (A/P42S, F103L, M106I, V149A, N200S, T47A, Supplementary Figure 3b); and four in NP (V41I, D210E, F253I, I353V, Supplementary Figure 3c). 2018 Frontiers in cellular and infection microbiology Result IV A3V;S515T;A42S;I116M;N154D;I198V;M26I;R143K;T223I;N390K;T63I;L89V;K251R;G309D;T339K;Q368R;H447Q;I471T;R477G;I495V;L13P;R207K;K328N;I368V;S375N;S375T;H436Y;A469T;L473V;V652A;M677T;V135A;H266R;F277S;C278Q;K356R;N383D;S409N;A515T;L653P;V15I;V15T;N30D;T215A;S31N;L55F;P42S;F103L;M106I;V149A;N200S;T47A;V41I;D210E;F253I;I353V 337;499;626;152;159;166;197;203;210;217;247;253;259;266;273;280;287;294;301;308;342;348;355;362;369;369;378;385;392;399;406;450;457;464;471;478;485;492;499;508;552;552;560;566;573;579;626;634;641;648;655;662;710;716;723;730 340;506;632;157;164;171;201;208;215;222;251;257;264;271;278;285;292;299;306;313;346;353;360;367;376;376;383;390;397;404;411;455;462;469;476;483;490;497;506;513;558;558;564;571;577;583;632;639;646;653;660;666;714;721;728;735 HA;NA;NP;NS;PA;PB1;PB2 148;193;706;622;446;332;242 150;195;708;624;448;335;245 30548432 Consecutive influenza surveillance of neuraminidase mutations and neuraminidase inhibitor resistance in Japan. D199N in A/H1N1pdm09, D151E, K249E, G320E, and S331R in A/H3N2, and I262T in B were extracted as RI/HRI-related AA mutations, based on their related references6, 24, 25, 26; however, no virus harboring these AA mutations showed substantial RI/HRI based on their IC50 values. 2019 Influenza and other respiratory viruses Result IV D199N;D151E;K249E;G320E;S331R;I262T 0;22;29;36;47;68 5;27;34;41;52;73 30548432 Consecutive influenza surveillance of neuraminidase mutations and neuraminidase inhibitor resistance in Japan. Most (10/13 mutations) of the AA mutations detected in the catalytic sites of A/H3N2 viruses were D151G/N mutations, which were found to be induced by an MDCK cultivation.21, 22 T148I in the non-catalytic sites was also reported to be associated with an MDCK passage.23 These AA mutations were not detected in any of unpassaged clinical samples.22 Finally, few AA mutations (3/4769, 0.06%, referred to Table 2) in the catalytic sites of A/H3N2 viruses occurred without their D151G/N mutations. 2019 Influenza and other respiratory viruses Result IV D151G;D151N;T148I;D151G;D151N 98;98;178;475;475 105;105;183;482;482 30548432 Consecutive influenza surveillance of neuraminidase mutations and neuraminidase inhibitor resistance in Japan. With regard to the substantial RI/HRI-related AA mutations detected in this study, four A/H1N1pdm09 viruses displaying HRI by oseltamivir and RI by peramivir contained H275Y mutations. 2019 Influenza and other respiratory viruses Result IV H275Y 168 173 30574137 Susceptibility of Influenza Viruses to the Novel Cap-Dependent Endonuclease Inhibitor Baloxavir Marboxil. Antiviral Susceptibilities of a Reference Influenza A Virus With a PA I38T Substitution. 2018 Frontiers in microbiology Result IV I38T 70 74 PA 67 69 30574137 Susceptibility of Influenza Viruses to the Novel Cap-Dependent Endonuclease Inhibitor Baloxavir Marboxil. Both the A/PR/8/34-PA/I38T mutant and the wild-type virus showed normal inhibition with all four NA inhibitors tested, whereas the A/PR/8/34-PA/I38T mutant virus exhibited 54- and 44-fold higher IC50 values to baloxavir in the plaque reduction and the focus reduction assay, respectively, compared with the wild-type virus, consistent with previous studies. 2018 Frontiers in microbiology Result IV I38T;I38T 22;144 26;148 NA;PA;PA 97;19;141 99;21;143 30574137 Susceptibility of Influenza Viruses to the Novel Cap-Dependent Endonuclease Inhibitor Baloxavir Marboxil. The influenza A(H1N1)pdm09-NA/H275Y, A(H3N2)-NA/E119V or -NA/R292K, and influenza B-NA/D197E mutant viruses exhibited HRI or RI against at least one of the four NA inhibitors, whereas no significant differences in baloxavir susceptibilities were found between the NA inhibitor-resistant and wild-type viruses by using either assay (Table 2); however, influenza B viruses showed higher IC50 values than influenza A viruses, as previously reported. 2018 Frontiers in microbiology Result IV H275Y;E119V;R292K;D197E 30;48;61;87 35;53;66;92 NA;NA;NA;NA;NA;NA 27;45;58;84;161;264 29;47;60;86;163;266 30574137 Susceptibility of Influenza Viruses to the Novel Cap-Dependent Endonuclease Inhibitor Baloxavir Marboxil. To examine whether the susceptibility of influenza viruses to baloxavir could be evaluated by using our cell-based screening systems (i.e., conventional plaque reduction and focus reduction assays), we conducted these assays using a reference influenza A(H1N1) virus with the PA I38T substitution that confers reduced susceptibility to baloxavir. 2018 Frontiers in microbiology Result IV I38T 279 283 PA 276 278 30619194 Influenza A Virus NS1 Protein Suppresses JNK1-Dependent Autophagosome Formation Mediated by Rab11a Recycling Endosomes. In agreement with previous reports, LC3 puncta were hardly colocalized with GFP-LAMP2, a lysosomal marker, in amantadine sensitive M2-N31S delNS1-infected cells (Figure 1G). 2018 Frontiers in microbiology Result IV N31S 134 138 M2 131 133 30619194 Influenza A Virus NS1 Protein Suppresses JNK1-Dependent Autophagosome Formation Mediated by Rab11a Recycling Endosomes. In contrast to wild-type virus, LC3 puncta were formed in R38AK41A- and Y89F-infected cells (Figures 2A-D). 2018 Frontiers in microbiology Result IV Y89F 72 76 30619194 Influenza A Virus NS1 Protein Suppresses JNK1-Dependent Autophagosome Formation Mediated by Rab11a Recycling Endosomes. In contrast, by adding 50 muM amantadine, a potent inhibitor of M2 ion channel activity, LAMP2 was colocalized with autophagosomes in M2-N31S delNS1-infected cells (Figures 1G,H). 2018 Frontiers in microbiology Result IV N31S 137 141 M2;M2 64;134 66;136 30619194 Influenza A Virus NS1 Protein Suppresses JNK1-Dependent Autophagosome Formation Mediated by Rab11a Recycling Endosomes. The LC3 lipidation was induced by wild-type-infected cells as previously reported, and the extent was not up-regulated in R38AK41A and Y89F-infected cells (Figure 2E). 2018 Frontiers in microbiology Result IV Y89F 135 139 30619194 Influenza A Virus NS1 Protein Suppresses JNK1-Dependent Autophagosome Formation Mediated by Rab11a Recycling Endosomes. To address the molecular mechanism of autophagy inhibition by NS1, HeLa cells (Figures 2A,B) and A549 cells (Figures 2C,D) were infected with either R38AK41A mutant deficient in the dsRNA-binding activity or Y89F mutant deficient in the stimulatory activity of class I PI3K, and then cells were subjected to indirect immunofluorescence assays with anti-LC3 antibody at 10 h post-infection. 2018 Frontiers in microbiology Result IV Y89F 208 212 NS1 62 65 30619194 Influenza A Virus NS1 Protein Suppresses JNK1-Dependent Autophagosome Formation Mediated by Rab11a Recycling Endosomes. We found that the amount of phosphorylated TSC2 increased in wild type-infected cells (Figure 2F, lane 2) but not in Y89F-infected cells (Figure 2F, lane 4) at 4 h post-infection. 2018 Frontiers in microbiology Result IV Y89F 117 121 30621708 Multiple amino acid substitutions involved in the adaption of three avian-origin H7N9 influenza viruses in mice. Moreover, E627K substitution in PB2 protein was the common substitution of the three mouse-adapted H7N9 viruses and PA T97I substitution was shared by H7N9-53 MA H7N9-ZSM MA. 2019 Virology journal Result IV E627K;T97I 10;119 15;123 PA;PB2 116;32 118;35 30640922 Molecular characterization of influenza A(H1N1)pdm09 in Cameroon during the 2014-2016 influenza seasons. None of the strains possessed the H275Y mutation that has been reported clinically to cause highly reduced inhibition to NAIs. 2019 PloS one Result IV H275Y 34 39 NAI 121 125 30640922 Molecular characterization of influenza A(H1N1)pdm09 in Cameroon during the 2014-2016 influenza seasons. The 2014 virus strains differed from the vaccine strain, by possessing 3 amino acid substitutions: K142R (antigenic site Ca), V234I and I286L. 2019 PloS one Result IV K142R;V234I;I286L 99;126;136 104;131;141 30640922 Molecular characterization of influenza A(H1N1)pdm09 in Cameroon during the 2014-2016 influenza seasons. The amino acid substitution S31N is the predominant amantadine-resistant M2 mutant and was found to be present in almost all of the circulating influenza A(H1N1)pdm09 strains except the two strains collected in 2014. 2019 PloS one Result IV S31N 28 32 M2 73 75 30640922 Molecular characterization of influenza A(H1N1)pdm09 in Cameroon during the 2014-2016 influenza seasons. We however noted some mutations in the NA gene following the results from FluSurver analyses, notably: I117M (84.2%), N248D (94.7%), and N369K (94.7%). 2019 PloS one Result IV I117M;N248D;N369K 103;118;137 108;123;142 39 41 30640922 Molecular characterization of influenza A(H1N1)pdm09 in Cameroon during the 2014-2016 influenza seasons. Whereas, 2015 and 2016 Cameroon strains differed from the vaccine strain by possessing the substitutions K163Q (antigenic site Sa) and A256T. 2019 PloS one Result IV K163Q;A256T 105;135 110;140 30733797 In silico thermodynamic stability of mammalian adaptation and virulence determinants in polymerase complex proteins of H9N2 virus. 391E, K318R, A661T, I504V and K526R were recognized in all viruses under study (Table 3). 2018 Journal, genetic engineering & biotechnology Result IV K318R;A661T;I504V;K526R 6;13;20;30 11;18;25;35 30733797 In silico thermodynamic stability of mammalian adaptation and virulence determinants in polymerase complex proteins of H9N2 virus. Additional substitutions that have been described to affect virulence in avian and/or mammalian hosts were found in PA encoding sequences are shown in (Table 2, Table 3); all Egyptian viruses under study show G186S. 2018 Journal, genetic engineering & biotechnology Result IV G186S 209 214 PA 116 118 30733797 In silico thermodynamic stability of mammalian adaptation and virulence determinants in polymerase complex proteins of H9N2 virus. Amino acid substitutions V127, L672, L550 and S409N residues were observed in all Egyptian LPAI-LPAI-H9N2 viruses. 2018 Journal, genetic engineering & biotechnology Result IV S409N 46 51 30733797 In silico thermodynamic stability of mammalian adaptation and virulence determinants in polymerase complex proteins of H9N2 virus. Despite that, the free-energy analysis of the substitutions (PB2-318, T661, and PA-S409N) suggested a destabilizing effect; the Predicting stability with i-Mutant2.0 SEQsuggesting stabilizing effect. 2018 Journal, genetic engineering & biotechnology Result IV S409N 83 88 PA;PB2 80;61 82;64 30733797 In silico thermodynamic stability of mammalian adaptation and virulence determinants in polymerase complex proteins of H9N2 virus. Like PB2; the nucleotide and amino acid similarity among Egyptian viruses to each other, Israel viruses, Middle East viruses and G1virus shown (Table 1), All Egyptian viruses under study had Isoleucine at position 317, L13P, V14A, and A473V. 2018 Journal, genetic engineering & biotechnology Result IV L13P;V14A;A473V 219;225;235 223;229;240 PB2 5 8 30733797 In silico thermodynamic stability of mammalian adaptation and virulence determinants in polymerase complex proteins of H9N2 virus. Six substitutions recorded in some viruses under study (K176R, I181V, R350K, R386K, E398D and S515P) which first recorded in Egyptian LPAI-H9N2 viruses. 2018 Journal, genetic engineering & biotechnology Result IV K176R;I181V;R350K;R386K;E398D;S515P 56;63;70;77;84;94 61;68;75;82;89;99 30733797 In silico thermodynamic stability of mammalian adaptation and virulence determinants in polymerase complex proteins of H9N2 virus. The Free-energy analysis revealed that out of the eighteen selected substitutions which known to affect the ability of virus replication and/or the pathogenicity, six mutations (PB1-F2 L82, PB2-K318R, and A661 and PA-S225, I400S, S409N) have a structural stabilizing effect on polymerase complex protein. 2018 Journal, genetic engineering & biotechnology Result IV K318R;I400S;S409N 194;223;230 199;228;235 PA;PB1F2;PB2 214;178;190 216;184;193 30733797 In silico thermodynamic stability of mammalian adaptation and virulence determinants in polymerase complex proteins of H9N2 virus. The PB1-F2 encoded a full-length protein of 90 AA and showing the substitutions N66S and L82S in all Egyptian LPAI-LPAI-H9N2 viruses, while the substitution T68I was not present, further mutations were described to foster replication in mammals and influence virulence was mentioned in (Table 2). 2018 Journal, genetic engineering & biotechnology Result IV N66S;L82S;T68I 80;89;157 84;93;161 PB1F2 4 10 30792414 Molecular evolution of influenza B virus during 2011-2017 in Chaoyang, Beijing, suggesting the free influenza vaccine policy. A portion of Victoria-lineage from 2011-2012 season was related to strain B/Brisbane/60/2008 and classified to clade 1B which had amino acids substitutions at L58P (8/8, 100%). 2019 Scientific reports Result IV L58P 159 163 30792414 Molecular evolution of influenza B virus during 2011-2017 in Chaoyang, Beijing, suggesting the free influenza vaccine policy. Aligned HA1 of Yamagata-lineage to reference influenza B vaccine strain (B/Massachusetts/2/2012), only N116K substitutions were found in 2013-2015 seasons was on the 120 loop. 2019 Scientific reports Result IV N116K 103 108 HA1 8 11 30792414 Molecular evolution of influenza B virus during 2011-2017 in Chaoyang, Beijing, suggesting the free influenza vaccine policy. All Victoria-lineage virus in 2011-2012 surveillance season shared amino acids substitutions at I146V (21/21), whereas Victoria-lineage virus in 2015-2017 surveillance seasons shared amino acids substitutions at I117V (23/29, 79.31%), N129D (29/29, 100%). 2019 Scientific reports Result IV I146V;I117V;N129D 96;212;235 101;217;240 30792414 Molecular evolution of influenza B virus during 2011-2017 in Chaoyang, Beijing, suggesting the free influenza vaccine policy. Comparing to strain B/Brisbane/60/2008, S41P, P42S substitutions in NA protein were showed in Victoria-lineage of 2011-2012 season, then strains of 2015-2017 seasons showed special amino acids substitutions I45T, I120V, D384G in NA protein. 2019 Scientific reports Result IV S41P;P42S;I45T;I120V;D384G 40;46;207;213;220 44;50;211;218;225 NA;NA 68;229 70;231 30792414 Molecular evolution of influenza B virus during 2011-2017 in Chaoyang, Beijing, suggesting the free influenza vaccine policy. Comparing to vaccine strain B/Wisconsin/1/2010, a series of amino acid changes were observed in the HA1 region of all strains: N116K, K299E and E313K. 2019 Scientific reports Result IV N116K;K299E;E313K 127;134;144 132;139;149 HA1 100 103 30792414 Molecular evolution of influenza B virus during 2011-2017 in Chaoyang, Beijing, suggesting the free influenza vaccine policy. The N129S and I146V substitutions were specially identified in 120 loop and 150 loop of HA1 region of Victoria-lineage in 2011-2012 surveillance season. 2019 Scientific reports Result IV N129S;I146V 4;14 9;19 HA1 88 91 30792414 Molecular evolution of influenza B virus during 2011-2017 in Chaoyang, Beijing, suggesting the free influenza vaccine policy. The Yamagata-lineage in 2011-2014 surveillance seasons shared special amino acids substitutions at R278K (9/33, 27.27%) (Tables 1, 2), whereas the Yamagata-lineage in 2014-2017 surveillance seasons shared amino acids substitutions at L172Q (34/34, 100%), K211R (8/34, 23.53%), M251V (26/34, 76.47%), which were related to B/Phuket/3073/2013 strain. 2019 Scientific reports Result IV R278K;L172Q;K211R;M251V 99;234;255;277 104;239;260;282 30792414 Molecular evolution of influenza B virus during 2011-2017 in Chaoyang, Beijing, suggesting the free influenza vaccine policy. The Yamagata-lineage was the prevail lineage in 2014-2015 season and amino acids substitutions I45V, A62T, L73P of NA protein showed in most strains comparing to strain B/Wisconsin/1/2010 (Tables 1, 2). 2019 Scientific reports Result IV I45V;A62T;L73P 95;101;107 99;105;111 115 117 30792414 Molecular evolution of influenza B virus during 2011-2017 in Chaoyang, Beijing, suggesting the free influenza vaccine policy. Whereas, I117V and N129D substitutions were characteristically showed in 120 loop of HA1 region of Victoria-lineage in 2015-2017 surveillance seasons (Table 3). 2019 Scientific reports Result IV I117V;N129D 9;19 14;24 HA1 85 88 30899824 Evolved avian influenza virus (H7N9) isolated from human cases in a middle Yangtze River city in China, from February to April 2017. A number of H7N9 viruses had acquired Arg292Lys substitution associated with oseltamivir-resistance in NA gene until April 2017. 2019 Heliyon Result IV R292K 38 47 103 105 30899824 Evolved avian influenza virus (H7N9) isolated from human cases in a middle Yangtze River city in China, from February to April 2017. Amantadine resistance was evident and the resistance-conferring mutation was identified as Ser31Asn in the M2 gene (Table 3). 2019 Heliyon Result IV S31N 91 99 M2 107 109 30899824 Evolved avian influenza virus (H7N9) isolated from human cases in a middle Yangtze River city in China, from February to April 2017. Another crucial mutant, a PB2 Asp701Asn substitution, was associated with increased viral polymerase activity, and was also present in A/changsha/26/2017 and A/changsha/58/2017. 2019 Heliyon Result IV D701N 30 39 PB2 26 29 30899824 Evolved avian influenza virus (H7N9) isolated from human cases in a middle Yangtze River city in China, from February to April 2017. But Arg292Lys substitution was not observed, and antivirals including oseltamivir were still administrated to all patients with H7N9 infections in our research. 2019 Heliyon Result IV R292K 4 13 Influenza A virus H7N9 infection 128 143 30899824 Evolved avian influenza virus (H7N9) isolated from human cases in a middle Yangtze River city in China, from February to April 2017. H7N9 viruses are incapable of transmitting between humans because of the absence of substitutions in the HA segment, including Asn158Asp, Asn224Lys, Gly228Ser, and Thr318Ile. 2019 Heliyon Result IV N158D;N224K;G228S;T318I 127;138;149;164 136;147;158;173 HA 105 107 30899824 Evolved avian influenza virus (H7N9) isolated from human cases in a middle Yangtze River city in China, from February to April 2017. Importantly, the PB2 gene Ala588Val and both Ala588Val/Glu627Lys mutations in the H7N9 virus have been demonstrated to enhance virulence in mice and the transmission of influenza viruses in mammals. 2019 Heliyon Result IV E627K;A588V;A588V;A588E;A588K 55;26;45;45;45 64;35;54;54;54 PB2 17 20 30899824 Evolved avian influenza virus (H7N9) isolated from human cases in a middle Yangtze River city in China, from February to April 2017. In addition, two of the strains, A/changsha/34/2017 and A/changsha/72/2017, acquired both Ala588Val/Glu627Lys mutations. 2019 Heliyon Result IV E627K;A588V;A588E;A588K 100;90;90;90 109;99;99;99 30899824 Evolved avian influenza virus (H7N9) isolated from human cases in a middle Yangtze River city in China, from February to April 2017. In changsha city, PB2 Ala588Val mutation site was presented in five of the isolates and K526R mutation site was presented in one of the isolates in this wave. 2019 Heliyon Result IV A588V;K526R 22;88 31;93 PB2 18 21 30899824 Evolved avian influenza virus (H7N9) isolated from human cases in a middle Yangtze River city in China, from February to April 2017. Substitutions of other segments, including Asn30Asp and Thr215Ala in M1, Pro42Ser in NS1, and Ile368Val in PB1, which increase virulence in mouse models, were observed in key functional loci of the isolates from the fifth H7N9 wave in our preliminary analyses. 2019 Heliyon Result IV N30D;T215A;P42S;I368V 43;56;73;94 51;65;81;103 M1;NS1;PB1 69;85;107 71;88;110 30899824 Evolved avian influenza virus (H7N9) isolated from human cases in a middle Yangtze River city in China, from February to April 2017. The Thr160Ala, Gly186Val, and Gln226Leu mutations in the HA segment, which are associated with the relative binding affinity between hemagglutinin and the sialic acid receptor on the host cell surface, and which prefer the alpha-2,6 sialic acid receptor, have been found in H7N9 strains in our research. 2019 Heliyon Result IV T160A;G186V;Q226L 4;15;30 13;24;39 HA;HA 57;133 59;146 30899824 Evolved avian influenza virus (H7N9) isolated from human cases in a middle Yangtze River city in China, from February to April 2017. We also found that the proportion of Ala588Val substitution in human infection cases was increasing from 2013 to 2017 years (Table 2). 2019 Heliyon Result IV A588V 37 46 30909490 The PB2 Polymerase Host Adaptation Substitutions Prime Avian Indonesia Sub Clade 2.1 H5N1 Viruses for Infecting Humans. Acquisition of the E627K substitution in PB2 following infection in humans or other mammalian hosts has been observed for avian H5N1, H7N7 and H7N9 viruses. 2019 Viruses Result IV E627K 19 24 PB2 41 44 30909490 The PB2 Polymerase Host Adaptation Substitutions Prime Avian Indonesia Sub Clade 2.1 H5N1 Viruses for Infecting Humans. Adaptation of E627K in PB2 was found to facilitate virus replication at a lower temperature in the upper respiratory tract. 2019 Viruses Result IV E627K 14 19 PB2 23 26 30909490 The PB2 Polymerase Host Adaptation Substitutions Prime Avian Indonesia Sub Clade 2.1 H5N1 Viruses for Infecting Humans. An adaptive E627K substitution in PB2 was found to enhance PB2 interaction with NP in the RNP complex. 2019 Viruses Result IV E627K 12 17 NP;PB2;PB2;RNP 80;34;59;90 82;37;62;93 30909490 The PB2 Polymerase Host Adaptation Substitutions Prime Avian Indonesia Sub Clade 2.1 H5N1 Viruses for Infecting Humans. Analysis using a minigenome reporter assay indicated that R288Q is relevant to RNP polymerase activity. 2019 Viruses Result IV R288Q 58 63 RNP 79 82 30909490 The PB2 Polymerase Host Adaptation Substitutions Prime Avian Indonesia Sub Clade 2.1 H5N1 Viruses for Infecting Humans. Apart from human cases infected with Qinghai-like viruses, which harbor 627K PB2 in avian species, and Indonesian viruses the later which rarely contain 627K PB2, about 30% of human isolates from rest of the affected areas mainly from China, Vietnam and Thailand contain 627K, with the E627K substitution presumably being acquired following infection. 2019 Viruses Result IV E627K 286 291 PB2;PB2 77;158 80;161 30909490 The PB2 Polymerase Host Adaptation Substitutions Prime Avian Indonesia Sub Clade 2.1 H5N1 Viruses for Infecting Humans. Apart from seasonal H3N2 viruses arising since the 1970s and the Indonesian H5N1 viruses, few other circulating influenza viruses carry the PB2 polymerase K526R substitution. 2019 Viruses Result IV K526R 155 160 PB2 140 143 30909490 The PB2 Polymerase Host Adaptation Substitutions Prime Avian Indonesia Sub Clade 2.1 H5N1 Viruses for Infecting Humans. As expected, Q288R reverse substitution in PB2 from IND5 decreases polymerase activity and dual reversal to Q288R and R526K severely diminishes polymerase activity (Figure 8B). 2019 Viruses Result IV Q288R;Q288R;R526K 13;108;118 18;113;123 PB2 43 46 30909490 The PB2 Polymerase Host Adaptation Substitutions Prime Avian Indonesia Sub Clade 2.1 H5N1 Viruses for Infecting Humans. As reported previously, about 80% of H5N1 human isolates from Indonesia contain K526R PB2. 2019 Viruses Result IV K526R 80 85 PB2 86 89 30909490 The PB2 Polymerase Host Adaptation Substitutions Prime Avian Indonesia Sub Clade 2.1 H5N1 Viruses for Infecting Humans. Consistent with the body weight curve, analysis of virus titers in lung tissues obtained 72 h post infection shows that K526R substitution in PB2 enhances virus replication in mice (Figure 6C). 2019 Viruses Result IV K526R 120 125 PB2 142 145 30909490 The PB2 Polymerase Host Adaptation Substitutions Prime Avian Indonesia Sub Clade 2.1 H5N1 Viruses for Infecting Humans. Examination of growth properties in A549 cells further demonstrated that R288Q and K526R together enhance virus replication in the CK2A background (Figure 8C). 2019 Viruses Result IV R288Q;K526R 73;83 78;88 30909490 The PB2 Polymerase Host Adaptation Substitutions Prime Avian Indonesia Sub Clade 2.1 H5N1 Viruses for Infecting Humans. However, E627K substitution was found in isolates from two of four mice fatally infected with reverse-mutated IND5-526K virus, suggesting that if 526R is absent then virus may adapt by gaining E627K so that it can replicate in mice. 2019 Viruses Result IV E627K;E627K 9;193 14;198 30909490 The PB2 Polymerase Host Adaptation Substitutions Prime Avian Indonesia Sub Clade 2.1 H5N1 Viruses for Infecting Humans. In contrast, RNP polymerase activity is significantly increased when the K526R substitution is introduced into the avian PB2 of the CK2A isolate. 2019 Viruses Result IV K526R 73 78 PB2;RNP 121;13 124;16 30909490 The PB2 Polymerase Host Adaptation Substitutions Prime Avian Indonesia Sub Clade 2.1 H5N1 Viruses for Infecting Humans. In summary, these animal experiments further demonstrate that K526R substitution in PB2 is important for in vitro virus replication in mammalian host. 2019 Viruses Result IV K526R 62 67 PB2 84 87 30909490 The PB2 Polymerase Host Adaptation Substitutions Prime Avian Indonesia Sub Clade 2.1 H5N1 Viruses for Infecting Humans. It appears that K526R PB2 was not present in Indonesian avian H5N1 viruses until 2005, the same year that the first human case of H5N1 infection was identified in Indonesia (Figure 1). 2019 Viruses Result IV K526R 16 21 PB2 22 25 Influenza A virus H5N1 infection 130 144 30909490 The PB2 Polymerase Host Adaptation Substitutions Prime Avian Indonesia Sub Clade 2.1 H5N1 Viruses for Infecting Humans. It is notable that at the lower dose, 102 PFU, WT IND5 still killed all infected mice, but mice infected with IND5 virus containing back mutated 526K PB2 showed no disease symptoms, being indistinguishable from the PBS control group, supporting the idea that the K526R substitution is critical for replication of Indonesian H5N1 viruses in mice. 2019 Viruses Result IV K526R 263 268 PB2 150 153 30909490 The PB2 Polymerase Host Adaptation Substitutions Prime Avian Indonesia Sub Clade 2.1 H5N1 Viruses for Infecting Humans. It was suggested that, subsequent to the 1968 reassortment event, which incorporated an avian PB1, acquisition of K526R in the PB2 gene of H3N2 enhanced the function of PB2-627K in the polymerase complex to optimize replication, and perhaps also transmission, of H3N2 in humans. 2019 Viruses Result IV K526R 114 119 PB1;PB2;PB2 94;127;169 97;130;172 30909490 The PB2 Polymerase Host Adaptation Substitutions Prime Avian Indonesia Sub Clade 2.1 H5N1 Viruses for Infecting Humans. K526R PB2 Enhances H5N1 Virus Replication in Mice. 2019 Viruses Result IV K526R 0 5 PB2 6 9 30909490 The PB2 Polymerase Host Adaptation Substitutions Prime Avian Indonesia Sub Clade 2.1 H5N1 Viruses for Infecting Humans. K526R Substitution Emerged in Avian H5N1 Virus, Coincident with Human Infections . 2019 Viruses Result IV K526R 0 5 30909490 The PB2 Polymerase Host Adaptation Substitutions Prime Avian Indonesia Sub Clade 2.1 H5N1 Viruses for Infecting Humans. K526R Substitution Emerged in Avian H5N1 Virus, Coincident with Human Infections. 2019 Viruses Result IV K526R 0 5 30909490 The PB2 Polymerase Host Adaptation Substitutions Prime Avian Indonesia Sub Clade 2.1 H5N1 Viruses for Infecting Humans. K526R Supports H5N1 Virus Replication in Mammalian Cells. 2019 Viruses Result IV K526R 0 5 30909490 The PB2 Polymerase Host Adaptation Substitutions Prime Avian Indonesia Sub Clade 2.1 H5N1 Viruses for Infecting Humans. Linkage of R288Q and K526R in Indonesian H5N1 Viruses. 2019 Viruses Result IV R288Q;K526R 11;21 16;26 30909490 The PB2 Polymerase Host Adaptation Substitutions Prime Avian Indonesia Sub Clade 2.1 H5N1 Viruses for Infecting Humans. Measurement of the MLD50 of these virus strains with 1 to 106 PFU infectious dose showed that back mutation to R526K in the human isolate (IND5) reduces virus virulence in mice (Table 1). 2019 Viruses Result IV R526K 111 116 30909490 The PB2 Polymerase Host Adaptation Substitutions Prime Avian Indonesia Sub Clade 2.1 H5N1 Viruses for Infecting Humans. Notably, no E627K or other known substitution was observed in any of the seven mice fatally infected with IND5 virus (Table 2). 2019 Viruses Result IV E627K 12 17 30909490 The PB2 Polymerase Host Adaptation Substitutions Prime Avian Indonesia Sub Clade 2.1 H5N1 Viruses for Infecting Humans. PB2-K526R Is Stable in both Avian and Mammalian Hosts. 2019 Viruses Result IV K526R 4 9 PB2 0 3 30909490 The PB2 Polymerase Host Adaptation Substitutions Prime Avian Indonesia Sub Clade 2.1 H5N1 Viruses for Infecting Humans. Similarly, an immunoprecipitation assay reveals that 526R-PB2 (IND5-WT or CK2A-K526R) has a higher affinity interaction with NP than 526K-PB2 does (Figure 5D). 2019 Viruses Result IV K526R 79 84 NP;PB2;PB2 125;58;138 127;61;141 30909490 The PB2 Polymerase Host Adaptation Substitutions Prime Avian Indonesia Sub Clade 2.1 H5N1 Viruses for Infecting Humans. Similarly, E627K substitution was found in one of five mice fatally infected with CK2A-526R virus, while viruses from three out of four mice infected with CK2A-WT avian isolate were found to contain this substitution. 2019 Viruses Result IV E627K 11 16 30909490 The PB2 Polymerase Host Adaptation Substitutions Prime Avian Indonesia Sub Clade 2.1 H5N1 Viruses for Infecting Humans. Since the majority of human isolates from Indonesia do not contain the 627K mutation, we evaluated whether these viruses have adapted to use a different mechanism, namely K526R, to facilitate replication in a mammalian host. 2019 Viruses Result IV K526R 171 176 30909490 The PB2 Polymerase Host Adaptation Substitutions Prime Avian Indonesia Sub Clade 2.1 H5N1 Viruses for Infecting Humans. Taken together, these results clearly show that K526R substitution in PB2 significantly enhances virus replication in MDCK and A549 cells, but does not attenuate virus replication in avian cells, supporting the contention that, similar to E627K, K526R is a host adaption marker important in the context of viral replicative function in humans. 2019 Viruses Result IV K526R;E627K;K526R 48;239;246 53;244;251 PB2 70 73 30909490 The PB2 Polymerase Host Adaptation Substitutions Prime Avian Indonesia Sub Clade 2.1 H5N1 Viruses for Infecting Humans. Taken together, these results indicate that host adaptive mutations in the PB2 gene enhance H5N1 virus replication in mice and that K526R PB2 is a pre-existing adaptive marker present in Indonesian H5N1 viruses currently circulating in avian species, which is necessary and sufficient to support virus replication in mammalian cells. 2019 Viruses Result IV K526R 132 137 PB2;PB2 75;138 78;141 30909490 The PB2 Polymerase Host Adaptation Substitutions Prime Avian Indonesia Sub Clade 2.1 H5N1 Viruses for Infecting Humans. These results suggest that E627K substitution is not required when the K526R PB2 adaptation is present. 2019 Viruses Result IV E627K;K526R 27;71 32;76 PB2 77 80 30909490 The PB2 Polymerase Host Adaptation Substitutions Prime Avian Indonesia Sub Clade 2.1 H5N1 Viruses for Infecting Humans. These results suggest that R288Q/K526R PB2 was selected for optimal function of RNP in Indonesian H5N1 viruses and that this constellation is independent of E627K function. 2019 Viruses Result IV K526R;R288Q;E627K 33;27;157 38;32;162 PB2;RNP 39;80 42;83 30909490 The PB2 Polymerase Host Adaptation Substitutions Prime Avian Indonesia Sub Clade 2.1 H5N1 Viruses for Infecting Humans. To examine if 627K may be acquired after virus infection in mice, or if K526R is sufficient to confer virus replication ability in mice, we examined viruses isolated from fatally-infected mice died from Day 5 post infection in our experiments. 2019 Viruses Result IV K526R 72 77 30909490 The PB2 Polymerase Host Adaptation Substitutions Prime Avian Indonesia Sub Clade 2.1 H5N1 Viruses for Infecting Humans. To further analyze if K526R PB2 is a specific pre-existing mammalian adaptation marker in Indonesian H5N1 viruses, we compared the differential effects of 526R and 627K on replication of the CK2A avian virus strain, which represents virus in the early epidemic in poultry before emergence of human infection occurred in Indonesia. 2019 Viruses Result IV K526R 22 27 PB2 28 31 30909490 The PB2 Polymerase Host Adaptation Substitutions Prime Avian Indonesia Sub Clade 2.1 H5N1 Viruses for Infecting Humans. To further test the impact of K526R in virus replication, the growth kinetics of the two pairs of reverse genetic versions of viruses containing either 526K or 526R in the CK2A or IND5 backbone were analyzed. 2019 Viruses Result IV K526R 30 35 30909490 The PB2 Polymerase Host Adaptation Substitutions Prime Avian Indonesia Sub Clade 2.1 H5N1 Viruses for Infecting Humans. To identify other genetic linkages that might be involved in the K526R PB2 adaptive strategy in H5N1 viruses from Indonesia, we examined available sequences in public databases and found that R288Q is exclusively associated with K526R in the PB2 of all characterized Indonesian H5N1 viruses. 2019 Viruses Result IV K526R;R288Q;K526R 65;192;229 70;197;234 PB2;PB2 71;242 74;245 30909490 The PB2 Polymerase Host Adaptation Substitutions Prime Avian Indonesia Sub Clade 2.1 H5N1 Viruses for Infecting Humans. To test if R288Q coordinates functionally with K526R, we analyzed RNP polymerase activity with PB2 containing the R288Q substitution in the background of the CK2A avian and IND5 human strains. 2019 Viruses Result IV R288Q;K526R;R288Q 11;47;114 16;52;119 PB2;RNP 95;66 98;69 30909490 The PB2 Polymerase Host Adaptation Substitutions Prime Avian Indonesia Sub Clade 2.1 H5N1 Viruses for Infecting Humans. To understand if K526R substitution contributes to virus replication, we created two pairs of reverse genetic viruses based on A/Chicken/Indonesia/2A/2003 (CK2A, avian) and A/Indonesia/5/2005 (IND5, human), which originally contained 526K and 526R PB2, respectively (Figure 1). 2019 Viruses Result IV K526R 17 22 PB2 248 251 30909490 The PB2 Polymerase Host Adaptation Substitutions Prime Avian Indonesia Sub Clade 2.1 H5N1 Viruses for Infecting Humans. To understand if the viruses acquired the K526R substitution prior to or after human infection, we analyzed public available sequences from avian and human isolates from Indonesia. 2019 Viruses Result IV K526R 42 47 30909490 The PB2 Polymerase Host Adaptation Substitutions Prime Avian Indonesia Sub Clade 2.1 H5N1 Viruses for Infecting Humans. Uniquely, the K526R PB2 substitution in Indonesian H5N1 viruses is rarely associated with either E627K or D701N. 2019 Viruses Result IV K526R;E627K;D701N 14;97;106 19;102;111 PB2 20 23 30909490 The PB2 Polymerase Host Adaptation Substitutions Prime Avian Indonesia Sub Clade 2.1 H5N1 Viruses for Infecting Humans. We previously showed that K526R enhances avian H7N9 virus replication in mice when combined with 627K. 2019 Viruses Result IV K526R 26 31 30909490 The PB2 Polymerase Host Adaptation Substitutions Prime Avian Indonesia Sub Clade 2.1 H5N1 Viruses for Infecting Humans. We tested if K526R substitution in H5N1 viruses from Indonesia may enhance interaction between NEP and viral polymerase complex. 2019 Viruses Result IV K526R 13 18 NEP 95 98 30909490 The PB2 Polymerase Host Adaptation Substitutions Prime Avian Indonesia Sub Clade 2.1 H5N1 Viruses for Infecting Humans. While introduction of R288Q into CK2A PB2 moderately increases RNP polymerase activity, the combination of R288Q and K526R substitutions significantly enhances the positive effects on polymerase activity exerted by R288Q or K526R alone (Figure 8A). 2019 Viruses Result IV R288Q;R288Q;K526R;R288Q;K526R 22;107;117;215;224 27;112;122;220;229 PB2;RNP 38;63 41;66 30909490 The PB2 Polymerase Host Adaptation Substitutions Prime Avian Indonesia Sub Clade 2.1 H5N1 Viruses for Infecting Humans. WT IND5 exhibits higher virulence than mutated avian CK2A-526R virus, which contains K526R PB2, suggesting that other mutations (see section below), yet to be defined, may also contribute to virus replication in mice. 2019 Viruses Result IV K526R 85 90 PB2 91 94 30996301 Bacterial glycosyltransferase-mediated cell-surface chemoenzymatic glycan modification. By treating LeX with Pm2,3ST-M144D and CMP-NeuAc, sLeX was produced. 2019 Nature communications Result IV M144D 29 34 30996301 Bacterial glycosyltransferase-mediated cell-surface chemoenzymatic glycan modification. Flow cytometry analysis revealed that Pm2,3ST-M144D- or Pd2,6ST-treated Lec2 cells were robustly labeled, and the labeling was time-dependent. 2019 Nature communications Result IV M144D 46 51 30996301 Bacterial glycosyltransferase-mediated cell-surface chemoenzymatic glycan modification. Further evaluation of the donor substrate scope of Pm2,3ST-M144D and Pd2,6ST revealed that besides the N-acyl modified CMP-SiaNAz, these two enzymes were capable of incorporating other CMP-Sia analogs, including CMP-9AzSia, CMP-SiaNAl, and CMP-SiaNPoc, onto cell-surface glycans. 2019 Nature communications Result IV M144D 59 64 30996301 Bacterial glycosyltransferase-mediated cell-surface chemoenzymatic glycan modification. HK68-MTA (G225M/L226T/ S228A), HK68-LSS (G225L/L226S), and HK68-QAS (G225Q/ L226A) share a very similar HA backbone conformation, but their binding affinity for NeuAcalpha2-6-Gal decreases following the order of HK68-MTA > HK68-LSS > HK68-QAS. 2019 Nature communications Result IV G225M;L226T;S228A;G225L;L226S;G225Q;L226A 10;16;23;41;47;69;76 15;21;28;46;52;74;81 HA 104 106 30996301 Bacterial glycosyltransferase-mediated cell-surface chemoenzymatic glycan modification. In this experiment, Lec2 cells were incubated with a sialyltransferase (Pm2,3ST-M144D or Pd2,6ST) and CMP-SiaNAz, or with a fucosyltransferase (Hp1,3FT or Hm1,2FT) and GDP-FucAz. 2019 Nature communications Result IV M144D 80 85 30996301 Bacterial glycosyltransferase-mediated cell-surface chemoenzymatic glycan modification. Interestingly, Pd2,6ST-labeling generated significantly higher signals than Pm2,3ST-M144D-labeling in bone structures, including the sections of leg, rib, spine, and skull. 2019 Nature communications Result IV M144D 84 89 30996301 Bacterial glycosyltransferase-mediated cell-surface chemoenzymatic glycan modification. Next, we evaluated the feasibility of labeling tissue specimens via one-step ST(Pm2,3ST-M144D or Pd2,6ST)-mediated glycan modification. 2019 Nature communications Result IV M144D 88 93 30996301 Bacterial glycosyltransferase-mediated cell-surface chemoenzymatic glycan modification. Originally reported by Chen and coworkers, Pm2,3ST-M144D and Pd2,6ST, are highly efficient for one-pot chemoenzymatic oligosaccharide synthesis. 2019 Nature communications Result IV M144D 51 56 30996301 Bacterial glycosyltransferase-mediated cell-surface chemoenzymatic glycan modification. Quantifying the cell-surface lectin staining signals, we discovered two sialyltransferases, Pm2,3ST-M144D and Pd2,6ST, and a fucosyltransferase, Hm1,2FT, that can install natural sialic acid or fucose, respectively, onto the cell surface. 2019 Nature communications Result IV M144D 100 105 30996301 Bacterial glycosyltransferase-mediated cell-surface chemoenzymatic glycan modification. Therefore, there are few acceptor substrates to be modified by ST(Pm2,3ST-M144D or Pd2,6ST). 2019 Nature communications Result IV M144D 74 79 30996301 Bacterial glycosyltransferase-mediated cell-surface chemoenzymatic glycan modification. Thin-layer chromatography (TLC) and liquid chromatography-mass spectrometry (LC/MS) analysis confirmed the formation of Fucalpha1-2-Galbeta1-4-GlcNAc, NeuAcalpha2-3-Galbeta1-4-GlcNAc, NeuAcalpha2-6-Galbeta1-4-GlcNAc, and LeX in Hm1,2FT, Pm2,3ST-M144D, Pd2,6ST, and Hp1,3FT-mediated transformations, respectively. 2019 Nature communications Result IV M144D 245 250 30996301 Bacterial glycosyltransferase-mediated cell-surface chemoenzymatic glycan modification. To further validate the activities of Hm1,2FT, Hp1,3FT, Pm2,3ST-M144D, and Pd2,6ST, we performed in vitro glycosylation reactions using the natural donor substrates, CMP-NeuAc (for STs) and GDP-Fuc (for FTs), and type 2 N-acetyllactosamine (LacNAc, Galbeta1-4-GlcNAc) as the acceptor. 2019 Nature communications Result IV M144D 64 69 30996301 Bacterial glycosyltransferase-mediated cell-surface chemoenzymatic glycan modification. To survey if the promiscuity of Pm2,3ST-M144D and Pd2,6ST could enable the transfer of biotin- or Cy3-functionalized CMP-Sia derivatives directly to the cell surface for one-step glycan labeling, Lec2 cells were incubated with either enzyme in the presence of crude conjugation product of CMP-SiaNAz-Cy3 or CMP-SiaNAz-biotin. 2019 Nature communications Result IV M144D 40 45 31008587 Hydrogen-Deuterium Exchange Supports Independent Membrane-Interfacial Fusion Peptide and Transmembrane Domains in Subunit 2 of Influenza Virus Hemagglutinin Protein, a Structured and Aqueous-Protected Connection between the Fusion Peptide and Soluble Ectodomain, and the Importance of Membrane Apposition by the Trimer-of-Hairpins Structure. 8 (center) displays a structural model for I173E-HA2 that is supported by our HDX-MS data. 2019 Biochemistry Result IV I173E 43 48 HA 49 51 31008587 Hydrogen-Deuterium Exchange Supports Independent Membrane-Interfacial Fusion Peptide and Transmembrane Domains in Subunit 2 of Influenza Virus Hemagglutinin Protein, a Structured and Aqueous-Protected Connection between the Fusion Peptide and Soluble Ectodomain, and the Importance of Membrane Apposition by the Trimer-of-Hairpins Structure. 8 (right) displays a model for G1E-HA2 with a I173E-like SE structure with dissociated C-terminal strand bound to unfolded FP. 2019 Biochemistry Result IV G1E;I173E 31;46 34;51 HA 35 37 31008587 Hydrogen-Deuterium Exchange Supports Independent Membrane-Interfacial Fusion Peptide and Transmembrane Domains in Subunit 2 of Influenza Virus Hemagglutinin Protein, a Structured and Aqueous-Protected Connection between the Fusion Peptide and Soluble Ectodomain, and the Importance of Membrane Apposition by the Trimer-of-Hairpins Structure. 8 model supports that highly-impaired fusion for I173E is due to greater inter-membrane distance that results from a more flexible SE hairpin. 2019 Biochemistry Result IV I173E 49 54 31008587 Hydrogen-Deuterium Exchange Supports Independent Membrane-Interfacial Fusion Peptide and Transmembrane Domains in Subunit 2 of Influenza Virus Hemagglutinin Protein, a Structured and Aqueous-Protected Connection between the Fusion Peptide and Soluble Ectodomain, and the Importance of Membrane Apposition by the Trimer-of-Hairpins Structure. Distinct G1E SE states similar to either WT or I173E structures are also evidenced by the bimodal behavior for 39-52, with one distribution of peaks in a m/z range similar to WT and the other in a m/z range similar to I173E. 2019 Biochemistry Result IV G1E;I173E;I173E 9;47;218 12;52;223 31008587 Hydrogen-Deuterium Exchange Supports Independent Membrane-Interfacial Fusion Peptide and Transmembrane Domains in Subunit 2 of Influenza Virus Hemagglutinin Protein, a Structured and Aqueous-Protected Connection between the Fusion Peptide and Soluble Ectodomain, and the Importance of Membrane Apposition by the Trimer-of-Hairpins Structure. For tHDX = 120 min, there are approximately equal sums of G1E peak intensities in the two ranges, and the calculated D% = 16 and 63% are similar to the 6 and 54% values for WT and I173E, respectively. 2019 Biochemistry Result IV G1E;I173E 58;180 61;185 31008587 Hydrogen-Deuterium Exchange Supports Independent Membrane-Interfacial Fusion Peptide and Transmembrane Domains in Subunit 2 of Influenza Virus Hemagglutinin Protein, a Structured and Aqueous-Protected Connection between the Fusion Peptide and Soluble Ectodomain, and the Importance of Membrane Apposition by the Trimer-of-Hairpins Structure. For the same peptide in 100-115 and 151-191, the (D%) are always larger for I173E vs. 2019 Biochemistry Result IV I173E 76 81 31008587 Hydrogen-Deuterium Exchange Supports Independent Membrane-Interfacial Fusion Peptide and Transmembrane Domains in Subunit 2 of Influenza Virus Hemagglutinin Protein, a Structured and Aqueous-Protected Connection between the Fusion Peptide and Soluble Ectodomain, and the Importance of Membrane Apposition by the Trimer-of-Hairpins Structure. FP/SE strand binding helps explain the G1E destabilization of the SE, where the latter observation was unanticipated because the trimer-of-hairpins structure of the SE is thermostable in the absence of the FP. 2019 Biochemistry Result IV G1E 39 42 31008587 Hydrogen-Deuterium Exchange Supports Independent Membrane-Interfacial Fusion Peptide and Transmembrane Domains in Subunit 2 of Influenza Virus Hemagglutinin Protein, a Structured and Aqueous-Protected Connection between the Fusion Peptide and Soluble Ectodomain, and the Importance of Membrane Apposition by the Trimer-of-Hairpins Structure. Partial dissociation of the C-terminal strand for G1E is consistent with (D%) values for the 151-191 region that are intermediate between the smaller WT and larger I173E values. 2019 Biochemistry Result IV G1E;I173E 50;164 53;169 31008587 Hydrogen-Deuterium Exchange Supports Independent Membrane-Interfacial Fusion Peptide and Transmembrane Domains in Subunit 2 of Influenza Virus Hemagglutinin Protein, a Structured and Aqueous-Protected Connection between the Fusion Peptide and Soluble Ectodomain, and the Importance of Membrane Apposition by the Trimer-of-Hairpins Structure. SE hairpin turns and C-terminal strands are on the exterior of the WT structure and exhibit significant (D%), but even larger (D%) for I173E in these segments supports strand dissociation and SE destabilization. 2019 Biochemistry Result IV I173E 135 140 31008587 Hydrogen-Deuterium Exchange Supports Independent Membrane-Interfacial Fusion Peptide and Transmembrane Domains in Subunit 2 of Influenza Virus Hemagglutinin Protein, a Structured and Aqueous-Protected Connection between the Fusion Peptide and Soluble Ectodomain, and the Importance of Membrane Apposition by the Trimer-of-Hairpins Structure. Structural destabilization of I173E- and G1E-HA2 underlies their fusion impairment. 2019 Biochemistry Result IV I173E;G1E 30;41 35;44 HA 45 47 31008587 Hydrogen-Deuterium Exchange Supports Independent Membrane-Interfacial Fusion Peptide and Transmembrane Domains in Subunit 2 of Influenza Virus Hemagglutinin Protein, a Structured and Aqueous-Protected Connection between the Fusion Peptide and Soluble Ectodomain, and the Importance of Membrane Apposition by the Trimer-of-Hairpins Structure. The bimodal data for G1E-HA239-52 are also consistent with this model, with one population with low exchange from protein that remains folded and a second population with high exchange from protein that has transiently unfolded. 2019 Biochemistry Result IV G1E 21 24 HA 25 27 31008587 Hydrogen-Deuterium Exchange Supports Independent Membrane-Interfacial Fusion Peptide and Transmembrane Domains in Subunit 2 of Influenza Virus Hemagglutinin Protein, a Structured and Aqueous-Protected Connection between the Fusion Peptide and Soluble Ectodomain, and the Importance of Membrane Apposition by the Trimer-of-Hairpins Structure. The C-terminal strand of I173E is dissociated from the N-terminal bundle with consequent much greater aqueous exposure of the bundle, as supported by much larger (D%) of 22-69 for I173E vs. 2019 Biochemistry Result IV I173E;I173E 25;180 30;185 31008587 Hydrogen-Deuterium Exchange Supports Independent Membrane-Interfacial Fusion Peptide and Transmembrane Domains in Subunit 2 of Influenza Virus Hemagglutinin Protein, a Structured and Aqueous-Protected Connection between the Fusion Peptide and Soluble Ectodomain, and the Importance of Membrane Apposition by the Trimer-of-Hairpins Structure. The I173E structure is the same as WT in the FP, 70-150 SE, TM, and endodomain regions, as supported by similar (D%) of I173E and WT for the 1-8, 70-99, 120-150, and 192-217 segments. 2019 Biochemistry Result IV I173E;I173E 4;120 9;125 31008587 Hydrogen-Deuterium Exchange Supports Independent Membrane-Interfacial Fusion Peptide and Transmembrane Domains in Subunit 2 of Influenza Virus Hemagglutinin Protein, a Structured and Aqueous-Protected Connection between the Fusion Peptide and Soluble Ectodomain, and the Importance of Membrane Apposition by the Trimer-of-Hairpins Structure. The lower Tm = 79 C for I173E and 75 C for G1E correlate with loss of SE structure and the consequent increased inter-membrane distance and impaired fusion. 2019 Biochemistry Result IV G1E;I173E 45;25 48;30 31008587 Hydrogen-Deuterium Exchange Supports Independent Membrane-Interfacial Fusion Peptide and Transmembrane Domains in Subunit 2 of Influenza Virus Hemagglutinin Protein, a Structured and Aqueous-Protected Connection between the Fusion Peptide and Soluble Ectodomain, and the Importance of Membrane Apposition by the Trimer-of-Hairpins Structure. There are similar (D%) for G1E and WT for peptides in the 22-38, 53-150, and 192-217 regions. 2019 Biochemistry Result IV G1E 27 30 31150476 Pathogenicity of the H1N1 influenza virus enhanced by functional synergy between the NPV100I and NAD248N pair. NP binds to viral RNA and is a component of the viral ribonucleoprotein (vRNP) complex, and V100I is located near the RNA-binding domain (S4 Fig). 2019 PloS one Result IV V100I 92 97 NP 0 2 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. A/Uruguay/716/2007 (NYMC X-175C) carried an egg-adaptive mutation, L194P, which has been extensively characterized, both structurally and antigenically, in our previous study using Bris07 HA. 2019 Cell host & microbe Result IV L194P 67 72 HA 188 190 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. Among them, G186V and L194P, which are located on opposite sides of the 190-helix, had particularly high-occurrence frequencies (Figure 1A). 2019 Cell host & microbe Result IV G186V;L194P 12;22 17;27 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. An ELISA experiment was then performed to assess binding of these sera to Bris07 WT, G186V, and L194P recombinant HA proteins (Figures 6A and S4A). 2019 Cell host & microbe Result IV G186V;L194P 85;96 90;101 HA 114 116 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. As expected, when the G186V mutant was passaged in eggs, the L194P mutation did not emerge. 2019 Cell host & microbe Result IV G186V;L194P 22;61 27;66 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. Besides IVR-165 HA, Wy03 HA also carried the G186V mutation. 2019 Cell host & microbe Result IV G186V 45 50 HA;HA 16;25 18;27 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. Both G186V and L194P single mutants could be rescued to a reasonable titer despite the lower titer of the L194P mutant. 2019 Cell host & microbe Result IV G186V;L194P;L194P 5;15;106 10;20;111 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. C05 exhibited high affinity to WT (Kd = 1.0 +- 0.1 nM) and to G186V (Kd = 1.4 +- 0.2 nM), but very weak binding to L194P (>1,000 nM). 2019 Cell host & microbe Result IV G186V;L194P 62;115 67;120 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. Consequently, the difference in receptor-binding mode between IVR-165 HA and the Bris07 HA L194P mutant can be explained by the opposing structural effects of the G186V and L194P mutations. 2019 Cell host & microbe Result IV L194P;G186V;L194P 91;163;173 96;168;178 HA;HA 70;88 72;90 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. Consistent with our observations above, these four strains carried G186V but not L194P. 2019 Cell host & microbe Result IV G186V;L194P 67;81 72;86 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. Consistently, the electron density for the receptor analogs 3'SLNLN and 6'SLNLN was also very weak in the complex with the Bris07 HA G186V/L194P double mutant. 2019 Cell host & microbe Result IV G186V;L194P 133;139 138;144 HA 130 132 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. Crystal structures of the Bris07 HA G186V/L194P double mutant were determined at 2.25 A, 2.1 A, and 2.4 A for the apo form, in complex with 3'SLNLN, and in complex with 6'SLNLN, respectively. 2019 Cell host & microbe Result IV G186V;L194P 36;42 41;47 HA 33 35 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. For 6'SLNLN, Gal-2 is rotated by 90 when binding to Bris07 HA L194P, as compared to the folded-back conformation when binding to IVR-165 HA (Figure 4D). 2019 Cell host & microbe Result IV L194P 63 68 HA;HA 60;138 62;140 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. For all serum samples, the binding to G186V was almost as strong as to WT, whereas binding to L194P was consistently weaker than to WT or G186V. 2019 Cell host & microbe Result IV G186V;L194P;G186V 38;94;138 43;99;143 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. Furthermore, based on a ferret study, L194P has been shown to significantly decrease virus immunogenicity. 2019 Cell host & microbe Result IV L194P 38 43 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. G186V and L194P Lead to Differences in Receptor-Binding Mode. 2019 Cell host & microbe Result IV G186V;L194P 0;10 5;15 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. G186V Imposes Minimum Change in Antigenicity. 2019 Cell host & microbe Result IV G186V 0 5 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. G186V Increases the Height of the HA RBS. 2019 Cell host & microbe Result IV G186V 0 5 HA 34 36 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. GlcNAc-3 of the 3'SLNLN in complex with the Bris07 HA L194P mutant shifts away from the RBS as compared to that of 3'SLNLN in complex with IVR-165 HA (Figure 4C). 2019 Cell host & microbe Result IV L194P 54 59 HA;HA 51;147 53;149 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. H156Q abolishes a hydrogen bond between the 150-loop and 190-helix (Figures S1A and S1B), whereas S219Y stabilizes the N165 glycan from the neighboring promoter of the trimer by forming a stacking interaction with the glycan (Figure S1C). 2019 Cell host & microbe Result IV H156Q;S219Y 0;98 5;103 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. HA G186V/L194P Double Mutant Disrupts the RBS. 2019 Cell host & microbe Result IV G186V;L194P 3;9 8;14 HA 0 2 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. Here, we further performed a side-by-side comparison of the HA antigenic changes resulting from the G186V and L194P mutations. 2019 Cell host & microbe Result IV G186V;L194P 100;110 105;115 HA 60 62 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. However, none of the nine vaccine seed strains carried both G186V and L194P. 2019 Cell host & microbe Result IV G186V;L194P 60;70 65;75 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. In all three structures, the electron density for the 190-helix was very weak to absent compared to that of the Bris07 HA L194P single mutant (Figure 5), whose structure was previously determined in the same crystallization condition. 2019 Cell host & microbe Result IV L194P 122 127 HA 119 121 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. In comparison, when the L194P mutant was passaged in eggs, no mutation was able to reach a frequency of >10% (Figure 2D). 2019 Cell host & microbe Result IV L194P 24 29 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. In contrast to mutation G186V, which increases the RBS height, mutation L194P appears to decrease its height (Figure 3C). 2019 Cell host & microbe Result IV G186V;L194P 24;72 29;77 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. In contrast, the G186V mutation has been shown to confer minimal HA antigenic differences, using ferret sera, sheep sera, and mouse monoclonal antibodies. 2019 Cell host & microbe Result IV G186V 17 22 HA 65 67 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. In contrast, the G186V/L194P double mutant could not be rescued. 2019 Cell host & microbe Result IV G186V;L194P 17;23 22;28 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. In fact, a previous study also failed to rescue the G186V/L194P double mutant in Bris07, as well as in another human H3N2 strain A/Wisconsin/67/05. 2019 Cell host & microbe Result IV G186V;L194P 52;58 57;63 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. Incompatibility of G186V and L194P. 2019 Cell host & microbe Result IV G186V;L194P 19;29 24;34 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. Instead, mutations I140K, I140R, N144K, H156R, H156Q, N189K, and D190N were observed with a frequency of >10% in any passage, on the background of G186V. 2019 Cell host & microbe Result IV I140K;I140R;N144K;H156R;H156Q;N189K;D190N;G186V 19;26;33;40;47;54;65;147 24;31;38;45;52;59;70;152 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. Interestingly, noticeable differences can be observed between the receptor-binding modes of IVR-165 HA and that of the Bris07 HA L194P mutant when their receptor-binding subdomains (HA1 residues 117-265) are aligned (Figures 4C and 4D). 2019 Cell host & microbe Result IV L194P 129 134 HA;HA;HA1 100;126;182 102;128;185 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. Next, we aimed to investigate whether there was any relationship between G186V and L194P. 2019 Cell host & microbe Result IV G186V;L194P 73;83 78;88 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. Nine mutations, namely H156Q, H156R, H183L, G186V, L194P, S219Y, S219F, N246H, and N246S, were classified as the major egg-adaptive mutations (see STAR Methods; Figures 1A and 1B; Table S1). 2019 Cell host & microbe Result IV H156Q;H156R;H183L;G186V;L194P;S219Y;S219F;N246H;N246S 23;30;37;44;51;58;65;72;83 28;35;42;49;56;63;70;77;88 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. Of note, the HA G186V/L194P double mutant abolishes virus replication but not HA protein expression. 2019 Cell host & microbe Result IV G186V;L194P 16;22 21;27 HA;HA 13;78 15;80 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. Overall, our analyses show that G186V and L194P are incompatible. 2019 Cell host & microbe Result IV G186V;L194P 32;42 37;47 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. Overall, our structural analysis indicates that G186V increases the height and, hence, the size of the HA RBS. 2019 Cell host & microbe Result IV G186V 48 53 HA 103 105 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. Overall, these results demonstrate that the evolutionary trajectories during H3N2 egg adaptation of G186V and L194P mutants are different, corroborating the incompatibility of G186V and L194P. 2019 Cell host & microbe Result IV G186V;L194P;G186V;L194P 100;110;176;186 105;115;181;191 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. Overall, these results substantiate the conclusion that G186V, unlike L194P, exhibits minimal antigenic change. 2019 Cell host & microbe Result IV G186V;L194P 56;70 61;75 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. Overall, this analysis demonstrates the potential clinical relevance of the egg-adaptive mutations and further suggests that G186V and L194P represent two distinct evolutionary pathways for egg adaptation. 2019 Cell host & microbe Result IV G186V;L194P 125;135 130;140 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. Previously, we and others demonstrated that the HA antigenicity is significantly altered by the L194P mutation, when using ferret sera, human sera, and human monoclonal antibodies. 2019 Cell host & microbe Result IV L194P 96 101 HA 48 50 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. Previously, we performed a thorough structural study of the L194P mutation. 2019 Cell host & microbe Result IV L194P 60 65 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. Sera from ferrets that were immunized with a virus that carried the G186V mutation cross-react well with the WT virus, with only a 2-fold decrease in hemagglutination inhibition (HAI) titer when compared to the sera from ferrets that were immunized with the WT virus. 2019 Cell host & microbe Result IV G186V 68 73 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. Similar to our previous observation with Bris07 L194P HA, IVR-165 HA had negligible binding to the glycan array (Figure S3). 2019 Cell host & microbe Result IV L194P 48 53 HA;HA 54;66 56;68 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. Six of the nine major egg-adaptive mutations, H156Q, H156R, G186V, L194P, S219Y, and S219F, could be found in the vaccine seed strains (Figure 1C). 2019 Cell host & microbe Result IV H156Q;H156R;G186V;L194P;S219Y;S219F 46;53;60;67;74;85 51;58;65;72;79;90 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. Such a difference can be attributed to the G186V mutation, which causes the 190-helix to move away from the 220-loop through an increase in the side-chain volume. 2019 Cell host & microbe Result IV G186V 43 48 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. The distance between OH98 and Calpha190 of the Bris07 HA L194P mutant is 8.3 A, whereas that of Bris07 wild-type (WT) HA is 8.7 A. 2019 Cell host & microbe Result IV L194P 57 62 HA;HA 54;118 56;120 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. The G186V mutant was passaged in eggs in triplicate (Figure 2C). 2019 Cell host & microbe Result IV G186V 4 9 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. The most commonly observed egg-adaptive mutations among these nine vaccine seed strains were G186V and L194P, each of which was carried by four vaccine seed strains. 2019 Cell host & microbe Result IV G186V;L194P 93;103 98;108 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. The other two egg-adaptive mutations H156Q and S219Y have little, if any, influence on the distance between the 190-helix and 220-loop. 2019 Cell host & microbe Result IV H156Q;S219Y 37;47 42;52 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. Therefore, the observed distance increase between the 190-helix and 220-loop is mainly a result of the G186V mutation. 2019 Cell host & microbe Result IV G186V 103 108 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. These observations are consistent with previous studies, which showed that growth of the H3N2 virus in eggs can be enhanced by H183L, G186V, L194P, S219Y, S219F, and loss of a glycosylation site at position 246. 2019 Cell host & microbe Result IV H183L;G186V;L194P;S219Y;S219F 127;134;141;148;155 132;139;146;153;160 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. This observation indicates that the 190-helix in Bris07 HA G186V/L194P double mutant is extremely disordered. 2019 Cell host & microbe Result IV G186V;L194P 59;65 64;70 HA 56 58 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. This structural analysis shows that combining HA mutations G186V and L194P dramatically destabilizes the 190-helix, causing a disruption of the RBS and also of antigenic site B, which is the major antigenic site in recent H3N2 viruses. 2019 Cell host & microbe Result IV G186V;L194P 59;69 64;74 HA 46 48 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. To dissect the impact of the G186V mutation, a crystal structure of IVR-165 HA, which is the triple mutant H156Q/G186V/S219Y of Vic11 HA, was determined at a resolution of 2.25 A (Table S3). 2019 Cell host & microbe Result IV G186V;G186V;H156Q;S219Y 29;113;107;119 34;118;112;124 HA;HA 76;134 78;136 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. To understand how G186V influences receptor binding, crystal structures of IVR-165 HA in complex the with avian receptor analog NeuAcalpha2-3Galbeta1-4GlcNAcbeta1-3Galbeta1-4GlcNAc (3'SLNLN) and the human receptor analog NeuAcalpha2-6Galbeta1-4GlcNAcbeta1-3Galbeta1-4GlcNAc (6'SLNLN) were determined at 2.1 and 2.4 A, respectively (Table S3; Figure S2). 2019 Cell host & microbe Result IV G186V 18 23 HA 83 85 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. We also tested binding of the HA-RBS-targeted antibody C05 to Bris07 WT, G186V, and L194P recombinant HA proteins using biolayer interferometry (BLI) (Figure 6B). 2019 Cell host & microbe Result IV G186V;L194P 73;84 78;89 HA;HA 30;102 32;104 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. We postulated that since G186V and L194P are mutually exclusive, the evolutionary trajectories of the H3N2 virus in eggs would be influenced by whichever mutation (i.e., G186V or L194P) appears first. 2019 Cell host & microbe Result IV G186V;L194P;G186V;L194P 25;35;170;179 30;40;175;184 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. We then performed an experiment by passaging the Bris07 G186V mutant to monitor the emergence of any mutations in the HA receptor-binding subdomain (HA1 residue 117-265) using next-generation sequencing. 2019 Cell host & microbe Result IV G186V 56 61 HA;HA1 118;149 120;152 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. We were therefore able to recombinantly express and purify the Bris07 HA G186V/L194P double mutant. 2019 Cell host & microbe Result IV G186V;L194P 73;79 78;84 HA 70 72 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. While G186V and L194P are the most commonly observed egg-adaptive mutations in H3N2, they did not co-occur in the same virus. 2019 Cell host & microbe Result IV G186V;L194P 6;16 11;21 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. While NYMC X-171 carried mutation G186V but not L194P, IVR-147 carried mutation L194P but not G186V. 2019 Cell host & microbe Result IV G186V;L194P;L194P;G186V 34;48;80;94 39;53;85;99 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. With the knowledge that HA mutations G186V and L194P exert an opposing structural effect on the RBS (Figures 3C, 4C, and 4D) and that the HA G186V/L194P double mutant was highly deleterious to the virus (Figure 2B), we were interested in examining the structural effect of the HA G186VL194P double mutant. 2019 Cell host & microbe Result IV G186V;L194P;G186V;L194P 37;47;141;147 42;52;146;152 HA;HA;HA 24;138;277 26;140;279 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. As shown in Table 1, two H9N2 viruses, A/chicken/Henan/5/1998 [CK/5(H9N2)] and A/chicken/Guangxi/9/1999 [CK/9(H9N2)], isolated in the 1990s did not acquire the PB2 E627K mutation even after being passaged six times in MDCK cells. 2019 mBio Result IV E627K 164 169 PB2 160 163 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. Because our study in mice showed that PA is important for PB2 E627K acquisition during mammalian adaptation of PG/S1421(H7N9), we next investigated whether PG/S1421(H7N9), CK/5(H9N2), and their reassortants had different RNP activities in HEK293T cells. 2019 mBio Result IV E627K 62 67 PA;PB2;RNP 38;58;221 40;61;224 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. CK/5(H9N2), a representative of viruses that maintain a stable PB2 627E during replication in mammals, was selected with PG/S1421(H7N9) to form a model virus pair to investigate the viral factors that drive the emergence of the PB2 E627K mutation during adaptation of H7N9 viruses to mammalian hosts. 2019 mBio Result IV E627K 232 237 PB2;PB2 63;228 66;231 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. Collectively, these results suggest that the replacement of the four PA residues (142K, 147I, 171I, and 182M) of PG/S1421(H7N9) with those of CK/5(H9N2) (142R, 147V, 171V, and 182L) may enhance the polymerase activity over a threshold capable of abolishing the need to acquire the PB2 E627K mutation in mammalian hosts. 2019 mBio Result IV E627K 285 290 PA;PB2 69;281 71;284 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. Deep sequencing of PG/S1421-CK/5PA(H7N9) recovered from the lungs of the second-passage mice demonstrated that the PB2 E627K mutation was not acquired (Table S1). 2019 mBio Result IV E627K 119 124 PB2 115 118 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. Different avian influenza viruses have different capabilities to acquire the PB2 E627K mutation during replication in MDCK cells and mice. 2019 mBio Result IV E627K 81 86 PB2 77 80 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. Four amino acids in the N-terminal PA domain are critical in mediating the acquisition of PB2 E627K. 2019 mBio Result IV E627K 94 99 PA;PB2 35;90 37;93 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. However, whether huANP32A directly plays a role in the acquisition of the PB2 E627K substitution during the mammalian adaptation of AIVs has not been resolved. 2019 mBio Result IV E627K 78 83 PB2 74 77 IAV infections 132 136 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. In contrast, the chimeric PA virus bearing domain 253-716 of CK/5(H9N2) PA acquired the PB2 E627K mutation during replication in mice. 2019 mBio Result IV E627K 92 97 PA;PA;PB2 26;72;88 28;74;91 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. In mice, PG/S1421-PA142R-147V-171V-182L(H7N9) maintained PB2 627E, whereas the four PG/S1421(H7N9) mutant viruses bearing the individual CK/5(H9N2) PA residues acquired the PB2 E627K mutation during replication. 2019 mBio Result IV E627K 177 182 PA;PA;PB2;PB2 18;148;57;173 20;150;60;176 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. Interestingly, the introduction of CK/5(H9N2) PB1 into the PG/S1421(H7N9) backbone yielded higher polymerase activity than that of parental PG/S1421(H7N9) and led to the appearance of another mammalian-adaptive marker, PB2 D701N, during the replication of PG/S1421-CK/5PB1(H7N9) in mice. 2019 mBio Result IV D701N 223 228 PB1;PB2 46;219 49;222 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. Next, we constructed another four PA chimeras containing amino acids 1 to 60, 1 to 86, 1 to 120, or 1 to 191 of CK/5(H9N2) PA in the backbone of PG/S1421(H7N9) PA to identify the key region in PAN that determines the emergence of the PB2 E627K mutation. 2019 mBio Result IV E627K 238 243 PA;PA;PA;PB2 34;123;160;234 36;125;162;237 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. Notably, PG/S1421(H7N9) replication was not detected in one of the five Anp32a-/- mice, PB2 627E was maintained in viruses recovered from two Anp32a-/- mice, and a PB2 D701N mutation emerged in viruses in the other two Anp32a-/- mice. 2019 mBio Result IV D701N 168 173 PB2;PB2 88;164 91;167 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. Of note, PG/S1421(H7N9) or single-gene reassortant viruses with low polymerase activities (RNP combinations 7PB27PB17PA7NP, 7PB27PB17PA9NP, and 9PB27PB17PA7NP) either failed to replicate in mice (PG/S1421-CK/5NP and PG/S1421-CK/5NS) or acquired the PB2 E627K substitution (PG/S1421, PG/S1421-CK/5PB2, PG/S1421-CK/5HA, PG/S1421-CK/5NA, and PG/S1421-CK/5M). 2019 mBio Result IV E627K 253 258 PB2;RNP 249;91 252;94 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. PG/S1421-CK/5PB1+PA(H7N9) maintained a stable PB2 627E, whereas PG/S1421-CK/5PB2+PB1(H7N9) acquired the PB2 E627K mutation during replication in mice (Table S2). 2019 mBio Result IV E627K 108 113 PA;PB1;PB2;PB2 17;81;46;104 19;84;49;107 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. PG/S1421(H7N9) quickly acquired the PB2 E627K mutation on day 5 after one passage in mice, CK/9(H9N2) acquired the PB2 E627K mutation after the second passage, whereas for CK/5(H9N2), the PB2 627E residue was stably maintained even after four passages in mice (Table 1). 2019 mBio Result IV E627K;E627K 40;119 45;124 PB2;PB2;PB2 36;115;188 39;118;191 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. Sequence analysis confirmed that the PB2 E627K mutation was acquired by virus in the lungs of the infected WT mice. 2019 mBio Result IV E627K 41 46 PB2 37 40 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. The absence of ANP32A protein abolished the acquisition of the PB2 E627K mutation and instead forced the virus down an alternative adaptive pathway to acquire the compensatory PB2 D701N mutation. 2019 mBio Result IV E627K;D701N 67;180 72;185 PB2;PB2 63;176 66;179 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. The chimeric PA virus containing domain 1-252 of CK/5(H9N2) PA replicated in mice without acquiring the PB2 E627K mutation. 2019 mBio Result IV E627K 108 113 PA;PA;PB2 13;60;104 15;62;107 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. The data showed that PG/S1421-CK/5PA1-120(H7N9) acquired the PB2 E627K mutation, whereas PG/S1421-CK/5PA1-191(H7N9) retained PB2 627E (Table S1). 2019 mBio Result IV E627K 65 70 PB2;PB2 61;125 64;128 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. The low polymerase activity attributed to PA drives the emergence of the mammalian-adaptive PB2 E627K mutation. 2019 mBio Result IV E627K 96 101 PA;PB2 42;92 44;95 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. The phenotypic emergence of PB2 E627K mutation was confirmed as occurring during virus passage because deep sequencing did not identify any subpopulations of PB2 627K in the original stocks of PG/S1421(H7N9) (see Table S1 in the supplemental material) and CK/SC197(H9N2) and CK/SC324(H9N2) virus. 2019 mBio Result IV E627K 32 37 PB2;PB2 28;158 31;161 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. The reassortant virus containing CK/5(H9N2) PB1 obtained a PB2 D701N mutation on day 5 p.i. 2019 mBio Result IV D701N 63 68 PB1;PB2 44;59 47;62 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. The reassortants containing the PB2, HA, NA, or M protein of CK/5(H9N2) acquired the PB2 E627K mutation on day 5 p.i. 2019 mBio Result IV E627K 89 94 HA;M;NA;PB2;PB2 37;48;41;32;85 39;49;43;35;88 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. The rescued single-gene reassortant viruses were intranasally inoculated into mice to monitor their ability to acquire the PB2 E627K mutation. 2019 mBio Result IV E627K 127 132 PB2 123 126 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. The role of these PA residues in determining the emergence of the PB2 E627K substitution was confirmed in the background of another H7N9 avian strain, A/chicken/Guangdong/SD008/2017 [CK/SD008(H7N9)] (Table S2). 2019 mBio Result IV E627K 70 75 PA;PB2 18;66 20;69 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. These results confirm that the low polymerase activity in human cells attributed to PG/S1421(H7N9) PA is associated with the emergence of the mammalian-adaptive PB2 E627K mutation. 2019 mBio Result IV E627K 165 170 PA;PB2 99;161 101;164 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. These results demonstrate that the N-terminal 1-252 domain of PA (PAN) is critical in mediating the acquisition of the PB2 E627K substitution during the replication of H7N9 virus in mammalian hosts. 2019 mBio Result IV E627K 123 128 PA;PB2 62;119 64;122 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. These results indicate that amino acid differences between PG/S1421(H7N9) and CK/5(H9N2) PA in region 121-191 are critical in determining the low polymerase activity of H7N9 AIVs and the emergence of the mammalian-adaptive PB2 E627K mutation. 2019 mBio Result IV E627K 227 232 PA;PB2 89;223 91;226 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. These results indicate that once the viral polymerase activity is compensated for by the PB2 E627K mutation, the polymerase function and virus growth are no longer influenced by huANP32A in human cells. 2019 mBio Result IV E627K 93 98 PB2 89 92 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. These results indicate that the PA gene carried by PG/S1421(H7N9) is responsible for driving the emergence of the PB2 E627K mutation in mice and that replacing PG/S1421(H7N9) PA with CK/5(H9N2) PA abolishes the acquisition of the adaptive PB2 E627K mutation in the mammalian host. 2019 mBio Result IV E627K;E627K 118;243 123;248 PA;PA;PA;PB2;PB2 32;175;194;114;239 34;177;196;117;242 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. These results suggest that the PA protein of PG/S1421(H7N9) is the causative viral factor for the low polymerase activity in human cells, which is associated with the emergence of the PB2 E627K substitution during virus replication in mice. 2019 mBio Result IV E627K 188 193 PA;PB2 31;184 33;187 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. Three other H9N2 viruses and the PG/S1421(H7N9) virus obtained the PB2 E627K mutation at passages 3 to 6 in MDCK cells (Table 1). 2019 mBio Result IV E627K 71 76 PB2 67 70 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. To explore the specific domain of PG/S1421(H7N9) PA that mediates the emergence of the PB2 E627K mutation of H7N9 viruses, we created two PA chimeras in which domain 1-252 or domain 253-716 of PG/S1421(H7N9) PA was replaced with that of CK/5(H9N2) PA. 2019 mBio Result IV E627K 91 96 PA;PA;PA;PA;PB2 49;138;208;248;87 51;140;210;250;90 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. To investigate whether the H7N9 and H9N2 viruses have the same capability to obtain the PB2 E627K mutation during replication in a mammalian host, we first selected an H7N9 avian strain, A/pigeon/Shanghai/S1421/2013 [PG/S1421(H7N9)], and five H9N2 avian strains and passaged them in MDCK cells. 2019 mBio Result IV E627K 92 97 PB2 88 91 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. We also found that three PG/S1421(H7N9) mutant viruses bearing three CK/5(H9N2) PA residues (i.e., PG/S1421-PA142R-147V-171V, PG/S1421-PA142R-147V-182L, and PG/S1421-PA147V-171V-182L) obtained the PB2 E627K mutation while replicating in mice, whereas a fourth triple-PA mutant PG/S1421(H7N9) virus (i.e., PG/S1421-PA142R-171V-182L) was not recovered from infected mouse lungs. 2019 mBio Result IV E627K 201 206 PA;PA;PA;PA;PA;PA;PB2 80;108;135;166;267;314;197 82;110;137;168;269;316;200 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. When we tested the PG/S1421(H7N9)-backbone viruses with PAN chimeras in mice, we found that the three H7N9 chimeric PAN viruses with low polymerase activities (i.e., PG/S1421-CK/5PA1-60, PG/S1421-CK/5PA1-86, and PG/S1421-CK/5PA1-120) acquired the PB2 E627K mutation after one passage in mice. 2019 mBio Result IV E627K 251 256 PB2 247 250 31223581 Genetic and Phylogenetic Characterization of the M Gene of Influenza A Virus Isolated from Iranian Patients. All Iranian H1N1 and H3N2 studied isolates possessed the most frequently adamantane-drug resistance mutation resulted in the amino acid substitution S31N in the M2 protein. 2019 Iranian journal of public health Result IV S31N 149 153 M2 161 163 31266524 Highly pathogenic avian influenza H7N9 viruses with reduced susceptibility to neuraminidase inhibitors showed comparable replication capacity to their sensitive counterparts. Furthermore, the substitution A246T in the NA protein induced a mean 10.97-fold increase in the IC50 of zanamivir (mean IC50 (nM) +- SD, 16.46 +- 0.59). 2019 Virology journal Result IV A246T 30 35 43 45 31266524 Highly pathogenic avian influenza H7N9 viruses with reduced susceptibility to neuraminidase inhibitors showed comparable replication capacity to their sensitive counterparts. However, the substitution E119V in the NA protein induced a mean 90.77-fold increase in the IC50 of oseltamivir (mean IC50 (nM) +- SD, 112.55 +- 17.25). 2019 Virology journal Result IV E119V 26 31 39 41 31266524 Highly pathogenic avian influenza H7N9 viruses with reduced susceptibility to neuraminidase inhibitors showed comparable replication capacity to their sensitive counterparts. In addition, the substitution H274Y in the NA protein induced a mean 23.40-fold increase in the IC50 of oseltamivir (mean IC50 (nM) +- SD, 29.01 +- 0.18). 2019 Virology journal Result IV H274Y 30 35 43 45 31266524 Highly pathogenic avian influenza H7N9 viruses with reduced susceptibility to neuraminidase inhibitors showed comparable replication capacity to their sensitive counterparts. The E119V mutation in N2 has been reported to significantly reduce the sensitivity of the virus to oseltamivir but not to zanamivir. 2019 Virology journal Result IV E119V 4 9 31266524 Highly pathogenic avian influenza H7N9 viruses with reduced susceptibility to neuraminidase inhibitors showed comparable replication capacity to their sensitive counterparts. The nucleotide changes were as follows: for E119V, E/GAA to V/GTA; for A246T, A/GCC to T/ACA; for H274Y, H/CAT to Y/TAT (Table 1). 2019 Virology journal Result IV E119V;A246T;H274Y 44;71;98 49;76;103 31267843 Mammalian-adaptive mutation NP-Q357K in Eurasian H1N1 Swine Influenza viruses determines the virulence phenotype in mice. All the rgHuN-NPK305R-, rgHuN-NPV313F-, rgHuN-NPK305R+V313F-, or rgHuN-NPV313F+K357Q-infected mice became severely ill, lost bodyweight from 2 dpi (> 30% from baseline), and eventually died or were humanly euthanized by 12 dpi (0% survival; Figure 4(C-D)). 2019 Emerging microbes & infections Result IV V313F;K357Q;V313F 54;79;73 59;84;78 NP;NP;NP;NP 14;30;46;71 16;32;48;73 31267843 Mammalian-adaptive mutation NP-Q357K in Eurasian H1N1 Swine Influenza viruses determines the virulence phenotype in mice. However, the introduction of substitution Q357K into JS1 NP resulted in significant bodyweight loss and 4/5 fatalities in the mice (Supplementary Figure 2(C-D)). 2019 Emerging microbes & infections Result IV Q357K 42 47 NP 57 59 31267843 Mammalian-adaptive mutation NP-Q357K in Eurasian H1N1 Swine Influenza viruses determines the virulence phenotype in mice. In contrast, the two cohorts of mice infected with rgHuN-NPK357Q or rgHuN-NPK305R+K357Q showed 100% survival for 14 dpi, a very modest bodyweight loss (< 10%), and few clinical symptoms (Figure 4(C-D)). 2019 Emerging microbes & infections Result IV K357Q;K357Q 82;59 87;64 NP;NP 57;74 59;76 31267843 Mammalian-adaptive mutation NP-Q357K in Eurasian H1N1 Swine Influenza viruses determines the virulence phenotype in mice. Substitution NP-K357Q decreases the infectivity, replication, and virulence of EA SIVs. 2019 Emerging microbes & infections Result IV K357Q 16 21 NP 13 15 31267843 Mammalian-adaptive mutation NP-Q357K in Eurasian H1N1 Swine Influenza viruses determines the virulence phenotype in mice. Substitutions R305K, F313V, and Q357K in the NP protein are mammalian signatures for the influenza A viruses. 2019 Emerging microbes & infections Result IV R305K;F313V;Q357K 14;21;32 19;26;37 NP 45 47 31267843 Mammalian-adaptive mutation NP-Q357K in Eurasian H1N1 Swine Influenza viruses determines the virulence phenotype in mice. Therefore, the substitution NP-K357Q reduced the virulence of the EA SIVs in mice. 2019 Emerging microbes & infections Result IV K357Q 31 36 NP 28 30 31267843 Mammalian-adaptive mutation NP-Q357K in Eurasian H1N1 Swine Influenza viruses determines the virulence phenotype in mice. These results indicate that NP-Q357K increases the viral replication of EA SIVs in mice. 2019 Emerging microbes & infections Result IV Q357K 31 36 NP 28 30 31267843 Mammalian-adaptive mutation NP-Q357K in Eurasian H1N1 Swine Influenza viruses determines the virulence phenotype in mice. This result indicated that the substitution NP-K357Q reduced the infectivity of the EA SIVs in mice. 2019 Emerging microbes & infections Result IV K357Q 47 52 NP 44 46 31267843 Mammalian-adaptive mutation NP-Q357K in Eurasian H1N1 Swine Influenza viruses determines the virulence phenotype in mice. To assess the contribution of the NP-Q357K substitution to the replication of EA SIVs in the respiratory tracts of mice, we inoculated mice with 105 TCID50 of each virus and analysed the viral titres in the nasal turbinate, tracheal tissue, and lung at various times after inoculation (Figure 5(C)). 2019 Emerging microbes & infections Result IV Q357K 37 42 NP 34 36 31267843 Mammalian-adaptive mutation NP-Q357K in Eurasian H1N1 Swine Influenza viruses determines the virulence phenotype in mice. To evaluate the contribution of substitution NP-Q357K to the virulence and infectivity of EA SIVs in mammals, the 50% mouse infective dose (MID50) and 50% mouse lethal dose (MLD5) were first determined. 2019 Emerging microbes & infections Result IV Q357K 48 53 NP 45 47 31267843 Mammalian-adaptive mutation NP-Q357K in Eurasian H1N1 Swine Influenza viruses determines the virulence phenotype in mice. To understand whether Q357K substitution affect the viral polymerase activity or virus replications in vitro, we firstly performed polymerase activities assay. 2019 Emerging microbes & infections Result IV Q357K 22 27 31267843 Mammalian-adaptive mutation NP-Q357K in Eurasian H1N1 Swine Influenza viruses determines the virulence phenotype in mice. When infected with 104 TCID50 of recombinant virus, the mice infected with the wild-type HuN (rgHuN-WT) or rgHuN-NPK305R+V313F+K357Q virus showed a reduction in bodyweight of up to 20% by 9 dpi, and 4/5 mice survived the infection (80% survival rate; Figure 4(C-D)). 2019 Emerging microbes & infections Result IV V313F;K357Q 121;127 126;132 NP 113 115 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. Aligned with SH2 HA, GD17 HA has 12 amino acid substitutions in addition to the insertion of the multibasic cleavage site, including S127N in antigenic site A, L226Q in the receptor-binding site (RBS) and antigenic site D, and A134V that was attributed to antigenic drift. 2019 Journal of virology Result IV S127N;L226Q;A134V 133;160;227 138;165;232 HA;HA 17;26 19;28 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. and the NA activities of rgSH2WT and rgSH2-G218E were similar in cleavage of the small soluble substrate 4-MU-NANA. 2019 Journal of virology Result IV G218E 43 48 8 10 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. Association of G218E in HA with MDCK adaptation and improved growth of H7 viruses. 2019 Journal of virology Result IV G218E 15 20 HA 24 26 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. Based on the findings that G218E resulted in reduced H7 virus binding to receptors and facilitated NA function, we further used electron microscopic techniques to determine whether G218E-induced MDCK adaptation is associated with facilitated nascent virus release from the infected cells. 2019 Journal of virology Result IV G218E;G218E 27;181 32;186 99 101 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. Based on the genetic and antigenic similarity between the HAs of SH2 and NL12, we introduced G218E into the HA of the low-yield A(H7N9) CVV rgSH2. 2019 Journal of virology Result IV G218E 93 98 HA 108 110 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. Both spherical and filamentous morphologies were observed in MDCK-grown rgSH2WT and rgSH2-G218E. 2019 Journal of virology Result IV G218E 90 95 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. but few aggregated viruses, among the individual viruses on the surfaces of rgSH2-G218E-infected cells. 2019 Journal of virology Result IV G218E 82 87 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. Compared to the association curve of rgSH2WT with 3'SLN, the association curve of rgSH2-G218E to 3'SLN showed a lower peak, followed by a steeper decay in the absence of NAi, indicating a more efficient cleavage of the sialic acids by NA. 2019 Journal of virology Result IV G218E 88 93 NA;NAI 235;170 237;173 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. Consistent with that observed in NL12ad and rgSH2-G218E, the binding avidity of rgGD-G218E to both avian- and human-type receptor analogs was reduced to approximately 25% of that measured in rgGD17. 2019 Journal of virology Result IV G218E;G218E 50;85 55;90 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. Consistently, the microneutralization (MN) antibody titers of the rgGD17 antiserum and the rgGD-G218E antiserum were both within a 2-fold difference in neutralizing GD17WT, rgGD17, and rgGD-G218E (Table 1, values in parentheses), suggesting that the G218E substitution in rgSH2 HA or rgGD17 HA did not cause significant antigenic change. 2019 Journal of virology Result IV G218E;G218E;G218E 96;190;250 101;195;255 HA;HA 278;291 280;293 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. Figure 4A showed the saturation binding curves of both rgSH2WT and rgSH2-G218E binding to 3'SLN with NAi (dashed lines) or without NAi (solid lines). 2019 Journal of virology Result IV G218E 73 78 NAI;NAI 101;131 104;134 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. Figure 4B demonstrated that the binding of rgSH2WT to 6'SLN was only slightly affected by the concurrent NA enzymatic activity (the difference between the blue solid line and blue dashed line), whereas binding of rgSH2-G218E to 6'SLN was more susceptible to the concurrent NA cleavage (red lines), indicating a stronger NA effect on binding to a human-type receptor analogs (6'SLN) of the rgSH2-G218E than that of the rgSH2WT. 2019 Journal of virology Result IV G218E;G218E 219;395 224;400 NA;NA;NA 105;273;320 107;275;322 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. G218E substitution facilitated N9 NA activity in H7N9 virus. 2019 Journal of virology Result IV G218E 0 5 N9;NA 31;34 33;36 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. G218E substitution facilitated the release of progeny H7 viruses from infected MDCK cells. 2019 Journal of virology Result IV G218E 0 5 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. In addition, the HI antibodies elicited by both rgSH2 and rgGD17 showed certain cross-reactivities among the H7N9 strains, whereas rgGD17 and rgGD-G218E rather than rgSH2 induced MN antibodies that reacted well with both homologous and heterologous H7N9 viruses. 2019 Journal of virology Result IV G218E 147 152 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. In addition, the multiple-step growth curves of rgNL12-G218E and rgNL12-G218E/K328R were similar, and rgNL12-K328R exhibited growth kinetics similar to those of rgNL12WT (data not shown), indicating that G218E was the determinant substitution for the NL12ad phenotype. 2019 Journal of virology Result IV G218E;G218E;K328R;K328R;G218E 55;72;78;109;204 60;77;83;114;209 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. In agreement with the G218E phenotype in NL12, rgSH2-G218E significantly outgrew rgSH2WT in both MDCK cells and eggs. 2019 Journal of virology Result IV G218E;G218E 22;53 27;58 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. In contrast, none of the rgGD17- or the rgGD-G218E-immunized ferrets showed obvious illness signs after GD17WT challenge. 2019 Journal of virology Result IV G218E 45 50 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. Intranasal inoculation with live rgGD17 or rgGD-G218E in ferrets induced specific antibody response against both homologous virus and the parental HPAI GD17WT in 2 weeks, as confirmed by HI assay. 2019 Journal of virology Result IV G218E 48 53 Influenza 147 151 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. Meanwhile, R292K, a mutation attributed to neuraminidase inhibitor (NAi) resistance, was identified in GD17 NA. 2019 Journal of virology Result IV R292K 11 16 NA;NAI;NA 108;68;43 110;71;56 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. Pretreatment of MDCK cells with cholera filtrate (receptor-destroying enzyme [RDE]) reduced the infectivity of both rgSH2WT and rgSH2-G218E in a concentration-dependent manner, but the latter showed a much steeper decline, suggesting that G218E substitution decreased the binding avidity of SH2 virus to MDCK cells. 2019 Journal of virology Result IV G218E;G218E 134;239 139;244 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. Reduced binding of G218E variants to both avian- and human-type receptor analogs. 2019 Journal of virology Result IV G218E 19 24 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. Reduced binding of G218E variants to MDCK cells. 2019 Journal of virology Result IV G218E 19 24 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. rgSH2-G218E formed large plaques and replicated more efficiently in MDCK cells. 2019 Journal of virology Result IV G218E 6 11 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. Sequencing analysis of NL12ad revealed two amino acid substitutions in HA, G218E and K328R (H3 numbering). 2019 Journal of virology Result IV G218E;K328R 75;85 80;90 HA 71 73 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. Similar results were obtained in the study using rgGD17 and rgGD-G218E (data not shown). 2019 Journal of virology Result IV G218E 65 70 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. Similar to the finding with NL12ad, rgSH2-G218E variant exhibited a significantly decreased binding avidity to both 3'SLN and 6'SLN, which was about 35% of that measured from rgSH2WT. 2019 Journal of virology Result IV G218E 42 47 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. Similarly, we introduced G218E into the HA of rgGD17 and achieved significantly improved virus growth in both MDCK cells (68.3% increase. 2019 Journal of virology Result IV G218E 25 30 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. The reduced binding to MDCK cells was also observed in rgSH2-G218E. 2019 Journal of virology Result IV G218E 61 66 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. The rgNL12-G218E formed large plaques with sizes similar to that formed by rgNL12-G218E/K328R, while the plaque size of rgNL12-K328R was similar to that formed by rgNL12WT (data not shown). 2019 Journal of virology Result IV G218E;G218E;K328R;K328R 11;82;88;127 16;87;93;132 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. The SEM and TEM findings confirmed the impeded release of WT NL12 and SH2 progenies from infected cells, which indicated that insufficient NA function cooperates with the HA binding and that the G218E substitution facilitates nascent virus release to initiate a new replication cycle by reducing HA receptor binding. 2019 Journal of virology Result IV G218E 195 200 HA;HA;NA 171;296;139 173;298;141 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. The total viral protein yield of rgSH2-G218E increased by 92.5% in MDCK cells and 154% in eggs compared to that of the wild-type counterpart. 2019 Journal of virology Result IV G218E 39 44 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. Therefore, we generated the low-pathogenic A(H7N9) CVV rgGD17 from the HPAI GD17WT by removing the multibasic motif in HA and introducing K292R in NA. 2019 Journal of virology Result IV K292R 138 143 HA;NA 119;147 121;149 Influenza;Influenza A virus H7N9 infection 45;71 49;75 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. These data demonstrated that (i) the concurrent HA binding and NA cleavage dynamically shaped the distinctive interaction of H7N9 virus with avian- and human-type receptors, (ii) the N9 NA functioned more efficiently on disrupting the H7 virus binding to avian-type receptor than the binding to human-type receptor, and (iii) the G218E substitution in H7 HA resulted in an enhanced effect of N9 NA on disrupting virus binding to both avian- and human-type receptors as a result of reduced H7N9 virus binding. 2019 Journal of virology Result IV G218E 330 335 HA;HA;N9;N9;NA;NA;NA 48;355;183;392;63;186;395 50;357;185;394;65;188;397 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. These results demonstrated that both low-pathogenic reassortants rgGD-G218E and rgGD17 induced specific immune response that effectively protected the immunized ferrets from lethal-dose challenge of parental HPAI GD17WT. 2019 Journal of virology Result IV G218E 70 75 Influenza 208 212 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. This finding is in agreement with the reduced binding of rgSH2-G218E to MDCK cells. 2019 Journal of virology Result IV G218E 63 68 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. To evaluate the effectiveness of the immune response elicited by rgGD17 and rgGD-G218E, the immunized ferrets were challenged with GD17WT virus. 2019 Journal of virology Result IV G218E 81 86 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. To examine the possible antigenic impact of G218E, we compared the antigenicity of G218E variants and the WT counterparts in ferrets. 2019 Journal of virology Result IV G218E;G218E 44;83 49;88 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. To identify the substitution responsible for the MDCK adaptation, we generated 7:1 (H7N1) reassortants rgNL12WT, rgNL12-G218E, rgNL12-K328R, and rgNL12-G218E/K328R. 2019 Journal of virology Result IV G218E;K328R;K328R;G218E 120;134;158;152 125;139;163;157 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. We further assessed the protection of the immune response to the rgGD17 and rgGD-G218E against GD17WT infection in a ferret model. 2019 Journal of virology Result IV G218E 81 86 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. When the NA activity was inhibited by NAi, the association curves of rgSH2WT and rgSH2-G218E were similar: a rapid rise, followed by a gradual increase to reach the plateau, the equilibrium of association and dissociation between the virus and receptor analog. 2019 Journal of virology Result IV G218E 87 92 NA;NAI 9;38 11;41 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. which indicated a more efficient SA cleavage by the rgSH2-G218E than by the rgSH2WT, although the expression of NA on both rgSH2WT and rgSH2-G218E was comparable, as determined by SDS-PAGE. 2019 Journal of virology Result IV G218E;G218E 58;141 63;146 112 114 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. which is a critical component of RBS, the G218E substitution is likely relevant to alteration in virus binding to host cells. 2019 Journal of virology Result IV G218E 42 47 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. With the two pairs of ferret antisera elicited by the rgSH2WT/rgSH2-G218E and rgGD17/rgGD-G218E, the two-way hemagglutination inhibition (HI) assay results determined that the HI titers of each pair were within 2-fold difference (Table 1). 2019 Journal of virology Result IV G218E;G218E 68;90 73;95 31305236 Prevailing I292V PB2 mutation in avian influenza H9N2 virus increases viral polymerase function and attenuates IFN-beta induction in human cells. Both PB2-292I and PB2-292V co-immunoprecipitated with Flag-MAVS fusion protein; PB2-292V was co-immunoprecipitated at twice the level of PB2-292I, demonstrating that PB2-I292V mutation increases the binding affinity of PB2 to MAVS. 2019 The Journal of general virology Result IV I292V 170 175 PB2;PB2;PB2;PB2;PB2;PB2 5;18;80;137;166;219 8;21;83;140;169;222 31305236 Prevailing I292V PB2 mutation in avian influenza H9N2 virus increases viral polymerase function and attenuates IFN-beta induction in human cells. PB2-I292V augments transcription and genomic RNA replication of H9N2 virus in human cells. 2019 The Journal of general virology Result IV I292V 4 9 PB2 0 3 31305236 Prevailing I292V PB2 mutation in avian influenza H9N2 virus increases viral polymerase function and attenuates IFN-beta induction in human cells. PB2-I292V confers in H9N2 virus higher polymerase activity in human cells. 2019 The Journal of general virology Result IV I292V 4 9 PB2 0 3 31305236 Prevailing I292V PB2 mutation in avian influenza H9N2 virus increases viral polymerase function and attenuates IFN-beta induction in human cells. PB2-I292V increases avian H9N2 influenza viral transcription and replication in human A549 cells. 2019 The Journal of general virology Result IV I292V 4 9 PB2 0 3 31305236 Prevailing I292V PB2 mutation in avian influenza H9N2 virus increases viral polymerase function and attenuates IFN-beta induction in human cells. PB2-I292V mutation increases replication of H9N2 virus in mammalian cells. 2019 The Journal of general virology Result IV I292V 4 9 PB2 0 3 31305236 Prevailing I292V PB2 mutation in avian influenza H9N2 virus increases viral polymerase function and attenuates IFN-beta induction in human cells. PB2-I292V mutation resulted in significant increase in polymerase activity in human 293T cells at both 33 and 37 C (P<0.05). 2019 The Journal of general virology Result IV I292V 4 9 PB2 0 3 31305236 Prevailing I292V PB2 mutation in avian influenza H9N2 virus increases viral polymerase function and attenuates IFN-beta induction in human cells. PB2-I292V mutational change in PB2 strongly attenuates virus induced IFN-beta expression in human cells. 2019 The Journal of general virology Result IV I292V 4 9 PB2;PB2 0;31 3;34 31305236 Prevailing I292V PB2 mutation in avian influenza H9N2 virus increases viral polymerase function and attenuates IFN-beta induction in human cells. Potential mammalian adaptative mutation of PB2-I292V is predominant in avian H9N2 influenza viruses. 2019 The Journal of general virology Result IV I292V 47 52 PB2 43 46 31305236 Prevailing I292V PB2 mutation in avian influenza H9N2 virus increases viral polymerase function and attenuates IFN-beta induction in human cells. Thus, PB2-I292V H9N2 virus replicates to a higher titre than that of PB2-292V virus in mammalian cells. 2019 The Journal of general virology Result IV I292V 10 15 PB2;PB2 6;69 9;72 31305236 Prevailing I292V PB2 mutation in avian influenza H9N2 virus increases viral polymerase function and attenuates IFN-beta induction in human cells. To ascertain whether vRNP polymerase activity is affected by PB2-I292V mutation, we produced wild-type (H9N2:PB2-292I), and mutant (H9N2:PB2-292V) viruses by reverse genetics. 2019 The Journal of general virology Result IV I292V 65 70 PB2;PB2;PB2 61;109;137 64;112;140 31305236 Prevailing I292V PB2 mutation in avian influenza H9N2 virus increases viral polymerase function and attenuates IFN-beta induction in human cells. To further investigate whether the PB2-I292V mutation has an effect on the expression of IFN-beta mRNA in response to influenza virus infection, A549 cells were separately infected with H9N2:PB2-292I and H9N2:PB2-292V virus and the IFN-beta mRNA levels were determined at 12 and 24 h p.i. 2019 The Journal of general virology Result IV I292V 39 44 PB2;PB2;PB2 35;191;209 38;194;212 IV infections 118 143 31305236 Prevailing I292V PB2 mutation in avian influenza H9N2 virus increases viral polymerase function and attenuates IFN-beta induction in human cells. To identify whether PB2-I292V enhances the RNP polymerase activity, viral mini-genome polymerase assays were performed by transfecting wild-type PB2 (PB2-292I) or mutant PB2 (PB2-292V) gene encoding plasmid with PB1, PA and NP expression plasmids of wild-type H9N2 virus. 2019 The Journal of general virology Result IV I292V 24 29 NP;PA;PB1;PB2;PB2;PB2;PB2;PB2;RNP 224;217;212;20;145;150;170;175;43 226;219;215;23;148;153;173;178;46 31329089 Biological properties of influenza A virus mutants with amino acid substitutions in the HA2 glycoprotein of the HA1/HA2 interaction region. Histidine was therefore introduced into the light chain of HA in two positions, namely at position 64 instead of threonine (T642H, referred to as mutant 64) and at position 66 instead of valine (V662H, referred to as mutant 66). 2019 The Journal of general virology Result IV T642H;V662H 124;195 129;200 HA 59 61 31329089 Biological properties of influenza A virus mutants with amino acid substitutions in the HA2 glycoprotein of the HA1/HA2 interaction region. T642H and V662H (this double mutant is referred to as 'D'). 2019 The Journal of general virology Result IV T642H;V662H 0;10 5;15 31356626 Severe cases of seasonal influenza in Russia in 2017-2018. Analysis of the HA D222G/N polymorphism using the next generation sequencing (NGS) data allowed us to detect and estimate the degree of the polymorphism in the studied cases. 2019 PloS one Result IV D222G;D222N 19;19 26;26 HA 16 18 31356626 Severe cases of seasonal influenza in Russia in 2017-2018. Analysis of the HA gene of 29 selected cases of A(H1N1)pdm09 influenza revealed in the major virus variant the presence of mutations D222G or D222N (H1 numbering) in the receptor-binding site in the MDCK isolates of four lethal cases out of 19 lethal cases included in the study (Table 2). 2019 PloS one Result IV D222G;D222N 133;142 138;147 HA 16 18 31356626 Severe cases of seasonal influenza in Russia in 2017-2018. Analysis of the NA of all studied A(H3N2) viruses for the presence of mutations conferring drug resistance revealed I222V amino acid substitution in the NA of A/Astrakhan/32/2017 strain. 2019 PloS one Result IV I222V 116 121 NA;NA 16;153 18;155 31356626 Severe cases of seasonal influenza in Russia in 2017-2018. Analysis of the neuraminidase (NA) gene of 29 A(H1N1)pdm09 viruses revealed the presence of the H275Y mutation (H1 numbering) in a single virus, A/Samara/117868/2018 (in the primary material and in the MDCK isolate). 2019 PloS one Result IV H275Y 96 101 NA;NA 31;16 33;29 31356626 Severe cases of seasonal influenza in Russia in 2017-2018. Another subgroup included a virus with HA gene that encodes the T135N substitution. 2019 PloS one Result IV T135N 64 69 HA 39 41 31356626 Severe cases of seasonal influenza in Russia in 2017-2018. For 3C.2a2 clade, a combination of T131K, R142K and R261Q substitutions was seen, and a combination of N121K and S144K substitutions was observed for 3C.2a3 clade. 2019 PloS one Result IV T131K;R142K;R261Q;N121K;S144K 35;42;52;103;113 40;47;57;108;118 31356626 Severe cases of seasonal influenza in Russia in 2017-2018. For clade 3C.2a1b the combination of K92R and H311Q substitutions in HA1 was observed (H3 numbering is used for all A(H3N2) amino acid substitutions). 2019 PloS one Result IV K92R;H311Q 37;46 41;51 HA1 69 72 31356626 Severe cases of seasonal influenza in Russia in 2017-2018. Genetic analysis revealed the presence of the H275Y amino acid substitution in the NA of this strain, which is associated with resistance to oseltamivir of A(H1N1) pdm09 viruses. 2019 PloS one Result IV H275Y 46 51 83 85 31356626 Severe cases of seasonal influenza in Russia in 2017-2018. In addition, all studied viruses had mutations in antigenic site B, one of which, P194L, is in a site of antibody recognition and another mutation, K160T, was shown to be associated with antigenic drift. 2019 PloS one Result IV P194L;K160T 82;148 87;153 31356626 Severe cases of seasonal influenza in Russia in 2017-2018. One of the subgroups included viruses with HA genes that encode E62G and R142G in HA1 with an additional substitution of T135K. 2019 PloS one Result IV E62G;R142G;T135K 64;73;121 68;78;126 HA;HA1 43;82 45;85 31356626 Severe cases of seasonal influenza in Russia in 2017-2018. T160K reverse mutation was shown to be an adaptation mutation to the growth in embryonated chicken eggs and it is absent in the cell-based A/HongKong/4801/2014 vaccine strain. 2019 PloS one Result IV T160K 0 5 31356626 Severe cases of seasonal influenza in Russia in 2017-2018. The H275Y substitution was previously associated with highly reduced inhibition by oseltamivir and reduced or highly reduced inhibition by peramivir of A(H1N1)pdm09 viruses (according to the criteria of the WHO expert working group on surveillance of influenza antiviral susceptibility). 2019 PloS one Result IV H275Y 4 9 31356626 Severe cases of seasonal influenza in Russia in 2017-2018. The presence of D222N mutation was not detected in the viral isolate of A/Irkutsk/1727/2018 lethal case (Table 2). 2019 PloS one Result IV D222N 16 21 31356626 Severe cases of seasonal influenza in Russia in 2017-2018. This analysis also revealed the simultaneous presence of viruses with D222G and D222N mutations in three studied lethal cases (in two viral isolates, A/Ulyanovsk/205/2018 and A/Irkutsk/1728/2018, and in the original clinical material of A/Irkutsk/1728/2018 and A/Krasnoyarsk/54/2018 cases) (Table 2). 2019 PloS one Result IV D222G;D222N 70;80 75;85 31356626 Severe cases of seasonal influenza in Russia in 2017-2018. This analysis revealed the presence of D222G and D222N mutations in minor amounts in the primary clinical material of A/Krasnoyarsk/54/2018 lethal case (MDCK isolate was not available) and D222N mutation was detected in a minor amount in the primary clinical material of A/Irkutsk/1727/2018 lethal case (Table 2). 2019 PloS one Result IV D222G;D222N;D222N 39;49;189 44;54;194 31420169 The structure and conformational plasticity of the nonstructural protein 1 of the 1918 influenza A virus. Both W187R and W187A mutations can abolish NS1-ED homodimerization; however, the W187R mutation is the only amino acid substitution allowed for position 187 of NS1 that does not affect the overlapping open reading frame of NS2, which is an alternatively spliced protein of the NS1 gene. 2019 Biochemical and biophysical research communications Result IV W187R;W187A;W187R 5;15;81 10;20;86 NS1;NS1;NS1;NS2 43;160;277;223 46;163;280;226 31420169 The structure and conformational plasticity of the nonstructural protein 1 of the 1918 influenza A virus. However, it remained unclear whether the 1918 NS1-ED W187A or W187R forms a dimer in solution. 2019 Biochemical and biophysical research communications Result IV W187A;W187R 53;62 58;67 NS1 46 49 31420169 The structure and conformational plasticity of the nonstructural protein 1 of the 1918 influenza A virus. However, we note that long-term solubility of 1918 NS1-ED W187R was limited. 2019 Biochemical and biophysical research communications Result IV W187R 58 63 NS1 51 54 31420169 The structure and conformational plasticity of the nonstructural protein 1 of the 1918 influenza A virus. However, while the NMR structure is a monomer, the crystal structure of the 1918 NS1-ED W187A showed a dimeric form. 2019 Biochemical and biophysical research communications Result IV W187A 88 93 NS1 81 84 31420169 The structure and conformational plasticity of the nonstructural protein 1 of the 1918 influenza A virus. In this study, we incorporated the W187R mutation into 1918 NS1-ED to abolish homodimerization. 2019 Biochemical and biophysical research communications Result IV W187R 35 40 NS1 60 63 31420169 The structure and conformational plasticity of the nonstructural protein 1 of the 1918 influenza A virus. The 1918 NS1-ED W187R exists as a monomer in solution. 2019 Biochemical and biophysical research communications Result IV W187R 16 21 NS1 9 12 31420169 The structure and conformational plasticity of the nonstructural protein 1 of the 1918 influenza A virus. The crystal structure contained two NS1-ED molecules in an asymmetric unit, although the W187A mutation is supposed to abolish the dimeric form. 2019 Biochemical and biophysical research communications Result IV W187A 89 94 NS1 36 39 31420169 The structure and conformational plasticity of the nonstructural protein 1 of the 1918 influenza A virus. The limited solubility suggests that even NS1-ED W187R undergoes oligomerization in slower timescale despite that its mechanism and relationship to biological function remain to be determined. 2019 Biochemical and biophysical research communications Result IV W187R 49 54 NS1 42 45 31420169 The structure and conformational plasticity of the nonstructural protein 1 of the 1918 influenza A virus. The overall structure of the 1918 NS1-ED W187R was highly similar to the recently reported crystal structure of the 1918 NS1-ED W187A (PDB ID: 6DGK) (Figure 2A). 2019 Biochemical and biophysical research communications Result IV W187R;W187A 41;128 46;133 NS1;NS1 34;121 37;124 31420169 The structure and conformational plasticity of the nonstructural protein 1 of the 1918 influenza A virus. The side chain of R187 was also fully exposed to solvent in the NMR structure of the Ud NS1-ED W187R. 2019 Biochemical and biophysical research communications Result IV W187R 95 100 NS1 88 91 31420169 The structure and conformational plasticity of the nonstructural protein 1 of the 1918 influenza A virus. The structure of the 1918 NS1-ED W187R (hereinafter 1918 NS1-ED unless otherwise defined) was determined using solution NMR spectroscopy as described in the Methods. 2019 Biochemical and biophysical research communications Result IV W187R 33 38 NS1;NS1 26;57 29;60 31420169 The structure and conformational plasticity of the nonstructural protein 1 of the 1918 influenza A virus. These results indicate that the W187R mutation does not affect the overall structure of the 1918 NS1-ED. 2019 Biochemical and biophysical research communications Result IV W187R 32 37 NS1 97 100 31420169 The structure and conformational plasticity of the nonstructural protein 1 of the 1918 influenza A virus. This shows that the 1918 NS1-ED W187R exists as a monomer in solution, although more thorough examination might be needed. 2019 Biochemical and biophysical research communications Result IV W187R 32 37 NS1 25 28 31420169 The structure and conformational plasticity of the nonstructural protein 1 of the 1918 influenza A virus. To address whether the 1918 NS1-ED-W187R exists as a monomer or dimer in solution, we measured the correlation time (tauc) for the rotational diffusion process of the 1918 NS1-ED using the NMR 15N R2/R1 ratio, which is a highly sensitive probe of molecular size and shape. 2019 Biochemical and biophysical research communications Result IV W187R 35 40 NS1;NS1 28;172 31;175 31420169 The structure and conformational plasticity of the nonstructural protein 1 of the 1918 influenza A virus. We speculate that the slow-timescale precipitation could be induced by alpha3-alpha3 or strand-strand dimeric interfaces, which are not suppressed by W187R mutation. 2019 Biochemical and biophysical research communications Result IV W187R 150 155 31477028 A study of the relationship between human infection with avian influenza a (H5N6) and environmental avian influenza viruses in Fujian, China. However, the Q226L and G228S mutations that may enhance the risk of human infection were not identified at the 210-loop in the HA proteins in all eight virus strains. 2019 BMC infectious diseases Result IV Q226L;G228S 13;23 18;28 HA 127 129 31477028 A study of the relationship between human infection with avian influenza a (H5N6) and environmental avian influenza viruses in Fujian, China. However, the S31 N substitution in the M2 gene was detected in one strain of A/Environment/Fujian/28681/2016. 2019 BMC infectious diseases Result IV S31N 13 18 M2 39 41 31477028 A study of the relationship between human infection with avian influenza a (H5N6) and environmental avian influenza viruses in Fujian, China. Neither R294K nor N294S substitution was detected in the NA genes of all the eight H5N6 viruses, indicating a general sensitivity to Oseltamivir and Zanamivir antiviral drugs. 2019 BMC infectious diseases Result IV R294K;N294S 8;18 13;23 57 59 31477028 A study of the relationship between human infection with avian influenza a (H5N6) and environmental avian influenza viruses in Fujian, China. Other mutations that have been shown to increase virulence in mice, such as L89 V, G309D, T339K, R477G and I495V in PB2, P42S in NS1, N30D and T215A in M1, were also detected. 2019 BMC infectious diseases Result IV L89V;G309D;T339K;R477G;I495V;P42S;N30D;T215A 76;83;90;97;107;121;134;143 81;88;95;102;112;125;138;148 M1;NS1;PB2 152;129;116 154;132;119 31538644 Baloxavir Marboxil in Japanese Pediatric Patients With Influenza: Safety and Clinical and Virologic Outcomes. A higher frequency of emergence of PA/I38T/M-substituted viruses occurred in patients with baseline A(H3N2) HAI antibody titer of less than 40 (42.3% [11/26]) than in those with titers of 40 or greater (17.1% [7/41]) (P = .0467; Table 6). 2020 Clinical infectious diseases Result IV I38M;I38T 38;38 44;44 PA 35 37 31538644 Baloxavir Marboxil in Japanese Pediatric Patients With Influenza: Safety and Clinical and Virologic Outcomes. All were infected with A(H3N2) virus; variants included PA/I38T (n = 10), PA/I38T/I mixture (n = 5), PA/I38M (n = 2) and PA/I38I/M mixture (n = 1). 2020 Clinical infectious diseases Result IV I38I;I38M;I38T;I38T;I38M;I38I 77;124;59;77;104;124 83;130;63;83;108;130 PA;PA;PA;PA 56;74;101;121 58;76;103;123 31538644 Baloxavir Marboxil in Japanese Pediatric Patients With Influenza: Safety and Clinical and Virologic Outcomes. Also, a higher frequency of PA/I38T/M-substituted virus detection was found in H3N2-infected children aged 5 years or younger (6/10) than in older children (12/57) (Table 5). 2020 Clinical infectious diseases Result IV I38M;I38T 31;31 37;37 PA 28 30 31538644 Baloxavir Marboxil in Japanese Pediatric Patients With Influenza: Safety and Clinical and Virologic Outcomes. Among those with emergence of PA/I38T/M-substituted viruses, the median TTIA was 29.4 hours longer in those with baseline HAI antibody titer of less than 40 than in those with a higher HAI antibody titer (Figure 4). 2020 Clinical infectious diseases Result IV I38M;I38T 33;33 39;39 PA 30 32 31538644 Baloxavir Marboxil in Japanese Pediatric Patients With Influenza: Safety and Clinical and Virologic Outcomes. By day 2 the mean change in virus titer from baseline was comparable in those with (4.75 log10 50% tissue culture infective dose [TCID50]/mL) or without (4.78 log10TCID50/mL) PA/I38T/M-substituted viruses. 2020 Clinical infectious diseases Result IV I38M;I38T 178;178 184;184 PA 175 177 31538644 Baloxavir Marboxil in Japanese Pediatric Patients With Influenza: Safety and Clinical and Virologic Outcomes. Factors Associated With Emergence of PA/I38T/M-Substituted Viruses. 2020 Clinical infectious diseases Result IV I38T;I38M 40;40 46;46 PA 37 39 31538644 Baloxavir Marboxil in Japanese Pediatric Patients With Influenza: Safety and Clinical and Virologic Outcomes. In the post-treatment samples, PA/I38T substitutions were found to have emerged as early as 48 hours in 2 patients, and variant viruses emerged by 120 hours in 8 patients (Figure 3A). 2020 Clinical infectious diseases Result IV I38T 34 38 PA 31 33 31538644 Baloxavir Marboxil in Japanese Pediatric Patients With Influenza: Safety and Clinical and Virologic Outcomes. Increases in viral titer (>0.7) at day 3 or later were observed in 72.2% of patients with emergence of PA/I38T/M-substituted viruses compared with 13.6% of those without such viruses. 2020 Clinical infectious diseases Result IV I38M;I38T 106;106 112;112 PA 103 105 31538644 Baloxavir Marboxil in Japanese Pediatric Patients With Influenza: Safety and Clinical and Virologic Outcomes. PA/I38T-substituted viruses were first detected when the plasma BXA concentration ranged from 8.34 to 23.5 ng/mL (Figure 3A, C). 2020 Clinical infectious diseases Result IV I38T 3 7 PA 0 2 31538644 Baloxavir Marboxil in Japanese Pediatric Patients With Influenza: Safety and Clinical and Virologic Outcomes. PA/I38T/M-substituted viruses were detected in 18 patients (23.4%), and their first detection was at days 3 (n = 1), 6 (n = 12) or 9 (n = 5). 2020 Clinical infectious diseases Result IV I38M;I38T 3;3 9;9 PA 0 2 31538644 Baloxavir Marboxil in Japanese Pediatric Patients With Influenza: Safety and Clinical and Virologic Outcomes. Post hoc analyses identified differences in age distribution, body weight, and baseline HAI antibody between patients with and without PA/I38T/M-substituted viruses (Table 5). 2020 Clinical infectious diseases Result IV I38M;I38T 138;138 144;144 PA 135 137 31538644 Baloxavir Marboxil in Japanese Pediatric Patients With Influenza: Safety and Clinical and Virologic Outcomes. Symptom recurrences resolved (score of 1 or 0) within 48 hours, with the exception of 2 patients without PA/I38T/M-substituted viruses. 2020 Clinical infectious diseases Result IV I38M;I38T 108;108 114;114 PA 105 107 31538644 Baloxavir Marboxil in Japanese Pediatric Patients With Influenza: Safety and Clinical and Virologic Outcomes. The emergence of PA/I38T-substituted viruses corresponded temporally with an increase in viral titers, which, in most cases, had been below the quantification limit for at least 1 day prior to PA/I38T-substituted virus emergence (Figure 3B). 2020 Clinical infectious diseases Result IV I38T;I38T 20;196 24;200 PA;PA 17;193 19;195 31538644 Baloxavir Marboxil in Japanese Pediatric Patients With Influenza: Safety and Clinical and Virologic Outcomes. The mean plasma C24 in patients with PA/I38T/M-substituted viruses (58.4 ng/mL) was similar to that in patients without such viruses (58.0 ng/mL). 2020 Clinical infectious diseases Result IV I38M;I38T 40;40 46;46 PA 37 39 31538644 Baloxavir Marboxil in Japanese Pediatric Patients With Influenza: Safety and Clinical and Virologic Outcomes. The median time to sustained cessation of viral shedding in patients with PA/I38T/M-substituted viruses was 180.0 hours (95% CI, 144.0-216.0 hours) compared with 24.0 hours (95% CI, 24.0-48.0 hours) in those without (Supplementary Table 6). 2020 Clinical infectious diseases Result IV I38M;I38T 77;77 83;83 PA 74 76 31538644 Baloxavir Marboxil in Japanese Pediatric Patients With Influenza: Safety and Clinical and Virologic Outcomes. The median TTIA and fever resolution in patients with PA/I38T/M-substituted viruses were 79.6 and 29.5 hours, respectively, compared with 42.8 and 20.8 hours, respectively, in those without PA/I38T/M-substituted viruses (Figure 2, Supplementary Table 6). 2020 Clinical infectious diseases Result IV I38M;I38M;I38T;I38T 57;193;57;193 63;199;63;199 PA;PA 54;190 56;192 31538644 Baloxavir Marboxil in Japanese Pediatric Patients With Influenza: Safety and Clinical and Virologic Outcomes. The PA/I38T viruses became dominant in most of the patients after 120 hours, except for 2 patients who had undetectable levels of viral RNAs. 2020 Clinical infectious diseases Result IV I38T 7 11 PA 4 6 31538644 Baloxavir Marboxil in Japanese Pediatric Patients With Influenza: Safety and Clinical and Virologic Outcomes. The time to sustained cessation of infectious viral shedding in patients with PA/I38T/M-substituted viruses was considerably longer than that in those without, regardless of baseline HAI antibody titer (Figure 5). 2020 Clinical infectious diseases Result IV I38M;I38T 81;81 87;87 PA 78 80 31538644 Baloxavir Marboxil in Japanese Pediatric Patients With Influenza: Safety and Clinical and Virologic Outcomes. To assess time course of emergence of PA/I38T/M-substituted viruses, next-generation sequencing (NGS) was used for the analysis on swab samples from 10 selected patients with I38T-substituted viruses (Supplementary Figure 3). 2020 Clinical infectious diseases Result IV I38M;I38T;I38T 41;41;175 47;47;179 PA 38 40 31538644 Baloxavir Marboxil in Japanese Pediatric Patients With Influenza: Safety and Clinical and Virologic Outcomes. Transient fever and symptom recurrence after 72 hours postdose were observed in 23.5% and 37.5% of patients, respectively, with PA/I38T/M-substituted viruses compared with 8.5% and 20.5%, respectively, in those without (Supplementary Table 7); transient symptom score increases were also observed at 72 hours postdose (Supplementary Figure 2). 2020 Clinical infectious diseases Result IV I38M;I38T 131;131 137;137 PA 128 130 31575766 Influenza Virus Polymerase Mutation Stabilizes a Foreign Gene Inserted into the Virus Genome by Enhancing the Transcription/Replication Efficiency of the Modified Segment. Accordingly, the difference in the transcription/replication efficiency of the NS segment was likely caused by the PB2-E712D. 2019 mBio Result IV E712D 119 124 NS;PB2 79;115 81;118 31575766 Influenza Virus Polymerase Mutation Stabilizes a Foreign Gene Inserted into the Virus Genome by Enhancing the Transcription/Replication Efficiency of the Modified Segment. Although PR8-PB1-V43I had fewer mutations than WT-PR8, the difference between PR8-PB1-V43I and WT-PR8 was small. 2019 mBio Result IV V43I;V43I 17;86 21;90 PB1;PB1 13;82 16;85 31575766 Influenza Virus Polymerase Mutation Stabilizes a Foreign Gene Inserted into the Virus Genome by Enhancing the Transcription/Replication Efficiency of the Modified Segment. Although the possibility that the PB2-E712D mutation affects virus polymerase fidelity cannot be excluded, the effect does not seem to be large enough to cause an appreciable difference in Venus stability. 2019 mBio Result IV E712D 38 43 PB2 34 37 31575766 Influenza Virus Polymerase Mutation Stabilizes a Foreign Gene Inserted into the Virus Genome by Enhancing the Transcription/Replication Efficiency of the Modified Segment. Although WT-Venus-PR8 showed a lower titer than Venus-PR8-PB2-E712D in MDCK cells, as described previously, the virus titer increased during virus passages as the proportion of Venus-positive plaques decreased. 2019 mBio Result IV E712D 62 67 PB2 58 61 31575766 Influenza Virus Polymerase Mutation Stabilizes a Foreign Gene Inserted into the Virus Genome by Enhancing the Transcription/Replication Efficiency of the Modified Segment. Due to the reduced transcription/replication efficiency of the NS segment, the expression level of the NS1 protein in WT-Venus-PR8-infected cells was much lower than that in Venus-PR8-PB2-E712D-infected cells. 2019 mBio Result IV E712D 188 193 NS;NS1;PB2 63;103;184 65;106;187 31575766 Influenza Virus Polymerase Mutation Stabilizes a Foreign Gene Inserted into the Virus Genome by Enhancing the Transcription/Replication Efficiency of the Modified Segment. MDCK cells were infected with WT-Venus-PR8 or Venus-PR8-PB2-E712D at an MOI of 1 or mock infected with medium only, and the relative expression levels of IFN-beta in infected cells were quantified at 9 h postinfection. 2019 mBio Result IV E712D 60 65 PB2 56 59 31575766 Influenza Virus Polymerase Mutation Stabilizes a Foreign Gene Inserted into the Virus Genome by Enhancing the Transcription/Replication Efficiency of the Modified Segment. Moreover, there was no clear difference in mutation number between WT-PR8 and PR8-PB2-E712D. 2019 mBio Result IV E712D 86 91 PB2 82 85 31575766 Influenza Virus Polymerase Mutation Stabilizes a Foreign Gene Inserted into the Virus Genome by Enhancing the Transcription/Replication Efficiency of the Modified Segment. PR8-PB1-V43I, which has been reported to be a high-fidelity mutant virus, and PR8-PB1-T123A, which has been reported to be a low-fidelity mutant virus, were also generated by reverse genetics and used as controls. 2019 mBio Result IV V43I;T123A 8;86 12;91 PB1;PB1 4;82 7;85 31575766 Influenza Virus Polymerase Mutation Stabilizes a Foreign Gene Inserted into the Virus Genome by Enhancing the Transcription/Replication Efficiency of the Modified Segment. Since a previous report suggested that PB1-V43I does not alter the mutation rate, the influence of PB1-V43I on the mutation rate might be dependent on the virus strain or experimental conditions. 2019 mBio Result IV V43I;V43I 43;103 47;107 PB1;PB1 39;99 42;102 31575766 Influenza Virus Polymerase Mutation Stabilizes a Foreign Gene Inserted into the Virus Genome by Enhancing the Transcription/Replication Efficiency of the Modified Segment. The amount of NS vRNA in WT-Venus-PR8-infected cells was 90% lower than that in Venus-PR8-PB2-E712D-infected cells. 2019 mBio Result IV E712D 94 99 NS;PB2 14;90 16;93 31575766 Influenza Virus Polymerase Mutation Stabilizes a Foreign Gene Inserted into the Virus Genome by Enhancing the Transcription/Replication Efficiency of the Modified Segment. The NS vRNA/NP vRNA ratio in WT-Venus-PR8-infected cells was 80% lower than that in Venus-PR8-PB2-E712D-infected cells. 2019 mBio Result IV E712D 98 103 NP;NS;PB2 12;4;94 14;6;97 31575766 Influenza Virus Polymerase Mutation Stabilizes a Foreign Gene Inserted into the Virus Genome by Enhancing the Transcription/Replication Efficiency of the Modified Segment. The PB2-E712D mutation does not cause an appreciable change in polymerase fidelity. 2019 mBio Result IV E712D 8 13 PB2 4 7 31575766 Influenza Virus Polymerase Mutation Stabilizes a Foreign Gene Inserted into the Virus Genome by Enhancing the Transcription/Replication Efficiency of the Modified Segment. The sequences of all of the plasmids used to generate viruses by reverse genetics were confirmed before use, and the NS segments of WT-Venus-PR8 and Venus-PR8-PB2-E712D were derived from the same NS-Venus plasmid. 2019 mBio Result IV E712D 163 168 NS;NS;PB2 117;196;159 119;198;162 31575766 Influenza Virus Polymerase Mutation Stabilizes a Foreign Gene Inserted into the Virus Genome by Enhancing the Transcription/Replication Efficiency of the Modified Segment. Therefore, it is unlikely that either WT-Venus-PR8 or Venus-PR8-PB2-E712D has a mutated promoter sequence in its NS segment. 2019 mBio Result IV E712D 68 73 NS;PB2 113;64 115;67 31575766 Influenza Virus Polymerase Mutation Stabilizes a Foreign Gene Inserted into the Virus Genome by Enhancing the Transcription/Replication Efficiency of the Modified Segment. To test this hypothesis, we generated WT-PR8, as well as PR8-PB2-E712D, which possesses aspartic acid at position 712 of PB2 and therefore differs from WT-PR8 by only this amino acid, by reverse genetics and compared their mutation rates. 2019 mBio Result IV E712D 65 70 PB2;PB2 61;121 64;124 31575766 Influenza Virus Polymerase Mutation Stabilizes a Foreign Gene Inserted into the Virus Genome by Enhancing the Transcription/Replication Efficiency of the Modified Segment. We confirmed that PR8-PB1-V43I, the high-fidelity control, had fewer mutations, and that PR8-PB1-T123A, the low-fidelity control, had more mutations than WT-PR8. 2019 mBio Result IV V43I;T123A 26;97 30;102 PB1;PB1 22;93 25;96 31575766 Influenza Virus Polymerase Mutation Stabilizes a Foreign Gene Inserted into the Virus Genome by Enhancing the Transcription/Replication Efficiency of the Modified Segment. We confirmed that the expression of Venus was lost immediately in WT-Venus-PR8, whereas all plaques of Venus-PR8-PB2-E712D showed Venus expression after four passages. 2019 mBio Result IV E712D 117 122 PB2 113 116 31575766 Influenza Virus Polymerase Mutation Stabilizes a Foreign Gene Inserted into the Virus Genome by Enhancing the Transcription/Replication Efficiency of the Modified Segment. We hypothesized that the PB2-E712D mutation increases viral polymerase fidelity in order to retain the inserted Venus gene during passages. 2019 mBio Result IV E712D 29 34 PB2 25 28 31575766 Influenza Virus Polymerase Mutation Stabilizes a Foreign Gene Inserted into the Virus Genome by Enhancing the Transcription/Replication Efficiency of the Modified Segment. We prepared WT-Venus-PR8 and Venus-PR8-PB2-E712D by using reverse genetics as previously described. 2019 mBio Result IV E712D 43 48 PB2 39 42 31575766 Influenza Virus Polymerase Mutation Stabilizes a Foreign Gene Inserted into the Virus Genome by Enhancing the Transcription/Replication Efficiency of the Modified Segment. WT-Venus-PR8 induced a higher level of IFN-beta expression than did Venus-PR8-PB2-E712D. 2019 mBio Result IV E712D 82 87 PB2 78 81 31581279 Influenza virus polymerase subunits co-evolve to ensure proper levels of dimerization of the heterotrimer. In addition, we inserted PB1 active site mutations (D445A-D446A) in both Gluc1- and Gluc2-tagged PB1 proteins, to avoid interference by FluPol activity in the FluPol dimerization read-out. 2019 PLoS pathogens Result IV D445A;D446A 52;58 57;63 PB1;PB1 25;97 28;100 31581279 Influenza virus polymerase subunits co-evolve to ensure proper levels of dimerization of the heterotrimer. In contrast, in the minigenome assay (Fig 6D), the PA-E31G mutations increased FluPol activity, as observed previously with the PA-28 (Fig 4A), to the same extent as did the PA-349, PB2-74 or PB1-577 mutations. 2019 PLoS pathogens Result IV E31G 54 58 PA;PA;PA;PB1;PB2 51;128;174;192;182 53;130;176;195;185 31581279 Influenza virus polymerase subunits co-evolve to ensure proper levels of dimerization of the heterotrimer. In order to mimic the binding of an Apo FluPol to a cRNP-associated FluPol, we inserted promoter binding mutations (M356A-E358A) in the PB1-Gluc2 construct. 2019 PLoS pathogens Result IV M356A;E358A 116;122 121;127 PB1 136 139 31581279 Influenza virus polymerase subunits co-evolve to ensure proper levels of dimerization of the heterotrimer. One of these, the PB2-D701N substitution, corresponded to a reversion from the WSN-PB2 towards the PR8-PB2 sequence at position 701; the other three changes (PB1-M195T, PA-L28R, and PA-E349K) occurred at residues of PR8-PB1 and -PA that were conserved between PR8 and WSN (Fig 1F). 2019 PLoS pathogens Result IV D701N;M195T;L28R;E349K 22;162;172;185 27;167;176;190 PA;PA;PA;PB1;PB1;PB2;PB2;PB2 169;182;229;158;220;18;83;103 171;184;231;161;223;21;86;106 31581279 Influenza virus polymerase subunits co-evolve to ensure proper levels of dimerization of the heterotrimer. The contribution of each of the PB2-D701N, PB1-M195T, PA-L28R, and PA-E349K mutations to the phenotypic reversion was analyzed using reverse genetics (below and in the figures they are referred to as mutations PB2-701, PB1-195, PA-28 and PA-349). 2019 PLoS pathogens Result IV D701N;M195T;L28R;E349K 36;47;57;70 41;52;61;75 PA;PA;PA;PA;PB1;PB1;PB2;PB2 54;67;228;238;43;219;32;210 56;69;230;240;46;222;35;213 31581279 Influenza virus polymerase subunits co-evolve to ensure proper levels of dimerization of the heterotrimer. The two other changes (NS1-L27P and HA-K187E,) were less likely to compensate for the presence of a heterologous PB2 subunit. 2019 PLoS pathogens Result IV L27P;K187E 27;39 31;44 HA;NS1;PB2 36;23;113 38;26;116 31581279 Influenza virus polymerase subunits co-evolve to ensure proper levels of dimerization of the heterotrimer. These observations suggest that the chimeric PxW FluPol has a major defect in its replication activity that can be partially trans-complemented by the R+/T- PB2 E361A. 2019 PLoS pathogens Result IV E361A 161 166 PB2 157 160 31581279 Influenza virus polymerase subunits co-evolve to ensure proper levels of dimerization of the heterotrimer. To further assess whether the chimeric PxW FluPol is impaired for transcription and/or replication, we trans-complemented it with a replication-competent/transcription-deficient (E361A, R+/T-,) or a replication-deficient/transcription-competent (R142A, R-/T+,) PR8-PB2 protein in the minigenome assay as described above. 2019 PLoS pathogens Result IV E361A;R142A 179;246 184;251 PB2 265 268 31581279 Influenza virus polymerase subunits co-evolve to ensure proper levels of dimerization of the heterotrimer. Upon sequencing, a combination of PB2-G74R and PA-E31G was found in one revertant virus, and the identical PB1-K577G mutation was found in the three others (mutations are referred to below and in the figures as PB2-74, PA-31 and PB1-577). 2019 PLoS pathogens Result IV G74R;E31G;K577G 38;50;111 42;54;116 PA;PA;PB1;PB1;PB2;PB2 47;219;107;229;34;211 49;221;110;232;37;214 31590265 Insights into the Acquisition of Virulence of Avian Influenza Viruses during a Single Passage in Ferrets. Amongst all of the ferrets inoculated with the ferret-passaged H5N1 viruses, extra-respiratory infection and/or substantial weight loss were only observed in those ferrets where the infecting virus had acquired either the PB2 E627K single AA substitution, or the combined AA substitutions PB2 S489P and NP V408I. 2019 Viruses Result IV E627K;S489P;V408I 226;293;306 231;298;311 NP;PB2;PB2 303;222;289 305;225;292 31590265 Insights into the Acquisition of Virulence of Avian Influenza Viruses during a Single Passage in Ferrets. Compared to the original inoculum, the virus recovered from the liver of ferret F8 showed three changes (PB2 I385V, PB2 N456D and PA E623G), whereas only a single AA change was detected in the A/Laos genome of the virus recovered from the liver of ferret F10 (PB2 E627K). 2019 Viruses Result IV I385V;N456D;E623G;E627K 109;120;133;264 114;125;138;269 PA;PB2;PB2;PB2 130;105;116;260 132;108;119;263 31590265 Insights into the Acquisition of Virulence of Avian Influenza Viruses during a Single Passage in Ferrets. Enhanced Pathogenicity of H5N1 in Ferrets Is Facilitated by the Combination of PB2 S489P or NP V408I, Not by Either PB2 S489P or NP V408I Individually. 2019 Viruses Result IV S489P;V408I;S489P;V408I 83;95;120;132 88;100;125;137 NP;NP;PB2;PB2 92;129;79;116 94;131;82;119 31590265 Insights into the Acquisition of Virulence of Avian Influenza Viruses during a Single Passage in Ferrets. Extra respiratory infection of the small intestine was observed in two ferrets from this group (F50 and F51) (Table 8), both of which acquired PB2 E627K AA substitutions (Table A3 and Table A4), in line with the frequency of 1-2 of four ferrets acquiring a high pathogenicity mutation within a single passage that we have consistently observed with the A/Laos viruses. 2019 Viruses Result IV E627K 147 152 PB2 143 146 31590265 Insights into the Acquisition of Virulence of Avian Influenza Viruses during a Single Passage in Ferrets. Ferrets infected with rgA/L/PB2/489P (Figure 4D) showed a similar pattern with two of the four ferrets (F59, F60) developing extra-respiratory tract infection (Table 8), and the PB2 E627K AA substitution detected in one of these (F60) (Table A3). 2019 Viruses Result IV E627K 182 187 PB2;PB2 28;178 31;181 31590265 Insights into the Acquisition of Virulence of Avian Influenza Viruses during a Single Passage in Ferrets. Ferrets inoculated with A/F10/NW (Figure 3E), an isolate that retained PB2 627E but had acquired PB2 S489P and NP V408I during the first virus passage, displayed a similar pattern of pathogenicity to that seen in ferrets inoculated with viruses that had acquired PB2 627K during the first virus passage. 2019 Viruses Result IV S489P;V408I 101;114 106;119 NP;PB2;PB2;PB2 111;71;97;263 113;74;100;266 31590265 Insights into the Acquisition of Virulence of Avian Influenza Viruses during a Single Passage in Ferrets. However, a limited extra-respiratory infection of the small intestine was discovered in two of the ferrets infected with this virus (F21, F22) (Table 6), and in each of these ferrets the PB2 E627K AA substitution could be detected by SNP analysis or sequencing (Table 7 and Table A2), suggesting later mutation/selection of the highly pathogenic variant. 2019 Viruses Result IV E627K 191 196 PB2 187 190 31590265 Insights into the Acquisition of Virulence of Avian Influenza Viruses during a Single Passage in Ferrets. However, one of the four ferrets (F38) exhibited weight loss of 6.7% by day 5, developed an extra-respiratory tract infection involving the small intestine, liver and spleen (Table 6), and sequencing (Table 7) of those tissues that failed to yield a PB2 627 SNP assay result (Table A2) revealed that virus within this ferret had acquired the PB2 E627K AA substitution during this second virus passage. 2019 Viruses Result IV E627K 346 351 PB2;PB2 250;342 253;345 31590265 Insights into the Acquisition of Virulence of Avian Influenza Viruses during a Single Passage in Ferrets. However, PB2 E627K AA substitutions were detected in respiratory samples from two ferrets (F54 and F56) (Table A3 and Table A4), again similar to the pattern observed with introduction of non-adapted virus, with acquisition of a pathogenic genotype in 1-2 of four ferrets. 2019 Viruses Result IV E627K 13 18 PB2 9 12 31590265 Insights into the Acquisition of Virulence of Avian Influenza Viruses during a Single Passage in Ferrets. In this way it was clearly observed that PB2 627K facilitated significantly increased polymerase activity, whereas the other introduced AA changes at PB2 S489P and NP V408I facilitated significantly increased polymerase activity only in combination, but not individually (Figure 5B). 2019 Viruses Result IV S489P;V408I 154;167 159;172 NP;PB2;PB2 164;41;150 166;44;153 31590265 Insights into the Acquisition of Virulence of Avian Influenza Viruses during a Single Passage in Ferrets. Of interest, this ferret also had virus in the trachea that showed the PB2 E627K AA substitution and a mixed population in the nasal wash, indicative of potentially independent adaption pathways occurring in localised sites. 2019 Viruses Result IV E627K 75 80 PB2 71 74 31590265 Insights into the Acquisition of Virulence of Avian Influenza Viruses during a Single Passage in Ferrets. Of these, only the PB2 E627K change led to an AA that corresponded to that in the equivalent position in A/Viet (Table 2). 2019 Viruses Result IV E627K 23 28 PB2 19 22 31590265 Insights into the Acquisition of Virulence of Avian Influenza Viruses during a Single Passage in Ferrets. PB2 E627K was also detected in virus from tissue samples of ferret F10 (liver, spleen and small intestine) but not the nasal wash. 2019 Viruses Result IV E627K 4 9 PB2 0 3 31590265 Insights into the Acquisition of Virulence of Avian Influenza Viruses during a Single Passage in Ferrets. Polymerase Activity in Mammalian Cells Is Enhanced by Either PB2 627K or the Combination of PB2 S489P and NP V408I. 2019 Viruses Result IV S489P;V408I 96;109 101;114 NP;PB2;PB2 106;61;92 108;64;95 31590265 Insights into the Acquisition of Virulence of Avian Influenza Viruses during a Single Passage in Ferrets. The PB2 I385V, PB2 N456D and PA E623G changes were only observed in virus from the liver of ferret F8 (Table 3). 2019 Viruses Result IV I385V;N456D;E623G 8;19;32 13;24;37 PA;PB2;PB2 29;4;15 31;7;18 31590265 Insights into the Acquisition of Virulence of Avian Influenza Viruses during a Single Passage in Ferrets. This would suggest that neither the PB2 S489P nor NP V408I AA substitution in isolation is sufficient to produce the high pathogenicity phenotype of human H5N1 isolates in the ferret model. 2019 Viruses Result IV S489P;V408I 40;53 45;58 NP;PB2 50;36 52;39 31590265 Insights into the Acquisition of Virulence of Avian Influenza Viruses during a Single Passage in Ferrets. To assess whether the increased pathogenicity observed in ferrets inoculated with A/F10/NW was due to the independent selection of viruses with individual adaptive mutations PB2 S489P or NP V408I, as opposed to a single population of virus with the two substitutions, the following reverse-engineered A/Laos viruses were generated and designated as follows: A/Laos encoding PB2 489P (rgA/L/PB2/489P) or NP 408I (rgA/L/NP/408I). 2019 Viruses Result IV S489P;V408I 178;190 183;195 NP;NP;NP;PB2;PB2;PB2 187;403;418;174;374;390 189;405;420;177;377;393 31597771 Identification of Key Amino Acids in the PB2 and M1 Proteins of H7N9 Influenza Virus That Affect Its Transmission in Guinea Pigs. and C); K627E in PB2 also significantly reduced the polymerase activity of the RNP complex of the AH/1 virus in 293T cells. 2019 Journal of virology Result IV K627E 8 13 PB2;RNP 17;79 20;82 31597771 Identification of Key Amino Acids in the PB2 and M1 Proteins of H7N9 Influenza Virus That Affect Its Transmission in Guinea Pigs. Our transmission study indicated that the D156E mutation in M1 abolished the transmissibility of the AH/1 virus in guinea pigs. 2019 Journal of virology Result IV D156E 42 47 M1 60 62 31597771 Identification of Key Amino Acids in the PB2 and M1 Proteins of H7N9 Influenza Virus That Affect Its Transmission in Guinea Pigs. Our transmission study indicated that the mutations V292I and K627E of PB2 independently abolished the transmission of the AH/1 virus; therefore, we investigated how these two mutations affect the polymerase activities of the RNP complex of the AH/1 virus in different cells at 33 C and/or 37 C. 2019 Journal of virology Result IV V292I;K627E 52;62 57;67 PB2;RNP 71;226 74;229 31597771 Identification of Key Amino Acids in the PB2 and M1 Proteins of H7N9 Influenza Virus That Affect Its Transmission in Guinea Pigs. Previous studies have reported that two amino acid mutations in PB2, E627K and D701N, increase the polymerase activities and thereby increase the virulence and transmissibility of different influenza viruses. 2019 Journal of virology Result IV E627K;D701N 69;79 74;84 PB2 64 67 31597771 Identification of Key Amino Acids in the PB2 and M1 Proteins of H7N9 Influenza Virus That Affect Its Transmission in Guinea Pigs. the mutation V292I in PB2 significantly reduced the polymerase activity of the RNP complex of the AH/1 virus in both chicken DF-1 fibroblasts. 2019 Journal of virology Result IV V292I 13 18 PB2;RNP 22;79 25;82 31597771 Identification of Key Amino Acids in the PB2 and M1 Proteins of H7N9 Influenza Virus That Affect Its Transmission in Guinea Pigs. These results indicate that the amino acids at positions 292 and 627 of PB2 affect the polymerase activity of the RNP complex of the H7N9 virus; the PB2 V292I mutation weakened the polymerase activity in both avian and mammalian cells, whereas the PB2 K627E mutation impaired the polymerase activity only in mammalian cells. 2019 Journal of virology Result IV V292I;K627E 153;252 158;257 PB2;PB2;PB2;RNP 72;149;248;114 75;152;251;117 31597771 Identification of Key Amino Acids in the PB2 and M1 Proteins of H7N9 Influenza Virus That Affect Its Transmission in Guinea Pigs. These results indicate that the mutation I26M in NA did not affect the transmissibility of the AH/1 virus, the NA gene of the CK/S1053 virus weakened the transmissibility of the AH/1 virus, and the mutations V292I and K627E in PB2 and D156E in M1 independently abolished the transmissibility of the AH/1 virus in guinea pigs. 2019 Journal of virology Result IV I26M;V292I;K627E;D156E 41;208;218;235 45;213;223;240 M1;NA;NA;PB2 244;49;111;227 246;51;113;230 31600274 Adaptation of H3N2 canine influenza virus to feline cell culture. All the viruses possessing HA1-K299R or HA2-T107I mutations grew better than rWT as did in epithelial-type CRFK cells. 2019 PloS one Result IV K299R;T107I 31;44 36;49 HA;HA1 40;27 42;30 31600274 Adaptation of H3N2 canine influenza virus to feline cell culture. Among them, we focused on mutations of envelope proteins such as HA1-K299R, HA2-T107I, NA-L35R, and M2-W41C mutations, three of which were observed in two or more Mad-CA viruses. 2019 PloS one Result IV K299R;T107I;L35R;W41C 69;80;90;103 74;85;94;107 HA;HA1;M2;NA 76;65;100;87 78;68;102;89 31600274 Adaptation of H3N2 canine influenza virus to feline cell culture. At pH 5.6, fused cells were observed only in mutant T107I HA expressing cells. 2019 PloS one Result IV T107I 52 57 HA 58 60 31600274 Adaptation of H3N2 canine influenza virus to feline cell culture. Both the HA mutants, rHA1-K299R and rHA2-T107I, enhanced virus growth at higher levels than that by rNA-L35R and rM2-W41C (Fig 2A). 2019 PloS one Result IV K299R;T107I;L35R;W41C 26;41;104;117 31;46;108;121 HA;NA 9;100 11;103 31600274 Adaptation of H3N2 canine influenza virus to feline cell culture. However, NA-L35R mutation enhanced the viral growth in combination with HA1-K299R mutation in a synergistic manner (Fig 6B). 2019 PloS one Result IV L35R;K299R 12;76 16;81 HA1;NA 72;9 75;11 31600274 Adaptation of H3N2 canine influenza virus to feline cell culture. In contrast, growth kinetics of the viruses possessing single NA-L35R or M-W41C mutations were similar to those of rWT (Fig 6A). 2019 PloS one Result IV L35R;W41C 65;75 69;79 M;NA 73;62 74;64 31600274 Adaptation of H3N2 canine influenza virus to feline cell culture. In contrast, the rNA-L35R and rM-W41C viruses exhibited similar growth properties to rWT (Fig 5A). 2019 PloS one Result IV L35R;W41C 21;33 25;37 17 20 31600274 Adaptation of H3N2 canine influenza virus to feline cell culture. Interestingly, the viruses possessing HA1-K299R or HA2-T107I mutations grew better than rWT at some time points, albeit small differences were observed in their titers. 2019 PloS one Result IV K299R;T107I 42;55 47;60 HA;HA1 51;38 53;41 31600274 Adaptation of H3N2 canine influenza virus to feline cell culture. These data indicated that HA1-K299R or HA2-T107I mutations were primary determinants for feline cell-adaptation of the CIV. 2019 PloS one Result IV K299R;T107I 30;43 35;48 HA;HA1 39;26 41;29 31600274 Adaptation of H3N2 canine influenza virus to feline cell culture. These data suggest that both the HA1-K299R and HA2-T107I mutations confer thermostability to the CIV, leading to its enhanced growth in CRFK cells. 2019 PloS one Result IV K299R;T107I 37;51 42;56 HA;HA1 47;33 49;36 31600274 Adaptation of H3N2 canine influenza virus to feline cell culture. These data suggest that HA2-T107I mutation widens the optimal pH range for virus membrane fusion in MDCK cells. 2019 PloS one Result IV T107I 28 33 HA 24 26 31600274 Adaptation of H3N2 canine influenza virus to feline cell culture. To characterize the mutations observed in the Mad-CA viruses, we generated viruses possessing single mutation (HA1-K299R, HA2-T107I, NA-L35R, or M2-W41C), viruses possessing double mutations (HA1-K299R/NA-L35R, or HA1-K299R/M2-W41C), and a virus possessing triple mutations (HA1-K299R/NA-L35R/M2-W41C), in addition to the wild-type virus by reverse genetics, referred as rHA1-K299R, rHA2-T107I, rNA-L35R, rM2-W41C, rHA1-K299R/NA-L35R, rHA1-K299R/M2-W41C, rHA1-K299R/NA-L35R/M2-W41C, and rWT, respectively. 2019 PloS one Result IV K299R;T107I;L35R;W41C;K299R;L35R;K299R;W41C;K299R;L35R;W41C;K299R;T107I;L35R;W41C;K299R;L35R;K299R;W41C;K299R;L35R;W41C 115;126;136;148;196;205;218;227;279;288;296;376;388;399;409;420;429;440;449;460;469;477 120;131;140;152;201;209;223;231;284;292;300;381;393;403;413;425;433;445;453;465;473;481 HA;HA1;HA1;HA1;HA1;M2;M2;M2;M2;M2;NA;NA;NA;NA;NA;NA 122;111;192;214;275;145;224;293;446;474;133;202;285;426;466;395 124;114;195;217;278;147;226;295;448;476;135;204;287;428;468;398 31600274 Adaptation of H3N2 canine influenza virus to feline cell culture. To investigate a mechanism why HA1-K299R and HA2-T107I mutations increased virus growth in CRFK cells, we analyzed the thermostability of the HA mutant viruses. 2019 PloS one Result IV K299R;T107I 35;49 40;54 HA;HA;HA1 45;142;31 47;144;34 31608791 Insights into species-specific regulation of ANP32A on the mammalian-restricted influenza virus polymerase activity. 293T cells were transfected with chANP32A-X1 or huANP32A for 24 h, and then infected with PR8-PB2 K627E or PR8-PB2 627K virus at an MOI = 5 and cultured for 4 h in DMEM with or without 100 mug/mL cycloheximide (CHX). 2019 Emerging microbes & infections Result IV K627E 98 103 PB2;PB2 94;111 97;114 31608791 Insights into species-specific regulation of ANP32A on the mammalian-restricted influenza virus polymerase activity. 293T cells were transfected with PR8 Myc-PB2 K627E or 627K, PB1, PA, and NP as well as cNA-Luc and chANP32A-X1 or huANP32A for 24 h. 2019 Emerging microbes & infections Result IV K627E 45 50 NP;PA;PB1;PB2 73;65;60;41 75;67;63;44 31608791 Insights into species-specific regulation of ANP32A on the mammalian-restricted influenza virus polymerase activity. Another chicken transcript, chANP32A-X2, increased the PB2 627E polymerase activity of H9N2 and H7N9 strains but could not stimulate PR8-derived PB2 K627E polymerase activity (Figure 2(A)). 2019 Emerging microbes & infections Result IV K627E 149 154 PB2;PB2 55;145 58;148 31608791 Insights into species-specific regulation of ANP32A on the mammalian-restricted influenza virus polymerase activity. As shown in Figure 7(B), compared with wild-type cNA-Luc, the mutations (A3G + U8C) in the 3' promoter significantly decreased PB2 K627E polymerase activity but not PB2 627K polymerase activity. 2019 Emerging microbes & infections Result IV A3G;K627E 73;131 76;136 PB2;PB2 127;165 130;168 31608791 Insights into species-specific regulation of ANP32A on the mammalian-restricted influenza virus polymerase activity. Being different from other influenza strains, PR8 virus acquired multiple mutations highly adapted to mammalian cells, which may contribute to the increased polymerase together with T598V or F636L mutation. 2019 Emerging microbes & infections Result IV T598V;F636L 182;191 187;196 31608791 Insights into species-specific regulation of ANP32A on the mammalian-restricted influenza virus polymerase activity. By comparison, PB2 E627K mutation promoted polymerase activity in 293T cells, but chANP32A-X1, chANP32A-X2 and huANP32A inhibited PB2 627K polymerase activity. 2019 Emerging microbes & infections Result IV E627K 19 24 PB2;PB2 15;130 18;133 31608791 Insights into species-specific regulation of ANP32A on the mammalian-restricted influenza virus polymerase activity. Collectively, these data demonstrated that chANP32A-X1 is specific for the enhancement of PB2 K627E RNPs formation and that chANP32A and huANP32A did not affect the primary cRNPs (PB2 K627E or 627K) assembly. 2019 Emerging microbes & infections Result IV K627E;K627E 94;184 99;189 PB2;PB2;RNP 90;180;100 93;183;104 31608791 Insights into species-specific regulation of ANP32A on the mammalian-restricted influenza virus polymerase activity. Comparatively, human influenza virus (PB2 627K) provides competent cRNPs for both pre-expressed PB2 K627E and PB2 627K polymerase to synthesize substantial amounts of vRNA in human cells. 2019 Emerging microbes & infections Result IV K627E 100 105 PB2;PB2;PB2 38;96;110 41;99;113 31608791 Insights into species-specific regulation of ANP32A on the mammalian-restricted influenza virus polymerase activity. Comparatively, in the presence of CHX, PR8-PB2 K627E and PR8-PB2 627K viruses exhibited similar mRNA levels in 293T cells or 293T cells expressing chANP32A-X1 or huANP32A (Figure 5(B)), indicating that overexpression of chANP32A-X1 and huANP32A have no remarkable influence on primary mRNA transcription. 2019 Emerging microbes & infections Result IV K627E 47 52 PB2;PB2 43;61 46;64 31608791 Insights into species-specific regulation of ANP32A on the mammalian-restricted influenza virus polymerase activity. Compared with H9N2 and H7N9 strains, PR8 exhibited the D567N, V598T, V613A and L636F mutations (Figure 4(A)). 2019 Emerging microbes & infections Result IV D567N;V598T;V613A;L636F 55;62;69;79 60;67;74;84 31608791 Insights into species-specific regulation of ANP32A on the mammalian-restricted influenza virus polymerase activity. Consistently, when huANP32A was overexpressed, PB2 K627E polymerase activity of PR8 was significantly inhibited in 293T cells, while the H9N2 and H7N9 strains were not significantly affected, showing strain-specific. 2019 Emerging microbes & infections Result IV K627E 51 56 PB2 47 50 31608791 Insights into species-specific regulation of ANP32A on the mammalian-restricted influenza virus polymerase activity. Correspondingly, in polymerase activity detection, chANP32A-X1 that resulted in the increased amount of PB2 K627E precipitated by NP increased polymerase activity and chANP32A and huANP32A could not rescue the inactive catalytic activity of the PB2 K627E and PB2 627K polymerases in PR8 virus with the PB1 D446Y mutation (Figure 8(C)). 2019 Emerging microbes & infections Result IV K627E;K627E;D446Y 108;249;306 113;254;311 NP;PB1;PB2;PB2;PB2 130;302;104;245;259 132;305;107;248;262 31608791 Insights into species-specific regulation of ANP32A on the mammalian-restricted influenza virus polymerase activity. Each type of RNA template was coexpressed with PR8-derived polymerase (PB1, PB2 K627E or 627K, PA) and NP in 293T cells. 2019 Emerging microbes & infections Result IV K627E 80 85 NP;PA;PB1;PB2 103;95;71;76 105;97;74;79 31608791 Insights into species-specific regulation of ANP32A on the mammalian-restricted influenza virus polymerase activity. Further, we observed that the low level of chANP32A-X2 promoted PR8 PB2 K627E polymerase activity and overdose expression had a negative effect. 2019 Emerging microbes & infections Result IV K627E 72 77 PB2 68 71 31608791 Insights into species-specific regulation of ANP32A on the mammalian-restricted influenza virus polymerase activity. Furthermore, chANP32A-X1, but not huANP32A, increased the amount of vRNA in cells pre-expressing PB2 K627E polymerase, while chANP32A-X1 and huANP32A inhibited the vRNA level in cells pre-expressing PB2 627K polymerase (Figure 5(C)). 2019 Emerging microbes & infections Result IV K627E 101 106 PB2;PB2 97;199 100;202 31608791 Insights into species-specific regulation of ANP32A on the mammalian-restricted influenza virus polymerase activity. However, when the mutations (3' promoter A3G + U8C mutation or 5' promoter C3U + G8A mutation) of cRNA template were used as a template, coexpression of polymerase (PB1, PB2 K627E or 627K, PA), NP and chANP32A-X1 or huANP32A showed that chANP32A-X1 increased PB2 K627E polymerase activity (Figure 7(C)). 2019 Emerging microbes & infections Result IV A3G;G8A;K627E;K627E 41;81;174;263 44;84;179;268 NP;PA;PB1;PB2;PB2 194;189;165;170;259 196;191;168;173;262 31608791 Insights into species-specific regulation of ANP32A on the mammalian-restricted influenza virus polymerase activity. In 293T cells infected with the PR8-PB2 K627E virus, chANP32A-X1, but not huANP32A, produced similar vRNA for both pre-expressed PB2 K627E and PB2 627K polymerase (Figure 5(C)). 2019 Emerging microbes & infections Result IV K627E;K627E 40;133 45;138 PB2;PB2;PB2 36;129;143 39;132;146 31608791 Insights into species-specific regulation of ANP32A on the mammalian-restricted influenza virus polymerase activity. In 293T cells, the viral titre of PR8-PB2 627K strain was higher than that of mutant PR8-PB2 K627E strain and chANP32A-X1 promoted the viral titre of mutant PR8-PB2 K627E strain (Figure 5(A)). 2019 Emerging microbes & infections Result IV K627E;K627E 93;165 98;170 PB2;PB2;PB2 38;89;161 41;92;164 31608791 Insights into species-specific regulation of ANP32A on the mammalian-restricted influenza virus polymerase activity. In addition, high level of chANP32A-X2 could not promote PR8 PB2 K627E polymerase activity (Figure 2(A,C)), but it could be promoted by chANP32A-X2 using the PB2 K627E protein with the three mutations of N567D, T598V or A613V, respectively (Figure 4(B)). 2019 Emerging microbes & infections Result IV K627E;K627E;N567D;T598V;A613V 65;162;204;211;220 70;167;209;216;225 PB2;PB2 61;158 64;161 31608791 Insights into species-specific regulation of ANP32A on the mammalian-restricted influenza virus polymerase activity. Interestingly, chANP32A-X1 did not show the ability to promote PB2 K627E polymerase activity for the PR8 virus, which was different from the results of the polymerase reconstitution assay with vNA-Luc as a template (Figure 2(A)). 2019 Emerging microbes & infections Result IV K627E 67 72 PB2 63 66 31608791 Insights into species-specific regulation of ANP32A on the mammalian-restricted influenza virus polymerase activity. On the basis of PB2 K627E mutation, we performed the mutation of N567D, T598V, A613V and F636L for PR8 virus, respectively. 2019 Emerging microbes & infections Result IV K627E;N567D;T598V;A613V;F636L 20;65;72;79;89 25;70;77;84;94 PB2 16 19 31608791 Insights into species-specific regulation of ANP32A on the mammalian-restricted influenza virus polymerase activity. One possibility is that the mutations of the three sites near to 627 site had an effect on PB2 K627E site, affecting the weak regulation of chANP32A-X2 in PB2 K627E polymerase. 2019 Emerging microbes & infections Result IV K627E;K627E 95;159 100;164 PB2;PB2 91;155 94;158 31608791 Insights into species-specific regulation of ANP32A on the mammalian-restricted influenza virus polymerase activity. Our data suggested that chANP32A-X1 compensated for the defective cRNPs for both pre-expressed PB2 K627E and 627K polymerase to produce vRNA. 2019 Emerging microbes & infections Result IV K627E 99 104 PB2 95 98 31608791 Insights into species-specific regulation of ANP32A on the mammalian-restricted influenza virus polymerase activity. The 598V and 636L are AIV signatures and the substitution of V598T and L636F increased polymerase activity in mammalian cells, respectively. 2019 Emerging microbes & infections Result IV V598T;L636F 61;71 66;76 31608791 Insights into species-specific regulation of ANP32A on the mammalian-restricted influenza virus polymerase activity. The additive facilitations reveals that chANP32A-X1 and the mutation of N567D, T598V, A613V and F636L promote PB2 627E polymerase in different manners. 2019 Emerging microbes & infections Result IV N567D;T598V;A613V;F636L 72;79;86;96 77;84;91;101 PB2 110 113 31608791 Insights into species-specific regulation of ANP32A on the mammalian-restricted influenza virus polymerase activity. The chANP32A-X1 and huANP32A were coexpressed with PB1, PB2 K627E or 627K, PA and NP as well as cNA-Luc and Renilla reporter control. 2019 Emerging microbes & infections Result IV K627E 60 65 NP;PA;PB1;PB2 82;75;51;56 84;77;54;59 31608791 Insights into species-specific regulation of ANP32A on the mammalian-restricted influenza virus polymerase activity. The different regulation of chANP32A-X1 in PB2 K627E polymerase activity depended on the cRNA promoter mutation. 2019 Emerging microbes & infections Result IV K627E 47 52 PB2 43 46 31608791 Insights into species-specific regulation of ANP32A on the mammalian-restricted influenza virus polymerase activity. The expression of chANP32A-X1 in 293T cells also supported PR8 PB2 K627E polymerase activity in a dose-dependent manner (Figure 2(C)). 2019 Emerging microbes & infections Result IV K627E 67 72 PB2 63 66 31608791 Insights into species-specific regulation of ANP32A on the mammalian-restricted influenza virus polymerase activity. The high level of chANP32A-X1 did not promote PR8 PB2 K627E polymerase activity with wild-type cNA-Luc template. 2019 Emerging microbes & infections Result IV K627E 54 59 PB2 50 53 31608791 Insights into species-specific regulation of ANP32A on the mammalian-restricted influenza virus polymerase activity. The mutations (3' promoter A3G + U8C mutations or 5' promoter C3U + G8A) of cRNA template could stabilize the panhandle structure (Figure 7(A)). 2019 Emerging microbes & infections Result IV A3G;G8A 27;68 30;71 31608791 Insights into species-specific regulation of ANP32A on the mammalian-restricted influenza virus polymerase activity. The mutations (C3U + G8A) in the 5' promoter significantly decreased PB2 K627E and 627K polymerase activity, but the difference in both PB2 K627E and 627K polymerases activity were also increased. 2019 Emerging microbes & infections Result IV G8A;K627E;K627E 21;73;140 24;78;145 PB2;PB2 69;136 72;139 31608791 Insights into species-specific regulation of ANP32A on the mammalian-restricted influenza virus polymerase activity. The PB2 K627E polymerase activity of H7N9 was also greatly increased by 71.2-fold in 293T cells expressing chANP32A-X1 using the cNA-Luc template, while only a 13.1-fold enhancement was observed in polymerase reconstitution assays with vNA-Luc template (Figure 2(A)). 2019 Emerging microbes & infections Result IV K627E 8 13 PB2 4 7 31608791 Insights into species-specific regulation of ANP32A on the mammalian-restricted influenza virus polymerase activity. The qRT-PCR assay showed that in the absence of CHX chANP32A-X1 promoted level of mRNA, vRNA and cRNA for PR8-PB2 K627E virus but not PR8-PB2 627K virus. 2019 Emerging microbes & infections Result IV K627E 114 119 PB2;PB2 110;138 113;141 31608791 Insights into species-specific regulation of ANP32A on the mammalian-restricted influenza virus polymerase activity. These mutations significantly promoted the PB2 K627E polymerase activity although western blot showed the mutant PB2 had the similar expression levels (Figure 4(A)). 2019 Emerging microbes & infections Result IV K627E 47 52 PB2;PB2 43;113 46;116 31608791 Insights into species-specific regulation of ANP32A on the mammalian-restricted influenza virus polymerase activity. Thus species-specific regulation of ANP32A in polymerase activity might be only related with PB2 E627K mutation. 2019 Emerging microbes & infections Result IV E627K 97 102 PB2 93 96 31608791 Insights into species-specific regulation of ANP32A on the mammalian-restricted influenza virus polymerase activity. To examine the effect of ANP32A on transcription and replication, the recombinant PR8 virus containing PB2 K627E (PR8-PB2 K627E) was generated in 293T cells by a plasmid-based reverse genetic system. 2019 Emerging microbes & infections Result IV K627E;K627E 107;122 112;127 PB2;PB2 103;118 106;121 31608791 Insights into species-specific regulation of ANP32A on the mammalian-restricted influenza virus polymerase activity. To further determine whether the vRNA levels were regulated by ANP32A, we pre-expressed PB1, PB2 K627E or 627K, PA and NP as well as chANP32A-X1 or huANP32A in 293T cells for 24h before infection with PR8-PB2 K627E or PR8-PB2 627K virus (MOI = 5) and CHX-treatment for 4 h. 2019 Emerging microbes & infections Result IV K627E;K627E 97;209 102;214 NP;PA;PB1;PB2;PB2;PB2 119;112;88;93;205;222 121;114;91;96;208;225 31608791 Insights into species-specific regulation of ANP32A on the mammalian-restricted influenza virus polymerase activity. We found that the pre-expressed PB2 627K polymerase seemed to produce more vRNA than PB2 K627E polymerase in 293T cells infected with the PR8-627K virus. 2019 Emerging microbes & infections Result IV K627E 89 94 PB2;PB2 32;85 35;88 31608791 Insights into species-specific regulation of ANP32A on the mammalian-restricted influenza virus polymerase activity. We observed that PB2 K627E polymerase exhibited the characteristic defect in RNPs formation and chANP32A-X1 but not huANP32A increased the amounts of PB2 627E in Co-IP, even if in absence of cNA-Luc ANP32A did not affect the amount of PB2 precipitated by NP (Figure 8(A)). 2019 Emerging microbes & infections Result IV K627E 21 26 NP;PB2;PB2;PB2;RNP 255;17;150;235;77 257;20;153;238;81 31608791 Insights into species-specific regulation of ANP32A on the mammalian-restricted influenza virus polymerase activity. When the E627K mutation occurs in pre-expressed PB2 polymerase, human influenza virus (PB2 627K) leads to optimal cRNPs, and the overexpression of chANP32A-X1 or huANP32A will be harmful. 2019 Emerging microbes & infections Result IV E627K 9 14 PB2;PB2 48;87 51;90 31608791 Insights into species-specific regulation of ANP32A on the mammalian-restricted influenza virus polymerase activity. When the PB1 D446Y mutation was introduced into the reconstituted polymerase with cNA-Luc, further CoIP assays showed that only cRNPs complex were formed and the amounts of PB2 K627E and PB2 627K polymerase immunoprecipitated by NP were not significantly different (Figure 8(B)). 2019 Emerging microbes & infections Result IV D446Y;K627E 13;177 18;182 NP;PB1;PB2;PB2 229;9;173;187 231;12;176;190 31635227 Antigenic Site Variation in the Hemagglutinin of Pandemic Influenza A(H1N1)pdm09 Viruses between 2009-2017 in Ukraine. Acquired amino acid substitutions, N31D and A186T, A/Dnipropetrovsk/445/2010 and A/Ukraine/220/2010 belonged to genetic group 2. 2019 Pathogens (Basel, Switzerland) Result IV N31D;A186T 35;44 39;49 31635227 Antigenic Site Variation in the Hemagglutinin of Pandemic Influenza A(H1N1)pdm09 Viruses between 2009-2017 in Ukraine. All viruses from genetic group 6B were characterized by acquired amino acid substitutions D97N, S185T, E47K and S124N. 2019 Pathogens (Basel, Switzerland) Result IV D97N;S185T;E47K;S124N 90;96;103;112 94;101;107;117 31635227 Antigenic Site Variation in the Hemagglutinin of Pandemic Influenza A(H1N1)pdm09 Viruses between 2009-2017 in Ukraine. Group 6B.2 is somewhat less numerous, and acquired substitutes are unique to this group, including V152T and V173I in HA1, and E164G and D174E in HA2. 2019 Pathogens (Basel, Switzerland) Result IV V152T;V173I;E164G;D174E 99;109;127;137 104;114;132;142 HA;HA1 146;118 148;121 31635227 Antigenic Site Variation in the Hemagglutinin of Pandemic Influenza A(H1N1)pdm09 Viruses between 2009-2017 in Ukraine. In 2013-2014, the genetic clade 6B emerged with a featured amino acid substitution from lysine (K) to glutamine (Q) at position 163 (K163Q, H1 numbering) in the hemagglutinin (HA), located at the Sa antigenic site. 2019 Pathogens (Basel, Switzerland) Result IV K163Q 133 138 HA;HA 176;161 178;174 31635227 Antigenic Site Variation in the Hemagglutinin of Pandemic Influenza A(H1N1)pdm09 Viruses between 2009-2017 in Ukraine. In addition, isolate from Odessa possessed an additional unique mutation, T232A. 2019 Pathogens (Basel, Switzerland) Result IV T232A 74 79 31635227 Antigenic Site Variation in the Hemagglutinin of Pandemic Influenza A(H1N1)pdm09 Viruses between 2009-2017 in Ukraine. Only isolate A/Zaporizza/417/2013 was somewhat different as lysine was replaced with isoleucine in position 163 instead of glutamine, as with all other viruses. 2019 Pathogens (Basel, Switzerland) Result IV K163I 60 111 31635227 Antigenic Site Variation in the Hemagglutinin of Pandemic Influenza A(H1N1)pdm09 Viruses between 2009-2017 in Ukraine. Only two of the analyzed isolates obtained in the 2010-2011 season belonged to genetic group 8, namely, A/Ukraine/60/2011 and A/Ukraine/3/2011, and had an A186T specific substitution. 2019 Pathogens (Basel, Switzerland) Result IV A186T 155 160 31635227 Antigenic Site Variation in the Hemagglutinin of Pandemic Influenza A(H1N1)pdm09 Viruses between 2009-2017 in Ukraine. Our isolates possessed the typical V234I substitution common to this group. 2019 Pathogens (Basel, Switzerland) Result IV V234I 35 40 31635227 Antigenic Site Variation in the Hemagglutinin of Pandemic Influenza A(H1N1)pdm09 Viruses between 2009-2017 in Ukraine. showed that substitution D222G in Ca HA causes the transition to a double a-2,3/a-2,6-mediated affinity for the upper and lower respiratory tract epithelium. 2019 Pathogens (Basel, Switzerland) Result IV D222G 25 30 HA 37 39 31635227 Antigenic Site Variation in the Hemagglutinin of Pandemic Influenza A(H1N1)pdm09 Viruses between 2009-2017 in Ukraine. Substitution D222N also causes changes in the specificity of the receptors resulting in viral infection of the lower respiratory tract. 2019 Pathogens (Basel, Switzerland) Result IV D222N 13 18 31635227 Antigenic Site Variation in the Hemagglutinin of Pandemic Influenza A(H1N1)pdm09 Viruses between 2009-2017 in Ukraine. Supposedly, this substitution is to a lesser extent pathogenic compared with D222G. 2019 Pathogens (Basel, Switzerland) Result IV D222G 77 82 31635227 Antigenic Site Variation in the Hemagglutinin of Pandemic Influenza A(H1N1)pdm09 Viruses between 2009-2017 in Ukraine. The 2010-2011 season isolate A/Ukraine/3/2011 had substitution E235V, whilst the 2014-2015 season isolate had substitution E235D. 2019 Pathogens (Basel, Switzerland) Result IV E235V;E235D 63;123 68;128 31635227 Antigenic Site Variation in the Hemagglutinin of Pandemic Influenza A(H1N1)pdm09 Viruses between 2009-2017 in Ukraine. The A/Lviv/N6/2009 and A/Ternopil/N11/2009 with D222G substitution resulted in fatalities. 2019 Pathogens (Basel, Switzerland) Result IV D222G 48 53 31635227 Antigenic Site Variation in the Hemagglutinin of Pandemic Influenza A(H1N1)pdm09 Viruses between 2009-2017 in Ukraine. The A/Odessa/166/2017 virus with this substitution resulted in fatality and was phylogenetically similar to the viruses from the Maldives (S74R, I295V). 2019 Pathogens (Basel, Switzerland) Result IV S74R;I295V 139;145 143;150 31635227 Antigenic Site Variation in the Hemagglutinin of Pandemic Influenza A(H1N1)pdm09 Viruses between 2009-2017 in Ukraine. The acquisition of a potential glycosylation site, which may increase the virulence of influenza viruses, determines significance of the S162T substitution. 2019 Pathogens (Basel, Switzerland) Result IV S162T 137 142 31635227 Antigenic Site Variation in the Hemagglutinin of Pandemic Influenza A(H1N1)pdm09 Viruses between 2009-2017 in Ukraine. The adjacent A186T substitution was discovered in two isolates: A/Dnipropetrovsk/445/2010 and A/Ukraine/60/2011, present in different epidemic seasons and in different genetic groups. 2019 Pathogens (Basel, Switzerland) Result IV A186T 13 18 31635227 Antigenic Site Variation in the Hemagglutinin of Pandemic Influenza A(H1N1)pdm09 Viruses between 2009-2017 in Ukraine. The first substitution S185T was detected among isolates from the 2010-2011 season and appeared consolidated in the virus population at the antigenic level. 2019 Pathogens (Basel, Switzerland) Result IV S185T 23 28 31635227 Antigenic Site Variation in the Hemagglutinin of Pandemic Influenza A(H1N1)pdm09 Viruses between 2009-2017 in Ukraine. The first substitution, A73S, was detected in one isolate A/Kharkiv/963/2016 belonging to the genetic group 6B.1. 2019 Pathogens (Basel, Switzerland) Result IV A73S 24 28 31635227 Antigenic Site Variation in the Hemagglutinin of Pandemic Influenza A(H1N1)pdm09 Viruses between 2009-2017 in Ukraine. The first substitution, S203T, emerged in the 2009-2010 season, almost immediately after the appearance of pandemic viruses. 2019 Pathogens (Basel, Switzerland) Result IV S203T 24 29 31635227 Antigenic Site Variation in the Hemagglutinin of Pandemic Influenza A(H1N1)pdm09 Viruses between 2009-2017 in Ukraine. The first, D222G, detected mostly in the 2009-2010 season, was found in eight isolates of this season and in one isolate A/Dnipro/580/2016 belonging to the 6B.2 genetic group. 2019 Pathogens (Basel, Switzerland) Result IV D222G 11 16 31635227 Antigenic Site Variation in the Hemagglutinin of Pandemic Influenza A(H1N1)pdm09 Viruses between 2009-2017 in Ukraine. The last substitution in the antigenic site Ca1 S236P (serine was replaced by proline) was detected in only one isolate A/Zaporizza/631/2016 of the season 2015-2016, belonging to group 6B.1. 2019 Pathogens (Basel, Switzerland) Result IV S236P 48 53 31635227 Antigenic Site Variation in the Hemagglutinin of Pandemic Influenza A(H1N1)pdm09 Viruses between 2009-2017 in Ukraine. The next substitution in the antigenic site Ca2 - A141T was detected only in three isolates from Khmelnitsky (A/Khmelnitsky/675/2016, A/Khmelnitsky/727/2016, A/Khmelnitsky/760/2016) in the 2016-2016 season. 2019 Pathogens (Basel, Switzerland) Result IV A141T 50 55 31635227 Antigenic Site Variation in the Hemagglutinin of Pandemic Influenza A(H1N1)pdm09 Viruses between 2009-2017 in Ukraine. The next substitution R205K was detected in various epidemic seasons: 2009-2010 and 2014-2015 in isolates A/Ukraine/123/2010 and A/Ukraine/434/2015, belonging to different genetic groups. 2019 Pathogens (Basel, Switzerland) Result IV R205K 22 27 31635227 Antigenic Site Variation in the Hemagglutinin of Pandemic Influenza A(H1N1)pdm09 Viruses between 2009-2017 in Ukraine. The substitution H138R was also found in the adjacent position 138. 2019 Pathogens (Basel, Switzerland) Result IV H138R 17 22 31635227 Antigenic Site Variation in the Hemagglutinin of Pandemic Influenza A(H1N1)pdm09 Viruses between 2009-2017 in Ukraine. The third and fourth substitutions include S190G (isolate A/Sumy/797/2009) and S190R (A/Khmelnitsky/88/2016). 2019 Pathogens (Basel, Switzerland) Result IV S190G;S190R 43;79 48;84 31635227 Antigenic Site Variation in the Hemagglutinin of Pandemic Influenza A(H1N1)pdm09 Viruses between 2009-2017 in Ukraine. These isolated viruses were characterized by the specific substitutions H138R and V249L. 2019 Pathogens (Basel, Switzerland) Result IV H138R;V249L 72;82 77;87 31635227 Antigenic Site Variation in the Hemagglutinin of Pandemic Influenza A(H1N1)pdm09 Viruses between 2009-2017 in Ukraine. Two substitutions were found at position 74, S74R (A/Ukraine/130/2011 and A/Odessa/166/2017) and S74N (A/Khmelnitsky/671/2016). 2019 Pathogens (Basel, Switzerland) Result IV S74R;S74N 45;97 49;101 31669761 Discovery of M2 channel blockers targeting the drug-resistant double mutants M2-S31N/L26I and M2-S31N/V27A from the influenza A viruses. All compounds (1-16) selected had potent inhibition against the M2-S31N mutant as tested before. 2020 European journal of pharmaceutical sciences Result IV S31N 67 71 M2 64 66 31669761 Discovery of M2 channel blockers targeting the drug-resistant double mutants M2-S31N/L26I and M2-S31N/V27A from the influenza A viruses. All three rH3N2 viruses, rH3N2 M2-S31N, rH3N2 M2-S31N/L26I, and rH3N2 M2-S31N/V27A, had similar growth curves, indicating no effect caused by the single or double mutation. 2020 European journal of pharmaceutical sciences Result IV S31N;S31N;L26I;S31N;V27A 34;49;54;73;78 38;53;58;77;82 M2;M2;M2 31;46;70 33;48;72 31669761 Discovery of M2 channel blockers targeting the drug-resistant double mutants M2-S31N/L26I and M2-S31N/V27A from the influenza A viruses. Amantadine derivatives such as WJ332 were developed to inhibit the single M2-S31N mutant with better potency than amantadine on WT channels. 2020 European journal of pharmaceutical sciences Result IV S31N 77 81 M2 74 76 31669761 Discovery of M2 channel blockers targeting the drug-resistant double mutants M2-S31N/L26I and M2-S31N/V27A from the influenza A viruses. Except for compounds 5 and 16, all compounds that inhibited the M2-S31N channel conductance had nearly identical inhibition for the M2-S31N/L26I double mutant channel as well. 2020 European journal of pharmaceutical sciences Result IV S31N;L26I;S31N 67;140;135 71;144;139 M2;M2 64;132 66;134 31669761 Discovery of M2 channel blockers targeting the drug-resistant double mutants M2-S31N/L26I and M2-S31N/V27A from the influenza A viruses. For the human H5N1 viruses, the highest number of isolates were collected during 2005-2007, whereby the V27A mutation was the most frequent mutant, followed by the double mutant S31N/L26I. 2020 European journal of pharmaceutical sciences Result IV V27A;L26I;S31N 104;183;178 108;187;182 31669761 Discovery of M2 channel blockers targeting the drug-resistant double mutants M2-S31N/L26I and M2-S31N/V27A from the influenza A viruses. For the rH3N2 M2-S31N/V27A virus, the EC50 values were approximately ten-fold higher than that of rH3N2 M2-S31N/L26I. 2020 European journal of pharmaceutical sciences Result IV V27A;S31N;L26I;S31N 22;17;112;107 26;21;116;111 M2;M2 14;104 16;106 31669761 Discovery of M2 channel blockers targeting the drug-resistant double mutants M2-S31N/L26I and M2-S31N/V27A from the influenza A viruses. From 2002-2007, the predominant amantadine-resistant M2 contained the S31N/L26I mutation as shown in. 2020 European journal of pharmaceutical sciences Result IV L26I;S31N 75;70 79;74 M2 53 55 31669761 Discovery of M2 channel blockers targeting the drug-resistant double mutants M2-S31N/L26I and M2-S31N/V27A from the influenza A viruses. From 2002-2019, the double mutant S31N/L26I remained the predominant amantadine-resistant mutant, accounting up to 50.6% of total drug-resistant isolates. 2020 European journal of pharmaceutical sciences Result IV L26I;S31N 39;34 43;38 31669761 Discovery of M2 channel blockers targeting the drug-resistant double mutants M2-S31N/L26I and M2-S31N/V27A from the influenza A viruses. H5N1 viruses are currently restricted to biosafety level 3 (BSL-3) containment labs, and clinical isolates of H5N1 viruses harboring the M2-S31N/L26I or the M2-S31N/V27A double mutants are not readily accessible. 2020 European journal of pharmaceutical sciences Result IV L26I;S31N;S31N;V27A 145;140;160;165 149;144;164;169 M2;M2 137;157 139;159 31669761 Discovery of M2 channel blockers targeting the drug-resistant double mutants M2-S31N/L26I and M2-S31N/V27A from the influenza A viruses. Identification of potent M2 channel blockers for S31N/L26I and S31N/V27A mutants. 2020 European journal of pharmaceutical sciences Result IV S31N;L26I;S31N;V27A 49;54;63;68 53;58;67;72 M2 25 27 31669761 Discovery of M2 channel blockers targeting the drug-resistant double mutants M2-S31N/L26I and M2-S31N/V27A from the influenza A viruses. In contrast, most of the compounds tested had reduced effect on the conductance of M2-S31N/V27A double mutant. 2020 European journal of pharmaceutical sciences Result IV S31N;V27A 86;91 90;95 M2 83 85 31669761 Discovery of M2 channel blockers targeting the drug-resistant double mutants M2-S31N/L26I and M2-S31N/V27A from the influenza A viruses. Nevertheless, three compounds, 6, 7 and 15 demonstrated 30-40% inhibition against the M2-S31N/V27A double mutant channel. 2020 European journal of pharmaceutical sciences Result IV S31N;V27A 89;94 93;98 M2 86 88 31669761 Discovery of M2 channel blockers targeting the drug-resistant double mutants M2-S31N/L26I and M2-S31N/V27A from the influenza A viruses. Other drug-resistant mutations such as the V27A or S31N/V27A were isolated in much fewer numbers. 2020 European journal of pharmaceutical sciences Result IV V27A;V27A;S31N 43;56;51 47;60;55 31669761 Discovery of M2 channel blockers targeting the drug-resistant double mutants M2-S31N/L26I and M2-S31N/V27A from the influenza A viruses. Strains resistant to amantadine in avian isolates between 2002-2019 are predominantly S31N (28.6% of amantadine-resistant strains) or S31N/L26I (60.9% of amantadine-resistant strains) (Fig 1). 2020 European journal of pharmaceutical sciences Result IV S31N;L26I;S31N 86;139;134 90;143;138 31669761 Discovery of M2 channel blockers targeting the drug-resistant double mutants M2-S31N/L26I and M2-S31N/V27A from the influenza A viruses. The EC50 values of compounds 6, 7 and 15 against rH3N2 M2-S31N/L26I virus were 0.5 +- 0.2, 1.2 +- 0.04, 2.0 +- 0.9 muM, respectively, slightly higher than that of the H1N1 M2-S31N virus. 2020 European journal of pharmaceutical sciences Result IV S31N;L26I;S31N 58;63;175 62;67;179 M2;M2 55;172 57;174 31669761 Discovery of M2 channel blockers targeting the drug-resistant double mutants M2-S31N/L26I and M2-S31N/V27A from the influenza A viruses. Therefore, we hypothesize that varying the isoxazole and aryl substitutions might lead to inhibitors targeting the M2 double mutants S31N/L26I and S31N/V27A. 2020 European journal of pharmaceutical sciences Result IV S31N;L26I;S31N;V27A 133;138;147;152 137;142;151;156 M2 115 117 31669761 Discovery of M2 channel blockers targeting the drug-resistant double mutants M2-S31N/L26I and M2-S31N/V27A from the influenza A viruses. Using two-electrode voltage clamp (TEVC) assay, we tested this series of M2-S31N inhibitors to profile their channel blockage efficacy against both S31N/L26I and S31N/V27A M2 double mutant channels expressed in oocytes. 2020 European journal of pharmaceutical sciences Result IV S31N;L26I;S31N;S31N;V27A 76;153;148;162;167 80;157;152;166;171 M2;M2 73;172 75;174 31669761 Discovery of M2 channel blockers targeting the drug-resistant double mutants M2-S31N/L26I and M2-S31N/V27A from the influenza A viruses. With our continuous interest in developing M2 channel blockers, we aimed to expand the spectrum of activity of S31N inhibitors to S31N/V27A and S31N/L26I as well. 2020 European journal of pharmaceutical sciences Result IV S31N;S31N;V27A;S31N;L26I 111;130;135;144;149 115;134;139;148;153 M2 43 45 31669761 Discovery of M2 channel blockers targeting the drug-resistant double mutants M2-S31N/L26I and M2-S31N/V27A from the influenza A viruses. With this strategy, we selected a library of M2-S31N inhibitors with diverse aryl or biaryl chemical modifications as shown in. 2020 European journal of pharmaceutical sciences Result IV S31N 48 52 M2 45 47 31669761 Discovery of M2 channel blockers targeting the drug-resistant double mutants M2-S31N/L26I and M2-S31N/V27A from the influenza A viruses. Within both human and avian H5N1 strains, we did not observe any M2-L26I/V27A double mutants, nor an appreciable amount of M2-S31N/L26I/V27A triple mutants (data not shown). 2020 European journal of pharmaceutical sciences Result IV L26I;V27A;S31N;V27A;L26I 68;73;126;136;131 72;77;130;140;135 M2;M2 65;123 67;125 31703251 Evolution of H5-Type Avian Influenza A Virus Towards Mammalian Tropism in Egypt, 2014 to 2015. All mice, infected with LP-S10739C, died naturally after the fourth day (Figure 5). 2019 Pathogens (Basel, Switzerland) Result IV S10739C 27 34 31703251 Evolution of H5-Type Avian Influenza A Virus Towards Mammalian Tropism in Egypt, 2014 to 2015. Although LP-S10739C showed the highest virulence, the infection was accompanied with the lowest virus shedding in the lung of infected mice (Figure 5c). 2019 Pathogens (Basel, Switzerland) Result IV S10739C 12 19 31703251 Evolution of H5-Type Avian Influenza A Virus Towards Mammalian Tropism in Egypt, 2014 to 2015. At later time points (24 to 36 h), LP-M7217B, LP-M2583A, LP-D10552B, LP-D10551C, LP-A/Du/Eg/4/2015, LP-S10739C, and LP-A10540A showed significantly improved replication kinetics as compared with the control LP-7271. 2019 Pathogens (Basel, Switzerland) Result IV M2583A;D10551C;S10739C;A10540A 49;72;103;119 55;79;110;126 31703251 Evolution of H5-Type Avian Influenza A Virus Towards Mammalian Tropism in Egypt, 2014 to 2015. Except for the H5-HA of influenza A/chicken/Egypt/1/2006 (H5N1, LP-2006, clade 2.2.1), which showed a lower affinity to human- and avian-type receptors than human LP-7271, the H5-HA proteins from influenza A/chicken/Egypt/Q1995D/2010 (H5N1, LP-Q1995D, clade 2.2.1.1), A/duck/Egypt/M2583A/2010 (H5N1, LP-M2583A, clade 2.2.1.1), and A/chicken/Egypt/M7217B/2013 (H5N1, LP-M7217B, clade 2.2.1.2) demonstrated binding affinity equal to that of human LP-7271 and were able to bind both types of receptors (Figure 2). 2019 Pathogens (Basel, Switzerland) Result IV Q1995D;M2583A;Q1995D;M2583A 244;303;222;281 250;309;228;287 HA;HA 18;179 20;181 31703251 Evolution of H5-Type Avian Influenza A Virus Towards Mammalian Tropism in Egypt, 2014 to 2015. However, in the second group, inoculated with LP-Q1995D, mice naturally died or had to be euthanized (weight body loss >= 25%). 2019 Pathogens (Basel, Switzerland) Result IV Q1995D 49 55 31703251 Evolution of H5-Type Avian Influenza A Virus Towards Mammalian Tropism in Egypt, 2014 to 2015. However, the affinities of the H5-HA proteins of influenza A/chicken/Egypt/S10738B/2015 (H5N1, LP- S10738B, clade 2.2.1.2), A/chicken/Egypt/A10540A/2014 (H5N1, LP-A10540A, clade 2.2.1.2), and A/chicken/Egypt/S10739C/2015 (H5N1, LP-S10739C, clade 2.2.1.2) to avian- and human-type receptors were slightly lower to comparable, respectively, as compared with the affinity of the human LP-7271 for both receptors (Figure 2). 2019 Pathogens (Basel, Switzerland) Result IV A10540A;A10540A;S10739C;S10739C 140;163;231;208 147;170;238;215 HA 34 36 31703251 Evolution of H5-Type Avian Influenza A Virus Towards Mammalian Tropism in Egypt, 2014 to 2015. In comparison to the human LP-7271 (Figure 3), LP 2006, LP-Q1995D, LP-M7217B, 2014 to 2015 LP-S10739C, and LP-D10552B replicated to significantly higher titers in MDCK-SIAT1 cells at 12 to 36 h and 24 to 36 h post-infection, respectively. 2019 Pathogens (Basel, Switzerland) Result IV Q1995D;S10739C 59;94 65;101 31703251 Evolution of H5-Type Avian Influenza A Virus Towards Mammalian Tropism in Egypt, 2014 to 2015. The data obtained revealed that the H5-HA proteins, derived from influenza A/chicken/Egypt/D10551C/2014 (H5N1, LP-D10551C, clade 2.2.1.2), A/chicken/Egypt/D10552B/2015 (H5N1, LP-D10552B, clade 2.2.1.2), A/chicken/Egypt/Q10920C/2015 (H5N1, LP-Q10920C, clade 2.2.1.2), and A/duck/Egypt/4/2015 (H5N1, LP-A/Du/Eg/4/2015, clade 2.2.1.2) of clade 2.2.1.2, demonstrated comparable to slightly lower affinities for human-type receptors but higher affinities to avian-type receptors, as compared with those for human LP-7271, respectively (Figure 2). 2019 Pathogens (Basel, Switzerland) Result IV D10551C;Q10920C;D10551C;Q10920C 114;242;91;219 121;249;98;226 HA 39 41 31703251 Evolution of H5-Type Avian Influenza A Virus Towards Mammalian Tropism in Egypt, 2014 to 2015. The following viruses were compared with other strains isolated from 2006 to 2013 for different clades as controls: influenza A/chicken/Egypt/1/2006 (clade 2.2.1), A/chicken/Egypt/Q1995D/2010 (clade 2.2.1.1), A/duck/Egypt/M2583A/2010 (clade 2.2.1.1), and A/chicken/Egypt/M7217B/2013 (clade 2.2.1.2)), in addition to the human strain A/Egypt/MOH-NRC7271/2014 (clade 2.2.1.2) (Table 1). 2019 Pathogens (Basel, Switzerland) Result IV Q1995D;M2583A 180;222 186;228 31703251 Evolution of H5-Type Avian Influenza A Virus Towards Mammalian Tropism in Egypt, 2014 to 2015. The LP-S10739C virus showed the highest morbidity (Figure 5a) and mortality (Figure 5b) in mice as compared with human LP-7271. 2019 Pathogens (Basel, Switzerland) Result IV S10739C 7 14 31703251 Evolution of H5-Type Avian Influenza A Virus Towards Mammalian Tropism in Egypt, 2014 to 2015. The replication efficiencies of LP 7+1 viruses expressing monobasic H5-HA of 2014 to 2015 viruses were comparable to human LP-7271, but lower than 2006 (LP-2006), 2010 (LP-Q1995D), and 2013 (LP-M7217B) at 6 to 36 h p.i. 2019 Pathogens (Basel, Switzerland) Result IV Q1995D 172 178 HA 71 73 31703251 Evolution of H5-Type Avian Influenza A Virus Towards Mammalian Tropism in Egypt, 2014 to 2015. Therefore, a representative H5N1 virus (clade 2.2.1.2) from each cluster was selected for further experimental validations (A/chicken/Egypt/A10540A/2014, A/chicken/Egypt/D10551C/2014, A/chicken/Egypt/D10552B/2015, A/chicken/Egypt/S10738B/2015, A/chicken/Egypt/S10739C/2015, A/chicken/Egypt/Q10920C/2015, and A/duck/Egypt/4/2015) (Figure 1). 2019 Pathogens (Basel, Switzerland) Result IV A10540A;D10551C;S10739C;Q10920C 140;170;260;290 147;177;267;297 31703251 Evolution of H5-Type Avian Influenza A Virus Towards Mammalian Tropism in Egypt, 2014 to 2015. To assess the in vivo pathogenicity of LP 7+1 H5-HA viruses, five groups of C57BL/6 female mice were infected with selected LP 7+1 H5-HA expressing reassortants of 2006 (LP-2006), Q1995D (LP-Q1995D), S10739C (LP-S10739C), and MOH-7271 (human LP-7271, positive control). 2019 Pathogens (Basel, Switzerland) Result IV Q1995D;Q1995D;S10739C;S10739C 180;191;200;212 186;197;207;219 HA;HA 49;134 51;136 31719554 Synergistic PA and HA mutations confer mouse adaptation of a contemporary A/H3N2 influenza virus. An additional amino acid mutation in the HA protein (N122D) was detected in the MA-H3N2 virus. 2019 Scientific reports Result IV N122D 53 58 HA 41 43 31719554 Synergistic PA and HA mutations confer mouse adaptation of a contemporary A/H3N2 influenza virus. Seven amino acid substitutions were identified in the PA (K615E), NP (G384R), NA (G320E) and HA (N122D, N144E, N246K, and A304T) proteins of MA-H3N2 compared to the parental virus (Table 1). 2019 Scientific reports Result IV K615E;G384R;G320E;N122D;N144E;N246K;A304T 58;70;82;97;104;111;122 63;75;87;102;109;116;127 HA;NA;NP;PA 93;78;66;54 95;80;68;56 31719554 Synergistic PA and HA mutations confer mouse adaptation of a contemporary A/H3N2 influenza virus. Since the only difference in the genome of the two viruses was the HA-N122D substitution, it could be concluded that this mutation was not responsible for the adaptation. 2019 Scientific reports Result IV N122D 70 75 HA 67 69 31719554 Synergistic PA and HA mutations confer mouse adaptation of a contemporary A/H3N2 influenza virus. Specifically, both passaged viruses harbored mutations in PA (K615E), HA (N144E, N246K and A304T), NP (G384R) and NA (G320E). 2019 Scientific reports Result IV K615E;N144E;N246K;A304T;G384R;G320E 62;74;81;91;103;118 67;79;86;96;108;123 HA;NA;NP;PA 70;114;99;58 72;116;101;60 31719554 Synergistic PA and HA mutations confer mouse adaptation of a contemporary A/H3N2 influenza virus. These results demonstrate that both MA-H3N2-PA containing one mutation (K615E) and MA-H3N2-HA containing all 3 mutations (N144E, N246K, and A304T) are required for the increased pathogenicity of MA-H3N2 virus in mice. 2019 Scientific reports Result IV K615E;N144E;N246K;A304T 72;122;129;140 77;127;134;145 HA;PA 91;44 93;46 31783761 Influenza A virus hemagglutinin mutations associated with use of neuraminidase inhibitors correlate with decreased inhibition by anti-influenza antibodies. Consistent with the HI results, the MN activity of mAbs 28665 and 28668 and human serum samples collected from three different donors was reduced by >170-fold against recombinant CA/04G155E and CA/04D222G compared to CA/04 (Table 3). 2019 Virology journal Result IV G155E;D222G 184;199 189;204 31783761 Influenza A virus hemagglutinin mutations associated with use of neuraminidase inhibitors correlate with decreased inhibition by anti-influenza antibodies. Examples include NA H275Y in the pre-2009-pandemic H1N1 lineage and M2 S31 N in the majority of currently circulating seasonal influenza viruses as well as other viruses. 2019 Virology journal Result IV H275Y;S31N 20;71 25;76 M2;NA 68;17 70;19 31783761 Influenza A virus hemagglutinin mutations associated with use of neuraminidase inhibitors correlate with decreased inhibition by anti-influenza antibodies. HI of goat and ferret antisera raised against pandemic A(H1N1)pdm09 viruses was significantly reduced (~ 20-fold ) against recombinant CA/04G155E and CA/04D222G viruses carrying the G155E and D222G substitutions, respectively, compared to the wild-type CA/04 virus (Table 2). 2019 Virology journal Result IV G155E;D222G 182;192 187;197 31783761 Influenza A virus hemagglutinin mutations associated with use of neuraminidase inhibitors correlate with decreased inhibition by anti-influenza antibodies. Substitution R208K mapped to the interior of the trimer below the surface-exposed globular domain distal to the HA1 antigenic sites. 2019 Virology journal Result IV R208K 13 18 HA1 112 115 31783761 Influenza A virus hemagglutinin mutations associated with use of neuraminidase inhibitors correlate with decreased inhibition by anti-influenza antibodies. The S183P substitution resulted in ~ 4-fold drop in 28665 titers and ~ 2-fold drop in 28666 and 28667 titers. 2019 Virology journal Result IV S183P 4 9 31783761 Influenza A virus hemagglutinin mutations associated with use of neuraminidase inhibitors correlate with decreased inhibition by anti-influenza antibodies. There were no significant changes in ferret antisera or mAb HI activity against V152I and S162 N. 2019 Virology journal Result IV V152I;S162N 80;90 85;96 31783761 Influenza A virus hemagglutinin mutations associated with use of neuraminidase inhibitors correlate with decreased inhibition by anti-influenza antibodies. These mutations included D125S, G155E, S162 N, and D222G (H1 numbering convention is used here and throughout the text). 2019 Virology journal Result IV D125S;G155E;S162N;D222G 25;32;39;51 30;37;45;56 31810278 Equine Mx1 Restricts Influenza A Virus Replication by Targeting at Distinct Site of its Nucleoprotein. As expected, point mutations in H3N8JL89 NP (H52Y) and H5N1 NP (Y52H) showed a reverse effect against eqMx1, confirming the importance of position 52. 2019 Viruses Result IV H52Y;Y52H 45;64 49;68 NP;NP 41;60 43;62 31810278 Equine Mx1 Restricts Influenza A Virus Replication by Targeting at Distinct Site of its Nucleoprotein. As expected, the reverse effect was observed for the mutation at site 52 of H7N9ZJ13 NP (N52H) (Figure 5B). 2019 Viruses Result IV N52H 89 93 NP 85 87 31810278 Equine Mx1 Restricts Influenza A Virus Replication by Targeting at Distinct Site of its Nucleoprotein. Expectedly, the mutant H3N8JL89-H52N-NP showed a strong interaction with eqMx1 (Figure 6A). 2019 Viruses Result IV H52N 32 36 NP 37 39 31810278 Equine Mx1 Restricts Influenza A Virus Replication by Targeting at Distinct Site of its Nucleoprotein. Flag-tagged eqMx1 was co-expressed in HEK293T cells, individually or in combination with expression plasmids of PB1, PB2, PA, viral reporter RNA (FF-luc), and NP from either H3N8JL89 and mutants (H3N8JL89-G34S-NP, H3N8JL89-H52N-NP) or H7N9ZJ13 and its mutants (H7N9ZJ13-S34G-NP, H7N9ZJ13-N52H-NP), to mimic the viral vRNPs. 2019 Viruses Result IV N52H;G34S;H52N;S34G 288;205;223;270 292;209;227;274 NP;NP;NP;NP;NP;PA;PB1;PB2 159;210;228;275;293;122;112;117 161;212;230;277;295;124;115;120 31810278 Equine Mx1 Restricts Influenza A Virus Replication by Targeting at Distinct Site of its Nucleoprotein. H5N1 contains Tyrosine (Y) at position 52 (Figure 5C). 2019 Viruses Result IV Y52Y 13 42 31810278 Equine Mx1 Restricts Influenza A Virus Replication by Targeting at Distinct Site of its Nucleoprotein. However, interestingly, mutating S34G in the H7N9ZJ13 NP had no distinguishable alteration in the activity towards eqMx1, rather a markedly less resistant phenotype was observed and the mutant behaved like a wild type H7N9ZJ13 NP. 2019 Viruses Result IV S34G 33 37 NP;NP 54;227 56;229 31810278 Equine Mx1 Restricts Influenza A Virus Replication by Targeting at Distinct Site of its Nucleoprotein. In contrast, Flag-tagged eqMx1 was co-immunoprecipitated with NP from H7N9ZJ13 and its mutant -S34G when they were co-expressed. 2019 Viruses Result IV S34G 95 99 NP 62 64 31810278 Equine Mx1 Restricts Influenza A Virus Replication by Targeting at Distinct Site of its Nucleoprotein. In H3N8JL89 NP, the mutants were G34S, G50S, H52N, K77R, M105V, and V186I. 2019 Viruses Result IV G34S;G50S;H52N;K77R;M105V;V186I 33;39;45;51;57;68 37;43;49;55;62;73 NP 12 14 31810278 Equine Mx1 Restricts Influenza A Virus Replication by Targeting at Distinct Site of its Nucleoprotein. In order to determine the effect of the two identified sites 34 and 52 in H3N8JL89 in resistance against huMxA, the polymerase activity of three H3N8JL89 NP mutants G34S, H52N, and H52Y, as well as two H7N9ZJ13 NP mutants S34G and N52H, were measured. 2019 Viruses Result IV G34S;H52N;H52Y;S34G;N52H 165;171;181;222;231 169;175;185;226;235 NP;NP 154;211 156;213 31810278 Equine Mx1 Restricts Influenza A Virus Replication by Targeting at Distinct Site of its Nucleoprotein. No PB2 was found co-immunoprecipitated with H3N8JL89-H52N-NP, H7N9ZJ13-NP, and H7N9ZJ13-S34G. 2019 Viruses Result IV H52N;S34G 53;88 57;92 NP;NP;PB2 58;71;3 60;73;6 31810278 Equine Mx1 Restricts Influenza A Virus Replication by Targeting at Distinct Site of its Nucleoprotein. On the other hand, in the complex where there was no interaction between eqMx1 and NP (H3N8JL89,-G34S and H7N9ZJ13,-N52H) PB2 was co-immunoprecipitated with the said variants of NP (Figure 6C,D; lanes 4 to 6). 2019 Viruses Result IV G34S;N52H 97;116 101;120 NP;NP;PB2 83;178;122 85;180;125 31810278 Equine Mx1 Restricts Influenza A Virus Replication by Targeting at Distinct Site of its Nucleoprotein. Out of eight substitutions of NP, two positions V85A and T197I were not selected for mutations as when the sequence of two strains of H3N8, H3N8JL89, and H3N8XJ07, were compared, the H3N8XJ07. 2019 Viruses Result IV V85A;T197I 48;57 52;62 NP 30 32 31810278 Equine Mx1 Restricts Influenza A Virus Replication by Targeting at Distinct Site of its Nucleoprotein. Results showed that when the eqMx1 was co-expressed with either H3N8JL89-NP or H3N8JL89-G34S-NP, no interaction was identified. 2019 Viruses Result IV G34S 88 92 NP;NP 73;93 75;95 31810278 Equine Mx1 Restricts Influenza A Virus Replication by Targeting at Distinct Site of its Nucleoprotein. Similarly, mutations at S50G, R77K, V105M, and I186V of H7N9ZJ13 NP showed no effect and mutation I186V showed more inhibition towards eqMx1. 2019 Viruses Result IV S50G;R77K;V105M;I186V;I186V 24;30;36;47;98 28;34;41;52;103 NP 65 67 31810278 Equine Mx1 Restricts Influenza A Virus Replication by Targeting at Distinct Site of its Nucleoprotein. Similarly, reverse mutations in H7N9ZJ13 NP, S34G, and N52H did not alter the sensitivity to huMxA (Figure 5E). 2019 Viruses Result IV S34G;N52H 45;55 49;59 NP 41 43 31810278 Equine Mx1 Restricts Influenza A Virus Replication by Targeting at Distinct Site of its Nucleoprotein. The mutants G34S, H52N, and H52Y showed less pronounced polymerase activity than the wild type H3N8JL89 NP but still could not escape the antiviral activity of huMxA (Figure 5D). 2019 Viruses Result IV G34S;H52N;H52Y 12;18;28 16;22;32 NP 104 106 31810278 Equine Mx1 Restricts Influenza A Virus Replication by Targeting at Distinct Site of its Nucleoprotein. This interaction was lost when site 52 mutated in H7N9ZJ13 to-N52H (Figure 6B). 2019 Viruses Result IV N52H 62 66 31810278 Equine Mx1 Restricts Influenza A Virus Replication by Targeting at Distinct Site of its Nucleoprotein. To further evaluate the importance of 52H of the NP protein in the resistance of eqMx1, we rescued viruses H3N8JL89 and H3N8JL89 with an H52N substitution in the NP using a reverse genetic system as previously described. 2019 Viruses Result IV H52N 137 141 NP;NP 49;162 51;164 31810278 Equine Mx1 Restricts Influenza A Virus Replication by Targeting at Distinct Site of its Nucleoprotein. We found mutations G34S (albeit not statistically significant) and H52N altered the restriction of eqMx1, whereas the mutants G50S, K77R, M105V, and V186I remained completely unaffected by eqMx1. 2019 Viruses Result IV G34S;H52N;G50S;K77R;M105V;V186I 19;67;126;132;138;149 23;71;130;136;143;154 31810278 Equine Mx1 Restricts Influenza A Virus Replication by Targeting at Distinct Site of its Nucleoprotein. We found that the wild type H3N8JL89 had almost the same number of copies in the presence or absence of eqMx1 during replication, whereas the number of copies of mutant virus (JL89-H52N) were drastically reduced in the cells expressing eqMx1, indicating that this mutant virus strain could be blocked by eqMx1, in contrast to the wild type H3N8JL89 virus (Figure 7A). 2019 Viruses Result IV H52N 181 185 31839904 Complete genome sequencing of H1N1pdm09 swine influenza isolates from Nigeria reveals likely reverse zoonotic transmission at the human-animal interface in intensive piggery. However, nucleotide alignment of the HA gene of the swine viruses from Nigeria differed by thirteen nucleotides and three amino acid substitutions at position N138S, Q240R (H1 numbering) and I312V compared to earlier H1N1pdm09 isolates from humans in Nigeria, Cameroon, Ghana and the prototype A/California/07/2009(H1N1) (Table 1). 2019 Infection ecology & epidemiology Result IV N138S;Q240R;I312V 159;166;191 164;171;196 HA 37 39 31839904 Complete genome sequencing of H1N1pdm09 swine influenza isolates from Nigeria reveals likely reverse zoonotic transmission at the human-animal interface in intensive piggery. S439G substitution in the amino acid is also unique to A/Swine/Nigeria/VIR44-09/2009. 2019 Infection ecology & epidemiology Result IV S439G 0 5 31839904 Complete genome sequencing of H1N1pdm09 swine influenza isolates from Nigeria reveals likely reverse zoonotic transmission at the human-animal interface in intensive piggery. Sequence analysis of the NA gene relative to A/California/07/2009 also revealed amino acid substitutions at positions V106I, N248D, Y351F, S439G. 2019 Infection ecology & epidemiology Result IV V106I;N248D;Y351F;S439G 118;125;132;139 123;130;137;144 25 27 31839904 Complete genome sequencing of H1N1pdm09 swine influenza isolates from Nigeria reveals likely reverse zoonotic transmission at the human-animal interface in intensive piggery. The PB2 protein of Nigerian isolate of H1N1pdm09 had D527G amino acid substitution, for PB1 G replaced K in position 736, for NS gene amino acid substitutions between A/Swine/Nigeria and prototype A/California include G28V, W103C, Q109K, I111M, I123V, W187E, G189D, V234M, S246N. 2019 Infection ecology & epidemiology Result IV D527G;G28V;W103C;Q109K;I111M;I123V;W187E;G189D;V234M;S246N 53;218;224;231;238;245;252;259;266;273 58;222;229;236;243;250;257;264;271;278 NS;PB1;PB2 126;88;4 128;91;7 31839904 Complete genome sequencing of H1N1pdm09 swine influenza isolates from Nigeria reveals likely reverse zoonotic transmission at the human-animal interface in intensive piggery. There were no observed substitutions in the matrix gene except S31N that has been described for most influenza A/H1N1pdm09 isolates as the predominant amantadine-resistant mutation in M2. 2019 Infection ecology & epidemiology Result IV S31N 63 67 M2;M 184;44 186;50 31842256 Antiviral Activity of Benzoic Acid Derivative NC-5 Against Influenza A Virus and Its Neuraminidase Inhibition. As in the case of H1N1-H275Y, the inhibition rate of NC-5 at 80 muM was 72.9%, while that of OC was only 4.0% (Figure 3F). 2019 International journal of molecular sciences Result IV H275Y 23 28 31842256 Antiviral Activity of Benzoic Acid Derivative NC-5 Against Influenza A Virus and Its Neuraminidase Inhibition. As shown in Figure 5E and Figure 6E, severe hyperemia appeared in the alveolar walls, and the spaces between the alveolar walls were filled with moderate inflammatory infiltrates of neutrophils, macrophages and lymphocytes in the H1N1 and H1N1-H275Y virus-infected models as well as in mice given OS following infection with H1N1-H275Y. 2019 International journal of molecular sciences Result IV H275Y;H275Y 244;330 249;335 31842256 Antiviral Activity of Benzoic Acid Derivative NC-5 Against Influenza A Virus and Its Neuraminidase Inhibition. Effective Protection by NC-5 in Mice Infected with Influenza Virus A/FM/1/47 (H1N1) and Oseltamivir-Resistant Mutant A/FM/1/47 (H1N1-H275Y) 2019 International journal of molecular sciences Result IV H275Y 133 138 31842256 Antiviral Activity of Benzoic Acid Derivative NC-5 Against Influenza A Virus and Its Neuraminidase Inhibition. Effective Protection by NC-5 in Mice Infected with Influenza Virus A/FM/1/47 (H1N1) and Oseltamivir-Resistant Mutant A/FM/1/47 (H1N1-H275Y). 2019 International journal of molecular sciences Result IV H275Y 133 138 31842256 Antiviral Activity of Benzoic Acid Derivative NC-5 Against Influenza A Virus and Its Neuraminidase Inhibition. H1N1, H1N1-H275Y and H3N2 were tested with oseltamivir carboxylate (OC) as a control. 2019 International journal of molecular sciences Result IV H275Y 11 16 31842256 Antiviral Activity of Benzoic Acid Derivative NC-5 Against Influenza A Virus and Its Neuraminidase Inhibition. In the case of H1N1-H275Y, the mice given OS all died on the ninth day, while NC-5 exhibited significant protection effect with 75 mg/kg/d and 100 mg/kg/d NC-5, increasing survival to 40% and 60% (Figure 6A), respectively. 2019 International journal of molecular sciences Result IV H275Y 20 25 31842256 Antiviral Activity of Benzoic Acid Derivative NC-5 Against Influenza A Virus and Its Neuraminidase Inhibition. NC-5 inhibited the Replication of Influenza Viruses A/FM/1/47 (H1N1), A/FM/1/47-H275Y (H1N1-H275Y) and A/Beijing/32/92 (H3N2) in Cell Culture. 2019 International journal of molecular sciences Result IV H275Y;H275Y 80;92 85;97 31842256 Antiviral Activity of Benzoic Acid Derivative NC-5 Against Influenza A Virus and Its Neuraminidase Inhibition. NC-5 suppressed the NA activity of H1N1-H275Y and H7N9-R294K and the inhibition rates were both 25.8% at 480 muM. 2019 International journal of molecular sciences Result IV H275Y;R294K 40;55 45;60 20 22 31842256 Antiviral Activity of Benzoic Acid Derivative NC-5 Against Influenza A Virus and Its Neuraminidase Inhibition. The lung parameters of mice infected with H1N1-H275Y and the mice administered OS (Figure 6C,D, lung index: 1.2, lung injury score: 7.3) were similar to those of the corresponding models (lung index: 1.4, lung injury score: 7.7), while the groups that received NC-5 at 100 mg/kg/d showed a significant improvement in condition (lung index: 1.0, lung injury score: 3.5). 2019 International journal of molecular sciences Result IV H275Y 47 52 Lung lesions;Lung lesions;Lung lesions 113;205;345 124;216;356 31842256 Antiviral Activity of Benzoic Acid Derivative NC-5 Against Influenza A Virus and Its Neuraminidase Inhibition. The NA activities of oseltamivir-resistant viruses H1N1-H275Y (Figure 2A) and H7N9-R294K (Figure 2C) were also inhibited by NC-5 with a weaker or similar inhibition effect. 2019 International journal of molecular sciences Result IV H275Y;R294K 56;83 61;88 4 6 31842256 Antiviral Activity of Benzoic Acid Derivative NC-5 Against Influenza A Virus and Its Neuraminidase Inhibition. The reduction in CPE caused by H1N1-H275Y was confirmed by direct microscopic observation, which detected a far lower CPE than the dimethyl sulfoxide (DMSO) control and the OC-treated cells (Figure 3E). 2019 International journal of molecular sciences Result IV H275Y 36 41 31852473 Continuing evolution of H6N2 influenza a virus in South African chickens and the implications for diagnosis and control. All sub-lineage I viruses isolated from 2015 onwards contained a V201I mutation in this epitope, and 338,087/2015, 344,378/2015 and 344,579/2015 had a M204 L mutation. 2019 BMC veterinary research Result IV V201I;M204L 65;151 70;157 31852473 Continuing evolution of H6N2 influenza a virus in South African chickens and the implications for diagnosis and control. All were absent from the South African H6N2 viruses apart from K702R (Additional file 7: Figure S3). 2019 BMC veterinary research Result IV K702R 63 68 31852473 Continuing evolution of H6N2 influenza a virus in South African chickens and the implications for diagnosis and control. D701N in the PB2 protein was associated with high pathogenicity in mice, this mutation was present in early sub-lineage I strain AL19/2002 but was not detected in any other South African H6N2 strains. 2019 BMC veterinary research Result IV D701N 0 5 PB2 13 16 31852473 Continuing evolution of H6N2 influenza a virus in South African chickens and the implications for diagnosis and control. H99Y and I368V mutations in the PB1 protein are associated with airborne transmission among ferrets but were absent from the H6N2 viruses. 2019 BMC veterinary research Result IV H99Y;I368V 0;9 4;14 PB1 32 35 31852473 Continuing evolution of H6N2 influenza a virus in South African chickens and the implications for diagnosis and control. Human-associated markers in the NP protein (V33I, I109V), M2 protein (L55F) NS1 protein (E227R/K) and NS2 protein (S70G) were similarly absent from the H6N2 viruses (data not shown). 2019 BMC veterinary research Result IV V33I;I109V;L55F;E227R;E227K;S70G 44;50;70;89;89;115 48;55;74;96;96;119 M2;NP;NS1;NS2 58;32;76;102 60;34;79;105 31852473 Continuing evolution of H6N2 influenza a virus in South African chickens and the implications for diagnosis and control. In the PB2 protein, K73R, A199S, L475 M, D567N, E627K, A661T and K702R mutations are associated with IAVs capacity to infect humans. 2019 BMC veterinary research Result IV K73R;A199S;L475M;D567N;E627K;A661T;K702R 20;26;33;41;48;55;65 24;31;39;46;53;60;70 PB2 7 10 31852473 Continuing evolution of H6N2 influenza a virus in South African chickens and the implications for diagnosis and control. In the third loop of the HBS, all sub-lineage I strains (but not sub-lineage II) except for H44934/2016 contain a Q432R mutation. 2019 BMC veterinary research Result IV Q432R 114 119 31852473 Continuing evolution of H6N2 influenza a virus in South African chickens and the implications for diagnosis and control. Key mutations near the receptor binding site in the HA protein implicated in the switch between H6 viruses binding avian-type receptors to human-type receptors include A138S, I55V, P186L, V187D, E190V, A193N, G225D, Q226L and G228S (H3 numbering;). 2019 BMC veterinary research Result IV A138S;I55V;P186L;V187D;E190V;A193N;G225D;Q226L;G228S 168;175;181;188;195;202;209;216;226 173;179;186;193;200;207;214;221;231 HA 52 54 31852473 Continuing evolution of H6N2 influenza a virus in South African chickens and the implications for diagnosis and control. Neither of the human-associated markers in the PB1-F2 protein, R79Q and L82S were detected, nor was N66S that is associated with increased virulence, replication efficiency and antiviral response in mice. 2019 BMC veterinary research Result IV R79Q;L82S;N66S 63;72;100 67;76;104 PB1F2 47 53 31852473 Continuing evolution of H6N2 influenza a virus in South African chickens and the implications for diagnosis and control. No human-associated markers in the PA protein, namely P28L, D55N, V100A, K356R, Q/T/S400 L or T552S were detected (data not shown). 2019 BMC veterinary research Result IV P28L;D55N;V100A;K356R;S400L;T552S 54;60;66;73;80;94 58;64;71;78;90;99 PA 35 37 31852473 Continuing evolution of H6N2 influenza a virus in South African chickens and the implications for diagnosis and control. Of the aforementioned, the A138S mutation was absent in the H6 ostrich progenitor but appeared in South African H6N2 sub-lineage I viruses as early as 2002, and have been maintained up until 2019, with the exception of 401,156/2016 and 402,385/2015 in which an 138 L mutation was present (Additional file 4: Figure S1). 2019 BMC veterinary research Result IV A138S 27 32 31852473 Continuing evolution of H6N2 influenza a virus in South African chickens and the implications for diagnosis and control. Of these, the R344K mutation first emerged in sub-lineage I viruses in 2012/2013 (Additional file 6: Figure S2) and was also found in four of the 12 viruses from 2015 onwards, namely 338,087/2015, 344,579/2015, 390,997/2016 and 404,573/2016. 2019 BMC veterinary research Result IV R344K 14 19 31852473 Continuing evolution of H6N2 influenza a virus in South African chickens and the implications for diagnosis and control. Six mutations are associated with the acquisition of resistance to neuramindase inhibitors, namely E119V, R152K, D198N, H274Y, R292K and N294S. 2019 BMC veterinary research Result IV E119V;R152K;D198N;H274Y;R292K;N294S 99;106;113;120;127;137 104;111;118;125;132;142 31852473 Continuing evolution of H6N2 influenza a virus in South African chickens and the implications for diagnosis and control. The A193N mutation was present in all sub-lineage I strains, but absent in the progenitor and sub-lineage II viruses apart from AL25/2002. 2019 BMC veterinary research Result IV A193N 4 9 31852473 Continuing evolution of H6N2 influenza a virus in South African chickens and the implications for diagnosis and control. The HA0 motif of PQVETRGIF was present in all viruses sequenced here, except for H44954/2016 that acquired an additional E343G mutation in its motif of PQVGTRGIF (Additional file 4: Figure S1). 2019 BMC veterinary research Result IV E343G 121 126 31852473 Continuing evolution of H6N2 influenza a virus in South African chickens and the implications for diagnosis and control. The K702R mutation was present in the H6N8 progenitor virus and in one early sub-lineage II isolate AL25/2002 but was absent from the later three sub-lineage II strains in 2012. 2019 BMC veterinary research Result IV K702R 4 9 31852473 Continuing evolution of H6N2 influenza a virus in South African chickens and the implications for diagnosis and control. The NA stalk region of sub-lineage I H6N2 viruses is characterised by a 21 amino acid deletion which was present in all the viruses analysed here (Additional file 6: Figure S2), but an additional single codon (serine) was deleted at residue 46 in isolate 432/2019. 2019 BMC veterinary research Result IV del 46 222 243 4 6 31852473 Continuing evolution of H6N2 influenza a virus in South African chickens and the implications for diagnosis and control. The remaining six mutations in the H6 HA, I155V, P186L, E190V, G225D, Q226L and G228S were not detected. 2019 BMC veterinary research Result IV I155V;P186L;E190V;G225D;Q226L;G228S 42;49;56;63;70;80 47;54;61;68;75;85 HA 38 40 31852473 Continuing evolution of H6N2 influenza a virus in South African chickens and the implications for diagnosis and control. The V187D mutation was already present in the H6N8 ostrich progenitor virus and has persisted through both sub-lineages I and II to the present time. 2019 BMC veterinary research Result IV V187D 4 9 31852473 Continuing evolution of H6N2 influenza a virus in South African chickens and the implications for diagnosis and control. V96A is specifically associated with resistance to zanamivir and oseltamivir, however none of these mutations were present in the neuraminidase proteins of the South African H6N2 viruses (Additional file 6: Figure S2). 2019 BMC veterinary research Result IV V96A 0 4 130 143 31864377 Changes in RNA secondary structure affect NS1 protein expression during early stage influenza virus infection. In order to change hairpin structure in the 497-564 NS (+) RNA region, we introduced three nucleotide substitutions(G511A, G512A and C537G) that lead to one amino acid mutation in the NS1 open reading frame (G166 N) and two mutations in the NEP ORF (V14 M and A22G) (Additional file 4: Figure S1). 2019 Virology journal Result IV G511A;G512A;C537G;G166N;V14M;A22G 116;123;133;208;250;260 121;128;138;214;255;264 NEP;NS;NS1 241;52;184 244;54;187 31864377 Changes in RNA secondary structure affect NS1 protein expression during early stage influenza virus infection. In the 82-148 region we introduced two synonymous mutations: G123A and A132G. 2019 Virology journal Result IV G123A;A132G 61;71 66;76 31864377 Changes in RNA secondary structure affect NS1 protein expression during early stage influenza virus infection. The reduced NS1 protein expression/accumulation observed is likely due to the role of the structures designed (via mutations G123A and A132G in the 82-148 NS RNA region). 2019 Virology journal Result IV G123A;A132G 125;135 130;140 NS;NS1 155;12 157;15 31894969 X-ray Crystal Structures of the Influenza M2 Proton Channel Drug-Resistant V27A Mutant Bound to a Spiro-Adamantyl Amine Inhibitor Reveal the Mechanism of Adamantane Resistance. All four Asp44 and Arg45 residues in the structure of M2(21-61) V27A face the aqueous pore. 2020 Biochemistry Result IV V27A 64 68 M2 54 56 31894969 X-ray Crystal Structures of the Influenza M2 Proton Channel Drug-Resistant V27A Mutant Bound to a Spiro-Adamantyl Amine Inhibitor Reveal the Mechanism of Adamantane Resistance. At residue Arg45, the minimum pore diameter is 2.8 A in the structure of M2(22-46) V27A and 1.0 A in the structure of M2(21-61) V27A. 2020 Biochemistry Result IV V27A;V27A 83;128 87;132 M2;M2 73;118 75;120 31894969 X-ray Crystal Structures of the Influenza M2 Proton Channel Drug-Resistant V27A Mutant Bound to a Spiro-Adamantyl Amine Inhibitor Reveal the Mechanism of Adamantane Resistance. Consistent with previous X-ray crystal structures of the WT and S31N mutant M2 channel, here we observe ordered water molecules above the channel's gating His37 residues. 2020 Biochemistry Result IV S31N 64 68 M2 76 78 31894969 X-ray Crystal Structures of the Influenza M2 Proton Channel Drug-Resistant V27A Mutant Bound to a Spiro-Adamantyl Amine Inhibitor Reveal the Mechanism of Adamantane Resistance. Crystal structure of the M2(21-61) V27A construct in complex with spiro-adamantyl amine. 2020 Biochemistry Result IV V27A 35 39 M2 25 27 31894969 X-ray Crystal Structures of the Influenza M2 Proton Channel Drug-Resistant V27A Mutant Bound to a Spiro-Adamantyl Amine Inhibitor Reveal the Mechanism of Adamantane Resistance. Here, Cys50 has been mutated to Ser to facilitate peptide synthesis and purification and to prevent oligomerization through the formation of disulfide bonds. 2020 Biochemistry Result IV C50S 6 35 31894969 X-ray Crystal Structures of the Influenza M2 Proton Channel Drug-Resistant V27A Mutant Bound to a Spiro-Adamantyl Amine Inhibitor Reveal the Mechanism of Adamantane Resistance. In the 2.5 A resolution structure of M2(22-46) V27A (6NV1), four ordered water molecules are within hydrogen bonding distance of Ala30 carbonyls ("Ala30 layer") and spiro-adamantyl amine, and four waters are observed forming hydrogen bonds to Gly34 carbonyls ("Gly34 layer"). 2020 Biochemistry Result IV V27A 47 51 M2 37 39 31894969 X-ray Crystal Structures of the Influenza M2 Proton Channel Drug-Resistant V27A Mutant Bound to a Spiro-Adamantyl Amine Inhibitor Reveal the Mechanism of Adamantane Resistance. In the crystal structure of M2(22-46) V27A bound to spiro-adamantyl amine, we observe that the width of the channel pore is 3.0 A at residue Ala27. 2020 Biochemistry Result IV V27A 38 42 M2 28 30 31894969 X-ray Crystal Structures of the Influenza M2 Proton Channel Drug-Resistant V27A Mutant Bound to a Spiro-Adamantyl Amine Inhibitor Reveal the Mechanism of Adamantane Resistance. In the following discussion of adamantane resistance in the V27A mutant and the spiro-adamantyl amine binding mechanism, we will focus on the structure of the M2(22-46) V27A construct (6NV1) because it was solved to higher resolution and shows the contents of the channel pore in greater detail. 2020 Biochemistry Result IV V27A;V27A 60;169 64;173 M2 159 161 31894969 X-ray Crystal Structures of the Influenza M2 Proton Channel Drug-Resistant V27A Mutant Bound to a Spiro-Adamantyl Amine Inhibitor Reveal the Mechanism of Adamantane Resistance. In the structure of the M2(22-46) V27A construct (6NV1), we observe a total of eight ordered monoolein molecules in the asymmetric unit interacting with the hydrophobic face of each monomer helix. 2020 Biochemistry Result IV V27A 34 38 M2 24 26 31894969 X-ray Crystal Structures of the Influenza M2 Proton Channel Drug-Resistant V27A Mutant Bound to a Spiro-Adamantyl Amine Inhibitor Reveal the Mechanism of Adamantane Resistance. In the structure of the spiro-adamantyl amine complex with V27A (6NV1), we observe that the ammonium group of the spiro-adamantyl amine inhibitor localizes to approximately the same position as the ammonium group of amantadine in complex with M2(22-46) WT (6BKK) from our previous work. 2020 Biochemistry Result IV V27A 59 63 M2 243 245 31894969 X-ray Crystal Structures of the Influenza M2 Proton Channel Drug-Resistant V27A Mutant Bound to a Spiro-Adamantyl Amine Inhibitor Reveal the Mechanism of Adamantane Resistance. Mechanism of amantadine and rimantadine resistance in the V27A mutant. 2020 Biochemistry Result IV V27A 58 62 31894969 X-ray Crystal Structures of the Influenza M2 Proton Channel Drug-Resistant V27A Mutant Bound to a Spiro-Adamantyl Amine Inhibitor Reveal the Mechanism of Adamantane Resistance. Molecular dynamics simulations of M2(22-46) V27A in complex with spiro-adamantyl amine. 2020 Biochemistry Result IV V27A 44 48 M2 34 36 31894969 X-ray Crystal Structures of the Influenza M2 Proton Channel Drug-Resistant V27A Mutant Bound to a Spiro-Adamantyl Amine Inhibitor Reveal the Mechanism of Adamantane Resistance. Nevertheless, after much optimization, we were able to grow crystals of M2(21-61) V27A in complex with spiro-adamantyl amine and solve a structure to 3.0 A resolution (6OUG). 2020 Biochemistry Result IV V27A 82 86 M2 72 74 31894969 X-ray Crystal Structures of the Influenza M2 Proton Channel Drug-Resistant V27A Mutant Bound to a Spiro-Adamantyl Amine Inhibitor Reveal the Mechanism of Adamantane Resistance. The contents of the M2 channel pore differ in the two crystal structures described here; fewer waters are observed in the structure of M2(21-61) V27A in complex with spiro-adamantyl amine. 2020 Biochemistry Result IV V27A 145 149 M2;M2 20;135 22;137 31894969 X-ray Crystal Structures of the Influenza M2 Proton Channel Drug-Resistant V27A Mutant Bound to a Spiro-Adamantyl Amine Inhibitor Reveal the Mechanism of Adamantane Resistance. The simulated M2(22-46) V27A - ligand complex was stable, and in all cases the M2(22-46) V27A tetramer showed no large conformational changes in the course of the simulations, as demonstrated by RMSDs smaller than 1.5 A for M2 (22-46) Calpha-carbons with respect to the starting structure (Table S2. 2020 Biochemistry Result IV V27A;V27A 24;89 28;93 31894969 X-ray Crystal Structures of the Influenza M2 Proton Channel Drug-Resistant V27A Mutant Bound to a Spiro-Adamantyl Amine Inhibitor Reveal the Mechanism of Adamantane Resistance. The spiro-adamantyl amine - M2(22-46) V27A complex in the X-ray structure was perfectly superimposed with the structure from the 300 ns MD simulation, with the RMSD of the ligand being less than 1 A. 2020 Biochemistry Result IV V27A 38 42 M2 28 30 31894969 X-ray Crystal Structures of the Influenza M2 Proton Channel Drug-Resistant V27A Mutant Bound to a Spiro-Adamantyl Amine Inhibitor Reveal the Mechanism of Adamantane Resistance. The spiro-adamantyl amine - M2(22-46) V27A protein complex was subjected to MD simulations in a POPC bilayer for 300 ns. 2020 Biochemistry Result IV V27A 38 42 M2 28 30 31894969 X-ray Crystal Structures of the Influenza M2 Proton Channel Drug-Resistant V27A Mutant Bound to a Spiro-Adamantyl Amine Inhibitor Reveal the Mechanism of Adamantane Resistance. The starting structure was produced after applying the V27A mutation to the structure of spiro-adamantyl amine in complex with M2(22-46) WT in the Inwardclosed state (6BMZ). 2020 Biochemistry Result IV V27A 55 59 M2 127 129 31894969 X-ray Crystal Structures of the Influenza M2 Proton Channel Drug-Resistant V27A Mutant Bound to a Spiro-Adamantyl Amine Inhibitor Reveal the Mechanism of Adamantane Resistance. The V27A mutant M2 channel conducts protons at an increased rate relative to the WT channel. 2020 Biochemistry Result IV V27A 4 8 M2 16 18 31894969 X-ray Crystal Structures of the Influenza M2 Proton Channel Drug-Resistant V27A Mutant Bound to a Spiro-Adamantyl Amine Inhibitor Reveal the Mechanism of Adamantane Resistance. The Val27 to Ala mutation at the N-terminus of M2 widens the channel pore at the adamantane binding site. 2020 Biochemistry Result IV V27A 4 16 M2 47 49 31894969 X-ray Crystal Structures of the Influenza M2 Proton Channel Drug-Resistant V27A Mutant Bound to a Spiro-Adamantyl Amine Inhibitor Reveal the Mechanism of Adamantane Resistance. This widening of the N-terminal channel pore is consistent with a previous solution NMR model of M2(18-60) V27A in DHPC micelles. 2020 Biochemistry Result IV V27A 107 111 M2 97 99 31894969 X-ray Crystal Structures of the Influenza M2 Proton Channel Drug-Resistant V27A Mutant Bound to a Spiro-Adamantyl Amine Inhibitor Reveal the Mechanism of Adamantane Resistance. Though mutation of Val27 to Ala prevents amantadine and rimantadine from inhibiting the channel, longer and bulkier inhibitors such as spiro-adamantyl amine can bind to the wider N-terminal pore of V27A mutant and inhibit its proton conduction. 2020 Biochemistry Result IV V27A;V27A 198;19 202;31 31894969 X-ray Crystal Structures of the Influenza M2 Proton Channel Drug-Resistant V27A Mutant Bound to a Spiro-Adamantyl Amine Inhibitor Reveal the Mechanism of Adamantane Resistance. Though rimantadine is slightly longer than amantadine, the length of the compound is not sufficient to allow for the drug ammonium group to form hydrogen bonds with Ala30 layer waters while also allowing the adamantyl group to engage in hydrophobic contacts with the N-terminal portion of the pore near residue 27, and so rimantadine is not able to inhibit the V27A channel. 2020 Biochemistry Result IV V27A 361 365 31894969 X-ray Crystal Structures of the Influenza M2 Proton Channel Drug-Resistant V27A Mutant Bound to a Spiro-Adamantyl Amine Inhibitor Reveal the Mechanism of Adamantane Resistance. Thus, the spiro-adamantyl amine inhibitor blocks proton conductance in both the WT and the adamantane-resistant V27A M2 channel by shifting its binding position depending on which residue is present at position 27. 2020 Biochemistry Result IV V27A 112 116 M2 117 119 31894969 X-ray Crystal Structures of the Influenza M2 Proton Channel Drug-Resistant V27A Mutant Bound to a Spiro-Adamantyl Amine Inhibitor Reveal the Mechanism of Adamantane Resistance. We have used LCP crystallization techniques to solve two X-ray crystal structures of the adamantane-resistant M2 V27A mutant: one 2.5 A structure of M2(22-46) V27A in complex with spiro-adamantyl amine (PDB ID 6NV1), and one 3.0 A structure of M2(21-61) V27A in complex with spiro-adamantyl amine (PDB ID 6OUG). 2020 Biochemistry Result IV V27A;V27A;V27A 113;159;254 117;163;258 M2;M2;M2 110;149;244 112;151;246 31894969 X-ray Crystal Structures of the Influenza M2 Proton Channel Drug-Resistant V27A Mutant Bound to a Spiro-Adamantyl Amine Inhibitor Reveal the Mechanism of Adamantane Resistance. We include structure 6OUG here as a comparison to the shorter M2(22-46) V27A construct and also because structural information about the helical turn immediately below residue 46 may prove useful for understanding proton conduction through the C-terminus of the channel. 2020 Biochemistry Result IV V27A 72 76 M2 62 64 31894969 X-ray Crystal Structures of the Influenza M2 Proton Channel Drug-Resistant V27A Mutant Bound to a Spiro-Adamantyl Amine Inhibitor Reveal the Mechanism of Adamantane Resistance. X-ray crystal structures of spiro-adamantyl amine bound to M2(22-46) V27A and M2(21-61) V27A. 2020 Biochemistry Result IV V27A;V27A 69;88 73;92 M2;M2 59;78 61;80 31906790 Contribution of Fc-dependent cell-mediated activity of a vestigial esterase-targeting antibody against H5N6 virus infection. 9F4-K322A treated mice also showed reduced tissue damage and polymorphonuclear cell inflammation compared to 1A4 treated mice, albeit to a lesser extent compared to mice that received 9F4-WT (Figure 5D and E). 2020 Emerging microbes & infections Result IV K322A 4 9 31906790 Contribution of Fc-dependent cell-mediated activity of a vestigial esterase-targeting antibody against H5N6 virus infection. 9F4-WT and 9F4-K322A treated mice had similar lung virus titres at 4 dpi and were both significantly lower compared to mice treated with 1A4 (Figure 5C). 2020 Emerging microbes & infections Result IV K322A 15 20 31906790 Contribution of Fc-dependent cell-mediated activity of a vestigial esterase-targeting antibody against H5N6 virus infection. All infected mice that were treated with 9F4-WT or 9F4-K322A survived the rgPR8 H5N6 challenge (Figure 5B). 2020 Emerging microbes & infections Result IV K322A 55 60 31906790 Contribution of Fc-dependent cell-mediated activity of a vestigial esterase-targeting antibody against H5N6 virus infection. Collectively these observations suggest that 9F4-K322A has similar anti-H5N6 potency compared to 9F4-WT and that CDC is dispensable for 9F4's capability to protect against H5N6 in vivo. 2020 Emerging microbes & infections Result IV K322A 49 54 31906790 Contribution of Fc-dependent cell-mediated activity of a vestigial esterase-targeting antibody against H5N6 virus infection. In contrast, infected mice treated with 9F4-K322A lost approximately 5% body weight between 1 and 3 dpi but maintained normal body weight profiles similar to that of mock-infected mice or infected mice that received 9F4-WT (Figure 5A). 2020 Emerging microbes & infections Result IV K322A 44 49 31906790 Contribution of Fc-dependent cell-mediated activity of a vestigial esterase-targeting antibody against H5N6 virus infection. In order to investigate whether these effector mechanisms play a role in the antiviral function of 9F4 against H5N6 infections, we have constructed two Fc mutants, namely 9F4-LALA and 9F4-K322A, by introducing point mutations L234A, L235A and K322A, respectively in the Fc region of 9F4. 2020 Emerging microbes & infections Result IV K322A;L234A;L235A;K322A 188;226;233;243 193;231;238;248 31906790 Contribution of Fc-dependent cell-mediated activity of a vestigial esterase-targeting antibody against H5N6 virus infection. Indeed, we observed reduced binding of C1q by 9F4-K322A compared to that of 9F4-WT or 9F4-LALA (p < 0.0001; Figure 3C). 2020 Emerging microbes & infections Result IV K322A 50 55 31906790 Contribution of Fc-dependent cell-mediated activity of a vestigial esterase-targeting antibody against H5N6 virus infection. mFcgammaRIV activation is induced by 9F4-WT and 9F4-K322A but not 9F4-LALA. 2020 Emerging microbes & infections Result IV K322A 52 57 31906790 Contribution of Fc-dependent cell-mediated activity of a vestigial esterase-targeting antibody against H5N6 virus infection. Nevertheless, the fold induction of both 9F4-WT and 9F4-K322A were significantly higher as compared to that of 1A4. 2020 Emerging microbes & infections Result IV K322A 56 61 31906790 Contribution of Fc-dependent cell-mediated activity of a vestigial esterase-targeting antibody against H5N6 virus infection. On the other hand, 9F4-K322A showed induction of mFcgammaRIV activation but the efficacy in eliciting ADCC was 1-fold lower than 9F4-WT (Figure 3B). 2020 Emerging microbes & infections Result IV K322A 23 28 31906790 Contribution of Fc-dependent cell-mediated activity of a vestigial esterase-targeting antibody against H5N6 virus infection. The introduction of LALA and K322A mutations to the Fc region of 9F4 have allowed us to study the importance ADCC/ADCP or CDC respectively in the context of 9F4's antiviral activity. 2020 Emerging microbes & infections Result IV K322A 29 34 31906790 Contribution of Fc-dependent cell-mediated activity of a vestigial esterase-targeting antibody against H5N6 virus infection. These results suggest that 9F4-WT and 9F4-K322A possess Fc binding affinity for mFcgammaRIV and are able to induce mFcgammaRIV signalling for effecting ADCC or ADCP. 2020 Emerging microbes & infections Result IV K322A 42 47 31906790 Contribution of Fc-dependent cell-mediated activity of a vestigial esterase-targeting antibody against H5N6 virus infection. To assess if the CDC pathway plays a major role in 9F4's anti-H5N6 activity, mice intranasally infected with 100 PFU of rgPR8 H5N6 were treated intraperitoneally 24 hpi with 10 mg/kg of 9F4-WT, 9F4-K322A or 1A4. 2020 Emerging microbes & infections Result IV K322A 198 203 31906790 Contribution of Fc-dependent cell-mediated activity of a vestigial esterase-targeting antibody against H5N6 virus infection. To determine if 9F4-K322A can bind C1q, we performed a C1q binding ELISA. 2020 Emerging microbes & infections Result IV K322A 20 25 31917822 The effect of mutations derived from mouse-adapted H3N2 seasonal influenza A virus to pathogenicity and host adaptation. Interestingly, there were five substitutions in only Balb/c-passaged clones, including V421F in PA, K18Q, and N160D in HA, D34N in NP, and S331R in NA. 2020 PloS one Result IV V421F;K18Q;N160D;D34N;S331R 87;100;110;123;139 92;104;115;127;144 HA;NA;NP;PA 119;148;131;96 121;150;133;98 31917822 The effect of mutations derived from mouse-adapted H3N2 seasonal influenza A virus to pathogenicity and host adaptation. The five mouse-adapted viruses had all of the following substitutions: F332L in PB2, and A144T, T183A, F209S, and N262T in HA. 2020 PloS one Result IV F332L;A144T;T183A;F209S;N262T 71;89;96;103;114 76;94;101;108;119 HA;PB2 123;80 125;83 31917822 The effect of mutations derived from mouse-adapted H3N2 seasonal influenza A virus to pathogenicity and host adaptation. This virus contained 13 amino acid substitutions related to mouse adaptation of seasonal H3N2 virus, and five mutations (V421F in PA; K18Q and N160D in HA; D34N in NP; and S331R in NA) were detected only in Balb/c-passaged clones (Table 5). 2020 PloS one Result IV V421F;K18Q;N160D;D34N;S331R 121;134;143;156;172 126;138;148;160;177 HA;NA;NP;PA 152;181;164;130 154;183;166;132 31932446 A molecularly engineered antiviral banana lectin inhibits fusion and is efficacious against influenza virus infection in vivo. Antiinfluenza activity is dependent on carbohydrate binding, as the D133G BanLec mutant lacking carbohydrate-binding activity has no antiinfluenza activity. 2020 Proc Natl Acad Sci U S A Result IV D133G 68 73 31932446 A molecularly engineered antiviral banana lectin inhibits fusion and is efficacious against influenza virus infection in vivo. D133G showed dramatically less binding than did H84T. 2020 Proc Natl Acad Sci U S A Result IV D133G 0 5 31932446 A molecularly engineered antiviral banana lectin inhibits fusion and is efficacious against influenza virus infection in vivo. In clear contrast, intraperitoneal administration of H84T was very well tolerated, resulting in no injection site lesions, no piloerection of back hair, and no weight loss upon administration of either dose, similar to administration of D133G BanLec, which in vitro lacks both mitogenicity and antiviral activity due to a mutation in the carbohydrate-binding site and so was not expected to elicit an inflammatory reaction. 2020 Proc Natl Acad Sci U S A Result IV D133G 237 242 31932446 A molecularly engineered antiviral banana lectin inhibits fusion and is efficacious against influenza virus infection in vivo. In rare D133G-treated cells, His tag staining resembled that in H84T-treated cells and colocalization between the His tag and LAMP1 was high (SI Appendix. 2020 Proc Natl Acad Sci U S A Result IV D133G 8 13 31932446 A molecularly engineered antiviral banana lectin inhibits fusion and is efficacious against influenza virus infection in vivo. Indeed, H84T inhibited replication of A/Mississippi/3/2001-H275Y (H1N1), a strain reported to be oseltamivir-resistant, in Madin-Darby canine kidney (MDCK) cells, with an EC90 value of 0.074 mug/mL (2.4 nM), as compared to >100 mug/mL for oseltamivir. 2020 Proc Natl Acad Sci U S A Result IV H275Y 59 64 31932446 A molecularly engineered antiviral banana lectin inhibits fusion and is efficacious against influenza virus infection in vivo. Inhibition was dependent on carbohydrate binding, as D133G did not block viral protein expression. 2020 Proc Natl Acad Sci U S A Result IV D133G 53 58 31932446 A molecularly engineered antiviral banana lectin inhibits fusion and is efficacious against influenza virus infection in vivo. S1), in which NA inhibitor resistance is conferred by the E119V and H275Y mutations, respectively, and adamantane resistance conferred by the S31N mutation. 2020 Proc Natl Acad Sci U S A Result IV E119V;H275Y;S31N 58;68;142 63;73;146 14 16 31932446 A molecularly engineered antiviral banana lectin inhibits fusion and is efficacious against influenza virus infection in vivo. S16) in both infected and uninfected cells; D133G is internalized into cells to a dramatically lesser extent. 2020 Proc Natl Acad Sci U S A Result IV D133G 44 49 31932446 A molecularly engineered antiviral banana lectin inhibits fusion and is efficacious against influenza virus infection in vivo. S17, Inset), suggesting that in the rare cases that D133G is internalized, it localizes to the same compartment as does H84T. 2020 Proc Natl Acad Sci U S A Result IV D133G 52 57 31932446 A molecularly engineered antiviral banana lectin inhibits fusion and is efficacious against influenza virus infection in vivo. S17), indicating that H84T localizes to the late endosome/lysosome, whereas D133G-treated cells exhibited minimal His tag staining, consistent with the low degree of BanLec staining in D133G-treated cells (SI Appendix. 2020 Proc Natl Acad Sci U S A Result IV D133G;D133G 76;185 81;190 31932446 A molecularly engineered antiviral banana lectin inhibits fusion and is efficacious against influenza virus infection in vivo. To ascertain whether H84T interacts with HA, we performed ELISAs using recombinant HA from A/California/07/2009 (H1N1)pdm09 and A/Perth/16/2009 (H3N2) derived from baculovirus, with the D133G BanLec mutant as a control, as it does not bind carbohydrates. 2020 Proc Natl Acad Sci U S A Result IV D133G 186 191 HA;HA 41;83 43;85 31932446 A molecularly engineered antiviral banana lectin inhibits fusion and is efficacious against influenza virus infection in vivo. To examine whether H84T is internalized into the late endosomal/lysosomal compartment in the absence of influenza virus infection, we next treated cells with His-tagged H84T or D133G and performed immunofluorescent staining for the His tag and LAMP1. 2020 Proc Natl Acad Sci U S A Result IV D133G 177 182 31932446 A molecularly engineered antiviral banana lectin inhibits fusion and is efficacious against influenza virus infection in vivo. We observed that H84T binds HA in a concentration-dependent manner, and D133G shows much reduced binding to HA (SI Appendix. 2020 Proc Natl Acad Sci U S A Result IV D133G 72 77 31948040 H7N9 Influenza Virus Containing a Polybasic HA Cleavage Site Requires Minimal Host Adaptation to Obtain a Highly Pathogenic Disease Phenotype in Mice. Although introduction of D347G (PA) or M483K (PB2) mutations alone appear to play no role in the pathogenicity of the H7N9-PBC virus at the doses tested, when combined with the A452T (HA) mutation a significant increase in pathogenicity was observed. 2020 Viruses Result IV D347G;M483K;A452T 25;39;177 30;44;182 HA;PA;PB2 184;32;46 186;34;49 31948040 H7N9 Influenza Virus Containing a Polybasic HA Cleavage Site Requires Minimal Host Adaptation to Obtain a Highly Pathogenic Disease Phenotype in Mice. From these results, the percentage of variants within each viral sample was determined and within the H7N9-PBC mP2 virus we found three dominant amino acid mutations in the following genes: HA (A452T, 66%), PA (D347G, 68%) and PB2 (M483K, 65%) (Table 1). 2020 Viruses Result IV A452T;D347G;M483K 194;211;232 199;216;237 HA;PA;PB2 190;207;227 192;209;230 31948040 H7N9 Influenza Virus Containing a Polybasic HA Cleavage Site Requires Minimal Host Adaptation to Obtain a Highly Pathogenic Disease Phenotype in Mice. H7N9-RG-mP2 viruses were also sequenced and mutations were found in NA (G389D, G389C), PB2 (M64R, D256G), and PB1 (A157V). 2020 Viruses Result IV G389D;G389C;M64R;D256G;A157V 72;79;92;98;115 77;84;96;103;120 NA;PB1;PB2 68;110;87 70;113;90 31948040 H7N9 Influenza Virus Containing a Polybasic HA Cleavage Site Requires Minimal Host Adaptation to Obtain a Highly Pathogenic Disease Phenotype in Mice. In line with the mammalian cell growth results, all H7N9-PBC mutants that contained the HA A452T mutation replicated to significantly higher levels at 24 h than the non-passaged H7N9-PBC virus, indicating a role for this mutation in replication efficiency. 2020 Viruses Result IV A452T 91 96 HA 88 90 31948040 H7N9 Influenza Virus Containing a Polybasic HA Cleavage Site Requires Minimal Host Adaptation to Obtain a Highly Pathogenic Disease Phenotype in Mice. Interestingly, amino acid mutations were found in PB2 (Q73R, D256G) and HA (I399M) that were unique compared to those found in H7N9-PBC mP2 virus (PB2 M483K, PA D347G, and HA A452T, Table 1). 2020 Viruses Result IV Q73R;D256G;I399M;M483K;D347G;A452T 55;61;76;151;161;175 59;66;81;156;166;180 HA;HA;PA;PB2;PB2 72;172;158;50;147 74;174;160;53;150 31951605 Reassortment and adaptive mutations of an emerging avian influenza virus H7N4 subtype in China. A unique feature of JS2018 among the novel H7N4 isolates was its E627K in PB2, similar to the H7N9 virus, a mutation that is thought to increase virulence. 2020 PloS one Result IV E627K 65 70 PB2 74 77 31951605 Reassortment and adaptive mutations of an emerging avian influenza virus H7N4 subtype in China. Again, JS2018 was the only H7N4 isolate with the E627K mutation in PB2 which was also present in human H7N9 viruses. 2020 PloS one Result IV E627K 49 54 PB2 67 70 31951605 Reassortment and adaptive mutations of an emerging avian influenza virus H7N4 subtype in China. In addition, a PB2 K683T mutation occurred in JS2018 and Ck2018 but not in the duck H7N4 viruses. 2020 PloS one Result IV K683T 19 24 PB2 15 18 31951605 Reassortment and adaptive mutations of an emerging avian influenza virus H7N4 subtype in China. None of the novel H7N4 viruses would be resistant to amantadine as no S31N in M2 was observed. 2020 PloS one Result IV S31N 70 74 M2 78 80 31951605 Reassortment and adaptive mutations of an emerging avian influenza virus H7N4 subtype in China. Of special note, four mutations in the JS2018 HA (H242Q, N283D, K321E, and I479M) were identified. 2020 PloS one Result IV H242Q;N283D;K321E;I479M 50;57;64;75 55;62;69;80 HA 46 48 31951605 Reassortment and adaptive mutations of an emerging avian influenza virus H7N4 subtype in China. Strikingly, no H274Y or R292K in NA changes, which had been associated with oseltamivir resistance, were identified in any of the H7N4 isolates, and not in A/Anhui/1/2013 or partly in A/Shanghai/1/2013, which explained the patient's positive response to oseltamivir treatment and full recovery. 2020 PloS one Result IV H274Y;R292K 15;24 20;29 33 35 31951605 Reassortment and adaptive mutations of an emerging avian influenza virus H7N4 subtype in China. We also noted that an N47S mutation in PB1-F2 was common to all human H7N4, H7N9 and H5N1 isolates, and a C19Y mutation in M2 occurred only in this human H7N4 isolate (Table 2). 2020 PloS one Result IV N47S;C19Y 22;106 26;110 M2;PB1F2 123;39 125;45 31955521 Antigenic variants of influenza B viruses isolated in Japan during the 2017-2018 and 2018-2019 influenza seasons. B/Colorado/06/2017 contains a two-amino-acid deletion at positions 162 and 163 in its HA. 2020 Influenza and other respiratory viruses Result IV del aa162 30 70 HA 86 88 31955521 Antigenic variants of influenza B viruses isolated in Japan during the 2017-2018 and 2018-2019 influenza seasons. B/Victoria-lineage viruses with the three-amino-acid deletion fell into two distinct subgroups (Figure 1B): one subgroup shared an amino acid substitution at position K136E, and the other subgroup had two common amino acid substitutions at I180T and K209N. 2020 Influenza and other respiratory viruses Result IV K136E;I180T;K209N 167;240;250 172;245;255 31955521 Antigenic variants of influenza B viruses isolated in Japan during the 2017-2018 and 2018-2019 influenza seasons. Sequence analysis revealed no mutations known to confer resistance to NA inhibitors in the influenza B isolates, except for one B/Yamagata-lineage isolate (B/Tokyo/UT-AC032/2018) that possessed a G407S mutation in its NA.15 A fluorescence NA inhibition assay with the MUNANA substrate was used to characterize the susceptibility of B/Tokyo/UT-AC032/2018 virus to oseltamivir carboxylate, peramivir, zanamivir, and laninamivir (Table 4). 2020 Influenza and other respiratory viruses Result IV G407S 196 201 NA;NA;NA 70;218;239 72;220;241 32064779 Rapid detection of an I38T amino acid substitution in influenza polymerase acidic subunit associated with reduced susceptibility to baloxavir marboxil. Among strains isolated in the 2017/2018 influenza season, 184 influenza A(H1N1)pdm09 strains, 91 influenza A(H3N2) strains, and 236 influenza B strains (Tables S1-S3) were tested by A/H1pdm PA_I38T rhPCR, A/H3 PA_I38T rhPCR, and B PA_I38T rhPCR, respectively. 2020 Influenza and other respiratory viruses Result IV I38T;I38T;I38T 193;213;234 197;217;238 PA;PA;PA 190;210;231 192;212;233 32064779 Rapid detection of an I38T amino acid substitution in influenza polymerase acidic subunit associated with reduced susceptibility to baloxavir marboxil. Four influenza A(H1N1)pdm09 strains isolated in the 2018/2019 influenza season and one clinical specimen positive for A(H1N1)pdm09 were tested by both A/H1pdm PA_I38T rhPCR and NGS. 2020 Influenza and other respiratory viruses Result IV I38T 162 166 PA 159 161 32064779 Rapid detection of an I38T amino acid substitution in influenza polymerase acidic subunit associated with reduced susceptibility to baloxavir marboxil. Similarly, eight influenza A(H3N2) strains and ten clinical specimens positive for A(H3N2) were tested by A/H3 PA_I38T rhPCR and NGS. 2020 Influenza and other respiratory viruses Result IV I38T 114 118 PA 111 113 32064779 Rapid detection of an I38T amino acid substitution in influenza polymerase acidic subunit associated with reduced susceptibility to baloxavir marboxil. The detection limits of A/H1pdm PA_I38T rhPCR for PA I38 and PA T38 were 36.8 and 34.9 copies/reaction, respectively. 2020 Influenza and other respiratory viruses Result IV I38T 35 39 PA;PA;PA 32;50;61 34;52;63 32064779 Rapid detection of an I38T amino acid substitution in influenza polymerase acidic subunit associated with reduced susceptibility to baloxavir marboxil. Those of A/H3 PA_I38T rhPCR for PA I38 and PA T38 were 29.6 and 32.5 copies/reaction, respectively, and those of B PA_I38T rhPCR for PA I38 and PA T38 were 29.3 and 33.9 copies/reaction, respectively. 2020 Influenza and other respiratory viruses Result IV I38T;I38T 17;118 21;122 PA;PA;PA;PA;PA;PA 14;32;43;115;133;144 16;34;45;117;135;146 32064779 Rapid detection of an I38T amino acid substitution in influenza polymerase acidic subunit associated with reduced susceptibility to baloxavir marboxil. Three rhPCR-based assays, A/H1pdm PA_I38T rhPCR, A/H3 PA_I38T rhPCR, and B PA_I38T rhPCR, were developed to discriminate between influenza A(H1N1)pdm09, A(H3N2), and B viruses carrying PA I38 and PA T38, respectively (Table 1). 2020 Influenza and other respiratory viruses Result IV I38T;I38T;I38T 37;57;78 41;61;82 PA;PA;PA;PA;PA 34;54;75;185;196 36;56;77;187;198 32093780 Acetylation at K108 of the NS1 protein is important for the replication and virulence of influenza virus. Deacetylation-mimic K108R substitution attenuates the mutant virus in a mouse model. 2020 Veterinary research Result IV K108R 20 25 32093780 Acetylation at K108 of the NS1 protein is important for the replication and virulence of influenza virus. Deacetylation-mimic K108R substitution retains the NS1 protein in the cytoplasm of infected cells. 2020 Veterinary research Result IV K108R 20 25 NS1 51 54 32093780 Acetylation at K108 of the NS1 protein is important for the replication and virulence of influenza virus. However, the deacetylated WSN-NS1-108R virus infection resulted in 80% mortality, and the mortality was delayed by 2 days compared with other viruses, which indicated that the deacetylation-mimic K108R substitution attenuated the WSN-NS1-108R virus in mice (Figures 3A and B). 2020 Veterinary research Result IV K108R 196 201 NS1;NS1 30;234 33;237 32093780 Acetylation at K108 of the NS1 protein is important for the replication and virulence of influenza virus. Moreover, to mimic constantly acetylated lysine at K108 of the NS1 protein, a K108Q substitution that is a known acetylation mimic was introduced into NS1, resulting in a mutant virus containing NS1-K108Q (WSN-NS1-108Q). 2020 Veterinary research Result IV K108Q;K108Q 78;199 83;204 NS1;NS1;NS1;NS1 63;151;195;210 66;154;198;213 32093780 Acetylation at K108 of the NS1 protein is important for the replication and virulence of influenza virus. The three proteins were expressed at similar levels in transfected 293T cells, which indicated that the K108R and K108Q mutations did not influence protein expression (Figure 4E). 2020 Veterinary research Result IV K108R;K108Q 104;114 109;119 32093780 Acetylation at K108 of the NS1 protein is important for the replication and virulence of influenza virus. This result indicated that the deacetylation-mimic K108R substitution retained NS1 protein in the cytoplasm of infected cells, suggesting that the acetylated K108 residue is important for the nuclear localization of the NS1 protein (Figures 5A-C). 2020 Veterinary research Result IV K108R 51 56 NS1;NS1 79;220 82;223 32093780 Acetylation at K108 of the NS1 protein is important for the replication and virulence of influenza virus. To determine whether K108R changes the subcellular localization of NS1 during infection, MDCK cells were infected with the three viruses. 2020 Veterinary research Result IV K108R 21 26 NS1 67 70 32093780 Acetylation at K108 of the NS1 protein is important for the replication and virulence of influenza virus. To determine whether the K108R and K108Q mutations affect the expression of the NS1 protein, the expression levels of FLAG-NS1-wt, FLAG-NS1-108Q, and FLAG-NS1-108R in 293T cells were compared. 2020 Veterinary research Result IV K108R;K108Q 25;35 30;40 NS1;NS1;NS1;NS1 80;123;136;155 83;126;139;158 32093780 Acetylation at K108 of the NS1 protein is important for the replication and virulence of influenza virus. To further explore how the K108R mutation attenuated the IFN-beta antagonistic ability of the NS1 protein, we co-transfected NS1 expression plasmids, an IFN-beta reporter plasmid and different type I interferon pathway components, including RIG-I CARD, TBK1, and the active form of IRF3, into 293T cells. 2020 Veterinary research Result IV K108R 27 32 NS1;NS1 94;125 97;128 32093780 Acetylation at K108 of the NS1 protein is important for the replication and virulence of influenza virus. To mimic deacetylated lysine, a K108R substitution was introduced into the NS1 protein, since an R substitution prevents acetylation but preserves the positive charge, and a mutant virus containing the NS1-K108R substitution was generated in the background of WSN virus (WSN-NS1-108R). 2020 Veterinary research Result IV K108R;K108R 32;206 37;211 NS1;NS1;NS1 75;202;275 78;205;278 32095441 Comparison of antigenic mutation during egg and cell passage cultivation of H3N2 influenza virus. In case of viruses passaged in eggs, hemagglutinin sequence of the 1st to 2nd passage viruses was the same as that of the parent virus, but there were three mutations identified from the 3rd to 8th passage viruses, A515G, G604A, and C942T, and from the 9th passaged virus, additional hemagglutinin sequence mutation with C704T were detected (Table 2). 2020 Clinical and experimental vaccine research Result IV A515G;G604A;C942T;C704T 215;222;233;321 220;227;238;326 HA;HA 37;284 50;297 32095441 Comparison of antigenic mutation during egg and cell passage cultivation of H3N2 influenza virus. The analysis revealed that the G186S mutation is relatively inward of the hemagglutinin, while the H156R and S219F mutations are located near the surface of receptor binding site and may cause structural changes. 2020 Clinical and experimental vaccine research Result IV G186S;H156R;S219F 31;99;109 36;104;114 HA 74 87 32130243 Epidemic of influenza A(H1N1)pdm09 analyzed by full genome sequences and the first case of oseltamivir-resistant strain in Myanmar 2017. All the analyzed Myanmar viruses belonged to genetic clade 6B.1 with amino acid substitutions of S84N, S162N, and I216T in HA (Fig 2). 2020 PloS one Result IV S84N;S162N;I216T 97;103;114 101;108;119 HA 123 125 32130243 Epidemic of influenza A(H1N1)pdm09 analyzed by full genome sequences and the first case of oseltamivir-resistant strain in Myanmar 2017. All the other A(H1N1)pdm09 isolates from Yangon and Pyinmana study sites did not show H275Y mutation in NA (Table 4). 2020 PloS one Result IV H275Y 86 91 104 106 32130243 Epidemic of influenza A(H1N1)pdm09 analyzed by full genome sequences and the first case of oseltamivir-resistant strain in Myanmar 2017. Among the viruses from this cluster, two out-patient viruses possessed T438A substitution. 2020 PloS one Result IV T438A 71 76 32130243 Epidemic of influenza A(H1N1)pdm09 analyzed by full genome sequences and the first case of oseltamivir-resistant strain in Myanmar 2017. Among them, 13 viruses from out-patients and 11 viruses from in-patients possessed a T314I substitution in HA. 2020 PloS one Result IV T314I 85 90 HA 107 109 32130243 Epidemic of influenza A(H1N1)pdm09 analyzed by full genome sequences and the first case of oseltamivir-resistant strain in Myanmar 2017. Around 60% of Myanmar out-patient viruses and all in-patient viruses shared the R173K amino acid substitution. 2020 PloS one Result IV R173K 80 85 32130243 Epidemic of influenza A(H1N1)pdm09 analyzed by full genome sequences and the first case of oseltamivir-resistant strain in Myanmar 2017. H275Y mutation on neuraminidase was found in one A(H1N1)pdm09 strain (A/Myanmar/17M307/2017), which was from an out-patient with no prior history of anti-viral treatment. 2020 PloS one Result IV H275Y 0 5 18 31 32130243 Epidemic of influenza A(H1N1)pdm09 analyzed by full genome sequences and the first case of oseltamivir-resistant strain in Myanmar 2017. In the phylogeny of the NA gene, all the Myanmar viruses possessed V13I, I34V, V264I, and N270K substitutions and belonged to clade 6B.1. 2020 PloS one Result IV V13I;I34V;V264I;N270K 67;73;79;90 71;77;84;95 24 26 32130243 Epidemic of influenza A(H1N1)pdm09 analyzed by full genome sequences and the first case of oseltamivir-resistant strain in Myanmar 2017. In vitro fluorescence-based NAI assay performed on the selected influenza A(H1N1)pdm09 isolates (12 isolates from out-patients and 12 from in-patients) revealed that the H275Y mutant A(H1N1)pdm09 virus has elevated IC50 value for oseltamivir (301.5 nM with 198-fold increase) and peramivir (21.9 nM with 274-fold increase) but not for zanamivir (0.58 nM with 0.9-fold difference) and laninamivir (0.72 nM with 2.7-fold difference), when compared to the IC50 value of the reference drug-sensitive strain A/Perth/265/2009 (275H), indicating resistance to oseltamivir and peramivir with highly reduced inhibition. 2020 PloS one Result IV H275Y 170 175 NAI 28 31 32130243 Epidemic of influenza A(H1N1)pdm09 analyzed by full genome sequences and the first case of oseltamivir-resistant strain in Myanmar 2017. Of the 233 influenza A(H1N1)pdm09 viruses from all the study sites, one isolate (0.4%) had the oseltamivir-resistance with H275Y mutation in the NA protein, as analyzed by cycling probe real-time PCR. 2020 PloS one Result IV H275Y 123 128 145 147 32130243 Epidemic of influenza A(H1N1)pdm09 analyzed by full genome sequences and the first case of oseltamivir-resistant strain in Myanmar 2017. The epidemiological link of the H275Y mutant virus is unknown. 2020 PloS one Result IV H275Y 32 37 32130243 Epidemic of influenza A(H1N1)pdm09 analyzed by full genome sequences and the first case of oseltamivir-resistant strain in Myanmar 2017. The majority (26, 87%) of viruses possessed S164T in HA and formed a clade with the Indian 2017 and Japanese 2017-2018 strains. 2020 PloS one Result IV S164T 44 49 HA 53 55 32130243 Epidemic of influenza A(H1N1)pdm09 analyzed by full genome sequences and the first case of oseltamivir-resistant strain in Myanmar 2017. This resistant virus and another sensitive out-patient virus exhibited P93H substitution in NA. 2020 PloS one Result IV P93H 71 75 92 94 32130243 Epidemic of influenza A(H1N1)pdm09 analyzed by full genome sequences and the first case of oseltamivir-resistant strain in Myanmar 2017. Three out-patient viruses (A/Myanmar/17M109/2017, A/Myanmar/17M309/2017, and A/Myanmar/17M310/2017) and one in-patient virus (A/Myanmar/17MP001/2017) shared A215G and S297P substitutions and formed a group with the Japanese strains in 2016 and 2017, having a bootstrap value of over 90%. 2020 PloS one Result IV A215G;S297P 157;167 162;172 32130243 Epidemic of influenza A(H1N1)pdm09 analyzed by full genome sequences and the first case of oseltamivir-resistant strain in Myanmar 2017. Three out-patient viruses and one in-patient virus exhibited the D451G substitution, which formed a small separate cluster as HA (Fig 2). 2020 PloS one Result IV D451G 65 70 HA 126 128 32130243 Epidemic of influenza A(H1N1)pdm09 analyzed by full genome sequences and the first case of oseltamivir-resistant strain in Myanmar 2017. We further characterized the amino acid substitutions in the remaining six segments of 25 Myanmar influenza A(H1N1)pdm09 strains, 13 out-patients including a case with NA/H275Y mutation and 12 in-patients, using next-generation sequencing. 2020 PloS one Result IV H275Y 171 176 168 170 32159230 Antigenic drift of hemagglutinin and neuraminidase in seasonal H1N1 influenza viruses from Saudi Arabia in 2014 to 2015. 49 Among the influenza A(H1N1)pdm09 HA sequences characterized in our study (Figure 2), one mutation, S179N (serine to asparagine), was observed that caused a predicted gain of a glycosylation motif. 2020 Journal of medical virology Result IV S179N 103 108 HA 37 39 32159230 Antigenic drift of hemagglutinin and neuraminidase in seasonal H1N1 influenza viruses from Saudi Arabia in 2014 to 2015. 54 As shown on a 3D model of the HA protein (RCSB PDB ID: 3LZG), 55 five mutations were found in previously characterized 48 Ab-binding sites: S179N and T180Q, in Sa; P200S and S202T, in Sb; and S220T, in Ca1 (Figure 2C and Table 1). 2020 Journal of medical virology Result IV S179N;T180Q;P200S;S202T;S220T 146;156;170;180;198 151;161;175;185;203 HA 34 36 32159230 Antigenic drift of hemagglutinin and neuraminidase in seasonal H1N1 influenza viruses from Saudi Arabia in 2014 to 2015. All strains encoded the same NA sequence, with the exception of MK228966 (A/Saudi Arabia/143/2014) and MK228893 (A/Saudi Arabia/10/2015) viruses, which did not have the mutations N248D and K432E respectively. 2020 Journal of medical virology Result IV N248D;K432E 179;189 184;194 29 31 32159230 Antigenic drift of hemagglutinin and neuraminidase in seasonal H1N1 influenza viruses from Saudi Arabia in 2014 to 2015. All the isolates had hemagglutinin (HA) gene corresponding to clade 6B (monophyletic) represented by global circulating strains of H1N1pdm09 (Figure 1) defined by four major reversions A13T, S101N, S179N, and I223T. 2020 Journal of medical virology Result IV A13T;S101N;S179N;I223T 185;191;198;209 189;196;203;214 HA;HA 36;21 38;34 32159230 Antigenic drift of hemagglutinin and neuraminidase in seasonal H1N1 influenza viruses from Saudi Arabia in 2014 to 2015. Almost 92% of Saudi viruses from our study formed a subclass branch with high bootstrap value (91/100) designated as 6B.1 48 mainly defined by S179N and I223T reversions. 2020 Journal of medical virology Result IV S179N;I223T 144;154 149;159 32159230 Antigenic drift of hemagglutinin and neuraminidase in seasonal H1N1 influenza viruses from Saudi Arabia in 2014 to 2015. Amino acid changes were found at key antigenic sites, such as position S101N, S179N (antigenic site-Sa), I233T (antigenic site-Sb) in the head domain. 2020 Journal of medical virology Result IV S101N;S179N;I233T 71;78;105 76;83;110 32159230 Antigenic drift of hemagglutinin and neuraminidase in seasonal H1N1 influenza viruses from Saudi Arabia in 2014 to 2015. Five out of the fourteen changes (N200S, N248D, I321V, N369K, and K432E) were at previously characterized Ab-binding sites. 2020 Journal of medical virology Result IV N200S;N248D;I321V;N369K;K432E 34;41;48;55;66 39;46;53;60;71 32159230 Antigenic drift of hemagglutinin and neuraminidase in seasonal H1N1 influenza viruses from Saudi Arabia in 2014 to 2015. Further analyses of HA protein of study strains (Table 1) showed amino acid change at position 13 in the signal peptide of HA (A13T), all belonging to clade 1 i.e. 2020 Journal of medical virology Result IV A13T 127 131 HA;HA 20;123 22;125 32159230 Antigenic drift of hemagglutinin and neuraminidase in seasonal H1N1 influenza viruses from Saudi Arabia in 2014 to 2015. Most of these isolates contained S179N (on the Sa antigenic site of HA resulting in a potential glycosylation site) and I233T amino acid substitutions in addition to the S101N substitution and formed a subclade subsequently designated as 6B.1. 2020 Journal of medical virology Result IV S179N;I233T;S101N 33;120;170 38;125;175 HA 68 70 32159230 Antigenic drift of hemagglutinin and neuraminidase in seasonal H1N1 influenza viruses from Saudi Arabia in 2014 to 2015. The circulating strains belonged to subclade 6B.1, defined by HA amino acid substitutions S101N, S179N, and I233T. 2020 Journal of medical virology Result IV S101N;S179N;I233T 90;97;108 95;102;113 HA 62 64 32159230 Antigenic drift of hemagglutinin and neuraminidase in seasonal H1N1 influenza viruses from Saudi Arabia in 2014 to 2015. The majority of the 2014/15 season Saudi isolates formed part of a large cluster possessing an S101N substitution in HA. 2020 Journal of medical virology Result IV S101N 95 100 HA 117 119 32159230 Antigenic drift of hemagglutinin and neuraminidase in seasonal H1N1 influenza viruses from Saudi Arabia in 2014 to 2015. The mutation at N11S among clade 6A strains resulted in a loss of potential glycosylation site at this position. 2020 Journal of medical virology Result IV N11S 16 20 32159230 Antigenic drift of hemagglutinin and neuraminidase in seasonal H1N1 influenza viruses from Saudi Arabia in 2014 to 2015. The remaining seven strains formed another cluster (96/100 bootstrap value) with an S101N, T169V, S179N, I190V, I223T, and G508E amino acid substitutions (designated as sub-clade 6B.2 in Figure 1). 2020 Journal of medical virology Result IV S101N;T169V;S179N;I190V;I223T;G508E 84;91;98;105;112;123 89;96;103;110;117;128 32159230 Antigenic drift of hemagglutinin and neuraminidase in seasonal H1N1 influenza viruses from Saudi Arabia in 2014 to 2015. Three of the mutations (K432E along the 430 loop, V241I, and N248D) were located near the catalytic site. 2020 Journal of medical virology Result IV K432E;V241I;N248D 25;51;62 30;56;67 32159230 Antigenic drift of hemagglutinin and neuraminidase in seasonal H1N1 influenza viruses from Saudi Arabia in 2014 to 2015. We did not find the D222G mutation commonly associated with increased virulence. 2020 Journal of medical virology Result IV D222G 20 25 32159230 Antigenic drift of hemagglutinin and neuraminidase in seasonal H1N1 influenza viruses from Saudi Arabia in 2014 to 2015. while MK246055 (A/Saudi Arabia/86/2015) and MK246063 (A/Saudi Arabia/94/2015) had the I338V amino acid change in the stalk domain which is a characteristic marker for all clades, when compared to the clade 1 viruses. 2020 Journal of medical virology Result IV I338V 86 91 32211197 Detection of H3N8 influenza A virus with multiple mammalian-adaptive mutations in a rescued Grey seal (Halichoerus grypus) pup. and S678N found in the seal PB1 gene has been associated with increased polymerase activity and virulence in mice. 2020 Virus evolution Result IV S678N 4 9 PB1 28 31 32211197 Detection of H3N8 influenza A virus with multiple mammalian-adaptive mutations in a rescued Grey seal (Halichoerus grypus) pup. Changes at positions 226 and 228 in HA (reference H3 numbering) which can change receptor-binding preferences between avian and mammalian hosts, were not found in either of the H3N8 seal viruses, but the H10 equivalent of H3-Q226L was identified in viruses from the 2014-15 H10N7 outbreak in European seals. 2020 Virus evolution Result IV Q226L 225 230 HA 36 38 32211197 Detection of H3N8 influenza A virus with multiple mammalian-adaptive mutations in a rescued Grey seal (Halichoerus grypus) pup. Many of these changes occur in the polymerase complex genes: D701N in the PB2 segment is a rare mutation, and a hallmark of mammalian adaptation of bird influenza viruses, regardless of genetic background. 2020 Virus evolution Result IV D701N 61 66 PB2 74 77 32211197 Detection of H3N8 influenza A virus with multiple mammalian-adaptive mutations in a rescued Grey seal (Halichoerus grypus) pup. Our reported seal virus retains F at position 110, but whether the mutation in the adjoining residue at S111G (reference H3 numbering 95) has any effect on HA fusion properties is unknown. 2020 Virus evolution Result IV S111G 104 109 HA 156 158 32211197 Detection of H3N8 influenza A virus with multiple mammalian-adaptive mutations in a rescued Grey seal (Halichoerus grypus) pup. PB1-I517V was found by Tamuri et al. 2020 Virus evolution Result IV I517V 4 9 PB1 0 3 32211197 Detection of H3N8 influenza A virus with multiple mammalian-adaptive mutations in a rescued Grey seal (Halichoerus grypus) pup. The HA of the 2011 Massachusetts seal virus had an F110S mutation, where the 110 residue has been previously found to be a critical component of the influenza viral fusion peptide, which may impact replication in mammalian cells. 2020 Virus evolution Result IV F110S 51 56 HA 4 6 32211197 Detection of H3N8 influenza A virus with multiple mammalian-adaptive mutations in a rescued Grey seal (Halichoerus grypus) pup. We compared all the substitutions with previously described mutations in seal influenza virus infections, and found that apart from D701N, which was also found in the H3N8 seal virus infection in Massachusetts in 2011, there were no convergent amino acid changes. 2020 Virus evolution Result IV D701N 132 137 IV infections 78 104 32231159 Insertion of Basic Amino Acids in the Hemagglutinin Cleavage Site of H4N2 Avian Influenza Virus (AIV)-Reduced Virus Fitness in Chickens is Restored by Reassortment with Highly Pathogenic H5N1 AIV. After IV infection, none of the H4N2_T327R injected chickens showed morbidity or mortality with IVPI values of 0. 2020 International journal of molecular sciences Result IV T327R 37 42 32231159 Insertion of Basic Amino Acids in the Hemagglutinin Cleavage Site of H4N2 Avian Influenza Virus (AIV)-Reduced Virus Fitness in Chickens is Restored by Reassortment with Highly Pathogenic H5N1 AIV. After ON inoculation, chickens challenged with H4N2_wt, H4N2_T327R, H4N2_T327K, H4N2_H5N2-HACS and H7N7_HA4 and contacts did not show any clinical signs with a PI of 0 (Table 2). 2020 International journal of molecular sciences Result IV T327R;T327K 61;73 66;78 32231159 Insertion of Basic Amino Acids in the Hemagglutinin Cleavage Site of H4N2 Avian Influenza Virus (AIV)-Reduced Virus Fitness in Chickens is Restored by Reassortment with Highly Pathogenic H5N1 AIV. All chickens inoculated with H5N1_HA4_T327R or H5N1_HA4_T327K died within 4 dpi with MDT values of 3.8 and two days, and PI values of 2.4 and 2.7, respectively. 2020 International journal of molecular sciences Result IV T327R;T327K 38;56 43;61 32231159 Insertion of Basic Amino Acids in the Hemagglutinin Cleavage Site of H4N2 Avian Influenza Virus (AIV)-Reduced Virus Fitness in Chickens is Restored by Reassortment with Highly Pathogenic H5N1 AIV. Altogether, T327R/K enabled partial activation of the HA in the absence of trypsin by a yet to be identified endogenous furin-like protease. 2020 International journal of molecular sciences Result IV T327K;T327R 12;12 19;19 HA 54 56 32231159 Insertion of Basic Amino Acids in the Hemagglutinin Cleavage Site of H4N2 Avian Influenza Virus (AIV)-Reduced Virus Fitness in Chickens is Restored by Reassortment with Highly Pathogenic H5N1 AIV. As H5N1_HA4_T327K killed all inoculated birds within two days, it was not possible to collect swabs at 4 dpi in this group. 2020 International journal of molecular sciences Result IV T327K 12 17 32231159 Insertion of Basic Amino Acids in the Hemagglutinin Cleavage Site of H4N2 Avian Influenza Virus (AIV)-Reduced Virus Fitness in Chickens is Restored by Reassortment with Highly Pathogenic H5N1 AIV. At 24 hpi, all viruses replicated without trypsin while viruses carrying H5N1 gene segments replicated at significantly higher titers than H4N2 viruses with or without T327R/K. 2020 International journal of molecular sciences Result IV T327K;T327R 168;168 175;175 32231159 Insertion of Basic Amino Acids in the Hemagglutinin Cleavage Site of H4N2 Avian Influenza Virus (AIV)-Reduced Virus Fitness in Chickens is Restored by Reassortment with Highly Pathogenic H5N1 AIV. Beside the recombinant H4N2_wt specifying CS 322PEKRRTR/G329, seven different viruses carrying the H4N2-HA with T327R (322PEKRRRR/G329), T327K (322PEKRRKR/G329) or (322PQRRRGKKR/G331) combined with the other seven gene segments from H4N2, HPAIV H5N1 or HPAIV H7N7 were successfully generated using reverse genetics (Table 1). 2020 International journal of molecular sciences Result IV T327R;T327K 112;137 117;142 HA 104 106 32231159 Insertion of Basic Amino Acids in the Hemagglutinin Cleavage Site of H4N2 Avian Influenza Virus (AIV)-Reduced Virus Fitness in Chickens is Restored by Reassortment with Highly Pathogenic H5N1 AIV. Both H5N1_HA4_T327R and H5N1_HA4_T327K were excreted from all contact birds (Figure 5B). 2020 International journal of molecular sciences Result IV T327R;T327K 14;33 19;38 32231159 Insertion of Basic Amino Acids in the Hemagglutinin Cleavage Site of H4N2 Avian Influenza Virus (AIV)-Reduced Virus Fitness in Chickens is Restored by Reassortment with Highly Pathogenic H5N1 AIV. Cell-to-Cell Spread of H4N2 Virus Was Significantly Increased by Reassortment with H7N7 or H5N1 Containing HA4_T327R/K. 2020 International journal of molecular sciences Result IV T327R 111 118 32231159 Insertion of Basic Amino Acids in the Hemagglutinin Cleavage Site of H4N2 Avian Influenza Virus (AIV)-Reduced Virus Fitness in Chickens is Restored by Reassortment with Highly Pathogenic H5N1 AIV. Conversely, 8/10 and 10/10 chickens injected IV with H5N1_HA4 or H5N1_HA4_T327K died with IVPI 2.1 or 2.8, respectively (Table 2). 2020 International journal of molecular sciences Result IV T327K 74 79 32231159 Insertion of Basic Amino Acids in the Hemagglutinin Cleavage Site of H4N2 Avian Influenza Virus (AIV)-Reduced Virus Fitness in Chickens is Restored by Reassortment with Highly Pathogenic H5N1 AIV. Furthermore, trypsin increased the replication of H5N1_HA4 to similar levels as H5N1_T327R/K (Figure 2). 2020 International journal of molecular sciences Result IV T327R 85 92 32231159 Insertion of Basic Amino Acids in the Hemagglutinin Cleavage Site of H4N2 Avian Influenza Virus (AIV)-Reduced Virus Fitness in Chickens is Restored by Reassortment with Highly Pathogenic H5N1 AIV. H4N2_T327R and H4N2_T327K were excreted in 3/6 and 6/6 in oropharyngeal swabs, respectively and only in 1/6 cloacal swabs in inoculated birds (Figure 5A). 2020 International journal of molecular sciences Result IV T327R;T327K 5;20 10;25 32231159 Insertion of Basic Amino Acids in the Hemagglutinin Cleavage Site of H4N2 Avian Influenza Virus (AIV)-Reduced Virus Fitness in Chickens is Restored by Reassortment with Highly Pathogenic H5N1 AIV. H5N1_HA4_T327K had significantly higher titers in the oropharyngeal swabs compared to H4N2_wt (Figure 5). 2020 International journal of molecular sciences Result IV T327K 9 14 32231159 Insertion of Basic Amino Acids in the Hemagglutinin Cleavage Site of H4N2 Avian Influenza Virus (AIV)-Reduced Virus Fitness in Chickens is Restored by Reassortment with Highly Pathogenic H5N1 AIV. H5N1_HA4_T327R was detected in oropharyngeal (n = 1/2) and cloacal (n = 2/2) swabs (Figure 5A). 2020 International journal of molecular sciences Result IV T327R 9 14 32231159 Insertion of Basic Amino Acids in the Hemagglutinin Cleavage Site of H4N2 Avian Influenza Virus (AIV)-Reduced Virus Fitness in Chickens is Restored by Reassortment with Highly Pathogenic H5N1 AIV. HAs with T327R/K were partially cleaved in the absence of trypsin but the addition of trypsin increased cleavability (Figure 4A). 2020 International journal of molecular sciences Result IV T327R;T327K 9;9 16;16 32231159 Insertion of Basic Amino Acids in the Hemagglutinin Cleavage Site of H4N2 Avian Influenza Virus (AIV)-Reduced Virus Fitness in Chickens is Restored by Reassortment with Highly Pathogenic H5N1 AIV. HAT and TMPRSS2 failed to activate HA_T327K (Figure 4B). 2020 International journal of molecular sciences Result IV T327K 38 43 HA 35 37 32231159 Insertion of Basic Amino Acids in the Hemagglutinin Cleavage Site of H4N2 Avian Influenza Virus (AIV)-Reduced Virus Fitness in Chickens is Restored by Reassortment with Highly Pathogenic H5N1 AIV. However, one out of two birds inoculated with H4N2_T327K had multifocal antigen distribution in the myocardium with mild, acute, focal to oligofocal necrotizing myocarditis as well as focal to oligofocal distribution in neuroglial cells with mild, acute, focal to oligofocal, necrotizing polioencephalitis (Figure 6 and Figure 7). 2020 International journal of molecular sciences Result IV T327K 51 56 Oligofocal necrotizing myocarditis;Polioencephalitis 138;276 172;305 32231159 Insertion of Basic Amino Acids in the Hemagglutinin Cleavage Site of H4N2 Avian Influenza Virus (AIV)-Reduced Virus Fitness in Chickens is Restored by Reassortment with Highly Pathogenic H5N1 AIV. In MDCK cells, H4N2 viruses carrying authentic HA, HA_T327R or HA_T327K showed no replication at 8 hpi without trypsin and only H4N2_HA_T327K produced viral progeny at very low titers in the presence of trypsin (Figure 2). 2020 International journal of molecular sciences Result IV T327R;T327K;T327K 54;66;136 59;71;141 HA;HA;HA 47;51;63 49;53;65 32231159 Insertion of Basic Amino Acids in the Hemagglutinin Cleavage Site of H4N2 Avian Influenza Virus (AIV)-Reduced Virus Fitness in Chickens is Restored by Reassortment with Highly Pathogenic H5N1 AIV. In the absence of exogenous protease, T327K was still cleaved. 2020 International journal of molecular sciences Result IV T327K 38 43 32231159 Insertion of Basic Amino Acids in the Hemagglutinin Cleavage Site of H4N2 Avian Influenza Virus (AIV)-Reduced Virus Fitness in Chickens is Restored by Reassortment with Highly Pathogenic H5N1 AIV. Likewise, H5N1_HA4_T327R was detected in the endothelium and parenchyma of almost all organs of at least one chicken, except for endothelial cells in the jejunum, heart and caecum and gizzard parenchyma. 2020 International journal of molecular sciences Result IV T327R 19 24 32231159 Insertion of Basic Amino Acids in the Hemagglutinin Cleavage Site of H4N2 Avian Influenza Virus (AIV)-Reduced Virus Fitness in Chickens is Restored by Reassortment with Highly Pathogenic H5N1 AIV. Likewise, the NP antigen was not detectable in the endothelium or parenchyma of any organ in birds inoculated with H4N2_T327R. 2020 International journal of molecular sciences Result IV T327R 120 125 NP 14 16 32231159 Insertion of Basic Amino Acids in the Hemagglutinin Cleavage Site of H4N2 Avian Influenza Virus (AIV)-Reduced Virus Fitness in Chickens is Restored by Reassortment with Highly Pathogenic H5N1 AIV. Mutation T327R/K Expanded the Organ Tropism of LPAIV H4N2 and Reassortment with HPAIV H5N1 Significantly Increased the Distribution and Severity of Lesions. 2020 International journal of molecular sciences Result IV T327R;T327K 9;9 16;16 32231159 Insertion of Basic Amino Acids in the Hemagglutinin Cleavage Site of H4N2 Avian Influenza Virus (AIV)-Reduced Virus Fitness in Chickens is Restored by Reassortment with Highly Pathogenic H5N1 AIV. Remarkably, H5N1_HA4_T327R induced a higher lymphatic depletion score in the thymus, bursa, cecal tonsils and bronchus-associated lymphoid tissues (BALT) compared to H5N1_HA4_T327K and H5N1_HA4. 2020 International journal of molecular sciences Result IV T327R;T327K 21;175 26;180 32231159 Insertion of Basic Amino Acids in the Hemagglutinin Cleavage Site of H4N2 Avian Influenza Virus (AIV)-Reduced Virus Fitness in Chickens is Restored by Reassortment with Highly Pathogenic H5N1 AIV. Replication of H4N2_T327R and H4N2_T327K with a point mutation in the HA was comparable to H4N2_wt irrespective of the presence of trypsin at 8 and 24 hpi (Figure 1), while the addition of trypsin significantly increased H4N2_T327R replication at 48 hpi (p < 0.03) (Figure 1). 2020 International journal of molecular sciences Result IV T327K 35 40 HA 70 72 32231159 Insertion of Basic Amino Acids in the Hemagglutinin Cleavage Site of H4N2 Avian Influenza Virus (AIV)-Reduced Virus Fitness in Chickens is Restored by Reassortment with Highly Pathogenic H5N1 AIV. T327K and H5N2_HACS compromised virus transmission as indicated by the lower number of contact birds with AIV antibodies. 2020 International journal of molecular sciences Result IV T327K 0 5 32231159 Insertion of Basic Amino Acids in the Hemagglutinin Cleavage Site of H4N2 Avian Influenza Virus (AIV)-Reduced Virus Fitness in Chickens is Restored by Reassortment with Highly Pathogenic H5N1 AIV. T327R/K Enabled Partial Trypsin-Independent Activation of the HA by Endogenous Furin-Like Protease. 2020 International journal of molecular sciences Result IV T327R;T327K 0;0 7;7 HA 62 64 32231159 Insertion of Basic Amino Acids in the Hemagglutinin Cleavage Site of H4N2 Avian Influenza Virus (AIV)-Reduced Virus Fitness in Chickens is Restored by Reassortment with Highly Pathogenic H5N1 AIV. The distribution of H4N2_T327K was more widespread than that of H4N2_T327R (Figure 6). 2020 International journal of molecular sciences Result IV T327K;T327R 25;69 30;74 32231159 Insertion of Basic Amino Acids in the Hemagglutinin Cleavage Site of H4N2 Avian Influenza Virus (AIV)-Reduced Virus Fitness in Chickens is Restored by Reassortment with Highly Pathogenic H5N1 AIV. The distribution of viruses carrying T327K was more widespread than viruses carrying T327R (Figure 6 and Figure 7), except for lymphoid depletion. 2020 International journal of molecular sciences Result IV T327K;T327R 37;85 42;90 32231159 Insertion of Basic Amino Acids in the Hemagglutinin Cleavage Site of H4N2 Avian Influenza Virus (AIV)-Reduced Virus Fitness in Chickens is Restored by Reassortment with Highly Pathogenic H5N1 AIV. The H4N2_T327K group exhibited moderate virulence with an IVPI of 0.6 and moderate to severe neurological disorders (e.g., torticollis, opisthotonos and paresis) starting at 9 dpi were observed in 7 out of 10 injected chickens. 2020 International journal of molecular sciences Result IV T327K 9 14 Neurological disorders 93 115 32231159 Insertion of Basic Amino Acids in the Hemagglutinin Cleavage Site of H4N2 Avian Influenza Virus (AIV)-Reduced Virus Fitness in Chickens is Restored by Reassortment with Highly Pathogenic H5N1 AIV. The NP of H5N1_HA4_T327K was detected in the endothelial and parenchymal cells of almost all organs (Figure 6A,B) and the intensity ranged from median scores of 0.5 in the hepatic endothelium as well as in the thymus, jejunum and caecum parenchyma to 3.0 in the lung parenchyma. 2020 International journal of molecular sciences Result IV T327K 19 24 NP 4 6 32231159 Insertion of Basic Amino Acids in the Hemagglutinin Cleavage Site of H4N2 Avian Influenza Virus (AIV)-Reduced Virus Fitness in Chickens is Restored by Reassortment with Highly Pathogenic H5N1 AIV. The plaque size of H4N2_T327R or H4N2_T 327K significantly increased by 52% and 125% in combination with the other seven H5N1 segments (Figure 3A). 2020 International journal of molecular sciences Result IV T327R 24 29 32231159 Insertion of Basic Amino Acids in the Hemagglutinin Cleavage Site of H4N2 Avian Influenza Virus (AIV)-Reduced Virus Fitness in Chickens is Restored by Reassortment with Highly Pathogenic H5N1 AIV. The spread of H4N2_T327R/K or H5N1_HA4 from cell-to-cell was comparable to H4N2_wt in the absence of trypsin. 2020 International journal of molecular sciences Result IV T327R;T327K 19;19 26;26 32231159 Insertion of Basic Amino Acids in the Hemagglutinin Cleavage Site of H4N2 Avian Influenza Virus (AIV)-Reduced Virus Fitness in Chickens is Restored by Reassortment with Highly Pathogenic H5N1 AIV. To determine the impact of expansion of the CS on HA cleavage, HEK293T cells were transfected with pCAGGS plasmids containing HA_wt, T327R or T327K with or without trypsin. 2020 International journal of molecular sciences Result IV T327R;T327K 133;142 138;147 HA 50 52 32231159 Insertion of Basic Amino Acids in the Hemagglutinin Cleavage Site of H4N2 Avian Influenza Virus (AIV)-Reduced Virus Fitness in Chickens is Restored by Reassortment with Highly Pathogenic H5N1 AIV. Virus Excretion in Inoculated and In-Contact Chickens Was Reduced by T327R/K and Increased by Reassortment with HPAIV H5N1 Segments. 2020 International journal of molecular sciences Result IV T327R;T327K 69;69 76;76 32231159 Insertion of Basic Amino Acids in the Hemagglutinin Cleavage Site of H4N2 Avian Influenza Virus (AIV)-Reduced Virus Fitness in Chickens is Restored by Reassortment with Highly Pathogenic H5N1 AIV. While all sentinels in-contact with H4N2_wt, H4N2_T327R, and H7N7_HA4 ON-inoculated chickens seroconverted, only 1/4 and 0/4 sentinel birds co-housed with chickens ON-inoculated with H4N2_T327K or H4N2_H5N2-HACS exhibited seroconversion (Table 2), indicating poor bird-to-bird transmission. 2020 International journal of molecular sciences Result IV T327R;T327K 50;188 55;193 32256457 Identification of Chebulinic Acid and Chebulagic Acid as Novel Influenza Viral Neuraminidase Inhibitors. To compare the antiviral potency of CHLA and CHLI with the marketed NA inhibitor oseltamivir carboxylate, a yield reduction assay was performed with six influenza virus strains, including A/H1N1/PR8, A/H3N2/NY, A/H3N2/Brisbane, B-Yamagate, B-Victoria, and an oseltamivir-resistant A/H1N1pdm(09), which contains the NA/H274Y substitution. 2020 Frontiers in microbiology Result IV H274Y 318 323 NA;NA 68;315 70;317 32256457 Identification of Chebulinic Acid and Chebulagic Acid as Novel Influenza Viral Neuraminidase Inhibitors. While compared to IAVs (Figures 5A-C), IBVs showed less sensitivity to CHLA and CHLI (Figures 5D,E).Interestingly, NA/H274Y in A/H1N1/pdm(09) virus conferred resistance to oseltamivir carboxylate, but the potency of CHLA and CHLI was not affected by the substitution (Figure 5F). 2020 Frontiers in microbiology Result IV H274Y 118 123 115 117 32272772 Influenza PB1-F2 Inhibits Avian MAVS Signaling. In human cells, the RIG-I d2CARD mutation A120D increased relative human IFN-beta promoter activity compared to the wildtype (Figure 3B), while the h2CARD mutation D122A almost completely abrogated relative IFN-beta promoter activity in HEK293T cells. 2020 Viruses Result IV A120D;D122A 42;164 47;169 32272772 Influenza PB1-F2 Inhibits Avian MAVS Signaling. Notably, the mutant D122A of human RIG-I can form 2CARD tetramers, but does not engage human MAVS to initiate signaling. 2020 Viruses Result IV D122A 20 25 32272772 Influenza PB1-F2 Inhibits Avian MAVS Signaling. The MAVS-CARD-RIG-I-CARD interface is poorly conserved between humans and ducks, but the overall structure is conserved such that the tandem T175K/T176E mutations on duck RIG-I permit interaction with human MAVS in HEK293T cells. 2020 Viruses Result IV T175K;T176E 141;147 146;152 32272772 Influenza PB1-F2 Inhibits Avian MAVS Signaling. The wildtype d2CARD induced high chIFN-beta promoter activity, while the A120D mutant d2CARD induced significantly less activity in DF-1 cells. 2020 Viruses Result IV A120D 73 78 32326238 Experimental Infection Using Mouse-Adapted Influenza B Virus in a Mouse Model. Additionally, nucleotide substitution in the HA segment (C641T) led to amino acid substitution in the HA protein (T214I). 2020 Viruses Result IV C641T;T214I 57;114 62;119 HA;HA 45;102 47;104 32326238 Experimental Infection Using Mouse-Adapted Influenza B Virus in a Mouse Model. B/2017-MA) showed the presence of synonymous (not leading to amino acid substitution) nucleotide substitution in the PB1 segment:A2175G. 2020 Viruses Result IV A2175G 129 135 PB1 117 120 32326238 Experimental Infection Using Mouse-Adapted Influenza B Virus in a Mouse Model. In addition, analysis of these strains of HA amino acid sequences revealed mutations (I117D, N129D, V146I) relative to earlier reference strains. 2020 Viruses Result IV I117D;N129D;V146I 86;93;100 91;98;105 HA 42 44 32326238 Experimental Infection Using Mouse-Adapted Influenza B Virus in a Mouse Model. In the sequence coding NA, a nucleotide substitution (G1294A), which leads to the amino acid change D432N, was detected. 2020 Viruses Result IV G1294A;D432N 54;100 60;105 23 25 32326238 Experimental Infection Using Mouse-Adapted Influenza B Virus in a Mouse Model. The strains NA substitutions were also found to feature amino acid substitutions characteristic of genetic group 1A of the B/Vic lineage (N340D, E358K, S295R, I120V, and K220N). 2020 Viruses Result IV N340D;E358K;S295R;I120V;K220N 138;145;152;159;170 143;150;157;164;175 12 14 32415096 mRNA display with library of even-distribution reveals cellular interactors of influenza virus NS1. Cells infected with IAV containing the D92Y mutation produce higher amounts of IFN compared with infection with WT, indicating an inability of this mutant NS1 to inhibit IFN induction, but the mechanism of this loss-of-function is unknown. 2020 Nature communications Result IV D92Y 39 43 NS1 155 158 32415096 mRNA display with library of even-distribution reveals cellular interactors of influenza virus NS1. Functionally, the R38A/K41A mutation failed to upregulate FASN protein expression. 2020 Nature communications Result IV R38A;K41A 18;23 22;27 32415096 mRNA display with library of even-distribution reveals cellular interactors of influenza virus NS1. Furthermore, purified CPSF1-FLAG was found to interact with NS1-HA in vitro, but this interaction was reduced by the D92Y mutation. 2020 Nature communications Result IV D92Y 117 121 HA;NS1 64;60 66;63 32415096 mRNA display with library of even-distribution reveals cellular interactors of influenza virus NS1. In comparison, the AP-MS-derived profiles of the wild-type protein and D92Y NS1 mutant revealed 80 proteins with loss of binding affinity to the mutant, including CPSF1 and the known CPSF complex member FIP1L1. 2020 Nature communications Result IV D92Y 71 75 NS1 76 79 32415096 mRNA display with library of even-distribution reveals cellular interactors of influenza virus NS1. In support of this, immunoprecipitation of HA-tagged NS1 in 293T cells resulted in co-immunoprecipitation of Flag-tagged CPSF1, but not the D92Y mutant. 2020 Nature communications Result IV D92Y 140 144 HA;NS1 43;53 45;56 32415096 mRNA display with library of even-distribution reveals cellular interactors of influenza virus NS1. Overexpression of CPSF1 results in significant inhibition of wild-type influenza A virus replication, but not of the D92Y mutant virus, which already lacks CPSF complex recruitment. 2020 Nature communications Result IV D92Y 117 121 32415096 mRNA display with library of even-distribution reveals cellular interactors of influenza virus NS1. To determine if this phenotype could be due to a change in the PPI profile, we applied md-LED on the NS1 D92Y (strain A/WSN/33). 2020 Nature communications Result IV D92Y 105 109 NS1 101 104 32415096 mRNA display with library of even-distribution reveals cellular interactors of influenza virus NS1. Together, the data from md-LED and AP-MS suggest that the D92Y mutation results in a loss of binding to the CPSF complex. 2020 Nature communications Result IV D92Y 58 62 32415096 mRNA display with library of even-distribution reveals cellular interactors of influenza virus NS1. Toward this end, we chose to investigate the interaction profile of a previously described NS1 mutant, D92Y, that was discovered in our high-throughput genetic screen for IFN-sensitive variants. 2020 Nature communications Result IV D92Y 103 107 NS1 91 94 32415096 mRNA display with library of even-distribution reveals cellular interactors of influenza virus NS1. we found that only one interactor, CPSF1, failed to bind the D92Y mutant. 2020 Nature communications Result IV D92Y 61 65 32415096 mRNA display with library of even-distribution reveals cellular interactors of influenza virus NS1. While wild-type NS1 efficiently down-regulated the expression of the GFP reporter, the D92Y mutant had no impact on GFP expression relative to the control. 2020 Nature communications Result IV D92Y 87 91 NS1 16 19 32433222 Baloxavir Marboxil 2% Granules in Japanese Children With Influenza: An Open-label Phase 3 Study. An increase in infectious virus around day 4 or 6 was observed in children with influenza B and in children with PA/I38T/M-substituted viruses, respectively (Figure, Supplemental Digital Content 7A, http://links.lww.com/INF/D974). 2020 The Pediatric infectious disease journal Result IV I38M;I38T 116;116 122;122 PA 113 115 32433222 Baloxavir Marboxil 2% Granules in Japanese Children With Influenza: An Open-label Phase 3 Study. Fever recurrence after day 4 was seen in 3 of 5 children with PA/I38T/M-substituted influenza A, 1 of 10 children with unsubstituted influenza A and 7 of 12 children with influenza B (Figure, Supplemental Digital Content 7B, http://links.lww.com/INF/D974). 2020 The Pediatric infectious disease journal Result IV I38M;I38T 65;65 71;71 PA 62 64 32433222 Baloxavir Marboxil 2% Granules in Japanese Children With Influenza: An Open-label Phase 3 Study. Of 33 children, 31 had baseline samples available for virus sequencing; no PA/I38X-substituted viruses were detected. 2020 The Pediatric infectious disease journal Result IV I38X 78 82 PA 75 77 32433222 Baloxavir Marboxil 2% Granules in Japanese Children With Influenza: An Open-label Phase 3 Study. Twenty-six children had baseline and posttreatment samples available; PA/I38T/M-substituted viruses were detected in 5 children at day 6 (n = 4) and day 9 (n = 1). 2020 The Pediatric infectious disease journal Result IV I38M;I38T 73;73 79;79 PA 70 72 32433222 Baloxavir Marboxil 2% Granules in Japanese Children With Influenza: An Open-label Phase 3 Study. Variants included 3 PA/I38T/I mixture (2 with A(H3N2) and 1 with A(H1N1)pdm09) and PA/I38M (2 with A(H3N2) virus). 2020 The Pediatric infectious disease journal Result IV I38I;I38T;I38M 23;23;86 29;29;90 PA;PA 20;83 22;85 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. All 28 Bulgarian viruses carried HA2 E150G substitution, the 19 subclade 3C.2a1b viruses were characterized by three HA1 substitutions, and the nine subclade 3C.2a2 viruses by four HA1 and one HA2 substitutions (Table 1). 2020 Journal of medical microbiology Result IV E150G 37 42 HA;HA;HA1;HA1 33;193;117;181 35;195;120;184 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. All 36 A(H1N1)pdm09 HA sequences contained three amino acid changes in HA1, S74R, S164T and I295V, that were fixed in globally circulating subclade 6B.1A viruses (Table 1). 2020 Journal of medical microbiology Result IV S74R;S164T;I295V 76;82;92 80;87;97 HA;HA1 20;71 22;74 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. All studied viruses that fell in subgroups of subclade 6B.1A carried HA1 S183P substitution. 2020 Journal of medical microbiology Result IV S183P 73 78 HA1 69 72 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. As with the vast majority of A(H1N1)pdm09 viruses, M2 proteins carried S31N substitution associated with resistance to M2-ion channel blockers (amantadine and rimantadine). 2020 Journal of medical microbiology Result IV S31N 71 75 M2;M2 51;119 53;121 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. Common substitutions in viruses of all genetic subgroups were G77R, V81A and N449D. 2020 Journal of medical microbiology Result IV G77R;V81A;N449D 62;68;77 66;72;82 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. NAs of Bulgarian A(H3N2) viruses all carried I212V and N329S substitutions compared to A/Singapore/INFIMH-16-019/2016. 2020 Journal of medical microbiology Result IV I212V;N329S 45;55 50;60 0 3 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. Of the amino acid substitutions, three were located in antigenic sites: S74R in site Cb; S164T and N129D in site Sa. 2020 Journal of medical microbiology Result IV S74R;S164T;N129D 72;89;99 76;94;104 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. Of the three egg-adaptation substitutions in the A/Singapore/INFIMH-16-0019/2016 vaccine virus (T160K resulting in the loss of a glycosylation sequon in antigenic site B, L194P in the 190-helix (residues 188-194) and D225G within the RBS), one Bulgarian virus (A/Bulgaria/1153/2019) carried T160K substitution and two (A/Bulgaria/1534/2018 and A/Bulgaria/900/2019) showed polymorphism at this position (T160X). 2020 Journal of medical microbiology Result IV T160K;L194P;D225G;T160K;T160X 96;171;217;291;403 101;176;222;296;408 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. Substitutions T160K/X (in antigenic site B), T128A and T135K (in antigenic site A) result in loss of N-glycosylation sequons, HA2 E155G falls within an N-glycosylation sequon (NET NGT). 2020 Journal of medical microbiology Result IV T160X;T160K;T128A;T135K;E155G 14;14;45;55;130 21;21;50;60;135 HA 126 128 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. Substitutions T72N, N234D and N329S identified in some or all Bulgarian viruses resulted in the loss of N-glycosylation sequons. 2020 Journal of medical microbiology Result IV T72N;N234D;N329S 14;20;30 18;25;35 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. Testing was performed on 280 detected A(H1N1)pdm09 viruses by real-time RT-PCR with respect to the NA H275Y oseltamivir resistance substitution at the NRL in Bulgaria; NA and PA sequences of all study A(H1N1)pdm09 and A(H3N2) viruses were screened for known markers of reduced susceptibility to NA inhibitors and baloxavir marboxil and phenotypic testing (by the MUNANA method) was performed on 13 influenza A(H1N1)pdm09 and 5 A(H3N2) influenza viruses. 2020 Journal of medical microbiology Result IV H275Y 102 107 NA;NA;NA;PA 99;168;295;175 101;170;297;177 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. The subclade 3C.2a1b viruses can be subdivided into two genetic groups: 11 with HA1 T128A and T135K substitutions and eight with HA1 T131K and HA2 V200I substitutions. 2020 Journal of medical microbiology Result IV T128A;T135K;T131K;V200I 84;94;133;147 89;99;138;152 HA;HA1;HA1 143;80;129 145;83;132 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. The substitution S164T modified the 162-164 sequon, NQS NQT, within the Sa antigenic site. 2020 Journal of medical microbiology Result IV S164T 17 22 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. The substitutions L85I, S105N, I188T, N449D and T452I occur at amino acid positions associated with NA antigenic sites. 2020 Journal of medical microbiology Result IV L85I;S105N;I188T;N449D;T452I 18;24;31;38;48 22;29;36;43;53 100 102 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. After analyzing the gene data for wild-type strains in the NCBI influenza database, it was found that the V186I and L466I mutations of NP genes do not exist in wild type, while the L77I mutation in the NS gene accounted for only 0.92%. 2020 AMB Express Result IV V186I;L466I;L77I 106;116;181 111;121;185 NP;NS 135;202 137;204 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. Among them, the 111-115 mutation hotspot contained E114K in 10 strains; the 196-200 mutation hotspot contained A198V in 66 strains; the 221-225 mutation hotspot contained M224K in 16 strains; and the 221-235 mutation hotspot contained Q234L in 25 strains. 2020 AMB Express Result IV E114K;A198V;M224K;Q234L 51;111;171;235 56;116;176;240 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. Among them, the 131-135 mutation hotspot contained K131R in 17 strains; the 166-170 mutation hotspot contained A168T in 3 strains; the 196-200 mutation hotspot contained A198V in 56 strains; the 201-205 mutation hotspot contained N201D in 3 strains; and the 231-235 mutation hotspot contained Q234L in 36 strains. 2020 AMB Express Result IV K131R;A168T;A198V;N201D;Q234L 51;111;170;230;293 56;116;175;235;298 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. Among them, the 196-200 mutation hotspot contained A198V in 55 strains; the 221-225 mutation hotspot contained M224K in 24 strains; the 231-235 mutation hotspot contained Q234L in 83 strains; the 281-285 mutation hotspot contained L281F in 9 strains; and the 281-285 mutation hotspot contained N285D in 4 strains. 2020 AMB Express Result IV A198V;M224K;Q234L;L281F;N285D 51;111;171;231;294 56;116;176;236;299 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. For the 15 strains isolated from the lungs in the twentieth generation after serial passaging without selection pressure, 1 strain had a V554I mutation (Table 5). 2020 AMB Express Result IV V554I 137 142 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. For the 15 strains isolated from the trachea in the twentieth generation after serial passaging without selection pressure, all 15 strains had a V186I mutation, and 14 strains had an L466I mutation, which shows that the V186I and L466I mutations were related to the mutation-prone nature of the virus. 2020 AMB Express Result IV V186I;L466I;V186I;L466I 145;183;220;230 150;188;225;235 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. For the 19 strains isolated from the trachea in the twentieth generation after serial passaging without selection pressure, 1 strain had an R185K mutation, 1 strain had an S190F mutation, 1 strain had an F646S mutation and 1 strain had a C693G mutation. 2020 AMB Express Result IV R185K;S190F;F646S;C693G 140;172;204;238 145;177;209;243 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. For the 19 strains isolated from the trachea in the twentieth generation after serial passaging without selection pressure, all 19 strains had a V186I mutation, and 9 strains had an L466I mutation. 2020 AMB Express Result IV V186I;L466I 145;182 150;187 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. For the 19 strains isolated from the trachea in the twentieth generation after serial passaging without selection pressure, the M1 gene of 2 strains had an F62L mutation, and the M2 gene of 1 strain had an R256H mutation; for the 15 strains isolated from the lung, the M2 gene of 1 strain had an A209T mutation (Table 5). 2020 AMB Express Result IV F62L;R256H;A209T 156;206;296 160;211;301 M1;M2;M2 128;179;269 130;181;271 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. For the 19 strains isolated from the trachea in the twentieth generation after serial passaging without selection pressure, the NS gene of 1 strain had an L33Q mutation, and the NS1 gene of 19 strains had an L77I mutation; for the 15 strains isolated from the lung, the NS gene of 15 strains had an L77I mutation, and the NS gene of 1 strain had a V84M mutation (Table 5). 2020 AMB Express Result IV L33Q;L77I;L77I;V84M 155;208;299;348 159;212;303;352 NS;NS;NS;NS1 128;270;322;178 130;272;324;181 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. For the 24 strains isolated from the lung in the twentieth generation after serial passaging with selection pressure, 1 strain had an F46L mutation, 1 strain had a V127I mutation, 1 strain had an L132I mutation and 1 strain had an E319V mutation. 2020 AMB Express Result IV F46L;V127I;L132I;E319V 134;164;196;231 138;169;201;236 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. For the M gene, compared with the F/98 sequence, for the 20 strains isolated from the trachea in the twentieth generation after serial passaging with selection pressure, the M1 gene of 1 strain had an L28P mutation, and the M1 gene of 2 strains of the 24 strains isolated from the lung had an R304G mutation. 2020 AMB Express Result IV L28P;R304G 201;293 205;298 M;M1;M1 8;174;224 9;176;226 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. For the NS gene, compared with the F/98 sequence, there were no mutations detected in the strains isolated from the trachea; for the 24 strains isolated from the lung, the NS gene of 1 strain had a P85L mutation. 2020 AMB Express Result IV P85L 198 202 NS;NS 8;172 10;174 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. For the viruses with and without selection pressure of vaccine antibodies, we selected 5 strains each, and the mutations in each strain were as follows (seen in Table 6): V1: HA (K131R, A198V, Q234L), NA (67-76 amino acid deletion), PB2 (R318K, R355K); V2: HA (K131R, A168T, A198T, L234Q), NA (67-76 amino acid deletion), PB2 (R318K); V3: HA (K131R, N201D, A198T, L234Q), NA (67-76 amino acid deletion); V4: HA (K131R, A198T, L234Q), NA (67-76 amino acid deletion), PB2 (R318K, R355K); V5: HA (K131R, A198T, L234Q), NA (67-76 amino acid deletion); N1: HA (A198V, M224K, Q234L, L281F, N285D), PB2 (R318K), NP (V186I, L466I), NS1 (L77I), M1 (F62L); N2: HA (A198V, M224K, Q234L, N285D), PB2 (R318K), NP (V186I, L466I), NS1 (L77I), M1 (F62L); N3: HA (A198V, M224K, Q234L, L281F, N285D), PB2 (R318K), NP (V186I, L466I), NS1 (L77I), M1 (F62L); N4: HA (E114K, A198V, M224K, Q234L, L281F, N285D), PB2 (R318K), NP (V186I, L466I), NS1 (L77I), M1 (F62L); and N5: HA (A198V, M224K, Q234L, L281F, N285D), PB2 (R318K), NP (V186I, L466I), NS1 (L77I), M1 (F62L). 2020 AMB Express Result IV K131R;A198V;Q234L;R318K;R355K;K131R;A168T;A198T;L234Q;R318K;K131R;N201D;A198T;L234Q;K131R;A198T;L234Q;R318K;R355K;K131R;A198T;L234Q;A198V;M224K;Q234L;L281F;N285D;R318K;V186I;L466I;L77I;F62L;A198V;M224K;Q234L;N285D;R318K;V186I;L466I;L77I;F62L;A198V;M224K;Q234L;L281F;N285D;R318K;V186I;L466I;L77I;F62L;E114K;A198V;M224K;Q234L;L281F;N285D;R318K;V186I;L466I;L77I;F62L;A198V;M224K;Q234L;L281F;N285D;R318K;V186I;L466I;L77I;F62L 179;186;193;238;245;261;268;275;282;327;343;350;357;364;412;419;426;471;478;494;501;508;556;563;570;577;584;597;609;616;629;640;655;662;669;676;689;701;708;721;732;747;754;761;768;775;788;800;807;820;831;846;853;860;867;874;881;894;906;913;926;937;956;963;970;977;984;997;1009;1016;1029;1040 184;191;198;243;250;266;273;280;287;332;348;355;362;369;417;424;431;476;483;499;506;513;561;568;575;582;589;602;614;621;633;644;660;667;674;681;694;706;713;725;736;752;759;766;773;780;793;805;812;824;835;851;858;865;872;879;886;899;911;918;930;941;961;968;975;982;989;1002;1014;1021;1033;1044 HA;HA;HA;HA;HA;HA;HA;HA;HA;HA;M1;M1;M1;M1;M1;NA;NA;NA;NA;NA;NP;NP;NP;NP;NP;NS1;NS1;NS1;NS1;NS1;PB2;PB2;PB2;PB2;PB2;PB2;PB2;PB2 175;257;339;408;490;552;651;743;842;952;636;728;827;933;1036;201;290;372;434;516;605;697;796;902;1005;624;716;815;921;1024;233;322;466;592;684;783;889;992 177;259;341;410;492;554;653;745;844;954;638;730;829;935;1038;203;292;374;436;518;607;699;798;904;1007;627;719;818;924;1027;236;325;469;595;687;786;892;995 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. In PB1 of 20 strains of quasispecies viruses isolated from the trachea in the twentieth generation after serial passaging with selection pressure of vaccine antibodies, there was only an I397V mutation in PB1 of 1 strain; in PB1 of 19 strains of quasispecies viruses isolated from the tracheas in the twentieth generation after serial passaging without selection pressure, there was only an I517V mutation in PB1 of 1 strain virus (Table 5). 2020 AMB Express Result IV I397V;I517V 187;391 192;396 PB1;PB1;PB1;PB1 3;205;225;409 6;208;228;412 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. In the 19 strains of viruses isolated from the tracheas of chickens without selection pressure, all the PB2 proteins of the 19 strains (100%) had an R318K mutation; in the 15 strains isolated from the tracheas of chickens without selection pressure, PB2 of 1 strain (6.6%) had an I63M mutation and PB2 of the 15 strains (100%) had an R318K mutation (Table 5). 2020 AMB Express Result IV R318K;I63M;R318K 149;280;334 154;284;339 PB2;PB2;PB2 104;250;298 107;253;301 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. In the 20 strains isolated from the tracheas of chickens with selection pressure, PB2 of 1 strain (5%) had a D256N mutation, PB2 of 13 strains (65%) had an R318K mutation and PB2 of 20 strain (100%) had an R355K mutation; in the 24 strains isolated from the tracheas of chickens with selection pressure, PB2 of 19 strains (79.1%) had an R318K mutation, PB2 of 24 strains (100%) had an R355K mutation PB2 of 1 strain (5.2%) had a K526R mutation, and PB2 of 2 strains (10.5%) had an A622V mutation. 2020 AMB Express Result IV D256N;R318K;R355K;R318K;R355K;K526R;A622V 109;156;206;337;385;429;481 114;161;211;342;390;434;486 PB2;PB2;PB2;PB2;PB2;PB2;PB2 82;125;175;304;353;400;449 85;128;178;307;356;403;452 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. Similarly, this result also indicates that the selection pressure of vaccine antibodies limits the NP gene to generate the V186I and L466I mutations (Table 5). 2020 AMB Express Result IV V186I;L466I 123;133 128;138 NP 99 101 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. The 131-135 mutation hotspot contained K131R in 18 strains; the 196-200 mutation hotspot contained A198V in 62 strains; and the 231-235 mutation hotspot contained Q234L in 32 strains. 2020 AMB Express Result IV K131R;A198V;Q234L 39;99;163 44;104;168 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. The PB2 gene of 100% of isolated strains from the tracheas and lungs of the twentieth-generation chickens without selection pressure had R318K mutations, but there was no R355K mutation, which signified that the R355K mutation in the PB2 genes was the result of the selection pressure of vaccine antibodies on F/98. 2020 AMB Express Result IV R318K;R355K;R355K 137;171;212 142;176;217 PB2;PB2 4;234 7;237 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. The R318K mutation in the PB2 gene appeared with and without selection pressure of vaccine antibodies, although the PB2 gene mutation rate of the isolated strains after serial passaging was lower than that without selection pressure of vaccine antibodies. 2020 AMB Express Result IV R318K 4 9 PB2;PB2 26;116 29;119 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. The results showed that all the PB2 genes of the viruses isolated from tracheas and lungs of the twentieth-generation chickens with selection pressure had R355K mutations, and 72% of the PB2 genes from isolated strains had R318K mutations. 2020 AMB Express Result IV R355K;R318K 155;223 160;228 PB2;PB2 32;187 35;190 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. The strains with I397V and I517V mutations in the PB1 genes were not advantageous, and their biological significance was not manifested in this study. 2020 AMB Express Result IV I397V;I517V 17;27 22;32 PB1 50 53 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. The V186I and L466I mutations of the NP gene and the L77I mutation of the NS gene occur in only the viruses passaging from generation to generation without the selection pressure of vaccine antibodies, which indicates that the selection pressure of vaccine antibodies was less effective for NS and NP than for other viral proteins. 2020 AMB Express Result IV V186I;L466I;L77I 4;14;53 9;19;57 NP;NP;NS;NS 37;298;74;291 39;300;76;293 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. We found that the HA gene mutations K131R, A168T, A198T and N201D of quasispecies viruses serially passaged from generation to generation with selection pressure of vaccine antibodies were all located in the head of HA protein; the mutations HA gene E114K, A198T, M224K and L234Q of quasispecies viruses serially passaged from generation to generation without selection pressure of vaccine antibodies were located in the head of HA protein, while L281F and N285D were located in the neck of the HA protein. 2020 AMB Express Result IV K131R;A168T;A198T;N201D;E114K;A198T;M224K;L234Q;L281F;N285D 36;43;50;60;250;257;264;274;447;457 41;48;55;65;255;262;269;279;452;462 HA;HA;HA;HA;HA 18;216;242;429;495 20;218;244;431;497 32483655 Genetic and antigenic characterization of influenza A/H5N1 viruses isolated from patients in Indonesia, 2008-2015. Additionally, substitutions in NS1 (N200S, G205R) as well as NS2 (T47A, M51I) proteins may result in decreased antiviral responses in the host. 2020 Virus genes Result IV N200S;G205R;T47A;M51I 36;43;66;72 41;48;70;76 NS1;NS2 31;61 34;64 32483655 Genetic and antigenic characterization of influenza A/H5N1 viruses isolated from patients in Indonesia, 2008-2015. Although Q136L is associated with reduced sensitivity to zanamivir and oseltamivir, Q136H had no effect on sensitivity to NAI when tested in H1N1pdm2009 or H3N2. 2020 Virus genes Result IV Q136L;Q136H 9;84 14;89 NAI 122 125 32483655 Genetic and antigenic characterization of influenza A/H5N1 viruses isolated from patients in Indonesia, 2008-2015. Both PB2-E627K (5 of 35 viruses) and PB2-D701N (1 virus) substitutions were observed in a limited number of the novel viruses presented in this study. 2020 Virus genes Result IV E627K;D701N 9;41 14;46 PB2;PB2 5;37 8;40 32483655 Genetic and antigenic characterization of influenza A/H5N1 viruses isolated from patients in Indonesia, 2008-2015. Furthermore, the N66S substitution in PB1-F2 known to increase virulence was not found in any of the novel viruses. 2020 Virus genes Result IV N66S 17 21 PB1F2 38 44 32483655 Genetic and antigenic characterization of influenza A/H5N1 viruses isolated from patients in Indonesia, 2008-2015. has previously shown that substitutions D183N and R189M are indeed responsible for the antigenic differences between these two clusters. 2020 Virus genes Result IV D183N;R189M 40;50 45;55 32483655 Genetic and antigenic characterization of influenza A/H5N1 viruses isolated from patients in Indonesia, 2008-2015. However, no substitution (i.e., N158X or T160X) removing this glycosylation site was observed in the new Indonesian samples. 2020 Virus genes Result IV N158X;T160X 32;41 37;46 32483655 Genetic and antigenic characterization of influenza A/H5N1 viruses isolated from patients in Indonesia, 2008-2015. However, none of the newly isolated viruses encoded known NAI resistance mutations (i.e., V116A, I117V, E119V, G136K, V149A, R156K, D198N, S246N, H275Y, R293K, N295S (N1 numbering)). 2020 Virus genes Result IV V116A;I117V;E119V;G136K;V149A;R156K;D198N;S246N;H275Y;R293K;N295S 90;97;104;111;118;125;132;139;146;153;160 95;102;109;116;123;130;137;144;151;158;165 NAI 58 61 32483655 Genetic and antigenic characterization of influenza A/H5N1 viruses isolated from patients in Indonesia, 2008-2015. In particular, PB2-E627K is a key molecular determinant of host range and a virulence factor during human infection with HPAI H5N1. 2020 Virus genes Result IV E627K 19 24 PB2 15 18 Influenza A virus H5N1 infection 121 130 32483655 Genetic and antigenic characterization of influenza A/H5N1 viruses isolated from patients in Indonesia, 2008-2015. Nonetheless, we did not find in any of the 35 virus isolates any HA substitutions (i.e., H103Y, T315I and Y351H, H352Q, an K387I (H3 numbering) that are known to increase replication and virulence of avian influenza virus H5N1 or H7N9 in mammalian animal models by mediating HA protein stability. 2020 Virus genes Result IV H103Y;T315I;Y351H;H352Q;K387I 89;96;106;113;123 94;101;111;118;128 HA;HA 65;275 67;277 32483655 Genetic and antigenic characterization of influenza A/H5N1 viruses isolated from patients in Indonesia, 2008-2015. NS1 mutations such as P42S, D87E, L98F and I101M were also found to modulate the virulence of H5N1 viruses. 2020 Virus genes Result IV P42S;D87E;L98F;I101M 22;28;34;43 26;32;38;48 NS1 0 3 32483655 Genetic and antigenic characterization of influenza A/H5N1 viruses isolated from patients in Indonesia, 2008-2015. Of note, Q136H was observed in 14 of the 35 isolates. 2020 Virus genes Result IV Q136H 9 14 32483655 Genetic and antigenic characterization of influenza A/H5N1 viruses isolated from patients in Indonesia, 2008-2015. PB2 substitutions such as E627K and D701N can dramatically increase polymerase activity of avian influenza viruses in mammalian cells. 2020 Virus genes Result IV E627K;D701N 26;36 31;41 PB2 0 3 32483655 Genetic and antigenic characterization of influenza A/H5N1 viruses isolated from patients in Indonesia, 2008-2015. The N183T substitution does not seem to have an antigenic effect, although the M189I could have a small antigenic effect as indicated by the placement on the outside of the cluster. 2020 Virus genes Result IV N183T;M189I 4;79 9;84 32483655 Genetic and antigenic characterization of influenza A/H5N1 viruses isolated from patients in Indonesia, 2008-2015. This is in strong contrast with human H5N1 viruses collected in other geographic regions where PB2-E627K substitution is common. 2020 Virus genes Result IV E627K 99 104 PB2 95 98 32483655 Genetic and antigenic characterization of influenza A/H5N1 viruses isolated from patients in Indonesia, 2008-2015. Various amantadine resistance substitutions in the M2 protein were also found in all 35 isolates, including V27A (34 viruses), V27T (1 virus), S31G (1 virus), and S31N (5 viruses). 2020 Virus genes Result IV V27A;V27T;S31G;S31N 108;127;143;163 112;131;147;167 M2 51 53 32486222 Antibody Neutralization of an Influenza Virus that Uses Neuraminidase for Receptor Binding. As described in the Introduction, the G147R mutation enables NA to bind receptor while retaining its catalytic receptor-cleaving activity. 2020 Viruses Result IV G147R 38 43 61 63 32486222 Antibody Neutralization of an Influenza Virus that Uses Neuraminidase for Receptor Binding. As expected, S364N greatly increased the resistance of the virus to HF5 neutralization (Figure 3). 2020 Viruses Result IV S364N 13 18 32486222 Antibody Neutralization of an Influenza Virus that Uses Neuraminidase for Receptor Binding. Based on prior work, it may be possible to generate D151N as a mixed cooperating population, but we did not attempt that here. 2020 Viruses Result IV D151N 52 57 32486222 Antibody Neutralization of an Influenza Virus that Uses Neuraminidase for Receptor Binding. Note that unlike the other HAs in this paper, this binding-deficient HA is H3 rather than H1:our rationale for using it is that it has been shown to completely lack receptor binding activity, whereas most characterized point mutants of HA in the receptor binding pocket (e.g., the widely used Y98F mutant) still retain a sufficient binding activity to enable HA-mediated infection in cell culture. 2020 Viruses Result IV Y98F 293 297 HA;HA;HA 69;236;359 71;238;361 32486222 Antibody Neutralization of an Influenza Virus that Uses Neuraminidase for Receptor Binding. One of the selected mutations, S364N, had previously been identified as an HF5 escape mutation in cell-based ELISAs using a panel of mutants and again after the passage of Cal09 virus in passively immunized animals. 2020 Viruses Result IV S364N 31 36 32486222 Antibody Neutralization of an Influenza Virus that Uses Neuraminidase for Receptor Binding. Since D151N ablates NA catalytic activity, it is not possible to rescue this virus as a clonal population, so we only tested the S364N mutation in subsequent validation. 2020 Viruses Result IV D151N;S364N 6;129 11;134 20 22 32486222 Antibody Neutralization of an Influenza Virus that Uses Neuraminidase for Receptor Binding. The HA also contains the mutation K62E in the HA stem domain, which has previously been shown to enhance viral growth in the context of the other HA mutations. 2020 Viruses Result IV K62E 34 38 HA;HA;HA 4;46;146 6;48;148 32486222 Antibody Neutralization of an Influenza Virus that Uses Neuraminidase for Receptor Binding. The second mutation was D151N:as discussed in the Introduction, this mutation confers receptor-binding properties on N2 NA. 2020 Viruses Result IV D151N 24 29 120 122 32486222 Antibody Neutralization of an Influenza Virus that Uses Neuraminidase for Receptor Binding. The second virus has the unmutated Cal09 HA, but the NA has the G147R mutation relative to the Cal09 sequence. 2020 Viruses Result IV G147R 64 69 HA;NA 41;53 43;55 32486222 Antibody Neutralization of an Influenza Virus that Uses Neuraminidase for Receptor Binding. Therefore, D151N might allow the virus to outcompete antibody binding by increasing NA binding avidity to cells, allowing rapid attachment and therefore reducing sensitivity to antibodies in a similar fashion to that shown for HA. 2020 Viruses Result IV D151N 11 16 HA;NA 227;84 229;86 32486222 Antibody Neutralization of an Influenza Virus that Uses Neuraminidase for Receptor Binding. This binding-deficient HA was paired with the G147R mutant of the Cal09 NA to create a virus that we will refer to as NAbind/HA bind. 2020 Viruses Result IV G147R 46 51 HA;HA;NA 23;125;72 25;127;74 32486222 Antibody Neutralization of an Influenza Virus that Uses Neuraminidase for Receptor Binding. This engineered HA contains amino-acid mutations at key residues in the receptor binding pocket (Y98F, H183F, and L194A in H3 numbering), deletion of residues 221-228 that form a loop near the receptor-binding pocket, and the addition of seven potential N-linked glycosylation sites (at residues 45, 63, 122, 126, 133, 144, and 246) that decrease HA receptor avidity. 2020 Viruses Result IV Y98F;H183F;L194A 97;103;114 101;108;119 HA;HA 16;347 18;349 32486222 Antibody Neutralization of an Influenza Virus that Uses Neuraminidase for Receptor Binding. To validate that S364N is an HF5 escape mutation in the NAbind/HA bind virus, we performed neutralization assays with the parental NAbind/HA bind virus and a reverse-genetics generated virus with S364N introduced into this background. 2020 Viruses Result IV S364N;S364N 17;196 22;201 HA;HA 63;138 65;140 32486222 Antibody Neutralization of an Influenza Virus that Uses Neuraminidase for Receptor Binding. We speculate that D151N indirectly increases antibody resistance by enhancing NA's affinity for receptors, similar to the "avidity" mutations that sometimes arise in HA under antibody pressure. 2020 Viruses Result IV D151N 18 23 HA;NA 166;78 168;80 32486222 Antibody Neutralization of an Influenza Virus that Uses Neuraminidase for Receptor Binding. We speculate that the correlation between neutralization of NAbind/HA bind and inhibitory activity in the ELLA assay reflects the fact that the G147R receptor-binding NA binds to cells using the NA active site. 2020 Viruses Result IV G147R 144 149 HA;NA;NA 67;167;195 69;169;197 32547518 Characterization of Influenza A and B Viruses Circulating in Southern China During the 2017-2018 Season. A previous study found that the amino acid substitution N180K altered the epitope and affected the viral antigenicity. 2020 Frontiers in microbiology Result IV N180K 56 61 32547518 Characterization of Influenza A and B Viruses Circulating in Southern China During the 2017-2018 Season. All of the A/H1N1 strains circulating during January to March, as well as the 2017-2019 vaccine strain (A/Michigan/45/2015), fell into clade 6B.1, which is defined by the HA1 amino acid substitutions S84N, S162N and I216T. 2020 Frontiers in microbiology Result IV S84N;S162N;I216T 200;206;216 204;211;221 HA1 171 174 32547518 Characterization of Influenza A and B Viruses Circulating in Southern China During the 2017-2018 Season. Another mutation P154S in the Ca2 antigenic site was also found in two isolates (SMU214 and SMU941). 2020 Frontiers in microbiology Result IV P154S 17 22 32547518 Characterization of Influenza A and B Viruses Circulating in Southern China During the 2017-2018 Season. Five mutations located in the HA antigenic epitopes were identified in the 19 B/Victoria isolates: K180N (19/19), I132V (16/19), N144D (15/19), I161V (3/19), H137Q or H137N (1/19), respectively (Figure 4C). 2020 Frontiers in microbiology Result IV K180N;I132V;N144D;I161V;H137Q;H137N 99;114;129;144;158;167 104;119;134;149;163;172 HA 30 32 32547518 Characterization of Influenza A and B Viruses Circulating in Southern China During the 2017-2018 Season. In the 150-loop, three isolates contained a mutation I161V. 2020 Frontiers in microbiology Result IV I161V 53 58 32547518 Characterization of Influenza A and B Viruses Circulating in Southern China During the 2017-2018 Season. Note that the mutations K180N, I132V, and N144D occurred in most of the isolates. 2020 Frontiers in microbiology Result IV K180N;I132V;N144D 24;31;42 29;36;47 32547518 Characterization of Influenza A and B Viruses Circulating in Southern China During the 2017-2018 Season. S181T was identified in all the 23 isolates, although the meaning of the mutation is unknown (Table 3). 2020 Frontiers in microbiology Result IV S181T 0 5 32547518 Characterization of Influenza A and B Viruses Circulating in Southern China During the 2017-2018 Season. The mutation L187Q was noted in all 80 isolates, but it was not found in any antigenic sites and therefore may not affect the antigenicity. 2020 Frontiers in microbiology Result IV L187Q 13 18 32547518 Characterization of Influenza A and B Viruses Circulating in Southern China During the 2017-2018 Season. When compared with the A/H1N1 2017-2019 vaccine strain (A/Michigan/45/2015), there were three major amino acid mutations within the HA gene of all 23 isolates (S91R, S181T, and I312V), of which one mutation, S91R, located in the Cb antigenic site was identified in all 23 isolates (Figure 4A). 2020 Frontiers in microbiology Result IV S91R;S181T;I312V;S91R 160;166;177;208 164;171;182;212 HA 132 134 32547518 Characterization of Influenza A and B Viruses Circulating in Southern China During the 2017-2018 Season. When compared with the B/Victoria 2016-2018 vaccine strain (B/Brisbane/60/2008), all 19 isolates had one common amino acid mutation (K180N), located in the HA 160-loop (Table 5). 2020 Frontiers in microbiology Result IV K180N 133 138 HA 156 158 32547518 Characterization of Influenza A and B Viruses Circulating in Southern China During the 2017-2018 Season. When compared with the B/Victoria 2018-2020 vaccine strain (B/Colorado/06/2017), surprisingly, all 19 isolates had K180N mutation in the 160-loop and 15 of 19 isolates had a G144D mutation in the 120-loop. 2020 Frontiers in microbiology Result IV K180N;G144D 115;174 120;179 32599753 Virtual Screening Identifies Chebulagic Acid as an Inhibitor of the M2(S31N) Viral Ion Channel and Influenza A Virus. After 20 hours' incubation, expression of M2(S31N) reduced yeast growth to 30.6 +- 11.6% (mean +- SD) of the strain treated with glucose, while expression of M2(S31) reduced growth to 24.4 +- 12.9% of glucose-treated cells. 2020 Molecules (Basel, Switzerland) Result IV S31N 45 49 M2;M2 42;158 44;160 32599753 Virtual Screening Identifies Chebulagic Acid as an Inhibitor of the M2(S31N) Viral Ion Channel and Influenza A Virus. Although not assessed by TEVC or plaque reduction assay, a thiophene derivative (compound 6) was selected as it restores growth of bacteria expressing M2(S31N), which would otherwise inhibit bacterial growth, with an EC50 of 25 microM. 2020 Molecules (Basel, Switzerland) Result IV S31N 154 158 M2 151 153 32599753 Virtual Screening Identifies Chebulagic Acid as an Inhibitor of the M2(S31N) Viral Ion Channel and Influenza A Virus. As expected, amantadine effectively inhibited PR8M2(S31) replication (EC50 = 0.16 +- 0.02 microM; mean +- s.e.m.) but not PR8M2(S31N) (EC50 > 5 microM), while M2WSJ352 selectively inhibited PR8M2(S31N) (EC50 = 3.2 +- 1.2 microM) over PR8M2(S31) (EC50 = 32.7 +- 16.1 microM). 2020 Molecules (Basel, Switzerland) Result IV S31N;S31N 128;196 132;200 32599753 Virtual Screening Identifies Chebulagic Acid as an Inhibitor of the M2(S31N) Viral Ion Channel and Influenza A Virus. Briefly, Saccharomyces cerevisiae strains contain a multicopy plasmid of M2(S31N) or M2(S31) from the Udorn strain of influenza A under the control of the inducible GAL1 promoter. 2020 Molecules (Basel, Switzerland) Result IV S31N 76 80 M2;M2 73;85 75;87 32599753 Virtual Screening Identifies Chebulagic Acid as an Inhibitor of the M2(S31N) Viral Ion Channel and Influenza A Virus. Chebulagic Acid Inhibits M2(S31N)Activity In Vitro. 2020 Molecules (Basel, Switzerland) Result IV S31N 28 32 M2 25 27 32599753 Virtual Screening Identifies Chebulagic Acid as an Inhibitor of the M2(S31N) Viral Ion Channel and Influenza A Virus. Compound 7, a pinanamine derivative, was reported to inhibit 27% of M2(S31N) and 96% of M2(S31)-dependent currents at 100 microM, as measured by TEVC, although it was effective only against M2(S31)-containing viruses in plaque reduction assays. 2020 Molecules (Basel, Switzerland) Result IV S31N 71 75 M2;M2;M2 68;88;190 70;90;192 32599753 Virtual Screening Identifies Chebulagic Acid as an Inhibitor of the M2(S31N) Viral Ion Channel and Influenza A Virus. Compounds 3 and 4 were also reported to inhibit replication of influenza A virus with M2(S31N), as measured by plaque reduction assay (reported half-maximal effective concentration (EC50) = 14 and 0.1 microM, respectively). 2020 Molecules (Basel, Switzerland) Result IV S31N 89 93 M2 86 88 32599753 Virtual Screening Identifies Chebulagic Acid as an Inhibitor of the M2(S31N) Viral Ion Channel and Influenza A Virus. Computed binding affinities for P1 and P2 towards M2(S31N) and M2(S31) are shown in Table 1. 2020 Molecules (Basel, Switzerland) Result IV S31N 53 57 M2;M2 50;63 52;65 32599753 Virtual Screening Identifies Chebulagic Acid as an Inhibitor of the M2(S31N) Viral Ion Channel and Influenza A Virus. Conversely, while M2WJ352 did not substantially restore growth of M2(S31N)-expressing yeast at up to 30 microM, amantadine restored growth with clear dose-dependence. 2020 Molecules (Basel, Switzerland) Result IV S31N 69 73 M2 66 68 32599753 Virtual Screening Identifies Chebulagic Acid as an Inhibitor of the M2(S31N) Viral Ion Channel and Influenza A Virus. Discovery of Chebulagic Acid as a Candidate M2(S31N)Inhibitor by Virtual Screening. 2020 Molecules (Basel, Switzerland) Result IV S31N 47 51 M2 44 46 32599753 Virtual Screening Identifies Chebulagic Acid as an Inhibitor of the M2(S31N) Viral Ion Channel and Influenza A Virus. However, while the growth of the M2(S31N)-expressing yeast strain was not affected by the addition of up to 30 microM amantadine (i.e., restoring < 10% of yeast growth), incubation with 30 microM M2WJ352 induced an average of 27.1 +- 8.3% increased growth relative to untreated M2(S31N)-expressing cells (Figure 3A), consistent with the selective inhibition of M2(S31N) by M2WJ352 but not amantadine. 2020 Molecules (Basel, Switzerland) Result IV S31N;S31N;S31N 36;281;364 40;285;368 M2;M2;M2 33;278;361 35;280;363 32599753 Virtual Screening Identifies Chebulagic Acid as an Inhibitor of the M2(S31N) Viral Ion Channel and Influenza A Virus. In both cases (docking with P1 and P2), we observed that conformations with lower binding energies were observed when the ligand interacted with the S31N form of M2. 2020 Molecules (Basel, Switzerland) Result IV S31N 149 153 M2 162 164 32599753 Virtual Screening Identifies Chebulagic Acid as an Inhibitor of the M2(S31N) Viral Ion Channel and Influenza A Virus. In contrast, chebulagic acid inhibited both PR8M2(S31N) and PR8M2(S31) (EC50s = 60.9 +- 22.0 and 50.3 +- 26.4 microM, respectively). 2020 Molecules (Basel, Switzerland) Result IV S31N 50 54 32599753 Virtual Screening Identifies Chebulagic Acid as an Inhibitor of the M2(S31N) Viral Ion Channel and Influenza A Virus. In contrast, compound 8, a derivative of hexamethylene amiloride, inhibited 32% of M2(S31N)-dependent currents at 100 microM, but not M2(S31) currents, as measured by single electrode voltage clamp electrophysiology of M2-transfected HEK cells. 2020 Molecules (Basel, Switzerland) Result IV S31N 86 90 M2;M2;M2 83;134;219 85;136;221 32599753 Virtual Screening Identifies Chebulagic Acid as an Inhibitor of the M2(S31N) Viral Ion Channel and Influenza A Virus. In contrast, neither blocked more than 20% of M2(S31) currents at 100 microM, indicating selectivity for M2(S31N). 2020 Molecules (Basel, Switzerland) Result IV S31N 108 112 M2;M2 46;105 48;107 32599753 Virtual Screening Identifies Chebulagic Acid as an Inhibitor of the M2(S31N) Viral Ion Channel and Influenza A Virus. In the context of M2(S31N), these interactions would be predicted to disrupt proton flow across the H37 proton shuttle, thereby inhibiting M2(S31N). 2020 Molecules (Basel, Switzerland) Result IV S31N;S31N 21;142 25;146 M2;M2 18;139 20;141 32599753 Virtual Screening Identifies Chebulagic Acid as an Inhibitor of the M2(S31N) Viral Ion Channel and Influenza A Virus. Notably, in this assay chebulagic acid also inhibited cytopathic effects due to PR8M2(S31N) with an inhibitory concentration of 17.2 +- 15.2 but also inhibited cytopathic effects due to PR8M2(S31) (inhibitory concentration = 32.4 +- 24.7 microM; Table 2). 2020 Molecules (Basel, Switzerland) Result IV S31N 86 90 32599753 Virtual Screening Identifies Chebulagic Acid as an Inhibitor of the M2(S31N) Viral Ion Channel and Influenza A Virus. P1 and P2 were separately docked to both M2(S31N) and M2(S31), and the top-ranking poses for each docked complex with the tightest binding affinities were selected and analyzed. 2020 Molecules (Basel, Switzerland) Result IV S31N 44 48 M2;M2 41;54 43;56 32599753 Virtual Screening Identifies Chebulagic Acid as an Inhibitor of the M2(S31N) Viral Ion Channel and Influenza A Virus. Similarly, M2WJ352 selectively inhibited cytopathic effects in monolayers infected with PR8M2(S31N) (inhibitory concentration = 17.6 +- 19.3 microM; mean +- SD) but not PR8M2(S31) (inhibitory concentration > 100 microM). 2020 Molecules (Basel, Switzerland) Result IV S31N 94 98 32599753 Virtual Screening Identifies Chebulagic Acid as an Inhibitor of the M2(S31N) Viral Ion Channel and Influenza A Virus. Taken together, these results indicate non-selective antiviral activity by chebulagic acid against both M2(S31N) and M2(S31)-containing strains of influenza. 2020 Molecules (Basel, Switzerland) Result IV S31N 107 111 M2;M2 104;117 106;119 32599753 Virtual Screening Identifies Chebulagic Acid as an Inhibitor of the M2(S31N) Viral Ion Channel and Influenza A Virus. The enthalpic contributions to the free binding energies of binding (DeltaG) obtained from the Affinity dG scoring shown in Table 1 further suggested more favorable binding of P1 and P2 within M2(S31N)(DeltaG = -39.75 and -30.17 kcal/mol, respectively), when compared with binding to the S31 form. 2020 Molecules (Basel, Switzerland) Result IV S31N 196 200 M2 193 195 32599753 Virtual Screening Identifies Chebulagic Acid as an Inhibitor of the M2(S31N) Viral Ion Channel and Influenza A Virus. The six selected M2(S31N) inhibitors, used to identify potentially bioactive pharmacophores, were split in two based on the presence (compounds 3 to 6) or absence (compounds 7 and 8) of the adamantane ring system. 2020 Molecules (Basel, Switzerland) Result IV S31N 20 24 M2 17 19 32599753 Virtual Screening Identifies Chebulagic Acid as an Inhibitor of the M2(S31N) Viral Ion Channel and Influenza A Virus. These included M2WJ352 and M2WJ332 (compounds 3 and 4, respectively), which are reported to selectively inhibit M2(S31N), as measured by two-electrode voltage clamp (TEVC)-based electrophysiology (reported half-maximal inhibitor concentration (IC50) of M2 current = 14, and 16 microM, respectively). 2020 Molecules (Basel, Switzerland) Result IV S31N 115 119 M2;M2 112;253 114;255 32599753 Virtual Screening Identifies Chebulagic Acid as an Inhibitor of the M2(S31N) Viral Ion Channel and Influenza A Virus. These results suggest that a subset of compounds identified by VS might counteract the detrimental effects of M2(S31N) expression on yeast growth, where the activity of 25 microg/mL (~26.2 microM) chebulagic acid is on par with the activity of 30 microM M2WJ352. 2020 Molecules (Basel, Switzerland) Result IV S31N 113 117 M2 110 112 32599753 Virtual Screening Identifies Chebulagic Acid as an Inhibitor of the M2(S31N) Viral Ion Channel and Influenza A Virus. These results suggest that chebulagic acid hydrolysis fragments selectively interact with M2(S31N) and its H37 residue to occlude the M2(S31N) pore. 2020 Molecules (Basel, Switzerland) Result IV S31N;S31N 93;137 97;141 M2;M2 90;134 92;136 32599753 Virtual Screening Identifies Chebulagic Acid as an Inhibitor of the M2(S31N) Viral Ion Channel and Influenza A Virus. These results suggest that chebulagic acid restores growth in yeast cells selectively expressing M2(S31N). 2020 Molecules (Basel, Switzerland) Result IV S31N 100 104 M2 97 99 32599753 Virtual Screening Identifies Chebulagic Acid as an Inhibitor of the M2(S31N) Viral Ion Channel and Influenza A Virus. To confirm whether the observed selectivity of chebulagic acid to inhibit M2(S31N) extended to antiviral activities, we assessed the ability of chebulagic acid to inhibit influenza A virus replication. 2020 Molecules (Basel, Switzerland) Result IV S31N 77 81 M2 74 76 32599753 Virtual Screening Identifies Chebulagic Acid as an Inhibitor of the M2(S31N) Viral Ion Channel and Influenza A Virus. To identify shared pharmacophores that may underlie M2(S31N) inhibition, we assembled a series of adamantane and non-adamantane-based compounds that were previously reported to inhibit M2(S31N) bioactivities (Figure 1B,C). 2020 Molecules (Basel, Switzerland) Result IV S31N;S31N 55;188 59;192 M2;M2 52;185 54;187 32599753 Virtual Screening Identifies Chebulagic Acid as an Inhibitor of the M2(S31N) Viral Ion Channel and Influenza A Virus. To validate the use of this assay, we induced expression of M2(S31N) in yeast in the presence of the control M2(S31N) inhibitor M2WJ352 (compound 3) or control M2(S31) inhibitor amantadine (1). 2020 Molecules (Basel, Switzerland) Result IV S31N;S31N 63;112 67;116 M2;M2;M2 60;109;160 62;111;162 32599753 Virtual Screening Identifies Chebulagic Acid as an Inhibitor of the M2(S31N) Viral Ion Channel and Influenza A Virus. Using this approach, amantadine was observed to selectively inhibit cytopathic effects in MDCK monolayers due to PR8M2(S31) (minimal inhibitory concentration = 1.8 +- 2.3 microM) but not PR8M2(S31N) as expected (inhibitory concentration > 100 microM; Table 2). 2020 Molecules (Basel, Switzerland) Result IV S31N 193 197 32599753 Virtual Screening Identifies Chebulagic Acid as an Inhibitor of the M2(S31N) Viral Ion Channel and Influenza A Virus. We also selected compound 5, a benzodiol derivative, which was reported to block both M2(S31) and M2(S31N) currents in TEVC (IC50s = 60 and 35 microM, respectively) and viral replication in plaque reduction assays (EC50s = 1 and 3.2 microM). 2020 Molecules (Basel, Switzerland) Result IV S31N 101 105 M2;M2 86;98 88;100 32599753 Virtual Screening Identifies Chebulagic Acid as an Inhibitor of the M2(S31N) Viral Ion Channel and Influenza A Virus. We also selected two non-adamantane based compounds with reported activity against M2(S31N) (Figure 1C). 2020 Molecules (Basel, Switzerland) Result IV S31N 86 90 M2 83 85 32599753 Virtual Screening Identifies Chebulagic Acid as an Inhibitor of the M2(S31N) Viral Ion Channel and Influenza A Virus. We next assessed the ability of the 8 compounds identified from the VS to restore growth of M2(S31N)-expressing yeast at 25 microg/mL (Figure 3C). 2020 Molecules (Basel, Switzerland) Result IV S31N 95 99 M2 92 94 32599753 Virtual Screening Identifies Chebulagic Acid as an Inhibitor of the M2(S31N) Viral Ion Channel and Influenza A Virus. We used a previously described reverse genetic system to generate A/Puerto Rico/8/34 (PR8) strains that encode M2 exclusively with N31 or S31 (PR8M2(S31N) or PR8M2(S31), respectively). 2020 Molecules (Basel, Switzerland) Result IV S31N 149 153 M2 111 113 32601336 Pre-existing immunity to influenza virus hemagglutinin stalk might drive selection for antibody-escape mutant viruses in a human challenge model. A388V mutation induces a stalk conformational change that disrupts epitopes that bind different HA stalk monoclonal antibodies. 2020 Nature medicine Result IV A388V 0 5 HA 96 98 32601336 Pre-existing immunity to influenza virus hemagglutinin stalk might drive selection for antibody-escape mutant viruses in a human challenge model. Association between pre-existing human serum anti-HA stalk immunity and A388V mutant virus expansion in challenge study participants. 2020 Nature medicine Result IV A388V 72 77 HA 50 52 32601336 Pre-existing immunity to influenza virus hemagglutinin stalk might drive selection for antibody-escape mutant viruses in a human challenge model. Because HA stalk mutations have often been shown to decrease viral fitness, we investigated the fitness of the A388V mutation using H1N1pdm viruses with A388 or V388 generated using a reverse genetics system. 2020 Nature medicine Result IV A388V 111 116 HA 8 10 32601336 Pre-existing immunity to influenza virus hemagglutinin stalk might drive selection for antibody-escape mutant viruses in a human challenge model. FI6V3 showed the smallest reduction in binding of the bNAbs tested, suggesting that FI6V3 binding is less sensitive to the A388V mutation. 2020 Nature medicine Result IV A388V 123 128 32601336 Pre-existing immunity to influenza virus hemagglutinin stalk might drive selection for antibody-escape mutant viruses in a human challenge model. Given the reductions in antibody binding to this region, it is probable that the alpha-helix of the HA stalk, the target of all known stalk bNAbs, could bulge or rotate to accommodate the A388V mutation, resulting in structural changes. 2020 Nature medicine Result IV A388V 188 193 HA 100 102 32601336 Pre-existing immunity to influenza virus hemagglutinin stalk might drive selection for antibody-escape mutant viruses in a human challenge model. Human challenge with an HA A388V polymorphic virus. 2020 Nature medicine Result IV A388V 27 32 HA 24 26 32601336 Pre-existing immunity to influenza virus hemagglutinin stalk might drive selection for antibody-escape mutant viruses in a human challenge model. Increased resistance of the A388V mutant to bNAbs. 2020 Nature medicine Result IV A388V 28 33 32601336 Pre-existing immunity to influenza virus hemagglutinin stalk might drive selection for antibody-escape mutant viruses in a human challenge model. Lack of effect of A388V stalk mutation on viral replication fitness and clinical disease. 2020 Nature medicine Result IV A388V 18 23 32601336 Pre-existing immunity to influenza virus hemagglutinin stalk might drive selection for antibody-escape mutant viruses in a human challenge model. Structural modeling indicated that the A388V mutation does not interface directly with bNAbs but would likely cause steric clashes against the bulky aromatic side chains of W365 and Y366 on the beta-hairpin structure of the HA stalk. 2020 Nature medicine Result IV A388V 39 44 HA 224 226 32601336 Pre-existing immunity to influenza virus hemagglutinin stalk might drive selection for antibody-escape mutant viruses in a human challenge model. The A388V polymorphism had arisen spontaneously from the clonal starting virus (A388) during the six passages in certified Vero cells used for its GMP manufacture. 2020 Nature medicine Result IV A388V 4 9 32601336 Pre-existing immunity to influenza virus hemagglutinin stalk might drive selection for antibody-escape mutant viruses in a human challenge model. The effect of the A388V mutation on stalk epitopes was investigated by measuring binding levels of various bNAbs to full-length wild-type or mutant HAs. 2020 Nature medicine Result IV A388V 18 23 32601336 Pre-existing immunity to influenza virus hemagglutinin stalk might drive selection for antibody-escape mutant viruses in a human challenge model. To evaluate the effect of immune pressure on the selection of A388V mutant, wild-type and mutant viruses were mixed in different ratios (50:50 and 95:5) and cultured with or without immune pressure in vitro. 2020 Nature medicine Result IV A388V 62 67 32629810 Replication of a Dog-Origin H6N1 Influenza Virus in Cell Culture and Mice. Regardless what the PB1 729 residue was, once the influenza virus had the PB2 E627K mutation, the RNP activity could increase dramatically. 2020 Viruses Result IV E627K 78 83 PB1;PB2;RNP 20;74;98 23;77;101 32631440 Characterization of neuraminidase inhibitor-resistant influenza virus isolates from immunocompromised patients in the Republic of Korea. A/Korea/S0002/2019 had six amino acid differences (T13I, Q51K, F74S, H275Y, D416N, and T452I) relative to A/Brisbane/02/2018 (Table 4), while A/Korea/S0003/2019 had eight (T13I, I29M, P93S, I99V, H275Y, G298A, V321I, and V394I). 2020 Virology journal Result IV T13I;Q51K;F74S;H275Y;D416N;T452I;T13I;I29M;P93S;I99V;H275Y;G298A;V321I;V394I 51;57;63;69;76;87;172;178;184;190;196;203;210;221 55;61;67;74;81;92;176;182;188;194;201;208;215;226 32631440 Characterization of neuraminidase inhibitor-resistant influenza virus isolates from immunocompromised patients in the Republic of Korea. Other NA drug-resistance substitutions (V116A, I117V, Q136K, D151A, Y155H, R156K, D198V, I222V, R224K, Q226H, E227D, E277Q, R293K, N294S, E425G, and I436N) were not detected. 2020 Virology journal Result IV V116A;I117V;Q136K;D151A;Y155H;R156K;D198V;I222V;R224K;Q226H;E227D;E277Q;R293K;N294S;E425G;I436N 40;47;54;61;68;75;82;89;96;103;110;117;124;131;138;149 45;52;59;66;73;80;87;94;101;108;115;122;129;136;143;154 6 8 32631440 Characterization of neuraminidase inhibitor-resistant influenza virus isolates from immunocompromised patients in the Republic of Korea. The H275Y NA substitution (N1 numbering), associated with strong drug resistance, was observed in (GISAID: EPI1602908 and EPI1602906) of A(H1N1)pdm09 isolates from both immunocompromised patients. 2020 Virology journal Result IV H275Y 4 9 10 12 32636820 Enhanced Potency of a Broad H7N9-Neutralizing Antibody HNIgGA6 Through Structure-Based Design. A slight increase in binding affinity was observed with Y103R on HCDR3 and Y51R on HCDR2. 2020 Frontiers in microbiology Result IV Y103R;Y51R 56;75 61;79 32636820 Enhanced Potency of a Broad H7N9-Neutralizing Antibody HNIgGA6 Through Structure-Based Design. All four mutants were able to neutralize the H7N9-AH pseudovirus in a dose-dependent manner similar to wild-type HNIgGA6, and the S28H mutant had the most potent neutralizing activity. 2020 Frontiers in microbiology Result IV S28H 130 134 32636820 Enhanced Potency of a Broad H7N9-Neutralizing Antibody HNIgGA6 Through Structure-Based Design. As expected, both HNIgGA6 and its S28H variant conferred substantial protection of the mice. 2020 Frontiers in microbiology Result IV S28H 34 38 32636820 Enhanced Potency of a Broad H7N9-Neutralizing Antibody HNIgGA6 Through Structure-Based Design. As shown in Figure 3B, similar to its parent HNIgGA6, S28H neutralized most of the H7N9 strains from 2013 to 2017. 2020 Frontiers in microbiology Result IV S28H 54 58 32636820 Enhanced Potency of a Broad H7N9-Neutralizing Antibody HNIgGA6 Through Structure-Based Design. Based on the crystal structure of the HNIgGA6/HA1 complex, mutations at Y51R, D100E and Y103R in HCDRs and at S28H in LCDR1 were constructed. 2020 Frontiers in microbiology Result IV Y51R;D100E;Y103R;S28H 72;78;88;110 76;83;93;114 HA1 46 49 32636820 Enhanced Potency of a Broad H7N9-Neutralizing Antibody HNIgGA6 Through Structure-Based Design. Enhancement of the Neutralizing Potency for the S28H Variant. 2020 Frontiers in microbiology Result IV S28H 48 52 32636820 Enhanced Potency of a Broad H7N9-Neutralizing Antibody HNIgGA6 Through Structure-Based Design. Finally, the protective efficacy of the S28H mAb was tested. 2020 Frontiers in microbiology Result IV S28H 40 44 32636820 Enhanced Potency of a Broad H7N9-Neutralizing Antibody HNIgGA6 Through Structure-Based Design. Improvement of the in vivo Neutralization Potency of the S28H Variant. 2020 Frontiers in microbiology Result IV S28H 57 61 32636820 Enhanced Potency of a Broad H7N9-Neutralizing Antibody HNIgGA6 Through Structure-Based Design. In contrast, although local alveolar septa can be seen with mild widening, the overall lesion was significantly inhibited in the mice that were immunized with the S28H mAb. 2020 Frontiers in microbiology Result IV S28H 163 167 32636820 Enhanced Potency of a Broad H7N9-Neutralizing Antibody HNIgGA6 Through Structure-Based Design. In contrast, viral proliferation was substantially inhibited by the S28H mAb and the viral titres were reduced by more than three orders of magnitude (Figure 4A). 2020 Frontiers in microbiology Result IV S28H 68 72 32636820 Enhanced Potency of a Broad H7N9-Neutralizing Antibody HNIgGA6 Through Structure-Based Design. Passive immunization with either HNIgGA6 or S28H variant had lower pathology scores compared with the control group, while S28H showed stronger inhibition of lung lesions due to more potent H7N9-neutralizing activity (Figure 4C). 2020 Frontiers in microbiology Result IV S28H;S28H 44;123 48;127 Lung lesions 158 170 32636820 Enhanced Potency of a Broad H7N9-Neutralizing Antibody HNIgGA6 Through Structure-Based Design. Protection of H7N9-Infected Mice by Optimized S28H mAb. 2020 Frontiers in microbiology Result IV S28H 46 50 32636820 Enhanced Potency of a Broad H7N9-Neutralizing Antibody HNIgGA6 Through Structure-Based Design. Strikingly, when serine was substituted by histidine at position 28 in LCDR1, the mutated antibody exhibited a noticeable increase in binding affinity (KD is 5.48e-12 M), which was an approximately three-fold increase compared to HNIgGA6. 2020 Frontiers in microbiology Result IV S28H 17 67 32636820 Enhanced Potency of a Broad H7N9-Neutralizing Antibody HNIgGA6 Through Structure-Based Design. The IC50 value for the S28H mutant was 4.38 ng/ml, compared to 41.66 ng/ml for HNIgGA6, indicating that S28H has a 10-fold more potent neutralization potency in vitro (Figure 3A). 2020 Frontiers in microbiology Result IV S28H;S28H 23;104 27;108 32636820 Enhanced Potency of a Broad H7N9-Neutralizing Antibody HNIgGA6 Through Structure-Based Design. The neutralizing activity of S28H against other H7N9 strains was also tested. 2020 Frontiers in microbiology Result IV S28H 29 33 32636820 Enhanced Potency of a Broad H7N9-Neutralizing Antibody HNIgGA6 Through Structure-Based Design. To determine the in vivo neutralization potency of the S28H variant, six mice were passively immunized with HNIgGA6 or S28H mAb by intraperitoneal injection at a final concentration of 5 mg kg-1. 2020 Frontiers in microbiology Result IV S28H;S28H 55;119 59;123 32636820 Enhanced Potency of a Broad H7N9-Neutralizing Antibody HNIgGA6 Through Structure-Based Design. Together, these results demonstrated that HNIgGA6 and its S28H mutant substantially decreased the mortality and morbidity of mice infected with H7N9. 2020 Frontiers in microbiology Result IV S28H 58 62 32636820 Enhanced Potency of a Broad H7N9-Neutralizing Antibody HNIgGA6 Through Structure-Based Design. We found that the D100E mutant on HCDR3 had a much lower binding capacity to that of the wild-type HNIgGA6. 2020 Frontiers in microbiology Result IV D100E 18 23 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. 13 are optical images of A4-based lateral flow system after detection of influenza-positive nasopharyngeal swab samples in the absence or presence of I223R/H275Y influenza viruses, in which positive test lines were clearly observed in influenza-positive nasopharyngeal swab samples taken with various subtypes of I223R/H275Y influenza virus. 2020 Nature communications Result IV I223R;H275Y;I223R;H275Y 150;156;313;319 155;161;318;324 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. 3B displays the interaction between A4 antibody and pH1N1/H275Y mutant virus (107 PFU mL-1) by dot-blot analysis. 2020 Nature communications Result IV H275Y 58 63 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. 5 shows the binding affinities of I223R/H275Y NA with respect to the two kinds of mutant A4 antibodies (H94A and W33A mutant A4 antibodies). 2020 Nature communications Result IV I223R;H275Y;H94A;W33A 34;40;104;113 39;45;108;117 46 48 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. A monoclonal A4 antibody specifically recognizing I223R/H275Y NA over wt NA was developed using a biopanning protocol and a phage display library of fragment antigen bindings (Fabs) against I223R/H275Y NA. 2020 Nature communications Result IV I223R;H275Y;I223R;H275Y 50;56;190;196 55;61;195;201 NA;NA;NA 62;73;202 64;75;204 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. A4 was further characterized for its binding specificity to I223R/H275Y NA compared to wt NA using a dot-blot test by spotting different amounts of I223R/H275Y and wt NA proteins on a nitrocellulose (NC) membrane. 2020 Nature communications Result IV I223R;H275Y;I223R;H275Y 60;66;148;154 65;71;153;159 NA;NA;NA 72;90;167 74;92;169 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. A4-based colorimetric detection of I223R/H275Y virus. 2020 Nature communications Result IV I223R;H275Y 35;41 40;46 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. A4-based LFA of I223R/H275Y virus. 2020 Nature communications Result IV I223R;H275Y 16;22 21;27 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. A4-based SERS detection of I223R/H275Y virus. 2020 Nature communications Result IV I223R;H275Y 27;33 32;38 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. After the third and fourth rounds of panning, the enriched pool was screened for I223R/H275Y NA-specific binders. 2020 Nature communications Result IV I223R;H275Y 81;87 86;92 93 95 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. Among them, clone strongly bound to I223R/H275Y NA was selected and subjected to DNA sequencing, which confirmed the presence of unique clone. 2020 Nature communications Result IV I223R;H275Y 36;42 41;47 48 50 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. Application of A4 antibody to I223R/H275Y virus detection. 2020 Nature communications Result IV I223R;H275Y 30;36 35;41 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. As a consequence of the double mutations, on the other hand, the side-chain phenolic moiety of Tyr275 binds to the hydrophobic pocket in the A4-I223R/H275Y NA complex instead of Leu224. 2020 Nature communications Result IV I223R;H275Y 144;150 149;155 156 158 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. As the concentration of I223R/H275Y pH1N1 virus decreased, the detection signal in the test line gradually decreased from strong to weak. 2020 Nature communications Result IV I223R;H275Y 24;30 29;35 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. Because the current diagnosis in the hospital does not confirm the presence of antiviral drug resistance of influenza viruses, nasopharyngeal samples from patients with influenza-like symptoms were collected and mixed with I223R/H275Y pH1N1 virus (103 PFU). 2020 Nature communications Result IV I223R;H275Y 223;229 228;234 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. Besides the increase in the number of hydrogen bonds, the strengthening of hydrophobic interactions may also be invoked to explain the higher binding affinity of the A4-I223R/H275Y NA complex than the A4-wt NA counterpart. 2020 Nature communications Result IV I223R;H275Y 169;175 174;180 NA;NA 181;207 183;209 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. Binding of A4 antibody to I223R/H275Y NA protein. 2020 Nature communications Result IV I223R;H275Y 26;32 31;37 38 40 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. By combining the developed A4 antibody and SERS-based immunoassay, we could detect I223R/H275Y mutant virus as low as 1.5 PFU. 2020 Nature communications Result IV I223R;H275Y 83;89 88;94 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. Each round of panning included a subtraction step against wt NA followed by panning against I223R/H275Y NA to remove wt NA binders. 2020 Nature communications Result IV I223R;H275Y 92;98 97;103 NA;NA;NA 61;104;120 63;106;122 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. Even with 102 PFU of I223R/H275Y pH1N1 virus, the Abs580/Abs520 value was approximately 0.7. 2020 Nature communications Result IV I223R;H275Y 21;27 26;32 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. Figure 3a, b are the comparative view of the docking poses of A4 in the wt NA and I223R/H275Y NA. 2020 Nature communications Result IV I223R;H275Y 82;88 87;93 NA;NA 75;94 77;96 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. Figure 6a is the SERS-based immunoassay results for I223R/H275Y pH1N1 (blue spectrum) and wt pH1N1 (black spectrum). 2020 Nature communications Result IV I223R;H275Y 52;58 57;63 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. Figure 8a is an optical image of A4-based lateral flow systems after detection of influenza-positive nasopharyngeal swab samples in the absence of I223R/H275Y pH1N1 virus where only the control line was observed. 2020 Nature communications Result IV I223R;H275Y 147;153 152;158 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. First, A4 antibody was applied to the Au NPs to distinguish I223R/H275Y pH1N1 with wt pH1N1 in the naked eye. 2020 Nature communications Result IV I223R;H275Y 60;66 65;71 NP 41 44 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. For the comparison, I223R/H275Y pH1N1 (107 PFU mL-1) and wt NA were also examined. 2020 Nature communications Result IV H275Y;I223R 26;20 31;25 60 62 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. For the detection of influenza viruses, the immune substrates were reacted with I223R/H275Y pH1N1, wt pH1N1, or H275Y pH1N1, and then the immunoprobes were reacted. 2020 Nature communications Result IV I223R;H275Y;H275Y 80;86;112 85;91;117 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. For the development of A4 antibody specific to I223R/H275Y NA, we first prepared influenza virus subtype H1N1 NA proteins, i.e., drug-susceptible wt NA and oseltamivir- and zanamivir-resistant mutant I223R/H275Y NA. 2020 Nature communications Result IV I223R;H275Y;I223R;H275Y 47;53;200;206 52;58;205;211 NA;NA;NA;NA 59;110;149;212 61;112;151;214 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. For the SERS-based immunoassay of I223R/H275Y pH1N1 virus, Au nanoplate and Au NP were selected as immune substrate and immunoprobe, respectively. 2020 Nature communications Result IV I223R;H275Y 34;40 39;45 NP 79 81 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. H275Y mutation is the most frequently observed drug-resistant mutation. 2020 Nature communications Result IV H275Y 0 5 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. Importantly, even in the cases of high concentrations of wt pH1N1 virus (106 PFU) and H275Y virus (106 PFU), only the control line was observed in the absence of the I223R/H275Y pH1N1 virus. 2020 Nature communications Result IV H275Y;H275Y;I223R 86;172;166 91;177;171 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. In addition, the dose effect of I223R/H275Y detection in nasopharyngeal swab samples was demonstrated. 2020 Nature communications Result IV I223R;H275Y 32;38 37;43 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. In addition, we tested the recognition of single-mutant influenza NA protein (H275Y NA) using A4 antibody. 2020 Nature communications Result IV H275Y 78 83 NA;NA 66;84 68;86 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. In contrast, very weak SERS signals were obtained when the sample has wt pH1N1 or H275Y pH1N1, because A4 does not bind to the wt influenza virus or single-mutant virus. 2020 Nature communications Result IV H275Y 82 87 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. In the presence of I223R/H275Y pH1N1, color of A4-Au NPs changes from red to purple. 2020 Nature communications Result IV I223R;H275Y 19;25 24;30 NP 53 56 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. In this study, we developed an A4 antibody specifically recognizing and binding to the mutant I223R/H275Y NA and demonstrated that it is possible to directly detect antiviral multidrug-resistant viruses in various sensing platforms. 2020 Nature communications Result IV I223R;H275Y 94;100 99;105 106 108 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. Judging from the structural features derived with docking simulations, the higher binding affinity of I223R/H275Y NA to A4 than the wt NA may be attributed in a large part to the strengthening of the hydrogen-bond interactions in the antibody-epitope complex. 2020 Nature communications Result IV I223R;H275Y 102;108 107;113 NA;NA 114;135 116;137 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. LFA is easy to use, cost-effective, and can diagnose influenza viruses rapidly, therefore A4-based LFA system can be used for the practical diagnosis of I223R/H275Y pH1N1 in real world. 2020 Nature communications Result IV I223R;H275Y 153;159 158;164 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. No signal was observed in the test line for the sample containing only the wt pH1N1 virus (1 x 104 PFU) and not the I223R/H275Y pH1N1 virus. 2020 Nature communications Result IV I223R;H275Y 116;122 121;127 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. On the other hand, the red test lines were observed clearly after detection of influenza-positive nasopharyngeal swab samples in the presence of I223R/H275Y pH1N1 virus. 2020 Nature communications Result IV I223R;H275Y 145;151 150;156 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. On the other hand, the side-chain carboxylate ion of Glu100 and the two backbone amidic moieties of Asn30 and Ser31 in the heavy chain are involved in the hydrogen-bond stabilization of I223R/H275Y NA in CDR of A4. 2020 Nature communications Result IV I223R;H275Y 186;192 191;197 198 200 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. On the other hand, wt pH1N1 virus and H275Y pH1N1 virus are not able to interact with A4-Au NPs; thus a signal from the test line is not observed. 2020 Nature communications Result IV H275Y 38 43 NP 92 95 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. Previously, it has been reported that I223R/H275Y NA exhibits an overall loose structure with disturbed positions but with a local rearrangement of the compact array at the drug-binding site. 2020 Nature communications Result IV I223R;H275Y 38;44 43;49 50 52 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. Randomly selected clones were subjected to soluble Fab expression and screened by enzyme-linked immunosorbent assay (ELISA) for their binding affinity to I223R/H275Y NA. 2020 Nature communications Result IV I223R;H275Y 154;160 159;165 166 168 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. Second, SERS-based immunoassay for I223R/H275Y mutant virus was demonstrated by using A4 antibody. 2020 Nature communications Result IV I223R;H275Y 35;41 40;46 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. Similarly, the Kd value of I223R/H275Y NA increases from 3.50 to 150 nM in going from the wt to the W33A mutant in the heavy chain. 2020 Nature communications Result IV I223R;H275Y;W33A 27;33;100 32;38;104 39 41 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. The A4 antibody bound to H275Y NA in a concentration-dependent manner with Kd of 0.12 microM. 2020 Nature communications Result IV H275Y 25 30 31 33 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. The Abs580/Abs520 values exhibited a linear correlation with the I223R/H275Y pH1N1 virus concentration. 2020 Nature communications Result IV I223R;H275Y 65;71 70;76 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. The affinity and kinetics of the A4 binding interaction to I223R/H275Y NA was also determined by surface plasmon resonance (SPR). 2020 Nature communications Result IV I223R;H275Y 59;65 64;70 71 73 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. The antiviral-resistant I223R/H275Y pH1N1 virus reacts and binds to A4-Au NPs, and then the complex is captured by immobilized anti-influenza A nucleoprotein IgG on the test line, resulting in a positive signal. 2020 Nature communications Result IV I223R;H275Y 24;30 29;35 NP;NP 74;144 77;157 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. the approximately 600-fold tighter binding of A4 to I223R/H275Y NA than to wt NA. 2020 Nature communications Result IV I223R;H275Y 52;58 57;63 NA;NA 64;78 66;80 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. The binding affinities of the purified whole antibodies to I223R/H275Y NA protein were measured by ELISA. 2020 Nature communications Result IV I223R;H275Y 59;65 64;70 71 73 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. The binding free energy of the A4-I223R/H275Y NA complex is 1.8 kcal mol-1 lower than that of the A4-wt NA complex, which is in agreement with the higher binding affinity of the former than the latter. 2020 Nature communications Result IV I223R;H275Y 34;40 39;45 NA;NA 46;104 48;106 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. The calculated binding modes of the epitope models for wt NA and I223R/H275Y NA reveal the different patterns for complexation. 2020 Nature communications Result IV I223R;H275Y 65;71 70;76 NA;NA 58;77 60;79 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. the color of the A4-Au NP solution obviously changed from deep red to purple as the I223R/H275Y pH1N1 virus concentration increased because the A4-Au NPs aggregated owing to the binding interaction between A4 and the I223R/H275Y NA of the virus. 2020 Nature communications Result IV I223R;H275Y;I223R;H275Y 84;90;217;223 89;95;222;228 NA;NP;NP 229;23;150 231;25;153 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. The diagnostic efficiency and specificity of the A4-based LFA was further verified by treating a mixture of antiviral-susceptible wt pH1N1 and oseltamivir- and zanamivir-resistant I223R/H275Y pH1N1 viruses at various ratios under human nasal fluid conditions. 2020 Nature communications Result IV I223R;H275Y 180;186 185;191 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. The intensity of the dots corresponding to the binding interaction between I223R/H275Y NA and A4 was significantly stronger than that between wt NA and A4. 2020 Nature communications Result IV I223R;H275Y 75;81 80;86 NA;NA 87;145 89;147 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. The KI of I223R/H275Y NA for oseltamivir was significantly increased by 7500 times compared to that of wt NA due to the increase in the dissociation rate constant (koff) for oseltamivir (15-fold). 2020 Nature communications Result IV I223R;H275Y 10;16 15;21 NA;NA 22;106 24;108 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. The KI of I223R/H275Y NA for zanamivir was 22-fold greater than that of wt NA due to the reduced association rate constant (kon) and increased koff. 2020 Nature communications Result IV I223R;H275Y 10;16 15;21 NA;NA 22;75 24;77 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. The kon and koff of A4 to I223R/H275Y NA were 2.84 x 103 M-1 s-1 and 7.22 x 10-5 s-1, respectively; thus steady state affinity (KD) was determined to be 0.254 nM. 2020 Nature communications Result IV I223R;H275Y 26;32 31;37 38 40 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. The presence of wt pH1N1 virus and H275Y pH1N1 virus in the A4-Au NP reaction solutions caused little change in color or absorption spectral shift. 2020 Nature communications Result IV H275Y 35 40 NP 66 68 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. The results of mutational analyses are thus consistent with those of docking simulations indicating that the strengthening of hydrophobic interactions with aromatic side chains are responsible for tight binding of I223R/H275Y NA in the CDR of A4. 2020 Nature communications Result IV I223R;H275Y 214;220 219;225 226 228 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. The selected A4 antibody bound to I223R/H275Y NA in a concentration-dependent manner with Kd of 3.50 nM. 2020 Nature communications Result IV I223R;H275Y 34;40 39;45 46 48 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. The sensitivity of A4-based LFA for the detection of I223R/H275Y pH1N1 virus was tested at various virus concentrations (106-102 PFU), and positive signals were confirmed for samples containing 106, 105, 104, and 103 PFU of I223R/H275Y pH1N1 virus in a concentration-dependent manner. 2020 Nature communications Result IV H275Y;I223R;H275Y;I223R 59;53;230;224 64;58;235;229 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. The SERS-based immunoassay result for H275Y pH1N1 is shown in Supplementary. 2020 Nature communications Result IV H275Y 38 43 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. The signal from the test line was observed even in a mixed sample containing a high concentration of the wt pH1N1 virus (9 x 103 PFU) and a small concentration of the I223R/H275Y pH1N1 virus (1 x 103 PFU). 2020 Nature communications Result IV I223R;H275Y 167;173 172;178 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. The virus samples were prepared by mixing each of the I223R/H275Y influenza viruses (103 PFU) with influenza-positive nasopharyngeal swab samples (n = 6). 2020 Nature communications Result IV I223R;H275Y 54;60 59;65 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. Therefore, two lines in the test indicate the presence of I223R/H275Y pH1N1 virus. 2020 Nature communications Result IV I223R;H275Y 58;64 63;69 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. These results demonstrate that A4-based LFA has a high detection specificity depending on the dose of mutant I223R/H275Y pH1N1 virus even in the mixture with wt virus, with an LOD of 103 PFU per test. 2020 Nature communications Result IV I223R;H275Y 109;115 114;120 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. These results demonstrate that this A4-based LFA has a high detection specificity depending on the dose of I223R/H275Y pH1N1 virus, with an limit of detection (LOD) of 103 PFU per test. 2020 Nature communications Result IV I223R;H275Y 107;113 112;118 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. Third, A4-based LFA system was developed for the diagnosis of I223R/H275Y pH1N1. 2020 Nature communications Result IV I223R;H275Y 62;68 67;73 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. This indicates that the oseltamivir- and zanamivir-resistant I223R/H275Y pH1N1 virus can be detected directly by the naked eye using the A4-Au NPs. 2020 Nature communications Result IV I223R;H275Y 61;67 66;72 NP 143 146 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. This prompted us to develop various kinds of I223R/H275Y mutant virus-sensing methods by using A4 antibody as shown in. 2020 Nature communications Result IV I223R;H275Y 45;51 50;56 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. We designed an A4-based colorimetric assay to directly detect I223R/H275Y mutant virus in the naked eye. 2020 Nature communications Result IV I223R;H275Y 62;68 67;73 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. We found that the A4 antibody exhibited highly increased binding capacity to the I223R/H275Y mutant virus. 2020 Nature communications Result IV I223R;H275Y 81;87 86;92 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. We note that the mutation of A4 antibody at position 94 in the light chain from His to Ala leads to approximately 50-fold increase in the Kd value associated with binding of I223R/H275Y NA (183 nM). 2020 Nature communications Result IV I223R;H275Y 174;180 179;185 186 188 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. When the I223R/H275Y pH1N1 virus samples were applied, the red test lines were observed clearly. 2020 Nature communications Result IV H275Y;I223R 15;9 20;14 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. When the sample includes I223R/H275Y mutant virus, Au NPs on a nanoplate (NPs-on-plate) structures can be constructed through the immunoreaction of A4-I223R/H275Y pH1N1-HA. 2020 Nature communications Result IV I223R;H275Y;I223R;H275Y 25;31;151;157 30;36;156;162 HA;NP;NP 169;54;74 171;57;77 32677963 Influenza A virus NS1 optimises virus infectivity by enhancing genome packaging in a dsRNA-binding dependent manner. 293 T RIG-I KO cells were infected with PR8-delNS1 in the absence or presence of NS1 WT or NS1 R38A as in. 2020 Virology journal Result IV R38A 95 99 NS1;NS1 81;91 84;94 32677963 Influenza A virus NS1 optimises virus infectivity by enhancing genome packaging in a dsRNA-binding dependent manner. 293 T RIG-I KO cells were used to produce VLP in the absence or presence NS1 WT or NS1 R38A. 2020 Virology journal Result IV R38A 87 91 NS1;NS1 73;83 76;86 32677963 Influenza A virus NS1 optimises virus infectivity by enhancing genome packaging in a dsRNA-binding dependent manner. Based on RT-qPCR, the amount of vRNA isolated from VLP produced from NS1 R38A-expressing donor cells was reduced by approximately 2-fold, comparable with empty control cells. 2020 Virology journal Result IV R38A 73 77 NS1 69 72 32677963 Influenza A virus NS1 optimises virus infectivity by enhancing genome packaging in a dsRNA-binding dependent manner. but these effects were attenuated when complemented with NS1 R38A (infected cells. 2020 Virology journal Result IV R38A 61 65 32677963 Influenza A virus NS1 optimises virus infectivity by enhancing genome packaging in a dsRNA-binding dependent manner. For this, we examined the R38A mutant of NS1. 2020 Virology journal Result IV R38A 26 30 NS1 41 44 32677963 Influenza A virus NS1 optimises virus infectivity by enhancing genome packaging in a dsRNA-binding dependent manner. Immunoblotting analysis revealed that the control, NS1 WT and NS1 R38A-expressing donor cells had similar NP, HA and M1 protein levels (donor cells. 2020 Virology journal Result IV R38A 66 70 32677963 Influenza A virus NS1 optimises virus infectivity by enhancing genome packaging in a dsRNA-binding dependent manner. Incorporation of NS1 into the virion was also impaired by R38A mutation. 2020 Virology journal Result IV R38A 58 62 NS1 17 20 32677963 Influenza A virus NS1 optimises virus infectivity by enhancing genome packaging in a dsRNA-binding dependent manner. NS1 WT increased virion associated M1 and HA2, but NS1 R38A exhibited markedly reduced effects (purified virion. 2020 Virology journal Result IV R38A 55 59 32677963 Influenza A virus NS1 optimises virus infectivity by enhancing genome packaging in a dsRNA-binding dependent manner. Of note, NS1 incorporation in VLP from NS1 R38A-expressing cells was significantly reduced (purified VLP. 2020 Virology journal Result IV R38A 43 47 32677963 Influenza A virus NS1 optimises virus infectivity by enhancing genome packaging in a dsRNA-binding dependent manner. R38 located at helix 2 of the NS1 RBD and R38A mutation abolishes its dsRNA-binding ability. 2020 Virology journal Result IV R38A 42 46 NS1 30 33 32677963 Influenza A virus NS1 optimises virus infectivity by enhancing genome packaging in a dsRNA-binding dependent manner. Similarly, NS1 R38A failed to fully rescue the attenuation of PR8-delNS1. 2020 Virology journal Result IV R38A 15 19 NS1 11 14 32677963 Influenza A virus NS1 optimises virus infectivity by enhancing genome packaging in a dsRNA-binding dependent manner. The level of NP was slightly increased in VLP produced from donor cell expressing NS1 WT but not NS1 R38A (purified VLP. 2020 Virology journal Result IV R38A 101 105 32677963 Influenza A virus NS1 optimises virus infectivity by enhancing genome packaging in a dsRNA-binding dependent manner. VLP produced from NS1 R38A mutant-expressing donor cells exhibited significantly reduced luciferase activity. 2020 Virology journal Result IV R38A 22 26 NS1 18 21 32677963 Influenza A virus NS1 optimises virus infectivity by enhancing genome packaging in a dsRNA-binding dependent manner. VLP produced in the presence of NS1 WT or NS1 R38A was inoculated to recipient cells (293 T RIG-I KO cells) and luciferase activity was examined. 2020 Virology journal Result IV R38A 46 50 NS1;NS1 32;42 35;45 32677963 Influenza A virus NS1 optimises virus infectivity by enhancing genome packaging in a dsRNA-binding dependent manner. We examined the effects of NS1 R38A mutation in the VLP system. 2020 Virology journal Result IV R38A 31 35 NS1 27 30 32709116 Genetic Characterization of a Novel North American-Origin Avian Influenza A (H6N5) Virus Isolated from Bean Goose of South Korea in 2018. However, the E119V mutation in NA was detected in all H6N5 isolates, suggesting their susceptibility to neuraminidase inhibitors, such as Oseltamivir, Peramivir, and Zanamivir. 2020 Viruses Result IV E119V 13 18 NA;NA 31;104 33;117 32709116 Genetic Characterization of a Novel North American-Origin Avian Influenza A (H6N5) Virus Isolated from Bean Goose of South Korea in 2018. K6 and K17 were variable in certain molecular aspects, such as mutation at A274T of PB2, S375N/T of PB1, or V105M of NP, each contributing to the potentially increased virulence of K6 in mammals (Table 2). 2020 Viruses Result IV A274T;S375N;S375T;V105M 75;89;89;108 80;96;96;113 NP;PB1;PB2 117;100;84 119;103;87 32709116 Genetic Characterization of a Novel North American-Origin Avian Influenza A (H6N5) Virus Isolated from Bean Goose of South Korea in 2018. Particularly, one human host marker mutation, E382D, in the PA gene was observed in two new strains imported from North America (K6 and K17), although they were not displayed in two old H6N5 isolates from Korea (CN5 and W69), which had originated from Eurasia. 2020 Viruses Result IV E382D 46 51 PA 60 62 32714761 Structural Basis of Human Helicase DDX21 in RNA Binding, Unwinding, and Antiviral Signal Activation. A similar increase of ATP binding for DEAD mutants was observed in DEAD-box helicase elF-4A.[26] However, in contrast to the increase of ATP binding by Asp339His mutation, the Glu340Gly mutation lost the inter-domain interaction with Arg499 and His523 (Figure 3F). 2020 Advanced science (Weinheim, Baden-Wurttemberg, Germany) Result IV D339H;E340G 152;176 161;185 32714761 Structural Basis of Human Helicase DDX21 in RNA Binding, Unwinding, and Antiviral Signal Activation. As shown in Figure6A, the RNA-binding defective mutant of DDX21 (4R to A) was associated with less of NS1 while the DDX21 DEV mutant (Asp339His, Glu340Gly) could pull-down more NS1 protein than WT DDX21. 2020 Advanced science (Weinheim, Baden-Wurttemberg, Germany) Result IV D339H;E340G 134;145 143;154 NS1;NS1 102;177 105;180 32714761 Structural Basis of Human Helicase DDX21 in RNA Binding, Unwinding, and Antiviral Signal Activation. Finally, the "3R to A" mutant lost most of the unwinding activity, whereas the Asp321Ala mutant had comparable unwinding activity (Figure 5F). 2020 Advanced science (Weinheim, Baden-Wurttemberg, Germany) Result IV D321A 79 88 32714761 Structural Basis of Human Helicase DDX21 in RNA Binding, Unwinding, and Antiviral Signal Activation. Furthermore, the Asp339His/Glu340Gly mutant exhibited barely detectable ATPase activity, while mutation Ser375Leu/Ala376Glu still retained some degree of ATPase activity (Figure S6C,D, Supporting Information). 2020 Advanced science (Weinheim, Baden-Wurttemberg, Germany) Result IV E340G;A376E;D339H;S375L;D339E;D339G;S375A;S375E 27;114;17;104;17;17;104;104 36;123;26;113;26;26;113;113 32714761 Structural Basis of Human Helicase DDX21 in RNA Binding, Unwinding, and Antiviral Signal Activation. In contrast, the "8A" mutant and "7A" mutant (excluding R255A) retained comparable RNA-crosslinking activity with WT DDX21. 2020 Advanced science (Weinheim, Baden-Wurttemberg, Germany) Result IV R255A 56 61 32714761 Structural Basis of Human Helicase DDX21 in RNA Binding, Unwinding, and Antiviral Signal Activation. In contrast, the Asp339His/Glu340Gly had the highest RNA-crosslinking activity, while Ser375Leu/Ala376Glu kept only about half of the activity (Figure 5A,B). 2020 Advanced science (Weinheim, Baden-Wurttemberg, Germany) Result IV E340G;A376E;D339H;S375L;S375A;S375E 27;96;17;86;86;86 36;105;26;95;95;95 32714761 Structural Basis of Human Helicase DDX21 in RNA Binding, Unwinding, and Antiviral Signal Activation. On the contrary, when Asp321Ala mutant with increased RNA binding affinity was used, the inhibition was enhanced (Figure S8F, Supporting Information). 2020 Advanced science (Weinheim, Baden-Wurttemberg, Germany) Result IV D321A 22 31 32714761 Structural Basis of Human Helicase DDX21 in RNA Binding, Unwinding, and Antiviral Signal Activation. Similarly, Thr315Ala and Thr494Ala abolished the ATPase activity but negligibly affected RNA-crosslinking activity (Figure 5A and Figure S6, Supporting Information). 2020 Advanced science (Weinheim, Baden-Wurttemberg, Germany) Result IV T315A;T494A 11;25 20;34 32714761 Structural Basis of Human Helicase DDX21 in RNA Binding, Unwinding, and Antiviral Signal Activation. The "4R to A" and "8A" mutants had similar results as "3R to A" and "7A" mutants, respectively, indicating that Arg255Ala did not involve with the RNA binding and ATPase activity. 2020 Advanced science (Weinheim, Baden-Wurttemberg, Germany) Result IV R255A 112 121 32714761 Structural Basis of Human Helicase DDX21 in RNA Binding, Unwinding, and Antiviral Signal Activation. The increase of RNA-crosslinking of Asp339His/Glu340Gly might be caused by the formation of the new salt bridge with ATP phosphate and a new cooperative bond with Mg2+ ion by the His substitution (Figure 3F). 2020 Advanced science (Weinheim, Baden-Wurttemberg, Germany) Result IV E340G;D339H;D339E;D339G 46;36;36;36 55;45;45;45 32714761 Structural Basis of Human Helicase DDX21 in RNA Binding, Unwinding, and Antiviral Signal Activation. The mutants Asp339His, Glu340Gly, Ser375Leu, and Ala376Glu significantly reduced the ATPase activity of DDX21 (Figure S6C,D, Supporting Information). 2020 Advanced science (Weinheim, Baden-Wurttemberg, Germany) Result IV D339H;S375L;E340G;A376E 12;34;23;49 21;43;32;58 32714761 Structural Basis of Human Helicase DDX21 in RNA Binding, Unwinding, and Antiviral Signal Activation. The results showed that single point mutation Arg270Ala, Arg318Ala, Gln352Ala, or Arg476Ala led to the apparent loss of the RNA-crosslinking activity, but not so effective as illustrated in the previous study with Vasa protein.[20] Nonetheless, the "3R to A" mutant (Arg270Ala, Arg318Ala, and Arg476Ala) or "4R to A" mutant remarkably reduced the RNA binding affinity by more than half. 2020 Advanced science (Weinheim, Baden-Wurttemberg, Germany) Result IV R270A;R318A;Q352A;R476A;R270A;R318A;R476A 46;57;68;82;267;278;293 55;66;77;91;276;287;302 32714761 Structural Basis of Human Helicase DDX21 in RNA Binding, Unwinding, and Antiviral Signal Activation. They included Arg270Ala, Thr315Ala, Arg318Ala, Asp321Ala, Gln352Ala, Arg476Ala, Thr494Ala, "4R to A" mutant (namely Arg255Ala/Arg270Ala/Arg318Ala/Arg476Ala), "8A" mutant (the eight residues were all mutated to alanine), Asp339His and Glu340Gly (from the conserved DExD motif), Ser375Leu and Ala376Glu (from conserved SAT motif), and the del-loop mutant. 2020 Advanced science (Weinheim, Baden-Wurttemberg, Germany) Result IV R270A;R318A;R270A;R318A;R476A;T315A;D321A;Q352A;R476A;T494A;R255A;D339H;E340G;S375L;A376E 14;36;126;136;146;25;47;58;69;80;116;220;234;277;291 23;45;135;145;155;34;56;67;78;89;125;229;243;286;300 32714761 Structural Basis of Human Helicase DDX21 in RNA Binding, Unwinding, and Antiviral Signal Activation. This might result from the Asp321Ala mutation, which probably enhanced the RNA-crosslinking by the elimination of the electrostatic repulsion between the Asp321 side chain and the RNA phosphates. 2020 Advanced science (Weinheim, Baden-Wurttemberg, Germany) Result IV D321A 27 36 32721992 Differential Viral-Host Immune Interactions Associated with Oseltamivir-Resistant H275Y and Wild-Type H1N1 A(pdm09) Influenza Virus Pathogenicity. Viral sequences between F and R6 were compared and mutations PB2 225S, PB1 T20I, PB1 A652V, PA K716E, PA L589I, and PA S594G were found. 2020 Viruses Result IV T20I;A652V;K716E;L589I;S594G 75;85;95;105;119 79;90;100;110;124 PA;PA;PA;PB1;PB1;PB2 92;102;116;71;81;61 94;104;118;74;84;64 32746754 A single N342D substitution in Influenza B Virus NA protein determines viral pathogenicity in mice. As shown in Figure 7(A), position of 342 is located near the enzyme active sites at positions 274 and 294 in the NA structure, indicating that an N342D substitution might affect the neuraminidase activity. 2020 Emerging microbes & infections Result IV N342D 146 151 NA;NA 113;182 115;195 32746754 A single N342D substitution in Influenza B Virus NA protein determines viral pathogenicity in mice. Our data show that the neuraminidase enzyme activity of rAH127/NAN342D was higher than that of rAH127, and the half-maximal effective concentration (EC50) value of rAH127/NAN342D was ~21-fold lower than that of rAH127, whereas those of rAH127/PB1V212I and rAH127/HAA390E were similar to that of rAH12. 2020 Emerging microbes & infections Result IV V212I 246 251 HA;NA;NA;NA;PB1 263;63;171;23;243 265;65;173;36;246 32750468 Functional neuraminidase inhibitor resistance motifs in avian influenza A(H5Nx) viruses. All three mutant viruses replicated significantly faster when compared to wt H5N6 (N294S at 8, 24 and 48 h p.i, p < 0.001; R292K at 8 and 24 h p.i, p < 0.01; E119V at 24 h p.i., p < 0.01 and 48 h p.i., p < 0.05). 2020 Antiviral research Result IV N294S;R292K;E119V 83;123;158 88;128;163 32750468 Functional neuraminidase inhibitor resistance motifs in avian influenza A(H5Nx) viruses. and in the plaque reduction assay the H5N6_R292K virus showed a 40% reduction in plaque size (10 muM of ZAN) compared to no drug, giving the phenotype of HRI when compared to wt H5N6. 2020 Antiviral research Result IV R292K 43 48 32750468 Functional neuraminidase inhibitor resistance motifs in avian influenza A(H5Nx) viruses. Both HA mutants showed significantly reduced receptor binding avidity as compared to wt: the Y98F HA mutation (R292K virus) led to 94% reduction and the A189T HA mutation (N294S virus) to 95% reduction in binding avidity (both p < 0.01). 2020 Antiviral research Result IV Y98F;R292K;A189T;N294S 93;111;153;172 97;116;158;177 HA;HA;HA 5;98;159 7;100;161 32750468 Functional neuraminidase inhibitor resistance motifs in avian influenza A(H5Nx) viruses. For H5N6 wt and R292K viruses we used plaque reduction assay (PRA) and determined the EC50 value for each drug by measuring reduction in plaque size as response to the NAIs. 2020 Antiviral research Result IV R292K 16 21 NAI 168 172 32750468 Functional neuraminidase inhibitor resistance motifs in avian influenza A(H5Nx) viruses. H5N8_E119V and H5N8_H274Y viruses both displayed HRI for PER whereas H5N8_N294S showed a more modest RI to the drug. 2020 Antiviral research Result IV E119V;H274Y;N294S 5;20;74 10;25;79 32750468 Functional neuraminidase inhibitor resistance motifs in avian influenza A(H5Nx) viruses. In contrast to other viruses, E119V showed a small increase in titre between 10 and 24 h p.i. 2020 Antiviral research Result IV E119V 30 35 32750468 Functional neuraminidase inhibitor resistance motifs in avian influenza A(H5Nx) viruses. In the avian H5N8 NA sequences a single sequence with a mutation from E119 to a Glutamine (Q) and in the avian H5N2 sequences a single sequence with an Arginine (R) at position 274 instead of a Histidine (H) were observed. 2020 Antiviral research Result IV R274R 151 181 18 20 32750468 Functional neuraminidase inhibitor resistance motifs in avian influenza A(H5Nx) viruses. In the plaque reduction assay addition of 10 muM PER reduced the plaque size of the H5N6_R292K by approximately 40%, and thus resulted in HRI when compared to the 100% reduction in wt H5N6 virus (Figure 2L & O). 2020 Antiviral research Result IV R292K 89 94 32750468 Functional neuraminidase inhibitor resistance motifs in avian influenza A(H5Nx) viruses. It was not possible to determine the IC50 value by MUNANA assay for the H5N6 and H5N8 R292K mutant as the fluorescent signal generated using MUNANA did not reach the recommended threshold for signal-to-background ratio. 2020 Antiviral research Result IV R292K 86 91 32750468 Functional neuraminidase inhibitor resistance motifs in avian influenza A(H5Nx) viruses. None of the avian or human H5N6 carried E119V signature, however 4.3% of human and 1.9% of avian strains contained Aspartic acid (D) at this position, a mutation recently reported to confer pan-resistance to available NAIs in pH1N1. 2020 Antiviral research Result IV E119V 40 45 NAI 218 222 32750468 Functional neuraminidase inhibitor resistance motifs in avian influenza A(H5Nx) viruses. Surprisingly, the NA E119V mutant, despite lack of compensatory mutations in HA also exhibited decreased receptor binding avidity by ~55% (p < 0.05). 2020 Antiviral research Result IV E119V 21 26 HA;NA 77;18 79;20 32750468 Functional neuraminidase inhibitor resistance motifs in avian influenza A(H5Nx) viruses. The differences in virus titres for all three mutants (E119V, R292K and N294S) were non-significant (p > 0.05) as compared to wt H5N6 with exception of R292K at 24 hpi which replicated to significantly higher titres (p < 0.01). 2020 Antiviral research Result IV E119V;R292K;N294S;R292K 55;62;72;152 60;67;77;157 32750468 Functional neuraminidase inhibitor resistance motifs in avian influenza A(H5Nx) viruses. The E119V and H274Y NAs were expressed at lower levels compared to the wt NA (64% and 69% of wt, respectively. 2020 Antiviral research Result IV E119V;H274Y 4;14 9;19 32750468 Functional neuraminidase inhibitor resistance motifs in avian influenza A(H5Nx) viruses. The four most common NAI reduced susceptibility associated mutations in human influenza strains (H1N1 and H3N2) are E119V, H274Y, R292K and N294S (N2 NA subtype numbering). 2020 Antiviral research Result IV E119V;H274Y;R292K;N294S 116;123;130;140 121;128;135;145 NA;NAI 150;21 152;24 Influenza 72 87 32750468 Functional neuraminidase inhibitor resistance motifs in avian influenza A(H5Nx) viruses. The H5N2_R292K virus demonstrated RI to ZAN. 2020 Antiviral research Result IV R292K 9 14 32750468 Functional neuraminidase inhibitor resistance motifs in avian influenza A(H5Nx) viruses. The highest concentration of OSE (10 muM) completely abrogated plaque formation of wt H5N6, whereas no reduction in plaque size was observed for H5N6_R292K. 2020 Antiviral research Result IV R292K 150 155 32750468 Functional neuraminidase inhibitor resistance motifs in avian influenza A(H5Nx) viruses. The IC50 measurements made using the MUNANA assay for PER with the panel of H5N6 mutants did not show any alteration in susceptibility to the drug, and for the H5N2 panel only the R292K showed RI for PER. 2020 Antiviral research Result IV R292K 180 185 32750468 Functional neuraminidase inhibitor resistance motifs in avian influenza A(H5Nx) viruses. the median titres of H5N6_E119V and N294S viruses reached ~1 x 104 PFU/ml, which was ~2-log more than wt H5N6 and R292K, however the differences were non-significant. 2020 Antiviral research Result IV N294S;R292K;E119V 36;114;26 41;119;31 32750468 Functional neuraminidase inhibitor resistance motifs in avian influenza A(H5Nx) viruses. The OSE IC50 values for the E119V mutation in all three viruses demonstrated RI, the H274Y mutation resulted in RI for the H5N6 NA and HRI for the H5N8 NA, and N294S mutation showed RI only in H5N8 background. 2020 Antiviral research Result IV E119V;H274Y;N294S 28;85;160 33;90;165 NA;NA 128;152 130;154 32750468 Functional neuraminidase inhibitor resistance motifs in avian influenza A(H5Nx) viruses. The R292K mutation in H5N2 resulted in HRI for OSE. 2020 Antiviral research Result IV R292K 4 9 32750468 Functional neuraminidase inhibitor resistance motifs in avian influenza A(H5Nx) viruses. The R292K mutation reduced NA activity to 6% of the wt NA, N294S to 35%, E119V to 37% and H274Y to 45%. 2020 Antiviral research Result IV R292K;N294S;E119V;H274Y 4;59;73;90 9;64;78;95 NA;NA 27;55 29;57 32750468 Functional neuraminidase inhibitor resistance motifs in avian influenza A(H5Nx) viruses. The results of MUNANA assay with ZAN showed that E119V mutation conferred HRI only in H5N8 virus, N294S mutation led to RI in H5N6 and H5N2 backgrounds and H274Y substitution did not affect the susceptibility to ZAN in any of the H5Nx viruses. 2020 Antiviral research Result IV E119V;N294S;H274Y 49;98;156 54;103;161 32750468 Functional neuraminidase inhibitor resistance motifs in avian influenza A(H5Nx) viruses. Three H5N6 mutant viruses, E119V, N294S and R292K showed reduced susceptibility to at least one drug. 2020 Antiviral research Result IV E119V;N294S;R292K 27;34;44 32;39;49 32750468 Functional neuraminidase inhibitor resistance motifs in avian influenza A(H5Nx) viruses. Two H5N6 mutants acquired single amino acid substitutions in their HA following rescue and stock preparation in eggs: Y98F (H3 numbering) in the R292K NA mutant and A189T in N294S NA mutant virus. 2020 Antiviral research Result IV Y98F;R292K;A189T;N294S 118;145;165;174 122;150;170;179 HA;NA;NA 67;151;180 69;153;182 32750468 Functional neuraminidase inhibitor resistance motifs in avian influenza A(H5Nx) viruses. Two of these mutations, R292K and E119V, have also been reported in human isolated H7N9 viruses following NAI drug treatment. 2020 Antiviral research Result IV R292K;E119V 24;34 29;39 NAI 106 109 32750468 Functional neuraminidase inhibitor resistance motifs in avian influenza A(H5Nx) viruses. We identified H274Y substitution in 1 viral sequence (0.1%) and N294S in 3 sequences (0.2%) of the 1356 avian H5N6 isolates (Table 1). 2020 Antiviral research Result IV H274Y;N294S 14;64 19;69 32750468 Functional neuraminidase inhibitor resistance motifs in avian influenza A(H5Nx) viruses. We used partly desialylated cRBCs to explore the impact of Y98F and A189T mutations in H5N6 HA on receptor binding avidity. 2020 Antiviral research Result IV Y98F;A189T 59;68 63;73 HA 92 94 32750468 Functional neuraminidase inhibitor resistance motifs in avian influenza A(H5Nx) viruses. With the exception of H274Y mutation in human H1N1 viruses (HRI to OSE and PER) there is currently not enough data to correlate these categories of IC50 change to clinical implication for an infected host. 2020 Antiviral research Result IV H274Y 22 27 32750468 Functional neuraminidase inhibitor resistance motifs in avian influenza A(H5Nx) viruses. wt H5N6 together with two NAI-resistant mutants, R292K and N294S replicated to their highest titres between 4 x 107-1.5 x 108 PFU/ml. 2020 Antiviral research Result IV R292K;N294S 49;59 54;64 NAI 26 29 32873642 Dynamic PB2-E627K substitution of influenza H7N9 virus indicates the in vivo genetic tuning and rapid host adaptation. Different D701N Substitution Patterns Compared with E627K. 2020 Proc Natl Acad Sci U S A Result IV D701N;E627K 10;52 15;57 32873642 Dynamic PB2-E627K substitution of influenza H7N9 virus indicates the in vivo genetic tuning and rapid host adaptation. Differential Patterns of E627K Substitution in the H7N9 Viruses from Patients and LPMs. 2020 Proc Natl Acad Sci U S A Result IV E627K 25 30 32873642 Dynamic PB2-E627K substitution of influenza H7N9 virus indicates the in vivo genetic tuning and rapid host adaptation. It has been demonstrated that, in addition to E627K, the substitution of D701N in PB2 is also responsible for the higher virulence of AIV in mammals. 2020 Proc Natl Acad Sci U S A Result IV E627K;D701N 46;73 51;78 PB2 82 85 32873642 Dynamic PB2-E627K substitution of influenza H7N9 virus indicates the in vivo genetic tuning and rapid host adaptation. Our analysis of the correlation between the adaptation of H7N9 PB2-E627K and the patient outcomes revealed a rapid E627K substitution in the patients who died. 2020 Proc Natl Acad Sci U S A Result IV E627K;E627K 67;115 72;120 PB2 63 66 32873642 Dynamic PB2-E627K substitution of influenza H7N9 virus indicates the in vivo genetic tuning and rapid host adaptation. Rapid Adaptation of PB2-E627K Predicts a Fatal Outcome. 2020 Proc Natl Acad Sci U S A Result IV E627K 24 29 PB2 20 23 32929001 RNA-seq accuracy and reproducibility for the mapping and quantification of influenza defective viral genomes. As shown in Figure 4A,B, DVGs were overall more frequent and diverse for the mutants (red and orange) than for the WT (blue), and more markedly so for the PA-K635A mutant (red). 2020 RNA (New York, N.Y.) Result IV K635A 158 163 PA 155 157 32929001 RNA-seq accuracy and reproducibility for the mapping and quantification of influenza defective viral genomes. For example, if the 5' and 3' portion of the read maps to positions 110-160 and 1200-1270 in the reference genome, respectively, the alignment identifies that the read is spanning the junction of a deletion from position 160 to position 1200. 2020 RNA (New York, N.Y.) Result IV del 160 198 224 32929001 RNA-seq accuracy and reproducibility for the mapping and quantification of influenza defective viral genomes. The K635A and R638A mutations in PA were shown to weaken the interaction between the influenza polymerase and the carboxy-terminal domain of cellular RNA polymerase II largest subunit, and in an independent study the PA-R638A mutation was shown to promote the generation of DVGs. 2020 RNA (New York, N.Y.) Result IV K635A;R638A;R638A 4;14;220 9;19;225 PA;PA 33;217 35;219 32929001 RNA-seq accuracy and reproducibility for the mapping and quantification of influenza defective viral genomes. The PA-K635A mutant was the only virus for which, notably, DVGs were detected from every single segment upon RT-seq, with an overall frequency around 0.1 for the PB1, PB2, and PA segments, 0.01 for the HA, NP, and NA segments, and 0.001 for the M and NS segments. 2020 RNA (New York, N.Y.) Result IV K635A 7 12 HA;M;NA;NP;NS;PA;PA;PB1;PB2 202;245;214;206;251;4;176;162;167 204;246;216;208;253;6;178;165;170 32929001 RNA-seq accuracy and reproducibility for the mapping and quantification of influenza defective viral genomes. To assess the reproducibility of DVG analysis using the DG-seq pipeline, vRNAs were extracted from three stocks of recombinant A/WSN/33 virus: the wild-type (WT) virus and two PA mutants (K635A and R638A), produced by reverse genetics and submitted to one round of amplification on MDCK cells upon plaque purification. 2020 RNA (New York, N.Y.) Result IV K635A;R638A 188;198 193;203 PA 176 178 32929001 RNA-seq accuracy and reproducibility for the mapping and quantification of influenza defective viral genomes. Upon analysis of the vRNAs purified from the WT, PA-K635A, and PA-R638A viral stocks in Expt 1, 90%-100% of the DVGs detected with the ViReMa-based pipeline were also detected with DG-seq. 2020 RNA (New York, N.Y.) Result IV K635A;R638A 52;66 57;71 PA;PA 49;63 51;65 32929001 RNA-seq accuracy and reproducibility for the mapping and quantification of influenza defective viral genomes. We next characterized separately the DVGs found upon DG-seq analysis of vRNAs purified from the WT, PA-K635A and PA-R638A viral stocks in Expt 1 (Supplemental Table S3). 2020 RNA (New York, N.Y.) Result IV K635A;R638A 103;116 108;121 PA;PA 100;113 102;115 32962203 PA from a Recent H9N2 (G1-Like) Avian Influenza a Virus (AIV) Strain Carrying Lysine 367 Confers Altered Replication Efficiency and Pathogenicity to Contemporaneous H5N1 in Mammalian Systems. At 37 C, the reassortant H5N1PA-H9N2EGY and the mutant H5N1PA_R367K showed significant higher virus replication than the wild-type virus at 12-48 h p.t. 2020 Viruses Result IV R367K 63 68 32962203 PA from a Recent H9N2 (G1-Like) Avian Influenza a Virus (AIV) Strain Carrying Lysine 367 Confers Altered Replication Efficiency and Pathogenicity to Contemporaneous H5N1 in Mammalian Systems. Based on the fact that the initial infection and onward transmission of an influenza virus depends on efficient virus replication in the human respiratory tract, we tested the replication of the mutant H5N1PA_R367K versus the wild-type H5N1EGY in A549 (Figure 7b) and Calu-3 (Figure 7c) at two different temperature settings, 33 C and 39 C, representing the initial site of infection and the subsequent alveolar infection, respectively. 2020 Viruses Result IV R367K 209 214 32962203 PA from a Recent H9N2 (G1-Like) Avian Influenza a Virus (AIV) Strain Carrying Lysine 367 Confers Altered Replication Efficiency and Pathogenicity to Contemporaneous H5N1 in Mammalian Systems. Even though the pattern of body weight reduction was comparable between the H5N1EGY and H5N1PA_R367K, the H5N1EGY-infected mice started to gain weight at day 9 p.i. 2020 Viruses Result IV R367K 95 100 32962203 PA from a Recent H9N2 (G1-Like) Avian Influenza a Virus (AIV) Strain Carrying Lysine 367 Confers Altered Replication Efficiency and Pathogenicity to Contemporaneous H5N1 in Mammalian Systems. Here it showed that while all mice infected with H9N2EGY and H5N1PA-H9N2EGY_K367R survived, only 80% of H5N1PA-H9N2EGY-infected mice and 60% of H5N1EGY-infected mice survived. 2020 Viruses Result IV K367R 76 81 32962203 PA from a Recent H9N2 (G1-Like) Avian Influenza a Virus (AIV) Strain Carrying Lysine 367 Confers Altered Replication Efficiency and Pathogenicity to Contemporaneous H5N1 in Mammalian Systems. However, H5N1PA_R367K showed significant higher replication than the wild-type at 36 h p.i. 2020 Viruses Result IV R367K 16 21 32962203 PA from a Recent H9N2 (G1-Like) Avian Influenza a Virus (AIV) Strain Carrying Lysine 367 Confers Altered Replication Efficiency and Pathogenicity to Contemporaneous H5N1 in Mammalian Systems. In Calu-3 cells, comparable replication kinetics were observed for H5N1PA_R367K and H5N1EGY at 39 C. 2020 Viruses Result IV R367K 74 79 32962203 PA from a Recent H9N2 (G1-Like) Avian Influenza a Virus (AIV) Strain Carrying Lysine 367 Confers Altered Replication Efficiency and Pathogenicity to Contemporaneous H5N1 in Mammalian Systems. In the light of these data, we conclude that the improved replication efficiency of H5N1PA_R367K is not directly related to an enhanced polymerase activity. 2020 Viruses Result IV R367K 91 96 32962203 PA from a Recent H9N2 (G1-Like) Avian Influenza a Virus (AIV) Strain Carrying Lysine 367 Confers Altered Replication Efficiency and Pathogenicity to Contemporaneous H5N1 in Mammalian Systems. Interestingly, H5N1PA_R367K showed significant higher replication than the wild-type H5N1EGY in A549 cells at 12-24 h p.i. 2020 Viruses Result IV R367K 22 27 32962203 PA from a Recent H9N2 (G1-Like) Avian Influenza a Virus (AIV) Strain Carrying Lysine 367 Confers Altered Replication Efficiency and Pathogenicity to Contemporaneous H5N1 in Mammalian Systems. Most strikingly, all mice infected with H5N1PA_R367K died without exceeding the 25% body weight reduction limit. 2020 Viruses Result IV R367K 47 52 32962203 PA from a Recent H9N2 (G1-Like) Avian Influenza a Virus (AIV) Strain Carrying Lysine 367 Confers Altered Replication Efficiency and Pathogenicity to Contemporaneous H5N1 in Mammalian Systems. Replication Efficiency of H5N1PA_R367K Is Not Associated with an Enhanced Polymerase Activity. 2020 Viruses Result IV R367K 33 38 32962203 PA from a Recent H9N2 (G1-Like) Avian Influenza a Virus (AIV) Strain Carrying Lysine 367 Confers Altered Replication Efficiency and Pathogenicity to Contemporaneous H5N1 in Mammalian Systems. The mice demonstrated around 10-20% of weight loss after infection with the wild-type H5N1EGY and the corresponding H5N1PA_R367K mutant. 2020 Viruses Result IV R367K 123 128 32962203 PA from a Recent H9N2 (G1-Like) Avian Influenza a Virus (AIV) Strain Carrying Lysine 367 Confers Altered Replication Efficiency and Pathogenicity to Contemporaneous H5N1 in Mammalian Systems. The mice infected with H9N2EGY, H5N1PA-H9N2EGY and H5N1PA-H9N2EGY_K367R virus showed less than 5% of weight loss in the next 14 days p.i. 2020 Viruses Result IV K367R 66 71 32962203 PA from a Recent H9N2 (G1-Like) Avian Influenza a Virus (AIV) Strain Carrying Lysine 367 Confers Altered Replication Efficiency and Pathogenicity to Contemporaneous H5N1 in Mammalian Systems. The PA_R367K Contributes to the Pathogenicity of H5N1EGY in Mice. 2020 Viruses Result IV R367K 7 12 32962203 PA from a Recent H9N2 (G1-Like) Avian Influenza a Virus (AIV) Strain Carrying Lysine 367 Confers Altered Replication Efficiency and Pathogenicity to Contemporaneous H5N1 in Mammalian Systems. The reassortant H5N1PA-H9N2EGY_K367R demonstrated lower replication efficiency than the H5N1PA-H9N2EGY and H5N1PA_R367K viruses, but still higher than the H5N1EGY (Figure 7a). 2020 Viruses Result IV K367R;R367K 31;114 36;119 32962203 PA from a Recent H9N2 (G1-Like) Avian Influenza a Virus (AIV) Strain Carrying Lysine 367 Confers Altered Replication Efficiency and Pathogenicity to Contemporaneous H5N1 in Mammalian Systems. The results show that both the H5N1EGY PA_R367K and the H5N1EGY PA-H9N2EGY_K367R slightly improved the polymerase activity of the Renilla luciferase expression by the H5N1EGY vRNP with PA alterations, but not significantly when compared to the wild type H5N1EGY vRNP. 2020 Viruses Result IV R367K;K367R 42;75 47;80 PA;PA;PA 39;64;185 41;66;187 32962203 PA from a Recent H9N2 (G1-Like) Avian Influenza a Virus (AIV) Strain Carrying Lysine 367 Confers Altered Replication Efficiency and Pathogenicity to Contemporaneous H5N1 in Mammalian Systems. These data suggest that the R367K substitution alone in the PA of H5N1EGY could contribute to the enhanced mortality of H5N1PA_R367K in mice. 2020 Viruses Result IV R367K;R367K 28;127 33;132 PA 60 62 32962203 PA from a Recent H9N2 (G1-Like) Avian Influenza a Virus (AIV) Strain Carrying Lysine 367 Confers Altered Replication Efficiency and Pathogenicity to Contemporaneous H5N1 in Mammalian Systems. This indicates a possible improvement of the viral fitness of H5N1PA_R367K at the initial site of infection. 2020 Viruses Result IV R367K 69 74 32962203 PA from a Recent H9N2 (G1-Like) Avian Influenza a Virus (AIV) Strain Carrying Lysine 367 Confers Altered Replication Efficiency and Pathogenicity to Contemporaneous H5N1 in Mammalian Systems. To better understand the impact of lysine at position 367 in the PA of H9N2EGY, primary human bronchial epithelial (NHBE) cells were infected (MOI = 1) with wild-type H5N1EGY, H5N1PA_R367K and H5N1PA-H9N2EGY_K367R mutants and reassortant H5N1PA-H9N2EGY. 2020 Viruses Result IV R367K;K367R 183;208 188;213 PA 65 67 32962203 PA from a Recent H9N2 (G1-Like) Avian Influenza a Virus (AIV) Strain Carrying Lysine 367 Confers Altered Replication Efficiency and Pathogenicity to Contemporaneous H5N1 in Mammalian Systems. To examine the effect of R367K mutation in the H9N2EGY to the pathogenicity in mice, we intranasally infected 6 to 8-week-old healthy female BALB/c mice (10 mice in each group) with a lower infectious dose (103 PFU) in 30 microL PBS of the recombinant wild-type strains (H5N1EGY and H9N2EGY), the reassortant (H5N1PA-H9N2EGY), and the H5N1 expressing PAH5N1EGY_R367K (H5N1PA_R367K) or the mutated PAH9N2EGY_K367R (H5N1PA-H9N2EGY_K367R). 2020 Viruses Result IV R367K;R367K;R367K;K367R;K367R 25;361;375;407;429 30;366;380;412;434 32962203 PA from a Recent H9N2 (G1-Like) Avian Influenza a Virus (AIV) Strain Carrying Lysine 367 Confers Altered Replication Efficiency and Pathogenicity to Contemporaneous H5N1 in Mammalian Systems. To investigate whether the improved replication efficiency of H5N1PA_R367K in mammalian cell culture models is linked to an improved polymerase activity, we further examined and compared the effect of the PA mutations in a mini-genome reporter assay using plasmids expressing the three subunits (PB2, PB1, PA) of the viral RNA-dependent RNA polymerase (RdRp) and the viral nucleoprotein (NP) of H5N1EGY or H9N2EGY (controls) or combinations of H5N1EGY PB2, PB1 and NP with mutated PA of H5N1EGY (PA_R367K) or of H9N2EGY (PA-H9N2EGY_K367R), as well as wild-type PA of H9N2EGY (PA-H9N2EGY). 2020 Viruses Result IV R367K;R367K;K367R 69;499;532 74;504;537 NP;NP;NP;PA;PA;PA;PA;PA;PA;PA;PB1;PB1;PB2;PB2 388;465;373;205;306;481;496;521;561;576;301;457;296;452 390;467;386;207;308;483;498;523;563;578;304;460;299;455 32962203 PA from a Recent H9N2 (G1-Like) Avian Influenza a Virus (AIV) Strain Carrying Lysine 367 Confers Altered Replication Efficiency and Pathogenicity to Contemporaneous H5N1 in Mammalian Systems. Unlike Q591K, the impact of the R367K substitution in the PA on the replication efficiency, polymerase activity and virulence of H5N1 strains has not been characterized yet. 2020 Viruses Result IV Q591K;R367K 7;32 12;37 PA 58 60 33024040 Structure-Based Modification of an Anti-neuraminidase Human Antibody Restores Protection Efficacy against the Drifted Influenza Virus. and the binding affinity of Z2B3-D102R to 18N1 (K432) decreased 3.07-fold compared with that of wild-type Z2B3 to 18N1. 2020 mBio Result IV D102R 33 38 33024040 Structure-Based Modification of an Anti-neuraminidase Human Antibody Restores Protection Efficacy against the Drifted Influenza Virus. Antiviral activity of Z2B3 and the D102R variant in vitro. 2020 mBio Result IV D102R 35 40 33024040 Structure-Based Modification of an Anti-neuraminidase Human Antibody Restores Protection Efficacy against the Drifted Influenza Virus. but could not bind to N1 from A/Serbia/NS-601/2014 H1N1 virus containing the K432E substitution (Serbia N1). 2020 mBio Result IV K432E 77 82 NS 39 41 33024040 Structure-Based Modification of an Anti-neuraminidase Human Antibody Restores Protection Efficacy against the Drifted Influenza Virus. In contrast, Z2B3-D102R regained an inhibitory effect against viral growth (IC50, 6.009 mug/ml). 2020 mBio Result IV D102R 18 23 33024040 Structure-Based Modification of an Anti-neuraminidase Human Antibody Restores Protection Efficacy against the Drifted Influenza Virus. In the prophylactic groups, mice treated with 5 mg/kg or 10 mg/kg of Z2B3-D102R showed 100% protection, while mice treated with the same dose of Z2B3 displayed no protection. 2020 mBio Result IV D102R 74 79 33024040 Structure-Based Modification of an Anti-neuraminidase Human Antibody Restores Protection Efficacy against the Drifted Influenza Virus. In the therapeutic groups, mice treated with 10 mg/kg or 20 mg/kg of Z2B3-D102R showed 80% and 100% survival, respectively, while neither counterpart doses of Z2B3 provided any protection. 2020 mBio Result IV D102R 74 79 33024040 Structure-Based Modification of an Anti-neuraminidase Human Antibody Restores Protection Efficacy against the Drifted Influenza Virus. It is not unexpected that the in vitro growth of diverse virus strains with K432 in NA, including CA/09, PR/34, and VN/04 viruses, was more effectively inhibited by Z2B3 than by Z2B3-D102R (Table 1). 2020 mBio Result IV D102R 183 188 84 86 33024040 Structure-Based Modification of an Anti-neuraminidase Human Antibody Restores Protection Efficacy against the Drifted Influenza Virus. On the other hand, 18N1 and Z2B3-D102R cannot survive in gel filtration. 2020 mBio Result IV D102R 33 38 33024040 Structure-Based Modification of an Anti-neuraminidase Human Antibody Restores Protection Efficacy against the Drifted Influenza Virus. Prophylactic and therapeutic efficiencies of Z2B3 antibody and the D102R variant. 2020 mBio Result IV D102R 67 72 33024040 Structure-Based Modification of an Anti-neuraminidase Human Antibody Restores Protection Efficacy against the Drifted Influenza Virus. Prophylactic and therapeutic studies were performed to explore the protection efficacy of both Z2B3 and Z2B3-D102R against challenge with different viruses in vivo. 2020 mBio Result IV D102R 109 114 33024040 Structure-Based Modification of an Anti-neuraminidase Human Antibody Restores Protection Efficacy against the Drifted Influenza Virus. The complex structure of Serbia N1 and Z2B3-D102R further demonstrated that a salt bridge was formed between the E432 of Serbia N1 and R102 of Z2B3-D102R as expected. 2020 mBio Result IV D102R;D102R 44;148 49;153 33024040 Structure-Based Modification of an Anti-neuraminidase Human Antibody Restores Protection Efficacy against the Drifted Influenza Virus. The MUNANA-based NA inhibition assay showed that both Z2B3 and Z2B3-D102R inhibit NA activity of the 18N1 protein, with 50% inhibitory concentrations (IC50s) of 118 and 386 nM, respectively. 2020 mBio Result IV D102R 68 73 NA;NA 17;82 19;84 33024040 Structure-Based Modification of an Anti-neuraminidase Human Antibody Restores Protection Efficacy against the Drifted Influenza Virus. The NA inhibition ability of Z2B3 and Z2B3-D102R displayed the same trend in the virus level (Table 1). 2020 mBio Result IV D102R 43 48 4 6 33024040 Structure-Based Modification of an Anti-neuraminidase Human Antibody Restores Protection Efficacy against the Drifted Influenza Virus. These data suggested that Z2B3 and Z2B3-D102R were able to inhibit virus yield in vitro and implicated their potential for protection in vivo. 2020 mBio Result IV D102R 40 45 33024040 Structure-Based Modification of an Anti-neuraminidase Human Antibody Restores Protection Efficacy against the Drifted Influenza Virus. These results indicate that D102R substitution could restore the protection by Z2B3 against A/Serbia/NS-601/2014 virus, which was in agreement with the restored inhibition of NA enzymatic activity and viral replication in vitro. 2020 mBio Result IV D102R 28 33 NA;NS 175;101 177;103 33024040 Structure-Based Modification of an Anti-neuraminidase Human Antibody Restores Protection Efficacy against the Drifted Influenza Virus. To investigate the protective efficacy of Z2B3-D102R antibody to A/Serbia/NS-601/2014 virus (with E432), we treated the DBA/2 mice with Z2B3-D102R 24 hours prior to intranasal infection in prophylactic study and 12 hours after intranasal infection in the therapeutic experiment. 2020 mBio Result IV D102R;D102R 47;141 52;146 NS 74 76 33024040 Structure-Based Modification of an Anti-neuraminidase Human Antibody Restores Protection Efficacy against the Drifted Influenza Virus. To test this hypothesis, we modified the antibody Z2B3 with D102R in the heavy chain and then purified the mutant antibody (Z2B3-D102R) in the baculoviral expression system. 2020 mBio Result IV D102R;D102R 60;129 65;134 33024040 Structure-Based Modification of an Anti-neuraminidase Human Antibody Restores Protection Efficacy against the Drifted Influenza Virus. Z2B3 with D102R may enable the binding of N1 with negatively charged E432. 2020 mBio Result IV D102R 10 15 33024040 Structure-Based Modification of an Anti-neuraminidase Human Antibody Restores Protection Efficacy against the Drifted Influenza Virus. Z2B3-D102R dramatically restored inhibition activity to Serbia N1, with an IC50 of 116 nM. 2020 mBio Result IV D102R 5 10 33028722 PA Mutations Inherited during Viral Evolution Act Cooperatively To Increase Replication of Contemporary H5N1 Influenza Virus with an Expanded Host Range. Ancestral D1/PA-wt and the EG13G18E/R388S/E448A reverse mutant caused only a limited inflammatory response in the lungs of infected mice. 2020 Journal of virology Result IV R388S;E448A 36;42 41;47 PA 13 15 33028722 PA Mutations Inherited during Viral Evolution Act Cooperatively To Increase Replication of Contemporary H5N1 Influenza Virus with an Expanded Host Range. As with most clade 2.2.1 viruses, both the EG13 and D1 viruses carry the PB2-E627K mutation. 2020 Journal of virology Result IV E627K 77 82 PB2 73 76 33028722 PA Mutations Inherited during Viral Evolution Act Cooperatively To Increase Replication of Contemporary H5N1 Influenza Virus with an Expanded Host Range. Based on the effects of the single mutations, we selected three PA substitutions (i.e., E18G, S388R, and A448E) for further study to investigate whether they might act cooperatively on polymerase activity. 2020 Journal of virology Result IV E18G;S388R;A448E 88;94;105 92;99;110 PA 64 66 33028722 PA Mutations Inherited during Viral Evolution Act Cooperatively To Increase Replication of Contemporary H5N1 Influenza Virus with an Expanded Host Range. D1/PAA448E/S388R and D1/PAA448E/S388R/E18G had MLD50 values of 1.8 x 102 FFU and 1.0 x 102 FFU, respectively, which were >2 logs lower than that of wild-type D1/PA. 2020 Journal of virology Result IV S388R;S388R;E18G 11;32;38 16;37;42 PA;PA;PA 3;24;161 5;26;163 33028722 PA Mutations Inherited during Viral Evolution Act Cooperatively To Increase Replication of Contemporary H5N1 Influenza Virus with an Expanded Host Range. Effect of the PA-A448E, -S388R, and -E18G mutations on the replication and virulence of clade 2.2.1 viruses in vivo in mice. 2020 Journal of virology Result IV A448E;S388R;E18G 17;25;37 22;30;41 PA 14 16 33028722 PA Mutations Inherited during Viral Evolution Act Cooperatively To Increase Replication of Contemporary H5N1 Influenza Virus with an Expanded Host Range. Effect of the PA-A448E, -S388R, and -E18G mutations on the replication of clade 2.2.1.2 viruses in human cells. 2020 Journal of virology Result IV A448E;S388R;E18G 17;25;37 22;30;41 PA 14 16 33028722 PA Mutations Inherited during Viral Evolution Act Cooperatively To Increase Replication of Contemporary H5N1 Influenza Virus with an Expanded Host Range. In addition, the E18G strain-specific mutations had a collateral effect on the increase of EG13 polymerase activity. 2020 Journal of virology Result IV E18G 17 21 33028722 PA Mutations Inherited during Viral Evolution Act Cooperatively To Increase Replication of Contemporary H5N1 Influenza Virus with an Expanded Host Range. In contrast, in the D1 background, the E18G, S388R, and A448E forward mutations each increased the polymerase activity by up to >1 log in human cells at 33 C, but the increase was greater with the reassorted EG13 PA subunit that was included as a control (denoted D1-EG13/PA here). 2020 Journal of virology Result IV E18G;S388R;A448E 39;45;56 43;50;61 PA;PA 213;272 215;274 33028722 PA Mutations Inherited during Viral Evolution Act Cooperatively To Increase Replication of Contemporary H5N1 Influenza Virus with an Expanded Host Range. In contrast, the EG13G18E/R388S/E448A reverse mutant replicated with an appreciably lower titer in the mouse lungs. 2020 Journal of virology Result IV R388S;E448A 26;32 31;37 33028722 PA Mutations Inherited during Viral Evolution Act Cooperatively To Increase Replication of Contemporary H5N1 Influenza Virus with an Expanded Host Range. In contrast, the same dose of PA carrying the forward mutants caused dramatic weight loss: 3 of 6 mice infected with D1/PAA448E survived, and none of the 6 mice infected with D1/PAA448E/S388R or D1/PAA448E/S388R/E18G survived, with death being faster for D1/PAA448E/S388R/E18G-infected mice than for D1/PAA448E/S388R-infected mice. 2020 Journal of virology Result IV S388R;S388R;E18G;E18G;S388R;S388R 186;206;212;272;266;311 191;211;216;276;271;316 PA;PA;PA;PA;PA;PA 30;120;178;198;258;303 32;122;180;200;260;305 33028722 PA Mutations Inherited during Viral Evolution Act Cooperatively To Increase Replication of Contemporary H5N1 Influenza Virus with an Expanded Host Range. In the apo form of the polymerase complex (PDB accession number 6QPF as the modeling template), our model indicated that PA-A448E, located on helix alpha16, created a hydrogen bond to PA-N444. 2020 Journal of virology Result IV A448E 124 129 PA;PA 121;184 123;186 33028722 PA Mutations Inherited during Viral Evolution Act Cooperatively To Increase Replication of Contemporary H5N1 Influenza Virus with an Expanded Host Range. In the EG13 background, the G18E, R388S, and E448A reverse mutations each decreased the polymerase activity, although the decrease was greatest with the reassorted D1/PA (denoted EG13-D1/PA here) that was included as a control. 2020 Journal of virology Result IV G18E;R388S;E448A 28;34;45 32;39;50 PA;PA 167;187 169;189 33028722 PA Mutations Inherited during Viral Evolution Act Cooperatively To Increase Replication of Contemporary H5N1 Influenza Virus with an Expanded Host Range. In the transcription preinitiation form (PDB accession number 6RR7 as the modeling template), A448E, S388R, and E18G were located on the outer side of the polymerase complex. 2020 Journal of virology Result IV A448E;S388R;E18G 94;101;112 99;106;116 33028722 PA Mutations Inherited during Viral Evolution Act Cooperatively To Increase Replication of Contemporary H5N1 Influenza Virus with an Expanded Host Range. indicating a limited ability of the virus carrying PB2-E627K to replicate in mice: the 50% mouse lethal dose (MLD50) was 2.5 x 104 FFU, which was in agreement with the MLD50 of ancestral clade 2.2.1 viruses reported previously. 2020 Journal of virology Result IV E627K 55 60 PB2 51 54 33028722 PA Mutations Inherited during Viral Evolution Act Cooperatively To Increase Replication of Contemporary H5N1 Influenza Virus with an Expanded Host Range. Multiple mutations were combined in their putative phylogenetic order, i.e., the G18E, R388S, and E448A reverse mutations and the A448E, S388R, and E18G forward mutations. 2020 Journal of virology Result IV G18E;R388S;E448A;A448E;S388R;E18G 81;87;98;130;137;148 85;92;103;135;142;152 33028722 PA Mutations Inherited during Viral Evolution Act Cooperatively To Increase Replication of Contemporary H5N1 Influenza Virus with an Expanded Host Range. PA forward mutants replicated more efficiently in the mouse lungs, with titers of D1/PAA448E/S388R(/E18G) being comparable to those of contemporary EG13. 2020 Journal of virology Result IV S388R;E18G 93;100 98;104 PA;PA 0;85 2;87 33028722 PA Mutations Inherited during Viral Evolution Act Cooperatively To Increase Replication of Contemporary H5N1 Influenza Virus with an Expanded Host Range. PA with the triple reverse mutation G18E/R388S/E448A (denoted EG13G18E/R388S/E448A here) had the lowest progeny virus yield in both cell lines, in particular by >2 logs in human cells at early times postinfection at 33 C, with the R388S/E448A mutation producing the greatest effect. 2020 Journal of virology Result IV G18E;R388S;E448A;R388S;E448A;R388S;E448A;G18E 36;41;47;71;77;231;237;66 40;46;52;76;82;236;242;70 PA 0 2 33028722 PA Mutations Inherited during Viral Evolution Act Cooperatively To Increase Replication of Contemporary H5N1 Influenza Virus with an Expanded Host Range. PA-E18 was located on helix alpha2 and contacted PA-R6 on the apposed helix alpha1, but the E18G substitution obviated this interaction, probably reducing structural stability at this position. 2020 Journal of virology Result IV E18G 92 96 PA;PA 0;49 2;51 33028722 PA Mutations Inherited during Viral Evolution Act Cooperatively To Increase Replication of Contemporary H5N1 Influenza Virus with an Expanded Host Range. The EG13-wt contemporary virus had a highly virulent phenotype, with an MLD50 of 7.0 x 100 FFU, whereas the EG13G18E/R388S/E448A reverse mutant had a markedly attenuated phenotype, with an MLD50 of 3.3 x 105 FFU. 2020 Journal of virology Result IV R388S;E448A 117;123 122;128 33028722 PA Mutations Inherited during Viral Evolution Act Cooperatively To Increase Replication of Contemporary H5N1 Influenza Virus with an Expanded Host Range. The most severe pathological changes were detected in the lungs of mice infected with D1/PAA448E/S388R(/E18G) or EG13-wt. 2020 Journal of virology Result IV S388R;E18G 97;104 102;108 PA 89 91 33028722 PA Mutations Inherited during Viral Evolution Act Cooperatively To Increase Replication of Contemporary H5N1 Influenza Virus with an Expanded Host Range. The PA-E18G, -S388R, and -A448E mutations act cooperatively to increase the polymerase activity of clade 2.2.1.2 viruses. 2020 Journal of virology Result IV E18G;S388R;A448E 7;14;26 11;19;31 PA 4 6 33028722 PA Mutations Inherited during Viral Evolution Act Cooperatively To Increase Replication of Contemporary H5N1 Influenza Virus with an Expanded Host Range. The polymerase with the G18E/R388S/E448A triple mutation had the lowest activity, with a level similar to that of EG13-D1/PA: the R388S/E448A double mutation produced the greatest reduction in polymerase activity. 2020 Journal of virology Result IV R388S;E448A;G18E;R388S;E448A 29;35;24;130;136 34;40;28;135;141 PA 122 124 33028722 PA Mutations Inherited during Viral Evolution Act Cooperatively To Increase Replication of Contemporary H5N1 Influenza Virus with an Expanded Host Range. The R388S/E448A reverse mutations were also included in this study because they were associated with the high polymerase activity in ancestral clade 2.2.1 viruses described below. 2020 Journal of virology Result IV R388S;E448A 4;10 9;15 33028722 PA Mutations Inherited during Viral Evolution Act Cooperatively To Increase Replication of Contemporary H5N1 Influenza Virus with an Expanded Host Range. The relative polymerase activities were D1-wt < A448E < A448E/S388R < A448E/S388R/E18G. 2020 Journal of virology Result IV A448E;A448E;S388R;S388R;A448E;E18G 48;56;62;76;70;82 53;61;67;81;75;86 33028722 PA Mutations Inherited during Viral Evolution Act Cooperatively To Increase Replication of Contemporary H5N1 Influenza Virus with an Expanded Host Range. The relative polymerase activities were wild-type EG13 (EG13-wt) > G18E > G18E/R388S > R388S/E448A > G18E/R388S/E448A. 2020 Journal of virology Result IV G18E;R388S;G18E;R388S;E448A;R388S;E448A;G18E 67;79;74;87;93;106;112;101 71;84;78;92;98;111;117;105 33028722 PA Mutations Inherited during Viral Evolution Act Cooperatively To Increase Replication of Contemporary H5N1 Influenza Virus with an Expanded Host Range. The S388R/E448A/G18E triple mutation had the highest polymerase activity, with a level comparable to that of D1-EG13/PA: the greatest increase was produced by the S388R/A448E mutation. 2020 Journal of virology Result IV G18E;E448A;S388R;S388R;A448E 16;10;4;163;169 20;15;9;168;174 PA 117 119 33028722 PA Mutations Inherited during Viral Evolution Act Cooperatively To Increase Replication of Contemporary H5N1 Influenza Virus with an Expanded Host Range. The triple mutant D1/PAA448E/S388E/E18G had the greatest progeny virus yield in both cells: D1/PA-wt < A448E < A448E/S388R < A448E/S388R/E18G, which was comparable to that of wild-type EG13. 2020 Journal of virology Result IV S388E;E18G;A448E;A448E;S388R;E18G;A448E;S388R 29;35;103;111;117;137;125;131 34;39;108;116;122;141;130;136 PA;PA 21;95 23;97 33028722 PA Mutations Inherited during Viral Evolution Act Cooperatively To Increase Replication of Contemporary H5N1 Influenza Virus with an Expanded Host Range. The V94I substitution was excluded from subsequent studies because it had little effect on polymerase activity and because of the similarity of the Val and Ile side chains, which differed from other substitutions. 2020 Journal of virology Result IV V94I 4 8 33028722 PA Mutations Inherited during Viral Evolution Act Cooperatively To Increase Replication of Contemporary H5N1 Influenza Virus with an Expanded Host Range. There were hydrogen bond bridges between PA-S388, PA-D389, and PB1-S361 in the PB1 beta-hairpin, but the S388R substitution obviated this bridge, presumably affecting interactions with the RNA 5' promoter. 2020 Journal of virology Result IV S388R 105 110 PA;PA;PB1;PB1 41;50;63;79 43;52;66;82 33028722 PA Mutations Inherited during Viral Evolution Act Cooperatively To Increase Replication of Contemporary H5N1 Influenza Virus with an Expanded Host Range. These results suggested that the phylogeny-associated A448E and S388R mutations acted cooperatively to increase the polymerase activity of the contemporary clade 2.2.1.2 viruses that have been circulating since 2010, with the effect being most prominent in infected human cells at 33 C. 2020 Journal of virology Result IV A448E;S388R 54;64 59;69 33028722 PA Mutations Inherited during Viral Evolution Act Cooperatively To Increase Replication of Contemporary H5N1 Influenza Virus with an Expanded Host Range. This suggested that a mutation(s) in polymerase-associated genes, other than PB2-E627K, accumulated in EG13 to produce its higher polymerase activity. 2020 Journal of virology Result IV E627K 81 86 PB2 77 80 33028722 PA Mutations Inherited during Viral Evolution Act Cooperatively To Increase Replication of Contemporary H5N1 Influenza Virus with an Expanded Host Range. To assess the relevance of the in vitro effects of the A448E/S388R/E18G mutation to in vivo infections, BALB/c mice were inoculated intranasally with serial dilutions of D1/PA-wt virus and D1/PA viruses carrying representative forward mutants (i.e., D1/PAA448E, D1/PAA448E/S388R, and D1/PAA448E/S388R/E18G) or with EG13-wt virus and the EG13G18E/R388S/E448A reverse mutant. 2020 Journal of virology Result IV A448E;S388R;E18G;S388R;S388R;E18G;R388S;E448A;A448E 55;61;67;273;295;301;346;352;289 60;66;71;278;300;305;351;357;294 PA;PA;PA;PA;PA 173;192;253;265;287 175;194;255;267;289 33028722 PA Mutations Inherited during Viral Evolution Act Cooperatively To Increase Replication of Contemporary H5N1 Influenza Virus with an Expanded Host Range. To investigate the structural basis for the increased clade 2.2.1 polymerase activity and replication by the PA mutations identified in this study (i.e., A448E, S388R, and E18G), we generated models of the D1/PA virus trimeric polymerase complex structure. 2020 Journal of virology Result IV A448E;S388R;E18G 154;161;172 159;166;176 PA;PA 109;209 111;211 33028722 PA Mutations Inherited during Viral Evolution Act Cooperatively To Increase Replication of Contemporary H5N1 Influenza Virus with an Expanded Host Range. Together, these results suggested that during the evolution of contemporary clade 2.2.1.2 viruses, the A448E and S388R mutations acted cooperatively to provide a more fit phenotype for replication in human cells at a lower temperature and that the E18G mutation produced strain-specific higher replication in EG13. 2020 Journal of virology Result IV A448E;S388R;E18G 103;113;248 108;118;252 33028722 PA Mutations Inherited during Viral Evolution Act Cooperatively To Increase Replication of Contemporary H5N1 Influenza Virus with an Expanded Host Range. We investigated the effect of the PA-A448E, -S388R, and -E18G substitution mutations on the replication kinetics of clade 2.2.1 viruses using recombinant viruses carrying these mutations. 2020 Journal of virology Result IV A448E;S388R;E18G 37;45;57 42;50;61 PA 34 36 33063654 Detection and discrimination of influenza B Victoria lineage deletion variant viruses by real-time RT-PCR. Influenza B viruses from the V1A, V1A-2DEL, V1A-3DEL and Yam lineages were antigenically characterised in HI tests using post-infection ferret sera raised against representative human influenza B viruses. 2020 Euro surveillance Result IV V1A;V1A;V1A 29;34;44 32;37;47 33063654 Detection and discrimination of influenza B Victoria lineage deletion variant viruses by real-time RT-PCR. Specificity was also demonstrated in V1A-3DEL viruses tested with the VIC 2_Del assay and vice versa. 2020 Euro surveillance Result IV V1A 37 40 33063654 Detection and discrimination of influenza B Victoria lineage deletion variant viruses by real-time RT-PCR. The HI assays demonstrated that both the V1A-2DEL and the V1A-3DEL variant influenza B viruses were antigenically distinct from each other and from the no-deletion B/VIC virus (V1A), as the viruses from each of the genetic groups were not well inhibited by antiserum raised against the other genetic groups (reductions in HI titres of 4-32-fold compared with the homologous HI titres) (Table 2). 2020 Euro surveillance Result IV V1A;V1A;V1A 41;58;177 44;61;180 33063654 Detection and discrimination of influenza B Victoria lineage deletion variant viruses by real-time RT-PCR. The LNA have been shown to increase stability and sequence mismatch detection, and we found that using a triplet of LNA centred on the mismatch allowed for successful detection of the V1A-3DEL viruses. 2020 Euro surveillance Result IV V1A 184 187 33063654 Detection and discrimination of influenza B Victoria lineage deletion variant viruses by real-time RT-PCR. The Vic deletion assay was successful in classifying the 77 B/VIC clinical specimens into their respective genetic groups (30 V1A-like, 27 V1A-2DEL-like and 20 V1A-3DEL-like) and, the rRT-PCR results were confirmed by sequencing (Table 5). 2020 Euro surveillance Result IV V1A;V1A;V1A 126;139;160 129;142;163 33063654 Detection and discrimination of influenza B Victoria lineage deletion variant viruses by real-time RT-PCR. Three quantified B/VIC viruses B/Maryland/15/2016 (V1A-2DEL), B/Hong Kong/269/2017 (V1A-3DEL) and B/Florida/103/2016 (V1A) were used to determine the limit of detection of the Vic 2_Del, Vic 3_Del and Vic No_Del assays, respectively. 2020 Euro surveillance Result IV V1A;V1A;V1A 51;84;118 54;87;121 33063654 Detection and discrimination of influenza B Victoria lineage deletion variant viruses by real-time RT-PCR. Two additional V1A viruses, B/Colorado/06/2017 (V1A-2DEL) and B/Brisbane/60/2008 (V1A), were used to evaluate the Vic deletion assay within the lower virus titres, and similar sensitivity was observed (Supplementary Table S2). 2020 Euro surveillance Result IV V1A;V1A;V1A 15;48;82 18;51;85 33063654 Detection and discrimination of influenza B Victoria lineage deletion variant viruses by real-time RT-PCR. We did not observe any cross-reactivity when V1A viruses were tested with the VIC 2_Del and VIC 3_Del assays. 2020 Euro surveillance Result IV V1A 45 48 33063654 Detection and discrimination of influenza B Victoria lineage deletion variant viruses by real-time RT-PCR. We did not observe cross-reactivity from the VIC No_Del assay when used to test V1A-2DEL and V1A-3DEL viruses. 2020 Euro surveillance Result IV V1A;V1A 80;93 83;96 33063654 Detection and discrimination of influenza B Victoria lineage deletion variant viruses by real-time RT-PCR. We used BHQplus chemistry to successfully design probes to the V1A and V1A-2DEL influenza B viruses (Table 1). 2020 Euro surveillance Result IV V1A;V1A 63;71 66;74 33063654 Detection and discrimination of influenza B Victoria lineage deletion variant viruses by real-time RT-PCR. When designing a probe for detection of the V1A-3DEL viruses, we attempted both a BHQplus design and a minor groove binding (MGB) probe for increased sequence specificity, but neither of these probe modifications were successful (data not shown). 2020 Euro surveillance Result IV V1A 44 47 33099886 Comprehensive assessment of amino acid substitutions in the trimeric RNA polymerase complex of influenza A virus detected in clinical trials of baloxavir marboxil. 26 The replicative capacities of the A(H1N1) and A(H3N2) viruses with I38V and L substitutions were comparable to those of the wild-type viruses in canine MDCK and human RPMI2650 cells (Figure 1 and Figure S1). 2021 Influenza and other respiratory viruses Result IV I38V 71 75 33099886 Comprehensive assessment of amino acid substitutions in the trimeric RNA polymerase complex of influenza A virus detected in clinical trials of baloxavir marboxil. Additionally, PA/I38T-, I38T/I-, and I38M-substituted A(H3N2) viruses were detected from 10, 2, and 1 BXM-treated subject, respectively, and PA/I38T-substituted type B viruses were detected from 1 BXM-treated patient. 2021 Influenza and other respiratory viruses Result IV I38T;I38T;I38I;I38M;I38T 17;24;24;37;144 21;30;30;41;148 PA;PA 14;141 16;143 33099886 Comprehensive assessment of amino acid substitutions in the trimeric RNA polymerase complex of influenza A virus detected in clinical trials of baloxavir marboxil. Assessment of novel PA/I38X substitutions detected in clinical trials. 2021 Influenza and other respiratory viruses Result IV I38X 23 27 PA 20 22 33099886 Comprehensive assessment of amino acid substitutions in the trimeric RNA polymerase complex of influenza A virus detected in clinical trials of baloxavir marboxil. Finally, PA/I38S-substituted A(H1N1)pdm09 viruses and polymorphic PA/I38V and PA/I38L were reported in the literature during 2018/19 influenza season. 2021 Influenza and other respiratory viruses Result IV I38S;I38V;I38L 12;69;81 16;73;85 PA;PA;PA 9;66;78 11;68;80 33099886 Comprehensive assessment of amino acid substitutions in the trimeric RNA polymerase complex of influenza A virus detected in clinical trials of baloxavir marboxil. Moreover, by using NGS analysis with higher sensitivity compared with Sanger sequencing, we found that PA/I38R was temporary detected at day 5 with a frequency of 7.6% in the virus population among one of the 10 subjects with PA/I38T A(H3N2) viruses. 2021 Influenza and other respiratory viruses Result IV I38R;I38T 106;229 110;233 PA;PA 103;226 105;228 33099886 Comprehensive assessment of amino acid substitutions in the trimeric RNA polymerase complex of influenza A virus detected in clinical trials of baloxavir marboxil. Plaque reduction assay revealed that the A(H1N1) viruses with polymorphic I38V and L substitutions displayed reduced BXA susceptibility by 2-fold and 6-fold, respectively (Table 1), consistent with a previous report. 2021 Influenza and other respiratory viruses Result IV I38V 74 78 33099886 Comprehensive assessment of amino acid substitutions in the trimeric RNA polymerase complex of influenza A virus detected in clinical trials of baloxavir marboxil. Resistance monitoring in phase 2 (T0821) and pediatric (T0822 [Japic CTI-163417]) trials revealed treatment-emergent I38T/F/M substitutions in PA, which confer reduced susceptibility to BXA (Table 1 and Table S1). 2021 Influenza and other respiratory viruses Result IV I38F;I38M;I38T 117;117;117 125;125;125 PA 143 145 33099886 Comprehensive assessment of amino acid substitutions in the trimeric RNA polymerase complex of influenza A virus detected in clinical trials of baloxavir marboxil. The I38R virus could not be obtained by reverse genetics, suggesting I38R conferred severe growth defect to the virus. 2021 Influenza and other respiratory viruses Result IV I38R;I38R 4;69 8;73 33099886 Comprehensive assessment of amino acid substitutions in the trimeric RNA polymerase complex of influenza A virus detected in clinical trials of baloxavir marboxil. Viruses bearing the I38N and I38S substitutions showed reduced BXA susceptibility by 24-fold and 12-fold, respectively (Table 1), but also, the recombinant A(H1N1) and A(H3N2) viruses with I38N and I38S substitutions exhibited significant fitness cost in MDCK and RPMI2650 cells (Figure 1 and Figure S1). 2021 Influenza and other respiratory viruses Result IV I38N;I38S;I38N;I38S 20;29;189;198 24;33;193;202 33099886 Comprehensive assessment of amino acid substitutions in the trimeric RNA polymerase complex of influenza A virus detected in clinical trials of baloxavir marboxil. While in the CAPSTONE-1 study, only I38T/M substitutions were detected, in the CAPSTONE-2 study, PA/I38N-substituted A(H1N1)pdm09 viruses were newly identified from one BXM-treated patient. 2021 Influenza and other respiratory viruses Result IV I38M;I38T;I38N 36;36;100 42;42;104 PA 97 99 33179567 Adsorptive mutation and N-linked glycosylation modulate influenza virus antigenicity and fitness. Finally, in the high avidity SKP-827/16 T180 V background virus, the addition of N-linked glycans was similar to their effect in SKP-827/16 T180 virus, such that N148 facilitated significantly greater viral titers in MDCK and CK cells (Figure 3(C,F)). 2020 Emerging microbes & infections Result IV T180V 40 46 33179567 Adsorptive mutation and N-linked glycosylation modulate influenza virus antigenicity and fitness. Finally, in the highest avidity SKP-827/16 T180 V background, N148 was again shown to completely ablate binding to 6SLN and 3SLN while reducing binding towards 3SLN(6Su) (Figure 2(K)). 2020 Emerging microbes & infections Result IV T180V 43 49 33179567 Adsorptive mutation and N-linked glycosylation modulate influenza virus antigenicity and fitness. However, in CK cells addition of N-linked glycans at residues 134 and 189 let to comparable virus replication kinetics with non-glycosylated SKP-827/16 T180 V. 2020 Emerging microbes & infections Result IV T180V 152 158 33179567 Adsorptive mutation and N-linked glycosylation modulate influenza virus antigenicity and fitness. However, in the low avidity background of SKP-827/16 T180A, the addition of N-linked glycans led to attenuation, although the difference in viral titers between glycosylated and non-glycosylated virus was greater in CK cells (Figure 3(A,D)). 2020 Emerging microbes & infections Result IV T180A 53 58 33179567 Adsorptive mutation and N-linked glycosylation modulate influenza virus antigenicity and fitness. In agreement with previous data, non-glycosylated high avidity viruses with T or V180 were attenuated compared to virus with low avidity T180A (from hereon, glycosylated and non-glycosylated viruses refers to those viruses which have had N-linked glycosylation motifs at sites 134, 148 and 189 introduced or not through mutagenesis; viruses still contain their naturally occurring N-linked glycosylation motifs at sites other than 134, 148 and 189). 2020 Emerging microbes & infections Result IV T180A 137 142 33179567 Adsorptive mutation and N-linked glycosylation modulate influenza virus antigenicity and fitness. In the case of SKP-827/16 T180 and T180A but not T180 V with N134 this was significantly enhanced (Figure 4(B)). 2020 Emerging microbes & infections Result IV T180A;T180V 35;49 40;55 33179567 Adsorptive mutation and N-linked glycosylation modulate influenza virus antigenicity and fitness. In the first instance, we utilized chicken polyclonal antisera raised against UDL-01/08 virus (which naturally has A180 and is therefore comparable to SKP-827/16 T180A) in HI assays against our panel of glycosylated and non-glycosylated viruses. 2020 Emerging microbes & infections Result IV T180A 162 167 33179567 Adsorptive mutation and N-linked glycosylation modulate influenza virus antigenicity and fitness. In the low avidity SKP-827/16 T180A virus background, N134 had a negligible effect on binding to 3SLN(6Su), while N148 and N189 both reduced binding avidity towards 3SLN(6Su) (Figure 2(B,C,D)). 2020 Emerging microbes & infections Result IV T180A 30 35 33179567 Adsorptive mutation and N-linked glycosylation modulate influenza virus antigenicity and fitness. Indeed, SKP-827/16 T180A and UDL-01/08 had comparable HI titers against UDL-01/08 antisera (Figure 4(A)), while non-glycosylated SKP-827/16 virus with T180 and T180 V had significantly lower HI titers by up to 4-fold. 2020 Emerging microbes & infections Result IV T180A;T180V 19;160 24;166 33179567 Adsorptive mutation and N-linked glycosylation modulate influenza virus antigenicity and fitness. Interestingly, the addition of N189 to the SKP-827/16 T180 and T180 V background viruses maintained significantly lower HI titers, and given that N189 in the background of T180A did not have a similar effect, it is possible that the impact of N189 on receptor binding avidity was not sufficient to counteract the enhanced avidity facilitated by T180 and T180 V with respect to antigenicity (Figure 4(A)). 2020 Emerging microbes & infections Result IV T180V;T180A;T180V 63;172;354 69;177;360 33179567 Adsorptive mutation and N-linked glycosylation modulate influenza virus antigenicity and fitness. The addition of N189 had a varied effect whereby it reduced binding avidity to 3SLN(6Su) in the T180A and T180 V backgrounds, had a negligible effect on 3SLN binding and slightly reduced binding avidity to 6SLN in the T180 background (Figure 2(D,H,L)). 2020 Emerging microbes & infections Result IV T180A;T180V 96;106 101;112 33179567 Adsorptive mutation and N-linked glycosylation modulate influenza virus antigenicity and fitness. These anti-high avidity virus antisera could reciprocate homologous-like HI titres for glycosylated and non-glycosylated T180, T180A and T180 V viruses in most cases (Figure 4(B)). 2020 Emerging microbes & infections Result IV T180A;T180V 127;137 132;143 33179567 Adsorptive mutation and N-linked glycosylation modulate influenza virus antigenicity and fitness. These effects corroborated well with MDCK plaque phenotype such that the addition of N-linked glycans to virus with T180A lead to significantly smaller plaques, and the addition of N148 to virus with T180 V lead to significantly larger plaques (Figure S1). 2020 Emerging microbes & infections Result IV T180A;T180V 116;200 121;206 33202790 Identification of Novel Influenza Polymerase PB2 Inhibitors Using a Cascade Docking Virtual Screening Approach. Except for compound 21B1 showing no activity against the A/Hong Kong/8/68 (HK/68, H3N2) strain, these compounds were active against a variety of influenza A virus strains, including HK/68 (H3N2), A/WSN/33 (H1N1), A/LiaoNing-ZhenXing/1109/2010 (ZX/1109, H1N1, natural isolate oseltamivir-resistant), the PR/8-R292K mutant (H1N1, recombinant oseltamivir-resistant), the PR/8-I38T mutant (H1N1, recombinant baloxavir-resistant), and influenza B/Lee/40 virus strains (Table 1). 2020 Molecules (Basel, Switzerland) Result IV R292K;I38T 308;373 313;377 33270431 Colorimetric Detection of SARS-CoV-2 and Drug-Resistant pH1N1 Using CRISPR/dCas9. As shown in Figure 5d, upper well surfaces were coated with dCas9/gRNA (H1) and lower with dCas9/gRNA (H275Y N1). 2020 ACS sensors Result IV H275Y 103 108 33270431 Colorimetric Detection of SARS-CoV-2 and Drug-Resistant pH1N1 Using CRISPR/dCas9. By adding a mismatched gRNA sequence, the H275Y SNP could be distinguished using the CRISPR/dCas9 system. 2020 ACS sensors Result IV H275Y 42 47 33270431 Colorimetric Detection of SARS-CoV-2 and Drug-Resistant pH1N1 Using CRISPR/dCas9. Figure 3d shows a plot of the OD450 nm value versus the type of gRNA, further confirming the identification of the pH1N1/H275Y mutation. 2020 ACS sensors Result IV H275Y 121 126 33270431 Colorimetric Detection of SARS-CoV-2 and Drug-Resistant pH1N1 Using CRISPR/dCas9. For the detection of the pH1N1/H275Y mutant virus, we designed gRNA, as shown in Figure 3a. 2020 ACS sensors Result IV H275Y 31 36 33270431 Colorimetric Detection of SARS-CoV-2 and Drug-Resistant pH1N1 Using CRISPR/dCas9. In this case, H275Y N1 RNA was clearly detected with the naked eye, and WT N1 RNA was also recognizable (Figure S6b). 2020 ACS sensors Result IV H275Y 14 19 33270431 Colorimetric Detection of SARS-CoV-2 and Drug-Resistant pH1N1 Using CRISPR/dCas9. Moreover, we intentionally spiked an additional mismatched gRNA sequence against both WT and H275Y N1 RNAs (italic and magenta background in Figure 3a,b). 2020 ACS sensors Result IV H275Y 93 98 33270431 Colorimetric Detection of SARS-CoV-2 and Drug-Resistant pH1N1 Using CRISPR/dCas9. Similar strategies for SNP identification have been employed in previous studies.Figure 3c is a photograph and the corresponding heat map after the detection of H275Y N1 RNA. 2020 ACS sensors Result IV H275Y 161 166 33270431 Colorimetric Detection of SARS-CoV-2 and Drug-Resistant pH1N1 Using CRISPR/dCas9. The dCas9/gRNA (H1)- and dCas9/gRNA (H275Y N1)-attached well microplates were prepared, and several target RNAs (100 nM) were investigated. 2020 ACS sensors Result IV H275Y 37 42 33270431 Colorimetric Detection of SARS-CoV-2 and Drug-Resistant pH1N1 Using CRISPR/dCas9. The gRNA sequence was matched to the pH1N1/H275Y N1 gene, including the SNP (italic and sky-blue background in Figure 3a) but mismatched those of pH1N1 wild-type (WT) N1 gene (italic and sky-blue background in Figure 3b). 2020 ACS sensors Result IV H275Y 43 48 33270431 Colorimetric Detection of SARS-CoV-2 and Drug-Resistant pH1N1 Using CRISPR/dCas9. The H275Y amino acid substitution of neuraminidase (NA) is the most common mutation in the N1 subtype of IFV, conferring oseltamivir resistance.- Since the first emergence of the pH1N1/H275Y mutant virus, the occurrence of mutant viruses has sharply increased, posing a threat to global public health.- Nevertheless, it has been difficult to identify the mutant virus routinely because the NA H275Y mutation of IFV is caused by a SNP. 2020 ACS sensors Result IV H275Y;H275Y;H275Y 4;185;393 9;190;398 NA;NA;NA 52;390;37 54;392;50 33270431 Colorimetric Detection of SARS-CoV-2 and Drug-Resistant pH1N1 Using CRISPR/dCas9. The results show that the H275Y mutation in IFV can be identified using the developed CRISPR/dCas9 system. 2020 ACS sensors Result IV H275Y 26 31 33270431 Colorimetric Detection of SARS-CoV-2 and Drug-Resistant pH1N1 Using CRISPR/dCas9. The well-designed gRNA enabled us to distinguish the pH1N1/H275Y SNP. 2020 ACS sensors Result IV H275Y 59 64 33270431 Colorimetric Detection of SARS-CoV-2 and Drug-Resistant pH1N1 Using CRISPR/dCas9. This mismatched sequence is five bases away from the H275Y SNP and plays an important role in the precise recognition of the H275Y SNP. 2020 ACS sensors Result IV H275Y;H275Y 53;125 58;130 33270431 Colorimetric Detection of SARS-CoV-2 and Drug-Resistant pH1N1 Using CRISPR/dCas9. We designed PAMmer sequences that can hybridize to the target RNAs of SARS-CoV-2, pH1N1, and pH1N1/H275Y viruses (Table S1). 2020 ACS sensors Result IV H275Y 99 104 33270431 Colorimetric Detection of SARS-CoV-2 and Drug-Resistant pH1N1 Using CRISPR/dCas9. We further investigated the identification of pH1N1 and pH1N1/H275Y mutant viruses in human nasopharyngeal aspirates and sputum samples. 2020 ACS sensors Result IV H275Y 62 67 33270431 Colorimetric Detection of SARS-CoV-2 and Drug-Resistant pH1N1 Using CRISPR/dCas9. When testing the mixture of H1 and H275Y N1 RNAs, both well surfaces exhibited a yellow color, implying the successful identification of the H275Y SNP. 2020 ACS sensors Result IV H275Y;H275Y 35;141 40;146 33270431 Colorimetric Detection of SARS-CoV-2 and Drug-Resistant pH1N1 Using CRISPR/dCas9. When the pH1N1/H275Y virus-spiked human nasopharyngeal aspirates and sputum samples were examined, the color signals turned on at both the dCas9/gRNA (H1)- and dCas9/gRNA (H275Y N1)-attached well surfaces. 2020 ACS sensors Result IV H275Y;H275Y 15;172 20;177 33270431 Colorimetric Detection of SARS-CoV-2 and Drug-Resistant pH1N1 Using CRISPR/dCas9. Without the spiked mismatched gRNA sequence, the gRNA perfectly matched the pH1N1/H275Y RNA and single mismatched to pH1N1 WT RNA (Figure S6a). 2020 ACS sensors Result IV H275Y 82 87 33281788 Altering Intracellular Localization of the RNA Interference Factors by Influenza A Virus Non-structural Protein 1. By comparison, infection with PR8-NS1 (D101H) induced enhanced inflammatory cell infiltration in the areas around the lung vasculature. 2020 Frontiers in microbiology Result IV D101H 39 44 NS1 34 37 33281788 Altering Intracellular Localization of the RNA Interference Factors by Influenza A Virus Non-structural Protein 1. Cell fractionation analysis showed that similar to IAV-PR8, infection with neither PR8-NS1 (A155T) nor PR8-NS1 (D189N) enhanced nuclear accumulation of AGO2 (Figure 4A lane 4,5). 2020 Frontiers in microbiology Result IV A155T;D189N 92;112 97;117 NS1;NS1 87;107 90;110 33281788 Altering Intracellular Localization of the RNA Interference Factors by Influenza A Virus Non-structural Protein 1. Furthermore, we found that endogenous miR-16 accumulated to much higher levels in the nucleus of 293T cells following infection with PR8 7 + 1 or PR8-NS1 (D101H), but not PR8-NS1 (A155T) or PR8-NS1 (D189N) (Figure 4A lanes 2, 3). 2020 Frontiers in microbiology Result IV D101H;A155T;D189N 155;180;199 160;185;204 NS1;NS1;NS1 150;175;194 153;178;197 33281788 Altering Intracellular Localization of the RNA Interference Factors by Influenza A Virus Non-structural Protein 1. In contrast, PR8-NS1 (D101H) infection enhanced nuclear accumulation of AGO2 (Figure 4A lane 3), which was thus similar to the infection with IAV-WSN or PR8 7 + 1. 2020 Frontiers in microbiology Result IV D101H 22 27 NS1 17 20 33281788 Altering Intracellular Localization of the RNA Interference Factors by Influenza A Virus Non-structural Protein 1. Sequence analysis of PR8-NS1 (D101H) recovered from the lung tissues of infected mice found that the introduced mutation was stably maintained and no reversion to the wild-type sequence was detected. 2020 Frontiers in microbiology Result IV D101H 30 35 NS1 25 28 33281788 Altering Intracellular Localization of the RNA Interference Factors by Influenza A Virus Non-structural Protein 1. The plaque morphology of PR8-NS1 (D101H), PR8-NS1 (A155T), and PR8-NS1 (D189N) was indistinguishable from each other or from IAV-PR8 and IAV-WSN (Figure 4C). 2020 Frontiers in microbiology Result IV D101H;A155T;D189N 34;51;72 39;56;77 NS1;NS1;NS1 29;46;67 32;49;70 33281788 Altering Intracellular Localization of the RNA Interference Factors by Influenza A Virus Non-structural Protein 1. Thus, we performed site-directed mutagenesis and rescued three mutants of IAV-PR8, PR8-NS1 (D101H), PR8-NS1 (A155T), and PR8-NS1 (D189N), each of which encoded a single amino acid substituted with that found in IAV-WSN NS1 at positions 101 (Asp/D to His/H), 155 (Ala/A to Thr/T), and 189 (D to Asn/N), respectively. 2020 Frontiers in microbiology Result IV D101H;A155T;D189N 92;109;130 97;114;135 NS1;NS1;NS1;NS1 87;104;125;219 90;107;128;222 33281788 Altering Intracellular Localization of the RNA Interference Factors by Influenza A Virus Non-structural Protein 1. We also found no obvious differences in the growth curves of PR8 7 + 1, PR8 D101H, and wild-type IAV-PR8 (Figure 4D). 2020 Frontiers in microbiology Result IV D101H 76 81 33281788 Altering Intracellular Localization of the RNA Interference Factors by Influenza A Virus Non-structural Protein 1. We also observed multiple necrotic lesions in the lungs of the mice infected with PR8-NS1 (D101H), and most of the necrosis was adjacent to bronchioles or small bronchioles (Figure 5B). 2020 Frontiers in microbiology Result IV D101H 91 96 NS1 86 89 33281788 Altering Intracellular Localization of the RNA Interference Factors by Influenza A Virus Non-structural Protein 1. We found that infection with the same dose of PR8-NS1 (D101H) caused significantly earlier mortality compared with IAV-PR8 infection (Figure 5A). 2020 Frontiers in microbiology Result IV D101H 55 60 NS1 50 53 IAV infections 115 132 33281788 Altering Intracellular Localization of the RNA Interference Factors by Influenza A Virus Non-structural Protein 1. We further compared the virus titers of IAV-PR8 and PR8-NS1 (D101H) in the infected lung tissues. 2020 Frontiers in microbiology Result IV D101H 61 66 NS1 56 59 33281788 Altering Intracellular Localization of the RNA Interference Factors by Influenza A Virus Non-structural Protein 1. We next compared the in vivo infection of mice with IAV-PR8 and PR8-NS1 (D101H), which differed by the single amino acid at position 101 of NS1. 2020 Frontiers in microbiology Result IV D101H 73 78 NS1;NS1 68;140 71;143 33408229 Next-Generation Sequencing Analysis of the Within-Host Genetic Diversity of Influenza A(H1N1)pdm09 Viruses in the Upper and Lower Respiratory Tracts of Patients with Severe Influenza. Among these substitutions, HA-A134T and HA-D222N have been characterized in the HA receptor-binding site. 2021 mSphere Result IV A134T;D222N 30;43 35;48 HA;HA;HA 27;40;80 29;42;82 33408229 Next-Generation Sequencing Analysis of the Within-Host Genetic Diversity of Influenza A(H1N1)pdm09 Viruses in the Upper and Lower Respiratory Tracts of Patients with Severe Influenza. Clade 6B.2 is characterized by the amino acid substitutions V152T, V173I, E491G, and D501E; viruses from Pt2 and Pt3 possessed these substitutions. 2021 mSphere Result IV V152T;V173I;E491G;D501E 60;67;74;85 65;72;79;90 33424035 The Effect of I155T, K156Q, K156E and N186K Mutations in Hemagglutinin on the Virulence and Reproduction of Influenza A/H5N1 Viruses. Accumulation of the RGK156Q and N186K viruses occurred with a lag, which was especially marked for the N186K mutant. 2020 Molecular biology Result IV N186K;N186K 32;103 37;108 33424035 The Effect of I155T, K156Q, K156E and N186K Mutations in Hemagglutinin on the Virulence and Reproduction of Influenza A/H5N1 Viruses. For example, the virulence of the RGN186K strain decreased by 4 orders of magnitude; the K156Q substitution also resulted in LD50 increase by almost 4 orders of magnitude. 2020 Molecular biology Result IV K156Q 89 94 33424035 The Effect of I155T, K156Q, K156E and N186K Mutations in Hemagglutinin on the Virulence and Reproduction of Influenza A/H5N1 Viruses. For the RGI155T and RG(K156E+V138A) mutants, the kinetics of accumulation of the virus was not very different from the original RGVN virus. 2020 Molecular biology Result IV K156E;V138A 23;29 28;34 33424035 The Effect of I155T, K156Q, K156E and N186K Mutations in Hemagglutinin on the Virulence and Reproduction of Influenza A/H5N1 Viruses. In the recombinant virus, this mutation was either absent or accompanied by an additional substitution: K156E+V138A or K156E+T160A. 2020 Molecular biology Result IV V138A;K156E;K156E;T160A 110;104;119;125 115;109;124;130 33424035 The Effect of I155T, K156Q, K156E and N186K Mutations in Hemagglutinin on the Virulence and Reproduction of Influenza A/H5N1 Viruses. The mutations causing amino acid substitutions in positions 155, 156, 138 and 186 of HA (I155T, K156Q, (K156E+V138A) and N186K, respectively) were introduced into the NA gene of the RGI155T, RGK156Q, RG(K156E+V138A) and RGN186K mutants by site-specific mutagenesis. 2020 Molecular biology Result IV I155T;K156Q;N186K;V138A;K156E;V138A;K156E 89;96;121;110;104;209;203 94;101;126;115;109;214;208 HA;NA 85;167 87;169 33424035 The Effect of I155T, K156Q, K156E and N186K Mutations in Hemagglutinin on the Virulence and Reproduction of Influenza A/H5N1 Viruses. There are no statistically significant differences between the RGI155T and RG(K156E+V138A) viruses and the original RGVN virus in the level of replication at different temperatures (Table 1). 2020 Molecular biology Result IV K156E;V138A 78;84 83;89 33424035 The Effect of I155T, K156Q, K156E and N186K Mutations in Hemagglutinin on the Virulence and Reproduction of Influenza A/H5N1 Viruses. Thus, it can be asserted that the K156Q and N186K amino acid substitutions promote a decrease in reproductive activity of the H5N1virus at elevated temperatures (40 S). 2020 Molecular biology Result IV K156Q;N186K 34;44 39;49 33424035 The Effect of I155T, K156Q, K156E and N186K Mutations in Hemagglutinin on the Virulence and Reproduction of Influenza A/H5N1 Viruses. Thus, the I155T, K156Q, K156E+V138A and N186K amino acid substitutions in the H5N1 influenza virus had different effects on its replication activity in chicken embryos. 2020 Molecular biology Result IV I155T;K156Q;K156E;V138A;N186K 10;17;24;30;40 15;22;29;35;45 33424035 The Effect of I155T, K156Q, K156E and N186K Mutations in Hemagglutinin on the Virulence and Reproduction of Influenza A/H5N1 Viruses. We failed to obtain a mutant with a single K156E substitution. 2020 Molecular biology Result IV K156E 43 48 33436086 N-linked glycosylation at site 158 of the HA protein of H5N6 highly pathogenic avian influenza virus is important for viral biological properties and host immune responses. We conducted a PCR-based site-directed mutagenesis to generate several viruses with a single amino acid change at 160, including T160A in RHX (RHX-160A) and A160T in RY6 (RY6-160T). 2021 Veterinary research Result IV T160A;A160T 129;157 134;162 33451024 Identification of Important N-Linked Glycosylation Sites in the Hemagglutinin Protein and Their Functional Impact on DC-SIGN Mediated Avian Influenza H5N1 Infection. A serial N-glycosylation mutation on HA extracellular domain (including HA1 and HA2) of H5N1 viruses were generated including N26Q, N27Q, N39Q, N170Q, N181Q, N209Q, N302Q, N500Q, and N559Q (Figure 4A). 2021 International journal of molecular sciences Result IV N26Q;N27Q;N39Q;N170Q;N181Q;N209Q;N302Q;N500Q;N559Q 126;132;138;144;151;158;165;172;183 130;136;142;149;156;163;170;177;188 HA;HA;HA1 37;80;72 39;82;75 33451024 Identification of Important N-Linked Glycosylation Sites in the Hemagglutinin Protein and Their Functional Impact on DC-SIGN Mediated Avian Influenza H5N1 Infection. Among these combinations, N27Q + N39Q and N27Q + N39Q + N181Q showed additively ameliorated effects when interacting with rDC-SIGN-Fc proteins (Figure 4D). 2021 International journal of molecular sciences Result IV N27Q;N39Q;N27Q;N39Q;N181Q 26;33;42;49;56 30;37;46;53;61 33451024 Identification of Important N-Linked Glycosylation Sites in the Hemagglutinin Protein and Their Functional Impact on DC-SIGN Mediated Avian Influenza H5N1 Infection. As the H5N1-RG virus with N27Q or N39Q on HA significantly ameliorated DC-SIGN mediated cis infection in iDCs, similarly, the H5N1-RG carrying N27Q + N39Q on HA additively reduced viral infectivity (p < 0.01) (Figure 7A). 2021 International journal of molecular sciences Result IV N27Q;N39Q;N27Q;N39Q 26;34;143;150 30;38;147;154 HA;HA 42;158 44;160 33451024 Identification of Important N-Linked Glycosylation Sites in the Hemagglutinin Protein and Their Functional Impact on DC-SIGN Mediated Avian Influenza H5N1 Infection. Combined, these results suggest that mutation on N27 or N39 N-glycosylation site or both sites of HA ameliorate DC-SIGN mediated H5N1 infection in cis. 2021 International journal of molecular sciences Result IV N39N 56 61 HA 98 100 Influenza A virus H5N1 infection 129 143 33451024 Identification of Important N-Linked Glycosylation Sites in the Hemagglutinin Protein and Their Functional Impact on DC-SIGN Mediated Avian Influenza H5N1 Infection. Further, we found that DC-SIGN mediated enhancement in viral infectivity could be significantly ameliorated on H5N1-PVs bearing the N27Q or N39Q mutation on the HA (p < 0.01). 2021 International journal of molecular sciences Result IV N27Q;N39Q 132;140 136;144 HA 161 163 33451024 Identification of Important N-Linked Glycosylation Sites in the Hemagglutinin Protein and Their Functional Impact on DC-SIGN Mediated Avian Influenza H5N1 Infection. Furthermore, significant lower titers of H5N1-RG viruses with N27Q or N39Q mutations on HA were detected in iDCs-transmitted MDCK cells (p < 0.01). 2021 International journal of molecular sciences Result IV N27Q;N39Q 62;70 66;74 HA 88 90 33451024 Identification of Important N-Linked Glycosylation Sites in the Hemagglutinin Protein and Their Functional Impact on DC-SIGN Mediated Avian Influenza H5N1 Infection. H5N1-RG carrying N27Q or N39Q or both mutations significantly reduced H5N1 induced apoptosis in iDCs (p < 0.05) (Figure 7D). 2021 International journal of molecular sciences Result IV N27Q;N39Q 17;25 21;29 33451024 Identification of Important N-Linked Glycosylation Sites in the Hemagglutinin Protein and Their Functional Impact on DC-SIGN Mediated Avian Influenza H5N1 Infection. H5N1-RG viruses carrying N27Q or N39Q or both mutations on HA were generated using site-directed mutagenesis. 2021 International journal of molecular sciences Result IV N27Q;N39Q 25;33 29;37 HA 59 61 33451024 Identification of Important N-Linked Glycosylation Sites in the Hemagglutinin Protein and Their Functional Impact on DC-SIGN Mediated Avian Influenza H5N1 Infection. However, H5N1-PVs with N181Q mutation did not influence DC-SIGN mediated H5N1 trans infection (p > 0.05), indicating most attenuated effect was resulted from N27 and N39 N-glycosylation mutation (Figure 6C). 2021 International journal of molecular sciences Result IV N181Q;N39N 23;166 28;171 Influenza A virus H5N1 infection 73 93 33451024 Identification of Important N-Linked Glycosylation Sites in the Hemagglutinin Protein and Their Functional Impact on DC-SIGN Mediated Avian Influenza H5N1 Infection. In addition, the H5N1-PVs carrying N27Q or N39Q significantly ameliorated DC-SIGN promoting effect on H5N1 trans infection (p < 0.05) (Figure 6C). 2021 International journal of molecular sciences Result IV N27Q;N39Q 35;43 39;47 Influenza A virus H5N1 infection 102 122 33451024 Identification of Important N-Linked Glycosylation Sites in the Hemagglutinin Protein and Their Functional Impact on DC-SIGN Mediated Avian Influenza H5N1 Infection. In our current study, we found that N27Q and N39Q on HA of H5N1-PVs significantly attenuated the virus interaction with DC-SIGN expressing cells. 2021 International journal of molecular sciences Result IV N27Q;N39Q 36;45 40;49 HA 53 55 33451024 Identification of Important N-Linked Glycosylation Sites in the Hemagglutinin Protein and Their Functional Impact on DC-SIGN Mediated Avian Influenza H5N1 Infection. Results indicated that H5N1-PVs HA with N27Q, N39Q, and N181Q single mutation significantly reduced the binding abilities with rDC-SIGN-Fc (p < 0.05). 2021 International journal of molecular sciences Result IV N27Q;N39Q;N181Q 40;46;56 44;50;61 HA 32 34 33451024 Identification of Important N-Linked Glycosylation Sites in the Hemagglutinin Protein and Their Functional Impact on DC-SIGN Mediated Avian Influenza H5N1 Infection. Results indicated that only N27Q and N39Q N-glycosylation single mutation on HA of H5N1-PVs significantly reduced viral attachment to DC-SIGN expressing cells (p < 0.05). 2021 International journal of molecular sciences Result IV N27Q;N39Q 28;37 32;41 HA 77 79 33451024 Identification of Important N-Linked Glycosylation Sites in the Hemagglutinin Protein and Their Functional Impact on DC-SIGN Mediated Avian Influenza H5N1 Infection. Similar significant and additive reducing effect was observed in H5N1-PVs carrying N27Q + N39Q or N27Q + N39Q + N181Q (p < 0.01). 2021 International journal of molecular sciences Result IV N27Q;N39Q;N27Q;N39Q;N181Q 83;90;98;105;112 87;94;102;109;117 33451024 Identification of Important N-Linked Glycosylation Sites in the Hemagglutinin Protein and Their Functional Impact on DC-SIGN Mediated Avian Influenza H5N1 Infection. The H5N1-PVs, which contained N27Q or N39Q and other combination of N-glycosylation mutants on the envelop were subjected to infectivity assay using Raji and Raji-DC-SIGN cells. 2021 International journal of molecular sciences Result IV N27Q;N39Q 30;38 34;42 33451024 Identification of Important N-Linked Glycosylation Sites in the Hemagglutinin Protein and Their Functional Impact on DC-SIGN Mediated Avian Influenza H5N1 Infection. We noted that the H5N1-PVs carrying N27Q + N39Q or N27Q + N39Q + N181Q combination displayed the lowest significant DC-SIGN mediated infectivity compared to the wild-type infected control (p < 0.01). 2021 International journal of molecular sciences Result IV N27Q;N39Q;N27Q;N39Q;N181Q 36;43;51;58;65 40;47;55;62;70 33518109 Characterization of the low-pathogenic H7N7 avian influenza virus in Shanghai, China. N30D and T215 A substitutions, which have been shown to increase pathogenicity to mammals, in the M1 protein were found (Table 2). 2021 Poultry science Result IV N30D;T215A 0;9 4;15 M1 98 100 33518109 Characterization of the low-pathogenic H7N7 avian influenza virus in Shanghai, China. The HA protein of CM1216 was found to have the T160 A mutation, which has been shown to increase the binding affinity of AIV to human-like (SA alpha-2, 6 Gal) receptors. 2021 Poultry science Result IV T160A 47 53 HA 4 6 33568453 Identification and Characterization of Novel Antibody Epitopes on the N2 Neuraminidase. All EMVs aside from the S331N EMV grew to similar, high levels in MDCK cells with titers peaking around 1 x 107 PFU/ml. 2021 mSphere Result IV S331N 24 29 33568453 Identification and Characterization of Novel Antibody Epitopes on the N2 Neuraminidase. Although the A272D EMV was generated using 229-1F06, we observed only a 4-fold increase in the MAb's NAI IC50 and no resistance against the other MAbs in the panel. 2021 mSphere Result IV A272D 13 18 NAI 101 104 33568453 Identification and Characterization of Novel Antibody Epitopes on the N2 Neuraminidase. Both A272D and S331N are located on the side of the NA. 2021 mSphere Result IV A272D;S331N 5;15 10;20 52 54 33568453 Identification and Characterization of Novel Antibody Epitopes on the N2 Neuraminidase. Both the irrelevant IgG control virus and the S331N virus grew poorly compared to the other EMVs. 2021 mSphere Result IV S331N 46 51 33568453 Identification and Characterization of Novel Antibody Epitopes on the N2 Neuraminidase. Both the K199T and the E258K EMVs grew to higher titers than the irrelevant IgG control virus (with peak titers of 3.12 x 105 and 5.3 x 105 PFU/ml, respectively, at 48 h postinfection). 2021 mSphere Result IV K199T;E258K 9;23 14;28 33568453 Identification and Characterization of Novel Antibody Epitopes on the N2 Neuraminidase. E258K is located on the bottom of the NA. 2021 mSphere Result IV E258K 0 5 38 40 33568453 Identification and Characterization of Novel Antibody Epitopes on the N2 Neuraminidase. However, we noticed that four of the six EMVs (K199E, A272D, S331N, and the irrelevant IgG control virus) contained the HA mutation N262T, which causes a loss of an N-linked glycosylation site (Table 2). 2021 mSphere Result IV K199E;A272D;S331N;N262T 47;54;61;132 52;59;66;137 HA 120 122 33568453 Identification and Characterization of Novel Antibody Epitopes on the N2 Neuraminidase. Interestingly, the EMVs containing mutations found in nature (K199E/T and E258K) had increased fitness in human lung epithelial cells compared to the irrelevant IgG control virus. 2021 mSphere Result IV K199E;K199T;E258K 62;62;74 69;69;79 33568453 Identification and Characterization of Novel Antibody Epitopes on the N2 Neuraminidase. NAI assays indicated that the K199E mutation caused complete escape from the MAb 235-1C02 and caused resistance to 235-1E06 (62-fold increase in NAI 50% inhibitory concentration [IC50]) and 229-1D05 (11-fold increase in NAI IC50). 2021 mSphere Result IV K199E 30 35 NAI;NAI;NAI 0;145;220 3;148;223 33568453 Identification and Characterization of Novel Antibody Epitopes on the N2 Neuraminidase. Notably, MAb 228-1B03, which does not have NAI or neutralizing activity, lost binding to the E258K EMV. 2021 mSphere Result IV E258K 93 98 NAI 43 46 33568453 Identification and Characterization of Novel Antibody Epitopes on the N2 Neuraminidase. The A272D EMV almost completely escaped from 229-1F06 (2,274-fold increase in neutralizing IC50). 2021 mSphere Result IV A272D 4 9 33568453 Identification and Characterization of Novel Antibody Epitopes on the N2 Neuraminidase. The E258K EMV exhibited complete escape from 229-2C06, along with resistance to 229-1F06 (66-fold increase in neutralizing IC50). 2021 mSphere Result IV E258K 4 9 33568453 Identification and Characterization of Novel Antibody Epitopes on the N2 Neuraminidase. The E258K mutation caused complete escape from MAb 229-2C06, but otherwise it did not have much impact on NAI activity. 2021 mSphere Result IV E258K 4 9 NAI 106 109 33568453 Identification and Characterization of Novel Antibody Epitopes on the N2 Neuraminidase. The K199E and A272D EMVs showed intermediate growth, reaching 1.2 x 105 PFU/ml and 2.1 x 104 PFU/ml at 48 h postinfection, respectively. 2021 mSphere Result IV K199E;A272D 4;14 9;19 33568453 Identification and Characterization of Novel Antibody Epitopes on the N2 Neuraminidase. The K199E/T mutations are the closest to the NA active site. 2021 mSphere Result IV K199E;K199T 4;4 11;11 45 47 33568453 Identification and Characterization of Novel Antibody Epitopes on the N2 Neuraminidase. The K199T and E258K EMVs did not contain this HA mutation and also grew to the highest titers in A549 cells, suggesting that N262T is altering viral fitness. 2021 mSphere Result IV K199T;E258K;N262T 4;14;125 9;19;130 HA 46 48 33568453 Identification and Characterization of Novel Antibody Epitopes on the N2 Neuraminidase. The K199T mutation also affected those same MAbs with a 47-fold increase in NAI IC50 for 235-1C02, a 30-fold increase in NAI IC50 for 235-1E06, and a 48-fold increase in NAI IC50 for 229-1D05. 2021 mSphere Result IV K199T 4 9 NAI;NAI;NAI 76;121;170 79;124;173 33568453 Identification and Characterization of Novel Antibody Epitopes on the N2 Neuraminidase. The K199T mutation had stronger effects on neutralization activity, although the same MAbs were impacted. 2021 mSphere Result IV K199T 4 9 33568453 Identification and Characterization of Novel Antibody Epitopes on the N2 Neuraminidase. The S331N EMV did not replicate above 1 x 103 PFU/ml. 2021 mSphere Result IV S331N 4 9 33568453 Identification and Characterization of Novel Antibody Epitopes on the N2 Neuraminidase. The S331N EMV, selected with 229-1G03, became slightly resistant toward 229-2C06 (5-fold increase in NAI IC50); however, it did not show resistance toward any other MAbs in the panel. 2021 mSphere Result IV S331N 4 9 NAI 101 104 33568453 Identification and Characterization of Novel Antibody Epitopes on the N2 Neuraminidase. The S331N mutation causes the gain of a putative N-linked glycosylation site in the NA. 2021 mSphere Result IV S331N 4 9 84 86 33568453 Identification and Characterization of Novel Antibody Epitopes on the N2 Neuraminidase. The S331N mutation had very little effect on MAb neutralization. 2021 mSphere Result IV S331N 4 9 33568453 Identification and Characterization of Novel Antibody Epitopes on the N2 Neuraminidase. We also identified an isolate circulating in New York City during the 2017-2018 influenza season that contained the same E258K mutation identified through escape mutagenesis, A/New York/PV190/2017 (Table 2). 2021 mSphere Result IV E258K 121 126 33568453 Identification and Characterization of Novel Antibody Epitopes on the N2 Neuraminidase. We found that these EMVs appeared after 2 to 10 passages and identified five distinct NA mutations: K199E/T (229-1D05 and 235-1C02/235-1E06, respectively), E258K (229-2C06), A272D (229-1F06), and S331N (229-1G03) (Table 2 and. 2021 mSphere Result IV K199T;K199E;E258K;A272D;S331N 100;100;156;174;196 107;105;161;179;201 86 88 33568453 Identification and Characterization of Novel Antibody Epitopes on the N2 Neuraminidase. We measured neutralization through PRNAs and found that the K199E mutation resulted in complete escape from the MAbs 235-1C02 and 229-1D05 and resistance to 229-1F06 (30-fold increase in neutralizing IC50), 235-1E06 (287-fold increase in neutralizing IC50), and 229-1G03 (23-fold increase in neutralizing IC50). 2021 mSphere Result IV K199E 60 65 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. As shown in Fig 2C, the 110-kDa PB1-SUMO1 band was detected when WSN-H1PB1, WSN-H1PB1/K379R, or WSN-H1PB1/K736R was cotransfected with SUMO1, whereas the indicated SUMOylated PB1 band disappeared when SUMO1mut was used instead of SUMO1. 2021 PLoS pathogens Result IV K379R;K736R 86;106 91;111 PB1;PB1 32;175 35;178 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. As shown in Fig 4B, both native PB1 and SUMOylated PB1 were present in cells expressing WSN-H1PB1, and the level of total PB1 remained stable across different time points; native PB1, but not the 110-kDa PB1-SUMO1, was detected in cells expressing WSN-H1PB1/K612R, whose level remained unchanged. 2021 PLoS pathogens Result IV K612R 258 263 PB1;PB1;PB1;PB1;PB1 32;51;122;179;204 35;54;125;182;207 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. As shown in Fig 8H, the amount of vRNA bound by WSN-H1PB1494-757 protein was much higher than that bound by WSN-H1PB1494-757/K612R. 2021 PLoS pathogens Result IV K612R 125 130 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. Both PB1 and PB1/K612R protein levels remained stable at 0, 2, 4, 6, 8, and 12 h under CHX treatment (Fig 4A), indicating that SUMOylation at K612 has no effect on the stability of IAV PB1. 2021 PLoS pathogens Result IV K612R 17 22 PB1;PB1;PB1 5;13;185 8;16;188 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. By contrast, in the FZ/1-PB1K612R (H1N1)-exposed group, the virus was detected in the nasal wash of only one ferret on day 3 p.e., and in the nasal wash of another ferret until day 7 p.e., with peak titers ranging from 3.9 to 6.3 log10 PFU/mL (Fig 10D). 2021 PLoS pathogens Result IV K612R 28 33 PB1 25 28 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. Cell lysates containing 100 mug of total protein that had previously been transfected with a plasmid expressing truncated WSN-H1PB1 protein (PB1494-757 or PB1494-757/K612R) or pCAGGS vector as a control were then added to the RNA-bound beads. 2021 PLoS pathogens Result IV K612R 166 171 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. Collectively, these results demonstrate that the K612R mutation in IAV PB1 impairs the ability of the PB1 protein to bind vRNA. 2021 PLoS pathogens Result IV K612R 49 54 PB1;PB1 71;102 74;105 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. Compared with the wild-type viruses, which formed large plaques, the PB1/K612R mutant viruses formed much smaller plaques, indicating that virus growth was greatly impaired by the lack of SUMOylation of PB1 at position 612 (Fig 7D-7F). 2021 PLoS pathogens Result IV K612R 73 78 PB1;PB1 69;203 72;206 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. Compared with wild-type VN-H5PB1 and AH-H7PB1, which were SUMOylated by SUMO1, analysis of the VN-H5PB1/K612R and AH-H7PB1/K612R mutants did not reveal the 110-kDa PB1-SUMO1 band (Fig 2D and 2E), indicating that the lysine residue at position 612 is also a major SUMOylation site of VN-H5PB1 and AH-H7PB1. 2021 PLoS pathogens Result IV K612R;K612R 104;123 109;128 PB1 164 167 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. Finally, we sought to determine whether the introduced PB1/K612R mutation was stably maintained during viral replication in ferrets. 2021 PLoS pathogens Result IV K612R 59 64 PB1 55 58 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. for the WSN-PB1K612R (H1N1), VN/1180-PB1K612R (H5N1), and AH/1-PB1K612R (H7N9) viruses, respectively, compared with the corresponding wild-type viruses. 2021 PLoS pathogens Result IV K612R;K612R;K612R 15;40;66 20;45;71 PB1;PB1;PB1 12;37;63 15;40;66 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. HEK293T cells transiently overexpressing Ubc9 and SUMO1-Flag or SUMO1mut-Flag were infected with WSN (H1N1), VN/1180 (H5N1), AH/1 (H7N9), or their PB1/K612R mutants at an MOI of 2. 2021 PLoS pathogens Result IV K612R 151 156 PB1 147 150 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. HEK293T cells were transfected for 48 h with WSN-H1PB1 or WSN-H1PB1/K612R mutant individually or simultaneously were transfected with WSN-H1PB2 or WSN-H1PA. 2021 PLoS pathogens Result IV K612R 68 73 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. HEK293T cells were transfected with an expression plasmid encoding WSN-H1PB1 or WSN-H1PB1/K612R mutant. 2021 PLoS pathogens Result IV K612R 90 95 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. HEK293T cells were transfected with plasmid expressing the Flag-tagged 494-757 region of wild-type PB1 or the PB1/K612R mutant of WSN (H1N1), VN/1180 (H5N1), or AH/1 (H7N9) virus (Fig 8B-8D). 2021 PLoS pathogens Result IV K612R 114 119 PB1;PB1 99;110 102;113 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. However, when the WSN-H1PB1/K612R mutant was cotransfected with SUMO1 or SUMO1mut, the 110-kDa PB1-SUMO1 band was not detected. 2021 PLoS pathogens Result IV K612R 28 33 PB1 95 98 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. In contrast, the 110-kDa PB1-SUMO1 band was not detectable in cells infected with the WSN-PB1K612R (H1N1) virus (Fig 3A). 2021 PLoS pathogens Result IV K612R 93 98 PB1;PB1 25;90 28;93 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. in the inoculated ferrets, and all of the viruses contained the R612K reversion mutation in the inoculated animals on day 4 p.i. 2021 PLoS pathogens Result IV R612K 64 69 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. Interestingly, the second virus-positive exposed ferret had already acquired the PB1 R612K reversion mutation when the virus was detected in the nasal wash on day 7 p.e. 2021 PLoS pathogens Result IV R612K 85 90 PB1 81 84 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. MDCK cells were infected with one of the wild-type viruses or with the PB1/K612R mutant viruses at an MOI of 0.001. 2021 PLoS pathogens Result IV K612R 75 80 PB1 71 74 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. No significant differences in the amounts of PB2, PA, and NP were observed between vRNP complexes bearing WSN-H1PB1 and those bearing WSN-H1PB1/K612R (S1 Fig). 2021 PLoS pathogens Result IV K612R 144 149 NP;PA;PB2 58;50;45 60;52;48 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. perivascular edema, infiltration of inflammatory cells, necrosis, and exfoliation of bronchiole epithelial cells) compared with the mice infected with the WSN-PB1K612R (H1N1) mutant virus. 2021 PLoS pathogens Result IV K612R 162 167 PB1 159 162 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. Similar results were observed in the lungs of mice infected with the wild-type VN/1180 (H5N1), AH/1 (H7N9) and their corresponding PB1/K612R mutant viruses (Fig 9N-9U). 2021 PLoS pathogens Result IV K612R 135 140 PB1 131 134 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. Similarly, the body weight loss of mice inoculated with AH/1 (H7N9) virus and AH/1-PB1K612R (H7N9) mutant virus were observed in the 105-107 PFU groups, with more severe body weight loss observed in mice inoculated with AH/1 (H7N9) virus than AH/1-PB1K612R (H7N9) mutant virus (S2E and S2F Fig); and the MLD50 was 105.5 PFU for AH/1 (H7N9) virus, whereas was >107.5 PFU for AH/1-PB1K612R (H7N9) mutant virus, displaying an at least 100-fold reduction compared with the wild-type virus (Fig 9H and 9I). 2021 PLoS pathogens Result IV K612R 382 387 PB1;PB1;PB1 83;248;379 86;251;382 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. Strikingly, PB1/K612R was not stably maintained during virus replication in ferrets. 2021 PLoS pathogens Result IV K612R 16 21 PB1 12 15 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. SUMOylation-defective PB1/K612R mutation impairs IAV replication. 2021 PLoS pathogens Result IV K612R 26 31 PB1 22 25 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. The amount of PB2 or PA that was immunoprecipitated by WSN-H1PB1 or WSN-H1PB1/K612R was comparable (Fig 6), indicating that the interactions between PB1-PB2 and PB1-PA were not affected by the SUMOylation at K612 of PB1. 2021 PLoS pathogens Result IV K612R 78 83 PA;PA;PB1;PB1;PB1;PB2;PB2 21;165;149;161;216;14;153 23;167;152;164;219;17;156 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. The K612R mutation impairs the ability of PB1 to bind vRNA. 2021 PLoS pathogens Result IV K612R 4 9 PB1 42 45 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. The main SUMOylated band was also present in the lanes transfected with the PB1/K379R and PB1/K736R mutants, but not the PB1/K612R mutant. 2021 PLoS pathogens Result IV K379R;K736R;K612R 80;94;125 85;99;130 PB1;PB1;PB1 76;90;121 79;93;124 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. The R612K reversion mutation in PB1 was found on day 2 p.i. 2021 PLoS pathogens Result IV R612K 4 9 PB1 32 35 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. The results showed that the vRNP complex activity of WSN (H1N1), VN/1180 (H5N1), and AH/1 (H7N9) virus decreased by approximately 50%, 55%, and 95%, respectively, in cells expressing PB1/K612R compared with that of PB1 (Fig 7A-7C). 2021 PLoS pathogens Result IV K612R 187 192 PB1;PB1 183;215 186;218 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. The virulence of SUMOylation-defective PB1/K612R mutant viruses is attenuated in mice. 2021 PLoS pathogens Result IV K612R 43 48 PB1 39 42 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. These data demonstrate that the K612R mutation impairs the vRNA-binding ability of PB1. 2021 PLoS pathogens Result IV K612R 32 37 PB1 83 86 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. These data indicate that the virulence of the SUMOylation-defective PB1/K612R mutant viruses is highly compromised compared with that of the wild-type viruses in mice. 2021 PLoS pathogens Result IV K612R 72 77 PB1 68 71 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. These data show that the PB1/K612R mutant viruses induce significantly less severe lung lesions compared with the wild-type viruses. 2021 PLoS pathogens Result IV K612R 29 34 PB1 25 28 Lung lesions 83 95 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. These results demonstrate that the SUMOylation-defective PB1/K612R mutation significantly attenuates the replication of IAVs in vivo. 2021 PLoS pathogens Result IV K612R 61 66 PB1 57 60 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. These results suggest that the SUMOylation-defective PB1/K612R mutation is correlated with the impaired replication and transmission of the FZ/1 (H1N1) virus in ferrets. 2021 PLoS pathogens Result IV K612R 57 62 PB1 53 56 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. These results suggest that the transmission of the FZ/1-PB1K612R (H1N1) virus may have occurred or have been enhanced after it acquired the R612K reversion mutation in its PB1 protein. 2021 PLoS pathogens Result IV R612K;K612R 140;59 145;64 PB1;PB1 56;172 59;175 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. To address whether the SUMOylation of PB1 protein occurs during IAV infection, SUMOylation-defective PB1/K612R mutants of WSN (H1N1), VN/1180 (H5N1), and AH/1 (H7N9) viruses (WSN-PB1K612R, VN/1180-PB1K612R, and AH/1-PB1K612R) were generated by reverse genetics and deep-sequenced to ensure that they contained no unwanted mutations (S2 Table). 2021 PLoS pathogens Result IV K612R 105 110 PB1;PB1;PB1;PB1;PB1 38;101;179;197;216 41;104;182;200;219 IAV infections 64 77 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. To determine the effect of the SUMOylation-defective PB1/K612R mutation on the in vitro replication of IAV, we first compared the plaque morphologies of the wild-type WSN (H1N1), VN/1180 (H5N1), and AH/1 (H7N9) viruses with those of the SUMOylation-defective PB1/K612R mutant viruses in MDCK cells. 2021 PLoS pathogens Result IV K612R;K612R 57;263 62;268 PB1;PB1 53;259 56;262 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. To determine whether the SUMOylation of PB1 at K612 affects the transmissibility of IAVs, a 2009 pandemic H1N1 virus, A/Fuzhou/1/2009 (FZ/1, H1N1), and its SUMOylation-defective PB1/K612R mutant FZ/1-PB1K612R (H1N1) were rescued by reverse genetics. 2021 PLoS pathogens Result IV K612R 182 187 PB1;PB1;PB1 40;178;200 43;181;203 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. To further confirm that the K612R mutation affects the binding of the PB1 protein to vRNA, we conducted an RNA-protein pull-down experiment. 2021 PLoS pathogens Result IV K612R 28 33 PB1 70 73 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. To further demonstrate that SUMOylation of PB1 at K612 does not alter protein stability, we cotransfected Flag-tagged WSN-H1PB1 or WSN-H1PB1/K612R mutant with Ubc9 and SUMO1 in HEK293T cells. 2021 PLoS pathogens Result IV K612R 141 146 PB1 43 46 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. To this end, a minigenome assay was performed in HEK293T cells, which were transfected with the four vRNP complex protein expression plasmids, PB2, PB1 or PB1/K612R, PA, and NP of WSN (H1N1), VN/1180 (H5N1), or AH/1 (H7N9) virus, together with a reporter plasmid, pHH21-SC09NS F-Luc, encoding a vRNA-like firefly luciferase gene. 2021 PLoS pathogens Result IV K612R 159 164 NP;PA;PB1;PB1;PB2 174;166;148;155;143 176;168;151;158;146 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. Viral RNP complexes, bearing WSN-H1PB1 or WSN-H1PB1/K612R, were reconstituted in HEK293T cells by co-transfection of expression plasmids for PB2, PB1 or PB1/K612R, PA, and NP of WSN (H1N1) virus, together with pHH21-SC09NS F-Luc, which was used to provide a vRNA-like template RNA. 2021 PLoS pathogens Result IV K612R;K612R 52;157 57;162 NP;PA;PB1;PB1;PB2;RNP 172;164;146;153;141;6 174;166;149;156;144;9 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. We also performed histopathological studies on lung sections from the wild-type- and PB1/K612R mutant virus-inoculated mice. 2021 PLoS pathogens Result IV K612R 89 94 PB1 85 88 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. We found that the PB1/K612R mutation led to 25- to 76-, 2- to 7-, and 3- to 22-fold reductions in growth titers from 12 to 48 h p.i. 2021 PLoS pathogens Result IV K612R 22 27 PB1 18 21 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. We found that the same amount of vRNA bound more WSN-H1PB1494-757 protein than WSN-H1PB1494-757/K612R protein (Fig 8K). 2021 PLoS pathogens Result IV K612R 96 101 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. We next determined the 50% mouse lethal dose (MLD50) of the PB1/K612R mutant viruses. 2021 PLoS pathogens Result IV K612R 64 69 PB1 60 63 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. We next examined the replication kinetics of the PB1/K612R mutant viruses. 2021 PLoS pathogens Result IV K612R 53 58 PB1 49 52 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. We therefore determined whether the SUMOylation-defective K612R mutation affects the ability of PB1 to bind to vRNA. 2021 PLoS pathogens Result IV K612R 58 63 PB1 96 99 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. When tested in the VN/1180 (H5N1) or AH/1 (H7N9) background, the VN/1180-H5PB1494-757 and AH/1-H7PB1494-757 proteins again bound much more model vRNA than the corresponding PB1/K612R mutant proteins, VN/1180-H5PB1494-757/K612R and AH/1-H7PB1494-757/K612R (Fig 8I and 8J). 2021 PLoS pathogens Result IV K612R;K612R;K612R 177;221;249 182;226;254 PB1 173 176 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. When we conducted this experiment in the VN/1180 (H5N1) and AH/1 (H7N9) backgrounds, we found that the amount of the PB1/K612R protein bound by vRNA was significantly lower than that of the wild-type protein (Fig 8L and 8M). 2021 PLoS pathogens Result IV K612R 121 126 PB1 117 120 33581212 Susceptibility of widely diverse influenza a viruses to PB2 polymerase inhibitor pimodivir. All 'variant' viruses tested were resistant to M2 inhibitors due to the presence of V27T or S31N substitutions in M2 protein. 2021 Antiviral research Result IV V27T;S31N 84;92 88;96 M2;M2 47;114 49;116 33581212 Susceptibility of widely diverse influenza a viruses to PB2 polymerase inhibitor pimodivir. As an internal quality control, a pair of A (H3N2) viruses was included in each test; their genomes were nearly identical, except substitution I38M in PA protein. 2021 Antiviral research Result IV I38M 143 147 PA 151 153 33581212 Susceptibility of widely diverse influenza a viruses to PB2 polymerase inhibitor pimodivir. Because their pimodivir IC50 values were low, average 3.48 nM, we concluded that H357N alone conferred the observed pimodivir resistance of ty/MN/80 virus. 2021 Antiviral research Result IV H357N 81 86 33581212 Susceptibility of widely diverse influenza a viruses to PB2 polymerase inhibitor pimodivir. However, the median pimodivir IC50 for the PA-I38M control virus was somewhat lower (5.77 vs 7.11 nM, p < 0.0001). 2021 Antiviral research Result IV I38M 46 50 PA 43 45 33581212 Susceptibility of widely diverse influenza a viruses to PB2 polymerase inhibitor pimodivir. However, two substitutions, H357N and L464M, residing in the cap-binding domain of the PB2, raised our interest. 2021 Antiviral research Result IV H357N;L464M 28;38 33;43 PB2 87 90 33581212 Susceptibility of widely diverse influenza a viruses to PB2 polymerase inhibitor pimodivir. However, we were able to obtain and test two A(H1N1)pdm09 viruses, A/Manitoba/RV0444/2018 and A/Kuwait/3812/2017, that carry the second substitution of interest - L464M. 2021 Antiviral research Result IV L464M 163 168 33581212 Susceptibility of widely diverse influenza a viruses to PB2 polymerase inhibitor pimodivir. In the multi-cycle replication-based FRA assay, S324C, N510K, and S324R conferred a 20-, 283-, and 688-fold reduction in pimodivir susceptibility, respectively (Table 2). 2021 Antiviral research Result IV S324C;N510K;S324R 48;55;66 53;60;71 33581212 Susceptibility of widely diverse influenza a viruses to PB2 polymerase inhibitor pimodivir. None of the H375N carrying viruses were available for testing. 2021 Antiviral research Result IV H375N 12 17 33581212 Susceptibility of widely diverse influenza a viruses to PB2 polymerase inhibitor pimodivir. Of these three, two A(H1N1)pdm09 viruses (A/Texas/70/2016 and A/Minnesota/11/2017) had S324C and N510K, respectively; while one A(H3N2) virus (A/Pennsylvania/242/2017) contained S324R. 2021 Antiviral research Result IV S324C;N510K;S324R 87;97;178 92;102;183 33581212 Susceptibility of widely diverse influenza a viruses to PB2 polymerase inhibitor pimodivir. PB2 sequences of 94,288 viruses (accessed from GISAID on September 23, 2020), including 63,923 (68%) viruses collected from humans, were analyzed for the presence of H357N. 2021 Antiviral research Result IV H357N 166 171 PB2 0 3 33581212 Susceptibility of widely diverse influenza a viruses to PB2 polymerase inhibitor pimodivir. Their replication was inhibited by pimodivir at low nanomolar concentrations, 2.77-28.59 nM (Table 4), except one NA inhibitor-resistant virus, A/turkey/Minnesota/833/80 (H4N2) carrying NA-R292K mutation (ty/MN/80-NA-R292K), which displayed highly elevated average pimodivir IC50, 644.17 nM. 2021 Antiviral research Result IV R292K;R292K 189;217 194;222 NA;NA;NA 114;186;214 116;188;216 33581212 Susceptibility of widely diverse influenza a viruses to PB2 polymerase inhibitor pimodivir. Therefore, it is reasonable to assume that the substitution H357N may affect pimodivir susceptibility. 2021 Antiviral research Result IV H357N 60 65 33581212 Susceptibility of widely diverse influenza a viruses to PB2 polymerase inhibitor pimodivir. These substitutions were as follows: F325L (n = 1), S337P (n = 1), K376R (n = 3), T378S (n = 3), M431L (n = 3), and N510K (n = 7) (Supplementary Table 1). 2021 Antiviral research Result IV T378S;F325L;S337P;K376R;M431L;N510K 82;37;52;67;97;116 87;42;57;72;102;121 33604005 In silico analysis and molecular characterization of Influenza A (H1N1) pdm09 virus circulating and causing major outbreaks in central India, 2009-2019. Analysis of amino acid sequence alignment revealed changes at two positions (T151A, D239G) at RBS of HA between genogroup 2 and 3, three positions (A151T, S200P, S202T) between genogroup 3 and 4, two positions (N114D, E279G) between 4 and 6A, four positions (N101S, Q180K, G279E, E300K) between 6A and 6B, three positions (S101N, K180Q, I251V) between 6B and 6C genogroup, four positions (G101S, T214A, V251I, K300E) between 6C and 7 genogroup (Table 4). 2020 Iranian journal of microbiology Result IV T151A;D239G;A151T;S200P;S202T;N114D;E279G;N101S;Q180K;G279E;E300K;S101N;K180Q;I251V;G101S;T214A;V251I;K300E 77;84;148;155;162;211;218;259;266;273;280;323;330;337;389;396;403;410 82;89;153;160;167;216;223;264;271;278;285;328;335;342;394;401;408;415 HA 101 103 33604005 In silico analysis and molecular characterization of Influenza A (H1N1) pdm09 virus circulating and causing major outbreaks in central India, 2009-2019. Mutational analysis of 2019 virus compared to A/Michigan/45/2015 revealed N179S, Q180K, T233I, R240Q amino acid substitutions whereas 2017 viruses showed A90V, S91R, N179S, Q180K, T233I, R240Q mutations in receptor binding sites (Table 3). 2020 Iranian journal of microbiology Result IV N179S;Q180K;T233I;R240Q;A90V;S91R;N179S;Q180K;T233I;R240Q 74;81;88;95;154;160;166;173;180;187 79;86;93;100;158;164;171;178;185;192 33604005 In silico analysis and molecular characterization of Influenza A (H1N1) pdm09 virus circulating and causing major outbreaks in central India, 2009-2019. The study included both partial and complete sequences and to keep up homogeneity, amino acid from position 151 to 300 used in study which revealed S220T highly frequent followed by S202T, K300E, A273T, K180Q and so on. 2020 Iranian journal of microbiology Result IV S220T;S202T;K300E;A273T;K180Q 148;182;189;196;203 153;187;194;201;208 33647314 The active form of the influenza cap-snatching endonuclease inhibitor baloxavir marboxil is a tight binding inhibitor. Cap-snatching endonuclease activity of FluB-ht wild-type (WT) and FluB-ht PA I38T. 2021 The Journal of biological chemistry Result IV I38T 77 81 PA 74 76 33647314 The active form of the influenza cap-snatching endonuclease inhibitor baloxavir marboxil is a tight binding inhibitor. Conversely, preincubation length had only negligible effects on the activity of the PA I38T FluB-ht. 2021 The Journal of biological chemistry Result IV I38T 87 91 PA 84 86 33647314 The active form of the influenza cap-snatching endonuclease inhibitor baloxavir marboxil is a tight binding inhibitor. Conversely, under the same conditions no inhibition of the PA I38T FluB-ht variant was observed. 2021 The Journal of biological chemistry Result IV I38T 62 66 PA 59 61 33647314 The active form of the influenza cap-snatching endonuclease inhibitor baloxavir marboxil is a tight binding inhibitor. Effect of BXA preincubation on inhibition of FluB-ht WT and FluB-ht PA I38T. 2021 The Journal of biological chemistry Result IV I38T 71 75 PA 68 70 33647314 The active form of the influenza cap-snatching endonuclease inhibitor baloxavir marboxil is a tight binding inhibitor. Effects of order of addition on inhibition of FluB-ht WT and FluB-ht PA I38T by BXA. 2021 The Journal of biological chemistry Result IV I38T 72 76 PA 69 71 33647314 The active form of the influenza cap-snatching endonuclease inhibitor baloxavir marboxil is a tight binding inhibitor. Here we used this approach to generate WT FluB-ht, a variant associated with BXM resistance (FluB-ht PA I38T), and a variant containing a catalytically inactive endonuclease (FluB-ht PA QNQ) where metal coordinating residues were mutated (E81Q, D109 N, E120Q). 2021 The Journal of biological chemistry Result IV I38T;E81Q;D109N;E120Q 104;239;245;253 108;243;251;258 PA;PA 101;183 103;185 33647314 The active form of the influenza cap-snatching endonuclease inhibitor baloxavir marboxil is a tight binding inhibitor. however, a quantitative comparison of WT and PA I38T FluB-ht reveals a reduction of the overall activity of the PA I38T FluB-ht as has been noted by others. 2021 The Journal of biological chemistry Result IV I38T;I38T 48;115 52;119 PA;PA 45;112 47;114 33647314 The active form of the influenza cap-snatching endonuclease inhibitor baloxavir marboxil is a tight binding inhibitor. However, the Kiapp of BXA for PA I38T of 217 nM is ~18-fold increased with respect to WT FluB-ht (12 nM). 2021 The Journal of biological chemistry Result IV I38T 33 37 PA 30 32 33647314 The active form of the influenza cap-snatching endonuclease inhibitor baloxavir marboxil is a tight binding inhibitor. Inhibition of FluB-ht WT and FluB-ht PA I38T endonuclease by BXA. 2021 The Journal of biological chemistry Result IV I38T 40 44 PA 37 39 33647314 The active form of the influenza cap-snatching endonuclease inhibitor baloxavir marboxil is a tight binding inhibitor. Plots of IC50 as a function of enzyme concentration for both WT and PA I38T FluB-ht yielded linear plots with slopes of ~0.5. 2021 The Journal of biological chemistry Result IV I38T 71 75 PA 68 70 33647314 The active form of the influenza cap-snatching endonuclease inhibitor baloxavir marboxil is a tight binding inhibitor. The difference observed between WT and PA I38T FluB-ht provides additional evidence to show that the association of BXA with FluB-ht is impaired by the PA I38T substitution. 2021 The Journal of biological chemistry Result IV I38T;I38T 42;155 46;159 PA;PA 39;152 41;154 33647314 The active form of the influenza cap-snatching endonuclease inhibitor baloxavir marboxil is a tight binding inhibitor. The endonuclease reaction in the absence of inhibitor for both WT and PA I38T FluB-ht was largely unaffected by the order of addition of FluB-ht (E), capped 20-nt Substrate (S), and Mg2. 2021 The Journal of biological chemistry Result IV I38T 73 77 33647314 The active form of the influenza cap-snatching endonuclease inhibitor baloxavir marboxil is a tight binding inhibitor. The FluB-ht PA I38T shows a very similar pattern as seen with the WT FluB-ht. 2021 The Journal of biological chemistry Result IV I38T 15 19 PA 12 14 33647314 The active form of the influenza cap-snatching endonuclease inhibitor baloxavir marboxil is a tight binding inhibitor. To quantify inhibition of WT and PA I38T FluB-ht by BXA, we initially determined IC50 values of 112 nM and 374 nM for the WT and I38T variants, respectively. 2021 The Journal of biological chemistry Result IV I38T;I38T 36;129 40;133 PA 33 35 33647314 The active form of the influenza cap-snatching endonuclease inhibitor baloxavir marboxil is a tight binding inhibitor. To test this hypothesis, IC50 values were determined for both WT and PA I38T FluB-ht at various concentrations of enzyme. 2021 The Journal of biological chemistry Result IV I38T 72 76 PA 69 71 33647314 The active form of the influenza cap-snatching endonuclease inhibitor baloxavir marboxil is a tight binding inhibitor. To this end, WT or PA I38T FluB-ht, and BXA were preincubated for a fixed period of time with 75 nM BXA to allow formation of an E:I:Mg2+ complex before initiating the reaction with substrate. 2021 The Journal of biological chemistry Result IV I38T 22 26 PA 19 21 33673017 Structural and Thermodynamic Analysis of the Resistance Development to Pimodivir (VX-787), the Clinical Inhibitor of Cap Binding to PB2 Subunit of Influenza A Polymerase. A considerably less negative Eint of the pimodivir: PB2-F404Y complex can be indicative of the less negative enthalpic term measured by isothermal titration calorimetry (ITC). 2021 Molecules (Basel, Switzerland) Result IV F404Y 57 62 PB2 53 56 33673017 Structural and Thermodynamic Analysis of the Resistance Development to Pimodivir (VX-787), the Clinical Inhibitor of Cap Binding to PB2 Subunit of Influenza A Polymerase. Additionally, the H357N and F404Y mutations considerably increased the binding affinity of the inhibitor. 2021 Molecules (Basel, Switzerland) Result IV H357N;F404Y 18;28 23;33 33673017 Structural and Thermodynamic Analysis of the Resistance Development to Pimodivir (VX-787), the Clinical Inhibitor of Cap Binding to PB2 Subunit of Influenza A Polymerase. Compared to WT, the M431I mutant had minor difference in the thermodynamic parameters of pimodivir binding. 2021 Molecules (Basel, Switzerland) Result IV M431I 20 25 33673017 Structural and Thermodynamic Analysis of the Resistance Development to Pimodivir (VX-787), the Clinical Inhibitor of Cap Binding to PB2 Subunit of Influenza A Polymerase. For the F404Y single mutant, the enthalpy change for pimodivir binding was substantially affected and was 4.8 kcal.mol-1 less favorable than the WT value. 2021 Molecules (Basel, Switzerland) Result IV F404Y 8 13 33673017 Structural and Thermodynamic Analysis of the Resistance Development to Pimodivir (VX-787), the Clinical Inhibitor of Cap Binding to PB2 Subunit of Influenza A Polymerase. For the H357N mutant, the enthalpic and entropic contributions were less favorable of 0.5 kcal.mol-1 and 2.5 kcal.mol-1, respectively. 2021 Molecules (Basel, Switzerland) Result IV H357N 8 13 33673017 Structural and Thermodynamic Analysis of the Resistance Development to Pimodivir (VX-787), the Clinical Inhibitor of Cap Binding to PB2 Subunit of Influenza A Polymerase. Pimodivir had comparable binding affinity to WT and M431I variants of PB2 in such a model. 2021 Molecules (Basel, Switzerland) Result IV M431I 52 57 PB2 70 73 33673017 Structural and Thermodynamic Analysis of the Resistance Development to Pimodivir (VX-787), the Clinical Inhibitor of Cap Binding to PB2 Subunit of Influenza A Polymerase. Since the thermodynamic analysis showed the greatest loss of the enthalpy contribution in the mutant PB2-F404Y, the structure was compared with that of PB2-WT in detail to identify any visible changes that could explain more unfavorable enthalpy. 2021 Molecules (Basel, Switzerland) Result IV F404Y 105 110 PB2;PB2 101;152 104;155 33673017 Structural and Thermodynamic Analysis of the Resistance Development to Pimodivir (VX-787), the Clinical Inhibitor of Cap Binding to PB2 Subunit of Influenza A Polymerase. The binding of pimodivir to the WT, F404Y, M431I, and H357N variants of PB2 was examined by using the semiempirical quantum mechanical PM6-D3H4X/COSMO2 based protein ligand scoring function. 2021 Molecules (Basel, Switzerland) Result IV F404Y;M431I;H357N 36;43;54 41;48;59 PB2 72 75 33673017 Structural and Thermodynamic Analysis of the Resistance Development to Pimodivir (VX-787), the Clinical Inhibitor of Cap Binding to PB2 Subunit of Influenza A Polymerase. The common atoms of mutated residues F404Y, M431I, and H357N possess similar positions as in the PB2-WT structure. 2021 Molecules (Basel, Switzerland) Result IV F404Y;M431I;H357N 37;44;55 42;49;60 PB2 97 100 33673017 Structural and Thermodynamic Analysis of the Resistance Development to Pimodivir (VX-787), the Clinical Inhibitor of Cap Binding to PB2 Subunit of Influenza A Polymerase. The H357N and F404Y mutations caused a considerable loss of the stabilization "free" energy for water molecules 1 to 4. 2021 Molecules (Basel, Switzerland) Result IV H357N;F404Y 4;14 9;19 33673017 Structural and Thermodynamic Analysis of the Resistance Development to Pimodivir (VX-787), the Clinical Inhibitor of Cap Binding to PB2 Subunit of Influenza A Polymerase. The M431I mutation had only a small impact on the "free" energy of the water molecules. 2021 Molecules (Basel, Switzerland) Result IV M431I 4 9 33673017 Structural and Thermodynamic Analysis of the Resistance Development to Pimodivir (VX-787), the Clinical Inhibitor of Cap Binding to PB2 Subunit of Influenza A Polymerase. The Mutated Forms M431I, F404Y and H357N of PB2 Impair Its Interaction with Pimodivir. 2021 Molecules (Basel, Switzerland) Result IV M431I;F404Y;H357N 18;25;35 23;30;40 PB2 44 47 33673017 Structural and Thermodynamic Analysis of the Resistance Development to Pimodivir (VX-787), the Clinical Inhibitor of Cap Binding to PB2 Subunit of Influenza A Polymerase. The RMDS of main chain atoms, Css and Cgamma for PB2-M431I is 0.12 A and for PB2-H357N is 0.09 A. 2021 Molecules (Basel, Switzerland) Result IV M431I;H357N 53;81 58;86 PB2;PB2 49;77 52;80 33673017 Structural and Thermodynamic Analysis of the Resistance Development to Pimodivir (VX-787), the Clinical Inhibitor of Cap Binding to PB2 Subunit of Influenza A Polymerase. The RMSD values for ligands referenced to the PB2-WT are PB2-F404Y-0.12 A, PB2-M431I-0.16 A, PB2-H357N-0.29 A. 2021 Molecules (Basel, Switzerland) Result IV F404Y;M431I;H357N 61;79;97 66;84;102 PB2;PB2;PB2;PB2 46;57;75;93 49;60;78;96 33673017 Structural and Thermodynamic Analysis of the Resistance Development to Pimodivir (VX-787), the Clinical Inhibitor of Cap Binding to PB2 Subunit of Influenza A Polymerase. The root-mean-square deviation for PB2-F404Y is 0.08 A up to Czeta. 2021 Molecules (Basel, Switzerland) Result IV F404Y 39 44 PB2 35 38 33673017 Structural and Thermodynamic Analysis of the Resistance Development to Pimodivir (VX-787), the Clinical Inhibitor of Cap Binding to PB2 Subunit of Influenza A Polymerase. The selected mutations in the cap-binding domains decreased the binding affinity of pimodivir by factors of 280 (F404Y mutant), 7 (M431I mutant) and 130 (H357N mutant). 2021 Molecules (Basel, Switzerland) Result IV F404Y;M431I;H357N 113;131;154 118;136;159 33673017 Structural and Thermodynamic Analysis of the Resistance Development to Pimodivir (VX-787), the Clinical Inhibitor of Cap Binding to PB2 Subunit of Influenza A Polymerase. These changes resulted in a larger decrease in binding affinity of pimodivir to PB2 upon the H357N and F404Y mutations. 2021 Molecules (Basel, Switzerland) Result IV H357N;F404Y 93;103 98;108 PB2 80 83 33673017 Structural and Thermodynamic Analysis of the Resistance Development to Pimodivir (VX-787), the Clinical Inhibitor of Cap Binding to PB2 Subunit of Influenza A Polymerase. This might be surprising especially for the F404Y because the residue 404 did not have a direct contact with the mentioned water molecules. 2021 Molecules (Basel, Switzerland) Result IV F404Y 44 49 33673017 Structural and Thermodynamic Analysis of the Resistance Development to Pimodivir (VX-787), the Clinical Inhibitor of Cap Binding to PB2 Subunit of Influenza A Polymerase. This model had the highest correlation with the experimental data and correctly ranked WT, M431I, H357N, and F404Y variant of PB2 by binding affinity of pimodivir. 2021 Molecules (Basel, Switzerland) Result IV M431I;H357N;F404Y 91;98;109 96;103;114 PB2 126 129 33673017 Structural and Thermodynamic Analysis of the Resistance Development to Pimodivir (VX-787), the Clinical Inhibitor of Cap Binding to PB2 Subunit of Influenza A Polymerase. W1 and W4 molecules become even more favorable and the other become less favorable (mainly W4, W6, and W10), which resulted in a decrease of the stabilization energy in the pimodivir:PB2-M431I complex. 2021 Molecules (Basel, Switzerland) Result IV M431I 187 192 PB2 183 186 33673017 Structural and Thermodynamic Analysis of the Resistance Development to Pimodivir (VX-787), the Clinical Inhibitor of Cap Binding to PB2 Subunit of Influenza A Polymerase. W2 and W3 became even repulsive upon the F404Y mutation. 2021 Molecules (Basel, Switzerland) Result IV F404Y 41 46 33679636 Improved in vitro Efficacy of Baloxavir Marboxil Against Influenza A Virus Infection by Combination Treatment With the MEK Inhibitor ATR-002. For both pairs of recombinant viruses (PA-mutant, WT) we found similar replication dynamics even though the titer for the PA mutants (rgH1N1-/rgH3N2-PA-I38T) was always below the titer of the WT viruses by 0.28 - 0.62 log10 (Figures 2A,B). 2021 Frontiers in microbiology Result IV I38T 152 156 PA;PA;PA 39;122;149 41;124;151 33679636 Improved in vitro Efficacy of Baloxavir Marboxil Against Influenza A Virus Infection by Combination Treatment With the MEK Inhibitor ATR-002. In contrast, BXA reduced the titer of the PA-mutants rgH1N1-PA-I38T and rgH3N2-PA-I38T only by 63 +- 3.23% and 60 +- 2.70%, whereas ATR-002 still achieved a reduction by 87.80 +- 2.20% and 99.70 +- 0.10%, respectively. 2021 Frontiers in microbiology Result IV I38T;I38T 63;82 67;86 PA;PA;PA 42;60;79 44;62;81 33679636 Improved in vitro Efficacy of Baloxavir Marboxil Against Influenza A Virus Infection by Combination Treatment With the MEK Inhibitor ATR-002. In order to determine the replication kinetics of the recombinant viruses (rgH1N1-PA-I38T, rgH3N2-PA-I38T) carrying the PA-I38T mutation in comparison to their respective recombinant wild type (rgH1N1-WT, rgH3N2-WT), we analyzed the increase in virus titer in the supernatant of cells infected with the different viruses at 6, 24, and 48 hpi. 2021 Frontiers in microbiology Result IV I38T;I38T;I38T 85;101;123 89;105;127 PA;PA;PA 82;98;120 84;100;122 33679636 Improved in vitro Efficacy of Baloxavir Marboxil Against Influenza A Virus Infection by Combination Treatment With the MEK Inhibitor ATR-002. This corroborates that the PA-I38T mutation confers resistance toward BXA and clearly indicates that BXA-resistant viruses are still highly sensitive toward MEK inhibition by ATR-002. 2021 Frontiers in microbiology Result IV I38T 30 34 PA 27 29 33679636 Improved in vitro Efficacy of Baloxavir Marboxil Against Influenza A Virus Infection by Combination Treatment With the MEK Inhibitor ATR-002. This is in agreement with published data indicating that the fitness of viruses isolated from BXA-treated persons, carrying the PA-I38T mutation, is reduced to a similar extent. 2021 Frontiers in microbiology Result IV I38T 131 135 PA 128 130 33679636 Improved in vitro Efficacy of Baloxavir Marboxil Against Influenza A Virus Infection by Combination Treatment With the MEK Inhibitor ATR-002. To confirm (i) reduced susceptibility toward BXA of the two recombinant PA-mutants (rgH1N1-PA-I38T, rgH3N2-PA-I38T) compared to the respective recombinant wild type viruses (rgH1N1-WT, rgH3N2-WT) and (ii) to further validate the antiviral activity of ATR-002 against the recombinant PA-mutants and WT viruses, we investigated the effect of ATR-002 versus BXA on the virus titer of the recombinant WT- and PA-mutant viruses 24 hpi compared to the untreated controls set to 100% (Figures 3A,B). 2021 Frontiers in microbiology Result IV I38T;I38T 94;110 98;114 PA;PA;PA;PA;PA 72;91;107;283;405 74;93;109;285;407 33782012 Discovery of a Novel Respiratory Syncytial Virus Replication Inhibitor. A total of 58 hits that showed similar inhibition against F_K394R virus and wild-type virus were subjected to further characterization. 2021 Antimicrobial agents and chemotherapy Result IV K394R 60 65 33782012 Discovery of a Novel Respiratory Syncytial Virus Replication Inhibitor. AY911262), which leads to a T-to-A change at amino acid 1684 of L polymerase, was found in all three clones but not in DMSO-p9 virus clones. 2021 Antimicrobial agents and chemotherapy Result IV T1684A 28 60 33782012 Discovery of a Novel Respiratory Syncytial Virus Replication Inhibitor. Because the K394R mutation in the fusion protein confers resistance to at least two fusion inhibitors with different structures, BMS-433771 and TMC353121, the CPE assay with this mutant virus (designated F_K394R) was used as a counterscreen assay to potentially filter out some entry inhibitors. 2021 Antimicrobial agents and chemotherapy Result IV K394R;K394R 12;206 17;211 33782012 Discovery of a Novel Respiratory Syncytial Virus Replication Inhibitor. L(T1684A) showed similar activation of RSV minigenome transcription as the wild-type L protein (data not shown). 2021 Antimicrobial agents and chemotherapy Result IV T1684A 2 8 33782012 Discovery of a Novel Respiratory Syncytial Virus Replication Inhibitor. The resistance of YM-53403 to triazole-1-resistant virus indicates the T1684A mutation had an impact on the YM-53403 binding pocket on L polymerase. 2021 Antimicrobial agents and chemotherapy Result IV T1684A 71 77 33782012 Discovery of a Novel Respiratory Syncytial Virus Replication Inhibitor. To further confirm if the T1684A mutation in the triazole-1-p9 virus alone contributed to the resistance to triazole-1, we introduced the mutation into the L expression construct, and the inhibitory effects of triazole-1 on the mutant protein L(T1684A)-driven minigenome expression were tested. 2021 Antimicrobial agents and chemotherapy Result IV T1684A;T1684A 26;245 32;251 33782012 Discovery of a Novel Respiratory Syncytial Virus Replication Inhibitor. Triazole-1 showed a similar IC50 (1.1 muM) in the CPE assay with the F_K394R mutant virus. 2021 Antimicrobial agents and chemotherapy Result IV K394R 71 76 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. A very high level of coverage (number of reads) of the region containing the HA 222 amino acid position and the possibility of detection of the presence of 0.2% of mutations made it possible to reveal the presence of D222G/N mutations in the minor virus variant with a frequency ranging from 0.2% to 0.6% in 14 samples from fatal cases with sufficient NGS coverage (Table 3). 2021 PloS one Result IV D222G;D222N 217;217 224;224 HA 77 79 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. An in-depth analysis of the D222G/N mutations revealed that all six tested samples with sufficient coverage had minor variants of the virus with D222G/N mutations (0.2-0.4%). 2021 PloS one Result IV D222G;D222N;D222G;D222N 28;28;145;145 35;35;152;152 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. Co-occurrence of mutations D222G and D222N (1% or more of both mutation variants in a sample) was observed in 11 samples out of 27, equivalent to 41% of the samples from fatal cases (the frequency of the mutations ranged from 4% to 97% in an individual sample). 2021 PloS one Result IV D222G;D222N 27;37 32;42 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. D222G/N mutations were also found in swabs (nasopharyngeal and oropharyngeal) taken from patients prior to their fatal outcome. 2021 PloS one Result IV D222N;D222G 0;0 7;7 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. Detection of minor A(H1N1)pdm09 virus variants with HA D222G/N mutations in samples from influenza cases with recovery. 2021 PloS one Result IV D222G;D222N 55;55 62;62 HA 52 54 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. For a more accurate assessment of the polymorphism data in the A(H1N1)pdm09 viruses, an optimized NGS analysis method was used to compare the content of D222G/N mutations in the primary material and in the A(H1N1)pdm09 virus isolates obtained using MDCK (Table 4). 2021 PloS one Result IV D222G;D222N 153;153 160;160 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. In 10 of these cases, the simultaneous presence of the D222G and D222N mutations was detected (Table 1). 2021 PloS one Result IV D222G;D222N 55;65 60;70 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. No major variants of the virus with D222G/N mutations were detected in 30 samples. 2021 PloS one Result IV D222G;D222N 36;36 43;43 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. Of the 77 A(H1N1)pdm2009 cases studied (including 47 fatal cases), in 18 cases D222G/N mutations were detected in major virus variants only in lethal cases (Table 1), which accounted for 38% of all studied fatal cases. 2021 PloS one Result IV D222G;D222N 79;79 86;86 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. Six samples had sufficient coverage (> 20,000) to detect minor variants of D222G/N mutations (Table 7). 2021 PloS one Result IV D222G;D222N 75;75 82;82 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. The analysis revealed an increase in the frequency of the D222G mutation in the lower respiratory tract compared to the upper respiratory tract, and also that the frequency of the D222N mutation was higher in the lung compared to the trachea. 2021 PloS one Result IV D222G;D222N 58;180 63;185 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. Thirty-eight percent of the samples from fatal cases had D222G/N mutations in the major virus variant and, in addition, 19% of the samples from fatal cases contained these mutations in the minor virus variants, with a frequency of more than 1% (1-47%). 2021 PloS one Result IV D222G;D222N 57;57 64;64 33975931 Analysis of the Evolution of Pandemic Influenza A(H1N1) Virus Neuraminidase Reveals Entanglement of Different Phenotypic Characteristics. After introduction of the K432E substitution (NC/13), an increased Km value (i.e., decreased substrate affinity) was observed using the MUNANA substrate. 2021 mBio Result IV K432E 26 31 33975931 Analysis of the Evolution of Pandemic Influenza A(H1N1) Virus Neuraminidase Reveals Entanglement of Different Phenotypic Characteristics. All NA proteins displayed the same ratio of specific activities comparing MUNANA to MUNGNA substrates, with the exception again of the NA proteins containing the K432E substitution, which consistently had a decreased ability to cleave MUNGNA. 2021 mBio Result IV K432E 162 167 NA;NA 4;135 6;137 33975931 Analysis of the Evolution of Pandemic Influenza A(H1N1) Virus Neuraminidase Reveals Entanglement of Different Phenotypic Characteristics. Although some substitutions are located relatively close to the active site (N200S, N248D, V241I, and K432E), none of them involves catalytic or framework residues. 2021 mBio Result IV N200S;N248D;V241I;K432E 77;84;91;102 82;89;96;107 33975931 Analysis of the Evolution of Pandemic Influenza A(H1N1) Virus Neuraminidase Reveals Entanglement of Different Phenotypic Characteristics. Analysis of the different NA gene sequences revealed that 16 amino acid substitutions (N248D, V106I, N369K, V241I, N44S, I106V, N200S, I321V, I34V/K432E, N386K, L40I, I314M, and V13I/V264I/N270K) became fixed in the virus population. 2021 mBio Result IV N248D;V106I;N369K;V241I;N44S;I106V;N200S;I321V;I34V;K432E;N386K;L40I;I314M;V264I;N270K;V13I 87;94;101;108;115;121;128;135;142;147;154;161;167;183;189;178 92;99;106;113;119;126;133;140;146;152;159;165;172;188;194;182 26 28 33975931 Analysis of the Evolution of Pandemic Influenza A(H1N1) Virus Neuraminidase Reveals Entanglement of Different Phenotypic Characteristics. Another consistent effect was the modestly increased specific activity resulting from the N386K substitution (introduced in WI/13). 2021 mBio Result IV N386K 90 95 33975931 Analysis of the Evolution of Pandemic Influenza A(H1N1) Virus Neuraminidase Reveals Entanglement of Different Phenotypic Characteristics. For some substitutions (I34V/K432E and V13I/V264I/N270K), the order in which they were acquired could not be resolved. 2021 mBio Result IV I34V;K432E;V264I;N270K;V13I 24;29;44;50;39 28;34;49;55;43 33975931 Analysis of the Evolution of Pandemic Influenza A(H1N1) Virus Neuraminidase Reveals Entanglement of Different Phenotypic Characteristics. In addition, we made a recombinant NA protein containing the I314M substitution in the background of the WI/13 NA protein. 2021 mBio Result IV I314M 61 66 NA;NA 35;111 37;113 33975931 Analysis of the Evolution of Pandemic Influenza A(H1N1) Virus Neuraminidase Reveals Entanglement of Different Phenotypic Characteristics. In contrast, the positive effect of the N386K substitution was still observed when transferrin was used. 2021 mBio Result IV N386K 40 45 33975931 Analysis of the Evolution of Pandemic Influenza A(H1N1) Virus Neuraminidase Reveals Entanglement of Different Phenotypic Characteristics. N386K results in the loss of a putative glycosylation site. 2021 mBio Result IV N386K 0 5 33975931 Analysis of the Evolution of Pandemic Influenza A(H1N1) Virus Neuraminidase Reveals Entanglement of Different Phenotypic Characteristics. No positive effect of the N369K substitution was observed when transferrin was used as the substrate, while the negative effect of the K432E substitution was much smaller and not significantly different. 2021 mBio Result IV N369K;K432E 26;135 31;140 33975931 Analysis of the Evolution of Pandemic Influenza A(H1N1) Virus Neuraminidase Reveals Entanglement of Different Phenotypic Characteristics. Of note, N386K and N44S disrupt and generate a potential N-glycosylation site, respectively. 2021 mBio Result IV N386K;N44S 9;19 14;23 33975931 Analysis of the Evolution of Pandemic Influenza A(H1N1) Virus Neuraminidase Reveals Entanglement of Different Phenotypic Characteristics. The location of these substitutions in the NA, excluding the substitutions located in the transmembrane domain or the stalk region (V13I, I34V, L40I, and N44S), the structure of which is not resolved, is shown in. 2021 mBio Result IV V13I;I34V;L40I;N44S 132;138;144;154 136;142;148;158 43 45 33975931 Analysis of the Evolution of Pandemic Influenza A(H1N1) Virus Neuraminidase Reveals Entanglement of Different Phenotypic Characteristics. The N369K substitution in MS/10, which is located in the 2SBS, like K432E, also had a relatively large effect on NA antigenicity. 2021 mBio Result IV N369K;K432E 4;68 9;73 113 115 33975931 Analysis of the Evolution of Pandemic Influenza A(H1N1) Virus Neuraminidase Reveals Entanglement of Different Phenotypic Characteristics. the results consistently show a positive effect of the N369K substitution (introduced in MS10) and a large negative effect of the K432E substitution (introduced in NC/13) on the cleavage of alpha2,3- and alpha2,6-linked SIA from fetuin. 2021 mBio Result IV N369K;K432E 55;130 60;135 33975931 Analysis of the Evolution of Pandemic Influenza A(H1N1) Virus Neuraminidase Reveals Entanglement of Different Phenotypic Characteristics. The substitutions N369K and K432E are located in the 2SBS at positions known to interact with SIA according to an N9 crystal structure. 2021 mBio Result IV N369K;K432E 18;28 23;33 N9 114 116 33975931 Analysis of the Evolution of Pandemic Influenza A(H1N1) Virus Neuraminidase Reveals Entanglement of Different Phenotypic Characteristics. The substitutions V264I and N270K in IN/15 consistently resulted in increased cleavage of alpha2,6-linked, but not alpha2,3-linked, SIAs, which was observed for both fetuin and transferrin. 2021 mBio Result IV V264I;N270K 18;28 23;33 33975931 Analysis of the Evolution of Pandemic Influenza A(H1N1) Virus Neuraminidase Reveals Entanglement of Different Phenotypic Characteristics. Thus, the K432E substitution (introduced in NC/13) has a positive effect on catalytic activity at low pH. 2021 mBio Result IV K432E 10 15 33975931 Analysis of the Evolution of Pandemic Influenza A(H1N1) Virus Neuraminidase Reveals Entanglement of Different Phenotypic Characteristics. When the antigenic distances of the NAs relative to their precursors were analyzed, which result from a single substitution, the largest antigenic change resulted from the K432E substitution introduced in NC13. 2021 mBio Result IV K432E 172 177 36 39 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. Although the cytosolic pH with Y17H 375K was less than that with Y17H 750 at 5 and 7 DPI, both groups returned to baseline pH at 10 DPI, whereas the cytosolic pH with WT 750 was below the limit of detection, with a low number of live cells (Fig 6). 2021 PloS one Result IV Y17H;Y17H 31;65 35;69 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. Although the mean tracheal cell membrane pH with Y17H 375K was 6.01 at 5 DPI, it sharply declined to 3.05 at 7 DPI. 2021 PloS one Result IV Y17H 49 53 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. At 10 DPI, the early endosome pH with WT 750 was below the limit of detection, whereas that with Y17H 750 remained at baseline and Y17H 375K slightly increased to 5.75 (Fig 6). 2021 PloS one Result IV Y17H;Y17H 97;131 101;135 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. At 10 DPI, the mean tracheal cell membrane pH with Y17H 750 recovered to baseline, whereas the pH with WT 750 and Y17H 375 were below the limit of detection with a low number of live cells (Fig 8). 2021 PloS one Result IV Y17H;Y17H 51;114 55;118 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. At 2 and 5 DPI, the nasal and soft palate temperatures did not change, except a 1-point increase at 5 DPI with Y17H 375K. 2021 PloS one Result IV Y17H 111 115 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. At 5 and 7 DPI, mice inoculated with Y17H 750 and WT 750 exhibited decreased cell membrane pH values to a mean of 5.23 at 5 DPI and 5.6 at 7 DPI for Y17H 750 and to 4.94 at 5 DPI and 4.7 at DPI for WT 750. 2021 PloS one Result IV Y17H;Y17H 37;149 41;153 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. At 5 DPI, all three IAVs significantly differed from PBS treatment (P < 0.0001), and WT 750 and Y17H 750 also significantly differed (P = 0.001). 2021 PloS one Result IV Y17H 96 100 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. At 5 DPI, salinity increased for all IAVs, and Y17H 750 differed from WT 750. 2021 PloS one Result IV Y17H 47 51 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. At 5 DPI, the cell membrane pH decreased in all groups, with significant differences between Y17H 750 and WT 750, and continuously decreased at 7 and 10 DPI. 2021 PloS one Result IV Y17H 93 97 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. At 5 DPI, WT 750 had lower saline concentrations than both Y17H 750 and Y17H 375K, and at 7 DPI, only WT 750 was significantly higher than PBS (Fig 4C). 2021 PloS one Result IV Y17H;Y17H 59;72 63;76 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. At 5 DPI, Y17H 750 recovered the microtubule mean pH to that of the baseline, which increased by 0.5 at 7 DPI and by 0.2 at 10 DPI. 2021 PloS one Result IV Y17H 10 14 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. At 7 DPI, mice infected with Y17H 750 had a naris pH of 6.89, which recovered to approximately 7.31 by 10 DPI. 2021 PloS one Result IV Y17H 29 33 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. At 7 DPI, only WT 750 and Y17H 375K significantly differed from PBS (Fig 4A). 2021 PloS one Result IV Y17H 26 30 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. At 7 DPI, the three IAVs increased the pH to 6.9 for Y17H 750, 6.7 for WT 750, and 6.6 for Y17H 375K. 2021 PloS one Result IV Y17H;Y17H 53;91 57;95 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. At 7 DPI, Y17H 750 salinity levels returned to baseline, which ranged from 0 to 10 parts per trillion. 2021 PloS one Result IV Y17H 10 14 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. Both Y17H 750 and WT 750 differed from Y17H 375K. 2021 PloS one Result IV Y17H;Y17H 5;39 9;43 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. Both Y17H 750 and Y17H 375K slightly decreased the mean pH from 5 to 10 DPI (Fig 8). 2021 PloS one Result IV Y17H;Y17H 5;18 9;22 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. By 7 DPI, the subcellular compartment pH of mice infected with Y17H IAVs returned to baseline, whereas mice infected with WT IAV had reduced populations of viable cells (Figs 6-8) 2021 PloS one Result IV Y17H 63 67 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. By 7 DPI, the subcellular compartment pH of mice infected with Y17H IAVs returned to baseline, whereas mice infected with WT IAV had reduced populations of viable cells (Figs 6-8). 2021 PloS one Result IV Y17H 63 67 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. CD11b-expressing cells peaked at 2 DPI with Y17H 750 and Y17H 375K and then rapidly declined at 5 DPI. 2021 PloS one Result IV Y17H;Y17H 44;57 48;61 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. CD4+ T cells peaked by 10 DPI in the noses of Y17H 750- and Y17H 375K-infected mice but did not increase with WT 750. 2021 PloS one Result IV Y17H;Y17H 46;60 50;64 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. DCs gradually increased with Y17H 750 and Y17H 375K starting 2 DPI and peaked at 5 DPI, followed by a decline at 7 DPI. 2021 PloS one Result IV Y17H;Y17H 29;42 33;46 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. In contrast, at 7 DPI WT 750 and Y17H 375K inoculation resulted in a naris pH of approximately 6.5 and was not restored to the naris uninfected pH by 10 DPI (Fig 3A). 2021 PloS one Result IV Y17H 33 37 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. In contrast, macrophage populations peaked at 2 DPI with Y17H 750 and Y17H 375K and gradually decreased until 10 DPI. 2021 PloS one Result IV Y17H;Y17H 57;70 61;74 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. In contrast, viral titers of Y17H 750 were lower by a factor of 3 log at 2 DPI and by 20-fold at 5 DPI. 2021 PloS one Result IV Y17H 29 33 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. In contrast, Y17H 750 cell membrane pH returned to that of baseline at 7 and 10 DPI (Fig 6). 2021 PloS one Result IV Y17H 13 17 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. In the nares, Y17H 375K resulted in the highest saline concentration at 2 DPI, in comparison with PBS, and no statistical difference with Y17H 750 or WT 750. 2021 PloS one Result IV Y17H;Y17H 14;138 18;142 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. In the nasal sinuses, saline concentrations at 2 DPI in both Y17H 750- and Y17H 375K-infected mice differed from that of PBS-treated mice. 2021 PloS one Result IV Y17H;Y17H 61;75 65;79 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. In the present study, infection with Y17H 750 did not sufficiently acidify the respiratory tract to a value that would be expected to inactivate the virus, while infection with higher-dose Y17H 375K resulted in a respiratory acidification sufficiently low to cause extracellular inactivation. 2021 PloS one Result IV Y17H;Y17H 37;189 41;193 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. In the soft palate epithelium, the microtubule mean pH slightly increased with Y17H 750 (5.15, P < 0.01) and Y17H 375K (5.28, P < 0.05 as compared with Y17H 750 and WT 750), with the highest increase in WT 750-infected mice (6.5, P < 0.001) at 2 DPI. 2021 PloS one Result IV Y17H;Y17H;Y17H 79;109;152 83;113;156 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. In the soft palate, WT 750 produced a mean viral titer that was 3 logs higher than that of Y17H 750 and 1 log higher than that of Y17H 375K at 2 DPI (Fig 2B). 2021 PloS one Result IV Y17H;Y17H 91;130 95;134 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. In the trachea, WT 750 and Y17H 375K exhibited the same kinetics during infection, with viral titers of 106 TCID50/mL at 2 and 5 DPI followed by gradual declines at 7 DPI (Fig 2C). 2021 PloS one Result IV Y17H 27 31 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. In the trachea, WT 750 and Y17H 750 differed from PBS at 2 DPI, whereas Y17H 375K did not differ from PBS or WT 750 and Y17H 750. 2021 PloS one Result IV Y17H;Y17H;Y17H 27;72;120 31;76;124 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. In the Y17H 750- and Y17H 375K-infected mice, T-cell populations began accumulating in the nose at 5 DPI, soft plate at 2 DPI, and trachea at 5 DPI (Fig 5C). 2021 PloS one Result IV Y17H;Y17H 7;21 11;25 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. Infection by Y17H 750 reduced nasal sinus pH to 7.25 at 2 DPI, 6.96 at 5 DPI, and 6.82 at 7 DPI before recovery to 7.5 at 10 DPI (Fig 3B). 2021 PloS one Result IV Y17H 13 17 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. Infection in the trachea of Y17H 375K yielded similar titers to WT 750 except for reduced titers in nasal, soft palate, and tracheal tissues that were approximately 0- to 0.5-log lower at 2 DPI (P = 0.017) and at 5 DPI (P = 0.01). 2021 PloS one Result IV Y17H 28 32 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. Infection with WT 750 and Y17H 375K reduced nasal sinus pH even lower (to 6.22 and 6.48, respectively) at 5 DPI and did not fully recover by 10 DPI. 2021 PloS one Result IV Y17H 26 30 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. Like the nasal pH values, Y17H 750 increased cytosolic pH to 6.01 and 7.36 at 7 and 10 DPI, respectively. 2021 PloS one Result IV Y17H 26 30 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. Like the pH changes in the early endosomes, the nasal cytosolic pH significantly increased at 2 DPI to 7.6 (P < 0.5) in Y17H (750PFU) and 7.52 in WT (750PFU) (P < 0.01) and slightly decreased to 6.25 (P < 0.5) in Y17H (375KPFU), as compared to that of PBS-treated mice. 2021 PloS one Result IV Y17H;Y17H 120;213 124;217 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. Mice inoculated with Y17H 375K and WT 750 resulted in mean nasal viral titers that were higher by approximately 2 logs at 2 DPI (P = 0.05) and at 5 DPI (P = 0.007) (Fig 2A) than were those of Y17H 750 PFU-infected mice. 2021 PloS one Result IV Y17H;Y17H 21;192 25;196 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. Overall, the HA-destabilizing Y17H substitution was highly attenuating but could be partially overcome by inoculation with a 500-fold higher dose. 2021 PloS one Result IV Y17H 30 34 HA 13 15 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. Overall, these data indicate that increasing the dose of Y17H IAV to 375,000 PFU caused similar weight loss and comparable (albeit unequal) nasal, soft palate, and tracheal viral titers with those of WT 750. 2021 PloS one Result IV Y17H 57 61 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. Previous studies showed that infectivity of WT virus in pH 6.4 media decayed at rate similar to neutral-pH media, while Y17H was much more rapidly inactivated when exposed to a pH of 6.4. 2021 PloS one Result IV Y17H 120 124 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. The cell membrane pH in the nasal epithelial cells in mice infected with all three IAVs increased significantly at 2 DPI, with mean pH values of 6.39 (P < 0.5), 5.69 (P < 0.5), and 6.73 (P < 0.5) for Y17H 750, WT 750, and Y17H 375K, respectively. 2021 PloS one Result IV Y17H;Y17H 200;222 204;226 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. The early endosome pH with Y17H 750 returned to a baseline pH of 6.44 (P < 0.5), whereas the early endosome pH with WT 750 and Y17H 375K decreased to mean values of 4.81 (P < 0.5) and 4.15 respectively at 7 DPI. 2021 PloS one Result IV Y17H;Y17H 27;127 31;131 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. The late endosome mean pH in the nasal epithelium increased to 6.6 (P < 0.5) with Y17H 750, to 5.7 (P < 0.5) with WT 750, and to 6.16 (P < 0.5) with Y17H 375K at 2 DPI. 2021 PloS one Result IV Y17H;Y17H 82;149 86;153 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. The late endosome mean pH then decreased at 5 DPI and differed between the Y17H and WT IAVs. 2021 PloS one Result IV Y17H 75 79 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. The late endosome pH in the soft palate and tracheal epithelium exhibited the same degree of changes as that of the nasal epithelium for all IAVs except for Y17H 750, which showed the highest mean pH mean at 7 DPI and then returned to within 0.5 of the baseline pH. 2021 PloS one Result IV Y17H 157 161 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. The macrophages in WT 750-infected mice peaked at 2 DPI and suddenly declined at 5 DPI, whereas the macrophages in Y17H 750- and Y17H 375K-infected mice increased at 2 DPI, peaking from 5 to 10 DPI. 2021 PloS one Result IV Y17H;Y17H 115;129 119;133 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. The mean pH at 2 DPI was reduced to 7.1, 6.5, and 6.4 for Y17H 750, WT 750, and Y17H 375K, respectively (Fig 3C). 2021 PloS one Result IV Y17H;Y17H 58;80 62;84 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. The mean pH in the naris of infected mice at 2 and 5 DPI decreased to approximately 7.37 and 6.96, respectively (P < 0.0003, compared to PBS-treated mice), for Y17H 750, to 7.02 and 6.68, respectively (P < 0.0001 compared to PBS-treated mice), for Y17H 375K, and 6.04 and 5.94, respectively, for WT 750. 2021 PloS one Result IV Y17H;Y17H 160;248 164;252 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. The mean pH of the tracheal epithelial cell membranes in infected mice 2 DPI increased to approximately 6.34 (P < 0.01), 6.5 (P < 0.001), and 6.21 for Y17H 750, WT 750, and Y17H 375K, respectively, as compared with that of PBS-treated mice. 2021 PloS one Result IV Y17H;Y17H 151;173 155;177 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. The mean pH returned to neutral with Y17H 750 at 10 DPI, whereas WT 750 and Y17H 375K maintained mildly acidic. 2021 PloS one Result IV Y17H;Y17H 37;76 41;80 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. The number of live cells at 10 DPI was low, except for those isolated from Y17H 750-infected mice, which maintained high numbers of live cells and a mean pH of 5.1 (P = 0.02) at 7 DPI and 5.2 at 10 DPI (Fig 7). 2021 PloS one Result IV Y17H 75 79 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. The pH in the cytosol of the soft palate epithelium was like the nasal cytosolic pH at 2 and 5 DPI for all groups, except that the mean pH value with Y17H 750 was acidic (4.85, P < 0.001) and even more acidic with WT 750 (3.11, P < 0.001), as compared to that of PBS-treated mice. 2021 PloS one Result IV Y17H 150 154 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. The population of CD4+ T cells notably increased with Y17H 750 and Y17H 375K at 7 DPI. 2021 PloS one Result IV Y17H;Y17H 54;67 58;71 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. The secretory vesicle and microtubule mean pH increased in the mean pH at 2 DPI, which was significantly increased in the nasal microtubule mean pH with both Y17H IAV inocula (P < 0.01 for Y17H 750 and P < 0.5 for Y17H375K), as compared to that of PBS-treated mice. 2021 PloS one Result IV Y17H;Y17H 158;189 162;193 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. The soft palate cell membrane mean pH sharply increased at 2 DPI, with mean values of 6.3 (P < 0.5), 6.11 (P < 0.02), and 7.82 (P < 0.01) for mice inoculated with Y17H 750, WT 750, and Y17H 375K, respectively, as compared to that of PBS-treated mice. 2021 PloS one Result IV Y17H;Y17H 163;185 167;189 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. The temperature slightly increased with Y17H 750 at 2 and 5 DPI and with Y17H 375K at 5 DPI (Fig 4E). 2021 PloS one Result IV Y17H;Y17H 40;73 44;77 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. The WT 750 and Y17H 375K groups had maximum body weight losses of approximately 20%, whereas the Y17H 750 group has significantly less (P < 0.05 at 7-10 DPI) (Fig 2D). 2021 PloS one Result IV Y17H;Y17H 15;97 19;101 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. The Y17H 750-infected mice had slightly decreased the mean pH (6.01) at 5 DPI followed by an increase to 6.81 (P < 0.01) at 7 DPI, with significantly increased mean pH values of 5.40 and 4.80 with WT 750 at 5 DPI (P < 0.01) and 7 DPI (P < 0.01), respectively. 2021 PloS one Result IV Y17H 4 8 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. Thus, Y17H 750 did not induce pathogenicity such as that caused by Y17H 375K of WT 750. 2021 PloS one Result IV Y17H;Y17H 6;67 10;71 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. To measure the extracellular pH in murine nasal, soft palate, and tracheal tissues, we intranasally inoculated 5-week-old mice with WT 750, Y17H 750, Y17H 375K, or PBS. 2021 PloS one Result IV Y17H;Y17H 140;150 144;154 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. To measure the subcellular pH in murine nose, soft palate, and tracheal cells, we intranasally inoculated mice with WT 750, Y17H 750, Y17H 375K, or PBS. 2021 PloS one Result IV Y17H;Y17H 124;134 128;138 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. To normalize the viral titers and body weight loss for subsequent studies of host responses, we included an additional group of mice infected with 375,000 PFU Y17H as we had established previously. 2021 PloS one Result IV Y17H 159 163 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. Tracheal pH decreased, but not less than 7, during infection with Y17H 750 (Fig 3D). 2021 PloS one Result IV Y17H 66 70 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. We inoculated groups of DBA/2J mice with 750 PFU of WT or HA1-Y17H. 2021 PloS one Result IV Y17H 62 66 HA1 58 61 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. WT 750 and Y17H 375 cell membrane pH remained low at 7 DPI and at 10 DPI, with a low number of live cells. 2021 PloS one Result IV Y17H 11 15 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. WT 750 and Y17H 375K continued to decrease the mean microtubule pH and the number of live cells during infection (Fig 7). 2021 PloS one Result IV Y17H 11 15 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. WT 750 and Y17H 375K cytosolic pH remained acidic at 7 DPI but was below the limit of detection at 10 DPI (Fig 7). 2021 PloS one Result IV Y17H 11 15 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. WT 750 and Y17H 375K differed from each other. 2021 PloS one Result IV Y17H 11 15 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. WT 750 and Y17H 375K salinity returned to baseline at 10 DPI (Fig 4A-4D). 2021 PloS one Result IV Y17H 11 15 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. WT 750 and Y17H375K decreased the microtubule mean pH until 10 DPI, whereas Y17H 750 recovered the mean baseline pH at 5 DPI and slightly increased at 7 and 10 DPI. 2021 PloS one Result IV Y17H 76 80 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. Y17H 375 and WT 750 continued to decrease the mean pH until 10 DPI, whereas the mean pH with Y17H 750 recovered. 2021 PloS one Result IV Y17H;Y17H 0;93 4;97 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. Y17H 375K had similar kinetics of tracheal acidification. 2021 PloS one Result IV Y17H 0 4 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. Adding the compensatory mutation, P653L, to K229R + N321K showed full compensation of polymerase activity to the level of N321K. 2021 PLoS pathogens Result IV P653L;K229R;N321K;N321K 34;44;52;122 39;49;57;127 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. As had been observed in the background of Eng195, Eng687 K229R resulted in low but appreciable polymerase activity which was fully compensated by the presence of P653L (Fig 4B). 2021 PLoS pathogens Result IV K229R;P653L 57;162 62;167 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. As the actual fitness values in ferrets remain unknown, the fitness values were chosen to qualitatively reflect the fitness advantage for P653L and the fitness cost of K229R seen in MDCKs. 2021 PLoS pathogens Result IV P653L;K229R 138;168 143;173 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. Despite the fitness advantage for P653L single mutant, the proportion of P653L did not increase above 3% after 20 generations. 2021 PLoS pathogens Result IV P653L;P653L 34;73 39;78 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. Eng195 PA N321K had higher polymerase activity compared to P653L (1-way ANOVA, p<0.001). 2021 PLoS pathogens Result IV N321K;P653L 10;59 15;64 PA 7 9 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. For mutation to increase the proportion of the P653L single mutant to the level seen in the baseline model, the mutation rate would have to be 10x higher than has been empirically measured or the fitness of P653L would have to be much higher (see S1 Appendix). 2021 PLoS pathogens Result IV P653L;P653L 47;207 52;212 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. Four donor ferrets were inoculated with K229R + P653L and Eng195 viruses in the ratio of 95:5. 2021 PLoS pathogens Result IV K229R;P653L 40;48 45;53 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. Given the large fitness advantage of the P653L mutant virus in ferrets, it is surprising that the mutation has not been observed in pH1N1 isolates. 2021 PLoS pathogens Result IV P653L 41 46 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. Here, we increased the fitness of K229R such that it was equal to WT and K229R + P653L (f = 1). 2021 PLoS pathogens Result IV K229R;K229R;P653L 34;73;81 39;78;86 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. However, cost to polymerase activity caused by K229R was noticeably less in Eng687 than in Eng195. 2021 PLoS pathogens Result IV K229R 47 52 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. However, the loss of the R229 allele was caused by the fitness advantage of the PA P653L single mutant not the fitness cost of the K229R mutant. 2021 PLoS pathogens Result IV P653L;K229R 83;131 88;136 PA 80 82 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. In addition, changing the fitness cost of K229R did not quantitatively affect the results of the model. 2021 PLoS pathogens Result IV K229R 42 47 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. In order to test whether P653L provided a benefit in a N321K background, we rescued a N321K + P653L virus. 2021 PLoS pathogens Result IV P653L;N321K;N321K;P653L 25;55;86;94 30;60;91;99 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. In the baseline model (Fig 3A), the initial proportions were, as in the inoculum of the experiment, 95% K229R + P653L and 5% wildtype. 2021 PLoS pathogens Result IV K229R;P653L 104;112 109;117 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. Introducing both K229R and N321K into Eng195 showed that N321K partially compensated for the loss of polymerase activity conferred by K229R but did not reach the level of polymerase activity of P653L + K229R (Fig 4A). 2021 PLoS pathogens Result IV K229R;N321K;N321K;K229R;P653L;K229R 17;27;57;134;194;202 22;32;62;139;199;207 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. Modelling shows a selective advantage for the P653L mutant coupled with reassortment drives genotype frequency changes. 2021 PLoS pathogens Result IV P653L 46 51 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. Mutation generated very few P653L single mutants compared to recombination. 2021 PLoS pathogens Result IV P653L 28 33 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. Next, we introduced the K229R and P653L mutations into the polymerase of a representative 3rd wave pandemic H1N1 virus, Eng687, which already contained N321K. 2021 PLoS pathogens Result IV K229R;P653L;N321K 24;34;152 29;39;157 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. Next, we sought to understand how the K229R and P653L mutations might change over time within an individual ferret. 2021 PLoS pathogens Result IV K229R;P653L 38;48 43;53 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. Next, we tested whether the fitness advantage of the P653L single mutant was sufficient to cause the observed increase of the K229 allele (Fig 3C). 2021 PLoS pathogens Result IV P653L 53 58 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. Next, we tested whether the observed increase of the K229 allele was due to the fitness advantage of P653L mutant (Fig 3B) or the fitness cost to the K229R mutant (Fig 3C). 2021 PLoS pathogens Result IV P653L;K229R 101;150 106;155 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. Next, we wanted to test whether N321K could affect the evolution of resistance of favipiravir by compensating for the defect in polymerase activity caused by PB1 K229R. 2021 PLoS pathogens Result IV N321K;K229R 32;162 37;167 PB1 158 161 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. Our previous work showed that the polymerase of Eng195 was less well adapted to human cells compared to later pandemic isolates and identified the N321K PA mutation as being a key mutation that led to improved polymerase activity in second and third wave pH1N1 virus isolates. 2021 PLoS pathogens Result IV N321K 147 152 PA 153 155 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. P653L only showed an increase in polymerase activity in the presence of K229R. 2021 PLoS pathogens Result IV P653L;K229R 0;72 5;77 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. PA P653L does not show a fitness benefit in more recent viruses. 2021 PLoS pathogens Result IV P653L 3 8 PA 0 2 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. PB1 and PA sequencing revealed that RNA ratio in the inoculum was 95% K229R + P653L and 5% Eng195. 2021 PLoS pathogens Result IV K229R;P653L 70;78 75;83 PA;PB1 8;0 10;3 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. Reassortment due to coinfection led to the generation of K229R and P653L single mutants. 2021 PLoS pathogens Result IV K229R;P653L 57;67 62;72 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. Sequencing of virus in the nasal wash showed high levels of both R229 in PB1 (>50%) and L653 in PA (>85%) in all infected ferrets indicating that the K229R + P653L virus could productively infect ferrets and was transmitted both through direct and indirect contact transmission routes (Fig 2). 2021 PLoS pathogens Result IV K229R;P653L 150;158 155;163 PA;PB1 96;73 98;76 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. Surprisingly, in MDCK cells a N321K virus showed lower growth after 24 hours than P653L or N321K + P653L (S3 Fig). 2021 PLoS pathogens Result IV N321K;P653L;N321K;P653L 30;82;91;99 35;87;96;104 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. Taken with the previous result, our model implies that when the WT virus reassorts the P653 allele is lost if there is a cost to the K229R mutant. 2021 PLoS pathogens Result IV K229R 133 138 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. The earliest sample after acquisition of virus in 2 of 4 contact ferrets and 2 of 3 indirect contact ferrets contained 100% K229R + P653L, with no transmission of any wild-type segments. 2021 PLoS pathogens Result IV K229R;P653L 124;132 129;137 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. The fitness advantage of the P653L mutant allowed it to outcompete both the WT and K229R + P653L. 2021 PLoS pathogens Result IV P653L;K229R;P653L 29;83;91 34;88;96 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. The fitness cost of the K229R mutation caused the loss of the P653 allele but did not replicate the loss of the R229 allele as seen in the baseline model. 2021 PLoS pathogens Result IV K229R 24 29 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. The nasal cavity may have a lower temperature and so we confirmed that this fitness advantage for P653L and cost for K229R was present in MDCKs at both 37 and 33 C (S1 Fig). 2021 PLoS pathogens Result IV P653L;K229R 98;117 103;122 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. The one exception was a mutation in M2 (T60A) which was present in both the direct and indirect contact from the same donor but in no other ferrets. 2021 PLoS pathogens Result IV T60A 40 44 M2 36 38 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. There was also a small proportion of K229R single mutant viruses which did not rise above 5%. 2021 PLoS pathogens Result IV K229R 37 42 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. There was no difference in polymerase activity between N321K and N321K + P653L (1-way ANOVA, p = 0.80). 2021 PLoS pathogens Result IV N321K;N321K;P653L 55;65;73 60;70;78 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. Therefore, for our baseline model, we assigned a relative fitness (f) of 1 to wild-type virus and K229R + P653L mutant, 1.25 for the P653L mutant and 0.01 for the K229R mutant. 2021 PLoS pathogens Result IV K229R;P653L;P653L;K229R 98;106;133;163 103;111;138;168 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. This confirmed that the K229R + P653L virus was able to productively infect and transmit between ferrets. 2021 PLoS pathogens Result IV K229R;P653L 24;32 29;37 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. This implied that N321K provides a greater increase in polymerase activity than P653L and P653L provided no additional benefit to polymerase activity in the presence of N321K. 2021 PLoS pathogens Result IV N321K;P653L;P653L;N321K 18;80;90;169 23;85;95;174 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. This was because co-infection with wild type and K229R + P653L, and thus the opportunity for the P653L single mutant to be generated through reassortment, occurs much more frequently than de novo mutation for the MOI and mutation rates assumed. 2021 PLoS pathogens Result IV K229R;P653L;P653L 49;57;97 54;62;102 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. To test whether favipiravir resistant virus could transmit by direct or indirect contact, we inoculated ferrets with a mix of resistant virus bearing PB1 K229R + PA P653L and the corresponding wild-type virus, Eng195, a prototypical first wave pH1N1 2009 virus. 2021 PLoS pathogens Result IV K229R;P653L 154;165 159;170 PA;PB1 162;150 164;153 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. To test whether there was epistasis between N321K and P653L, we introduced the N321K mutation into Eng195 and tested polymerase using the minigenome activity (Fig 4A). 2021 PLoS pathogens Result IV N321K;P653L;N321K 44;54;79 49;59;84 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. Viruses shed in nasal wash underwent whole genome sequencing to search for additional mutations which might be required for efficient transmission or to further compensate for K229R or P653L. 2021 PLoS pathogens Result IV K229R;P653L 176;185 181;190 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. We do not know the reason for the loss of fitness of N321K in MDCK cells but it is reassuring that minigenome assays reflected the fitness advantage of N321K previously seen in HAEs. 2021 PLoS pathogens Result IV N321K;N321K 53;152 58;157 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. We hypothesized that one reason the mutation might not be present is that more recent mutations in the pH1N1 virus polymerase also confer a fitness advantage, achieving the same increase in polymerase activity as P653L. 2021 PLoS pathogens Result IV P653L 213 218 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. We kept other parameters the same including the fitness of K229R (0.01). 2021 PLoS pathogens Result IV K229R 59 64 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. We maintained a fitness advantage for P653L (1.25). 2021 PLoS pathogens Result IV P653L 38 43 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. We noted that previous fitness data we generated in MDCK cells showed a large fitness disadvantage for the K229R mutant, little difference between wild type and the double mutants, and a fitness advantage for the P653L mutant. 2021 PLoS pathogens Result IV K229R;P653L 107;213 112;218 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. We reduced the fitness of P653L such that it was equal to WT and K229R + P653L (f = 1). 2021 PLoS pathogens Result IV P653L;K229R;P653L 26;65;73 31;70;78 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. We showed that varying the initial proportions of WT and K229R + P653L did not lead to qualitative changes in our results nor did varying the viral load. 2021 PLoS pathogens Result IV K229R;P653L 57;65 62;70 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. Without a fitness advantage to the P653L single mutant, the WT virus was still lost after 20 generations but the frequency of P653L did not rise above 5%, the starting frequency in the inoculum (Fig 3B). 2021 PLoS pathogens Result IV P653L;P653L 35;126 40;131 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. Without a fitness cost to the K229R mutant, there was an increase in the P653L single mutant and a loss of WT virus. 2021 PLoS pathogens Result IV K229R;P653L 30;73 35;78 34065033 Novel Clade 2.3.4.4b Highly Pathogenic Avian Influenza A H5N8 and H5N5 Viruses in Denmark, 2020. In addition, one of the H5N8 viruses (A/barnacle goose/Denmark/14139-3/2020) had a PB2-M64T amino acid substitution that is highly conserved in human influenza A H1N1, H2N2, and H3N2 viruses. 2021 Viruses Result IV M64T 87 91 PB2 83 86 34065033 Novel Clade 2.3.4.4b Highly Pathogenic Avian Influenza A H5N8 and H5N5 Viruses in Denmark, 2020. The PB2-M64T substitution was not present in A/Astrakhan/3212/2020(H5N8) (EPI_ISL_1038924) virus detected in workers at a poultry farm in Russia on 12 December 2020. 2021 Viruses Result IV M64T 8 12 PB2 4 7 34068322 Dual R108K and G189D Mutations in the NS1 Protein of A/H1N1 Influenza Virus Counteract Host Innate Immune Responses. Compared with the WT rXJ49 NS1 protein, the rXJ49-NS1mut protein harboring R108K/G189D inhibited activation of the IFN-beta promotor. 2021 Viruses Result IV R108K;G189D 75;81 80;86 NS1 27 30 34068322 Dual R108K and G189D Mutations in the NS1 Protein of A/H1N1 Influenza Virus Counteract Host Innate Immune Responses. Impact of the R108K/G189D Mutation on Expression of Genes Involved in Cytokine Responses In Vitro. 2021 Viruses Result IV R108K;G189D 14;20 19;25 34068322 Dual R108K and G189D Mutations in the NS1 Protein of A/H1N1 Influenza Virus Counteract Host Innate Immune Responses. In Vivo Characterization of the Recombinant pdmH1N1 Virus XJ49 Expression NS1 with Dual R108K/G189D Mutant. 2021 Viruses Result IV R108K;G189D 88;94 93;99 NS1 74 77 34068322 Dual R108K and G189D Mutations in the NS1 Protein of A/H1N1 Influenza Virus Counteract Host Innate Immune Responses. Sequencing of the NS fragment of rXJ49-NS1mut showed that the dual R108K/G189D mutation was stable over time. 2021 Viruses Result IV R108K;G189D 67;73 72;78 NS 18 20 34068322 Dual R108K and G189D Mutations in the NS1 Protein of A/H1N1 Influenza Virus Counteract Host Innate Immune Responses. The Dual R108K/G189D Mutant in NS1 Suppresses Expression of IFN-beta. 2021 Viruses Result IV R108K;G189D 9;15 14;20 NS1 31 34 34068322 Dual R108K and G189D Mutations in the NS1 Protein of A/H1N1 Influenza Virus Counteract Host Innate Immune Responses. The NS1 Dual R108K/G189D Mutant Virus Exhibited Similar Viral Replication Ability Compared with WT Strain. 2021 Viruses Result IV R108K;G189D 13;19 18;24 NS1 4 7 34068322 Dual R108K and G189D Mutations in the NS1 Protein of A/H1N1 Influenza Virus Counteract Host Innate Immune Responses. These results suggest that the dual R108K/G189D mutation in the NS1 protein has little effect on viral replication but increases the pathogenicity of the XJ49 virus in mice. 2021 Viruses Result IV R108K;G189D 36;42 41;47 NS1 64 67 34068322 Dual R108K and G189D Mutations in the NS1 Protein of A/H1N1 Influenza Virus Counteract Host Innate Immune Responses. These results suggest that the R108K and G189D mutations in NS1 significantly inhibit expression of host-innate immunity-related proteins that function at the early stage of virus infection and that NS1 shutoff activity reported in previous studies is not the only mechanism of blocking antiviral responses in human hosts. 2021 Viruses Result IV R108K;G189D 31;41 36;46 NS1;NS1 60;199 63;202 34068322 Dual R108K and G189D Mutations in the NS1 Protein of A/H1N1 Influenza Virus Counteract Host Innate Immune Responses. These results suggest that the R108K/G189D mutation in NS1 inhibits expression of genes related to host innate immunity. 2021 Viruses Result IV R108K;G189D 31;37 36;42 NS1 55 58 34068322 Dual R108K and G189D Mutations in the NS1 Protein of A/H1N1 Influenza Virus Counteract Host Innate Immune Responses. This suggests that the influenza virus NS1 protein inhibits host gene expression and that the R108K/G189D mutation increases this effect. 2021 Viruses Result IV R108K;G189D 94;100 99;105 NS1 39 42 34068322 Dual R108K and G189D Mutations in the NS1 Protein of A/H1N1 Influenza Virus Counteract Host Innate Immune Responses. Thus, the R108K/G189D mutation increases the ability of NS1 to impair host innate immune responses. 2021 Viruses Result IV R108K;G189D 10;16 15;21 NS1 56 59 34068322 Dual R108K and G189D Mutations in the NS1 Protein of A/H1N1 Influenza Virus Counteract Host Innate Immune Responses. To determine whether mutations R108K and G189D in the XJ49 NS1 protein affect IFN-beta expression, we measured the promoter activity of IFN-beta using a luciferase reporter gene assay. 2021 Viruses Result IV R108K;G189D 31;41 36;46 NS1 59 62 34068322 Dual R108K and G189D Mutations in the NS1 Protein of A/H1N1 Influenza Virus Counteract Host Innate Immune Responses. Using this reverse genetics system, dual R108K/G189D mutations were introduced into NS1 segments, and a recombinant mutant, rXJ49-NS1mut, was rescued successfully (Figure 1B). 2021 Viruses Result IV R108K;G189D 41;47 46;52 NS1 84 87 34070388 Molecular Characterization of Seasonal Influenza A and B from Hospitalized Patients in Thailand in 2018-2019. Additional amino acid substitutions were found at P99S, C123S, and S139C for segment NA, T285I for segment M, and V453A at the NP segment (Tables S7 and S8). 2021 Viruses Result IV P99S;C123S;S139C;T285I;V453A 50;56;67;89;114 54;61;72;94;119 M;NA;NP 107;85;127 108;87;129 34070388 Molecular Characterization of Seasonal Influenza A and B from Hospitalized Patients in Thailand in 2018-2019. Among these Thai strains, we found additional mutations at antigenic sites; S91R (Cb), S181T(Sa), and T202I (Sb) (Figure 2B). 2021 Viruses Result IV S91R;S181T;T202I 76;87;102 80;92;107 34070388 Molecular Characterization of Seasonal Influenza A and B from Hospitalized Patients in Thailand in 2018-2019. Determination of amino acid substitutions among the A/H1N1 isolates also revealed the mutation Q51K, F74S, G77R, V81A, I188T, and T462I for segment NA, T80A, A155T, and A242T for segment NS, V431I for segment NP, V200I and K386R for segment PB1, and G225S and V667I for segment PB2 (Tables S3 and S4). 2021 Viruses Result IV Q51K;F74S;G77R;V81A;I188T;T462I;T80A;A155T;A242T;V431I;V200I;K386R;G225S;V667I 95;101;107;113;119;130;152;158;169;191;213;223;250;260 99;105;111;117;124;135;156;163;174;196;218;228;255;265 NA;NP;NS;PB1;PB2 148;209;187;241;278 150;211;189;244;281 34070388 Molecular Characterization of Seasonal Influenza A and B from Hospitalized Patients in Thailand in 2018-2019. In comparison to the B/Colorado/06/2017 vaccine strain, these substitutions include G129D, G133R, K136E, and V180R for segment HA (Figure 7). 2021 Viruses Result IV G129D;G133R;K136E;V180R 84;91;98;109 89;96;103;114 HA 127 129 34070388 Molecular Characterization of Seasonal Influenza A and B from Hospitalized Patients in Thailand in 2018-2019. Moreover, a unique mutation (S200P) was observed at the receptor binding site (Figure 3A). 2021 Viruses Result IV S200P 29 34 34070388 Molecular Characterization of Seasonal Influenza A and B from Hospitalized Patients in Thailand in 2018-2019. Substitution at positions P100S, S101N, D114S, S179N, K180Q, S181T, T214A, S220T, and I233R were detected in the head domain of H1N1 strain isolates in this study. 2021 Viruses Result IV P100S;S101N;D114S;S179N;K180Q;S181T;T214A;S220T;I233R 26;33;40;47;54;61;68;75;86 31;38;45;52;59;66;73;80;91 34070388 Molecular Characterization of Seasonal Influenza A and B from Hospitalized Patients in Thailand in 2018-2019. The isolates of the 3C.2a1b clade also contain amino acid substitutions at P126L, K220N, and V303I in NA, K158R in PA, and S107N in PB2. 2021 Viruses Result IV P126L;K220N;V303I;K158R;S107N 75;82;93;106;123 80;87;98;111;128 NA;PA;PB2 102;115;132 104;117;135 34070388 Molecular Characterization of Seasonal Influenza A and B from Hospitalized Patients in Thailand in 2018-2019. The mutation S200P results in the loss of coordination with a water molecule, and may interfere with the hydrogen bond to the Sialic molecule (Figure 3B). 2021 Viruses Result IV S200P 13 18 34070388 Molecular Characterization of Seasonal Influenza A and B from Hospitalized Patients in Thailand in 2018-2019. These isolates contain substitutions of T144A/I, T151K at antigenic site A, Q213R, S214P, and T176K at antigenic site B, D69N and Q277R at antigenic site C, N137K and N187K at antigenic site D and E78K/G at antigenic site E (Figure 5C). 2021 Viruses Result IV E78G;T144A;T144I;T151K;Q213R;S214P;T176K;D69N;Q277R;N137K;N187K;E78K 197;40;40;49;76;83;94;121;130;157;167;197 203;47;47;54;81;88;99;125;135;162;172;203 34131512 Identification of H3N2 NA and PB1-F2 genetic variants and their association with disease symptoms during the 2014-15 influenza season. Again, the NAg+F2P viruses clustered together providing further support for the presence of a single common ancestor from which all the NAg+F2P genotype viruses derived. 2021 Virus evolution Result IV F2P;F2P 15;140 18;143 34131512 Identification of H3N2 NA and PB1-F2 genetic variants and their association with disease symptoms during the 2014-15 influenza season. Although the presence of one as a passenger mutation linked with the other cannot be formally excluded, the expansion of NAg+F2P genotype viruses suggests selection according to a fitness advantage of that genotype over other viruses within the 3C.2a clade. 2021 Virus evolution Result IV F2P 125 128 34131512 Identification of H3N2 NA and PB1-F2 genetic variants and their association with disease symptoms during the 2014-15 influenza season. Evolution of NA glycosylation and PB1-F275P. 2021 Virus evolution Result IV F275P 38 43 NA;PB1 13;34 15;37 34131512 Identification of H3N2 NA and PB1-F2 genetic variants and their association with disease symptoms during the 2014-15 influenza season. In addition, eighteen of the twenty isolates had another non-synonymous mutation (ntT739A), which changed the Serine residue to Threonine (T) at AA 247. 2021 Virus evolution Result IV T739A 84 89 34131512 Identification of H3N2 NA and PB1-F2 genetic variants and their association with disease symptoms during the 2014-15 influenza season. In samples from 2013 to 2014, only the NAg-F2H genotype was detected. 2021 Virus evolution Result IV F2H 43 46 34131512 Identification of H3N2 NA and PB1-F2 genetic variants and their association with disease symptoms during the 2014-15 influenza season. In the PB1 phylogenetic tree, all F2P and all F2R viruses shared a single node. 2021 Virus evolution Result IV F2P;F2R 34;46 37;49 PB1 7 10 34131512 Identification of H3N2 NA and PB1-F2 genetic variants and their association with disease symptoms during the 2014-15 influenza season. In the PB1 phylogenetic tree, the large set of burgundy colored branches at the top similarly indicates that all detected F2P isolates arose from a common ancestor. 2021 Virus evolution Result IV F2P 122 125 PB1 7 10 34131512 Identification of H3N2 NA and PB1-F2 genetic variants and their association with disease symptoms during the 2014-15 influenza season. JHMI isolates had a non-synonymous nucleotide mutation (ntG734A; ORF numbering throughout) in the NA segment. 2021 Virus evolution Result IV G734A 58 63 98 100 34131512 Identification of H3N2 NA and PB1-F2 genetic variants and their association with disease symptoms during the 2014-15 influenza season. NAg+F2R isolates seem to have been selected in the opposite order. 2021 Virus evolution Result IV F2R 4 7 34131512 Identification of H3N2 NA and PB1-F2 genetic variants and their association with disease symptoms during the 2014-15 influenza season. None of the 3C.2a clade isolates from the WPAFB had the F2P genotype. 2021 Virus evolution Result IV F2P 56 59 34131512 Identification of H3N2 NA and PB1-F2 genetic variants and their association with disease symptoms during the 2014-15 influenza season. Since the NAg+ and F2P genotypes appear together in most virus strains. 2021 Virus evolution Result IV F2P 19 22 34131512 Identification of H3N2 NA and PB1-F2 genetic variants and their association with disease symptoms during the 2014-15 influenza season. Taken together, the data indicate that the NAg+F2P genotype rapidly became dominant among clade 3C.2a viruses (compare. 2021 Virus evolution Result IV F2P 47 50 34131512 Identification of H3N2 NA and PB1-F2 genetic variants and their association with disease symptoms during the 2014-15 influenza season. The branches of the NA and PB1 phylogenetic trees use the HA clade color scheme, with the exception of viruses encoding the NAg+ or F2P mutations, which use the 3C.2a genotype color scheme from. 2021 Virus evolution Result IV F2P 132 135 HA;NA;PB1 58;20;27 60;22;30 34131512 Identification of H3N2 NA and PB1-F2 genetic variants and their association with disease symptoms during the 2014-15 influenza season. The branching of the three NAg+F2R viruses (yellow) among a small group of NAg-F2R viruses (magenta) indicates that a subset of F2R viruses created a background in which NAg+ was selected, but this group was short-lived and did not lead to the emergence of the NAg+F2P genotype. 2021 Virus evolution Result IV F2R;F2R;F2R;F2P 31;79;128;265 34;82;131;268 34131512 Identification of H3N2 NA and PB1-F2 genetic variants and their association with disease symptoms during the 2014-15 influenza season. The clinical and demographic information from twenty patients infected with the NAg+F2P genotype was compared to the thirty-four patients infected with clade 3C.2a NAg-F2H genotype viruses (Table 3). 2021 Virus evolution Result IV F2P;F2H 84;168 87;171 34131512 Identification of H3N2 NA and PB1-F2 genetic variants and their association with disease symptoms during the 2014-15 influenza season. The frequency of NAg+F2P isolates grew to sixty-eight per cent of all clade 3C.2a isolates in 2015-16 while the NAg-F2H genotype shrank from seventy-five per cent to twelve per cent. 2021 Virus evolution Result IV F2P;F2H 21;116 24;119 34131512 Identification of H3N2 NA and PB1-F2 genetic variants and their association with disease symptoms during the 2014-15 influenza season. The group of NAg+F2H viruses (plum) that branched from the trunk of the tree before the NAg+F2P group, and the other NAg+F2H virus branch locations, scattered among NAg-F2H branches, suggests that the NAg+ mutation was selected numerous times and that in one case, it was selected slightly before acquisition of the H75P mutation. 2021 Virus evolution Result IV F2H;F2P;F2H;F2H;H75P 17;92;121;169;316 20;95;124;172;320 34131512 Identification of H3N2 NA and PB1-F2 genetic variants and their association with disease symptoms during the 2014-15 influenza season. The locations of the NAg-F2P viruses (cyan branches) within the NAg+F2P viruses (salmon branches) indicate that the NAg-F2P genotype likely arose from mutations that reversed the NAg+ to the NAg- genotype in the NAg+F2P genotype lineage. 2021 Virus evolution Result IV F2P;F2P;F2P;F2P 25;68;120;216 28;71;123;219 34131512 Identification of H3N2 NA and PB1-F2 genetic variants and their association with disease symptoms during the 2014-15 influenza season. The NAg-F2H genotype was dominant during the 2014-15 winter season (75%) with the NAg+F2P genotype being the second most common genotype (19%). 2021 Virus evolution Result IV F2H;F2P 8;86 11;89 34131512 Identification of H3N2 NA and PB1-F2 genetic variants and their association with disease symptoms during the 2014-15 influenza season. The NAg-F2H virus grew to higher titers on hNEC cultures compared with NAg+ F2P. 2021 Virus evolution Result IV F2H;F2P 8;76 11;79 34131512 Identification of H3N2 NA and PB1-F2 genetic variants and their association with disease symptoms during the 2014-15 influenza season. The NAg+F2P genotype viruses all clustered together from a single branch of the tree (salmon color at top of tree), indicating that a common ancestor acquired both the NAg+ and the F2P mutations. 2021 Virus evolution Result IV F2P;F2P 8;181 11;184 34131512 Identification of H3N2 NA and PB1-F2 genetic variants and their association with disease symptoms during the 2014-15 influenza season. The only clinical factors that differed between the patient populations was an increased reporting of coughing and shortness of breath in individuals infected with the NAg+F2P genotype. 2021 Virus evolution Result IV F2P 172 175 34131512 Identification of H3N2 NA and PB1-F2 genetic variants and their association with disease symptoms during the 2014-15 influenza season. The only other genotype to increase in frequency was NAg+F2H, which grew from four per cent to nineteen per cent. 2021 Virus evolution Result IV F2H 57 60 34131512 Identification of H3N2 NA and PB1-F2 genetic variants and their association with disease symptoms during the 2014-15 influenza season. The only other non-synonymous mutation that occurred with greater than twenty-five per cent frequency among the 3C.2a clade JHMI isolates was an ntA318C mutation in the PB1 ORF, which was a synonymous change in the PB1 ORF but resulted in a change from Histidine (H) to Proline (P) at AA 75 (H75P) of the PB1-F2 ORF (F2P). 2021 Virus evolution Result IV A318C;F2P;H75P 147;317;292 152;320;296 PB1;PB1;PB1F2 169;215;305 172;218;311 34131512 Identification of H3N2 NA and PB1-F2 genetic variants and their association with disease symptoms during the 2014-15 influenza season. The phylogenetic analysis suggests that the two mutations of the NAg+F2P genotype clade 3C.2a viruses descended from a common ancestor. 2021 Virus evolution Result IV F2P 69 72 34131512 Identification of H3N2 NA and PB1-F2 genetic variants and their association with disease symptoms during the 2014-15 influenza season. The same twenty JHMI 3C.2a clade viruses that were NAg+ contained the F2P mutation while all other 3C.2a isolates lacked both mutations (NAg-F2H). 2021 Virus evolution Result IV F2P;F2H 70;141 73;144 34131512 Identification of H3N2 NA and PB1-F2 genetic variants and their association with disease symptoms during the 2014-15 influenza season. There was no evidence that the F2P mutation was gained by NAg- viruses. 2021 Virus evolution Result IV F2P 31 34 34131512 Identification of H3N2 NA and PB1-F2 genetic variants and their association with disease symptoms during the 2014-15 influenza season. These data indicated that the NAg+ and F2P genotypes were co-selected in clade 3C.2a viruses. 2021 Virus evolution Result IV F2P 39 42 34131512 Identification of H3N2 NA and PB1-F2 genetic variants and their association with disease symptoms during the 2014-15 influenza season. Viruses from the 3C.2a NAg+F2P genotype associated with breathing difficulties. 2021 Virus evolution Result IV F2P 27 30 34131512 Identification of H3N2 NA and PB1-F2 genetic variants and their association with disease symptoms during the 2014-15 influenza season. Viruses representative of the two 3C.2a genotypes:A/Columbia/P0041/2014 (NAg-F2H) and A/Bethesda/P0055/2015 (NAg+F2P):were expanded and assessed for differences in replication on three different cell types: MDCK cells, MDCK-SIAT cells, and hNECs. 2021 Virus evolution Result IV F2H;F2P 77;113 80;116 34131512 Identification of H3N2 NA and PB1-F2 genetic variants and their association with disease symptoms during the 2014-15 influenza season. Viruses with NAg+ accounted for eighty-seven per cent of isolates in the 2015-16 season showing that NAg+ viruses were more frequent than viruses with the PB1-F2P mutation. 2021 Virus evolution Result IV F2P 159 162 PB1 155 158 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. dRIN of H274Y mutant NA. 2021 PeerJ Result IV H274Y 8 13 21 23 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. Figure 2 represents snapshot images obtained from the MD simulations for the WT and H274Y mutant NA-OTV complexes, showing the OTV binding site and the region adjacent to residue 274. 2021 PeerJ Result IV H274Y 84 89 97 99 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. Figure 3 shows the dRIN graphs for the WT and H274Y mutant NA complexed with OTV. 2021 PeerJ Result IV H274Y 46 51 59 61 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. Figure 4B indicates that the occupancy of ligand-residue interactions between the OTV and its surrounding residues, E119, D151, R152, and S246 decreased after H274Y mutation, whereas the occupancy of the OTV-Y406 interaction increased. 2021 PeerJ Result IV H274Y 159 164 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. Figure 4B shows the change in the occupancies of residues interacting with each of the WT and H274Y mutant NA. 2021 PeerJ Result IV H274Y 94 99 107 109 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. Figure 5A shows the decomposed protein-ligand complex binding free energies of the WT and H274Y mutant NA on a per-residue basis according to the MM-PBSA calculations. 2021 PeerJ Result IV H274Y 90 95 103 105 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. Figure 5B shows the change in the decomposed binding free energies between the WT and H274Y mutant NA. 2021 PeerJ Result IV H274Y 86 91 99 101 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. His-to-Tyr mutation of residue 274 caused significant changes in the dRIN at the interface region. 2021 PeerJ Result IV Y274H 0 34 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. However, the H274Y mutation resulted in decreased hydrogen-bond interaction occupancy compared to that in the WT NA, thereby making vdW interaction more prevalent (Tables 2 and 3). 2021 PeerJ Result IV H274Y 13 18 113 115 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. In contrast, the occupancy of close contacts between S246 and OTV was 54% in WT NA; this occupancy decreased after H274Y mutation, but the difference was small, about 17% (Tables 2 and 3). 2021 PeerJ Result IV H274Y 115 120 80 82 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. In particular, it was observed that the occupancies of interactions with OTV were greatly reduced by more than 80% for the residues D151 and R152, and could be expected to contribute significantly to the decreased binding affinity of OTV with H274Y mutant NA. 2021 PeerJ Result IV H274Y 243 248 256 258 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. In particular, two histidine moieties overlapped with each other through vdW and pi-pi stacking interactions in the pair of H296 and H274 in WT NA, whereas no interaction was observed between the two aromatic rings in H274Y mutant NA. 2021 PeerJ Result IV H274Y 218 223 NA;NA 144;231 146;233 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. In the pair of residues 246 and 274, weak interactions were observed between S246 and H274, with an overall occupancy of approximately 23% in WT NA, and H274Y mutation increased close contacts to approximately 80% and an overall occupancy to approximately 90% (Tables 2 and 3). 2021 PeerJ Result IV H274Y 153 158 145 147 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. Notably, no interaction was observed between E276 and H274 in WT NA; however, in the H274Y mutant NA, a pair of residues E276 and Y274 formed a solid hydrogen-bond interaction with an occupancy of about 100%. 2021 PeerJ Result IV H274Y 85 90 NA;NA 65;98 67;100 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. On the contrary, R292 formed a robust hydrogen-bond interaction with OTV with an occupancy of 100% in the WT NA, and this occupancy remained unchanged in the H274Y mutant NA (Tables 2 and 3). 2021 PeerJ Result IV H274Y 158 163 NA;NA 109;171 111;173 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. On the contrary, there were close contacts between E276 and OTV, with an occupancy of approximately 50% in WT NA, and this occupancy remained unchanged after the H274Y mutation. 2021 PeerJ Result IV H274Y 162 167 110 112 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. Previous studies have reported that the H274Y mutation in NA can change the structure of the 150-loop region from a closed to an open form (). 2021 PeerJ Result IV H274Y 40 45 58 60 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. Several computational studies have been conducted on the change in the binding free energy of OTV due to the H274Y mutation (). 2021 PeerJ Result IV H274Y 109 114 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. Similarly, for the interaction between D293 and residue 274, the overall occupancy of the interactions was about 80% in both the WT and H274Y mutant NA, but the preferred interaction in WT NA was the vdW interaction, and that in the H274Y mutant NA was close contact (Tables 2 and 3). 2021 PeerJ Result IV H274Y;H274Y 136;233 141;238 NA;NA;NA 149;189;246 151;191;248 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. Table 1 summarizes the computed binding free energies (DeltaG) of OTV for the WT and H274Y mutant NA obtained from the MM-PBSA calculations, along with the enthalpy (DeltaH) and entropy (TDeltaS). 2021 PeerJ Result IV H274Y 85 90 98 100 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. The 7.20 kcal mol-1 increase in the binding free energy of OTV due to the H274Y mutation could significantly reduce the efficiency of this inhibitor against NA. 2021 PeerJ Result IV H274Y 74 79 157 159 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. The binding free energies of OTV were computed to be -11.54 and -4.34 kcal mol-1 for the WT and H274Y mutant NA, respectively. 2021 PeerJ Result IV H274Y 96 101 109 111 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. the characteristics of dRIN in the H274Y mutant NA changed significantly as compared to the dRIN in the WT NA. 2021 PeerJ Result IV H274Y 35 40 NA;NA 48;107 50;109 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. The difference in the binding free energy of the WT and H274Y mutant NA to OTV was calculated to be approximately 4.4 kcal mol-1, based on the experimentally measured IC50 value (). 2021 PeerJ Result IV H274Y 56 61 69 71 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. The dRIN structure of the H274Y mutation site remained almost unchanged, even after the His-to-Tyr mutation, except for a few residue-residue pairs and the interface bordering the OTV. 2021 PeerJ Result IV H274Y 26 31 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. the H274Y mutation resulted in significantly increased components of decomposed binding free energy at E119, D151, and R152, destabilizing the interaction between OTV and H274Y mutant NA. 2021 PeerJ Result IV H274Y;H274Y 4;171 9;176 184 186 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. the occupancies of interactions between residue 274 and the residues S246, E276, and R292, which form the interface, increased after the H274Y mutation, whereas the occupancies of interactions with OTV remained almost unchanged. 2021 PeerJ Result IV H274Y 137 142 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. The pair of residues 292 and 274 in WT NA had no interaction between R292 and H274, but that in H274Y mutant NA had close contact with an occupancy of about 40% (Tables 2 and 3). 2021 PeerJ Result IV H274Y 96 101 NA;NA 39;109 41;111 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. The pocket cavity volume of the H274Y mutant NA was increased more than twofold compared to that of the WT NA. 2021 PeerJ Result IV H274Y 32 37 NA;NA 45;107 47;109 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. The results analyzed for the last 40 ns of the MD simulations showed that the average pocket cavity volumes were computed to be 394 and 853 A3, for the WT and H274Y mutant NA, respectively. 2021 PeerJ Result IV H274Y 159 164 172 174 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. The results calculated with epsilon = 1.0 showed a larger difference in binding free energies (10.48 kcal mol-1) than those calculated with epsilon = 4.0 (7.20 kcal mol-1), further reducing the affinity of NA for OTV after the H274Y mutation. 2021 PeerJ Result IV H274Y 227 232 206 208 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. there were three residues, S246, E276, and R292, at the interface between the OTV binding site of NA and its H274Y mutation site, that were observed to interact directly with both OTV and residue 274 in the H274Y mutant NA. 2021 PeerJ Result IV H274Y;H274Y 109;207 114;212 NA;NA 98;220 100;222 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. Therefore, the decrease in binding affinity between OTV and NA due to the H274Y mutation can be the result of indirect effects caused by changes in the residue interaction network. 2021 PeerJ Result IV H274Y 74 79 60 62 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. This is supported by the experimental fact that the H274Y mutant NA has a 300- to 1700-fold decrease in relative susceptibility to OTV compared with the WT NA in H5N1 viruses (). 2021 PeerJ Result IV H274Y 52 57 NA;NA 65;156 67;158 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. Thus, the H274Y mutation reduced the binding affinity of OTV to NA by cleaving the ligand-residue interaction. 2021 PeerJ Result IV H274Y 10 15 64 66 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. To further analyze the structural changes associated with the H274Y mutation, the pocket cavity volumes of the WT and mutant NA were examined using the POVME 3.0 software (). 2021 PeerJ Result IV H274Y 62 67 125 127 34164347 Risk of Environmental Exposure to H7N9 Influenza Virus via Airborne and Surface Routes in a Live Poultry Market in Hebei, China. The sequence analysis revealed that two amino acid substitutions in the MA-P5 virus, one in the PB1 subunit (H115Q) and another in the PB2 subunit (E627K) ( Table 1 ). 2021 Frontiers in cellular and infection microbiology Result IV H115Q;E627K 109;148 114;153 PB1;PB2 96;135 99;138 34194404 Host Adaptive Evolution of Avian-Origin H3N2 Canine Influenza Virus. For the NA protein, a T16A substitution occurs at a site located in the transmembrane region of this protein (Figure 4). 2021 Frontiers in microbiology Result IV T16A 22 26 8 10 34194404 Host Adaptive Evolution of Avian-Origin H3N2 Canine Influenza Virus. Given the role of the NS1 protein in suppressing host cellular immune responses, the NS1-E227K mutation might be a molecular determinant to hone the function of the immune suppression by H3N2 CIV. 2021 Frontiers in microbiology Result IV E227K 89 94 NS1;NS1 22;85 25;88 34194404 Host Adaptive Evolution of Avian-Origin H3N2 Canine Influenza Virus. However, it is interesting to note that 11 out of the 54 (20.37%) effective substitutions in H3N2 CIV, including HA-G146S, HA-V242I, HA-V418I, M1-V15I, M2-R18K, PA-N347D, PB1-V200I, PB2-K251R, PB2-I292T, PB2-V511I, and PB2-G590S, are fixed in H3N8 CIV (Table 1), indicating that convergent evolution has occurred on different lineages of CIVs at these sites. 2021 Frontiers in microbiology Result IV G146S;V242I;V418I;V15I;R18K;N347D;V200I;K251R;I292T;V511I;G590S 116;126;136;146;155;164;175;186;197;208;223 121;131;141;150;159;169;180;191;202;213;228 HA;HA;HA;M1;M2;PA;PB1;PB2;PB2;PB2;PB2 113;123;133;143;152;161;171;182;193;204;219 115;125;135;145;154;163;174;185;196;207;222 34194404 Host Adaptive Evolution of Avian-Origin H3N2 Canine Influenza Virus. In addition, M1-V15I, PA-C241Y, PB1-R187K, PB2-K251R, and PB2-G590S substitutions have all been reported to enhance pathogenicity and virulence of AIVs in mammalian hosts due to their contributions to improving replicative efficacy and assembly fitness. 2021 Frontiers in microbiology Result IV V15I;C241Y;R187K;K251R;G590S 16;25;36;47;62 20;30;41;52;67 M1;PA;PB1;PB2;PB2 13;22;32;43;58 15;24;35;46;61 34194404 Host Adaptive Evolution of Avian-Origin H3N2 Canine Influenza Virus. In addition, N188D, G146S, and V242I mutations are located at the antigenic epitope B, antigenic epitope A, and antigenic epitope D of the HA protein, respectively (Figure 3), where substitutions at these sites may lead to antigenic drift in IAVs and the subsequent evasion of host immune responses. 2021 Frontiers in microbiology Result IV N188D;G146S;V242I 13;20;31 18;25;36 HA 139 141 34194404 Host Adaptive Evolution of Avian-Origin H3N2 Canine Influenza Virus. In addition, the I153T and H155Y are located close to the enzymatic site of the NA protein (Figure 4). 2021 Frontiers in microbiology Result IV I153T;H155Y 17;27 22;32 80 82 34194404 Host Adaptive Evolution of Avian-Origin H3N2 Canine Influenza Virus. Some of the effective substitutions, such as HA-V418I, NA-L390S, M2-R18K, NS1-E227K, and PB2-K251R, were also seen in the majority of the AIV sequences with a proportion of greater than 75% (Table 1). 2021 Frontiers in microbiology Result IV V418I;L390S;R18K;E227K;K251R 48;58;68;78;93 53;63;72;83;98 HA;M2;NA;NS1;PB2 45;65;55;74;89 47;67;57;77;92 34194404 Host Adaptive Evolution of Avian-Origin H3N2 Canine Influenza Virus. The N188D substitution, located at the receptor-binding region (190 helix) of HA protein (Figure 3), is a notable replacement. 2021 Frontiers in microbiology Result IV N188D 4 9 HA 78 80 34207098 Virus Adaptation Following Experimental Infection of Chickens with a Domestic Duck Low Pathogenic Avian Influenza Isolate from the 2017 USA H7N9 Outbreak Identifies Polymorphic Mutations in Multiple Gene Segments. At the consensus level (above 50%), the following substitutions were observed: V203I in PB2 at 3 dpc (D3CL) and A337T in NP at 7 dpc (D7CL) (Table 3). 2021 Viruses Result IV V203I;A337T 79;112 84;117 NP;PB2 121;88 123;91 34207098 Virus Adaptation Following Experimental Infection of Chickens with a Domestic Duck Low Pathogenic Avian Influenza Isolate from the 2017 USA H7N9 Outbreak Identifies Polymorphic Mutations in Multiple Gene Segments. Furthermore, minor populations of viruses carried substitutions (>5%) including T530A at D1OP and V109A and N639S at D3 CL in PB2; L42F at D1OP and E457K at D3CL in PA; M12V, T321A, and F409Y at D1OP and A169V and K337N at D3CL in HA; G356E at D1OP, V67A at D3CL in NP; S22P in M2 and F251S in M1 at D1OP (Table 3). 2021 Viruses Result IV T530A;V109A;N639S;L42F;E457K;M12V;T321A;F409Y;A169V;K337N;G356E;V67A;S22P;F251S 80;98;108;131;148;169;175;186;204;214;235;250;270;285 85;103;113;135;153;173;180;191;209;219;240;254;274;290 HA;M1;M2;NP;PA;PB2 231;294;278;266;165;126 233;296;280;268;167;129 34207098 Virus Adaptation Following Experimental Infection of Chickens with a Domestic Duck Low Pathogenic Avian Influenza Isolate from the 2017 USA H7N9 Outbreak Identifies Polymorphic Mutations in Multiple Gene Segments. In addition, two non-synonymous changes in NP (N450D and A336T) and two non-synonymous changes in NS (K27M and M79I) were found (Table 1). 2021 Viruses Result IV N450D;A336T;K27M;M79I 47;57;102;111 52;62;106;115 NP;NS 43;98 45;100 34207098 Virus Adaptation Following Experimental Infection of Chickens with a Domestic Duck Low Pathogenic Avian Influenza Isolate from the 2017 USA H7N9 Outbreak Identifies Polymorphic Mutations in Multiple Gene Segments. Interestingly, 30.5% of viruses caried substitution S150L (S143L, H3 numbering) in the HA segment. 2021 Viruses Result IV S150L;S143L 52;59 57;64 HA 87 89 34207098 Virus Adaptation Following Experimental Infection of Chickens with a Domestic Duck Low Pathogenic Avian Influenza Isolate from the 2017 USA H7N9 Outbreak Identifies Polymorphic Mutations in Multiple Gene Segments. Interestingly, K337N (K328N H3 numbering) substitution in the HA segment was carried by almost 40% of viruses while A169V (A160V H3 numbering) (13% of viruses) recovered from clinically ill chicken (Table 3). 2021 Viruses Result IV K337N;K328N;A169V;A160V 15;22;116;123 20;27;121;128 HA 62 64 34207098 Virus Adaptation Following Experimental Infection of Chickens with a Domestic Duck Low Pathogenic Avian Influenza Isolate from the 2017 USA H7N9 Outbreak Identifies Polymorphic Mutations in Multiple Gene Segments. Interestingly, the duck H7N9 LPAIV sample carried the same M105I substitution in the NP segment as the H7N9 HPAIV chicken isolates, contrary to chicken H7N9 LPAIVs (Figure S2). 2021 Viruses Result IV M105I 59 64 NP 85 87 34240696 Nanopore metagenomic sequencing of influenza virus directly from respiratory samples: diagnosis, drug resistance and nosocomial transmission, United Kingdom, 2018/19 influenza season. From consensus sequences covering drug-resistant positions, we identified the S31N amino acid mutation in the M2 protein in 20/20 H1N1 and 11/11 H3N2 sequences, which is known to be widespread, conferring reduced inhibition by amantadine. 2021 Euro surveillance Result IV S31N 78 82 M2 110 112 34240696 Nanopore metagenomic sequencing of influenza virus directly from respiratory samples: diagnosis, drug resistance and nosocomial transmission, United Kingdom, 2018/19 influenza season. In 2018/19, the proportion of sequences with the S331R mutation increased to 139/9,274 (1.5%), and all belonged to the R-genotype. 2021 Euro surveillance Result IV S331R 49 54 34240696 Nanopore metagenomic sequencing of influenza virus directly from respiratory samples: diagnosis, drug resistance and nosocomial transmission, United Kingdom, 2018/19 influenza season. In the 2017/18 dataset, 13/7,129 (0.2%) sequences carried the S331R mutation, with HA and NA segments from clade 3C.2a2 or 3C.2a3. 2021 Euro surveillance Result IV S331R 62 67 HA;NA 83;90 85;92 34240696 Nanopore metagenomic sequencing of influenza virus directly from respiratory samples: diagnosis, drug resistance and nosocomial transmission, United Kingdom, 2018/19 influenza season. Interestingly, the S331R mutation occurred in the same sample (sample 5), motivating us to further investigate the prevalence of this mutation in seasonal IAV using all global H3N2 sequences published in GISAID from the last two influenza seasons (2017/18 and 2018/19). 2021 Euro surveillance Result IV S331R 19 24 34240696 Nanopore metagenomic sequencing of influenza virus directly from respiratory samples: diagnosis, drug resistance and nosocomial transmission, United Kingdom, 2018/19 influenza season. One of 13 H3N2 sequences (sample 5) carried the S331R amino acid mutation in the NA protein, which has been reported to confer reduced inhibition by oseltamivir. 2021 Euro surveillance Result IV S331R 48 53 81 83 34240696 Nanopore metagenomic sequencing of influenza virus directly from respiratory samples: diagnosis, drug resistance and nosocomial transmission, United Kingdom, 2018/19 influenza season. Other drug resistance mutations, such as H275Y in the NA protein associated with oseltamivir resistance, were not present in our dataset. 2021 Euro surveillance Result IV H275Y 41 46 54 56 34240696 Nanopore metagenomic sequencing of influenza virus directly from respiratory samples: diagnosis, drug resistance and nosocomial transmission, United Kingdom, 2018/19 influenza season. These results suggest a potential association between the increase in prevalence of the S331R mutation and the emergence of this distinct R-genotype. 2021 Euro surveillance Result IV S331R 88 93 34253060 In Vivo Therapy with M2e-Specific IgG Selects for an Influenza A Virus Mutant with Delayed Matrix Protein 2 Expression. A delay in M2 expression compared to that in wild-type PR8 infection was not observed following infection with PR8-M2-I11T virus. 2021 mBio Result IV I11T 118 122 M2;M2 11;115 13;117 34253060 In Vivo Therapy with M2e-Specific IgG Selects for an Influenza A Virus Mutant with Delayed Matrix Protein 2 Expression. Based on these results, we can conclude that in the context of PR8 virus, the combination of K443R in PB2, I550T in PA, and A231S, I361M, and V458M in HA is associated with delayed expression of M2, HA, NP, PA, and PB2. 2021 mBio Result IV K443R;I550T;A231S;I361M;V458M 93;107;124;131;142 98;112;129;136;147 HA;HA;M2;NP;PA;PA;PB2;PB2 151;199;195;203;116;207;102;215 153;201;197;205;118;209;105;218 34253060 In Vivo Therapy with M2e-Specific IgG Selects for an Influenza A Virus Mutant with Delayed Matrix Protein 2 Expression. Cells that were infected with PR8-M2-P10L or PR8-M2-P10H viruses were not recognized by MAb 37 or MAb 65. 2021 mBio Result IV P10L;P10H 37;52 41;56 M2;M2 34;49 36;51 34253060 In Vivo Therapy with M2e-Specific IgG Selects for an Influenza A Virus Mutant with Delayed Matrix Protein 2 Expression. Deep sequencing of the viral RNA present in the BAL fluid of the mouse that had been treated with MAb 37 (experiment 1, mouse 5, dpi 33) revealed a wild-type M2 sequence and five prevalent nonsynonymous mutations in other parts of the virus, namely, K443R in PB2 (62.7%), I550T in PA (98.09%), A231S in HA (96.32%), I361M (I18M in HA2) in HA (96.15%), and V458M (V115M in HA2) in HA (99.6%) (Table S4). 2021 mBio Result IV K443R;I550T;A231S;I361M;I18M;V458M;V115M 250;272;294;316;323;356;363 255;277;299;321;327;361;368 HA;HA;HA;HA;HA;M2;PA;PB2 303;331;339;372;380;158;281;259 305;333;341;374;382;160;283;262 34253060 In Vivo Therapy with M2e-Specific IgG Selects for an Influenza A Virus Mutant with Delayed Matrix Protein 2 Expression. For the other viral proteins, including HA, PA, and PB2, the expression profile was comparable between PR8-HPP- and PR8-M2-I11T-infected HEK293S cells. 2021 mBio Result IV I11T 123 127 HA;M2;PA;PB2 40;120;44;52 42;122;46;55 34253060 In Vivo Therapy with M2e-Specific IgG Selects for an Influenza A Virus Mutant with Delayed Matrix Protein 2 Expression. However, the I11T mutation in M2e was only detected in MAb 37-treated mice, suggesting that position 11 of M2e is more critical for binding of MAb 37 than for binding of MAb 65. 2021 mBio Result IV I11T 13 17 34253060 In Vivo Therapy with M2e-Specific IgG Selects for an Influenza A Virus Mutant with Delayed Matrix Protein 2 Expression. In addition, MAb 37 bound only weakly to PR8-M2-I11T-infected cells, while MAb 65 efficiently recognized this M2e mutant. 2021 mBio Result IV I11T 48 52 M2 45 47 34253060 In Vivo Therapy with M2e-Specific IgG Selects for an Influenza A Virus Mutant with Delayed Matrix Protein 2 Expression. In addition, mutation PA I550T was included, since this mutation was identified in multiple escape virus populations in our study and it has been reported that PA I550L can enhance viral replication. 2021 mBio Result IV I550T;I550L 25;163 30;168 PA;PA 22;160 24;162 34253060 In Vivo Therapy with M2e-Specific IgG Selects for an Influenza A Virus Mutant with Delayed Matrix Protein 2 Expression. In addition, the double mutation M374K and Q556H in PA occurred together with a D309N mutation in PB2 in viruses isolated from a MAb 65-treated mouse (experiment 2, mouse 1, 37 dpi). 2021 mBio Result IV M374K;Q556H;D309N 33;43;80 38;48;85 PA;PB2 52;98 54;101 34253060 In Vivo Therapy with M2e-Specific IgG Selects for an Influenza A Virus Mutant with Delayed Matrix Protein 2 Expression. In contrast, polymerase activity was slightly reduced in the presence of PA I550T. 2021 mBio Result IV I550T 76 81 PA 73 75 34253060 In Vivo Therapy with M2e-Specific IgG Selects for an Influenza A Virus Mutant with Delayed Matrix Protein 2 Expression. In MAb 37-treated mice, PR8 virus with a mutation at position T765C (I11T) was also observed. 2021 mBio Result IV T765C;I11T 62;69 67;73 34253060 In Vivo Therapy with M2e-Specific IgG Selects for an Influenza A Virus Mutant with Delayed Matrix Protein 2 Expression. Moreover, when combined with the polymerase activity-enhancing mutants PB2 R443K and PB2 I504V, PA I550T resulted in lower polymerase activity than that of the wild-type control. 2021 mBio Result IV R443K;I504V;I550T 75;89;99 80;94;104 PA;PB2;PB2 96;71;85 98;74;88 34253060 In Vivo Therapy with M2e-Specific IgG Selects for an Influenza A Virus Mutant with Delayed Matrix Protein 2 Expression. Polymerase activity was significantly enhanced when PB2 D309N, PB2 I504V, or PB2 K443R were present in the otherwise wild-type polymerase complex. 2021 mBio Result IV D309N;I504V;K443R 56;67;81 61;72;86 PB2;PB2;PB2 52;63;77 55;66;80 34253060 In Vivo Therapy with M2e-Specific IgG Selects for an Influenza A Virus Mutant with Delayed Matrix Protein 2 Expression. The ability of the M2e-specific MAbs to bind to the M2 mutant viruses was investigated using cell-based enzyme-limited immunosorbent assay (ELISA) with rescued recombinant PR8 viruses that carried either the P10L, P10H, or I11T mutation. 2021 mBio Result IV P10L;P10H;I11T 208;214;223 212;218;227 M2 52 54 34253060 In Vivo Therapy with M2e-Specific IgG Selects for an Influenza A Virus Mutant with Delayed Matrix Protein 2 Expression. The M2e mutations P10H, P10L, and I11T were detected at a frequency that ranged from 0.61% to 90.18% in 6 out of 10 mice treated with MAb 37 that reached the ethical endpoint. 2021 mBio Result IV P10H;P10L;I11T 18;24;34 22;28;38 34253060 In Vivo Therapy with M2e-Specific IgG Selects for an Influenza A Virus Mutant with Delayed Matrix Protein 2 Expression. The mutations K443R (62.7%) in PB2 and I550T (98.09%) in PA occurred together in viruses that were isolated from a mouse that had been treated with MAb 37 (experiment 1, mouse 5, 33 dpi). 2021 mBio Result IV K443R;I550T 14;39 19;44 PA;PB2 57;31 59;34 34253060 In Vivo Therapy with M2e-Specific IgG Selects for an Influenza A Virus Mutant with Delayed Matrix Protein 2 Expression. The PB2 mutation I504V, for example, was found at a frequency of 59.6% or greater in 7 BAL fluid samples derived from mice that had been treated with MAbs 37, 148, or 65, whereas PB1 and PA mutations were undetectable or were only present at low frequency (below 20%) in these samples (Tables S4 to S7). 2021 mBio Result IV I504V 17 22 PA;PB1;PB2 187;179;4 189;182;7 34253060 In Vivo Therapy with M2e-Specific IgG Selects for an Influenza A Virus Mutant with Delayed Matrix Protein 2 Expression. The variation in the M2e sequence was limited to nucleotide positions C762A (P10H) and C762T (P10L) for MAb 65. 2021 mBio Result IV C762A;P10H;C762T;P10L 70;77;87;94 75;81;92;98 34253060 In Vivo Therapy with M2e-Specific IgG Selects for an Influenza A Virus Mutant with Delayed Matrix Protein 2 Expression. This differential recognition of virus with M2-I11T by MAb 37 and MAb 65 is thus in line with the deep sequence analysis of the in vivo escape selection, in which M2-I11T mutant viruses were only observed in the MAb 37-treated mice. 2021 mBio Result IV I11T;I11T 47;166 51;170 M2;M2 44;163 46;165 34253060 In Vivo Therapy with M2e-Specific IgG Selects for an Influenza A Virus Mutant with Delayed Matrix Protein 2 Expression. Three types of variation were detected in M2e in virus samples derived from MAb 37- and MAb 65-treated mice, M2-P10H, M2-P10L, and M2-I11T. 2021 mBio Result IV P10H;P10L;I11T 112;121;134 116;125;138 M2;M2;M2 109;118;131 111;120;133 34253060 In Vivo Therapy with M2e-Specific IgG Selects for an Influenza A Virus Mutant with Delayed Matrix Protein 2 Expression. To evaluate whether the acquired I11T mutation in M2 would suffice to escape MAb 37 treatment in our model, SCID mice were treated with MAb 37 or control IgG1 prior to and weekly after infection with 10 PFU of PR8 or PR8-M2-I11T virus. 2021 mBio Result IV I11T;I11T 33;224 37;228 M2;M2 50;221 52;223 34253060 In Vivo Therapy with M2e-Specific IgG Selects for an Influenza A Virus Mutant with Delayed Matrix Protein 2 Expression. Two out of three control IgG-treated and two out of four MAb 37-treated SCID mice did not survive the PR8-M2-I11T challenge, suggesting that PR8 virus with a M2e-I11T mutation can escape MAb 37 treatment. 2021 mBio Result IV I11T;I11T 109;162 113;166 M2 106 108 34253060 In Vivo Therapy with M2e-Specific IgG Selects for an Influenza A Virus Mutant with Delayed Matrix Protein 2 Expression. Viral RNA with two mutations in PA, V127I and S405N, combined with I504V in PB2 was detected in BAL fluid from a MAb 37-treated mouse (experiment 2, mouse 5, 39 dpi). 2021 mBio Result IV V127I;S405N;I504V 36;46;67 41;51;72 PA;PB2 32;76 34;79 34253060 In Vivo Therapy with M2e-Specific IgG Selects for an Influenza A Virus Mutant with Delayed Matrix Protein 2 Expression. We tested these mutations, as well as PB2-R493K, which emerged in another MAb 37-treated animal (experiment 1, mouse 8, 29 dpi), together with the well-documented I504V mutation in PB2 as a positive control, in a minireplicon assay on HEK cells. 2021 mBio Result IV R493K;I504V 42;163 47;168 PB2;PB2 38;181 41;184 34337007 Full Genomic Sequences of H5N1 Highly Pathogenic Avian Influenza Virus in Human Autopsy Specimens Reveal Genetic Variability and Adaptive Changes for Growth in MDCK Cell Cultures. On the other hand, both the autopsy specimens and the virus isolates contained the S31N substitution in the M2 protein, indicating the amantadine and rimantadine resistance. 2021 BioMed research international Result IV S31N 83 87 M2 108 110 34337007 Full Genomic Sequences of H5N1 Highly Pathogenic Avian Influenza Virus in Human Autopsy Specimens Reveal Genetic Variability and Adaptive Changes for Growth in MDCK Cell Cultures. The H274Y substitution, which indicated the oseltamivir and peramivir resistance, was not present in both the autopsy specimens and the virus isolates, even though the patient received a full course of oseltamivir treatment before his death. 2021 BioMed research international Result IV H274Y 4 9 34337007 Full Genomic Sequences of H5N1 Highly Pathogenic Avian Influenza Virus in Human Autopsy Specimens Reveal Genetic Variability and Adaptive Changes for Growth in MDCK Cell Cultures. This led to the nonsynonymous mutation of M315I in the virus isolate from the trachea. 2021 BioMed research international Result IV M315I 42 47 34337007 Full Genomic Sequences of H5N1 Highly Pathogenic Avian Influenza Virus in Human Autopsy Specimens Reveal Genetic Variability and Adaptive Changes for Growth in MDCK Cell Cultures. This M315I amino acid change may be necessary for adaptation to grow in MDCK cells since the 315I was found in virus isolates from all kinds of clinical specimens. 2021 BioMed research international Result IV M315I 5 10 34358217 Mutation E48K in PB1 Polymerase Subunit Improves Stability of a Candidate Live Attenuated Influenza B Virus Vaccine. High-throughput sequencing of the viral genome of B/Bris PB1att 4M further confirmed that key mutations (E48K, K391E, E580G, and S660A) were maintained after four passages in both MDCK cells and SPF eggs. 2021 Vaccines Result IV E48K;K391E;E580G;S660A 105;111;118;129 109;116;123;134 34358217 Mutation E48K in PB1 Polymerase Subunit Improves Stability of a Candidate Live Attenuated Influenza B Virus Vaccine. In contrast, two new mutations were identified in the PB1 of the B/Bris PB1 3M virus at passage sE4 (E48K and G161C), but not at sP1 or sP4 (MDCK cell passages). 2021 Vaccines Result IV E48K;G161C 101;110 105;115 PB1;PB1 54;72 57;75 34358217 Mutation E48K in PB1 Polymerase Subunit Improves Stability of a Candidate Live Attenuated Influenza B Virus Vaccine. In order to assess the efficacy of the B/Bris PB1att 4M vaccine strain, mice were challenged at 21 dpb with a lethal dose (107 EID50/mouse) of the B/Bris PB2-F406Y mutant strain. 2021 Vaccines Result IV F406Y 158 163 PB2 154 157 34358217 Mutation E48K in PB1 Polymerase Subunit Improves Stability of a Candidate Live Attenuated Influenza B Virus Vaccine. Mutations E48K and K391E Remain Stable in Combination after Serial Passages in MDCKs and SPF Eggs. 2021 Vaccines Result IV E48K;K391E 10;19 14;24 34358217 Mutation E48K in PB1 Polymerase Subunit Improves Stability of a Candidate Live Attenuated Influenza B Virus Vaccine. Sanger sequencing analysis of the PB1 segment confirmed that the B/Bris PB1att 4M virus stably retained all modifications introduced (E48K, K391E, E580G, and S660A) after four serial passages in MDCK cells and in SPF eggs. 2021 Vaccines Result IV E48K;K391E;E580G;S660A 134;140;147;158 138;145;152;163 PB1 34 37 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. Altogether, the single-turnover NTP incorporation kinetics assays allow us to quantify the transcription fidelity of K235R mutant against the wild-type RdRp from the derived incorporation constant (kpol) and apparent substrate dissociation constant (Kd,app) for the cognate CTP and the noncognate UTP. 2021 Nucleic acids research Result IV K235R 117 122 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. As a result, the IAV genome will not be dominated by the high-fidelity mutant K235R. 2021 Nucleic acids research Result IV K235R 78 83 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. As expected, K235R mutant RdRp incorporates both the 3'dCTP and 2'F-dCTP at much lower efficiency compared to wild-type RdRp (Supplementary Figure S18). 2021 Nucleic acids research Result IV K235R 13 18 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. As shown in Figure 6C and D, we found the number of SNV sites in wild-type live virus is 19.25 +- 0.50 (mean +- SD), whereas the number of SNV sites in K235R is 12 +- 2.94 (mean +- SD). 2021 Nucleic acids research Result IV K235R 152 157 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. As the K235R RdRp has higher efficiency to incorporate the cognate CTP but a lower efficiency to incorporate the noncognate UTP than the wild-type, the transcription fidelity for K235R RdRp is around 4.6-fold higher than that for wild-type RdRp (Figure 4D). 2021 Nucleic acids research Result IV K235R;K235R 7;179 12;184 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. Based on the specificity for UTP, we computed the discrimination factor for both wild-type and K235R, which serves as a quantitative measurement for the transcription fidelity by computing the ratio of specificities for cognate CTP:G(template) and wobble UTP:G(template). 2021 Nucleic acids research Result IV K235R 95 100 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. Consistent with the results from the mini-genome assay (Figure 3A), mutations of K235 to amino acids with neutral side-chains abolished RdRp activity, while K235R mutant possessed a 2-fold increase in transcription efficiency to synthesize the full product with all four NTPs (Figure 3B and C). 2021 Nucleic acids research Result IV K235R 157 162 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. For example, a previous study identified a mutant HIV-1 with a K65R substitution on the p66 subunit of reverse transcriptase (RT). 2021 Nucleic acids research Result IV K65R 63 67 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. For example, the previously identified high-fidelity V43I and K229R mutants show accurate incorporation at the cost of decreased transcription rate. 2021 Nucleic acids research Result IV V43I;K229R 53;62 57;67 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. For NTP binding, we have computed the free energy of NTP binding to the active site in the revision of this manuscript and further examined the impact of K235R on the cognate versus noncognate NTP binding (Supplementary Figure S15, see Supplementary Section S1.13 for details). 2021 Nucleic acids research Result IV K235R 154 159 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. Further structural analysis indicated the conformational flexibility is most pronounced in the K235R mutant RdRp with noncognate UTP (Supplementary Figures S16 and S17, see Supplementary Section S1.14 for details), possibly due to larger fluctuations of the phosphate tail induced by the relatively unstable wobble base pair. 2021 Nucleic acids research Result IV K235R 95 100 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. Furthermore, MD simulations by substituting R239 with alanine demonstrate that the distance between R239A and NTP is extended to ~8 A (Figure 2F), implicating that the point mutation completely abolishes its role in facilitating catalysis. 2021 Nucleic acids research Result IV R239A 100 105 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. Furthermore, the K235R mutation well maintains other critical distances for catalysis (Supplementary Figure S12, see Supplementary Section S1.11 for details), and simultaneously maintained or imposed extra interactions with the Palpha & Pgamma groups of CTP (Supplementary Figure S13, see Supplementary Sections 1.10 and 1.11 for details). 2021 Nucleic acids research Result IV K235R 17 22 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. Furthermore, we calculated the substrate specificity (kpol/Kd,app) to measure the polymerase transcription efficiency and discrimination factor (substrate specificity of cognate over noncognate NTP) to profile the fidelity in both wild-type and K235R mutant RdRps. 2021 Nucleic acids research Result IV K235R 245 250 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. However, Kd,app for wobble base pair in K235R (448.8 +- 88.2 muM) is obviously higher than that in wild-type RdRp (163.2 +- 38.7 muM) (Figure 4B and Supplementary Figure S6). 2021 Nucleic acids research Result IV K235R 40 45 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. However, the Kd,app for CTP incorporation in K235R is 186.0 +- 77.4 muM, comparable with the 126.4 +- 56.0 muM in wild-type. 2021 Nucleic acids research Result IV K235R 45 50 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. However, this distance fluctuates more obviously and has a fractional distribution in the region of 6-7 A, consistent with the experimental observation that the K235R mutant has a less evident increase in kpol for UTP:G(template) wobble pair than the CTP:G(template) canonical pair (Figure 5A). 2021 Nucleic acids research Result IV K235R 161 166 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. In this study, we show that the K235R mutant IAV RdRp exhibits increased fidelity and activity compared to the wild-type K235 IAV RdRp. 2021 Nucleic acids research Result IV K235R 32 37 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. Indeed, the high-fidelity phenotype K235R is only present in a small number of swine and avian strains (e.g. 2021 Nucleic acids research Result IV K235R 36 41 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. Intriguingly, our results show that in the determination of CTP:G(template), the CTP incorporation rate in K235R RdRp (kpol = 620.0 min-1) significantly increased by 2.8-fold compared to the wild-type RdRp (kpol = 219.3 min-1) (Figure 4A; Supplementary Figure S6 and Supplementary Table S1). 2021 Nucleic acids research Result IV K235R 107 112 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. isolation of A/swine/Guangdong/wxl/2004(H9N2)) but not in human isolations, implying that K235R renders the virus incapable of effective cross-species transmission. 2021 Nucleic acids research Result IV K235R 90 95 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. It is noted that the sufficient space in the active site of IAV RdRp is important to ensure the K235R mutant with a longer side chain while maintaining the positive charge could work together with R239 to approach the triphosphate moiety of CTP without imposing any steric hindrance, thereby exerting a higher propensity for withdrawing electron density from the phosphate and facilitating the phosphodiester bond formation. 2021 Nucleic acids research Result IV K235R 96 101 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. K235R mutation enhances the transcription activity of IAV RdRp. 2021 Nucleic acids research Result IV K235R 0 5 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. K235R mutation renders IAV RdRp higher fidelity. 2021 Nucleic acids research Result IV K235R 0 5 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. Meanwhile, the mutant shows lower transcription efficiency to incorporate the noncognate UTP mainly due to the higher Kd,app for the K235R mutant. 2021 Nucleic acids research Result IV K235R 133 138 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. More importantly, our findings suggest that the higher fidelity of K235R mutant is originated from higher transcription efficiency for incorporating cognate NTP over noncognate NTP. 2021 Nucleic acids research Result IV K235R 67 72 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. Mutational frequencies carrying the PB1-K235R mutation measured by NGS. 2021 Nucleic acids research Result IV K235R 40 45 PB1 36 39 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. Our discovery of the K235R mutant IAV may have significant implications to vaccine development by overcoming two main challenges. 2021 Nucleic acids research Result IV K235R 21 26 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. Our finding is consistent with a previous work demonstrating that the alanine substitutions on the positively charged residues in Motif F of IAV RdRp could lead to various degrees of loss in polymerase activity, such as the R239A mutation that led to a complete loss of enzyme activity. 2021 Nucleic acids research Result IV R239A 224 229 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. Overall, the distance analysis from MD simulations explains the closer distance between K235R and substrate NTP can lead to a faster incorporation rate (kpol). 2021 Nucleic acids research Result IV K235R 88 93 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. Overall, the K235R mutant not only preserves distances that are critical to catalysis but also forms extra interactions between K235R and CTP to further stabilize the catalytically active conformation. 2021 Nucleic acids research Result IV K235R;K235R 13;128 18;133 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. Strikingly, we discovered that K235R mutation by preserving the positive charge while modifying the size of the side chain results in up to as much as two-fold enhanced polymerase activity over wild-type RdRp. 2021 Nucleic acids research Result IV K235R 31 36 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. The average sequencing depths of both wild-type and K235R are ~105 per replicate (Figure 6B). 2021 Nucleic acids research Result IV K235R 52 57 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. The incorporation rate for K235R mutant (kpol = 7.8 min-1) is slightly higher than that for wild-type (kpol = 6.8 min-1). 2021 Nucleic acids research Result IV K235R 27 32 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. The K65 in HIV-1 RT is structurally equivalent to K235 in IAV RdRp (Supplementary Figures S1A, S14A and S14C), where the disturbed enzyme activity of K65R was probably caused by a bulkier side chain of the substituted arginine in the highly compacted active site (Supplementary Figure S14A and S14B, see Supplementary Section S1.12 for details). 2021 Nucleic acids research Result IV S14A;S14C;K65R;S14A 95;104;150;285 99;108;154;289 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. The longer side chain imposed by the K235R mutant renders the residue closer to the triphosphate moiety of CTP and thereby considerably facilitates the incorporation of the cognate CTP (faster kpol), leading to higher transcription efficiency than the wild-type. 2021 Nucleic acids research Result IV K235R 37 42 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. The NGS results indicated that the K235R mutant live virus had a significantly lower mutation rate than that of the wild-type live virus, which are also consistent with our findings based on biochemical assays and confirm that K235R is indeed a high-fidelity mutant at the live virus level. 2021 Nucleic acids research Result IV K235R;K235R 35;227 40;232 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. The recombinant viruses carrying the K235R mutation also show no compromise on the viral replication (Figure 3D). 2021 Nucleic acids research Result IV K235R 37 42 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. Therefore, the specificity of CTP:G(template) of K235R and wild-type are 3.3 and 1.7 min-1muM-1, respectively (Figure 4C). 2021 Nucleic acids research Result IV K235R 49 54 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. Therefore, the transcription efficiency for the noncognate UTP incorporation in K235R mutant (kpol/Kd,app = 0.02 min-1muM-1) is lower than that in the wildtype (kpol/Kd,app = 0.04 min-1muM-1) (Figure 4C and Supplementary Table S1). 2021 Nucleic acids research Result IV K235R 80 85 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. These results demonstrate that the K235R mutant can significantly promote transcription activity and maintain normal viral growth kinetics compared to wild-type. 2021 Nucleic acids research Result IV K235R 35 40 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. These results further support our discovery that the K235R mutant has higher transcription fidelity than the wild-type to distinguish the cognate NTP from the mismatched NTP and the NTP analogs. 2021 Nucleic acids research Result IV K235R 53 58 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. These results suggest that the K235R mutant exerts increased transcription efficiency for the cognate CTP by 1.9-fold. 2021 Nucleic acids research Result IV K235R 31 36 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. This also explains the discrepancy in the transcription activity of K235R mutant IAV RdRp and other RdRp with the corresponding mutation. 2021 Nucleic acids research Result IV K235R 68 73 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. This is consistent with the experimental observations that the transcription activity of R239K RdRp is decreased orders of magnitudes compared to the wild-type RdRp. 2021 Nucleic acids research Result IV R239K 89 94 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. This is in sharp contrast to IAV RdRp, wherein the active site has enough space to accommodate K235R and R239 without steric hindrance (Supplementary Figure S14D). 2021 Nucleic acids research Result IV K235R;S14D 95;157 100;161 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. This observed conformational flexibility together with the results of the free energy calculations explains how the K235R mutation deters the UTP binding. 2021 Nucleic acids research Result IV K235R 116 121 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. This provides the mechanistic interpretation for the higher kpol in K235R (Figure 5A). 2021 Nucleic acids research Result IV K235R 68 73 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. To confirm the high-fidelity phenotype of live viruses with the PB1-K235R mutation, we rescued the wild-type and PB1-K235R mutant A/WSN/1933(H1N1) recombinant viruses from pHW2000 plasmids. 2021 Nucleic acids research Result IV K235R;K235R 68;117 73;122 PB1;PB1 64;113 67;116 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. To further explore the molecular mechanisms by which K235R enhanced the incorporation rate (kpol) in comparison with wild-type (Figure 5A), we performed MD simulations to survey the active site of wild-type and K235R mutant RdRps (five 100-ns simulations for each system, see Supplementary Sections 1.9-1.10 for details). 2021 Nucleic acids research Result IV K235R;K235R 53;211 58;216 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. We also attempted to rescue recombinant viruses carrying the R239K mutation at the RdRp, but they were not viable (Figure 2D). 2021 Nucleic acids research Result IV R239K 61 66 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. We expect that the K235R substitution will not become prevalent because the virus's high fidelity RdRp may prevent it from initiating the required mutational changes, rendering it incapable of adapting to its environment. 2021 Nucleic acids research Result IV K235R 19 24 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. We further assessed if K235R could exhibit better discrimination for NTP analogs. 2021 Nucleic acids research Result IV K235R 23 28 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. We next determined the specificity for UTP incorporation in both the wild-type and K235R mutant RdRps. 2021 Nucleic acids research Result IV K235R 83 88 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. We note that this difference is still at the level of thermal fluctuation (~1.3 kBT), nevertheless it is converged in our alchemical free energy calculations (Supplementary Figure S15C). 2021 Nucleic acids research Result IV S15C 180 184 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. When UTP is present at the active site to form the wobble pair with the template G, the K235R mutant also shows a closer distance to the beta-phosphate group of UTP than wild-type (Figure 5D). 2021 Nucleic acids research Result IV K235R 88 93 34702977 Ancestral sequence reconstruction pinpoints adaptations that enable avian influenza virus transmission in pigs. Among 20 amino acids that differentiate the internal proteins of RG-EA2 and -EA3 viruses, PB1-Q621R and NP-R351K were detected at high frequencies (> 90%) among EA swine influenza viruses isolated from 1979 to 2018. 2021 Nature microbiology Result IV Q621R;R351K 94;107 99;112 NP;PB1 104;90 106;93 34702977 Ancestral sequence reconstruction pinpoints adaptations that enable avian influenza virus transmission in pigs. Among the 12 amino acid differences found in the HA protein of RG-EA2 and EA3 viruses, HA1-N121T, HA1-Y138H, HA1-N207Y, HA1-K311Q, HA2-A65S, and HA2-D158N (H1 numbering) were detected at high frequencies (>90%) among EA swine viruses isolated from 1979-2016. 2021 Nature microbiology Result IV N121T;Y138H;N207Y;K311Q;A65S;D158N 91;102;113;124;135;149 96;107;118;129;139;154 HA;HA;HA;HA1;HA1;HA1;HA1 49;131;145;87;98;109;120 51;133;147;90;101;112;123 34702977 Ancestral sequence reconstruction pinpoints adaptations that enable avian influenza virus transmission in pigs. Both PB1-R621Q and NP-K351R mutations reduced the polymerase activity of RG-EA3 (P < 0.01. 2021 Nature microbiology Result IV R621Q;K351R 9;22 14;27 34702977 Ancestral sequence reconstruction pinpoints adaptations that enable avian influenza virus transmission in pigs. In contact pigs, viral load shed by RG-EA2NP-R351K infected contacts (mean +- SD AUC = 3.04 +- 1.57) was slightly lower than that of the RG-EA2PB1-Q621R,NP-R351K infected contacts (5.4 +- 1.31; two-sided Mann-Whitney test, P = 0.11). 2021 Nature microbiology Result IV R351K;Q621R;R351K 45;147;156 50;152;161 NP 153 155 34702977 Ancestral sequence reconstruction pinpoints adaptations that enable avian influenza virus transmission in pigs. In NPTr cells, RG-EA2 PB1-Q621R,NP-R351K replicated to higher titers than RG-EA2 and RG-EA2 NP-R351K viruses at 24 hpi (P = 0.019) and 36 hpi (P = 0.024), respectively. 2021 Nature microbiology Result IV Q621R;R351K;R351K 26;35;95 31;40;100 NP;NP;PB1 32;92;22 34;94;25 34702977 Ancestral sequence reconstruction pinpoints adaptations that enable avian influenza virus transmission in pigs. In the NA protein, RG-EA2 and RG-EA3 differed by the Y344N mutation (N1 numbering). 2021 Nature microbiology Result IV Y344N 53 58 7 9 34702977 Ancestral sequence reconstruction pinpoints adaptations that enable avian influenza virus transmission in pigs. Interestingly, the NP-R351K mutation facilitated accumulation of viral RNP in the nucleus at earlier time points when compared to RG-EA2 virus (P < 0.05. 2021 Nature microbiology Result IV R351K 22 27 34702977 Ancestral sequence reconstruction pinpoints adaptations that enable avian influenza virus transmission in pigs. Introduction of the PB1-Q621R but not the NP-R351K mutation increased the polymerase activity of RG-EA2 (One-way ANOVA and Tukey's post hoc test, P < 0.01. 2021 Nature microbiology Result IV Q621R;R351K 24;45 29;50 34702977 Ancestral sequence reconstruction pinpoints adaptations that enable avian influenza virus transmission in pigs. Next-generation sequencing analyses were performed on the peak-titer nasal swab samples of each contact pig infected with RG-EA2NP-R351K or RG-EA2PB1-Q621R,NP-R351K and we did not observe common adaptive mutations in more than 1 pig (Supplementary Table 3). 2021 Nature microbiology Result IV R351K;Q621R;R351K 131;150;159 136;155;164 NP 156 158 34702977 Ancestral sequence reconstruction pinpoints adaptations that enable avian influenza virus transmission in pigs. RG-EA2NP-R351K was detected from the nasal swabs of all donors and contacts. 2021 Nature microbiology Result IV R351K 9 14 34702977 Ancestral sequence reconstruction pinpoints adaptations that enable avian influenza virus transmission in pigs. RG-EA2PB1-Q621R,NP-R351K was detected from the nasal swabs of all donors and contacts. 2021 Nature microbiology Result IV Q621R;R351K 10;19 15;24 NP 16 18 34702977 Ancestral sequence reconstruction pinpoints adaptations that enable avian influenza virus transmission in pigs. Taken together, these results showed that introducing the NP-R351K mutation was sufficient to enhance the transmissibility of the reconstructed early EA2 swine virus. 2021 Nature microbiology Result IV R351K 61 66 NP 58 60 34702977 Ancestral sequence reconstruction pinpoints adaptations that enable avian influenza virus transmission in pigs. The total amount of virus shed by the RG-EA2NP-R351K inoculated donors (mean +- SD AUC = 2.74 +- 2.63) was comparable to that of the RG-EA2PB1-Q621R,NP-R351K inoculated donors (3.78 +- 1.67; two-sided Mann-Whitney test, P = 0.69). 2021 Nature microbiology Result IV R351K;Q621R;R351K 47;143;152 52;148;157 NP 149 151 34702977 Ancestral sequence reconstruction pinpoints adaptations that enable avian influenza virus transmission in pigs. We further focused on these two mutations and compared the transmissibility of RG-EA2NP-R351K and RG-EA2PB1-Q621R, NP-R351K viruses in pigs. 2021 Nature microbiology Result IV Q621R;R351K;R351K 108;88;118 113;93;123 NP 115 117 35044215 N-Glycolylneuraminic Acid Binding of Avian and Equine H7 Influenza A Viruses. A combination of A135E and S128T resulted in a loss of glycan binding on the array. 2022 Journal of virology Result IV A135E;S128T 17;27 22;32 35044215 N-Glycolylneuraminic Acid Binding of Avian and Equine H7 Influenza A Viruses. Adding the T189A mutation in the A135E+K193R background switched the H7tu HA to binding mainly NeuGc. 2022 Journal of virology Result IV T189A;K193R;A135E 11;39;33 16;44;38 HA 74 76 35044215 N-Glycolylneuraminic Acid Binding of Avian and Equine H7 Influenza A Viruses. After the introduction of the five reciprocal mutations (T128S, V130I, E135A, A189T, R189K), the equine HA still seemed specific for NeuGc on the glycan array. 2022 Journal of virology Result IV T128S;V130I;E135A;A189T;R189K 57;64;71;78;85 62;69;76;83;90 HA 104 106 35044215 N-Glycolylneuraminic Acid Binding of Avian and Equine H7 Influenza A Viruses. As controls for the presence of NeuAc and NeuGc on erythrocytes and tracheal epithelium, we used our previously studied wild-type (WT) and Y161A mutant HAs of A/Vietnam/1203/2004 H5N1 (H5VN), which specifically bind alpha2,3-linked NeuAc and alpha2,3-linked NeuGc, respectively. 2022 Journal of virology Result IV Y161A 139 144 35044215 N-Glycolylneuraminic Acid Binding of Avian and Equine H7 Influenza A Viruses. As soon as the key mutation A135E was introduced, the HA showed similar binding patterns as the avian H7 Has, with binding to both NeuAc and NeuGc and both chicken and horse erythrocytes and tissue. 2022 Journal of virology Result IV A135E 28 33 HA 54 56 35044215 N-Glycolylneuraminic Acid Binding of Avian and Equine H7 Influenza A Viruses. Despite residue 219 being very close to the 220-loop, mutation A219P did not change the binding properties of the H7tu HA from NeuAc to NeuGc. 2022 Journal of virology Result IV A219P 63 68 HA 119 121 35044215 N-Glycolylneuraminic Acid Binding of Avian and Equine H7 Influenza A Viruses. Furthermore, NeuGc binding specificity on the glycan array was achieved by combining mutation A135E with mutations I130V or T189A+K193R. 2022 Journal of virology Result IV A135E;I130V;T189A;K193R 94;115;124;130 99;120;129;135 35044215 N-Glycolylneuraminic Acid Binding of Avian and Equine H7 Influenza A Viruses. However, both types of erythrocytes were still bound by HAs with combinations of all investigated mutations (A135E, A135E+S128T, A135E+I130V, and A135E+T189A+K193R). 2022 Journal of virology Result IV A135E;S128T;A135E;A135E;I130V;A135E;T189A;K193R 109;122;116;129;135;146;152;158 114;127;121;134;140;151;157;163 35044215 N-Glycolylneuraminic Acid Binding of Avian and Equine H7 Influenza A Viruses. However, introducing Y161A in other HA subtypes (H1, H2, and H4) did not change binding specificity. 2022 Journal of virology Result IV Y161A 21 26 HA 36 38 35044215 N-Glycolylneuraminic Acid Binding of Avian and Equine H7 Influenza A Viruses. In H7eq, R144 forms salt bridges with the 130-loop residue E135, but mutation G144R alone in the H7tu HA did not change the binding specificity. 2022 Journal of virology Result IV G144R 78 83 HA 102 104 35044215 N-Glycolylneuraminic Acid Binding of Avian and Equine H7 Influenza A Viruses. In short, we were able to modify the H7tu HA for binding NeuGc specifically on the glycan microarray by combinations of mutations A135E+S128T, A135E+I130V, or A135E+T189A+K193R. 2022 Journal of virology Result IV A135E;S128T;A135E;I130V;A135E;K193R;T189A 130;136;143;149;159;171;165 135;141;148;154;164;176;170 HA 42 44 35044215 N-Glycolylneuraminic Acid Binding of Avian and Equine H7 Influenza A Viruses. In summary, while most mutations performed on the H7tu HA did not affect binding specificity, the introduction of mutation K193R abolished glycan binding and A135E seemed to be key for binding NeuGc while maintaining binding to NeuAc. 2022 Journal of virology Result IV K193R;A135E 123;158 128;163 HA 55 57 35044215 N-Glycolylneuraminic Acid Binding of Avian and Equine H7 Influenza A Viruses. In the 130-loop, mutations S128T and I130V did not induce clear changes in the NeuAc/NeuGc specificity. 2022 Journal of virology Result IV S128T;I130V 27;37 32;42 35044215 N-Glycolylneuraminic Acid Binding of Avian and Equine H7 Influenza A Viruses. Introducing K193R into the H7tu HA seemed to abolish all binding to the glycan array. 2022 Journal of virology Result IV K193R 12 17 HA 32 34 35044215 N-Glycolylneuraminic Acid Binding of Avian and Equine H7 Influenza A Viruses. Mutating more amino acids in the 130-loop, at position 128 (S128T) or 130 (I130V), appeared to abolish NeuAc binding while maintaining binding to NeuGc on the glycan microarray. 2022 Journal of virology Result IV S128T;I130V 60;75 65;80 35044215 N-Glycolylneuraminic Acid Binding of Avian and Equine H7 Influenza A Viruses. Mutation T189A in the H7tu HA did not change receptor specificity when introduced on its own. 2022 Journal of virology Result IV T189A 9 14 HA 27 29 35044215 N-Glycolylneuraminic Acid Binding of Avian and Equine H7 Influenza A Viruses. Previously, it was demonstrated that a Y161A mutation changed the binding properties of an H5 HA from NeuAc to NeuGc. 2022 Journal of virology Result IV Y161A 39 44 HA 94 96 35044215 N-Glycolylneuraminic Acid Binding of Avian and Equine H7 Influenza A Viruses. Since mutations A135E and K193R both affected the receptor-binding properties, we further combined these two mutations with mutations that did not change binding specificity so far. 2022 Journal of virology Result IV A135E;K193R 16;26 21;31 35044215 N-Glycolylneuraminic Acid Binding of Avian and Equine H7 Influenza A Viruses. Since we did not observe exclusive NeuGc binding with the double and triple mutants, we combined the five mutations S128T, I130V, A135E, T189A, and K193R in the H7tu HA. 2022 Journal of virology Result IV S128T;I130V;A135E;T189A;K193R 116;123;130;137;148 121;128;135;142;153 HA 166 168 35044215 N-Glycolylneuraminic Acid Binding of Avian and Equine H7 Influenza A Viruses. Starting from the key mutation A135E, we continued mutagenesis in the recombinantly expressed HAs by adding mutations at the previously stated positions. 2022 Journal of virology Result IV A135E 31 36 35044215 N-Glycolylneuraminic Acid Binding of Avian and Equine H7 Influenza A Viruses. the addition of mutation A135E restored binding to both NeuAc and NeuGc. 2022 Journal of virology Result IV A135E 25 30 35044215 N-Glycolylneuraminic Acid Binding of Avian and Equine H7 Influenza A Viruses. The addition of mutation A219P did not affect the binding specificity, since both NeuAc and NeuGc were still bound almost equally. 2022 Journal of virology Result IV A219P 25 30 35044215 N-Glycolylneuraminic Acid Binding of Avian and Equine H7 Influenza A Viruses. The combination of A135E+S128T+I130V did not change the binding specificities in comparison to that of only A135E. 2022 Journal of virology Result IV S128T;I130V;A135E;A135E 25;31;19;108 30;36;24;113 35044215 N-Glycolylneuraminic Acid Binding of Avian and Equine H7 Influenza A Viruses. The combination of mutation A135E with mutation G144R, A159G+A160V, T189A, or A219P did not change binding specificity compared to that of mutation A135E alone, since both NeuAc and NeuGc were still bound. 2022 Journal of virology Result IV G144R;A135E;A159G;A160V;T189A;A219P;A135E 48;28;55;61;68;78;148 53;33;60;66;73;83;153 35044215 N-Glycolylneuraminic Acid Binding of Avian and Equine H7 Influenza A Viruses. The combination of mutations A135E, T189A, and K193R did not change the binding specificity in the hemagglutination assay either, but binding to both chicken and horse tracheal tissue was lost. 2022 Journal of virology Result IV A135E;T189A;K193R 29;36;47 34;41;52 35044215 N-Glycolylneuraminic Acid Binding of Avian and Equine H7 Influenza A Viruses. The combinations of mutations A135E, A135E+S128T, and A135E+I130V did not change the binding specificity of the HA in the hemagglutination assay using chicken or horse erythrocytes. 2022 Journal of virology Result IV A135E;S128T;A135E;A135E;I130V 30;43;37;54;60 35;48;42;59;65 HA 112 114 35044215 N-Glycolylneuraminic Acid Binding of Avian and Equine H7 Influenza A Viruses. The NeuGc-Gal bond of 3'-GcLN in the H7eq complex adopts a cis conformation, which is consistent with our previous findings for the structure of 3'-GcLN in complex with the A/Vietnam/1203/2004 H5N1 Y161A mutant that shifts receptor specificity from NeuAc to NeuGc. 2022 Journal of virology Result IV Y161A 198 203 35044215 N-Glycolylneuraminic Acid Binding of Avian and Equine H7 Influenza A Viruses. The sole introduction of mutation A135E enabled NeuGc binding and seemed to abolish some binding to NeuAc. 2022 Journal of virology Result IV A135E 34 39 35044215 N-Glycolylneuraminic Acid Binding of Avian and Equine H7 Influenza A Viruses. We found that adding mutation G144R or A159G+A160V abolished binding to the array. 2022 Journal of virology Result IV G144R;A159G;A160V 30;39;45 35;44;50 35044215 N-Glycolylneuraminic Acid Binding of Avian and Equine H7 Influenza A Viruses. We made mutations A159G and A160V simultaneously in the H7tu HA, but unlike with the Y161A mutation in H5, we did not observe NeuGc binding with this double mutation. 2022 Journal of virology Result IV A159G;A160V;Y161A 18;28;85 23;33;90 HA 61 63 35044215 N-Glycolylneuraminic Acid Binding of Avian and Equine H7 Influenza A Viruses. We observed that mutating position 135 (A135E) resulted in a gain of binding of the H7tu HA to NeuGc while maintaining binding to NeuAc. 2022 Journal of virology Result IV A135E 40 45 HA 89 91 35044215 N-Glycolylneuraminic Acid Binding of Avian and Equine H7 Influenza A Viruses. When we, however, combined mutations A135E, D189A, and K193R or all five mutations, the H15 HA became specific for NeuGc on the glycan array. 2022 Journal of virology Result IV A135E;D189A;K193R 37;44;55 42;49;60 HA 92 94 35044215 N-Glycolylneuraminic Acid Binding of Avian and Equine H7 Influenza A Viruses. Whereas almost all binding was abolished when mutation K193R was introduced by itself. 2022 Journal of virology Result IV K193R 55 60 18325270 Mutations in influenza A virus (H5N1) and possible limited spread, Turkey, 2006. The Q447L and E627K mutations in FK and MAK virus isolates indicate a common origin of viruses in the 2 siblings. 2008 Emerging infectious diseases Conclusion IV Q447L;E627K 4;14 9;19 18325270 Mutations in influenza A virus (H5N1) and possible limited spread, Turkey, 2006. Unique mutations (D158N and S227N in HA and N556K and R46K in PB2) in only the MAK isolate suggest virus evolution in 1 patient. 2008 Emerging infectious diseases Conclusion IV D158N;S227N;N556K;R46K 18;28;44;54 23;33;49;58 HA;PB2 37;62 39;65 19958488 Prediction of avian influenza A binding preference to human receptor using conformational analysis of receptor bound to hemagglutinin. The results could be used to explain why the L129V/A134V Kan-1 and Q222L/G224S Sing-97 could bind better to human receptor analog in in vitro assays. 2009 BMC genomics Conclusion IV L129V;A134V;Q222L;G224S 45;51;67;73 50;56;72;78 20459681 Oseltamivir-resistant pandemic (H1N1)2009 in Yemen - case report. Both clinical specimens contained the mutation H274Y in NA gene associated with resistance to oseltamivir. 2010 Virology journal Conclusion IV H274Y 47 52 56 58 20459681 Oseltamivir-resistant pandemic (H1N1)2009 in Yemen - case report. Both clinical specimens presented the mutation S31N in the M2 gene associated with resistance to adamantanes. 2010 Virology journal Conclusion IV S31N 47 51 M2 59 61 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. HA-E391K is a globally fast growing mutation in 2009 (H1N1) samples and could alter the salt bridge pattern and stability in a region of the HA oligomerization interface that is important for membrane fusion and also a known antigenic site. 2010 PLoS currents Conclusion IV E391K 3 8 HA;HA 0;141 2;143 20591072 Increasing antiviral activity of surfactant protein d trimers by introducing residues from bovine serum collectins: dissociation of mannan-binding and antiviral activity. The combined effect of the hydrophobic substitution at R343 and the RAK insertion adjacent to D325 alters both ridges surrounding the primary carbohydrate binding site leading to substantially greater mannan binding than occurs with either R343I or RAK alone. 2010 Scandinavian journal of immunology Conclusion IV R343I 240 245 20591072 Increasing antiviral activity of surfactant protein d trimers by introducing residues from bovine serum collectins: dissociation of mannan-binding and antiviral activity. Unexpectedly, the RAK+R343I (or V) combined mutants had reduced viral binding and inhibiting activity compared to R343I (or V) single mutants. 2010 Scandinavian journal of immunology Conclusion IV R343I;R343I 22;114 27;119 20591072 Increasing antiviral activity of surfactant protein d trimers by introducing residues from bovine serum collectins: dissociation of mannan-binding and antiviral activity. We demonstrate that the CL-43 NCRD and a mutant version of the human SP-D NCRD incorporating key distinctive features surrounding the lectin site of CL-43 (RAK+R343I) have greatly increased binding to mannan. 2010 Scandinavian journal of immunology Conclusion IV R343I 160 165 20833142 Solution NMR structure of the V27A drug resistant mutant of influenza A M2 channel. The solution NMR structure of the V27A amantadine-resistant mutant reveals a number of interesting features that have not been observed in any of the known experimental structures and models of the M2 protein. 2010 Biochemical and biophysical research communications Conclusion IV V27A 34 38 M2 198 200 20833142 Solution NMR structure of the V27A drug resistant mutant of influenza A M2 channel. The structure shows a substantially increased channel opening at the N-terminal end, which may explain the faster proton conduction observed for the V27A mutant. 2010 Biochemical and biophysical research communications Conclusion IV V27A 149 153 21364825 Identification of sequence mutations affecting hemagglutinin specificity to sialic acid receptor in influenza A virus subtypes. These mutation patterns identified include 1) mutations in positions 190 and 225 to aspartic acid (E190D in A/Brevig Mission/1/18(H1N1), A/New York/1/18(H1N1) and A/South Carolina/1/1918(H1N1) and G225D on A/South Carolina/1/1918(H1N1), A/South Carolina/1/1918(H1N1), and A/Puerto Rico/8/34(H1N1)) and 2) mutations in position 226 and 228 to leucine and serine (Q226L and G228S in A/Guiyang/1/1957(H2N2), A/Kayano/57(H2N2), A/Aichi/2/1968(H3N2) and A/Hong Kong/1/1968(H3N2), A/Memphis/1/68(H3N2)). 2010 Bioinformation Conclusion IV E190D;G225D;Q226L;G228S 101;200;368;378 106;205;373;383 21744829 Molecular dynamics simulation directed rational design of inhibitors targeting drug-resistant mutants of influenza A virus M2. Relatively long simulations have allowed one to address mobile water as well as conformational mobility and resulted in a deeper understanding of the mechanism of inhibition that translated into tight-binding inhibitors of V27A. 2011 Journal of the American Chemical Society Conclusion IV V27A 223 227 21744829 Molecular dynamics simulation directed rational design of inhibitors targeting drug-resistant mutants of influenza A virus M2. This insight paved the way to an understanding of the potential mode of binding of our initial hits for V27A, and to enhance their affinity by maximizing the fit with this mutant while simultaneously retaining affinity for WT through a related but distinct predicted binding mode. 2011 Journal of the American Chemical Society Conclusion IV V27A 104 108 22111074 First Fatal Oseltamivir-Resistant 2009 Pandemic Influenza A (H1N1) Case in an Adult in Korea. Sequence analysis performed at the Korea Centers for Disease Control and Prevention revealed an H275Y neuraminidase gene mutation, as described elsewhere. 2011 Chonnam medical journal Conclusion IV H275Y 96 101 102 115 23437766 Discovery of novel dual inhibitors of the wild-type and the most prevalent drug-resistant mutant, S31N, of the M2 proton channel from influenza A virus. On the basis of this work, several more potent series of S31N inhibitors have been discovered, one series has already been published, and others will be the subject of future reports. 2013 Journal of medicinal chemistry Conclusion IV S31N 57 61 23437766 Discovery of novel dual inhibitors of the wild-type and the most prevalent drug-resistant mutant, S31N, of the M2 proton channel from influenza A virus. Using a combination of structural information of M2 proton channel and medicinal chemistry approaches, we report the discovery of promising dual M2 inhibitors for S31N and WT M2 channels, demonstrating that M2 S31N is a druggable target. 2013 Journal of medicinal chemistry Conclusion IV S31N;S31N 163;210 167;214 M2;M2;M2;M2 49;145;175;207 51;147;177;209 23902660 Frequency of D222G haemagglutinin mutant of pandemic (H1N1) pdm09 influenza virus in Tunisia between 2009 and 2011. The altered receptor specificity and distinctive cell tropism of the D222G mutants of influenza A(H1N1)pdm09 are hallmarks of a more dangerous pathogen, emphasizing the importance of close monitoring of the evolution of these viruses. 2013 Diagnostic pathology Conclusion IV D222G 69 74 23902660 Frequency of D222G haemagglutinin mutant of pandemic (H1N1) pdm09 influenza virus in Tunisia between 2009 and 2011. Whether the selection of the D222G mutation is a cause or a consequence of more severe lower respiratory tract infection is still to be resolved. 2013 Diagnostic pathology Conclusion IV D222G 29 34 24074585 Mutation from arginine to lysine at the position 189 of hemagglutinin contributes to the antigenic drift in H3N2 swine influenza viruses. In summary, we experimentally demonstrated that a single mutation (i.e., R189K) in hemagglutinin contributed to the antigenic drift of contemporary H3N2 SIVs. 2013 Virology Conclusion IV R189K 73 78 HA 83 96 24074585 Mutation from arginine to lysine at the position 189 of hemagglutinin contributes to the antigenic drift in H3N2 swine influenza viruses. To our knowledge, it is the first study to demonstrate contribution of R189K mutation to antigenic drift among swine H3N2 isolates. 2013 Virology Conclusion IV R189K 71 76 24237039 3-Azatetracyclo[5.2.1.1(5,8).0(1,5)]undecane derivatives: from wild-type inhibitors of the M2 ion channel of influenza A virus to derivatives with potent activity against the V27A mutant. Interestingly, the compounds reported here are the first examples of non-adamantane derivatives endowed with low micromolar activity against the V27A/M2 mutant channel, opening the way to the design of novel M2 inhibitors structurally based on non-adamantane scaffolds. 2013 Journal of medicinal chemistry Conclusion IV V27A 145 149 M2;M2 150;208 152;210 24237039 3-Azatetracyclo[5.2.1.1(5,8).0(1,5)]undecane derivatives: from wild-type inhibitors of the M2 ion channel of influenza A virus to derivatives with potent activity against the V27A mutant. The present works showed that, starting from compounds active against the wt A/M2 channel it is possible to design compounds active against both the wt and the V27A mutant A/M2 channels. 2013 Journal of medicinal chemistry Conclusion IV V27A 160 164 M2;M2 79;174 81;176 24521884 Mass spectrometry analysis coupled with de novo sequencing reveals amino acid substitutions in nucleocapsid protein from influenza A virus. One of identified amino acid substitutions, R452K, was located within the tryptic peptide MP1 (447-461), whereas the other two amino acid substitutions, T423A and N430T, were located within tryptic peptide MP2 (423-436). 2014 International journal of molecular sciences Conclusion IV R452K;T423A;N430T 44;153;163 49;158;168 24558492 Study of oseltamivir and zanamivir resistance-related mutations in influenza viruses isolated from wild mallards in Sweden. The presence of R118K mutation in N9, R152K in N6 and probably even majority of other mutations in N1 and N3 are rather due to natural variation of NA than induction by NAI. 2014 PloS one Conclusion IV R118K;R152K 16;38 21;43 N9;NA;NAI 34;148;169 36;150;172 24751348 PCR for detection of oseltamivir resistance mutation in influenza A(H7N9) virus. A similar phenomenon was observed in patients infected with the HA D222G mutant of influenza A(H1N1)pdm09 virus; this virus showed preferential replication in the lower respiratory tract and this infection was correlated with severe outcomes or deaths. 2014 Emerging infectious diseases Conclusion IV D222G 67 72 HA 64 66 24751348 PCR for detection of oseltamivir resistance mutation in influenza A(H7N9) virus. We have developed an SNP real-time RT-PCR for detection of a drug-resistant NA R292K mutant of influenza A(H7N9) virus. 2014 Emerging infectious diseases Conclusion IV R292K 79 84 76 78 24941437 Easily accessible polycyclic amines that inhibit the wild-type and amantadine-resistant mutants of the M2 channel of influenza A virus. Furthermore, compound 18 showed strong activity against the A/PR/8/34 strain, an A/H1N1 virus with two mutations (S31N and V27T) in the M2 protein. 2014 Journal of medicinal chemistry Conclusion IV S31N;V27T 114;123 118;127 M2 136 138 24941437 Easily accessible polycyclic amines that inhibit the wild-type and amantadine-resistant mutants of the M2 channel of influenza A virus. In particular, amine 18 and guanidine 19 emerged as promising compounds, being low micromolar inhibitors against the wt channel and the L26F mutant, while being endowed with submicromolar IC50 against the V27A variant. 2014 Journal of medicinal chemistry Conclusion IV L26F;V27A 136;205 140;209 24941437 Easily accessible polycyclic amines that inhibit the wild-type and amantadine-resistant mutants of the M2 channel of influenza A virus. The present work shows the feasibility of designing easily accessible compounds able to successfully inhibit the wt and the V27A and L26F variants of the A/M2 channels of influenza A virus. 2014 Journal of medicinal chemistry Conclusion IV V27A;L26F 124;133 128;137 M2 156 158 25470189 Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel. All unambiguous NOEs indicated that the inhibitors bind to the WT and S31N channels in opposite orientations, although we cannot rule out the possibility of other minor conformational states of the drug in the WT protein due to spectral overlap. 2014 Journal of the American Chemical Society Conclusion IV S31N 70 74 25470189 Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel. Our design was based on the hypothesis that dual inhibitors bind to WT and M2-S31N channels with opposite orientations: the aromatic headgroup faces down toward the C-termini and toward N-terminus in WT and S31N channel, respectively. 2014 Journal of the American Chemical Society Conclusion IV S31N;S31N 78;207 82;211 M2 75 77 25470189 Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel. The antiviral activity of the most potent inhibitor, 11, in inhibiting WT and the S31N mutant is on par with that of amantadine (1) in inhibiting WT virus. 2014 Journal of the American Chemical Society Conclusion IV S31N 82 86 25470189 Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel. We designed a class of such broad-spectrum dual inhibitors with EC50 values against WT and M2 S31N influenza viruses, which is comparable with that of amantadine (1) in inhibiting WT influenza virus. 2014 Journal of the American Chemical Society Conclusion IV S31N 94 98 M2 91 93 25589893 Identification of novel compounds against an R294K substitution of influenza A (H7N9) virus using ensemble based drug virtual screening. In this study, we demonstrated resistant mechanism of mutant strain H7N9 (R294K) in Shanghai virus by comparing binding poses and binding affinity between inhibitors as well as the substrate and X-ray structure of mutant and wild type NA in H7N9 virus. 2015 International journal of medical sciences Conclusion IV R294K 74 79 235 237 25589893 Identification of novel compounds against an R294K substitution of influenza A (H7N9) virus using ensemble based drug virtual screening. Therefore, we concluded that 7181 is the best potential compound for NA (R294K) inhibition and should be further analyzed and served as drug candidate for in vivo testing. 2015 International journal of medical sciences Conclusion IV R294K 73 78 69 71 25721488 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2013-2014. Almost all recently circulating A(H1N1)pdm09 viruses possess the NA V241I and N369K substitutions, indicating increased risk of H275Y variant viruses emerging and spreading globally. 2015 Antiviral research Conclusion IV V241I;N369K;H275Y 68;78;128 73;83;133 65 67 25721488 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2013-2014. However, a large community cluster of A(H1N1)pdm09 viruses with the NA H275Y substitution occurred in Hokkaido, Japan between November 2013 and February 2014. 2015 Antiviral research Conclusion IV H275Y 71 76 68 70 25721488 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2013-2014. In 2011, a widespread community cluster of NA H275Y variant A(H1N1)pdm09 viruses occurred in Newcastle, Australia. 2015 Antiviral research Conclusion IV H275Y 46 51 43 45 25721488 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2013-2014. The Hokkaido cluster viruses carried these two substitutions and shared NA N386K substitution with the H275Y variant viruses detected in China. 2015 Antiviral research Conclusion IV N386K;H275Y 75;103 80;108 72 74 25721488 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2013-2014. The latter H275Y variant viruses possessed V241I and N369K substitutions in the NA which partially overcame the detrimental effects of the H275Y substitution on virus fitness. 2015 Antiviral research Conclusion IV H275Y;V241I;N369K;H275Y 11;43;53;139 16;48;58;144 80 82 25721488 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2013-2014. The slight increase in 2013-2014 is due to several clusters of untreated cases of A(H1N1)pdm09 viruses carrying NA H275Y substitution in China, Japan and the United States. 2015 Antiviral research Conclusion IV H275Y 115 120 112 114 25721488 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2013-2014. The WHO-AVWG is currently developing the WHO database (FluNet) to collect this basic information, together with H275Y screening data for influenza A(H1N1)pdm09 viruses, from all NICs who perform such testing. 2015 Antiviral research Conclusion IV H275Y 112 117 25721488 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2013-2014. Therefore, the H275Y variant viruses of the Hokkaido cluster and those of China may be derived from a common ancestor. 2015 Antiviral research Conclusion IV H275Y 15 20 25793397 Characterization of a novel mutation in NS1 protein of influenza A virus induced by a chemical substance for the attenuation of pathogenicity. Although the antiviral activity of MFPT against IAVs was not a potent one (the 50% inhibitory concentration for virus replication = 2.8 mM), MFPTr viruses were attenuated both in vitro and in vivo as expected, and had a common novel mutation, P164S in NS1. 2015 PloS one Conclusion IV P164S 243 248 NS1 252 255 26056814 Molecular Characterisation of the Haemagglutinin Glycan-Binding Specificity of Egg-Adapted Vaccine Strains of the Pandemic 2009 H1N1 Swine Influenza A Virus. Our glycan binding data support the introduction of the D225G or Q226R mutations in recombinant H1N1 viruses to achieve high egg-growth to for rapid generation of vaccine production candidates. 2015 Molecules (Basel, Switzerland) Conclusion IV D225G;Q226R 56;65 61;70 26754751 Coupling high-throughput genetics with phylogenetic information reveals an epistatic interaction on the influenza A virus M segment. We successfully identified the epistatic interaction between influenza A virus M1 substitutions A209T and Q214H. 2016 BMC genomics Conclusion IV A209T;Q214H 96;106 101;111 M1 79 81 26845764 Genomic Signatures for Avian H7N9 Viruses Adapting to Humans. Numerous human-isolated avian influenza A viruses exhibit PB2 627K, which is a human-specific signature, and strong biological evidence indicates that an E627K mutation promotes avian viral replication in mammals. 2016 PloS one Conclusion IV E627K 154 159 PB2 58 61 26845764 Genomic Signatures for Avian H7N9 Viruses Adapting to Humans. We used a reporter assay to test all of these substitutions and showed that either Q591K, M535L, or D701N mutation increases the viral RNP activity in human cells with PB2 627E, suggesting that E627K, Q591K, M535L, and D701N are crucial markers for assessing the potential of an avian virus to infect humans, as well as for potentially increasing adaptation for the virus to gain human-to-human transmission capability in leading to a pandemic in the future. 2016 PloS one Conclusion IV Q591K;M535L;D701N;E627K;Q591K;M535L;D701N 83;90;100;194;201;208;219 88;95;105;199;206;213;224 PB2;RNP 168;135 171;138 27405392 G45R mutation in the nonstructural protein 1 of A/Puerto Rico/8/1934 (H1N1) enhances viral replication independent of dsRNA-binding activity and type I interferon biology. As we have demonstrated that G45R/NS1 virus induced the type I IFN induction and response in infected A549 cells, it is also interesting to investigate virus virulence for further studies. 2016 Virology journal Conclusion IV G45R 29 33 NS1 34 37 27405392 G45R mutation in the nonstructural protein 1 of A/Puerto Rico/8/1934 (H1N1) enhances viral replication independent of dsRNA-binding activity and type I interferon biology. G45R/NS1 does not increase the efficiency of binding to dsRNA or suppress IFNbeta induction, which are the established functions of NS1. 2016 Virology journal Conclusion IV G45R 0 4 NS1;NS1 5;132 8;135 27405392 G45R mutation in the nonstructural protein 1 of A/Puerto Rico/8/1934 (H1N1) enhances viral replication independent of dsRNA-binding activity and type I interferon biology. Thus, increased viral replication of G45R/NS is independent of dsRNA binding and type I IFN induction, suggesting that a non-characterized function of NS1 was responsible for the enhanced viral replication observed in this study. 2016 Virology journal Conclusion IV G45R 37 41 NS;NS1 42;151 44;154 27657178 Discovery of Potent Antivirals against Amantadine-Resistant Influenza A Viruses by Targeting the M2-S31N Proton Channel. However, our recent studies demonstrated that unlike amantadine, M2-S31N channel blockers have a higher genetic barrier of drug resistance that is comparable to oseltamivir. 2016 ACS infectious diseases Conclusion IV S31N 68 72 M2 65 67 27657178 Discovery of Potent Antivirals against Amantadine-Resistant Influenza A Viruses by Targeting the M2-S31N Proton Channel. In addressing this unmet medical need, we revisited the M2 proton channel and aim to develop the next generation of antivirals by targeting the M2-S31N mutant. 2016 ACS infectious diseases Conclusion IV S31N 147 151 M2;M2 56;144 58;146 27657178 Discovery of Potent Antivirals against Amantadine-Resistant Influenza A Viruses by Targeting the M2-S31N Proton Channel. In this study, we developed a late-stage diversification synthesis strategy that enabled us to expeditiously synthesize a focused library of M2-S31N inhibitors. 2016 ACS infectious diseases Conclusion IV S31N 144 148 M2 141 143 27657178 Discovery of Potent Antivirals against Amantadine-Resistant Influenza A Viruses by Targeting the M2-S31N Proton Channel. It was found that a hydrophobic substitution, preferentially piperidine and azepane, is required at the para-position of the aromatic head group for potent M2-S31N channel blockage. 2016 ACS infectious diseases Conclusion IV S31N 159 163 M2 156 158 27657178 Discovery of Potent Antivirals against Amantadine-Resistant Influenza A Viruses by Targeting the M2-S31N Proton Channel. The most potent compounds 10c and 16d have single-digit micromolar efficacy against all three M2-S31N-containing influenza A viruses, A/WSN/22 (H1N1), A/Switzerland/9715293/2013 (H1N1), and A/California/07/2009 (H1N1). 2016 ACS infectious diseases Conclusion IV S31N 97 101 M2 94 96 27657178 Discovery of Potent Antivirals against Amantadine-Resistant Influenza A Viruses by Targeting the M2-S31N Proton Channel. The reason why we chose M2-S31N mutant as the drug target is because it is one of the most conserved viral proteins among circulating influenza A viruses. 2016 ACS infectious diseases Conclusion IV S31N 27 31 M2 24 26 27657178 Discovery of Potent Antivirals against Amantadine-Resistant Influenza A Viruses by Targeting the M2-S31N Proton Channel. Therefore, M2-S31N remains a high-profile antiviral drug target to combat drug resistance. 2016 ACS infectious diseases Conclusion IV S31N 14 18 M2 11 13 28182419 Expeditious Lead Optimization of Isoxazole-Containing Influenza A Virus M2-S31N Inhibitors Using the Suzuki-Miyaura Cross-Coupling Reaction. It is worth highlighting that this was the first attempt to systematically correlate the channel blockage activity with antiviral activity for AM2-S31N inhibitors. 2017 Journal of medicinal chemistry Conclusion IV S31N 147 151 28182419 Expeditious Lead Optimization of Isoxazole-Containing Influenza A Virus M2-S31N Inhibitors Using the Suzuki-Miyaura Cross-Coupling Reaction. The major therapeutic value of AM2-S31N inhibitors is that they are active against both oseltamivir-sensitive and -resistant strains; therefore, they can be used either alone to combat oseltamivir-resistant strains or used in combination with oseltamivir to delay the evolution of resistant strains. 2017 Journal of medicinal chemistry Conclusion IV S31N 35 39 28182419 Expeditious Lead Optimization of Isoxazole-Containing Influenza A Virus M2-S31N Inhibitors Using the Suzuki-Miyaura Cross-Coupling Reaction. To corroborate with this conclusion, the most potent compound emerging from this study was compound 9q, which had single- to sub-micromolar efficacy against all four AM2-S31N-containing influenza A viruses (A/California/07/2009 (H1N1), A/Washington/29/2009 (H1N1), A/Denmark/528/2009 (H1N1), and A/Switzerland/9715293/2013 (H3N2)). 2017 Journal of medicinal chemistry Conclusion IV S31N 170 174 28182419 Expeditious Lead Optimization of Isoxazole-Containing Influenza A Virus M2-S31N Inhibitors Using the Suzuki-Miyaura Cross-Coupling Reaction. With our continuous efforts in developing antivirals to target the predominant drug-resistant AM2-S31N mutant, we aimed to develop an expeditious synthesis strategy in order to speed up the iterative cycles of design, synthesis, and biological characterization. 2017 Journal of medicinal chemistry Conclusion IV S31N 98 102 28418242 Slow but Steady Wins the Race: Dissimilarities among New Dual Inhibitors of the Wild-Type and the V27A Mutant M2 Channels of Influenza A Virus. (3) The weak affinity observed in our compounds for the V27A A/M2 mutant channel, goes in line with the proposed drug resistance mechanism by in silico and structural approaches. 2017 Journal of medicinal chemistry Conclusion IV V27A 56 60 M2 63 65 28418242 Slow but Steady Wins the Race: Dissimilarities among New Dual Inhibitors of the Wild-Type and the V27A Mutant M2 Channels of Influenza A Virus. Its guanidine derivative, 7, behaves in both channels as a fast and weak binder (Figures 2C and 2G), meanwhile the compound 8, its 2-piperidine isomer, shows a very slow but strong binding with the wt M2 channel (Figure 2D) and no remarkable binding at all with the V27A mutant channel (Figure 2H). 2017 Journal of medicinal chemistry Conclusion IV V27A 266 270 M2 201 203 28418242 Slow but Steady Wins the Race: Dissimilarities among New Dual Inhibitors of the Wild-Type and the V27A Mutant M2 Channels of Influenza A Virus. Namely, amine 2 is a strong binder of the wt channel (IC50 = 3.6 muM, Table 1, see also Figure 2B), while its binding being fast and weak in the V27A channel (Figure 2F). 2017 Journal of medicinal chemistry Conclusion IV V27A 145 149 28418242 Slow but Steady Wins the Race: Dissimilarities among New Dual Inhibitors of the Wild-Type and the V27A Mutant M2 Channels of Influenza A Virus. Nevertheless, while all the guanidine derivatives were pointed out to be potent dual inhibitors of the M2 and V27A channels by TEVC assays, their inactivity in the plaque reduction assays proved the TEVC predictions to be completely wrong. 2017 Journal of medicinal chemistry Conclusion IV V27A 110 114 M2 103 105 28418242 Slow but Steady Wins the Race: Dissimilarities among New Dual Inhibitors of the Wild-Type and the V27A Mutant M2 Channels of Influenza A Virus. The novel 4-(1-adamantyl)piperidine 2 and its guanidine derivative 7, were low micromolar blockers of the wt and V27A mutant M2 channels. 2017 Journal of medicinal chemistry Conclusion IV V27A 113 117 M2 125 127 28418242 Slow but Steady Wins the Race: Dissimilarities among New Dual Inhibitors of the Wild-Type and the V27A Mutant M2 Channels of Influenza A Virus. This is the first time the drug resistance mechanism of the V27A A/M2 mutant channel is experimentally evidenced. 2017 Journal of medicinal chemistry Conclusion IV V27A 60 64 M2 67 69 28433777 Design and expeditious synthesis of organosilanes as potent antivirals targeting multidrug-resistant influenza A viruses. In summary, guided by the pharmacophore of AM2-S31N inhibitors, we were able to design organosilanes as potent AM2-S31N channel blockers. 2017 European journal of medicinal chemistry Conclusion IV S31N;S31N 47;115 51;119 28433777 Design and expeditious synthesis of organosilanes as potent antivirals targeting multidrug-resistant influenza A viruses. The major therapeutic importance of AM2-S31N inhibitors such as organosilane 5b is that they are active against both oseltamivir-sensitive and -resistant influenza viruses. 2017 European journal of medicinal chemistry Conclusion IV S31N 40 44 28498306 A Conserved Residue, Tyrosine (Y) 84, in H5N1 Influenza A Virus NS1 Regulates IFN Signaling Responses to Enhance Viral Infection. Specifically, using rIAVs expressing a wildtype NS1 or NS1 encoding a Y84F mutation, we show in vitro and in vivo that targeting the conserved tyrosine residue inhibits virus replication and confers greater sensitivity to the antiviral effects of IFN. 2017 Viruses Conclusion IV Y84F 70 74 NS1;NS1 48;55 51;58 28754164 Data-driven interdisciplinary mathematical modelling quantitatively unveils competition dynamics of co-circulating influenza strains. Our study provides quantitative descriptions about the transmission efficiency of each circulating clade per se and brings to light the transmission dynamics of the A/H1N1 H275Y strains during the 2007-2009 influenza seasons worldwide. 2017 Journal of translational medicine Conclusion IV H275Y 172 177 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. Another new NA H134N AAS was found in three B/Victoria-lineage viruses from Lao DPR that displayed HRI by zanamivir, peramivir and laninamivir. 2017 Antiviral research Conclusion IV H134N 15 20 12 14 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. Consistent with the previous global updates, the frequency of viruses displaying RI or HRI was higher (~1.8%) among A(H1N1)pdm09 viruses, with the majority of such viruses containing NA H275Y AAS. 2017 Antiviral research Conclusion IV H275Y 186 191 183 185 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. Presence of NA H134N AAS was confirmed in the respective clinical specimens, as for NA S247R AAS in A(H1N1)pdm09 viruses, thus ruling out their emergence due to tissue-culture selection. 2017 Antiviral research Conclusion IV H134N;S247R 15;87 20;92 NA;NA 12;84 14;86 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. This finding is in agreement with previous reports on the limited transmission of oseltamivir-resistant viruses containing NA H275Y AAS. 2017 Antiviral research Conclusion IV H275Y 126 131 123 125 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. Three other A(H1N1)pdm09 viruses, collected in widely-dispersed regions of the world, contained a rare NA S247R AAS that conferred RI/HRI against all four NAIs; the AAS was detected in the corresponding clinical specimens. 2017 Antiviral research Conclusion IV S247R 106 111 NA;NAI 103;155 105;159 28951584 Identification of neuraminidase inhibitors against dual H274Y/I222R mutant strains. Furthermore, the identified inhibitors showed inhibition for oseltamivir-resistant NA strains containing with H274Y and I222R mutations. 2017 Scientific reports Conclusion IV H274Y;I222R 110;120 115;125 83 85 29587792 Major contribution of the RNA-binding domain of NS1 in the pathogenicity and replication potential of an avian H7N1 influenza virus in chickens. Our data clearly showed that the double substitution R38A-K41A severely impacted the viral phenotype, much more than the A149V substitution. 2018 Virology journal Conclusion IV K41A;R38A;A149V 58;53;121 62;57;126 29587792 Major contribution of the RNA-binding domain of NS1 in the pathogenicity and replication potential of an avian H7N1 influenza virus in chickens. The severely altered phenotype of the 3841AA-mutant, as compared to the slighter impact of the A149V substitution, emphasized the essential role of the RBD and the relative dispensability of the effector domain, which have been discussed previously and are further supported by the unaltered pathogenicity of a modified bat-influenza virus expressing an RBD-only NS1. 2018 Virology journal Conclusion IV A149V 95 100 NS1 363 366 29593694 Amino Acid Substitutions HA A150V, PA A343T, and PB2 E627K Increase the Virulence of H5N6 Influenza Virus in Mice. This study revealed the significance of HA A150V, PA A343T, and PB2 E627K in the mammalian adaption process of an H5N6 avian influenza virus. 2018 Frontiers in microbiology Conclusion IV A150V;A343T;E627K 43;53;68 48;58;73 HA;PA;PB2 40;50;64 42;52;67 29750015 Symmetric dimeric adamantanes for exploring the structure of two viroporins: influenza virus M2 and hepatitis C virus p7. These findings, although disappointing, are consistent with previously proposed ligand-binding mechanisms: ligand binds to the M2-WT with its positively charged ammonium facing the C-terminal His37, while M2-S31N inhibitors need to have the adamantane-NH2+-CH2-aryl pharmacophore and bind to the M2-S31N channel with their aryl group facing the N-terminal Val27. 2018 Drug design, development and therapy Conclusion IV S31N;S31N 208;299 212;303 M2;M2;M2 127;205;296 129;207;298 29750015 Symmetric dimeric adamantanes for exploring the structure of two viroporins: influenza virus M2 and hepatitis C virus p7. Upon testing on M2 protein, the extra adamantane moiety caused a decrease in potency relative to the reference monomeric compounds amantadine and rimantadine, implying that these dimers could not be accommodated by either M2-WT or M2-S31N proton channels. 2018 Drug design, development and therapy Conclusion IV S31N 234 238 M2;M2;M2 16;222;231 18;224;233 30050898 Structurally Diverse Polyketides From the Mangrove-Derived Fungus Diaporthe sp. SCSIO 41011 With Their Anti-influenza A Virus Activities. Amongst, pestalotiopsone F (14), pestalotiopsone B (15), 3,8-dihydroxy-6-methyl-9-oxo-9H-xanthene-1-carboxylate (26), and 5-chloroisorotiorin displayed pronounced anti-IAV activities against three IAV virus subtypes, including A/Puerto Rico/8/34 H274Y (H1N1), A/FM-1/1/47 (H1N1), and A/Aichi/2/68 (H3N2) with IC50 values in the range of 2.52-39.97 muM. 2018 Frontiers in chemistry Conclusion IV H274Y 246 251 30349332 Antiviral resistance markers in influenza virus sequences in Mexico, 2000-2017. These resistant viruses increased their presence as of 2009; among them, H275Y (or H274Y) has been maintained and disseminated by different influenza virus subtypes around the world. 2018 Infection and drug resistance Conclusion IV H275Y;H274Y 73;83 78;88 30439983 Influenza B viruses circulated during last 5 years in Mongolia. G104R substitution in NA gene of resistant isolate was identified as a novel mutation, responsible for drug resistance. 2018 PloS one Conclusion IV G104R 0 5 22 24 30509291 Conserved methionine 165 of matrix protein contributes to the nuclear import and is essential for influenza A virus replication. Mutation of M165 was lethal and affected transport of M165A and NP proteins to the nuclei of transfected cells. 2018 Virology journal Conclusion IV M165A 54 59 NP 64 66 30509291 Conserved methionine 165 of matrix protein contributes to the nuclear import and is essential for influenza A virus replication. Single R163A, Q164A and V166A substitution resulted in the production of viable viruses. 2018 Virology journal Conclusion IV R163A;Q164A;V166A 7;14;24 12;19;29 30621708 Multiple amino acid substitutions involved in the adaption of three avian-origin H7N9 influenza viruses in mice. Moreover, PB2 E627K and PA T97I may play important roles in H7N9 mammal adaption, but the exact role and other substitutions need further verification. 2019 Virology journal Conclusion IV E627K;T97I 14;27 19;31 PA;PB2 24;10 26;13 31008587 Hydrogen-Deuterium Exchange Supports Independent Membrane-Interfacial Fusion Peptide and Transmembrane Domains in Subunit 2 of Influenza Virus Hemagglutinin Protein, a Structured and Aqueous-Protected Connection between the Fusion Peptide and Soluble Ectodomain, and the Importance of Membrane Apposition by the Trimer-of-Hairpins Structure. G1E has aqueous exposure of these regions intermediate between WT and I173E, as well as increased protection of the fusion peptide. 2019 Biochemistry Conclusion IV I173E 70 75 31008587 Hydrogen-Deuterium Exchange Supports Independent Membrane-Interfacial Fusion Peptide and Transmembrane Domains in Subunit 2 of Influenza Virus Hemagglutinin Protein, a Structured and Aqueous-Protected Connection between the Fusion Peptide and Soluble Ectodomain, and the Importance of Membrane Apposition by the Trimer-of-Hairpins Structure. HDX-MS was also done on the G1E and I173E mutants that result in highly-impaired fusion. 2019 Biochemistry Conclusion IV G1E;I173E 28;36 31;41 31008587 Hydrogen-Deuterium Exchange Supports Independent Membrane-Interfacial Fusion Peptide and Transmembrane Domains in Subunit 2 of Influenza Virus Hemagglutinin Protein, a Structured and Aqueous-Protected Connection between the Fusion Peptide and Soluble Ectodomain, and the Importance of Membrane Apposition by the Trimer-of-Hairpins Structure. I173E shows much greater aqueous exposure vs. 2019 Biochemistry Conclusion IV I173E 0 5 31008587 Hydrogen-Deuterium Exchange Supports Independent Membrane-Interfacial Fusion Peptide and Transmembrane Domains in Subunit 2 of Influenza Virus Hemagglutinin Protein, a Structured and Aqueous-Protected Connection between the Fusion Peptide and Soluble Ectodomain, and the Importance of Membrane Apposition by the Trimer-of-Hairpins Structure. The HDX-MS data support a model in which reduced fusion by the mutants is due to larger distance between the apposed membranes, and for G1E, also loss of fusion peptide contact with the target membrane. 2019 Biochemistry Conclusion IV G1E 136 139 31008587 Hydrogen-Deuterium Exchange Supports Independent Membrane-Interfacial Fusion Peptide and Transmembrane Domains in Subunit 2 of Influenza Virus Hemagglutinin Protein, a Structured and Aqueous-Protected Connection between the Fusion Peptide and Soluble Ectodomain, and the Importance of Membrane Apposition by the Trimer-of-Hairpins Structure. These data are consistent with binding of the G1E fusion peptide to the dissociated C-terminal strands. 2019 Biochemistry Conclusion IV G1E 46 49 31266524 Highly pathogenic avian influenza H7N9 viruses with reduced susceptibility to neuraminidase inhibitors showed comparable replication capacity to their sensitive counterparts. As a result, all 4 amino acid substitutions (R292 K, E119V, A246T or H274Y) in the NA protein reduced the susceptibility of HPAI H7N9 to oseltamivir or zanamivir. 2019 Virology journal Conclusion IV R292K;E119V;A246T;H274Y 45;53;60;69 51;58;65;74 83 85 Influenza A virus H7N9 infection 124 133 31356626 Severe cases of seasonal influenza in Russia in 2017-2018. Of the 87 analyzed viral isolates only one strain of A(H1N1)pdm09 influenza virus was resistant to oseltamivir and had the H275Y amino acid substitution in the NA protein. 2019 PloS one Conclusion IV H275Y 123 128 160 162 31356626 Severe cases of seasonal influenza in Russia in 2017-2018. The next generation sequencing of the original clinical material and isolated influenza strains of A(H1N1)pdm09 viruses revealed major or minor viral variants with HA containing D222G/N mutations, which were previously associated with the increased severity of the disease and mortality, in 32% of the analyzed lethal cases. 2019 PloS one Conclusion IV D222G;D222N 178;178 185;185 HA 164 166 31356626 Severe cases of seasonal influenza in Russia in 2017-2018. This study demonstrated the importance of monitoring D222G/N polymorphism in the HA of A(H1N1)pdm09, including detection of minor virus variants with the mutations for epidemiological surveillance. 2019 PloS one Conclusion IV D222G;D222N 53;53 60;60 HA 81 83 31436527 Human-to-Human Transmission of Influenza A(H3N2) Virus with Reduced Susceptibility to Baloxavir, Japan, February 2019. Almost all mutant viruses isolated from baloxavir-treated patients possessed mixed PA I38T/I, I38M/I, I38R/I, I38T/M/I, I38T/K/I, or I38T/M/R substitutions, indicating these mutant viruses emerged under the selective pressure of baloxavir. 2019 Emerging infectious diseases Conclusion IV I38I;I38I;I38T;I38M;I38I;I38K;I38I;I38M;I38R;I38T;I38M;I38I;I38R;I38T;I38T 86;102;110;110;110;120;120;133;133;86;94;94;102;120;133 92;108;118;118;118;128;128;141;141;92;100;100;108;128;141 PA 83 85 31436527 Human-to-Human Transmission of Influenza A(H3N2) Virus with Reduced Susceptibility to Baloxavir, Japan, February 2019. In contrast, the 4 mutant viruses recovered from children without prior baloxavir treatment, including the virus described in this study, contained the PA I38T substitution and not a mixture including wild-type 3I8. 2019 Emerging infectious diseases Conclusion IV I38T 155 159 PA 152 154 31436527 Human-to-Human Transmission of Influenza A(H3N2) Virus with Reduced Susceptibility to Baloxavir, Japan, February 2019. One mutant virus was detected the day after baloxavir administration in a 2-year-old child from a family cluster, and this virus possessed a mixture of I38T/I substitutions (50% T and 50% I). 2019 Emerging infectious diseases Conclusion IV I38I;I38T 152;152 158;158 31436527 Human-to-Human Transmission of Influenza A(H3N2) Virus with Reduced Susceptibility to Baloxavir, Japan, February 2019. These observations suggest 2 possibilities: the infant was infected by the sibling who was infected by another host harboring the virus with the PA I38T substitution, or both children were infected by another host harboring the virus with the PA I38T substitution. 2019 Emerging infectious diseases Conclusion IV I38T;I38T 148;246 152;250 PA;PA 145;243 147;245 31436527 Human-to-Human Transmission of Influenza A(H3N2) Virus with Reduced Susceptibility to Baloxavir, Japan, February 2019. This child might have been infected with a mixed population containing mutant and wild-type viruses; this incident suggested possible human-to-human transmission of the mutant influenza A(H3N2) virus encoding the PA I38T substitution. 2019 Emerging infectious diseases Conclusion IV I38T 216 220 PA 213 215 31669761 Discovery of M2 channel blockers targeting the drug-resistant double mutants M2-S31N/L26I and M2-S31N/V27A from the influenza A viruses. Although M2-S31N/V27A occurs at a low frequency among H5N1 viruses, its importance should not be ignored. 2020 European journal of pharmaceutical sciences Conclusion IV V27A;S31N 17;12 21;16 M2 9 11 31669761 Discovery of M2 channel blockers targeting the drug-resistant double mutants M2-S31N/L26I and M2-S31N/V27A from the influenza A viruses. and V27A mutation might have a direct impact on drug binding. 2020 European journal of pharmaceutical sciences Conclusion IV V27A 4 8 31669761 Discovery of M2 channel blockers targeting the drug-resistant double mutants M2-S31N/L26I and M2-S31N/V27A from the influenza A viruses. From the WJ332/M2-S31N complex structure. 2020 European journal of pharmaceutical sciences Conclusion IV S31N 18 22 M2 15 17 31669761 Discovery of M2 channel blockers targeting the drug-resistant double mutants M2-S31N/L26I and M2-S31N/V27A from the influenza A viruses. However, the rise of double mutants such as S31N/V27A and S31N/L26I with similar fitness levels as WT may allow for sustained presence in circulating seasonal and pandemic strains. 2020 European journal of pharmaceutical sciences Conclusion IV S31N;V27A;S31N;L26I 44;49;58;63 48;53;62;67 31669761 Discovery of M2 channel blockers targeting the drug-resistant double mutants M2-S31N/L26I and M2-S31N/V27A from the influenza A viruses. In contrast, M2-S31N/V27A double mutant channel appeared to be significant different from the M2-S31N channel, as majority of the M2-S31N inhibitors tested were less active against the M2-S31N/V27A mutant, except three compounds 6, 7 and 15. 2020 European journal of pharmaceutical sciences Conclusion IV S31N;V27A;S31N;S31N;V27A;S31N 16;21;97;133;193;188 20;25;101;137;197;192 M2;M2;M2;M2 13;94;130;185 15;96;132;187 31669761 Discovery of M2 channel blockers targeting the drug-resistant double mutants M2-S31N/L26I and M2-S31N/V27A from the influenza A viruses. In this study, we identified two amantadine-resistant M2 double mutants among avian and human H5N1 viruses: the predominant M2-S31N/L26I mutant and the less frequent M2-S31N/V27A mutant. 2020 European journal of pharmaceutical sciences Conclusion IV L26I;S31N;V27A;S31N 132;127;174;169 136;131;178;173 M2;M2;M2 54;124;166 56;126;168 31669761 Discovery of M2 channel blockers targeting the drug-resistant double mutants M2-S31N/L26I and M2-S31N/V27A from the influenza A viruses. It was found that M2-S31N inhibitors in general also inhibit M2-S31N/L26I channel in both electrophysiological assay and cellular antiviral assay, suggesting an additional L26I did not significantly alter the M2 structure and drug sensitivity. 2020 European journal of pharmaceutical sciences Conclusion IV S31N;L26I;S31N;L26I 21;69;64;172 25;73;68;176 M2;M2;M2 18;61;209 20;63;211 31669761 Discovery of M2 channel blockers targeting the drug-resistant double mutants M2-S31N/L26I and M2-S31N/V27A from the influenza A viruses. M2-S31N remains the dominant amantadine-resistant strain in avian, swine and human influenza viruses, and is believed to have emerged prior to amantadine use in the early 19th century. 2020 European journal of pharmaceutical sciences Conclusion IV S31N 3 7 M2 0 2 31669761 Discovery of M2 channel blockers targeting the drug-resistant double mutants M2-S31N/L26I and M2-S31N/V27A from the influenza A viruses. The three compounds we identified herein 6, 7, and 15 are promising candidates for further optimization into potent channel blockers against not only M2-S31N but also M2-S31N/L26I and M2-S31N/V27A. 2020 European journal of pharmaceutical sciences Conclusion IV S31N;S31N;L26I;S31N;V27A 153;170;175;187;192 157;174;179;191;196 M2;M2;M2 150;167;184 152;169;186 31669761 Discovery of M2 channel blockers targeting the drug-resistant double mutants M2-S31N/L26I and M2-S31N/V27A from the influenza A viruses. Therefore, the focus on targeting the single-mutant S31N should continue. 2020 European journal of pharmaceutical sciences Conclusion IV S31N 52 56 31669761 Discovery of M2 channel blockers targeting the drug-resistant double mutants M2-S31N/L26I and M2-S31N/V27A from the influenza A viruses. This is because the M2-S31N/V27A mutant virus had similar fitness of replication as the WT, but is more virulent. 2020 European journal of pharmaceutical sciences Conclusion IV V27A;S31N 28;23 32;27 M2 20 22 31842256 Antiviral Activity of Benzoic Acid Derivative NC-5 Against Influenza A Virus and Its Neuraminidase Inhibition. This compound can inhibit influenza A viruses A/FM/1/47 (H1N1), A/Beijing/32/92 (H3N2) and oseltamivir-resistant mutant A/FM/1/47-H275Y (H1N1-H275Y) in a dose-dependent manner. 2019 International journal of molecular sciences Conclusion IV H275Y;H275Y 130;142 135;147 31894969 X-ray Crystal Structures of the Influenza M2 Proton Channel Drug-Resistant V27A Mutant Bound to a Spiro-Adamantyl Amine Inhibitor Reveal the Mechanism of Adamantane Resistance. Hydrophobic contacts critical for drug binding are removed when Val27 is mutated to Ala. 2020 Biochemistry Conclusion IV V27A 64 87 31894969 X-ray Crystal Structures of the Influenza M2 Proton Channel Drug-Resistant V27A Mutant Bound to a Spiro-Adamantyl Amine Inhibitor Reveal the Mechanism of Adamantane Resistance. MD simulations in POPC hydrated bilayers accurately predict the X-ray M2 V27A structure (6NV1). 2020 Biochemistry Conclusion IV V27A 73 77 M2 70 72 31894969 X-ray Crystal Structures of the Influenza M2 Proton Channel Drug-Resistant V27A Mutant Bound to a Spiro-Adamantyl Amine Inhibitor Reveal the Mechanism of Adamantane Resistance. These X-ray crystal structures reveal the mechanism of adamantane resistance in the V27A channel. 2020 Biochemistry Conclusion IV V27A 84 88 31894969 X-ray Crystal Structures of the Influenza M2 Proton Channel Drug-Resistant V27A Mutant Bound to a Spiro-Adamantyl Amine Inhibitor Reveal the Mechanism of Adamantane Resistance. We also observe that the spiro-adamantyl amine inhibitor blocks proton conduction in both the WT and V27A mutant M2 channels by shifting its binding site depending on whether Val or Ala are present at position 27, and that a network of either one or two layers of hydrogen-bonded waters is formed. 2020 Biochemistry Conclusion IV V27A 101 105 M2 113 115 32266186 Childhood Nephrotic Syndrome Complicated by Catastrophic Multiple Arterial Thrombosis Requiring Bilateral Above-Knee Amputation. Whole-exome sequencing revealed negativity for factor V Leiden and prothrombin G20210A, which are well-known causes of thrombosis, but showed a missense variant in the PROS1 gene encoding protein S (NM_000313.3: c.1889C>T: Thr630Ile), which is recurrently reported in patients with thrombosis. 2020 Frontiers in pediatrics Conclusion IV G20210A;T630I 79;223 86;232 32326238 Experimental Infection Using Mouse-Adapted Influenza B Virus in a Mouse Model. Apparently, selective accumulation of amino acid substitutions in the mouse-adapted IBV, including changes to HA (T214I) and NA (D432N), may increase pathogenicity following the adaptation and be important for the virions to attach to hosts airways. 2020 Viruses Conclusion IV T214I;D432N 114;129 119;134 HA;NA 110;125 112;127 32631240 Successful treatment with baloxavir marboxil of a patient with peramivir-resistant influenza A/H3N2 with a dual E119D/R292K substitution after allogeneic hematopoietic cell transplantation: a case report. We examined the HD15-influenza-positive sample by polymerase chain reaction and sequence analysis, which detected a dual E119D/R292K mutant influenza A/H3N2. 2020 BMC infectious diseases Conclusion IV E119D;R292K 121;127 126;132 32631440 Characterization of neuraminidase inhibitor-resistant influenza virus isolates from immunocompromised patients in the Republic of Korea. The NA H275Y substitution and some HA or NA substitutions in drug-resistant A(H1N1)pdm09 viruses isolated from immunocompromised patients influence both antigenicity and NAI resistance. 2020 Virology journal Conclusion IV H275Y 7 12 HA;NA;NA;NAI 35;4;41;170 37;6;43;173 33063654 Detection and discrimination of influenza B Victoria lineage deletion variant viruses by real-time RT-PCR. Combining the CDC Vic deletion assay with the CDC Flu rRT-PCR Dx Panel Influenza B Lineage Genotyping Kit will allow for rapid identification of the distinct influenza B viral genetic groups B/YAM, B/VIC V1A, V1A-2DEL and V1A-3DEL. 2020 Euro surveillance Conclusion IV V1A;V1A;V1A 204;209;222 207;212;225 33202790 Identification of Novel Influenza Polymerase PB2 Inhibitors Using a Cascade Docking Virtual Screening Approach. Among these, four compounds, namely, compound 11D4, 12C5, 21A5, and 21B1, could inhibit a broad spectrum of influenza virus strains, including HK/68 (H3N2), A/WSN/33 (H1N1), ZX/1109 (H1N1, natural isolate, oseltamivir-resistant), the PR/8-R292K mutant (H1N1, recombinant oseltamivir-resistant strain), and the influenza B/Lee/40 virus. 2020 Molecules (Basel, Switzerland) Conclusion IV R292K 239 244 33270431 Colorimetric Detection of SARS-CoV-2 and Drug-Resistant pH1N1 Using CRISPR/dCas9. For the use of this method for clinical samples, virus-spiked human nasopharyngeal aspirates and sputum samples were tested, and distinct color changes were observed in the presence of SARS-CoV-2, pH1N1, and pH1N1/H275Y mutant viruses. 2020 ACS sensors Conclusion IV H275Y 214 219 33270431 Colorimetric Detection of SARS-CoV-2 and Drug-Resistant pH1N1 Using CRISPR/dCas9. In addition, viruses including SARS-CoV-2, pH1N1, and oseltamivir-resistant pH1N1/H275Y were successfully detected in dCas9/gRNA-immobilized well microplates. 2020 ACS sensors Conclusion IV H275Y 82 87 33270431 Colorimetric Detection of SARS-CoV-2 and Drug-Resistant pH1N1 Using CRISPR/dCas9. We evaluated the method using RNAs of SARS-CoV-2 N1, N2, and N3, pH1N1 H1, and pH1N1/H275Y N1 genes. 2020 ACS sensors Conclusion IV H275Y 85 90 33673017 Structural and Thermodynamic Analysis of the Resistance Development to Pimodivir (VX-787), the Clinical Inhibitor of Cap Binding to PB2 Subunit of Influenza A Polymerase. Compared to the wild-type, the dissociation constant changed by the factor of 7 for PB2-M431I, 280 for PB2-F404Y, and 130 for PB2-H357N. 2021 Molecules (Basel, Switzerland) Conclusion IV M431I;F404Y;H357N 88;107;130 93;112;135 PB2;PB2;PB2 84;103;126 87;106;129 33673017 Structural and Thermodynamic Analysis of the Resistance Development to Pimodivir (VX-787), the Clinical Inhibitor of Cap Binding to PB2 Subunit of Influenza A Polymerase. From our four high-resolution structures, the atoms of F404Y, M431I, and H357N possess similar positions as in the PB2-WT. 2021 Molecules (Basel, Switzerland) Conclusion IV F404Y;M431I;H357N 55;62;73 60;67;78 PB2 115 118 33673017 Structural and Thermodynamic Analysis of the Resistance Development to Pimodivir (VX-787), the Clinical Inhibitor of Cap Binding to PB2 Subunit of Influenza A Polymerase. Of those, we have selected three major mutations: F404Y, M431I, and H357N that have been described as the most important for the resistance phenotype of the virus. 2021 Molecules (Basel, Switzerland) Conclusion IV F404Y;M431I;H357N 50;57;68 55;62;73 33673017 Structural and Thermodynamic Analysis of the Resistance Development to Pimodivir (VX-787), the Clinical Inhibitor of Cap Binding to PB2 Subunit of Influenza A Polymerase. The F404Y and H357N mutations caused a loss of the stabilization "free" energy for water molecules. 2021 Molecules (Basel, Switzerland) Conclusion IV F404Y;H357N 4;14 9;19 33673017 Structural and Thermodynamic Analysis of the Resistance Development to Pimodivir (VX-787), the Clinical Inhibitor of Cap Binding to PB2 Subunit of Influenza A Polymerase. The M431I mutation had only minor influence on the "free" energy of the water molecules. 2021 Molecules (Basel, Switzerland) Conclusion IV M431I 4 9 33673017 Structural and Thermodynamic Analysis of the Resistance Development to Pimodivir (VX-787), the Clinical Inhibitor of Cap Binding to PB2 Subunit of Influenza A Polymerase. The mutation F404Y is not in a direct contact with these water molecules. 2021 Molecules (Basel, Switzerland) Conclusion IV F404Y 13 18 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. In addition this analysis revealed the presence of the D222G/N mutations at a frequency of 0.2-98% in samples from all studied fatal cases that had sufficient NGS coverage. 2021 PloS one Conclusion IV D222G;D222N 55;55 62;62 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. The application of targeted NGS sequencing enabled us to conduct a thorough evaluation of A(H1N1)pdm09 HA D222G/N mutations, which correlate with high morbidity and mortality. 2021 PloS one Conclusion IV D222G;D222N 106;106 113;113 HA 103 105 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. The ubiquitous presence of the D222G/N mutations revealed in all studied samples (fatal and non-fatal) may indicate that they either come from a limited circulation of the viruses with the mutations in the human population or that they can arise and be further selected for in the host's lower respiratory tract. 2021 PloS one Conclusion IV D222G;D222N 31;31 38;38 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. This may lead to an overall higher probability of the origin of the mutation D222G (GAT-GGT) in contrast to D222N (GAT-AAT). 2021 PloS one Conclusion IV D222G;D222N 77;108 82;113 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. This may occur due to the high mutation rate in the influenza A virus genome and due to the high prevalence of alpha2,3-linked sialic acid receptors, specific for D222G/N-hemagglutinin binding, in the lower respiratory tract. 2021 PloS one Conclusion IV D222G;D222N 163;163 170;170 HA 171 184 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. H274Y mutation significantly enhanced the interaction between residue 274 and the three interface residues in NA, resulting in significantly decreased interaction between OTV and its surrounding loop 150 residues. 2021 PeerJ Conclusion IV H274Y 0 5 110 112 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. In conclusion, using dRIN analysis, we succeeded in understanding the characteristic changes in residue interactions associated with the H274Y mutation, which can elucidate the molecular mechanism of OTV resistance in influenza viruses. 2021 PeerJ Conclusion IV H274Y 137 142 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. In this study, we theoretically investigated the molecular mechanism of drug resistance to OTV in influenza virus with H274Y mutation of N1 NA using MD simulations. 2021 PeerJ Conclusion IV H274Y 119 124 140 142 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. The dRIN graphs quantitatively showed how the His-to-Tyr mutation at residue 274 altered the residue interactions within the OTV binding site of NA and its H274Y mutation site. 2021 PeerJ Conclusion IV H274Y;H274Y 156;46 161;80 145 147 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. The results of dRIN analysis revealed that the OTV binding site of NA and its H274Y mutation site interact via three interface residues connecting the two sites. 2021 PeerJ Conclusion IV H274Y 78 83 67 69 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. When altering the side chain of K235 while preserving its positive charge, we showed that K235R exhibited a much-enhanced NTP incorporation rate for cognate NTP and a higher transcription fidelity by distinguishing cognate NTP against the mismatched NTP and NTP analogs. 2021 Nucleic acids research Conclusion IV K235R 90 95 17055070 H5N1 Oseltamivir-resistance detection by real-time PCR using two high sensitivity labeled TaqMan probes. H274Y 2007 Journal of virological methods Table IV H274Y 0 5 18325270 Mutations in influenza A virus (H5N1) and possible limited spread, Turkey, 2006. D158N 2008 Emerging infectious diseases Table IV D158N 0 5 18325270 Mutations in influenza A virus (H5N1) and possible limited spread, Turkey, 2006. E627K 2008 Emerging infectious diseases Table IV E627K 0 5 18325270 Mutations in influenza A virus (H5N1) and possible limited spread, Turkey, 2006. I28V 2008 Emerging infectious diseases Table IV I28V 0 4 18325270 Mutations in influenza A virus (H5N1) and possible limited spread, Turkey, 2006. I42T 2008 Emerging infectious diseases Table IV I42T 0 4 18325270 Mutations in influenza A virus (H5N1) and possible limited spread, Turkey, 2006. N556K 2008 Emerging infectious diseases Table IV N556K 0 5 18325270 Mutations in influenza A virus (H5N1) and possible limited spread, Turkey, 2006. Q447L 2008 Emerging infectious diseases Table IV Q447L 0 5 18325270 Mutations in influenza A virus (H5N1) and possible limited spread, Turkey, 2006. R46K 2008 Emerging infectious diseases Table IV R46K 0 4 18325270 Mutations in influenza A virus (H5N1) and possible limited spread, Turkey, 2006. S133A 2008 Emerging infectious diseases Table IV S133A 0 5 18325270 Mutations in influenza A virus (H5N1) and possible limited spread, Turkey, 2006. S227N 2008 Emerging infectious diseases Table IV S227N 0 5 18404209 Human-like receptor specificity does not affect the neuraminidase-inhibitor susceptibility of H5N1 influenza viruses. G228S 2008 PLoS pathogens Table IV G228S 0 5 18404209 Human-like receptor specificity does not affect the neuraminidase-inhibitor susceptibility of H5N1 influenza viruses. H183N 2008 PLoS pathogens Table IV H183N 0 5 18404209 Human-like receptor specificity does not affect the neuraminidase-inhibitor susceptibility of H5N1 influenza viruses. K222I 2008 PLoS pathogens Table IV K222I 0 5 18404209 Human-like receptor specificity does not affect the neuraminidase-inhibitor susceptibility of H5N1 influenza viruses. N158S 2008 PLoS pathogens Table IV N158S 0 5 18404209 Human-like receptor specificity does not affect the neuraminidase-inhibitor susceptibility of H5N1 influenza viruses. N248D 2008 PLoS pathogens Table IV N248D 0 5 18404209 Human-like receptor specificity does not affect the neuraminidase-inhibitor susceptibility of H5N1 influenza viruses. Q226L 2008 PLoS pathogens Table IV Q226L 0 5 18404209 Human-like receptor specificity does not affect the neuraminidase-inhibitor susceptibility of H5N1 influenza viruses. R229S 2008 PLoS pathogens Table IV R229S 0 5 18404209 Human-like receptor specificity does not affect the neuraminidase-inhibitor susceptibility of H5N1 influenza viruses. S159N 2008 PLoS pathogens Table IV S159N 0 5 18404209 Human-like receptor specificity does not affect the neuraminidase-inhibitor susceptibility of H5N1 influenza viruses. S227N 2008 PLoS pathogens Table IV S227N 0 5 18404209 Human-like receptor specificity does not affect the neuraminidase-inhibitor susceptibility of H5N1 influenza viruses. T160A 2008 PLoS pathogens Table IV T160A 0 5 18404209 Human-like receptor specificity does not affect the neuraminidase-inhibitor susceptibility of H5N1 influenza viruses. Y161H 2008 PLoS pathogens Table IV Y161H 0 5 18601954 Treatment of influenza A (H1N1) virus infections in mice and ferrets with cyanovirin-N. Asp225Gly 2008 Antiviral research Table IV D225G 0 9 19394063 The origin and global emergence of adamantane resistant A/H3N2 influenza viruses. S31N 2009 Virology Table IV S31N 0 4 19857993 Evaluation of a rapid molecular algorithm for detection of pandemic influenza A (H1N1) 2009 virus and screening for a key oseltamivir resistance (H275Y) substitution in neuraminidase. H274Y 2010 Journal of clinical virology Table IV H274Y 0 5 19893747 Novel pandemic influenza A(H1N1) viruses are potently inhibited by DAS181, a sialidase fusion protein. H274Y 2009 PloS one Table IV H274Y 0 5 19893749 Inhibition of neuraminidase inhibitor-resistant influenza virus by DAS181, a novel sialidase fusion protein. H274Y 2009 PloS one Table IV H274Y 0 5 19905033 Design and pharmacological characterization of inhibitors of amantadine-resistant mutants of the M2 ion channel of influenza A virus. A30T 2009 Biochemistry Table IV A30T 0 4 19905033 Design and pharmacological characterization of inhibitors of amantadine-resistant mutants of the M2 ion channel of influenza A virus. G34E 2009 Biochemistry Table IV G34E 0 4 19905033 Design and pharmacological characterization of inhibitors of amantadine-resistant mutants of the M2 ion channel of influenza A virus. L26F 2009 Biochemistry Table IV L26F 0 4 19905033 Design and pharmacological characterization of inhibitors of amantadine-resistant mutants of the M2 ion channel of influenza A virus. S31N 2009 Biochemistry Table IV S31N 0 4 19905033 Design and pharmacological characterization of inhibitors of amantadine-resistant mutants of the M2 ion channel of influenza A virus. V27A 2009 Biochemistry Table IV V27A 0 4 19905033 Design and pharmacological characterization of inhibitors of amantadine-resistant mutants of the M2 ion channel of influenza A virus. V27G 2009 Biochemistry Table IV V27G 0 4 19958488 Prediction of avian influenza A binding preference to human receptor using conformational analysis of receptor bound to hemagglutinin. A134V 2009 BMC genomics Table IV A134V 0 5 19958488 Prediction of avian influenza A binding preference to human receptor using conformational analysis of receptor bound to hemagglutinin. G224S 2009 BMC genomics Table IV G224S 0 5 19958488 Prediction of avian influenza A binding preference to human receptor using conformational analysis of receptor bound to hemagglutinin. L129V 2009 BMC genomics Table IV L129V 0 5 19958488 Prediction of avian influenza A binding preference to human receptor using conformational analysis of receptor bound to hemagglutinin. Q222L 2009 BMC genomics Table IV Q222L 0 5 19995550 X-ray structures of NS1 effector domain mutants. W187A 2010 Archives of biochemistry and biophysics Table IV W187A 0 5 19995550 X-ray structures of NS1 effector domain mutants. W187Y 2010 Archives of biochemistry and biophysics Table IV W187Y 0 5 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. E119A 2010 PLoS pathogens Table IV E119A 0 5 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. H274Y 2010 PLoS pathogens Table IV H274Y 0 5 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. I117V 2010 PLoS pathogens Table IV I117V 0 5 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. K150N 2010 PLoS pathogens Table IV K150N 0 5 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. N294S 2010 PLoS pathogens Table IV N294S 0 5 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. V116A 2010 PLoS pathogens Table IV V116A 0 5 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. Y252H 2010 PLoS pathogens Table IV Y252H 0 5 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. A203V 2010 PLoS currents Table IV A203V 0 5 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. A302T 2010 PLoS currents Table IV A302T 0 5 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. D114N 2010 PLoS currents Table IV D114N 0 5 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. E189K 2010 PLoS currents Table IV E189K 0 5 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. E391K 2010 PLoS currents Table IV E391K 0 5 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. E516K 2010 PLoS currents Table IV E516K 0 5 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. F347L 2010 PLoS currents Table IV F347L 0 5 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. I123V 2010 PLoS currents Table IV I123V 0 5 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. I22V 2010 PLoS currents Table IV I22V 0 4 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. I392S 2010 PLoS currents Table IV I392S 0 5 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. I78V 2010 PLoS currents Table IV I78V 0 4 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. K340N 2010 PLoS currents Table IV K340N 0 5 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. K460E 2010 PLoS currents Table IV K460E 0 5 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. K60E 2010 PLoS currents Table IV K60E 0 4 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. K716Q 2010 PLoS currents Table IV K716Q 0 5 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. K71N 2010 PLoS currents Table IV K71N 0 4 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. K736G 2010 PLoS currents Table IV K736G 0 5 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. M274I 2010 PLoS currents Table IV M274I 0 5 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. N142D 2010 PLoS currents Table IV N142D 0 5 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. N248D 2010 PLoS currents Table IV N248D 0 5 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. N277D 2010 PLoS currents Table IV N277D 0 5 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. N55D 2010 PLoS currents Table IV N55D 0 4 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. R467K 2010 PLoS currents Table IV R467K 0 5 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. R563K 2010 PLoS currents Table IV R563K 0 5 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. S220T 2010 PLoS currents Table IV S220T 0 5 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. S88P 2010 PLoS currents Table IV S88P 0 4 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. S91R 2010 PLoS currents Table IV S91R 0 4 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. V100I 2010 PLoS currents Table IV V100I 0 5 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. V106I 2010 PLoS currents Table IV V106I 0 5 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. V14I 2010 PLoS currents Table IV V14I 0 4 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. V190I 2010 PLoS currents Table IV V190I 0 5 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. V36I 2010 PLoS currents Table IV V36I 0 4 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. V428I 2010 PLoS currents Table IV V428I 0 5 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. V47A 2010 PLoS currents Table IV V47A 0 4 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. V544I 2010 PLoS currents Table IV V544I 0 5 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. V7I 2010 PLoS currents Table IV V7I 0 3 20661429 Oseltamivir-resistant pandemic A/H1N1 virus is as virulent as its wild-type counterpart in mice and ferrets. H274Y 2010 PLoS pathogens Table IV H274Y 0 5 20689744 The PB2-E627K mutation attenuates viruses containing the 2009 H1N1 influenza pandemic polymerase. D701N 2010 mBio Table IV D701N 0 5 20689744 The PB2-E627K mutation attenuates viruses containing the 2009 H1N1 influenza pandemic polymerase. E627K 2010 mBio Table IV E627K 0 5 20689744 The PB2-E627K mutation attenuates viruses containing the 2009 H1N1 influenza pandemic polymerase. K627E 2010 mBio Table IV K627E 0 5 20738882 Clinical importance and impact on the households of oseltamivir-resistant seasonal A/H1N1 influenza virus in healthy children in Italy. H275Y 2010 Virology journal Table IV H275Y 0 5 20836794 Oseltamivir-resistant influenza A 2009 H1N1 virus in immunocompromised patients. H275Y 2010 Influenza and other respiratory viruses Table IV H275Y 0 5 21116343 Does pandemic A/H1N1 virus have the potential to become more pathogenic? D87N 2010 mBio Table IV D87N 0 4 21116343 Does pandemic A/H1N1 virus have the potential to become more pathogenic? K154Q 2010 mBio Table IV K154Q 0 5 21116343 Does pandemic A/H1N1 virus have the potential to become more pathogenic? L295P 2010 mBio Table IV L295P 0 5 21349290 Development of a real-time RT-PCR assay for detection of resistance to oseltamivir in influenza A pandemic (H1N1) 2009 virus using single nucleotide polymorphism probes. C823T 2011 Journal of virological methods Table IV C823T 0 5 21407805 A single base-pair change in 2009 H1N1 hemagglutinin increases human receptor affinity and leads to efficient airborne viral transmission in ferrets. Ile219->Lys 2011 PloS one Table IV I219K 0 11 21407805 A single base-pair change in 2009 H1N1 hemagglutinin increases human receptor affinity and leads to efficient airborne viral transmission in ferrets. Ile219Lys 2011 PloS one Table IV I219K 0 9 21455300 Assessing the in vitro fitness of an oseltamivir-resistant seasonal A/H1N1 influenza strain using a mathematical model. H275Y 2011 PloS one Table IV H275Y 0 5 21572517 Mutation analysis of 2009 pandemic influenza A(H1N1) viruses collected in Japan during the peak phase of the pandemic. A156T 2011 PloS one Table IV A156T 0 5 21572517 Mutation analysis of 2009 pandemic influenza A(H1N1) viruses collected in Japan during the peak phase of the pandemic. D185N 2011 PloS one Table IV D185N 0 5 21572517 Mutation analysis of 2009 pandemic influenza A(H1N1) viruses collected in Japan during the peak phase of the pandemic. H275Y 2011 PloS one Table IV H275Y 0 5 21572517 Mutation analysis of 2009 pandemic influenza A(H1N1) viruses collected in Japan during the peak phase of the pandemic. N248D 2011 PloS one Table IV N248D 0 5 21572517 Mutation analysis of 2009 pandemic influenza A(H1N1) viruses collected in Japan during the peak phase of the pandemic. N295S 2011 PloS one Table IV N295S 0 5 21572517 Mutation analysis of 2009 pandemic influenza A(H1N1) viruses collected in Japan during the peak phase of the pandemic. S220T 2011 PloS one Table IV S220T 0 5 21572517 Mutation analysis of 2009 pandemic influenza A(H1N1) viruses collected in Japan during the peak phase of the pandemic. V106I 2011 PloS one Table IV V106I 0 5 21586098 Recent avian influenza virus A/H5N1 evolution in vaccinated and unvaccinated poultry from farms in Southern Vietnam, January-March 2010. A184G 2011 Transboundary and emerging diseases Table IV A184G 0 5 21586098 Recent avian influenza virus A/H5N1 evolution in vaccinated and unvaccinated poultry from farms in Southern Vietnam, January-March 2010. A185E 2011 Transboundary and emerging diseases Table IV A185E 0 5 21586098 Recent avian influenza virus A/H5N1 evolution in vaccinated and unvaccinated poultry from farms in Southern Vietnam, January-March 2010. A214S 2011 Transboundary and emerging diseases Table IV A214S 0 5 21586098 Recent avian influenza virus A/H5N1 evolution in vaccinated and unvaccinated poultry from farms in Southern Vietnam, January-March 2010. C42R 2011 Transboundary and emerging diseases Table IV C42R 0 4 21586098 Recent avian influenza virus A/H5N1 evolution in vaccinated and unvaccinated poultry from farms in Southern Vietnam, January-March 2010. C42W 2011 Transboundary and emerging diseases Table IV C42W 0 4 21586098 Recent avian influenza virus A/H5N1 evolution in vaccinated and unvaccinated poultry from farms in Southern Vietnam, January-March 2010. D45G 2011 Transboundary and emerging diseases Table IV D45G 0 4 21586098 Recent avian influenza virus A/H5N1 evolution in vaccinated and unvaccinated poultry from farms in Southern Vietnam, January-March 2010. I514V 2011 Transboundary and emerging diseases Table IV I514V 0 5 21586098 Recent avian influenza virus A/H5N1 evolution in vaccinated and unvaccinated poultry from farms in Southern Vietnam, January-March 2010. I71T 2011 Transboundary and emerging diseases Table IV I71T 0 4 21586098 Recent avian influenza virus A/H5N1 evolution in vaccinated and unvaccinated poultry from farms in Southern Vietnam, January-March 2010. K161R 2011 Transboundary and emerging diseases Table IV K161R 0 5 21586098 Recent avian influenza virus A/H5N1 evolution in vaccinated and unvaccinated poultry from farms in Southern Vietnam, January-March 2010. L41H 2011 Transboundary and emerging diseases Table IV L41H 0 4 21586098 Recent avian influenza virus A/H5N1 evolution in vaccinated and unvaccinated poultry from farms in Southern Vietnam, January-March 2010. N236S 2011 Transboundary and emerging diseases Table IV N236S 0 5 21586098 Recent avian influenza virus A/H5N1 evolution in vaccinated and unvaccinated poultry from farms in Southern Vietnam, January-March 2010. N309T 2011 Transboundary and emerging diseases Table IV N309T 0 5 21586098 Recent avian influenza virus A/H5N1 evolution in vaccinated and unvaccinated poultry from farms in Southern Vietnam, January-March 2010. P136S 2011 Transboundary and emerging diseases Table IV P136S 0 5 21586098 Recent avian influenza virus A/H5N1 evolution in vaccinated and unvaccinated poultry from farms in Southern Vietnam, January-March 2010. R458K 2011 Transboundary and emerging diseases Table IV R458K 0 5 21586098 Recent avian influenza virus A/H5N1 evolution in vaccinated and unvaccinated poultry from farms in Southern Vietnam, January-March 2010. S155G 2011 Transboundary and emerging diseases Table IV S155G 0 5 21586098 Recent avian influenza virus A/H5N1 evolution in vaccinated and unvaccinated poultry from farms in Southern Vietnam, January-March 2010. S155N 2011 Transboundary and emerging diseases Table IV S155N 0 5 21586098 Recent avian influenza virus A/H5N1 evolution in vaccinated and unvaccinated poultry from farms in Southern Vietnam, January-March 2010. T204M 2011 Transboundary and emerging diseases Table IV T204M 0 5 21586098 Recent avian influenza virus A/H5N1 evolution in vaccinated and unvaccinated poultry from farms in Southern Vietnam, January-March 2010. T36A 2011 Transboundary and emerging diseases Table IV T36A 0 4 21586098 Recent avian influenza virus A/H5N1 evolution in vaccinated and unvaccinated poultry from farms in Southern Vietnam, January-March 2010. V200I 2011 Transboundary and emerging diseases Table IV V200I 0 5 21951678 Comparative safety, immunogenicity, and efficacy of several anti-H5N1 influenza experimental vaccines in a mouse and chicken models (Testing of killed and live H5 vaccine). Asp54/Asn 2012 Influenza and other respiratory viruses Table IV D54N 0 9 21951678 Comparative safety, immunogenicity, and efficacy of several anti-H5N1 influenza experimental vaccines in a mouse and chicken models (Testing of killed and live H5 vaccine). Lys131/Thr 2012 Influenza and other respiratory viruses Table IV K131T 0 10 21951678 Comparative safety, immunogenicity, and efficacy of several anti-H5N1 influenza experimental vaccines in a mouse and chicken models (Testing of killed and live H5 vaccine). Lys222/Thr 2012 Influenza and other respiratory viruses Table IV K222T 0 10 21951678 Comparative safety, immunogenicity, and efficacy of several anti-H5N1 influenza experimental vaccines in a mouse and chicken models (Testing of killed and live H5 vaccine). Val48/Ile 2012 Influenza and other respiratory viruses Table IV V48I 0 9 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. D222G 2011 PloS one Table IV D222G 0 5 22022458 Minor changes in the hemagglutinin of influenza A(H1N1)2009 virus alter its antigenic properties. A134T 2011 PloS one Table IV A134T 0 5 22022458 Minor changes in the hemagglutinin of influenza A(H1N1)2009 virus alter its antigenic properties. E374K 2011 PloS one Table IV E374K 0 5 22022458 Minor changes in the hemagglutinin of influenza A(H1N1)2009 virus alter its antigenic properties. I321V 2011 PloS one Table IV I321V 0 5 22022458 Minor changes in the hemagglutinin of influenza A(H1N1)2009 virus alter its antigenic properties. I460T 2011 PloS one Table IV I460T 0 5 22022458 Minor changes in the hemagglutinin of influenza A(H1N1)2009 virus alter its antigenic properties. N125D 2011 PloS one Table IV N125D 0 5 22022458 Minor changes in the hemagglutinin of influenza A(H1N1)2009 virus alter its antigenic properties. N462D 2011 PloS one Table IV N462D 0 5 22022458 Minor changes in the hemagglutinin of influenza A(H1N1)2009 virus alter its antigenic properties. S183P 2011 PloS one Table IV S183P 0 5 22022458 Minor changes in the hemagglutinin of influenza A(H1N1)2009 virus alter its antigenic properties. S185T 2011 PloS one Table IV S185T 0 5 22022458 Minor changes in the hemagglutinin of influenza A(H1N1)2009 virus alter its antigenic properties. S203T 2011 PloS one Table IV S203T 0 5 22022458 Minor changes in the hemagglutinin of influenza A(H1N1)2009 virus alter its antigenic properties. S451N 2011 PloS one Table IV S451N 0 5 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. H275Y 2011 PLoS pathogens Table IV H275Y 0 5 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. M234V 2011 PLoS pathogens Table IV M234V 0 5 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. N344D 2011 PLoS pathogens Table IV N344D 0 5 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. Q222R 2011 PLoS pathogens Table IV Q222R 0 5 22217077 Surveillance in Eastern India (2007-2009) revealed reassortment event involving NS and PB1-F2 gene segments among co-circulating influenza A subtypes. A569C 2012 Virology journal Table IV A569C 0 5 22217077 Surveillance in Eastern India (2007-2009) revealed reassortment event involving NS and PB1-F2 gene segments among co-circulating influenza A subtypes. A594T 2012 Virology journal Table IV A594T 0 5 22217077 Surveillance in Eastern India (2007-2009) revealed reassortment event involving NS and PB1-F2 gene segments among co-circulating influenza A subtypes. C150T 2012 Virology journal Table IV C150T 0 5 22217077 Surveillance in Eastern India (2007-2009) revealed reassortment event involving NS and PB1-F2 gene segments among co-circulating influenza A subtypes. C303A 2012 Virology journal Table IV C303A 0 5 22217077 Surveillance in Eastern India (2007-2009) revealed reassortment event involving NS and PB1-F2 gene segments among co-circulating influenza A subtypes. D101E 2012 Virology journal Table IV D101E 0 5 22217077 Surveillance in Eastern India (2007-2009) revealed reassortment event involving NS and PB1-F2 gene segments among co-circulating influenza A subtypes. G378A 2012 Virology journal Table IV G378A 0 5 22217077 Surveillance in Eastern India (2007-2009) revealed reassortment event involving NS and PB1-F2 gene segments among co-circulating influenza A subtypes. N190T 2012 Virology journal Table IV N190T 0 5 22217077 Surveillance in Eastern India (2007-2009) revealed reassortment event involving NS and PB1-F2 gene segments among co-circulating influenza A subtypes. T273C 2012 Virology journal Table IV T273C 0 5 22230322 Highly pathogenic avian influenza virus H5N1 controls type I IFN induction in chicken macrophage HD-11 cells: a polygenic trait that involves NS1 and the polymerase complex. A144V 2012 Virology journal Table IV A144V 0 5 22238617 Mutational analyses of the influenza A virus polymerase subunit PA reveal distinct functions related and unrelated to RNA polymerase activity. D478A 2012 PloS one Table IV D478A 0 5 22238617 Mutational analyses of the influenza A virus polymerase subunit PA reveal distinct functions related and unrelated to RNA polymerase activity. D514A 2012 PloS one Table IV D514A 0 5 22238617 Mutational analyses of the influenza A virus polymerase subunit PA reveal distinct functions related and unrelated to RNA polymerase activity. D516A 2012 PloS one Table IV D516A 0 5 22238617 Mutational analyses of the influenza A virus polymerase subunit PA reveal distinct functions related and unrelated to RNA polymerase activity. E372A 2012 PloS one Table IV E372A 0 5 22238617 Mutational analyses of the influenza A virus polymerase subunit PA reveal distinct functions related and unrelated to RNA polymerase activity. E656A 2012 PloS one Table IV E656A 0 5 22238617 Mutational analyses of the influenza A virus polymerase subunit PA reveal distinct functions related and unrelated to RNA polymerase activity. F480A 2012 PloS one Table IV F480A 0 5 22238617 Mutational analyses of the influenza A virus polymerase subunit PA reveal distinct functions related and unrelated to RNA polymerase activity. F503A 2012 PloS one Table IV F503A 0 5 22238617 Mutational analyses of the influenza A virus polymerase subunit PA reveal distinct functions related and unrelated to RNA polymerase activity. G502A 2012 PloS one Table IV G502A 0 5 22238617 Mutational analyses of the influenza A virus polymerase subunit PA reveal distinct functions related and unrelated to RNA polymerase activity. G507A 2012 PloS one Table IV G507A 0 5 22238617 Mutational analyses of the influenza A virus polymerase subunit PA reveal distinct functions related and unrelated to RNA polymerase activity. I504A 2012 PloS one Table IV I504A 0 5 22238617 Mutational analyses of the influenza A virus polymerase subunit PA reveal distinct functions related and unrelated to RNA polymerase activity. I505A 2012 PloS one Table IV I505A 0 5 22238617 Mutational analyses of the influenza A virus polymerase subunit PA reveal distinct functions related and unrelated to RNA polymerase activity. K361A 2012 PloS one Table IV K361A 0 5 22238617 Mutational analyses of the influenza A virus polymerase subunit PA reveal distinct functions related and unrelated to RNA polymerase activity. K362A 2012 PloS one Table IV K362A 0 5 22238617 Mutational analyses of the influenza A virus polymerase subunit PA reveal distinct functions related and unrelated to RNA polymerase activity. K367A 2012 PloS one Table IV K367A 0 5 22238617 Mutational analyses of the influenza A virus polymerase subunit PA reveal distinct functions related and unrelated to RNA polymerase activity. K378A 2012 PloS one Table IV K378A 0 5 22238617 Mutational analyses of the influenza A virus polymerase subunit PA reveal distinct functions related and unrelated to RNA polymerase activity. K385A 2012 PloS one Table IV K385A 0 5 22238617 Mutational analyses of the influenza A virus polymerase subunit PA reveal distinct functions related and unrelated to RNA polymerase activity. K497A 2012 PloS one Table IV K497A 0 5 22238617 Mutational analyses of the influenza A virus polymerase subunit PA reveal distinct functions related and unrelated to RNA polymerase activity. K506A 2012 PloS one Table IV K506A 0 5 22238617 Mutational analyses of the influenza A virus polymerase subunit PA reveal distinct functions related and unrelated to RNA polymerase activity. L500A 2012 PloS one Table IV L500A 0 5 22238617 Mutational analyses of the influenza A virus polymerase subunit PA reveal distinct functions related and unrelated to RNA polymerase activity. L511A 2012 PloS one Table IV L511A 0 5 22238617 Mutational analyses of the influenza A virus polymerase subunit PA reveal distinct functions related and unrelated to RNA polymerase activity. N499A 2012 PloS one Table IV N499A 0 5 22238617 Mutational analyses of the influenza A virus polymerase subunit PA reveal distinct functions related and unrelated to RNA polymerase activity. N513A 2012 PloS one Table IV N513A 0 5 22238617 Mutational analyses of the influenza A virus polymerase subunit PA reveal distinct functions related and unrelated to RNA polymerase activity. R508A 2012 PloS one Table IV R508A 0 5 22238617 Mutational analyses of the influenza A virus polymerase subunit PA reveal distinct functions related and unrelated to RNA polymerase activity. R512A 2012 PloS one Table IV R512A 0 5 22238617 Mutational analyses of the influenza A virus polymerase subunit PA reveal distinct functions related and unrelated to RNA polymerase activity. S509A 2012 PloS one Table IV S509A 0 5 22238617 Mutational analyses of the influenza A virus polymerase subunit PA reveal distinct functions related and unrelated to RNA polymerase activity. T498A 2012 PloS one Table IV T498A 0 5 22238617 Mutational analyses of the influenza A virus polymerase subunit PA reveal distinct functions related and unrelated to RNA polymerase activity. T515A 2012 PloS one Table IV T515A 0 5 22238617 Mutational analyses of the influenza A virus polymerase subunit PA reveal distinct functions related and unrelated to RNA polymerase activity. V517A 2012 PloS one Table IV V517A 0 5 22238617 Mutational analyses of the influenza A virus polymerase subunit PA reveal distinct functions related and unrelated to RNA polymerase activity. V518A 2012 PloS one Table IV V518A 0 5 22238617 Mutational analyses of the influenza A virus polymerase subunit PA reveal distinct functions related and unrelated to RNA polymerase activity. Y501A 2012 PloS one Table IV Y501A 0 5 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. R361A 2012 PloS one Table IV R361A 0 5 22363521 Frequency of D222G and Q223R hemagglutinin mutants of pandemic (H1N1) 2009 influenza virus in Japan between 2009 and 2010. D187E 2012 PloS one Table IV D187E 0 5 22363521 Frequency of D222G and Q223R hemagglutinin mutants of pandemic (H1N1) 2009 influenza virus in Japan between 2009 and 2010. D222G 2012 PloS one Table IV D222G 0 5 22363521 Frequency of D222G and Q223R hemagglutinin mutants of pandemic (H1N1) 2009 influenza virus in Japan between 2009 and 2010. K119N 2012 PloS one Table IV K119N 0 5 22363521 Frequency of D222G and Q223R hemagglutinin mutants of pandemic (H1N1) 2009 influenza virus in Japan between 2009 and 2010. N125D 2012 PloS one Table IV N125D 0 5 22363521 Frequency of D222G and Q223R hemagglutinin mutants of pandemic (H1N1) 2009 influenza virus in Japan between 2009 and 2010. Q223R 2012 PloS one Table IV Q223R 0 5 22438920 Mutations in polymerase genes enhanced the virulence of 2009 pandemic H1N1 influenza virus in mice. A36T 2012 PloS one Table IV A36T 0 4 22438920 Mutations in polymerase genes enhanced the virulence of 2009 pandemic H1N1 influenza virus in mice. H357N 2012 PloS one Table IV H357N 0 5 22615752 Functional analysis of conserved motifs in influenza virus PB1 protein. A448V 2012 PloS one Table IV A448V 0 5 22615752 Functional analysis of conserved motifs in influenza virus PB1 protein. D439E 2012 PloS one Table IV D439E 0 5 22615752 Functional analysis of conserved motifs in influenza virus PB1 protein. D445C 2012 PloS one Table IV D445C 0 5 22615752 Functional analysis of conserved motifs in influenza virus PB1 protein. D445E 2012 PloS one Table IV D445E 0 5 22615752 Functional analysis of conserved motifs in influenza virus PB1 protein. D445G 2012 PloS one Table IV D445G 0 5 22615752 Functional analysis of conserved motifs in influenza virus PB1 protein. D445S 2012 PloS one Table IV D445S 0 5 22615752 Functional analysis of conserved motifs in influenza virus PB1 protein. D446N 2012 PloS one Table IV D446N 0 5 22615752 Functional analysis of conserved motifs in influenza virus PB1 protein. D446S 2012 PloS one Table IV D446S 0 5 22615752 Functional analysis of conserved motifs in influenza virus PB1 protein. F447L 2012 PloS one Table IV F447L 0 5 22615752 Functional analysis of conserved motifs in influenza virus PB1 protein. F447V 2012 PloS one Table IV F447V 0 5 22615752 Functional analysis of conserved motifs in influenza virus PB1 protein. I475V 2012 PloS one Table IV I475V 0 5 22615752 Functional analysis of conserved motifs in influenza virus PB1 protein. K480R 2012 PloS one Table IV K480R 0 5 22615752 Functional analysis of conserved motifs in influenza virus PB1 protein. K481E 2012 PloS one Table IV K481E 0 5 22615752 Functional analysis of conserved motifs in influenza virus PB1 protein. K481N 2012 PloS one Table IV K481N 0 5 22615752 Functional analysis of conserved motifs in influenza virus PB1 protein. K481T 2012 PloS one Table IV K481T 0 5 22615752 Functional analysis of conserved motifs in influenza virus PB1 protein. L449I 2012 PloS one Table IV L449I 0 5 22615752 Functional analysis of conserved motifs in influenza virus PB1 protein. M409T 2012 PloS one Table IV M409T 0 5 22615752 Functional analysis of conserved motifs in influenza virus PB1 protein. M477T 2012 PloS one Table IV M477T 0 5 22615752 Functional analysis of conserved motifs in influenza virus PB1 protein. N306T 2012 PloS one Table IV N306T 0 5 22615752 Functional analysis of conserved motifs in influenza virus PB1 protein. N476D 2012 PloS one Table IV N476D 0 5 22615752 Functional analysis of conserved motifs in influenza virus PB1 protein. N476L 2012 PloS one Table IV N476L 0 5 22615752 Functional analysis of conserved motifs in influenza virus PB1 protein. N476T 2012 PloS one Table IV N476T 0 5 22615752 Functional analysis of conserved motifs in influenza virus PB1 protein. N476Y 2012 PloS one Table IV N476Y 0 5 22615752 Functional analysis of conserved motifs in influenza virus PB1 protein. Q442L 2012 PloS one Table IV Q442L 0 5 22615752 Functional analysis of conserved motifs in influenza virus PB1 protein. Q442R 2012 PloS one Table IV Q442R 0 5 22615752 Functional analysis of conserved motifs in influenza virus PB1 protein. S444P 2012 PloS one Table IV S444P 0 5 22615752 Functional analysis of conserved motifs in influenza virus PB1 protein. S478R 2012 PloS one Table IV S478R 0 5 22615752 Functional analysis of conserved motifs in influenza virus PB1 protein. S478T 2012 PloS one Table IV S478T 0 5 22615752 Functional analysis of conserved motifs in influenza virus PB1 protein. T303I 2012 PloS one Table IV T303I 0 5 22615752 Functional analysis of conserved motifs in influenza virus PB1 protein. T303S 2012 PloS one Table IV T303S 0 5 22615752 Functional analysis of conserved motifs in influenza virus PB1 protein. Y483H 2012 PloS one Table IV Y483H 0 5 22621130 The new temperature-sensitive mutation PA-F35S for developing recombinant avian live attenuated H5N1 influenza vaccine. F35S 2012 Virology journal Table IV F35S 0 4 22661221 Intrahost emergent dynamics of oseltamivir-resistant virus of pandemic influenza A (H1N1) 2009 in a fatally immunocompromised patient. H275Y 2012 Journal of infection and chemotherapy Table IV H275Y 0 5 22788742 Comprehensive global amino acid sequence analysis of PB1F2 protein of influenza A H5N1 viruses and the influenza A virus subtypes responsible for the 20th-century pandemics. N66S 2013 Influenza and other respiratory viruses Table IV N66S 0 4 22788742 Comprehensive global amino acid sequence analysis of PB1F2 protein of influenza A H5N1 viruses and the influenza A virus subtypes responsible for the 20th-century pandemics. N84S 2013 Influenza and other respiratory viruses Table IV N84S 0 4 22808250 Mouse-adapted H9N2 influenza A virus PB2 protein M147L and E627K mutations are critical for high virulence. E627K 2012 PloS one Table IV E627K 0 5 22808250 Mouse-adapted H9N2 influenza A virus PB2 protein M147L and E627K mutations are critical for high virulence. M147L 2012 PloS one Table IV M147L 0 5 22808250 Mouse-adapted H9N2 influenza A virus PB2 protein M147L and E627K mutations are critical for high virulence. V250G 2012 PloS one Table IV V250G 0 5 22851656 Emergence of fatal avian influenza in New England harbor seals. C1347T 2012 mBio Table IV C1347T 0 6 22851656 Emergence of fatal avian influenza in New England harbor seals. C1499A 2012 mBio Table IV C1499A 0 6 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. H275Y 2012 PLoS pathogens Table IV H275Y 0 5 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. I223R 2012 PLoS pathogens Table IV I223R 0 5 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. N248D 2012 PLoS pathogens Table IV N248D 0 5 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. V106I 2012 PLoS pathogens Table IV V106I 0 5 23326573 An assay suitable for high throughput screening of anti-influenza drugs. V27 A 2013 PloS one Table IV V27A 0 5 23326573 An assay suitable for high throughput screening of anti-influenza drugs. V27A 2013 PloS one Table IV V27A 0 4 23397331 Influenza virus A(H1N1)pdm09 hemagglutinin polymorphism and associated disease in southern Germany during the 2010/11 influenza season. H275Y 2013 Archives of virology Table IV H275Y 0 5 23437217 Parallel screening of wild-type and drug-resistant targets for anti-resistance neuraminidase inhibitors. H275Y 2013 PloS one Table IV H275Y 0 5 23437217 Parallel screening of wild-type and drug-resistant targets for anti-resistance neuraminidase inhibitors. I223R 2013 PloS one Table IV I223R 0 5 23451169 Simultaneous detection of oseltamivir- and amantadine-resistant influenza by oligonucleotide microarray visualization. V27A 2013 PloS one Table IV V27A 0 4 23555270 Monomeric nucleoprotein of influenza A virus. R416A 2013 PLoS pathogens Table IV R416A 0 5 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. A136S 2013 Influenza and other respiratory viruses Table IV A136S 0 5 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. A138S 2013 Influenza and other respiratory viruses Table IV A138S 0 5 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. D151D/G 2013 Influenza and other respiratory viruses Table IV D151D;D151G 0;0 7;7 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. D151G 2013 Influenza and other respiratory viruses Table IV D151G 0 5 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. D198D/N 2013 Influenza and other respiratory viruses Table IV D198D;D198N 0;0 7;7 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. D198N 2013 Influenza and other respiratory viruses Table IV D198N 0 5 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. D199D/N 2013 Influenza and other respiratory viruses Table IV D199D;D199N 0;0 7;7 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. D199N 2013 Influenza and other respiratory viruses Table IV D199N 0 5 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. F173V 2013 Influenza and other respiratory viruses Table IV F173V 0 5 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. F174V 2013 Influenza and other respiratory viruses Table IV F174V 0 5 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. G140R 2013 Influenza and other respiratory viruses Table IV G140R 0 5 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. G142R 2013 Influenza and other respiratory viruses Table IV G142R 0 5 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. G460S 2013 Influenza and other respiratory viruses Table IV G460S 0 5 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. G461S 2013 Influenza and other respiratory viruses Table IV G461S 0 5 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. H273Y 2013 Influenza and other respiratory viruses Table IV H273Y 0 5 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. H274H/Y 2013 Influenza and other respiratory viruses Table IV H274H;H274Y 0;0 7;7 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. H274Y 2013 Influenza and other respiratory viruses Table IV H274Y 0 5 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. H275H/Y 2013 Influenza and other respiratory viruses Table IV H275H;H275Y 0;0 7;7 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. H275Y 2013 Influenza and other respiratory viruses Table IV H275Y 0 5 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. I120V 2013 Influenza and other respiratory viruses Table IV I120V 0 5 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. M400V 2013 Influenza and other respiratory viruses Table IV M400V 0 5 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. M403V 2013 Influenza and other respiratory viruses Table IV M403V 0 5 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. N144K 2013 Influenza and other respiratory viruses Table IV N144K 0 5 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. N146K 2013 Influenza and other respiratory viruses Table IV N146K 0 5 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. N325K 2013 Influenza and other respiratory viruses Table IV N325K 0 5 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. S244P 2013 Influenza and other respiratory viruses Table IV S244P 0 5 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. S245P 2013 Influenza and other respiratory viruses Table IV S245P 0 5 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. S246N 2013 Influenza and other respiratory viruses Table IV S246N 0 5 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. S247N 2013 Influenza and other respiratory viruses Table IV S247N 0 5 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. T106N 2013 Influenza and other respiratory viruses Table IV T106N 0 5 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. T110N 2013 Influenza and other respiratory viruses Table IV T110N 0 5 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. A643V 2013 PLoS pathogens Table IV A643V 0 5 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. D14E 2013 PLoS pathogens Table IV D14E 0 4 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. D187E 2013 PLoS pathogens Table IV D187E 0 5 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. D187N 2013 PLoS pathogens Table IV D187N 0 5 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. D187V 2013 PLoS pathogens Table IV D187V 0 5 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. D21G 2013 PLoS pathogens Table IV D21G 0 4 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. D60N 2013 PLoS pathogens Table IV D60N 0 4 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. D87N 2013 PLoS pathogens Table IV D87N 0 4 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. G131S 2013 PLoS pathogens Table IV G131S 0 5 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. G155E 2013 PLoS pathogens Table IV G155E 0 5 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. H214Y 2013 PLoS pathogens Table IV H214Y 0 5 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. I28T 2013 PLoS pathogens Table IV I28T 0 4 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. I46F 2013 PLoS pathogens Table IV I46F 0 4 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. K142N 2013 PLoS pathogens Table IV K142N 0 5 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. K153E 2013 PLoS pathogens Table IV K153E 0 5 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. K154E 2013 PLoS pathogens Table IV K154E 0 5 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. K154N 2013 PLoS pathogens Table IV K154N 0 5 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. K156E 2013 PLoS pathogens Table IV K156E 0 5 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. K691N 2013 PLoS pathogens Table IV K691N 0 5 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. L191I 2013 PLoS pathogens Table IV L191I 0 5 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. M15I 2013 PLoS pathogens Table IV M15I 0 4 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. M239V 2013 PLoS pathogens Table IV M239V 0 5 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. M410V 2013 PLoS pathogens Table IV M410V 0 5 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. M66I 2013 PLoS pathogens Table IV M66I 0 4 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. N125D 2013 PLoS pathogens Table IV N125D 0 5 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. N125S 2013 PLoS pathogens Table IV N125S 0 5 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. N156D 2013 PLoS pathogens Table IV N156D 0 5 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. N156E 2013 PLoS pathogens Table IV N156E 0 5 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. N156K 2013 PLoS pathogens Table IV N156K 0 5 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. N156N 2013 PLoS pathogens Table IV N156N 0 5 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. N348S 2013 PLoS pathogens Table IV N348S 0 5 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. N38N 2013 PLoS pathogens Table IV N38N 0 4 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. P69P/A 2013 PLoS pathogens Table IV P69P;P69A 0;0 6;6 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. Q223R 2013 PLoS pathogens Table IV Q223R 0 5 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. R223Q 2013 PLoS pathogens Table IV R223Q 0 5 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. R251K 2013 PLoS pathogens Table IV R251K 0 5 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. R254R/Q 2013 PLoS pathogens Table IV R254R;R254Q 0;0 7;7 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. R293M 2013 PLoS pathogens Table IV R293M 0 5 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. S183P 2013 PLoS pathogens Table IV S183P 0 5 23759670 Virological self-sampling to monitor influenza antiviral susceptibility in a community cohort. H275Y 2013 The Journal of antimicrobial chemotherapy Table IV H275Y 0 5 23860768 Resistance to neuraminidase inhibitors conferred by an R292K mutation in a human influenza virus H7N9 isolate can be masked by a mixed R/K viral population. A122S 2013 mBio Table IV A122S 0 5 23860768 Resistance to neuraminidase inhibitors conferred by an R292K mutation in a human influenza virus H7N9 isolate can be masked by a mixed R/K viral population. A479T 2013 mBio Table IV A479T 0 5 23860768 Resistance to neuraminidase inhibitors conferred by an R292K mutation in a human influenza virus H7N9 isolate can be masked by a mixed R/K viral population. D513N 2013 mBio Table IV D513N 0 5 23860768 Resistance to neuraminidase inhibitors conferred by an R292K mutation in a human influenza virus H7N9 isolate can be masked by a mixed R/K viral population. E121G 2013 mBio Table IV E121G 0 5 23860768 Resistance to neuraminidase inhibitors conferred by an R292K mutation in a human influenza virus H7N9 isolate can be masked by a mixed R/K viral population. G218E 2013 mBio Table IV G218E 0 5 23860768 Resistance to neuraminidase inhibitors conferred by an R292K mutation in a human influenza virus H7N9 isolate can be masked by a mixed R/K viral population. G65E 2013 mBio Table IV G65E 0 4 23860768 Resistance to neuraminidase inhibitors conferred by an R292K mutation in a human influenza virus H7N9 isolate can be masked by a mixed R/K viral population. I118T 2013 mBio Table IV I118T 0 5 23860768 Resistance to neuraminidase inhibitors conferred by an R292K mutation in a human influenza virus H7N9 isolate can be masked by a mixed R/K viral population. T547P 2013 mBio Table IV T547P 0 5 23894575 Analysis of adaptation mutants in the hemagglutinin of the influenza A(H1N1)pdm09 virus. A134T 2013 PloS one Table IV A134T 0 5 23894575 Analysis of adaptation mutants in the hemagglutinin of the influenza A(H1N1)pdm09 virus. D222E 2013 PloS one Table IV D222E 0 5 23894575 Analysis of adaptation mutants in the hemagglutinin of the influenza A(H1N1)pdm09 virus. E374K 2013 PloS one Table IV E374K 0 5 23894575 Analysis of adaptation mutants in the hemagglutinin of the influenza A(H1N1)pdm09 virus. P297S 2013 PloS one Table IV P297S 0 5 23894575 Analysis of adaptation mutants in the hemagglutinin of the influenza A(H1N1)pdm09 virus. S143G 2013 PloS one Table IV S143G 0 5 23894575 Analysis of adaptation mutants in the hemagglutinin of the influenza A(H1N1)pdm09 virus. S185T 2013 PloS one Table IV S185T 0 5 23902660 Frequency of D222G haemagglutinin mutant of pandemic (H1N1) pdm09 influenza virus in Tunisia between 2009 and 2011. D222E 2013 Diagnostic pathology Table IV D222E 0 5 23902660 Frequency of D222G haemagglutinin mutant of pandemic (H1N1) pdm09 influenza virus in Tunisia between 2009 and 2011. D222G 2013 Diagnostic pathology Table IV D222G 0 5 23902660 Frequency of D222G haemagglutinin mutant of pandemic (H1N1) pdm09 influenza virus in Tunisia between 2009 and 2011. K374E 2013 Diagnostic pathology Table IV K374E 0 5 23951116 Resistance mutation R292K is induced in influenza A(H6N2) virus by exposure of infected mallards to low levels of oseltamivir. R292K 2013 PloS one Table IV R292K 0 5 24147093 Emerging antigenic variants at the antigenic site Sb in pandemic A(H1N1)2009 influenza virus in Japan detected by a human monoclonal antibody. A189T 2013 PloS one Table IV A189T 0 5 24147093 Emerging antigenic variants at the antigenic site Sb in pandemic A(H1N1)2009 influenza virus in Japan detected by a human monoclonal antibody. D190E 2013 PloS one Table IV D190E 0 5 24391498 A single amino acid in the stalk region of the H1N1pdm influenza virus HA protein affects viral fusion, stability and infectivity. E47K 2014 PLoS pathogens Table IV E47K 0 4 24391498 A single amino acid in the stalk region of the H1N1pdm influenza virus HA protein affects viral fusion, stability and infectivity. K47E 2014 PLoS pathogens Table IV K47E 0 4 24558492 Study of oseltamivir and zanamivir resistance-related mutations in influenza viruses isolated from wild mallards in Sweden. D151K 2014 PloS one Table IV D151K 0 5 24558492 Study of oseltamivir and zanamivir resistance-related mutations in influenza viruses isolated from wild mallards in Sweden. D151N 2014 PloS one Table IV D151N 0 5 24558492 Study of oseltamivir and zanamivir resistance-related mutations in influenza viruses isolated from wild mallards in Sweden. D198N 2014 PloS one Table IV D198N 0 5 24558492 Study of oseltamivir and zanamivir resistance-related mutations in influenza viruses isolated from wild mallards in Sweden. I222V 2014 PloS one Table IV I222V 0 5 24558492 Study of oseltamivir and zanamivir resistance-related mutations in influenza viruses isolated from wild mallards in Sweden. R118K 2014 PloS one Table IV R118K 0 5 24558492 Study of oseltamivir and zanamivir resistance-related mutations in influenza viruses isolated from wild mallards in Sweden. R152K 2014 PloS one Table IV R152K 0 5 24558492 Study of oseltamivir and zanamivir resistance-related mutations in influenza viruses isolated from wild mallards in Sweden. R156K 2014 PloS one Table IV R156K 0 5 24667168 Low 2012-13 influenza vaccine effectiveness associated with mutation in the egg-adapted H3N2 vaccine strain not antigenic drift in circulating viruses. D53N 2014 PloS one Table IV D53N 0 4 24667168 Low 2012-13 influenza vaccine effectiveness associated with mutation in the egg-adapted H3N2 vaccine strain not antigenic drift in circulating viruses. E280A 2014 PloS one Table IV E280A 0 5 24667168 Low 2012-13 influenza vaccine effectiveness associated with mutation in the egg-adapted H3N2 vaccine strain not antigenic drift in circulating viruses. E62G 2014 PloS one Table IV E62G 0 4 24667168 Low 2012-13 influenza vaccine effectiveness associated with mutation in the egg-adapted H3N2 vaccine strain not antigenic drift in circulating viruses. I140M 2014 PloS one Table IV I140M 0 5 24667168 Low 2012-13 influenza vaccine effectiveness associated with mutation in the egg-adapted H3N2 vaccine strain not antigenic drift in circulating viruses. I192V 2014 PloS one Table IV I192V 0 5 24667168 Low 2012-13 influenza vaccine effectiveness associated with mutation in the egg-adapted H3N2 vaccine strain not antigenic drift in circulating viruses. I230V 2014 PloS one Table IV I230V 0 5 24667168 Low 2012-13 influenza vaccine effectiveness associated with mutation in the egg-adapted H3N2 vaccine strain not antigenic drift in circulating viruses. I48T 2014 PloS one Table IV I48T 0 4 24667168 Low 2012-13 influenza vaccine effectiveness associated with mutation in the egg-adapted H3N2 vaccine strain not antigenic drift in circulating viruses. L157S 2014 PloS one Table IV L157S 0 5 24667168 Low 2012-13 influenza vaccine effectiveness associated with mutation in the egg-adapted H3N2 vaccine strain not antigenic drift in circulating viruses. N145S 2014 PloS one Table IV N145S 0 5 24667168 Low 2012-13 influenza vaccine effectiveness associated with mutation in the egg-adapted H3N2 vaccine strain not antigenic drift in circulating viruses. N278K 2014 PloS one Table IV N278K 0 5 24667168 Low 2012-13 influenza vaccine effectiveness associated with mutation in the egg-adapted H3N2 vaccine strain not antigenic drift in circulating viruses. N45S 2014 PloS one Table IV N45S 0 4 24667168 Low 2012-13 influenza vaccine effectiveness associated with mutation in the egg-adapted H3N2 vaccine strain not antigenic drift in circulating viruses. R142G 2014 PloS one Table IV R142G 0 5 24667168 Low 2012-13 influenza vaccine effectiveness associated with mutation in the egg-adapted H3N2 vaccine strain not antigenic drift in circulating viruses. S198A 2014 PloS one Table IV S198A 0 5 24667168 Low 2012-13 influenza vaccine effectiveness associated with mutation in the egg-adapted H3N2 vaccine strain not antigenic drift in circulating viruses. S198A/T 2014 PloS one Table IV S198A;S198T 0;0 7;7 24667168 Low 2012-13 influenza vaccine effectiveness associated with mutation in the egg-adapted H3N2 vaccine strain not antigenic drift in circulating viruses. S312N 2014 PloS one Table IV S312N 0 5 24667168 Low 2012-13 influenza vaccine effectiveness associated with mutation in the egg-adapted H3N2 vaccine strain not antigenic drift in circulating viruses. S54G 2014 PloS one Table IV S54G 0 4 24667168 Low 2012-13 influenza vaccine effectiveness associated with mutation in the egg-adapted H3N2 vaccine strain not antigenic drift in circulating viruses. T128A 2014 PloS one Table IV T128A 0 5 24667168 Low 2012-13 influenza vaccine effectiveness associated with mutation in the egg-adapted H3N2 vaccine strain not antigenic drift in circulating viruses. T128S 2014 PloS one Table IV T128S 0 5 24667168 Low 2012-13 influenza vaccine effectiveness associated with mutation in the egg-adapted H3N2 vaccine strain not antigenic drift in circulating viruses. V88I 2014 PloS one Table IV V88I 0 4 24667168 Low 2012-13 influenza vaccine effectiveness associated with mutation in the egg-adapted H3N2 vaccine strain not antigenic drift in circulating viruses. Y94H/Q 2014 PloS one Table IV Y94H;Y94Q 0;0 6;6 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. H275Y 2014 PLoS pathogens Table IV H275Y 0 5 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. I241V 2014 PLoS pathogens Table IV I241V 0 5 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. K369N 2014 PLoS pathogens Table IV K369N 0 5 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. N369K 2014 PLoS pathogens Table IV N369K 0 5 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. V241I 2014 PLoS pathogens Table IV V241I 0 5 24941437 Easily accessible polycyclic amines that inhibit the wild-type and amantadine-resistant mutants of the M2 channel of influenza A virus. L26F 2014 Journal of medicinal chemistry Table IV L26F 0 4 24941437 Easily accessible polycyclic amines that inhibit the wild-type and amantadine-resistant mutants of the M2 channel of influenza A virus. S31N 2014 Journal of medicinal chemistry Table IV S31N 0 4 24941437 Easily accessible polycyclic amines that inhibit the wild-type and amantadine-resistant mutants of the M2 channel of influenza A virus. V27A 2014 Journal of medicinal chemistry Table IV V27A 0 4 25078692 A single amino acid substitution in the novel H7N9 influenza A virus NS1 protein increases CPSF30 binding and virulence. I106M 2014 Journal of virology Table IV I106M 0 5 25713566 PB2 segment promotes high-pathogenicity of H5N1 avian influenza viruses in mice. Ala143Thr 2015 Frontiers in microbiology Table IV A143T 0 9 25713566 PB2 segment promotes high-pathogenicity of H5N1 avian influenza viruses in mice. Ala684Thr 2015 Frontiers in microbiology Table IV A684T 0 9 25713566 PB2 segment promotes high-pathogenicity of H5N1 avian influenza viruses in mice. Arg340Lys 2015 Frontiers in microbiology Table IV R340K 0 9 25713566 PB2 segment promotes high-pathogenicity of H5N1 avian influenza viruses in mice. Arg353Lys 2015 Frontiers in microbiology Table IV R353K 0 9 25713566 PB2 segment promotes high-pathogenicity of H5N1 avian influenza viruses in mice. Asn201Ser 2015 Frontiers in microbiology Table IV N201S 0 9 25713566 PB2 segment promotes high-pathogenicity of H5N1 avian influenza viruses in mice. Asn289Ser 2015 Frontiers in microbiology Table IV N289S 0 9 25713566 PB2 segment promotes high-pathogenicity of H5N1 avian influenza viruses in mice. Asn296Ser 2015 Frontiers in microbiology Table IV N296S 0 9 25713566 PB2 segment promotes high-pathogenicity of H5N1 avian influenza viruses in mice. Asn648Ser 2015 Frontiers in microbiology Table IV N648S 0 9 25713566 PB2 segment promotes high-pathogenicity of H5N1 avian influenza viruses in mice. Asn715Ser 2015 Frontiers in microbiology Table IV N715S 0 9 25713566 PB2 segment promotes high-pathogenicity of H5N1 avian influenza viruses in mice. Asn82Ser 2015 Frontiers in microbiology Table IV N82S 0 8 25713566 PB2 segment promotes high-pathogenicity of H5N1 avian influenza viruses in mice. Asp166Gly 2015 Frontiers in microbiology Table IV D166G 0 9 25713566 PB2 segment promotes high-pathogenicity of H5N1 avian influenza viruses in mice. Gln39Lys 2015 Frontiers in microbiology Table IV Q39K 0 8 25713566 PB2 segment promotes high-pathogenicity of H5N1 avian influenza viruses in mice. Glu327Gly 2015 Frontiers in microbiology Table IV E327G 0 9 25713566 PB2 segment promotes high-pathogenicity of H5N1 avian influenza viruses in mice. Glu66Ala 2015 Frontiers in microbiology Table IV E66A 0 8 25713566 PB2 segment promotes high-pathogenicity of H5N1 avian influenza viruses in mice. Gly368Arg 2015 Frontiers in microbiology Table IV G368R 0 9 25713566 PB2 segment promotes high-pathogenicity of H5N1 avian influenza viruses in mice. Ile649Val 2015 Frontiers in microbiology Table IV I649V 0 9 25713566 PB2 segment promotes high-pathogenicity of H5N1 avian influenza viruses in mice. Ile83Val 2015 Frontiers in microbiology Table IV I83V 0 8 25713566 PB2 segment promotes high-pathogenicity of H5N1 avian influenza viruses in mice. Leu154Gln 2015 Frontiers in microbiology Table IV L154Q 0 9 25713566 PB2 segment promotes high-pathogenicity of H5N1 avian influenza viruses in mice. Leu261Phe 2015 Frontiers in microbiology Table IV L261F 0 9 25713566 PB2 segment promotes high-pathogenicity of H5N1 avian influenza viruses in mice. Lys205Arg 2015 Frontiers in microbiology Table IV K205R 0 9 25713566 PB2 segment promotes high-pathogenicity of H5N1 avian influenza viruses in mice. Lys39Gln 2015 Frontiers in microbiology Table IV K39Q 0 8 25713566 PB2 segment promotes high-pathogenicity of H5N1 avian influenza viruses in mice. Lys544Glu 2015 Frontiers in microbiology Table IV K544E 0 9 25713566 PB2 segment promotes high-pathogenicity of H5N1 avian influenza viruses in mice. Met14Val 2015 Frontiers in microbiology Table IV M14V 0 8 25713566 PB2 segment promotes high-pathogenicity of H5N1 avian influenza viruses in mice. Met49Val 2015 Frontiers in microbiology Table IV M49V 0 8 25713566 PB2 segment promotes high-pathogenicity of H5N1 avian influenza viruses in mice. Met59Ile 2015 Frontiers in microbiology Table IV M59I 0 8 25713566 PB2 segment promotes high-pathogenicity of H5N1 avian influenza viruses in mice. Pro157Ser 2015 Frontiers in microbiology Table IV P157S 0 9 25713566 PB2 segment promotes high-pathogenicity of H5N1 avian influenza viruses in mice. Pro25Leu 2015 Frontiers in microbiology Table IV P25L 0 8 25713566 PB2 segment promotes high-pathogenicity of H5N1 avian influenza viruses in mice. Ser100Asn 2015 Frontiers in microbiology Table IV S100N 0 9 25713566 PB2 segment promotes high-pathogenicity of H5N1 avian influenza viruses in mice. Ser31Asn 2015 Frontiers in microbiology Table IV S31N 0 8 25713566 PB2 segment promotes high-pathogenicity of H5N1 avian influenza viruses in mice. Ser653Pro 2015 Frontiers in microbiology Table IV S653P 0 9 25713566 PB2 segment promotes high-pathogenicity of H5N1 avian influenza viruses in mice. Ser715Asn 2015 Frontiers in microbiology Table IV S715N 0 9 25713566 PB2 segment promotes high-pathogenicity of H5N1 avian influenza viruses in mice. Thr115Ala 2015 Frontiers in microbiology Table IV T115A 0 9 25713566 PB2 segment promotes high-pathogenicity of H5N1 avian influenza viruses in mice. Thr172Ala 2015 Frontiers in microbiology Table IV T172A 0 9 25713566 PB2 segment promotes high-pathogenicity of H5N1 avian influenza viruses in mice. Thr337Ala 2015 Frontiers in microbiology Table IV T337A 0 9 25713566 PB2 segment promotes high-pathogenicity of H5N1 avian influenza viruses in mice. Thr339Lys 2015 Frontiers in microbiology Table IV T339K 0 9 25713566 PB2 segment promotes high-pathogenicity of H5N1 avian influenza viruses in mice. Thr684Ala 2015 Frontiers in microbiology Table IV T684A 0 9 25713566 PB2 segment promotes high-pathogenicity of H5N1 avian influenza viruses in mice. Tyr133Phe 2015 Frontiers in microbiology Table IV Y133F 0 9 25713566 PB2 segment promotes high-pathogenicity of H5N1 avian influenza viruses in mice. Val129Phe 2015 Frontiers in microbiology Table IV V129F 0 9 25713566 PB2 segment promotes high-pathogenicity of H5N1 avian influenza viruses in mice. Val354Ile 2015 Frontiers in microbiology Table IV V354I 0 9 25713566 PB2 segment promotes high-pathogenicity of H5N1 avian influenza viruses in mice. Val649Ile 2015 Frontiers in microbiology Table IV V649I 0 9 25742269 Oseltamivir-resistant influenza A(H1N1)pdm2009 strains found in Brazil are endowed with permissive mutations, which compensate the loss of fitness imposed by antiviral resistance. H275Y 2015 Memorias do Instituto Oswaldo Cruz Table IV H275Y 0 5 25768797 Adamantane-resistant influenza a viruses in the world (1902-2013): frequency and distribution of M2 gene mutations. A30T 2015 PloS one Table IV A30T 0 4 25768797 Adamantane-resistant influenza a viruses in the world (1902-2013): frequency and distribution of M2 gene mutations. A30V 2015 PloS one Table IV A30V 0 4 25768797 Adamantane-resistant influenza a viruses in the world (1902-2013): frequency and distribution of M2 gene mutations. G34E 2015 PloS one Table IV G34E 0 4 25768797 Adamantane-resistant influenza a viruses in the world (1902-2013): frequency and distribution of M2 gene mutations. L26F 2015 PloS one Table IV L26F 0 4 25768797 Adamantane-resistant influenza a viruses in the world (1902-2013): frequency and distribution of M2 gene mutations. L38F 2015 PloS one Table IV L38F 0 4 25768797 Adamantane-resistant influenza a viruses in the world (1902-2013): frequency and distribution of M2 gene mutations. S31N 2015 PloS one Table IV S31N 0 4 25768797 Adamantane-resistant influenza a viruses in the world (1902-2013): frequency and distribution of M2 gene mutations. V27A 2015 PloS one Table IV V27A 0 4 25876137 SNPer: an R library for quantitative variant analysis on single nucleotide polymorphisms among influenza virus populations. A1195C 2015 PloS one Table IV A1195C 0 6 25876137 SNPer: an R library for quantitative variant analysis on single nucleotide polymorphisms among influenza virus populations. A1323G 2015 PloS one Table IV A1323G 0 6 25876137 SNPer: an R library for quantitative variant analysis on single nucleotide polymorphisms among influenza virus populations. A1671G 2015 PloS one Table IV A1671G 0 6 25876137 SNPer: an R library for quantitative variant analysis on single nucleotide polymorphisms among influenza virus populations. A405G 2015 PloS one Table IV A405G 0 5 25876137 SNPer: an R library for quantitative variant analysis on single nucleotide polymorphisms among influenza virus populations. A482G 2015 PloS one Table IV A482G 0 5 25876137 SNPer: an R library for quantitative variant analysis on single nucleotide polymorphisms among influenza virus populations. A973G 2015 PloS one Table IV A973G 0 5 25876137 SNPer: an R library for quantitative variant analysis on single nucleotide polymorphisms among influenza virus populations. C1606T 2015 PloS one Table IV C1606T 0 6 25876137 SNPer: an R library for quantitative variant analysis on single nucleotide polymorphisms among influenza virus populations. C629T 2015 PloS one Table IV C629T 0 5 25876137 SNPer: an R library for quantitative variant analysis on single nucleotide polymorphisms among influenza virus populations. G413A 2015 PloS one Table IV G413A 0 5 25876137 SNPer: an R library for quantitative variant analysis on single nucleotide polymorphisms among influenza virus populations. G640T 2015 PloS one Table IV G640T 0 5 25876137 SNPer: an R library for quantitative variant analysis on single nucleotide polymorphisms among influenza virus populations. G715A 2015 PloS one Table IV G715A 0 5 25928577 Amino acid substitutions in the neuraminidase protein of an H9N2 avian influenza virus affect its airborne transmission in chickens. D368E 2015 Veterinary research Table IV D368E 0 5 25928577 Amino acid substitutions in the neuraminidase protein of an H9N2 avian influenza virus affect its airborne transmission in chickens. E313K 2015 Veterinary research Table IV E313K 0 5 25928577 Amino acid substitutions in the neuraminidase protein of an H9N2 avian influenza virus affect its airborne transmission in chickens. G381D 2015 Veterinary research Table IV G381D 0 5 25928577 Amino acid substitutions in the neuraminidase protein of an H9N2 avian influenza virus affect its airborne transmission in chickens. S370L 2015 Veterinary research Table IV S370L 0 5 25966032 Virological characterization of influenza H1N1pdm09 in Vietnam, 2010-2013. A197T 2015 Influenza and other respiratory viruses Table IV A197T 0 5 25966032 Virological characterization of influenza H1N1pdm09 in Vietnam, 2010-2013. D222N 2015 Influenza and other respiratory viruses Table IV D222N 0 5 25966032 Virological characterization of influenza H1N1pdm09 in Vietnam, 2010-2013. D416N 2015 Influenza and other respiratory viruses Table IV D416N 0 5 25966032 Virological characterization of influenza H1N1pdm09 in Vietnam, 2010-2013. D97N 2015 Influenza and other respiratory viruses Table IV D97N 0 4 25966032 Virological characterization of influenza H1N1pdm09 in Vietnam, 2010-2013. E374K 2015 Influenza and other respiratory viruses Table IV E374K 0 5 25966032 Virological characterization of influenza H1N1pdm09 in Vietnam, 2010-2013. E499K 2015 Influenza and other respiratory viruses Table IV E499K 0 5 25966032 Virological characterization of influenza H1N1pdm09 in Vietnam, 2010-2013. G155E 2015 Influenza and other respiratory viruses Table IV G155E 0 5 25966032 Virological characterization of influenza H1N1pdm09 in Vietnam, 2010-2013. G41R 2015 Influenza and other respiratory viruses Table IV G41R 0 4 25966032 Virological characterization of influenza H1N1pdm09 in Vietnam, 2010-2013. H138R 2015 Influenza and other respiratory viruses Table IV H138R 0 5 25966032 Virological characterization of influenza H1N1pdm09 in Vietnam, 2010-2013. I122V 2015 Influenza and other respiratory viruses Table IV I122V 0 5 25966032 Virological characterization of influenza H1N1pdm09 in Vietnam, 2010-2013. I216M 2015 Influenza and other respiratory viruses Table IV I216M 0 5 25966032 Virological characterization of influenza H1N1pdm09 in Vietnam, 2010-2013. I321V 2015 Influenza and other respiratory viruses Table IV I321V 0 5 25966032 Virological characterization of influenza H1N1pdm09 in Vietnam, 2010-2013. K283E 2015 Influenza and other respiratory viruses Table IV K283E 0 5 25966032 Virological characterization of influenza H1N1pdm09 in Vietnam, 2010-2013. K84R 2015 Influenza and other respiratory viruses Table IV K84R 0 4 25966032 Virological characterization of influenza H1N1pdm09 in Vietnam, 2010-2013. N156K 2015 Influenza and other respiratory viruses Table IV N156K 0 5 25966032 Virological characterization of influenza H1N1pdm09 in Vietnam, 2010-2013. N200S 2015 Influenza and other respiratory viruses Table IV N200S 0 5 25966032 Virological characterization of influenza H1N1pdm09 in Vietnam, 2010-2013. N248D 2015 Influenza and other respiratory viruses Table IV N248D 0 5 25966032 Virological characterization of influenza H1N1pdm09 in Vietnam, 2010-2013. N260D 2015 Influenza and other respiratory viruses Table IV N260D 0 5 25966032 Virological characterization of influenza H1N1pdm09 in Vietnam, 2010-2013. N369K 2015 Influenza and other respiratory viruses Table IV N369K 0 5 25966032 Virological characterization of influenza H1N1pdm09 in Vietnam, 2010-2013. N386S 2015 Influenza and other respiratory viruses Table IV N386S 0 5 25966032 Virological characterization of influenza H1N1pdm09 in Vietnam, 2010-2013. N38D 2015 Influenza and other respiratory viruses Table IV N38D 0 4 25966032 Virological characterization of influenza H1N1pdm09 in Vietnam, 2010-2013. N44S 2015 Influenza and other respiratory viruses Table IV N44S 0 4 25966032 Virological characterization of influenza H1N1pdm09 in Vietnam, 2010-2013. P83S 2015 Influenza and other respiratory viruses Table IV P83S 0 4 25966032 Virological characterization of influenza H1N1pdm09 in Vietnam, 2010-2013. Q313R 2015 Influenza and other respiratory viruses Table IV Q313R 0 5 25966032 Virological characterization of influenza H1N1pdm09 in Vietnam, 2010-2013. R223Q 2015 Influenza and other respiratory viruses Table IV R223Q 0 5 25966032 Virological characterization of influenza H1N1pdm09 in Vietnam, 2010-2013. S143G 2015 Influenza and other respiratory viruses Table IV S143G 0 5 25966032 Virological characterization of influenza H1N1pdm09 in Vietnam, 2010-2013. S185T 2015 Influenza and other respiratory viruses Table IV S185T 0 5 25966032 Virological characterization of influenza H1N1pdm09 in Vietnam, 2010-2013. S203T 2015 Influenza and other respiratory viruses Table IV S203T 0 5 25966032 Virological characterization of influenza H1N1pdm09 in Vietnam, 2010-2013. S451N 2015 Influenza and other respiratory viruses Table IV S451N 0 5 25966032 Virological characterization of influenza H1N1pdm09 in Vietnam, 2010-2013. T241I 2015 Influenza and other respiratory viruses Table IV T241I 0 5 25966032 Virological characterization of influenza H1N1pdm09 in Vietnam, 2010-2013. V106I 2015 Influenza and other respiratory viruses Table IV V106I 0 5 25966032 Virological characterization of influenza H1N1pdm09 in Vietnam, 2010-2013. V234I 2015 Influenza and other respiratory viruses Table IV V234I 0 5 25966032 Virological characterization of influenza H1N1pdm09 in Vietnam, 2010-2013. V241I 2015 Influenza and other respiratory viruses Table IV V241I 0 5 25966032 Virological characterization of influenza H1N1pdm09 in Vietnam, 2010-2013. V249L 2015 Influenza and other respiratory viruses Table IV V249L 0 5 25966032 Virological characterization of influenza H1N1pdm09 in Vietnam, 2010-2013. V83L 2015 Influenza and other respiratory viruses Table IV V83L 0 4 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. H275Y 2015 PloS one Table IV H275Y 0 5 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. I223V 2015 PloS one Table IV I223V 0 5 26056814 Molecular Characterisation of the Haemagglutinin Glycan-Binding Specificity of Egg-Adapted Vaccine Strains of the Pandemic 2009 H1N1 Swine Influenza A Virus. Asp225Gly 2015 Molecules (Basel, Switzerland) Table IV D225G 0 9 26056814 Molecular Characterisation of the Haemagglutinin Glycan-Binding Specificity of Egg-Adapted Vaccine Strains of the Pandemic 2009 H1N1 Swine Influenza A Virus. D225G 2015 Molecules (Basel, Switzerland) Table IV D225G 0 5 26056814 Molecular Characterisation of the Haemagglutinin Glycan-Binding Specificity of Egg-Adapted Vaccine Strains of the Pandemic 2009 H1N1 Swine Influenza A Virus. Gln226Arg 2015 Molecules (Basel, Switzerland) Table IV Q226R 0 9 26056814 Molecular Characterisation of the Haemagglutinin Glycan-Binding Specificity of Egg-Adapted Vaccine Strains of the Pandemic 2009 H1N1 Swine Influenza A Virus. K123N 2015 Molecules (Basel, Switzerland) Table IV K123N 0 5 26056814 Molecular Characterisation of the Haemagglutinin Glycan-Binding Specificity of Egg-Adapted Vaccine Strains of the Pandemic 2009 H1N1 Swine Influenza A Virus. Q226R 2015 Molecules (Basel, Switzerland) Table IV Q226R 0 5 26077257 Influenza A(H7N9) virus acquires resistance-related neuraminidase I222T substitution when infected mallards are exposed to low levels of oseltamivir in water. I222T 2015 Antimicrobial agents and chemotherapy Table IV I222T 0 5 26422258 Oseltamivir Resistance in Influenza A(H6N2) Caused by an R292K Substitution in Neuraminidase Is Not Maintained in Mallards without Drug Pressure. D113N 2015 PloS one Table IV D113N 0 5 26422258 Oseltamivir Resistance in Influenza A(H6N2) Caused by an R292K Substitution in Neuraminidase Is Not Maintained in Mallards without Drug Pressure. D141N 2015 PloS one Table IV D141N 0 5 26422258 Oseltamivir Resistance in Influenza A(H6N2) Caused by an R292K Substitution in Neuraminidase Is Not Maintained in Mallards without Drug Pressure. R292K 2015 PloS one Table IV R292K 0 5 26583707 Influenza A(H6N1) Virus in Dogs, Taiwan. D701Q 2015 Emerging infectious diseases Table IV D701Q 0 5 26583707 Influenza A(H6N1) Virus in Dogs, Taiwan. D92E 2015 Emerging infectious diseases Table IV D92E 0 4 26583707 Influenza A(H6N1) Virus in Dogs, Taiwan. E627K 2015 Emerging infectious diseases Table IV E627K 0 5 26583707 Influenza A(H6N1) Virus in Dogs, Taiwan. G228S 2015 Emerging infectious diseases Table IV G228S 0 5 26583707 Influenza A(H6N1) Virus in Dogs, Taiwan. H275Y 2015 Emerging infectious diseases Table IV H275Y 0 5 26583707 Influenza A(H6N1) Virus in Dogs, Taiwan. N66S 2015 Emerging infectious diseases Table IV N66S 0 4 26583707 Influenza A(H6N1) Virus in Dogs, Taiwan. Q226L 2015 Emerging infectious diseases Table IV Q226L 0 5 26583707 Influenza A(H6N1) Virus in Dogs, Taiwan. S31N 2015 Emerging infectious diseases Table IV S31N 0 4 26845764 Genomic Signatures for Avian H7N9 Viruses Adapting to Humans. D701N 2016 PloS one Table IV D701N 0 5 26845764 Genomic Signatures for Avian H7N9 Viruses Adapting to Humans. E627K 2016 PloS one Table IV E627K 0 5 26845764 Genomic Signatures for Avian H7N9 Viruses Adapting to Humans. K627E 2016 PloS one Table IV K627E 0 5 26845764 Genomic Signatures for Avian H7N9 Viruses Adapting to Humans. Q226L 2016 PloS one Table IV Q226L 0 5 26845764 Genomic Signatures for Avian H7N9 Viruses Adapting to Humans. Q235L 2016 PloS one Table IV Q235L 0 5 26974849 Effects of egg-adaptation on receptor-binding and antigenic properties of recent influenza A (H3N2) vaccine viruses. D190E 2016 The Journal of general virology Table IV D190E 0 5 26974849 Effects of egg-adaptation on receptor-binding and antigenic properties of recent influenza A (H3N2) vaccine viruses. G186V 2016 The Journal of general virology Table IV G186V 0 5 26974849 Effects of egg-adaptation on receptor-binding and antigenic properties of recent influenza A (H3N2) vaccine viruses. H156Q 2016 The Journal of general virology Table IV H156Q 0 5 26974849 Effects of egg-adaptation on receptor-binding and antigenic properties of recent influenza A (H3N2) vaccine viruses. H156R 2016 The Journal of general virology Table IV H156R 0 5 26974849 Effects of egg-adaptation on receptor-binding and antigenic properties of recent influenza A (H3N2) vaccine viruses. I226N 2016 The Journal of general virology Table IV I226N 0 5 26974849 Effects of egg-adaptation on receptor-binding and antigenic properties of recent influenza A (H3N2) vaccine viruses. R156H 2016 The Journal of general virology Table IV R156H 0 5 26974849 Effects of egg-adaptation on receptor-binding and antigenic properties of recent influenza A (H3N2) vaccine viruses. R156Q 2016 The Journal of general virology Table IV R156Q 0 5 26974849 Effects of egg-adaptation on receptor-binding and antigenic properties of recent influenza A (H3N2) vaccine viruses. S219F 2016 The Journal of general virology Table IV S219F 0 5 26974849 Effects of egg-adaptation on receptor-binding and antigenic properties of recent influenza A (H3N2) vaccine viruses. S219Y 2016 The Journal of general virology Table IV S219Y 0 5 26974849 Effects of egg-adaptation on receptor-binding and antigenic properties of recent influenza A (H3N2) vaccine viruses. V186G 2016 The Journal of general virology Table IV V186G 0 5 27097026 Novel Polymerase Gene Mutations for Human Adaptation in Clinical Isolates of Avian H5N1 Influenza Viruses. K198R 2016 PLoS pathogens Table IV K198R 0 5 27097026 Novel Polymerase Gene Mutations for Human Adaptation in Clinical Isolates of Avian H5N1 Influenza Viruses. K214R 2016 PLoS pathogens Table IV K214R 0 5 27097026 Novel Polymerase Gene Mutations for Human Adaptation in Clinical Isolates of Avian H5N1 Influenza Viruses. L384S 2016 PLoS pathogens Table IV L384S 0 5 27097026 Novel Polymerase Gene Mutations for Human Adaptation in Clinical Isolates of Avian H5N1 Influenza Viruses. P627L 2016 PLoS pathogens Table IV P627L 0 5 27097026 Novel Polymerase Gene Mutations for Human Adaptation in Clinical Isolates of Avian H5N1 Influenza Viruses. T182I 2016 PLoS pathogens Table IV T182I 0 5 27268229 Detection of reassortant avian influenza A (H11N9) virus in environmental samples from live poultry markets in China. D701N 2016 Infectious diseases of poverty Table IV D701N 0 5 27268229 Detection of reassortant avian influenza A (H11N9) virus in environmental samples from live poultry markets in China. E119V 2016 Infectious diseases of poverty Table IV E119V 0 5 27268229 Detection of reassortant avian influenza A (H11N9) virus in environmental samples from live poultry markets in China. E627K 2016 Infectious diseases of poverty Table IV E627K 0 5 27268229 Detection of reassortant avian influenza A (H11N9) virus in environmental samples from live poultry markets in China. H274Y 2016 Infectious diseases of poverty Table IV H274Y 0 5 27268229 Detection of reassortant avian influenza A (H11N9) virus in environmental samples from live poultry markets in China. N30D 2016 Infectious diseases of poverty Table IV N30D 0 4 27268229 Detection of reassortant avian influenza A (H11N9) virus in environmental samples from live poultry markets in China. Q226L 2016 Infectious diseases of poverty Table IV Q226L 0 5 27268229 Detection of reassortant avian influenza A (H11N9) virus in environmental samples from live poultry markets in China. R152K 2016 Infectious diseases of poverty Table IV R152K 0 5 27268229 Detection of reassortant avian influenza A (H11N9) virus in environmental samples from live poultry markets in China. S31N 2016 Infectious diseases of poverty Table IV S31N 0 4 27268229 Detection of reassortant avian influenza A (H11N9) virus in environmental samples from live poultry markets in China. T215A 2016 Infectious diseases of poverty Table IV T215A 0 5 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. D391G 2016 PLoS pathogens Table IV D391G 0 5 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. D391Y 2016 PLoS pathogens Table IV D391Y 0 5 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. F175Y 2016 PLoS pathogens Table IV F175Y 0 5 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. Q387K 2016 PLoS pathogens Table IV Q387K 0 5 27535054 NS1 Protein Mutation I64T Affects Interferon Responses and Virulence of Circulating H3N2 Human Influenza A Viruses. E26K 2016 Journal of virology Table IV E26K 0 4 27535054 NS1 Protein Mutation I64T Affects Interferon Responses and Virulence of Circulating H3N2 Human Influenza A Viruses. I64T 2016 Journal of virology Table IV I64T 0 4 27535054 NS1 Protein Mutation I64T Affects Interferon Responses and Virulence of Circulating H3N2 Human Influenza A Viruses. R224G 2016 Journal of virology Table IV R224G 0 5 27630240 Human Monoclonal Antibody 81.39a Effectively Neutralizes Emerging Influenza A Viruses of Group 1 and 2 Hemagglutinins. D19A 2016 Journal of virology Table IV D19A 0 4 27630240 Human Monoclonal Antibody 81.39a Effectively Neutralizes Emerging Influenza A Viruses of Group 1 and 2 Hemagglutinins. E119V 2016 Journal of virology Table IV E119V 0 5 27630240 Human Monoclonal Antibody 81.39a Effectively Neutralizes Emerging Influenza A Viruses of Group 1 and 2 Hemagglutinins. H274Y 2016 Journal of virology Table IV H274Y 0 5 27630240 Human Monoclonal Antibody 81.39a Effectively Neutralizes Emerging Influenza A Viruses of Group 1 and 2 Hemagglutinins. L26I 2016 Journal of virology Table IV L26I 0 4 27630240 Human Monoclonal Antibody 81.39a Effectively Neutralizes Emerging Influenza A Viruses of Group 1 and 2 Hemagglutinins. R292K 2016 Journal of virology Table IV R292K 0 5 27630240 Human Monoclonal Antibody 81.39a Effectively Neutralizes Emerging Influenza A Viruses of Group 1 and 2 Hemagglutinins. S247P 2016 Journal of virology Table IV S247P 0 5 27630240 Human Monoclonal Antibody 81.39a Effectively Neutralizes Emerging Influenza A Viruses of Group 1 and 2 Hemagglutinins. S31N 2016 Journal of virology Table IV S31N 0 4 27714496 Community- and hospital-acquired infections with oseltamivir- and peramivir-resistant influenza A(H1N1)pdm09 viruses during the 2015-2016 season in Japan. H275Y 2017 Virus genes Table IV H275Y 0 5 27741319 Cross-Neutralising Nanobodies Bind to a Conserved Pocket in the Hemagglutinin Stem Region Identified Using Yeast Display and Deep Mutational Scanning. asparagine (N) at residue 46 2016 PloS one Table IV N46N 0 28 27741319 Cross-Neutralising Nanobodies Bind to a Conserved Pocket in the Hemagglutinin Stem Region Identified Using Yeast Display and Deep Mutational Scanning. D46N 2016 PloS one Table IV D46N 0 4 28100622 Glycosylation of the Hemagglutinin Protein of H5N1 Influenza Virus Increases Its Virulence in Mice by Exacerbating the Host Immune Response. N158G 2017 Journal of virology Table IV N158G 0 5 28128091 Development of oseltamivir and zanamivir resistance in influenza A(H1N1)pdm09 virus, Denmark, 2014. H275Y 2017 Euro surveillance Table IV H275Y 0 5 28282440 H1N1 influenza viruses varying widely in hemagglutinin stability transmit efficiently from swine to swine and to ferrets. R106K 2017 PLoS pathogens Table IV R106K 0 5 28282440 H1N1 influenza viruses varying widely in hemagglutinin stability transmit efficiently from swine to swine and to ferrets. Y17H 2017 PLoS pathogens Table IV Y17H 0 4 28410396 Evolution of the neuraminidase gene of seasonal influenza A and B viruses in Thailand between 2010 and 2015. A395E 2017 PloS one Table IV A395E 0 5 28410396 Evolution of the neuraminidase gene of seasonal influenza A and B viruses in Thailand between 2010 and 2015. D197N 2017 PloS one Table IV D197N 0 5 28410396 Evolution of the neuraminidase gene of seasonal influenza A and B viruses in Thailand between 2010 and 2015. H275Y 2017 PloS one Table IV H275Y 0 5 28410396 Evolution of the neuraminidase gene of seasonal influenza A and B viruses in Thailand between 2010 and 2015. S247N 2017 PloS one Table IV S247N 0 5 28465552 A reassortant H9N2 influenza virus containing 2009 pandemic H1N1 internal-protein genes acquired enhanced pig-to-pig transmission after serial passages in swine. Ala115Val 2017 Scientific reports Table IV A115V 0 9 28465552 A reassortant H9N2 influenza virus containing 2009 pandemic H1N1 internal-protein genes acquired enhanced pig-to-pig transmission after serial passages in swine. Asp225Gly 2017 Scientific reports Table IV D225G 0 9 28465552 A reassortant H9N2 influenza virus containing 2009 pandemic H1N1 internal-protein genes acquired enhanced pig-to-pig transmission after serial passages in swine. Gly179Gln 2017 Scientific reports Table IV G179Q 0 9 28465552 A reassortant H9N2 influenza virus containing 2009 pandemic H1N1 internal-protein genes acquired enhanced pig-to-pig transmission after serial passages in swine. Gly22Arg 2017 Scientific reports Table IV G22R 0 8 28465552 A reassortant H9N2 influenza virus containing 2009 pandemic H1N1 internal-protein genes acquired enhanced pig-to-pig transmission after serial passages in swine. Ile615Thr 2017 Scientific reports Table IV I615T 0 9 28465552 A reassortant H9N2 influenza virus containing 2009 pandemic H1N1 internal-protein genes acquired enhanced pig-to-pig transmission after serial passages in swine. Leu119Phe 2017 Scientific reports Table IV L119F 0 9 28465552 A reassortant H9N2 influenza virus containing 2009 pandemic H1N1 internal-protein genes acquired enhanced pig-to-pig transmission after serial passages in swine. Thr535Met 2017 Scientific reports Table IV T535M 0 9 28465552 A reassortant H9N2 influenza virus containing 2009 pandemic H1N1 internal-protein genes acquired enhanced pig-to-pig transmission after serial passages in swine. Thr58Ala 2017 Scientific reports Table IV T58A 0 8 28465552 A reassortant H9N2 influenza virus containing 2009 pandemic H1N1 internal-protein genes acquired enhanced pig-to-pig transmission after serial passages in swine. Trp406Arg 2017 Scientific reports Table IV W406R 0 9 28588133 Novel Nonreplicating Vaccinia Virus Vector Enhances Expression of Heterologous Genes and Suppresses Synthesis of Endogenous Viral Proteins. A23R 2017 mBio Table IV A23R 0 4 28744280 Amino Acid Substitution K470R in the Nucleoprotein Increases the Virulence of H5N1 Influenza A Virus in Mammals. K198R 2017 Frontiers in microbiology Table IV K198R 0 5 28744280 Amino Acid Substitution K470R in the Nucleoprotein Increases the Virulence of H5N1 Influenza A Virus in Mammals. K227R 2017 Frontiers in microbiology Table IV K227R 0 5 28744280 Amino Acid Substitution K470R in the Nucleoprotein Increases the Virulence of H5N1 Influenza A Virus in Mammals. K229R 2017 Frontiers in microbiology Table IV K229R 0 5 28744280 Amino Acid Substitution K470R in the Nucleoprotein Increases the Virulence of H5N1 Influenza A Virus in Mammals. K470R 2017 Frontiers in microbiology Table IV K470R 0 5 28744280 Amino Acid Substitution K470R in the Nucleoprotein Increases the Virulence of H5N1 Influenza A Virus in Mammals. K91R 2017 Frontiers in microbiology Table IV K91R 0 4 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. D151N/D 2017 Antiviral research Table IV D151N;D151D 0;0 7;7 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. D197N 2017 Antiviral research Table IV D197N 0 5 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. D432G 2017 Antiviral research Table IV D432G 0 5 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. E105K/E 2017 Antiviral research Table IV E105K;E105E 0;0 7;7 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. G104E 2017 Antiviral research Table IV G104E 0 5 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. G147R 2017 Antiviral research Table IV G147R 0 5 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. G243S/G 2017 Antiviral research Table IV G243S;G243G 0;0 7;7 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. H134N 2017 Antiviral research Table IV H134N 0 5 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. H134Y 2017 Antiviral research Table IV H134Y 0 5 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. H273Y 2017 Antiviral research Table IV H273Y 0 5 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. H275Y 2017 Antiviral research Table IV H275Y 0 5 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. H275Y/H 2017 Antiviral research Table IV H275Y;H275H 0;0 7;7 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. I117R 2017 Antiviral research Table IV I117R 0 5 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. I221T 2017 Antiviral research Table IV I221T 0 5 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. I221V 2017 Antiviral research Table IV I221V 0 5 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. I223K 2017 Antiviral research Table IV I223K 0 5 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. I262T 2017 Antiviral research Table IV I262T 0 5 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. K152N 2017 Antiviral research Table IV K152N 0 5 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. K186R 2017 Antiviral research Table IV K186R 0 5 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. P165L 2017 Antiviral research Table IV P165L 0 5 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. Q136R/Q 2017 Antiviral research Table IV Q136R;Q136Q 0;0 7;7 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. Q391K 2017 Antiviral research Table IV Q391K 0 5 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. S247R 2017 Antiviral research Table IV S247R 0 5 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. T106I 2017 Antiviral research Table IV T106I 0 5 28802866 Global update on the susceptibility of human influenza viruses to neuraminidase inhibitors, 2015-2016. T106P 2017 Antiviral research Table IV T106P 0 5 28814518 A Single-Amino-Acid Substitution at Position 225 in Hemagglutinin Alters the Transmissibility of Eurasian Avian-Like H1N1 Swine Influenza Virus in Guinea Pigs. A103T 2017 Journal of virology Table IV A103T 0 5 28814518 A Single-Amino-Acid Substitution at Position 225 in Hemagglutinin Alters the Transmissibility of Eurasian Avian-Like H1N1 Swine Influenza Virus in Guinea Pigs. E225G 2017 Journal of virology Table IV E225G 0 5 28814518 A Single-Amino-Acid Substitution at Position 225 in Hemagglutinin Alters the Transmissibility of Eurasian Avian-Like H1N1 Swine Influenza Virus in Guinea Pigs. G225E 2017 Journal of virology Table IV G225E 0 5 28814518 A Single-Amino-Acid Substitution at Position 225 in Hemagglutinin Alters the Transmissibility of Eurasian Avian-Like H1N1 Swine Influenza Virus in Guinea Pigs. H256Y 2017 Journal of virology Table IV H256Y 0 5 28814518 A Single-Amino-Acid Substitution at Position 225 in Hemagglutinin Alters the Transmissibility of Eurasian Avian-Like H1N1 Swine Influenza Virus in Guinea Pigs. I183V 2017 Journal of virology Table IV I183V 0 5 28814518 A Single-Amino-Acid Substitution at Position 225 in Hemagglutinin Alters the Transmissibility of Eurasian Avian-Like H1N1 Swine Influenza Virus in Guinea Pigs. L160P 2017 Journal of virology Table IV L160P 0 5 28814518 A Single-Amino-Acid Substitution at Position 225 in Hemagglutinin Alters the Transmissibility of Eurasian Avian-Like H1N1 Swine Influenza Virus in Guinea Pigs. R27Q 2017 Journal of virology Table IV R27Q 0 4 28814518 A Single-Amino-Acid Substitution at Position 225 in Hemagglutinin Alters the Transmissibility of Eurasian Avian-Like H1N1 Swine Influenza Virus in Guinea Pigs. S138A 2017 Journal of virology Table IV S138A 0 5 28814518 A Single-Amino-Acid Substitution at Position 225 in Hemagglutinin Alters the Transmissibility of Eurasian Avian-Like H1N1 Swine Influenza Virus in Guinea Pigs. T235I 2017 Journal of virology Table IV T235I 0 5 28814518 A Single-Amino-Acid Substitution at Position 225 in Hemagglutinin Alters the Transmissibility of Eurasian Avian-Like H1N1 Swine Influenza Virus in Guinea Pigs. V15I 2017 Journal of virology Table IV V15I 0 4 28814737 Susceptibility of influenza A(H1N1)/pdm2009, seasonal A(H3N2) and B viruses to Oseltamivir in Guangdong, China between 2009 and 2014. H275Y 2017 Scientific reports Table IV H275Y 0 5 28860593 Prerequisites for the acquisition of mammalian pathogenicity by influenza A virus with a prototypic avian PB2 gene. A674T 2017 Scientific reports Table IV A674T 0 5 28860593 Prerequisites for the acquisition of mammalian pathogenicity by influenza A virus with a prototypic avian PB2 gene. E627K 2017 Scientific reports Table IV E627K 0 5 28860593 Prerequisites for the acquisition of mammalian pathogenicity by influenza A virus with a prototypic avian PB2 gene. I109V 2017 Scientific reports Table IV I109V 0 5 28860593 Prerequisites for the acquisition of mammalian pathogenicity by influenza A virus with a prototypic avian PB2 gene. I133V 2017 Scientific reports Table IV I133V 0 5 28860593 Prerequisites for the acquisition of mammalian pathogenicity by influenza A virus with a prototypic avian PB2 gene. I66M 2017 Scientific reports Table IV I66M 0 4 28860593 Prerequisites for the acquisition of mammalian pathogenicity by influenza A virus with a prototypic avian PB2 gene. K340R 2017 Scientific reports Table IV K340R 0 5 28860593 Prerequisites for the acquisition of mammalian pathogenicity by influenza A virus with a prototypic avian PB2 gene. K627E 2017 Scientific reports Table IV K627E 0 5 28860593 Prerequisites for the acquisition of mammalian pathogenicity by influenza A virus with a prototypic avian PB2 gene. K88R 2017 Scientific reports Table IV K88R 0 4 28860593 Prerequisites for the acquisition of mammalian pathogenicity by influenza A virus with a prototypic avian PB2 gene. L373I 2017 Scientific reports Table IV L373I 0 5 28860593 Prerequisites for the acquisition of mammalian pathogenicity by influenza A virus with a prototypic avian PB2 gene. R157K 2017 Scientific reports Table IV R157K 0 5 28860593 Prerequisites for the acquisition of mammalian pathogenicity by influenza A virus with a prototypic avian PB2 gene. V575M 2017 Scientific reports Table IV V575M 0 5 29299533 Cooperating H3N2 Influenza Virus Variants Are Not Detectable in Primary Clinical Samples. A425A 2018 mSphere Table IV A425A 0 5 29299533 Cooperating H3N2 Influenza Virus Variants Are Not Detectable in Primary Clinical Samples. D513Y 2018 mSphere Table IV D513Y 0 5 29299533 Cooperating H3N2 Influenza Virus Variants Are Not Detectable in Primary Clinical Samples. E325K 2018 mSphere Table IV E325K 0 5 29299533 Cooperating H3N2 Influenza Virus Variants Are Not Detectable in Primary Clinical Samples. E40G 2018 mSphere Table IV E40G 0 4 29299533 Cooperating H3N2 Influenza Virus Variants Are Not Detectable in Primary Clinical Samples. E731E 2018 mSphere Table IV E731E 0 5 29299533 Cooperating H3N2 Influenza Virus Variants Are Not Detectable in Primary Clinical Samples. E83K 2018 mSphere Table IV E83K 0 4 29299533 Cooperating H3N2 Influenza Virus Variants Are Not Detectable in Primary Clinical Samples. F254F 2018 mSphere Table IV F254F 0 5 29299533 Cooperating H3N2 Influenza Virus Variants Are Not Detectable in Primary Clinical Samples. F42F 2018 mSphere Table IV F42F 0 4 29299533 Cooperating H3N2 Influenza Virus Variants Are Not Detectable in Primary Clinical Samples. G47S 2018 mSphere Table IV G47S 0 4 29299533 Cooperating H3N2 Influenza Virus Variants Are Not Detectable in Primary Clinical Samples. H562Y 2018 mSphere Table IV H562Y 0 5 29299533 Cooperating H3N2 Influenza Virus Variants Are Not Detectable in Primary Clinical Samples. I202V 2018 mSphere Table IV I202V 0 5 29299533 Cooperating H3N2 Influenza Virus Variants Are Not Detectable in Primary Clinical Samples. I392M 2018 mSphere Table IV I392M 0 5 29299533 Cooperating H3N2 Influenza Virus Variants Are Not Detectable in Primary Clinical Samples. M372I 2018 mSphere Table IV M372I 0 5 29299533 Cooperating H3N2 Influenza Virus Variants Are Not Detectable in Primary Clinical Samples. M631V 2018 mSphere Table IV M631V 0 5 29299533 Cooperating H3N2 Influenza Virus Variants Are Not Detectable in Primary Clinical Samples. N518N 2018 mSphere Table IV N518N 0 5 29299533 Cooperating H3N2 Influenza Virus Variants Are Not Detectable in Primary Clinical Samples. N86T 2018 mSphere Table IV N86T 0 4 29299533 Cooperating H3N2 Influenza Virus Variants Are Not Detectable in Primary Clinical Samples. P238P 2018 mSphere Table IV P238P 0 5 29299533 Cooperating H3N2 Influenza Virus Variants Are Not Detectable in Primary Clinical Samples. P419P 2018 mSphere Table IV P419P 0 5 29299533 Cooperating H3N2 Influenza Virus Variants Are Not Detectable in Primary Clinical Samples. R175K 2018 mSphere Table IV R175K 0 5 29299533 Cooperating H3N2 Influenza Virus Variants Are Not Detectable in Primary Clinical Samples. R208S 2018 mSphere Table IV R208S 0 5 29308074 Neuraminidase Gene Variations in Influenza A(H1N1)pdm09 Virus among Patients Admitted to Refferal Pulmonary Hospital, Tehran, Iran in 2009-2013. H275Y 2017 Tanaffos Table IV H275Y 0 5 29324781 Neuraminidase inhibitor susceptibility and neuraminidase enzyme kinetics of human influenza A and B viruses circulating in Thailand in 2010-2015. A395D 2018 PloS one Table IV A395D 0 5 29324781 Neuraminidase inhibitor susceptibility and neuraminidase enzyme kinetics of human influenza A and B viruses circulating in Thailand in 2010-2015. A395T 2018 PloS one Table IV A395T 0 5 29324781 Neuraminidase inhibitor susceptibility and neuraminidase enzyme kinetics of human influenza A and B viruses circulating in Thailand in 2010-2015. A395V 2018 PloS one Table IV A395V 0 5 29324781 Neuraminidase inhibitor susceptibility and neuraminidase enzyme kinetics of human influenza A and B viruses circulating in Thailand in 2010-2015. D342S 2018 PloS one Table IV D342S 0 5 29324781 Neuraminidase inhibitor susceptibility and neuraminidase enzyme kinetics of human influenza A and B viruses circulating in Thailand in 2010-2015. I222V 2018 PloS one Table IV I222V 0 5 29324781 Neuraminidase inhibitor susceptibility and neuraminidase enzyme kinetics of human influenza A and B viruses circulating in Thailand in 2010-2015. S331G 2018 PloS one Table IV S331G 0 5 29324781 Neuraminidase inhibitor susceptibility and neuraminidase enzyme kinetics of human influenza A and B viruses circulating in Thailand in 2010-2015. S331R 2018 PloS one Table IV S331R 0 5 29409570 Early season co-circulation of influenza A(H3N2) and B(Yamagata): interim estimates of 2017/18 vaccine effectiveness, Canada, January 2018. A212T 2018 Euro surveillance Table IV A212T 0 5 29409570 Early season co-circulation of influenza A(H3N2) and B(Yamagata): interim estimates of 2017/18 vaccine effectiveness, Canada, January 2018. D53N 2018 Euro surveillance Table IV D53N 0 4 29409570 Early season co-circulation of influenza A(H3N2) and B(Yamagata): interim estimates of 2017/18 vaccine effectiveness, Canada, January 2018. E62G 2018 Euro surveillance Table IV E62G 0 4 29409570 Early season co-circulation of influenza A(H3N2) and B(Yamagata): interim estimates of 2017/18 vaccine effectiveness, Canada, January 2018. G78D 2018 Euro surveillance Table IV G78D 0 4 29409570 Early season co-circulation of influenza A(H3N2) and B(Yamagata): interim estimates of 2017/18 vaccine effectiveness, Canada, January 2018. H311Q 2018 Euro surveillance Table IV H311Q 0 5 29409570 Early season co-circulation of influenza A(H3N2) and B(Yamagata): interim estimates of 2017/18 vaccine effectiveness, Canada, January 2018. I192T 2018 Euro surveillance Table IV I192T 0 5 29409570 Early season co-circulation of influenza A(H3N2) and B(Yamagata): interim estimates of 2017/18 vaccine effectiveness, Canada, January 2018. K92R 2018 Euro surveillance Table IV K92R 0 4 29409570 Early season co-circulation of influenza A(H3N2) and B(Yamagata): interim estimates of 2017/18 vaccine effectiveness, Canada, January 2018. L172Q 2018 Euro surveillance Table IV L172Q 0 5 29409570 Early season co-circulation of influenza A(H3N2) and B(Yamagata): interim estimates of 2017/18 vaccine effectiveness, Canada, January 2018. M251V 2018 Euro surveillance Table IV M251V 0 5 29409570 Early season co-circulation of influenza A(H3N2) and B(Yamagata): interim estimates of 2017/18 vaccine effectiveness, Canada, January 2018. N121K 2018 Euro surveillance Table IV N121K 0 5 29409570 Early season co-circulation of influenza A(H3N2) and B(Yamagata): interim estimates of 2017/18 vaccine effectiveness, Canada, January 2018. N122D 2018 Euro surveillance Table IV N122D 0 5 29409570 Early season co-circulation of influenza A(H3N2) and B(Yamagata): interim estimates of 2017/18 vaccine effectiveness, Canada, January 2018. N171D 2018 Euro surveillance Table IV N171D 0 5 29409570 Early season co-circulation of influenza A(H3N2) and B(Yamagata): interim estimates of 2017/18 vaccine effectiveness, Canada, January 2018. N171K 2018 Euro surveillance Table IV N171K 0 5 29409570 Early season co-circulation of influenza A(H3N2) and B(Yamagata): interim estimates of 2017/18 vaccine effectiveness, Canada, January 2018. N31S 2018 Euro surveillance Table IV N31S 0 4 29409570 Early season co-circulation of influenza A(H3N2) and B(Yamagata): interim estimates of 2017/18 vaccine effectiveness, Canada, January 2018. Q197H 2018 Euro surveillance Table IV Q197H 0 5 29409570 Early season co-circulation of influenza A(H3N2) and B(Yamagata): interim estimates of 2017/18 vaccine effectiveness, Canada, January 2018. R142G 2018 Euro surveillance Table IV R142G 0 5 29409570 Early season co-circulation of influenza A(H3N2) and B(Yamagata): interim estimates of 2017/18 vaccine effectiveness, Canada, January 2018. R142K 2018 Euro surveillance Table IV R142K 0 5 29409570 Early season co-circulation of influenza A(H3N2) and B(Yamagata): interim estimates of 2017/18 vaccine effectiveness, Canada, January 2018. R150K 2018 Euro surveillance Table IV R150K 0 5 29409570 Early season co-circulation of influenza A(H3N2) and B(Yamagata): interim estimates of 2017/18 vaccine effectiveness, Canada, January 2018. R261Q 2018 Euro surveillance Table IV R261Q 0 5 29409570 Early season co-circulation of influenza A(H3N2) and B(Yamagata): interim estimates of 2017/18 vaccine effectiveness, Canada, January 2018. S144K 2018 Euro surveillance Table IV S144K 0 5 29409570 Early season co-circulation of influenza A(H3N2) and B(Yamagata): interim estimates of 2017/18 vaccine effectiveness, Canada, January 2018. S144R 2018 Euro surveillance Table IV S144R 0 5 29409570 Early season co-circulation of influenza A(H3N2) and B(Yamagata): interim estimates of 2017/18 vaccine effectiveness, Canada, January 2018. S262N 2018 Euro surveillance Table IV S262N 0 5 29409570 Early season co-circulation of influenza A(H3N2) and B(Yamagata): interim estimates of 2017/18 vaccine effectiveness, Canada, January 2018. T131K 2018 Euro surveillance Table IV T131K 0 5 29409570 Early season co-circulation of influenza A(H3N2) and B(Yamagata): interim estimates of 2017/18 vaccine effectiveness, Canada, January 2018. T135K 2018 Euro surveillance Table IV T135K 0 5 29409570 Early season co-circulation of influenza A(H3N2) and B(Yamagata): interim estimates of 2017/18 vaccine effectiveness, Canada, January 2018. T135N 2018 Euro surveillance Table IV T135N 0 5 29409570 Early season co-circulation of influenza A(H3N2) and B(Yamagata): interim estimates of 2017/18 vaccine effectiveness, Canada, January 2018. V182I 2018 Euro surveillance Table IV V182I 0 5 29409570 Early season co-circulation of influenza A(H3N2) and B(Yamagata): interim estimates of 2017/18 vaccine effectiveness, Canada, January 2018. Y94H 2018 Euro surveillance Table IV Y94H 0 4 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. A138S 2018 Influenza and other respiratory viruses Table IV A138S 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. A197T 2018 Influenza and other respiratory viruses Table IV A197T 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. A201V 2018 Influenza and other respiratory viruses Table IV A201V 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. A202T 2018 Influenza and other respiratory viruses Table IV A202T 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. A212S 2018 Influenza and other respiratory viruses Table IV A212S 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. A261T 2018 Influenza and other respiratory viruses Table IV A261T 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. A343T 2018 Influenza and other respiratory viruses Table IV A343T 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. A455G 2018 Influenza and other respiratory viruses Table IV A455G 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. A559V 2018 Influenza and other respiratory viruses Table IV A559V 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. A560V 2018 Influenza and other respiratory viruses Table IV A560V 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. D151N 2018 Influenza and other respiratory viruses Table IV D151N 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. D160N 2018 Influenza and other respiratory viruses Table IV D160N 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. D188G 2018 Influenza and other respiratory viruses Table IV D188G 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. D195N 2018 Influenza and other respiratory viruses Table IV D195N 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. D209N 2018 Influenza and other respiratory viruses Table IV D209N 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. D21G 2018 Influenza and other respiratory viruses Table IV D21G 0 4 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. D339N 2018 Influenza and other respiratory viruses Table IV D339N 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. D396E 2018 Influenza and other respiratory viruses Table IV D396E 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. D581N 2018 Influenza and other respiratory viruses Table IV D581N 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. E221D 2018 Influenza and other respiratory viruses Table IV E221D 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. E252V 2018 Influenza and other respiratory viruses Table IV E252V 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. E26K 2018 Influenza and other respiratory viruses Table IV E26K 0 4 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. E351D 2018 Influenza and other respiratory viruses Table IV E351D 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. E47K 2018 Influenza and other respiratory viruses Table IV E47K 0 4 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. E50K 2018 Influenza and other respiratory viruses Table IV E50K 0 4 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. E97G 2018 Influenza and other respiratory viruses Table IV E97G 0 4 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. F159S 2018 Influenza and other respiratory viruses Table IV F159S 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. F159Y 2018 Influenza and other respiratory viruses Table IV F159Y 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. G154D 2018 Influenza and other respiratory viruses Table IV G154D 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. G16E 2018 Influenza and other respiratory viruses Table IV G16E 0 4 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. G170R 2018 Influenza and other respiratory viruses Table IV G170R 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. G240V 2018 Influenza and other respiratory viruses Table IV G240V 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. G262E 2018 Influenza and other respiratory viruses Table IV G262E 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. H273N 2018 Influenza and other respiratory viruses Table IV H273N 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. H456Y 2018 Influenza and other respiratory viruses Table IV H456Y 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. H713Y 2018 Influenza and other respiratory viruses Table IV H713Y 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. I111T 2018 Influenza and other respiratory viruses Table IV I111T 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. I123V 2018 Influenza and other respiratory viruses Table IV I123V 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. I136L 2018 Influenza and other respiratory viruses Table IV I136L 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. I149T 2018 Influenza and other respiratory viruses Table IV I149T 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. I182V 2018 Influenza and other respiratory viruses Table IV I182V 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. I183V 2018 Influenza and other respiratory viruses Table IV I183V 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. I20T 2018 Influenza and other respiratory viruses Table IV I20T 0 4 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. I222V 2018 Influenza and other respiratory viruses Table IV I222V 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. I308V 2018 Influenza and other respiratory viruses Table IV I308V 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. I30T 2018 Influenza and other respiratory viruses Table IV I30T 0 4 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. I321V 2018 Influenza and other respiratory viruses Table IV I321V 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. I354L 2018 Influenza and other respiratory viruses Table IV I354L 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. I380V 2018 Influenza and other respiratory viruses Table IV I380V 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. I392T 2018 Influenza and other respiratory viruses Table IV I392T 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. I397M 2018 Influenza and other respiratory viruses Table IV I397M 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. I39M 2018 Influenza and other respiratory viruses Table IV I39M 0 4 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. I435T 2018 Influenza and other respiratory viruses Table IV I435T 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. I554V 2018 Influenza and other respiratory viruses Table IV I554V 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. I589T 2018 Influenza and other respiratory viruses Table IV I589T 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. K160T 2018 Influenza and other respiratory viruses Table IV K160T 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. K163I 2018 Influenza and other respiratory viruses Table IV K163I 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. K229E 2018 Influenza and other respiratory viruses Table IV K229E 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. K230R 2018 Influenza and other respiratory viruses Table IV K230R 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. K258E 2018 Influenza and other respiratory viruses Table IV K258E 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. K326R 2018 Influenza and other respiratory viruses Table IV K326R 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. K357R 2018 Influenza and other respiratory viruses Table IV K357R 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. K39R 2018 Influenza and other respiratory viruses Table IV K39R 0 4 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. K470M 2018 Influenza and other respiratory viruses Table IV K470M 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. K605R 2018 Influenza and other respiratory viruses Table IV K605R 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. K78R 2018 Influenza and other respiratory viruses Table IV K78R 0 4 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. L108I 2018 Influenza and other respiratory viruses Table IV L108I 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. L384I 2018 Influenza and other respiratory viruses Table IV L384I 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. L40V 2018 Influenza and other respiratory viruses Table IV L40V 0 4 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. L424M 2018 Influenza and other respiratory viruses Table IV L424M 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. L90I 2018 Influenza and other respiratory viruses Table IV L90I 0 4 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. M124I 2018 Influenza and other respiratory viruses Table IV M124I 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. M192V 2018 Influenza and other respiratory viruses Table IV M192V 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. M317T 2018 Influenza and other respiratory viruses Table IV M317T 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. M374I 2018 Influenza and other respiratory viruses Table IV M374I 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. M407I 2018 Influenza and other respiratory viruses Table IV M407I 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. M440V 2018 Influenza and other respiratory viruses Table IV M440V 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. M476L 2018 Influenza and other respiratory viruses Table IV M476L 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. M481I 2018 Influenza and other respiratory viruses Table IV M481I 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. M66T 2018 Influenza and other respiratory viruses Table IV M66T 0 4 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. N144S 2018 Influenza and other respiratory viruses Table IV N144S 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. N145S 2018 Influenza and other respiratory viruses Table IV N145S 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. N200S 2018 Influenza and other respiratory viruses Table IV N200S 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. N205S 2018 Influenza and other respiratory viruses Table IV N205S 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. N225D 2018 Influenza and other respiratory viruses Table IV N225D 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. N246Y 2018 Influenza and other respiratory viruses Table IV N246Y 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. N248D 2018 Influenza and other respiratory viruses Table IV N248D 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. N262K 2018 Influenza and other respiratory viruses Table IV N262K 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. N272S 2018 Influenza and other respiratory viruses Table IV N272S 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. N278K 2018 Influenza and other respiratory viruses Table IV N278K 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. N321K 2018 Influenza and other respiratory viruses Table IV N321K 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. N369K 2018 Influenza and other respiratory viruses Table IV N369K 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. N44S 2018 Influenza and other respiratory viruses Table IV N44S 0 4 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. N675K 2018 Influenza and other respiratory viruses Table IV N675K 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. P224S 2018 Influenza and other respiratory viruses Table IV P224S 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. P273R 2018 Influenza and other respiratory viruses Table IV P273R 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. P83S 2018 Influenza and other respiratory viruses Table IV P83S 0 4 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. Q256K 2018 Influenza and other respiratory viruses Table IV Q256K 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. Q311H 2018 Influenza and other respiratory viruses Table IV Q311H 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. Q33R 2018 Influenza and other respiratory viruses Table IV Q33R 0 4 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. R142G 2018 Influenza and other respiratory viruses Table IV R142G 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. R194Q 2018 Influenza and other respiratory viruses Table IV R194Q 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. R255T 2018 Influenza and other respiratory viruses Table IV R255T 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. R293K 2018 Influenza and other respiratory viruses Table IV R293K 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. R356K 2018 Influenza and other respiratory viruses Table IV R356K 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. R361K 2018 Influenza and other respiratory viruses Table IV R361K 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. R389K 2018 Influenza and other respiratory viruses Table IV R389K 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. R390K 2018 Influenza and other respiratory viruses Table IV R390K 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. R52K 2018 Influenza and other respiratory viruses Table IV R52K 0 4 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. R673S 2018 Influenza and other respiratory viruses Table IV R673S 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. S124N 2018 Influenza and other respiratory viruses Table IV S124N 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. S143G 2018 Influenza and other respiratory viruses Table IV S143G 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. S185T 2018 Influenza and other respiratory viruses Table IV S185T 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. S203T 2018 Influenza and other respiratory viruses Table IV S203T 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. S217G 2018 Influenza and other respiratory viruses Table IV S217G 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. S245N 2018 Influenza and other respiratory viruses Table IV S245N 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. S247T 2018 Influenza and other respiratory viruses Table IV S247T 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. S359P 2018 Influenza and other respiratory viruses Table IV S359P 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. S482N 2018 Influenza and other respiratory viruses Table IV S482N 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. S52N 2018 Influenza and other respiratory viruses Table IV S52N 0 4 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. S643T 2018 Influenza and other respiratory viruses Table IV S643T 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. S644T 2018 Influenza and other respiratory viruses Table IV S644T 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. S709N 2018 Influenza and other respiratory viruses Table IV S709N 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. S710N 2018 Influenza and other respiratory viruses Table IV S710N 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. S84G 2018 Influenza and other respiratory viruses Table IV S84G 0 4 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. T128A 2018 Influenza and other respiratory viruses Table IV T128A 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. T267K 2018 Influenza and other respiratory viruses Table IV T267K 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. T289I 2018 Influenza and other respiratory viruses Table IV T289I 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. T329N 2018 Influenza and other respiratory viruses Table IV T329N 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. T400K 2018 Influenza and other respiratory viruses Table IV T400K 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. T48A 2018 Influenza and other respiratory viruses Table IV T48A 0 4 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. V100I 2018 Influenza and other respiratory viruses Table IV V100I 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. V117M 2018 Influenza and other respiratory viruses Table IV V117M 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. V186G 2018 Influenza and other respiratory viruses Table IV V186G 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. V193A 2018 Influenza and other respiratory viruses Table IV V193A 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. V197A 2018 Influenza and other respiratory viruses Table IV V197A 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. V22F 2018 Influenza and other respiratory viruses Table IV V22F 0 4 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. V241I 2018 Influenza and other respiratory viruses Table IV V241I 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. V338I 2018 Influenza and other respiratory viruses Table IV V338I 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. V344M 2018 Influenza and other respiratory viruses Table IV V344M 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. V407I 2018 Influenza and other respiratory viruses Table IV V407I 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. V51I 2018 Influenza and other respiratory viruses Table IV V51I 0 4 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. V606A 2018 Influenza and other respiratory viruses Table IV V606A 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. V63I 2018 Influenza and other respiratory viruses Table IV V63I 0 4 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. V668I 2018 Influenza and other respiratory viruses Table IV V668I 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. V669I 2018 Influenza and other respiratory viruses Table IV V669I 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. V731I 2018 Influenza and other respiratory viruses Table IV V731I 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. V73A 2018 Influenza and other respiratory viruses Table IV V73A 0 4 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. V80I 2018 Influenza and other respiratory viruses Table IV V80I 0 4 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. W383C 2018 Influenza and other respiratory viruses Table IV W383C 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. W580C 2018 Influenza and other respiratory viruses Table IV W580C 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. Y161F 2018 Influenza and other respiratory viruses Table IV Y161F 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. Y351F 2018 Influenza and other respiratory viruses Table IV Y351F 0 5 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. Y55F 2018 Influenza and other respiratory viruses Table IV Y55F 0 4 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. Y67F 2018 Influenza and other respiratory viruses Table IV Y67F 0 4 29489903 Design and synthesis of constrained bicyclic molecules as candidate inhibitors of influenza A neuraminidase. H274Y 2018 PloS one Table IV H274Y 0 5 29587786 Effects of the S42 residue of the H1N1 swine influenza virus NS1 protein on interferon responses and virus replication. D92E 2018 Virology journal Table IV D92E 0 4 29630683 The use of plant lectins to regulate H1N1 influenza A virus receptor binding activity. A1026G 2018 PloS one Table IV A1026G 0 6 29630683 The use of plant lectins to regulate H1N1 influenza A virus receptor binding activity. G155E 2018 PloS one Table IV G155E 0 5 29630683 The use of plant lectins to regulate H1N1 influenza A virus receptor binding activity. G201E 2018 PloS one Table IV G201E 0 5 29630683 The use of plant lectins to regulate H1N1 influenza A virus receptor binding activity. N129D 2018 PloS one Table IV N129D 0 5 29630683 The use of plant lectins to regulate H1N1 influenza A virus receptor binding activity. S183P 2018 PloS one Table IV S183P 0 5 29643248 A Single Amino Acid in the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses. A193T 2018 Journal of virology Table IV A193T 0 5 29643248 A Single Amino Acid in the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses. A541T 2018 Journal of virology Table IV A541T 0 5 29643248 A Single Amino Acid in the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses. E162G 2018 Journal of virology Table IV E162G 0 5 29643248 A Single Amino Acid in the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses. E550K 2018 Journal of virology Table IV E550K 0 5 29643248 A Single Amino Acid in the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses. K338R 2018 Journal of virology Table IV K338R 0 5 29643248 A Single Amino Acid in the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses. P295T 2018 Journal of virology Table IV P295T 0 5 29643248 A Single Amino Acid in the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses. Q78K 2018 Journal of virology Table IV Q78K 0 4 29688498 Dynamic Variation and Reversion in the Signature Amino Acids of H7N9 Virus During Human Infection. D701N 2018 The Journal of infectious diseases Table IV D701N 0 5 29688498 Dynamic Variation and Reversion in the Signature Amino Acids of H7N9 Virus During Human Infection. E627K 2018 The Journal of infectious diseases Table IV E627K 0 5 29688498 Dynamic Variation and Reversion in the Signature Amino Acids of H7N9 Virus During Human Infection. G186V/I 2018 The Journal of infectious diseases Table IV G186V;G186I 0;0 7;7 29688498 Dynamic Variation and Reversion in the Signature Amino Acids of H7N9 Virus During Human Infection. H274Y 2018 The Journal of infectious diseases Table IV H274Y 0 5 29688498 Dynamic Variation and Reversion in the Signature Amino Acids of H7N9 Virus During Human Infection. K526R 2018 The Journal of infectious diseases Table IV K526R 0 5 29688498 Dynamic Variation and Reversion in the Signature Amino Acids of H7N9 Virus During Human Infection. Q226L/I 2018 The Journal of infectious diseases Table IV Q226L;Q226I 0;0 7;7 29688498 Dynamic Variation and Reversion in the Signature Amino Acids of H7N9 Virus During Human Infection. R292K 2018 The Journal of infectious diseases Table IV R292K 0 5 29688498 Dynamic Variation and Reversion in the Signature Amino Acids of H7N9 Virus During Human Infection. T160A 2018 The Journal of infectious diseases Table IV T160A 0 5 29688498 Dynamic Variation and Reversion in the Signature Amino Acids of H7N9 Virus During Human Infection. V473L 2018 The Journal of infectious diseases Table IV V473L 0 5 29691337 Identification of the I38T PA Substitution as a Resistance Marker for Next-Generation Influenza Virus Endonuclease Inhibitors. I38T 2018 mBio Table IV I38T 0 4 29743603 Unexpected infection outcomes of China-origin H7N9 low pathogenicity avian influenza virus in turkeys. L235Q 2018 Scientific reports Table IV L235Q 0 5 29743603 Unexpected infection outcomes of China-origin H7N9 low pathogenicity avian influenza virus in turkeys. L235X 2018 Scientific reports Table IV L235X 0 5 29743603 Unexpected infection outcomes of China-origin H7N9 low pathogenicity avian influenza virus in turkeys. N10H 2018 Scientific reports Table IV N10H 0 4 29743603 Unexpected infection outcomes of China-origin H7N9 low pathogenicity avian influenza virus in turkeys. R269K 2018 Scientific reports Table IV R269K 0 5 29743603 Unexpected infection outcomes of China-origin H7N9 low pathogenicity avian influenza virus in turkeys. T10I 2018 Scientific reports Table IV T10I 0 4 29743603 Unexpected infection outcomes of China-origin H7N9 low pathogenicity avian influenza virus in turkeys. T10S 2018 Scientific reports Table IV T10S 0 4 29743603 Unexpected infection outcomes of China-origin H7N9 low pathogenicity avian influenza virus in turkeys. Y360H 2018 Scientific reports Table IV Y360H 0 5 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. K41A 2018 Frontiers in cellular and infection microbiology Table IV K41A 0 4 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. R38A 2018 Frontiers in cellular and infection microbiology Table IV R38A 0 4 29927982 Influenza D virus M2 protein exhibits ion channel activity in Xenopus laevis oocytes. K76A 2018 PloS one Table IV K76A 0 4 29927982 Influenza D virus M2 protein exhibits ion channel activity in Xenopus laevis oocytes. Y72A 2018 PloS one Table IV Y72A 0 4 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. A20S 2018 Scientific reports Table IV A20S 0 4 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. A36V 2018 Scientific reports Table IV A36V 0 4 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. A37T 2018 Scientific reports Table IV A37T 0 4 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. E119D 2018 Scientific reports Table IV E119D 0 5 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. E120D 2018 Scientific reports Table IV E120D 0 5 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. E199G 2018 Scientific reports Table IV E199G 0 5 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. E23K 2018 Scientific reports Table IV E23K 0 4 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. E623K 2018 Scientific reports Table IV E623K 0 5 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. F36A 2018 Scientific reports Table IV F36A 0 4 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. F36V 2018 Scientific reports Table IV F36V 0 4 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. G548R 2018 Scientific reports Table IV G548R 0 5 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. H274Y 2018 Scientific reports Table IV H274Y 0 5 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. I38F 2018 Scientific reports Table IV I38F 0 4 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. I38M 2018 Scientific reports Table IV I38M 0 4 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. I38T 2018 Scientific reports Table IV I38T 0 4 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. I38V 2018 Scientific reports Table IV I38V 0 4 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. L28P 2018 Scientific reports Table IV L28P 0 4 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. N412D 2018 Scientific reports Table IV N412D 0 5 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. R356K 2018 Scientific reports Table IV R356K 0 5 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. S632P 2018 Scientific reports Table IV S632P 0 5 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. V517A 2018 Scientific reports Table IV V517A 0 5 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. V545T 2018 Scientific reports Table IV V545T 0 5 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. V63I 2018 Scientific reports Table IV V63I 0 4 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. A214V 2018 PloS one Table IV A214V 0 5 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. A320P 2018 PloS one Table IV A320P 0 5 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. A320V 2018 PloS one Table IV A320V 0 5 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. A350T 2018 PloS one Table IV A350T 0 5 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. A537V 2018 PloS one Table IV A537V 0 5 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. A85T 2018 PloS one Table IV A85T 0 4 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. C30R 2018 PloS one Table IV C30R 0 4 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. C42R 2018 PloS one Table IV C42R 0 4 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. D120N 2018 PloS one Table IV D120N 0 5 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. D287A 2018 PloS one Table IV D287A 0 5 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. D309G 2018 PloS one Table IV D309G 0 5 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. D330E 2018 PloS one Table IV D330E 0 5 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. D69N 2018 PloS one Table IV D69N 0 4 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. D83K 2018 PloS one Table IV D83K 0 4 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. E419G 2018 PloS one Table IV E419G 0 5 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. E442G 2018 PloS one Table IV E442G 0 5 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. E83K 2018 PloS one Table IV E83K 0 4 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. F15S 2018 PloS one Table IV F15S 0 4 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. F274S 2018 PloS one Table IV F274S 0 5 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. F348L 2018 PloS one Table IV F348L 0 5 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. F516L 2018 PloS one Table IV F516L 0 5 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. F536L 2018 PloS one Table IV F536L 0 5 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. F550S 2018 PloS one Table IV F550S 0 5 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. F95L 2018 PloS one Table IV F95L 0 4 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. G132D 2018 PloS one Table IV G132D 0 5 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. G21R 2018 PloS one Table IV G21R 0 4 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. G21V 2018 PloS one Table IV G21V 0 4 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. G286D 2018 PloS one Table IV G286D 0 5 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. H200P 2018 PloS one Table IV H200P 0 5 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. I222N 2018 PloS one Table IV I222N 0 5 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. I242F 2018 PloS one Table IV I242F 0 5 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. I246M 2018 PloS one Table IV I246M 0 5 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. I26T 2018 PloS one Table IV I26T 0 4 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. I276T 2018 PloS one Table IV I276T 0 5 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. I28V 2018 PloS one Table IV I28V 0 4 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. I57T 2018 PloS one Table IV I57T 0 4 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. K308N 2018 PloS one Table IV K308N 0 5 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. K403N 2018 PloS one Table IV K403N 0 5 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. L140I 2018 PloS one Table IV L140I 0 5 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. L29P 2018 PloS one Table IV L29P 0 4 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. L443F 2018 PloS one Table IV L443F 0 5 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. L463Q 2018 PloS one Table IV L463Q 0 5 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. L52M 2018 PloS one Table IV L52M 0 4 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. M284I 2018 PloS one Table IV M284I 0 5 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. M478I 2018 PloS one Table IV M478I 0 5 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. N205I 2018 PloS one Table IV N205I 0 5 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. N208S 2018 PloS one Table IV N208S 0 5 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. N232S 2018 PloS one Table IV N232S 0 5 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. N329T 2018 PloS one Table IV N329T 0 5 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. N440K 2018 PloS one Table IV N440K 0 5 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. N47D 2018 PloS one Table IV N47D 0 4 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. P119A 2018 PloS one Table IV P119A 0 5 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. P126S 2018 PloS one Table IV P126S 0 5 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. P285L 2018 PloS one Table IV P285L 0 5 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. P324S 2018 PloS one Table IV P324S 0 5 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. P46L 2018 PloS one Table IV P46L 0 4 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. R292K 2018 PloS one Table IV R292K 0 5 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. R323K 2018 PloS one Table IV R323K 0 5 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. R472K 2018 PloS one Table IV R472K 0 5 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. R508G 2018 PloS one Table IV R508G 0 5 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. S111G 2018 PloS one Table IV S111G 0 5 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. S165N 2018 PloS one Table IV S165N 0 5 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. S225R 2018 PloS one Table IV S225R 0 5 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. S263N 2018 PloS one Table IV S263N 0 5 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. S281R 2018 PloS one Table IV S281R 0 5 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. T151A 2018 PloS one Table IV T151A 0 5 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. T195A 2018 PloS one Table IV T195A 0 5 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. T242I 2018 PloS one Table IV T242I 0 5 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. T34A 2018 PloS one Table IV T34A 0 4 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. T34I 2018 PloS one Table IV T34I 0 4 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. T386I 2018 PloS one Table IV T386I 0 5 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. T69N 2018 PloS one Table IV T69N 0 4 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. V30A 2018 PloS one Table IV V30A 0 4 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. V33A 2018 PloS one Table IV V33A 0 4 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. V418F 2018 PloS one Table IV V418F 0 5 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. V424G 2018 PloS one Table IV V424G 0 5 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. V50A 2018 PloS one Table IV V50A 0 4 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. Y40H 2018 PloS one Table IV Y40H 0 4 30050898 Structurally Diverse Polyketides From the Mangrove-Derived Fungus Diaporthe sp. SCSIO 41011 With Their Anti-influenza A Virus Activities. H274Y 2018 Frontiers in chemistry Table IV H274Y 0 5 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. A224P 2018 Scientific reports Table IV A224P 0 5 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. A343T 2018 Scientific reports Table IV A343T 0 5 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. A689S 2018 Scientific reports Table IV A689S 0 5 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. D394G 2018 Scientific reports Table IV D394G 0 5 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. D398E 2018 Scientific reports Table IV D398E 0 5 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. D701N 2018 Scientific reports Table IV D701N 0 5 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. E610D 2018 Scientific reports Table IV E610D 0 5 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. E613V 2018 Scientific reports Table IV E613V 0 5 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. F562Y 2018 Scientific reports Table IV F562Y 0 5 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. G685R 2018 Scientific reports Table IV G685R 0 5 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. H134R 2018 Scientific reports Table IV H134R 0 5 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. K190R 2018 Scientific reports Table IV K190R 0 5 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. K745R 2018 Scientific reports Table IV K745R 0 5 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. L226F 2018 Scientific reports Table IV L226F 0 5 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. L466F 2018 Scientific reports Table IV L466F 0 5 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. L618M 2018 Scientific reports Table IV L618M 0 5 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. M111I 2018 Scientific reports Table IV M111I 0 5 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. M315I 2018 Scientific reports Table IV M315I 0 5 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. M744T 2018 Scientific reports Table IV M744T 0 5 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. M86V 2018 Scientific reports Table IV M86V 0 4 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. N115S 2018 Scientific reports Table IV N115S 0 5 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. N222S 2018 Scientific reports Table IV N222S 0 5 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. N314S 2018 Scientific reports Table IV N314S 0 5 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. N328K 2018 Scientific reports Table IV N328K 0 5 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. S65P 2018 Scientific reports Table IV S65P 0 4 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. T156V 2018 Scientific reports Table IV T156V 0 5 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. T21S 2018 Scientific reports Table IV T21S 0 4 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. T430A 2018 Scientific reports Table IV T430A 0 5 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. T81A 2018 Scientific reports Table IV T81A 0 4 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. T85A 2018 Scientific reports Table IV T85A 0 4 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. V344M 2018 Scientific reports Table IV V344M 0 5 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. Y305F 2018 Scientific reports Table IV Y305F 0 5 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. Y658H 2018 Scientific reports Table IV Y658H 0 5 30227889 Effects of mutations in the effector domain of influenza A virus NS1 protein. E96A 2018 BMC research notes Table IV E96A 0 4 30227889 Effects of mutations in the effector domain of influenza A virus NS1 protein. F103S 2018 BMC research notes Table IV F103S 0 5 30227889 Effects of mutations in the effector domain of influenza A virus NS1 protein. R38A 2018 BMC research notes Table IV R38A 0 4 30227889 Effects of mutations in the effector domain of influenza A virus NS1 protein. W187R 2018 BMC research notes Table IV W187R 0 5 30227889 Effects of mutations in the effector domain of influenza A virus NS1 protein. Y89A 2018 BMC research notes Table IV Y89A 0 4 30227889 Effects of mutations in the effector domain of influenza A virus NS1 protein. Y89F 2018 BMC research notes Table IV Y89F 0 4 30282714 Amino Acid Residue 217 in the Hemagglutinin Glycoprotein Is a Key Mediator of Avian Influenza H7N9 Virus Antigenicity. A125T 2019 Journal of virology Table IV A125T 0 5 30282714 Amino Acid Residue 217 in the Hemagglutinin Glycoprotein Is a Key Mediator of Avian Influenza H7N9 Virus Antigenicity. A125V 2019 Journal of virology Table IV A125V 0 5 30282714 Amino Acid Residue 217 in the Hemagglutinin Glycoprotein Is a Key Mediator of Avian Influenza H7N9 Virus Antigenicity. A151T 2019 Journal of virology Table IV A151T 0 5 30282714 Amino Acid Residue 217 in the Hemagglutinin Glycoprotein Is a Key Mediator of Avian Influenza H7N9 Virus Antigenicity. L217Q 2019 Journal of virology Table IV L217Q 0 5 30282714 Amino Acid Residue 217 in the Hemagglutinin Glycoprotein Is a Key Mediator of Avian Influenza H7N9 Virus Antigenicity. Q217L 2019 Journal of virology Table IV Q217L 0 5 30282714 Amino Acid Residue 217 in the Hemagglutinin Glycoprotein Is a Key Mediator of Avian Influenza H7N9 Virus Antigenicity. V125A 2019 Journal of virology Table IV V125A 0 5 30301950 Tree shrew as a new animal model to study the pathogenesis of avian influenza (H9N2) virus infection. E627K 2018 Emerging microbes & infections Table IV E627K 0 5 30353004 Genome-wide characterization of the seasonal H3N2 virus in Shanghai reveals natural temperature-sensitive strains conferred by the I668V mutation in the PA subunit. D339N 2018 Emerging microbes & infections Table IV D339N 0 5 30353004 Genome-wide characterization of the seasonal H3N2 virus in Shanghai reveals natural temperature-sensitive strains conferred by the I668V mutation in the PA subunit. H75P 2018 Emerging microbes & infections Table IV H75P 0 4 30353004 Genome-wide characterization of the seasonal H3N2 virus in Shanghai reveals natural temperature-sensitive strains conferred by the I668V mutation in the PA subunit. I140T 2018 Emerging microbes & infections Table IV I140T 0 5 30353004 Genome-wide characterization of the seasonal H3N2 virus in Shanghai reveals natural temperature-sensitive strains conferred by the I668V mutation in the PA subunit. I668V 2018 Emerging microbes & infections Table IV I668V 0 5 30353004 Genome-wide characterization of the seasonal H3N2 virus in Shanghai reveals natural temperature-sensitive strains conferred by the I668V mutation in the PA subunit. K220N 2018 Emerging microbes & infections Table IV K220N 0 5 30353004 Genome-wide characterization of the seasonal H3N2 virus in Shanghai reveals natural temperature-sensitive strains conferred by the I668V mutation in the PA subunit. K340R 2018 Emerging microbes & infections Table IV K340R 0 5 30353004 Genome-wide characterization of the seasonal H3N2 virus in Shanghai reveals natural temperature-sensitive strains conferred by the I668V mutation in the PA subunit. K92R 2018 Emerging microbes & infections Table IV K92R 0 4 30353004 Genome-wide characterization of the seasonal H3N2 virus in Shanghai reveals natural temperature-sensitive strains conferred by the I668V mutation in the PA subunit. N121K 2018 Emerging microbes & infections Table IV N121K 0 5 30353004 Genome-wide characterization of the seasonal H3N2 virus in Shanghai reveals natural temperature-sensitive strains conferred by the I668V mutation in the PA subunit. N127S 2018 Emerging microbes & infections Table IV N127S 0 5 30353004 Genome-wide characterization of the seasonal H3N2 virus in Shanghai reveals natural temperature-sensitive strains conferred by the I668V mutation in the PA subunit. N171K 2018 Emerging microbes & infections Table IV N171K 0 5 30353004 Genome-wide characterization of the seasonal H3N2 virus in Shanghai reveals natural temperature-sensitive strains conferred by the I668V mutation in the PA subunit. N329S 2018 Emerging microbes & infections Table IV N329S 0 5 30353004 Genome-wide characterization of the seasonal H3N2 virus in Shanghai reveals natural temperature-sensitive strains conferred by the I668V mutation in the PA subunit. R142K 2018 Emerging microbes & infections Table IV R142K 0 5 30353004 Genome-wide characterization of the seasonal H3N2 virus in Shanghai reveals natural temperature-sensitive strains conferred by the I668V mutation in the PA subunit. R15K 2018 Emerging microbes & infections Table IV R15K 0 4 30353004 Genome-wide characterization of the seasonal H3N2 virus in Shanghai reveals natural temperature-sensitive strains conferred by the I668V mutation in the PA subunit. R25Q 2018 Emerging microbes & infections Table IV R25Q 0 4 30353004 Genome-wide characterization of the seasonal H3N2 virus in Shanghai reveals natural temperature-sensitive strains conferred by the I668V mutation in the PA subunit. R261Q 2018 Emerging microbes & infections Table IV R261Q 0 5 30353004 Genome-wide characterization of the seasonal H3N2 virus in Shanghai reveals natural temperature-sensitive strains conferred by the I668V mutation in the PA subunit. R299K 2018 Emerging microbes & infections Table IV R299K 0 5 30353004 Genome-wide characterization of the seasonal H3N2 virus in Shanghai reveals natural temperature-sensitive strains conferred by the I668V mutation in the PA subunit. T114S 2018 Emerging microbes & infections Table IV T114S 0 5 30353004 Genome-wide characterization of the seasonal H3N2 virus in Shanghai reveals natural temperature-sensitive strains conferred by the I668V mutation in the PA subunit. T131K 2018 Emerging microbes & infections Table IV T131K 0 5 30353004 Genome-wide characterization of the seasonal H3N2 virus in Shanghai reveals natural temperature-sensitive strains conferred by the I668V mutation in the PA subunit. T135K 2018 Emerging microbes & infections Table IV T135K 0 5 30353004 Genome-wide characterization of the seasonal H3N2 virus in Shanghai reveals natural temperature-sensitive strains conferred by the I668V mutation in the PA subunit. T135N 2018 Emerging microbes & infections Table IV T135N 0 5 30353004 Genome-wide characterization of the seasonal H3N2 virus in Shanghai reveals natural temperature-sensitive strains conferred by the I668V mutation in the PA subunit. V303I 2018 Emerging microbes & infections Table IV V303I 0 5 30439983 Influenza B viruses circulated during last 5 years in Mongolia. E105K 2018 PloS one Table IV E105K 0 5 30439983 Influenza B viruses circulated during last 5 years in Mongolia. G104R 2018 PloS one Table IV G104R 0 5 30439983 Influenza B viruses circulated during last 5 years in Mongolia. G140R 2018 PloS one Table IV G140R 0 5 30439983 Influenza B viruses circulated during last 5 years in Mongolia. H101N 2018 PloS one Table IV H101N 0 5 30439983 Influenza B viruses circulated during last 5 years in Mongolia. I114T 2018 PloS one Table IV I114T 0 5 30439983 Influenza B viruses circulated during last 5 years in Mongolia. I117V 2018 PloS one Table IV I117V 0 5 30439983 Influenza B viruses circulated during last 5 years in Mongolia. I146V 2018 PloS one Table IV I146V 0 5 30439983 Influenza B viruses circulated during last 5 years in Mongolia. N116K 2018 PloS one Table IV N116K 0 5 30439983 Influenza B viruses circulated during last 5 years in Mongolia. N129D 2018 PloS one Table IV N129D 0 5 30466301 Activity of enisamium, an isonicotinic acid derivative, against influenza viruses in differentiated normal human bronchial epithelial cells. H275Y 2018 Antiviral chemistry & chemotherapy Table IV H275Y 0 5 30548432 Consecutive influenza surveillance of neuraminidase mutations and neuraminidase inhibitor resistance in Japan. D151E 2019 Influenza and other respiratory viruses Table IV D151E 0 5 30548432 Consecutive influenza surveillance of neuraminidase mutations and neuraminidase inhibitor resistance in Japan. D151G 2019 Influenza and other respiratory viruses Table IV D151G 0 5 30548432 Consecutive influenza surveillance of neuraminidase mutations and neuraminidase inhibitor resistance in Japan. D151N 2019 Influenza and other respiratory viruses Table IV D151N 0 5 30548432 Consecutive influenza surveillance of neuraminidase mutations and neuraminidase inhibitor resistance in Japan. D199N 2019 Influenza and other respiratory viruses Table IV D199N 0 5 30548432 Consecutive influenza surveillance of neuraminidase mutations and neuraminidase inhibitor resistance in Japan. G320E 2019 Influenza and other respiratory viruses Table IV G320E 0 5 30548432 Consecutive influenza surveillance of neuraminidase mutations and neuraminidase inhibitor resistance in Japan. H275Y 2019 Influenza and other respiratory viruses Table IV H275Y 0 5 30548432 Consecutive influenza surveillance of neuraminidase mutations and neuraminidase inhibitor resistance in Japan. I262T 2019 Influenza and other respiratory viruses Table IV I262T 0 5 30548432 Consecutive influenza surveillance of neuraminidase mutations and neuraminidase inhibitor resistance in Japan. K249E 2019 Influenza and other respiratory viruses Table IV K249E 0 5 30548432 Consecutive influenza surveillance of neuraminidase mutations and neuraminidase inhibitor resistance in Japan. S331R 2019 Influenza and other respiratory viruses Table IV S331R 0 5 30548432 Consecutive influenza surveillance of neuraminidase mutations and neuraminidase inhibitor resistance in Japan. T148I 2019 Influenza and other respiratory viruses Table IV T148I 0 5 30574137 Susceptibility of Influenza Viruses to the Novel Cap-Dependent Endonuclease Inhibitor Baloxavir Marboxil. D197E 2018 Frontiers in microbiology Table IV D197E 0 5 30574137 Susceptibility of Influenza Viruses to the Novel Cap-Dependent Endonuclease Inhibitor Baloxavir Marboxil. E119V 2018 Frontiers in microbiology Table IV E119V 0 5 30574137 Susceptibility of Influenza Viruses to the Novel Cap-Dependent Endonuclease Inhibitor Baloxavir Marboxil. H275Y 2018 Frontiers in microbiology Table IV H275Y 0 5 30574137 Susceptibility of Influenza Viruses to the Novel Cap-Dependent Endonuclease Inhibitor Baloxavir Marboxil. I38T 2018 Frontiers in microbiology Table IV I38T 0 4 30574137 Susceptibility of Influenza Viruses to the Novel Cap-Dependent Endonuclease Inhibitor Baloxavir Marboxil. R292K 2018 Frontiers in microbiology Table IV R292K 0 5 30640922 Molecular characterization of influenza A(H1N1)pdm09 in Cameroon during the 2014-2016 influenza seasons. A141V 2019 PloS one Table IV A141V 0 5 30640922 Molecular characterization of influenza A(H1N1)pdm09 in Cameroon during the 2014-2016 influenza seasons. A48S 2019 PloS one Table IV A48S 0 4 30640922 Molecular characterization of influenza A(H1N1)pdm09 in Cameroon during the 2014-2016 influenza seasons. H273N 2019 PloS one Table IV H273N 0 5 30640922 Molecular characterization of influenza A(H1N1)pdm09 in Cameroon during the 2014-2016 influenza seasons. I216T 2019 PloS one Table IV I216T 0 5 30640922 Molecular characterization of influenza A(H1N1)pdm09 in Cameroon during the 2014-2016 influenza seasons. K142R 2019 PloS one Table IV K142R 0 5 30640922 Molecular characterization of influenza A(H1N1)pdm09 in Cameroon during the 2014-2016 influenza seasons. K163Q 2019 PloS one Table IV K163Q 0 5 30640922 Molecular characterization of influenza A(H1N1)pdm09 in Cameroon during the 2014-2016 influenza seasons. K283E 2019 PloS one Table IV K283E 0 5 30640922 Molecular characterization of influenza A(H1N1)pdm09 in Cameroon during the 2014-2016 influenza seasons. P83S 2019 PloS one Table IV P83S 0 4 30640922 Molecular characterization of influenza A(H1N1)pdm09 in Cameroon during the 2014-2016 influenza seasons. S162N 2019 PloS one Table IV S162N 0 5 30640922 Molecular characterization of influenza A(H1N1)pdm09 in Cameroon during the 2014-2016 influenza seasons. S162R/N 2019 PloS one Table IV S162R;S162N 0;0 7;7 30640922 Molecular characterization of influenza A(H1N1)pdm09 in Cameroon during the 2014-2016 influenza seasons. S185T 2019 PloS one Table IV S185T 0 5 30640922 Molecular characterization of influenza A(H1N1)pdm09 in Cameroon during the 2014-2016 influenza seasons. S84N 2019 PloS one Table IV S84N 0 4 30640922 Molecular characterization of influenza A(H1N1)pdm09 in Cameroon during the 2014-2016 influenza seasons. T120A 2019 PloS one Table IV T120A 0 5 30670142 Detection of influenza A(H3N2) viruses exhibiting reduced susceptibility to the novel cap-dependent endonuclease inhibitor baloxavir in Japan, December 2018. I38T 2019 Euro surveillance Table IV I38T 0 4 30670142 Detection of influenza A(H3N2) viruses exhibiting reduced susceptibility to the novel cap-dependent endonuclease inhibitor baloxavir in Japan, December 2018. Y277F 2019 Euro surveillance Table IV Y277F 0 5 30792414 Molecular evolution of influenza B virus during 2011-2017 in Chaoyang, Beijing, suggesting the free influenza vaccine policy. I117V 2019 Scientific reports Table IV I117V 0 5 30792414 Molecular evolution of influenza B virus during 2011-2017 in Chaoyang, Beijing, suggesting the free influenza vaccine policy. I146V 2019 Scientific reports Table IV I146V 0 5 30792414 Molecular evolution of influenza B virus during 2011-2017 in Chaoyang, Beijing, suggesting the free influenza vaccine policy. N116K 2019 Scientific reports Table IV N116K 0 5 30792414 Molecular evolution of influenza B virus during 2011-2017 in Chaoyang, Beijing, suggesting the free influenza vaccine policy. N129D 2019 Scientific reports Table IV N129D 0 5 30899824 Evolved avian influenza virus (H7N9) isolated from human cases in a middle Yangtze River city in China, from February to April 2017. Ala144Thr 2019 Heliyon Table IV A144T 0 9 30899824 Evolved avian influenza virus (H7N9) isolated from human cases in a middle Yangtze River city in China, from February to April 2017. Ala588Val 2019 Heliyon Table IV A588V 0 9 30899824 Evolved avian influenza virus (H7N9) isolated from human cases in a middle Yangtze River city in China, from February to April 2017. Arg292Lys 2019 Heliyon Table IV R292K 0 9 30899824 Evolved avian influenza virus (H7N9) isolated from human cases in a middle Yangtze River city in China, from February to April 2017. Asn30Asp 2019 Heliyon Table IV N30D 0 8 30899824 Evolved avian influenza virus (H7N9) isolated from human cases in a middle Yangtze River city in China, from February to April 2017. Asp701Asn 2019 Heliyon Table IV D701N 0 9 30899824 Evolved avian influenza virus (H7N9) isolated from human cases in a middle Yangtze River city in China, from February to April 2017. Gln235Leu 2019 Heliyon Table IV Q235L 0 9 30899824 Evolved avian influenza virus (H7N9) isolated from human cases in a middle Yangtze River city in China, from February to April 2017. Glu627Lys 2019 Heliyon Table IV E627K 0 9 30899824 Evolved avian influenza virus (H7N9) isolated from human cases in a middle Yangtze River city in China, from February to April 2017. Gly195Val 2019 Heliyon Table IV G195V 0 9 30899824 Evolved avian influenza virus (H7N9) isolated from human cases in a middle Yangtze River city in China, from February to April 2017. His99Tyr 2019 Heliyon Table IV H99Y 0 8 30899824 Evolved avian influenza virus (H7N9) isolated from human cases in a middle Yangtze River city in China, from February to April 2017. Ile292Val 2019 Heliyon Table IV I292V 0 9 30899824 Evolved avian influenza virus (H7N9) isolated from human cases in a middle Yangtze River city in China, from February to April 2017. Ile368Val 2019 Heliyon Table IV I368V 0 9 30899824 Evolved avian influenza virus (H7N9) isolated from human cases in a middle Yangtze River city in China, from February to April 2017. Leu89Val 2019 Heliyon Table IV L89V 0 8 30899824 Evolved avian influenza virus (H7N9) isolated from human cases in a middle Yangtze River city in China, from February to April 2017. Pro42Ser 2019 Heliyon Table IV P42S 0 8 30899824 Evolved avian influenza virus (H7N9) isolated from human cases in a middle Yangtze River city in China, from February to April 2017. Ser31Asn 2019 Heliyon Table IV S31N 0 8 30899824 Evolved avian influenza virus (H7N9) isolated from human cases in a middle Yangtze River city in China, from February to April 2017. Thr169Ala 2019 Heliyon Table IV T169A 0 9 30899824 Evolved avian influenza virus (H7N9) isolated from human cases in a middle Yangtze River city in China, from February to April 2017. Thr215Ala 2019 Heliyon Table IV T215A 0 9 30914078 Influenza A(H3N2) virus exhibiting reduced susceptibility to baloxavir due to a polymerase acidic subunit I38T substitution detected from a hospitalised child without prior baloxavir treatment, Japan, January 2019. I38M 2019 Euro surveillance Table IV I38M 0 4 30914078 Influenza A(H3N2) virus exhibiting reduced susceptibility to baloxavir due to a polymerase acidic subunit I38T substitution detected from a hospitalised child without prior baloxavir treatment, Japan, January 2019. I38T 2019 Euro surveillance Table IV I38T 0 4 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. G186V 2019 Cell host & microbe Table IV G186V 0 5 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. L194P 2019 Cell host & microbe Table IV L194P 0 5 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. R0176L 2019 Cell host & microbe Table IV R0176L 0 6 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. E627K 2019 mBio Table IV E627K 0 5 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. G218E 2019 Journal of virology Table IV G218E 0 5 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. K328R 2019 Journal of virology Table IV K328R 0 5 31356626 Severe cases of seasonal influenza in Russia in 2017-2018. D222G/N 2019 PloS one Table IV D222G;D222N 0;0 7;7 31436527 Human-to-Human Transmission of Influenza A(H3N2) Virus with Reduced Susceptibility to Baloxavir, Japan, February 2019. I38T 2019 Emerging infectious diseases Table IV I38T 0 4 31477028 A study of the relationship between human infection with avian influenza a (H5N6) and environmental avian influenza viruses in Fujian, China. D701N 2019 BMC infectious diseases Table IV D701N 0 5 31477028 A study of the relationship between human infection with avian influenza a (H5N6) and environmental avian influenza viruses in Fujian, China. D92E 2019 BMC infectious diseases Table IV D92E 0 4 31477028 A study of the relationship between human infection with avian influenza a (H5N6) and environmental avian influenza viruses in Fujian, China. E627K 2019 BMC infectious diseases Table IV E627K 0 5 31477028 A study of the relationship between human infection with avian influenza a (H5N6) and environmental avian influenza viruses in Fujian, China. G228S 2019 BMC infectious diseases Table IV G228S 0 5 31477028 A study of the relationship between human infection with avian influenza a (H5N6) and environmental avian influenza viruses in Fujian, China. G309D 2019 BMC infectious diseases Table IV G309D 0 5 31477028 A study of the relationship between human infection with avian influenza a (H5N6) and environmental avian influenza viruses in Fujian, China. H99Y 2019 BMC infectious diseases Table IV H99Y 0 4 31477028 A study of the relationship between human infection with avian influenza a (H5N6) and environmental avian influenza viruses in Fujian, China. I368V 2019 BMC infectious diseases Table IV I368V 0 5 31477028 A study of the relationship between human infection with avian influenza a (H5N6) and environmental avian influenza viruses in Fujian, China. I495V 2019 BMC infectious diseases Table IV I495V 0 5 31477028 A study of the relationship between human infection with avian influenza a (H5N6) and environmental avian influenza viruses in Fujian, China. L89V 2019 BMC infectious diseases Table IV L89V 0 4 31477028 A study of the relationship between human infection with avian influenza a (H5N6) and environmental avian influenza viruses in Fujian, China. N294S 2019 BMC infectious diseases Table IV N294S 0 5 31477028 A study of the relationship between human infection with avian influenza a (H5N6) and environmental avian influenza viruses in Fujian, China. N30D 2019 BMC infectious diseases Table IV N30D 0 4 31477028 A study of the relationship between human infection with avian influenza a (H5N6) and environmental avian influenza viruses in Fujian, China. P42S 2019 BMC infectious diseases Table IV P42S 0 4 31477028 A study of the relationship between human infection with avian influenza a (H5N6) and environmental avian influenza viruses in Fujian, China. Q226L 2019 BMC infectious diseases Table IV Q226L 0 5 31477028 A study of the relationship between human infection with avian influenza a (H5N6) and environmental avian influenza viruses in Fujian, China. R294K 2019 BMC infectious diseases Table IV R294K 0 5 31477028 A study of the relationship between human infection with avian influenza a (H5N6) and environmental avian influenza viruses in Fujian, China. R477G 2019 BMC infectious diseases Table IV R477G 0 5 31477028 A study of the relationship between human infection with avian influenza a (H5N6) and environmental avian influenza viruses in Fujian, China. T215A 2019 BMC infectious diseases Table IV T215A 0 5 31477028 A study of the relationship between human infection with avian influenza a (H5N6) and environmental avian influenza viruses in Fujian, China. T339K 2019 BMC infectious diseases Table IV T339K 0 5 31538644 Baloxavir Marboxil in Japanese Pediatric Patients With Influenza: Safety and Clinical and Virologic Outcomes. I38M 2020 Clinical infectious diseases Table IV I38M 0 4 31538644 Baloxavir Marboxil in Japanese Pediatric Patients With Influenza: Safety and Clinical and Virologic Outcomes. I38T 2020 Clinical infectious diseases Table IV I38T 0 4 31538644 Baloxavir Marboxil in Japanese Pediatric Patients With Influenza: Safety and Clinical and Virologic Outcomes. isoleucine substituted by methionine at position 38 2020 Clinical infectious diseases Table IV I38M 0 51 31538644 Baloxavir Marboxil in Japanese Pediatric Patients With Influenza: Safety and Clinical and Virologic Outcomes. isoleucine substituted by threonine at position 38 2020 Clinical infectious diseases Table IV I38T 0 50 31783761 Influenza A virus hemagglutinin mutations associated with use of neuraminidase inhibitors correlate with decreased inhibition by anti-influenza antibodies. A197T 2019 Virology journal Table IV A197T 0 5 31783761 Influenza A virus hemagglutinin mutations associated with use of neuraminidase inhibitors correlate with decreased inhibition by anti-influenza antibodies. D222G 2019 Virology journal Table IV D222G 0 5 31783761 Influenza A virus hemagglutinin mutations associated with use of neuraminidase inhibitors correlate with decreased inhibition by anti-influenza antibodies. E119G 2019 Virology journal Table IV E119G 0 5 31783761 Influenza A virus hemagglutinin mutations associated with use of neuraminidase inhibitors correlate with decreased inhibition by anti-influenza antibodies. E119V 2019 Virology journal Table IV E119V 0 5 31783761 Influenza A virus hemagglutinin mutations associated with use of neuraminidase inhibitors correlate with decreased inhibition by anti-influenza antibodies. G155E 2019 Virology journal Table IV G155E 0 5 31783761 Influenza A virus hemagglutinin mutations associated with use of neuraminidase inhibitors correlate with decreased inhibition by anti-influenza antibodies. G70C 2019 Virology journal Table IV G70C 0 4 31783761 Influenza A virus hemagglutinin mutations associated with use of neuraminidase inhibitors correlate with decreased inhibition by anti-influenza antibodies. H151Q 2019 Virology journal Table IV H151Q 0 5 31783761 Influenza A virus hemagglutinin mutations associated with use of neuraminidase inhibitors correlate with decreased inhibition by anti-influenza antibodies. L151P 2019 Virology journal Table IV L151P 0 5 31783761 Influenza A virus hemagglutinin mutations associated with use of neuraminidase inhibitors correlate with decreased inhibition by anti-influenza antibodies. N125D 2019 Virology journal Table IV N125D 0 5 31783761 Influenza A virus hemagglutinin mutations associated with use of neuraminidase inhibitors correlate with decreased inhibition by anti-influenza antibodies. N146S 2019 Virology journal Table IV N146S 0 5 31783761 Influenza A virus hemagglutinin mutations associated with use of neuraminidase inhibitors correlate with decreased inhibition by anti-influenza antibodies. R208K 2019 Virology journal Table IV R208K 0 5 31783761 Influenza A virus hemagglutinin mutations associated with use of neuraminidase inhibitors correlate with decreased inhibition by anti-influenza antibodies. S183F 2019 Virology journal Table IV S183F 0 5 31783761 Influenza A virus hemagglutinin mutations associated with use of neuraminidase inhibitors correlate with decreased inhibition by anti-influenza antibodies. S183P 2019 Virology journal Table IV S183P 0 5 31783761 Influenza A virus hemagglutinin mutations associated with use of neuraminidase inhibitors correlate with decreased inhibition by anti-influenza antibodies. T152A 2019 Virology journal Table IV T152A 0 5 31783761 Influenza A virus hemagglutinin mutations associated with use of neuraminidase inhibitors correlate with decreased inhibition by anti-influenza antibodies. V114I 2019 Virology journal Table IV V114I 0 5 31783761 Influenza A virus hemagglutinin mutations associated with use of neuraminidase inhibitors correlate with decreased inhibition by anti-influenza antibodies. V152I 2019 Virology journal Table IV V152I 0 5 31783761 Influenza A virus hemagglutinin mutations associated with use of neuraminidase inhibitors correlate with decreased inhibition by anti-influenza antibodies. Y155H 2019 Virology journal Table IV Y155H 0 5 31839904 Complete genome sequencing of H1N1pdm09 swine influenza isolates from Nigeria reveals likely reverse zoonotic transmission at the human-animal interface in intensive piggery. D375N 2019 Infection ecology & epidemiology Table IV D375N 0 5 31839904 Complete genome sequencing of H1N1pdm09 swine influenza isolates from Nigeria reveals likely reverse zoonotic transmission at the human-animal interface in intensive piggery. D527G 2019 Infection ecology & epidemiology Table IV D527G 0 5 31839904 Complete genome sequencing of H1N1pdm09 swine influenza isolates from Nigeria reveals likely reverse zoonotic transmission at the human-animal interface in intensive piggery. G189D 2019 Infection ecology & epidemiology Table IV G189D 0 5 31839904 Complete genome sequencing of H1N1pdm09 swine influenza isolates from Nigeria reveals likely reverse zoonotic transmission at the human-animal interface in intensive piggery. G28V 2019 Infection ecology & epidemiology Table IV G28V 0 4 31839904 Complete genome sequencing of H1N1pdm09 swine influenza isolates from Nigeria reveals likely reverse zoonotic transmission at the human-animal interface in intensive piggery. I111M 2019 Infection ecology & epidemiology Table IV I111M 0 5 31839904 Complete genome sequencing of H1N1pdm09 swine influenza isolates from Nigeria reveals likely reverse zoonotic transmission at the human-animal interface in intensive piggery. I123V 2019 Infection ecology & epidemiology Table IV I123V 0 5 31839904 Complete genome sequencing of H1N1pdm09 swine influenza isolates from Nigeria reveals likely reverse zoonotic transmission at the human-animal interface in intensive piggery. I312Y 2019 Infection ecology & epidemiology Table IV I312Y 0 5 31839904 Complete genome sequencing of H1N1pdm09 swine influenza isolates from Nigeria reveals likely reverse zoonotic transmission at the human-animal interface in intensive piggery. I338Y 2019 Infection ecology & epidemiology Table IV I338Y 0 5 31839904 Complete genome sequencing of H1N1pdm09 swine influenza isolates from Nigeria reveals likely reverse zoonotic transmission at the human-animal interface in intensive piggery. I505V 2019 Infection ecology & epidemiology Table IV I505V 0 5 31839904 Complete genome sequencing of H1N1pdm09 swine influenza isolates from Nigeria reveals likely reverse zoonotic transmission at the human-animal interface in intensive piggery. K716Q 2019 Infection ecology & epidemiology Table IV K716Q 0 5 31839904 Complete genome sequencing of H1N1pdm09 swine influenza isolates from Nigeria reveals likely reverse zoonotic transmission at the human-animal interface in intensive piggery. K736G 2019 Infection ecology & epidemiology Table IV K736G 0 5 31839904 Complete genome sequencing of H1N1pdm09 swine influenza isolates from Nigeria reveals likely reverse zoonotic transmission at the human-animal interface in intensive piggery. L122Q 2019 Infection ecology & epidemiology Table IV L122Q 0 5 31839904 Complete genome sequencing of H1N1pdm09 swine influenza isolates from Nigeria reveals likely reverse zoonotic transmission at the human-animal interface in intensive piggery. M111I 2019 Infection ecology & epidemiology Table IV M111I 0 5 31839904 Complete genome sequencing of H1N1pdm09 swine influenza isolates from Nigeria reveals likely reverse zoonotic transmission at the human-animal interface in intensive piggery. N248D 2019 Infection ecology & epidemiology Table IV N248D 0 5 31839904 Complete genome sequencing of H1N1pdm09 swine influenza isolates from Nigeria reveals likely reverse zoonotic transmission at the human-animal interface in intensive piggery. P100S 2019 Infection ecology & epidemiology Table IV P100S 0 5 31839904 Complete genome sequencing of H1N1pdm09 swine influenza isolates from Nigeria reveals likely reverse zoonotic transmission at the human-animal interface in intensive piggery. P224S 2019 Infection ecology & epidemiology Table IV P224S 0 5 31839904 Complete genome sequencing of H1N1pdm09 swine influenza isolates from Nigeria reveals likely reverse zoonotic transmission at the human-animal interface in intensive piggery. Q109K 2019 Infection ecology & epidemiology Table IV Q109K 0 5 31839904 Complete genome sequencing of H1N1pdm09 swine influenza isolates from Nigeria reveals likely reverse zoonotic transmission at the human-animal interface in intensive piggery. Q240R 2019 Infection ecology & epidemiology Table IV Q240R 0 5 31839904 Complete genome sequencing of H1N1pdm09 swine influenza isolates from Nigeria reveals likely reverse zoonotic transmission at the human-animal interface in intensive piggery. S138N 2019 Infection ecology & epidemiology Table IV S138N 0 5 31839904 Complete genome sequencing of H1N1pdm09 swine influenza isolates from Nigeria reveals likely reverse zoonotic transmission at the human-animal interface in intensive piggery. S246N 2019 Infection ecology & epidemiology Table IV S246N 0 5 31839904 Complete genome sequencing of H1N1pdm09 swine influenza isolates from Nigeria reveals likely reverse zoonotic transmission at the human-animal interface in intensive piggery. S439G 2019 Infection ecology & epidemiology Table IV S439G 0 5 31839904 Complete genome sequencing of H1N1pdm09 swine influenza isolates from Nigeria reveals likely reverse zoonotic transmission at the human-animal interface in intensive piggery. T23S 2019 Infection ecology & epidemiology Table IV T23S 0 4 31839904 Complete genome sequencing of H1N1pdm09 swine influenza isolates from Nigeria reveals likely reverse zoonotic transmission at the human-animal interface in intensive piggery. T396A 2019 Infection ecology & epidemiology Table IV T396A 0 5 31839904 Complete genome sequencing of H1N1pdm09 swine influenza isolates from Nigeria reveals likely reverse zoonotic transmission at the human-animal interface in intensive piggery. V100I 2019 Infection ecology & epidemiology Table IV V100I 0 5 31839904 Complete genome sequencing of H1N1pdm09 swine influenza isolates from Nigeria reveals likely reverse zoonotic transmission at the human-animal interface in intensive piggery. V106I 2019 Infection ecology & epidemiology Table IV V106I 0 5 31839904 Complete genome sequencing of H1N1pdm09 swine influenza isolates from Nigeria reveals likely reverse zoonotic transmission at the human-animal interface in intensive piggery. V14I 2019 Infection ecology & epidemiology Table IV V14I 0 4 31839904 Complete genome sequencing of H1N1pdm09 swine influenza isolates from Nigeria reveals likely reverse zoonotic transmission at the human-animal interface in intensive piggery. V235M 2019 Infection ecology & epidemiology Table IV V235M 0 5 31839904 Complete genome sequencing of H1N1pdm09 swine influenza isolates from Nigeria reveals likely reverse zoonotic transmission at the human-animal interface in intensive piggery. W102C 2019 Infection ecology & epidemiology Table IV W102C 0 5 31839904 Complete genome sequencing of H1N1pdm09 swine influenza isolates from Nigeria reveals likely reverse zoonotic transmission at the human-animal interface in intensive piggery. W187E 2019 Infection ecology & epidemiology Table IV W187E 0 5 31839904 Complete genome sequencing of H1N1pdm09 swine influenza isolates from Nigeria reveals likely reverse zoonotic transmission at the human-animal interface in intensive piggery. Y351F 2019 Infection ecology & epidemiology Table IV Y351F 0 5 31842256 Antiviral Activity of Benzoic Acid Derivative NC-5 Against Influenza A Virus and Its Neuraminidase Inhibition. H275Y 2019 International journal of molecular sciences Table IV H275Y 0 5 31842256 Antiviral Activity of Benzoic Acid Derivative NC-5 Against Influenza A Virus and Its Neuraminidase Inhibition. R294K 2019 International journal of molecular sciences Table IV R294K 0 5 31917822 The effect of mutations derived from mouse-adapted H3N2 seasonal influenza A virus to pathogenicity and host adaptation. A144T 2020 PloS one Table IV A144T 0 5 31917822 The effect of mutations derived from mouse-adapted H3N2 seasonal influenza A virus to pathogenicity and host adaptation. D34N 2020 PloS one Table IV D34N 0 4 31917822 The effect of mutations derived from mouse-adapted H3N2 seasonal influenza A virus to pathogenicity and host adaptation. F209S 2020 PloS one Table IV F209S 0 5 31917822 The effect of mutations derived from mouse-adapted H3N2 seasonal influenza A virus to pathogenicity and host adaptation. F323L 2020 PloS one Table IV F323L 0 5 31917822 The effect of mutations derived from mouse-adapted H3N2 seasonal influenza A virus to pathogenicity and host adaptation. K18Q 2020 PloS one Table IV K18Q 0 4 31917822 The effect of mutations derived from mouse-adapted H3N2 seasonal influenza A virus to pathogenicity and host adaptation. K609R 2020 PloS one Table IV K609R 0 5 31917822 The effect of mutations derived from mouse-adapted H3N2 seasonal influenza A virus to pathogenicity and host adaptation. M86I 2020 PloS one Table IV M86I 0 4 31917822 The effect of mutations derived from mouse-adapted H3N2 seasonal influenza A virus to pathogenicity and host adaptation. N160D 2020 PloS one Table IV N160D 0 5 31917822 The effect of mutations derived from mouse-adapted H3N2 seasonal influenza A virus to pathogenicity and host adaptation. N262T 2020 PloS one Table IV N262T 0 5 31917822 The effect of mutations derived from mouse-adapted H3N2 seasonal influenza A virus to pathogenicity and host adaptation. S331R 2020 PloS one Table IV S331R 0 5 31917822 The effect of mutations derived from mouse-adapted H3N2 seasonal influenza A virus to pathogenicity and host adaptation. T183A 2020 PloS one Table IV T183A 0 5 31917822 The effect of mutations derived from mouse-adapted H3N2 seasonal influenza A virus to pathogenicity and host adaptation. V421F 2020 PloS one Table IV V421F 0 5 31917822 The effect of mutations derived from mouse-adapted H3N2 seasonal influenza A virus to pathogenicity and host adaptation. Y713H 2020 PloS one Table IV Y713H 0 5 31955521 Antigenic variants of influenza B viruses isolated in Japan during the 2017-2018 and 2018-2019 influenza seasons. E117A 2020 Influenza and other respiratory viruses Table IV E117A 0 5 31955521 Antigenic variants of influenza B viruses isolated in Japan during the 2017-2018 and 2018-2019 influenza seasons. G407S 2020 Influenza and other respiratory viruses Table IV G407S 0 5 32064779 Rapid detection of an I38T amino acid substitution in influenza polymerase acidic subunit associated with reduced susceptibility to baloxavir marboxil. I38T 2020 Influenza and other respiratory viruses Table IV I38T 0 4 32130243 Epidemic of influenza A(H1N1)pdm09 analyzed by full genome sequences and the first case of oseltamivir-resistant strain in Myanmar 2017. H275Y 2020 PloS one Table IV H275Y 0 5 32211197 Detection of H3N8 influenza A virus with multiple mammalian-adaptive mutations in a rescued Grey seal (Halichoerus grypus) pup. A105K 2020 Virus evolution Table IV A105K 0 5 32211197 Detection of H3N8 influenza A virus with multiple mammalian-adaptive mutations in a rescued Grey seal (Halichoerus grypus) pup. A154T 2020 Virus evolution Table IV A154T 0 5 32211197 Detection of H3N8 influenza A virus with multiple mammalian-adaptive mutations in a rescued Grey seal (Halichoerus grypus) pup. D161N 2020 Virus evolution Table IV D161N 0 5 32211197 Detection of H3N8 influenza A virus with multiple mammalian-adaptive mutations in a rescued Grey seal (Halichoerus grypus) pup. D701N 2020 Virus evolution Table IV D701N 0 5 32211197 Detection of H3N8 influenza A virus with multiple mammalian-adaptive mutations in a rescued Grey seal (Halichoerus grypus) pup. G101N 2020 Virus evolution Table IV G101N 0 5 32211197 Detection of H3N8 influenza A virus with multiple mammalian-adaptive mutations in a rescued Grey seal (Halichoerus grypus) pup. I517V 2020 Virus evolution Table IV I517V 0 5 32211197 Detection of H3N8 influenza A virus with multiple mammalian-adaptive mutations in a rescued Grey seal (Halichoerus grypus) pup. I81V 2020 Virus evolution Table IV I81V 0 4 32211197 Detection of H3N8 influenza A virus with multiple mammalian-adaptive mutations in a rescued Grey seal (Halichoerus grypus) pup. R753T 2020 Virus evolution Table IV R753T 0 5 32211197 Detection of H3N8 influenza A virus with multiple mammalian-adaptive mutations in a rescued Grey seal (Halichoerus grypus) pup. S111G 2020 Virus evolution Table IV S111G 0 5 32211197 Detection of H3N8 influenza A virus with multiple mammalian-adaptive mutations in a rescued Grey seal (Halichoerus grypus) pup. S235Y 2020 Virus evolution Table IV S235Y 0 5 32211197 Detection of H3N8 influenza A virus with multiple mammalian-adaptive mutations in a rescued Grey seal (Halichoerus grypus) pup. S321I 2020 Virus evolution Table IV S321I 0 5 32211197 Detection of H3N8 influenza A virus with multiple mammalian-adaptive mutations in a rescued Grey seal (Halichoerus grypus) pup. S395T 2020 Virus evolution Table IV S395T 0 5 32211197 Detection of H3N8 influenza A virus with multiple mammalian-adaptive mutations in a rescued Grey seal (Halichoerus grypus) pup. S41D 2020 Virus evolution Table IV S41D 0 4 32211197 Detection of H3N8 influenza A virus with multiple mammalian-adaptive mutations in a rescued Grey seal (Halichoerus grypus) pup. S678N 2020 Virus evolution Table IV S678N 0 5 32211197 Detection of H3N8 influenza A virus with multiple mammalian-adaptive mutations in a rescued Grey seal (Halichoerus grypus) pup. T176S 2020 Virus evolution Table IV T176S 0 5 32211197 Detection of H3N8 influenza A virus with multiple mammalian-adaptive mutations in a rescued Grey seal (Halichoerus grypus) pup. T383A 2020 Virus evolution Table IV T383A 0 5 32211197 Detection of H3N8 influenza A virus with multiple mammalian-adaptive mutations in a rescued Grey seal (Halichoerus grypus) pup. T64A 2020 Virus evolution Table IV T64A 0 4 32211197 Detection of H3N8 influenza A virus with multiple mammalian-adaptive mutations in a rescued Grey seal (Halichoerus grypus) pup. T676I 2020 Virus evolution Table IV T676I 0 5 32211197 Detection of H3N8 influenza A virus with multiple mammalian-adaptive mutations in a rescued Grey seal (Halichoerus grypus) pup. V104M 2020 Virus evolution Table IV V104M 0 5 32211197 Detection of H3N8 influenza A virus with multiple mammalian-adaptive mutations in a rescued Grey seal (Halichoerus grypus) pup. V667I 2020 Virus evolution Table IV V667I 0 5 32211197 Detection of H3N8 influenza A virus with multiple mammalian-adaptive mutations in a rescued Grey seal (Halichoerus grypus) pup. V91I 2020 Virus evolution Table IV V91I 0 4 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. A155T 2020 Journal of medical microbiology Table IV A155T 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. A166T 2020 Journal of medical microbiology Table IV A166T 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. A212T 2020 Journal of medical microbiology Table IV A212T 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. A27V 2020 Journal of medical microbiology Table IV A27V 0 4 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. D145N 2020 Journal of medical microbiology Table IV D145N 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. D174E 2020 Journal of medical microbiology Table IV D174E 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. D222N 2020 Journal of medical microbiology Table IV D222N 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. D291E 2020 Journal of medical microbiology Table IV D291E 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. D394N 2020 Journal of medical microbiology Table IV D394N 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. D399N 2020 Journal of medical microbiology Table IV D399N 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. D416K 2020 Journal of medical microbiology Table IV D416K 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. D416N 2020 Journal of medical microbiology Table IV D416N 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. D53N 2020 Journal of medical microbiology Table IV D53N 0 4 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. D94N 2020 Journal of medical microbiology Table IV D94N 0 4 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. E14G 2020 Journal of medical microbiology Table IV E14G 0 4 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. E150G 2020 Journal of medical microbiology Table IV E150G 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. E179D 2020 Journal of medical microbiology Table IV E179D 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. E344K 2020 Journal of medical microbiology Table IV E344K 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. E618D 2020 Journal of medical microbiology Table IV E618D 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. E62G 2020 Journal of medical microbiology Table IV E62G 0 4 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. E688G 2020 Journal of medical microbiology Table IV E688G 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. F74L 2020 Journal of medical microbiology Table IV F74L 0 4 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. F74S 2020 Journal of medical microbiology Table IV F74S 0 4 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. G142R 2020 Journal of medical microbiology Table IV G142R 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. G225D 2020 Journal of medical microbiology Table IV G225D 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. G225S 2020 Journal of medical microbiology Table IV G225S 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. G346D 2020 Journal of medical microbiology Table IV G346D 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. G77R 2020 Journal of medical microbiology Table IV G77R 0 4 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. G93S 2020 Journal of medical microbiology Table IV G93S 0 4 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. H311Q 2020 Journal of medical microbiology Table IV H311Q 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. I111M 2020 Journal of medical microbiology Table IV I111M 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. I176M 2020 Journal of medical microbiology Table IV I176M 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. I188T 2020 Journal of medical microbiology Table IV I188T 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. I212V 2020 Journal of medical microbiology Table IV I212V 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. I295V 2020 Journal of medical microbiology Table IV I295V 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. I34T 2020 Journal of medical microbiology Table IV I34T 0 4 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. I365T 2020 Journal of medical microbiology Table IV I365T 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. I436V 2020 Journal of medical microbiology Table IV I436V 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. I77M 2020 Journal of medical microbiology Table IV I77M 0 4 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. I96V 2020 Journal of medical microbiology Table IV I96V 0 4 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. K121N 2020 Journal of medical microbiology Table IV K121N 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. K158R 2020 Journal of medical microbiology Table IV K158R 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. K160T 2020 Journal of medical microbiology Table IV K160T 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. K161R 2020 Journal of medical microbiology Table IV K161R 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. K171N 2020 Journal of medical microbiology Table IV K171N 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. K220N 2020 Journal of medical microbiology Table IV K220N 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. K299R 2020 Journal of medical microbiology Table IV K299R 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. K302T 2020 Journal of medical microbiology Table IV K302T 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. K340R 2020 Journal of medical microbiology Table IV K340R 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. K386R 2020 Journal of medical microbiology Table IV K386R 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. K83E 2020 Journal of medical microbiology Table IV K83E 0 4 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. K92R 2020 Journal of medical microbiology Table IV K92R 0 4 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. L105F 2020 Journal of medical microbiology Table IV L105F 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. L161I 2020 Journal of medical microbiology Table IV L161I 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. L233I 2020 Journal of medical microbiology Table IV L233I 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. L314M 2020 Journal of medical microbiology Table IV L314M 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. L338F 2020 Journal of medical microbiology Table IV L338F 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. L418I 2020 Journal of medical microbiology Table IV L418I 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. L85I 2020 Journal of medical microbiology Table IV L85I 0 4 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. M314I 2020 Journal of medical microbiology Table IV M314I 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. M410V 2020 Journal of medical microbiology Table IV M410V 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. M65T 2020 Journal of medical microbiology Table IV M65T 0 4 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. N128T 2020 Journal of medical microbiology Table IV N128T 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. N129D 2020 Journal of medical microbiology Table IV N129D 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. N169S 2020 Journal of medical microbiology Table IV N169S 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. N207H 2020 Journal of medical microbiology Table IV N207H 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. N234D 2020 Journal of medical microbiology Table IV N234D 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. N260D 2020 Journal of medical microbiology Table IV N260D 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. N329S 2020 Journal of medical microbiology Table IV N329S 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. N339K 2020 Journal of medical microbiology Table IV N339K 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. N449D 2020 Journal of medical microbiology Table IV N449D 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. P126L 2020 Journal of medical microbiology Table IV P126L 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. P194L 2020 Journal of medical microbiology Table IV P194L 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. P289S 2020 Journal of medical microbiology Table IV P289S 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. P386S 2020 Journal of medical microbiology Table IV P386S 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. P453T 2020 Journal of medical microbiology Table IV P453T 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. Q51K 2020 Journal of medical microbiology Table IV Q51K 0 4 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. R223Q 2020 Journal of medical microbiology Table IV R223Q 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. R261Q 2020 Journal of medical microbiology Table IV R261Q 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. R299K 2020 Journal of medical microbiology Table IV R299K 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. R33Q 2020 Journal of medical microbiology Table IV R33Q 0 4 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. R356K 2020 Journal of medical microbiology Table IV R356K 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. S105N 2020 Journal of medical microbiology Table IV S105N 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. S107D 2020 Journal of medical microbiology Table IV S107D 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. S164T 2020 Journal of medical microbiology Table IV S164T 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. S183P 2020 Journal of medical microbiology Table IV S183P 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. S198P 2020 Journal of medical microbiology Table IV S198P 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. S23N 2020 Journal of medical microbiology Table IV S23N 0 4 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. S315R 2020 Journal of medical microbiology Table IV S315R 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. S74R 2020 Journal of medical microbiology Table IV S74R 0 4 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. S79P 2020 Journal of medical microbiology Table IV S79P 0 4 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. T120A 2020 Journal of medical microbiology Table IV T120A 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. T128A 2020 Journal of medical microbiology Table IV T128A 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. T131K 2020 Journal of medical microbiology Table IV T131K 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. T135K 2020 Journal of medical microbiology Table IV T135K 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. T185I 2020 Journal of medical microbiology Table IV T185I 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. T398I 2020 Journal of medical microbiology Table IV T398I 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. T452I 2020 Journal of medical microbiology Table IV T452I 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. T64I 2020 Journal of medical microbiology Table IV T64I 0 4 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. T72I 2020 Journal of medical microbiology Table IV T72I 0 4 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. T72N 2020 Journal of medical microbiology Table IV T72N 0 4 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. T80A 2020 Journal of medical microbiology Table IV T80A 0 4 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. T81I 2020 Journal of medical microbiology Table IV T81I 0 4 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. V193A 2020 Journal of medical microbiology Table IV V193A 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. V193I 2020 Journal of medical microbiology Table IV V193I 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. V197I 2020 Journal of medical microbiology Table IV V197I 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. V200I 2020 Journal of medical microbiology Table IV V200I 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. V303I 2020 Journal of medical microbiology Table IV V303I 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. V319I 2020 Journal of medical microbiology Table IV V319I 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. V398I 2020 Journal of medical microbiology Table IV V398I 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. V431I 2020 Journal of medical microbiology Table IV V431I 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. V43I 2020 Journal of medical microbiology Table IV V43I 0 4 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. V47L 2020 Journal of medical microbiology Table IV V47L 0 4 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. V667I 2020 Journal of medical microbiology Table IV V667I 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. V668I 2020 Journal of medical microbiology Table IV V668I 0 5 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. V67I 2020 Journal of medical microbiology Table IV V67I 0 4 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. V77I 2020 Journal of medical microbiology Table IV V77I 0 4 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. V81A 2020 Journal of medical microbiology Table IV V81A 0 4 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. A168T 2020 AMB Express Table IV A168T 0 5 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. A198T 2020 AMB Express Table IV A198T 0 5 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. A198V 2020 AMB Express Table IV A198V 0 5 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. A209T 2020 AMB Express Table IV A209T 0 5 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. A622V 2020 AMB Express Table IV A622V 0 5 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. C693G 2020 AMB Express Table IV C693G 0 5 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. D256N 2020 AMB Express Table IV D256N 0 5 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. E114K 2020 AMB Express Table IV E114K 0 5 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. E319V 2020 AMB Express Table IV E319V 0 5 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. E533G 2020 AMB Express Table IV E533G 0 5 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. F46L 2020 AMB Express Table IV F46L 0 4 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. F62L 2020 AMB Express Table IV F62L 0 4 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. F646S 2020 AMB Express Table IV F646S 0 5 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. I397V 2020 AMB Express Table IV I397V 0 5 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. I517V 2020 AMB Express Table IV I517V 0 5 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. I63M 2020 AMB Express Table IV I63M 0 4 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. K131R 2020 AMB Express Table IV K131R 0 5 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. K526R 2020 AMB Express Table IV K526R 0 5 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. L132I 2020 AMB Express Table IV L132I 0 5 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. L234Q 2020 AMB Express Table IV L234Q 0 5 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. L281F 2020 AMB Express Table IV L281F 0 5 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. L28P 2020 AMB Express Table IV L28P 0 4 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. L33Q 2020 AMB Express Table IV L33Q 0 4 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. L466I 2020 AMB Express Table IV L466I 0 5 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. L77I 2020 AMB Express Table IV L77I 0 4 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. M224K 2020 AMB Express Table IV M224K 0 5 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. N201D 2020 AMB Express Table IV N201D 0 5 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. N285D 2020 AMB Express Table IV N285D 0 5 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. P85L 2020 AMB Express Table IV P85L 0 4 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. Q234L 2020 AMB Express Table IV Q234L 0 5 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. R185K 2020 AMB Express Table IV R185K 0 5 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. R256H 2020 AMB Express Table IV R256H 0 5 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. R304G 2020 AMB Express Table IV R304G 0 5 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. R318K 2020 AMB Express Table IV R318K 0 5 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. R355K 2020 AMB Express Table IV R355K 0 5 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. S190F 2020 AMB Express Table IV S190F 0 5 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. V127I 2020 AMB Express Table IV V127I 0 5 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. V186I 2020 AMB Express Table IV V186I 0 5 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. V554I 2020 AMB Express Table IV V554I 0 5 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. V84M 2020 AMB Express Table IV V84M 0 4 32631440 Characterization of neuraminidase inhibitor-resistant influenza virus isolates from immunocompromised patients in the Republic of Korea. A158E 2020 Virology journal Table IV A158E 0 5 32631440 Characterization of neuraminidase inhibitor-resistant influenza virus isolates from immunocompromised patients in the Republic of Korea. F74S 2020 Virology journal Table IV F74S 0 4 32631440 Characterization of neuraminidase inhibitor-resistant influenza virus isolates from immunocompromised patients in the Republic of Korea. H275Y 2020 Virology journal Table IV H275Y 0 5 32631440 Characterization of neuraminidase inhibitor-resistant influenza virus isolates from immunocompromised patients in the Republic of Korea. I29M 2020 Virology journal Table IV I29M 0 4 32631440 Characterization of neuraminidase inhibitor-resistant influenza virus isolates from immunocompromised patients in the Republic of Korea. Q51K 2020 Virology journal Table IV Q51K 0 4 32631440 Characterization of neuraminidase inhibitor-resistant influenza virus isolates from immunocompromised patients in the Republic of Korea. R240Q 2020 Virology journal Table IV R240Q 0 5 32631440 Characterization of neuraminidase inhibitor-resistant influenza virus isolates from immunocompromised patients in the Republic of Korea. T13I 2020 Virology journal Table IV T13I 0 4 32631440 Characterization of neuraminidase inhibitor-resistant influenza virus isolates from immunocompromised patients in the Republic of Korea. T202I 2020 Virology journal Table IV T202I 0 5 32709116 Genetic Characterization of a Novel North American-Origin Avian Influenza A (H6N5) Virus Isolated from Bean Goose of South Korea in 2018. A127N 2020 Viruses Table IV A127N 0 5 32709116 Genetic Characterization of a Novel North American-Origin Avian Influenza A (H6N5) Virus Isolated from Bean Goose of South Korea in 2018. A138S 2020 Viruses Table IV A138S 0 5 32709116 Genetic Characterization of a Novel North American-Origin Avian Influenza A (H6N5) Virus Isolated from Bean Goose of South Korea in 2018. A274T 2020 Viruses Table IV A274T 0 5 32709116 Genetic Characterization of a Novel North American-Origin Avian Influenza A (H6N5) Virus Isolated from Bean Goose of South Korea in 2018. A469T 2020 Viruses Table IV A469T 0 5 32709116 Genetic Characterization of a Novel North American-Origin Avian Influenza A (H6N5) Virus Isolated from Bean Goose of South Korea in 2018. A515T 2020 Viruses Table IV A515T 0 5 32709116 Genetic Characterization of a Novel North American-Origin Avian Influenza A (H6N5) Virus Isolated from Bean Goose of South Korea in 2018. A676T 2020 Viruses Table IV A676T 0 5 32709116 Genetic Characterization of a Novel North American-Origin Avian Influenza A (H6N5) Virus Isolated from Bean Goose of South Korea in 2018. C278Q 2020 Viruses Table IV C278Q 0 5 32709116 Genetic Characterization of a Novel North American-Origin Avian Influenza A (H6N5) Virus Isolated from Bean Goose of South Korea in 2018. D701N 2020 Viruses Table IV D701N 0 5 32709116 Genetic Characterization of a Novel North American-Origin Avian Influenza A (H6N5) Virus Isolated from Bean Goose of South Korea in 2018. E119V 2020 Viruses Table IV E119V 0 5 32709116 Genetic Characterization of a Novel North American-Origin Avian Influenza A (H6N5) Virus Isolated from Bean Goose of South Korea in 2018. E173G/D 2020 Viruses Table IV E173G;E173D 0;0 7;7 32709116 Genetic Characterization of a Novel North American-Origin Avian Influenza A (H6N5) Virus Isolated from Bean Goose of South Korea in 2018. E190D 2020 Viruses Table IV E190D 0 5 32709116 Genetic Characterization of a Novel North American-Origin Avian Influenza A (H6N5) Virus Isolated from Bean Goose of South Korea in 2018. E382D 2020 Viruses Table IV E382D 0 5 32709116 Genetic Characterization of a Novel North American-Origin Avian Influenza A (H6N5) Virus Isolated from Bean Goose of South Korea in 2018. F253I 2020 Viruses Table IV F253I 0 5 32709116 Genetic Characterization of a Novel North American-Origin Avian Influenza A (H6N5) Virus Isolated from Bean Goose of South Korea in 2018. F277S 2020 Viruses Table IV F277S 0 5 32709116 Genetic Characterization of a Novel North American-Origin Avian Influenza A (H6N5) Virus Isolated from Bean Goose of South Korea in 2018. G225D 2020 Viruses Table IV G225D 0 5 32709116 Genetic Characterization of a Novel North American-Origin Avian Influenza A (H6N5) Virus Isolated from Bean Goose of South Korea in 2018. G228S 2020 Viruses Table IV G228S 0 5 32709116 Genetic Characterization of a Novel North American-Origin Avian Influenza A (H6N5) Virus Isolated from Bean Goose of South Korea in 2018. G309D 2020 Viruses Table IV G309D 0 5 32709116 Genetic Characterization of a Novel North American-Origin Avian Influenza A (H6N5) Virus Isolated from Bean Goose of South Korea in 2018. H266R 2020 Viruses Table IV H266R 0 5 32709116 Genetic Characterization of a Novel North American-Origin Avian Influenza A (H6N5) Virus Isolated from Bean Goose of South Korea in 2018. H436Y 2020 Viruses Table IV H436Y 0 5 32709116 Genetic Characterization of a Novel North American-Origin Avian Influenza A (H6N5) Virus Isolated from Bean Goose of South Korea in 2018. H447Q 2020 Viruses Table IV H447Q 0 5 32709116 Genetic Characterization of a Novel North American-Origin Avian Influenza A (H6N5) Virus Isolated from Bean Goose of South Korea in 2018. I353V 2020 Viruses Table IV I353V 0 5 32709116 Genetic Characterization of a Novel North American-Origin Avian Influenza A (H6N5) Virus Isolated from Bean Goose of South Korea in 2018. I495V 2020 Viruses Table IV I495V 0 5 32709116 Genetic Characterization of a Novel North American-Origin Avian Influenza A (H6N5) Virus Isolated from Bean Goose of South Korea in 2018. K251R 2020 Viruses Table IV K251R 0 5 32709116 Genetic Characterization of a Novel North American-Origin Avian Influenza A (H6N5) Virus Isolated from Bean Goose of South Korea in 2018. K328N 2020 Viruses Table IV K328N 0 5 32709116 Genetic Characterization of a Novel North American-Origin Avian Influenza A (H6N5) Virus Isolated from Bean Goose of South Korea in 2018. L102F 2020 Viruses Table IV L102F 0 5 32709116 Genetic Characterization of a Novel North American-Origin Avian Influenza A (H6N5) Virus Isolated from Bean Goose of South Korea in 2018. L13P 2020 Viruses Table IV L13P 0 4 32709116 Genetic Characterization of a Novel North American-Origin Avian Influenza A (H6N5) Virus Isolated from Bean Goose of South Korea in 2018. L473V 2020 Viruses Table IV L473V 0 5 32709116 Genetic Characterization of a Novel North American-Origin Avian Influenza A (H6N5) Virus Isolated from Bean Goose of South Korea in 2018. L653P 2020 Viruses Table IV L653P 0 5 32709116 Genetic Characterization of a Novel North American-Origin Avian Influenza A (H6N5) Virus Isolated from Bean Goose of South Korea in 2018. L89V 2020 Viruses Table IV L89V 0 4 32709116 Genetic Characterization of a Novel North American-Origin Avian Influenza A (H6N5) Virus Isolated from Bean Goose of South Korea in 2018. M677T 2020 Viruses Table IV M677T 0 5 32709116 Genetic Characterization of a Novel North American-Origin Avian Influenza A (H6N5) Virus Isolated from Bean Goose of South Korea in 2018. N205K 2020 Viruses Table IV N205K 0 5 32709116 Genetic Characterization of a Novel North American-Origin Avian Influenza A (H6N5) Virus Isolated from Bean Goose of South Korea in 2018. N30D 2020 Viruses Table IV N30D 0 4 32709116 Genetic Characterization of a Novel North American-Origin Avian Influenza A (H6N5) Virus Isolated from Bean Goose of South Korea in 2018. N379T 2020 Viruses Table IV N379T 0 5 32709116 Genetic Characterization of a Novel North American-Origin Avian Influenza A (H6N5) Virus Isolated from Bean Goose of South Korea in 2018. N66S 2020 Viruses Table IV N66S 0 4 32709116 Genetic Characterization of a Novel North American-Origin Avian Influenza A (H6N5) Virus Isolated from Bean Goose of South Korea in 2018. P42S 2020 Viruses Table IV P42S 0 4 32709116 Genetic Characterization of a Novel North American-Origin Avian Influenza A (H6N5) Virus Isolated from Bean Goose of South Korea in 2018. Q226L 2020 Viruses Table IV Q226L 0 5 32709116 Genetic Characterization of a Novel North American-Origin Avian Influenza A (H6N5) Virus Isolated from Bean Goose of South Korea in 2018. Q368R 2020 Viruses Table IV Q368R 0 5 32709116 Genetic Characterization of a Novel North American-Origin Avian Influenza A (H6N5) Virus Isolated from Bean Goose of South Korea in 2018. R207K 2020 Viruses Table IV R207K 0 5 32709116 Genetic Characterization of a Novel North American-Origin Avian Influenza A (H6N5) Virus Isolated from Bean Goose of South Korea in 2018. R477G 2020 Viruses Table IV R477G 0 5 32709116 Genetic Characterization of a Novel North American-Origin Avian Influenza A (H6N5) Virus Isolated from Bean Goose of South Korea in 2018. S375N/T 2020 Viruses Table IV S375N;S375T 0;0 7;7 32709116 Genetic Characterization of a Novel North American-Origin Avian Influenza A (H6N5) Virus Isolated from Bean Goose of South Korea in 2018. S37A 2020 Viruses Table IV S37A 0 4 32709116 Genetic Characterization of a Novel North American-Origin Avian Influenza A (H6N5) Virus Isolated from Bean Goose of South Korea in 2018. T215A 2020 Viruses Table IV T215A 0 5 32709116 Genetic Characterization of a Novel North American-Origin Avian Influenza A (H6N5) Virus Isolated from Bean Goose of South Korea in 2018. T339K 2020 Viruses Table IV T339K 0 5 32709116 Genetic Characterization of a Novel North American-Origin Avian Influenza A (H6N5) Virus Isolated from Bean Goose of South Korea in 2018. T48N 2020 Viruses Table IV T48N 0 4 32709116 Genetic Characterization of a Novel North American-Origin Avian Influenza A (H6N5) Virus Isolated from Bean Goose of South Korea in 2018. T63I 2020 Viruses Table IV T63I 0 4 32709116 Genetic Characterization of a Novel North American-Origin Avian Influenza A (H6N5) Virus Isolated from Bean Goose of South Korea in 2018. V105M 2020 Viruses Table IV V105M 0 5 32709116 Genetic Characterization of a Novel North American-Origin Avian Influenza A (H6N5) Virus Isolated from Bean Goose of South Korea in 2018. V149A 2020 Viruses Table IV V149A 0 5 32709116 Genetic Characterization of a Novel North American-Origin Avian Influenza A (H6N5) Virus Isolated from Bean Goose of South Korea in 2018. V41I 2020 Viruses Table IV V41I 0 4 32709116 Genetic Characterization of a Novel North American-Origin Avian Influenza A (H6N5) Virus Isolated from Bean Goose of South Korea in 2018. V652A 2020 Viruses Table IV V652A 0 5 32750468 Functional neuraminidase inhibitor resistance motifs in avian influenza A(H5Nx) viruses. E119D 2020 Antiviral research Table IV E119D 0 5 32750468 Functional neuraminidase inhibitor resistance motifs in avian influenza A(H5Nx) viruses. E119Q 2020 Antiviral research Table IV E119Q 0 5 32750468 Functional neuraminidase inhibitor resistance motifs in avian influenza A(H5Nx) viruses. E119V 2020 Antiviral research Table IV E119V 0 5 32750468 Functional neuraminidase inhibitor resistance motifs in avian influenza A(H5Nx) viruses. E119V/D 2020 Antiviral research Table IV E119V;E119D 0;0 7;7 32750468 Functional neuraminidase inhibitor resistance motifs in avian influenza A(H5Nx) viruses. H274R 2020 Antiviral research Table IV H274R 0 5 32750468 Functional neuraminidase inhibitor resistance motifs in avian influenza A(H5Nx) viruses. H274Y 2020 Antiviral research Table IV H274Y 0 5 32750468 Functional neuraminidase inhibitor resistance motifs in avian influenza A(H5Nx) viruses. N294S 2020 Antiviral research Table IV N294S 0 5 32750468 Functional neuraminidase inhibitor resistance motifs in avian influenza A(H5Nx) viruses. R292K 2020 Antiviral research Table IV R292K 0 5 33024040 Structure-Based Modification of an Anti-neuraminidase Human Antibody Restores Protection Efficacy against the Drifted Influenza Virus. D102R 2020 mBio Table IV D102R 0 5 33099886 Comprehensive assessment of amino acid substitutions in the trimeric RNA polymerase complex of influenza A virus detected in clinical trials of baloxavir marboxil. I38F 2021 Influenza and other respiratory viruses Table IV I38F 0 4 33099886 Comprehensive assessment of amino acid substitutions in the trimeric RNA polymerase complex of influenza A virus detected in clinical trials of baloxavir marboxil. I38L 2021 Influenza and other respiratory viruses Table IV I38L 0 4 33099886 Comprehensive assessment of amino acid substitutions in the trimeric RNA polymerase complex of influenza A virus detected in clinical trials of baloxavir marboxil. I38M 2021 Influenza and other respiratory viruses Table IV I38M 0 4 33099886 Comprehensive assessment of amino acid substitutions in the trimeric RNA polymerase complex of influenza A virus detected in clinical trials of baloxavir marboxil. I38N 2021 Influenza and other respiratory viruses Table IV I38N 0 4 33099886 Comprehensive assessment of amino acid substitutions in the trimeric RNA polymerase complex of influenza A virus detected in clinical trials of baloxavir marboxil. I38R 2021 Influenza and other respiratory viruses Table IV I38R 0 4 33099886 Comprehensive assessment of amino acid substitutions in the trimeric RNA polymerase complex of influenza A virus detected in clinical trials of baloxavir marboxil. I38S 2021 Influenza and other respiratory viruses Table IV I38S 0 4 33099886 Comprehensive assessment of amino acid substitutions in the trimeric RNA polymerase complex of influenza A virus detected in clinical trials of baloxavir marboxil. I38T 2021 Influenza and other respiratory viruses Table IV I38T 0 4 33099886 Comprehensive assessment of amino acid substitutions in the trimeric RNA polymerase complex of influenza A virus detected in clinical trials of baloxavir marboxil. I38V 2021 Influenza and other respiratory viruses Table IV I38V 0 4 33281788 Altering Intracellular Localization of the RNA Interference Factors by Influenza A Virus Non-structural Protein 1. A155T 2020 Frontiers in microbiology Table IV A155T 0 5 33281788 Altering Intracellular Localization of the RNA Interference Factors by Influenza A Virus Non-structural Protein 1. D101H 2020 Frontiers in microbiology Table IV D101H 0 5 33281788 Altering Intracellular Localization of the RNA Interference Factors by Influenza A Virus Non-structural Protein 1. D189N 2020 Frontiers in microbiology Table IV D189N 0 5 33424035 The Effect of I155T, K156Q, K156E and N186K Mutations in Hemagglutinin on the Virulence and Reproduction of Influenza A/H5N1 Viruses. I155T 2020 Molecular biology Table IV I155T 0 5 33424035 The Effect of I155T, K156Q, K156E and N186K Mutations in Hemagglutinin on the Virulence and Reproduction of Influenza A/H5N1 Viruses. K156E 2020 Molecular biology Table IV K156E 0 5 33424035 The Effect of I155T, K156Q, K156E and N186K Mutations in Hemagglutinin on the Virulence and Reproduction of Influenza A/H5N1 Viruses. K156Q 2020 Molecular biology Table IV K156Q 0 5 33424035 The Effect of I155T, K156Q, K156E and N186K Mutations in Hemagglutinin on the Virulence and Reproduction of Influenza A/H5N1 Viruses. N186K 2020 Molecular biology Table IV N186K 0 5 33424035 The Effect of I155T, K156Q, K156E and N186K Mutations in Hemagglutinin on the Virulence and Reproduction of Influenza A/H5N1 Viruses. V138A 2020 Molecular biology Table IV V138A 0 5 33518109 Characterization of the low-pathogenic H7N7 avian influenza virus in Shanghai, China. E190D 2021 Poultry science Table IV E190D 0 5 33518109 Characterization of the low-pathogenic H7N7 avian influenza virus in Shanghai, China. E276D 2021 Poultry science Table IV E276D 0 5 33518109 Characterization of the low-pathogenic H7N7 avian influenza virus in Shanghai, China. G228S 2021 Poultry science Table IV G228S 0 5 33518109 Characterization of the low-pathogenic H7N7 avian influenza virus in Shanghai, China. H99Y 2021 Poultry science Table IV H99Y 0 4 33518109 Characterization of the low-pathogenic H7N7 avian influenza virus in Shanghai, China. N30D 2021 Poultry science Table IV N30D 0 4 33518109 Characterization of the low-pathogenic H7N7 avian influenza virus in Shanghai, China. N383D 2021 Poultry science Table IV N383D 0 5 33518109 Characterization of the low-pathogenic H7N7 avian influenza virus in Shanghai, China. P42S 2021 Poultry science Table IV P42S 0 4 33518109 Characterization of the low-pathogenic H7N7 avian influenza virus in Shanghai, China. R118I 2021 Poultry science Table IV R118I 0 5 33518109 Characterization of the low-pathogenic H7N7 avian influenza virus in Shanghai, China. S224P 2021 Poultry science Table IV S224P 0 5 33518109 Characterization of the low-pathogenic H7N7 avian influenza virus in Shanghai, China. T136S 2021 Poultry science Table IV T136S 0 5 33518109 Characterization of the low-pathogenic H7N7 avian influenza virus in Shanghai, China. V15I 2021 Poultry science Table IV V15I 0 4 33568453 Identification and Characterization of Novel Antibody Epitopes on the N2 Neuraminidase. A272D 2021 mSphere Table IV A272D 0 5 33568453 Identification and Characterization of Novel Antibody Epitopes on the N2 Neuraminidase. D101G 2021 mSphere Table IV D101G 0 5 33568453 Identification and Characterization of Novel Antibody Epitopes on the N2 Neuraminidase. D339N 2021 mSphere Table IV D339N 0 5 33568453 Identification and Characterization of Novel Antibody Epitopes on the N2 Neuraminidase. E258K 2021 mSphere Table IV E258K 0 5 33568453 Identification and Characterization of Novel Antibody Epitopes on the N2 Neuraminidase. E623G 2021 mSphere Table IV E623G 0 5 33568453 Identification and Characterization of Novel Antibody Epitopes on the N2 Neuraminidase. G102R 2021 mSphere Table IV G102R 0 5 33568453 Identification and Characterization of Novel Antibody Epitopes on the N2 Neuraminidase. G349R 2021 mSphere Table IV G349R 0 5 33568453 Identification and Characterization of Novel Antibody Epitopes on the N2 Neuraminidase. H172R 2021 mSphere Table IV H172R 0 5 33568453 Identification and Characterization of Novel Antibody Epitopes on the N2 Neuraminidase. I380V 2021 mSphere Table IV I380V 0 5 33568453 Identification and Characterization of Novel Antibody Epitopes on the N2 Neuraminidase. K199E 2021 mSphere Table IV K199E 0 5 33568453 Identification and Characterization of Novel Antibody Epitopes on the N2 Neuraminidase. K199T 2021 mSphere Table IV K199T 0 5 33568453 Identification and Characterization of Novel Antibody Epitopes on the N2 Neuraminidase. L109F 2021 mSphere Table IV L109F 0 5 33568453 Identification and Characterization of Novel Antibody Epitopes on the N2 Neuraminidase. L338F 2021 mSphere Table IV L338F 0 5 33568453 Identification and Characterization of Novel Antibody Epitopes on the N2 Neuraminidase. N262T 2021 mSphere Table IV N262T 0 5 33568453 Identification and Characterization of Novel Antibody Epitopes on the N2 Neuraminidase. N290D 2021 mSphere Table IV N290D 0 5 33568453 Identification and Characterization of Novel Antibody Epitopes on the N2 Neuraminidase. N329S 2021 mSphere Table IV N329S 0 5 33568453 Identification and Characterization of Novel Antibody Epitopes on the N2 Neuraminidase. P468H 2021 mSphere Table IV P468H 0 5 33568453 Identification and Characterization of Novel Antibody Epitopes on the N2 Neuraminidase. R222H 2021 mSphere Table IV R222H 0 5 33568453 Identification and Characterization of Novel Antibody Epitopes on the N2 Neuraminidase. S161N 2021 mSphere Table IV S161N 0 5 33568453 Identification and Characterization of Novel Antibody Epitopes on the N2 Neuraminidase. S245N 2021 mSphere Table IV S245N 0 5 33568453 Identification and Characterization of Novel Antibody Epitopes on the N2 Neuraminidase. S247T 2021 mSphere Table IV S247T 0 5 33568453 Identification and Characterization of Novel Antibody Epitopes on the N2 Neuraminidase. S331N 2021 mSphere Table IV S331N 0 5 33568453 Identification and Characterization of Novel Antibody Epitopes on the N2 Neuraminidase. T267K 2021 mSphere Table IV T267K 0 5 33568453 Identification and Characterization of Novel Antibody Epitopes on the N2 Neuraminidase. T392I 2021 mSphere Table IV T392I 0 5 33568453 Identification and Characterization of Novel Antibody Epitopes on the N2 Neuraminidase. Y235S 2021 mSphere Table IV Y235S 0 5 33568453 Identification and Characterization of Novel Antibody Epitopes on the N2 Neuraminidase. Y239F 2021 mSphere Table IV Y239F 0 5 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. D222G/N 2021 PloS one Table IV D222G;D222N 0;0 7;7 33975931 Analysis of the Evolution of Pandemic Influenza A(H1N1) Virus Neuraminidase Reveals Entanglement of Different Phenotypic Characteristics. I106V 2021 mBio Table IV I106V 0 5 33975931 Analysis of the Evolution of Pandemic Influenza A(H1N1) Virus Neuraminidase Reveals Entanglement of Different Phenotypic Characteristics. I314M 2021 mBio Table IV I314M 0 5 33975931 Analysis of the Evolution of Pandemic Influenza A(H1N1) Virus Neuraminidase Reveals Entanglement of Different Phenotypic Characteristics. I321V 2021 mBio Table IV I321V 0 5 33975931 Analysis of the Evolution of Pandemic Influenza A(H1N1) Virus Neuraminidase Reveals Entanglement of Different Phenotypic Characteristics. K432E 2021 mBio Table IV K432E 0 5 33975931 Analysis of the Evolution of Pandemic Influenza A(H1N1) Virus Neuraminidase Reveals Entanglement of Different Phenotypic Characteristics. N200S 2021 mBio Table IV N200S 0 5 33975931 Analysis of the Evolution of Pandemic Influenza A(H1N1) Virus Neuraminidase Reveals Entanglement of Different Phenotypic Characteristics. N248D 2021 mBio Table IV N248D 0 5 33975931 Analysis of the Evolution of Pandemic Influenza A(H1N1) Virus Neuraminidase Reveals Entanglement of Different Phenotypic Characteristics. N270K 2021 mBio Table IV N270K 0 5 33975931 Analysis of the Evolution of Pandemic Influenza A(H1N1) Virus Neuraminidase Reveals Entanglement of Different Phenotypic Characteristics. N369K 2021 mBio Table IV N369K 0 5 33975931 Analysis of the Evolution of Pandemic Influenza A(H1N1) Virus Neuraminidase Reveals Entanglement of Different Phenotypic Characteristics. N386K 2021 mBio Table IV N386K 0 5 33975931 Analysis of the Evolution of Pandemic Influenza A(H1N1) Virus Neuraminidase Reveals Entanglement of Different Phenotypic Characteristics. N44S 2021 mBio Table IV N44S 0 4 33975931 Analysis of the Evolution of Pandemic Influenza A(H1N1) Virus Neuraminidase Reveals Entanglement of Different Phenotypic Characteristics. V106I 2021 mBio Table IV V106I 0 5 33975931 Analysis of the Evolution of Pandemic Influenza A(H1N1) Virus Neuraminidase Reveals Entanglement of Different Phenotypic Characteristics. V241I 2021 mBio Table IV V241I 0 5 33975931 Analysis of the Evolution of Pandemic Influenza A(H1N1) Virus Neuraminidase Reveals Entanglement of Different Phenotypic Characteristics. V264I 2021 mBio Table IV V264I 0 5 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. H274Y 2021 PeerJ Table IV H274Y 0 5 34194404 Host Adaptive Evolution of Avian-Origin H3N2 Canine Influenza Virus. A661T 2021 Frontiers in microbiology Table IV A661T 0 5 34194404 Host Adaptive Evolution of Avian-Origin H3N2 Canine Influenza Virus. C241Y 2021 Frontiers in microbiology Table IV C241Y 0 5 34194404 Host Adaptive Evolution of Avian-Origin H3N2 Canine Influenza Virus. D27G 2021 Frontiers in microbiology Table IV D27G 0 4 34194404 Host Adaptive Evolution of Avian-Origin H3N2 Canine Influenza Virus. D313N 2021 Frontiers in microbiology Table IV D313N 0 5 34194404 Host Adaptive Evolution of Avian-Origin H3N2 Canine Influenza Virus. E227K 2021 Frontiers in microbiology Table IV E227K 0 5 34194404 Host Adaptive Evolution of Avian-Origin H3N2 Canine Influenza Virus. E227R 2021 Frontiers in microbiology Table IV E227R 0 5 34194404 Host Adaptive Evolution of Avian-Origin H3N2 Canine Influenza Virus. E243D 2021 Frontiers in microbiology Table IV E243D 0 5 34194404 Host Adaptive Evolution of Avian-Origin H3N2 Canine Influenza Virus. E357D 2021 Frontiers in microbiology Table IV E357D 0 5 34194404 Host Adaptive Evolution of Avian-Origin H3N2 Canine Influenza Virus. E97K 2021 Frontiers in microbiology Table IV E97K 0 4 34194404 Host Adaptive Evolution of Avian-Origin H3N2 Canine Influenza Virus. G146S 2021 Frontiers in microbiology Table IV G146S 0 5 34194404 Host Adaptive Evolution of Avian-Origin H3N2 Canine Influenza Virus. G14E 2021 Frontiers in microbiology Table IV G14E 0 4 34194404 Host Adaptive Evolution of Avian-Origin H3N2 Canine Influenza Virus. G590S 2021 Frontiers in microbiology Table IV G590S 0 5 34194404 Host Adaptive Evolution of Avian-Origin H3N2 Canine Influenza Virus. G684E 2021 Frontiers in microbiology Table IV G684E 0 5 34194404 Host Adaptive Evolution of Avian-Origin H3N2 Canine Influenza Virus. H155Y 2021 Frontiers in microbiology Table IV H155Y 0 5 34194404 Host Adaptive Evolution of Avian-Origin H3N2 Canine Influenza Virus. I153T 2021 Frontiers in microbiology Table IV I153T 0 5 34194404 Host Adaptive Evolution of Avian-Origin H3N2 Canine Influenza Virus. I25M 2021 Frontiers in microbiology Table IV I25M 0 4 34194404 Host Adaptive Evolution of Avian-Origin H3N2 Canine Influenza Virus. I292T 2021 Frontiers in microbiology Table IV I292T 0 5 34194404 Host Adaptive Evolution of Avian-Origin H3N2 Canine Influenza Virus. K251R 2021 Frontiers in microbiology Table IV K251R 0 5 34194404 Host Adaptive Evolution of Avian-Origin H3N2 Canine Influenza Virus. K326R 2021 Frontiers in microbiology Table IV K326R 0 5 34194404 Host Adaptive Evolution of Avian-Origin H3N2 Canine Influenza Virus. L390S 2021 Frontiers in microbiology Table IV L390S 0 5 34194404 Host Adaptive Evolution of Avian-Origin H3N2 Canine Influenza Virus. L40F 2021 Frontiers in microbiology Table IV L40F 0 4 34194404 Host Adaptive Evolution of Avian-Origin H3N2 Canine Influenza Virus. M76I 2021 Frontiers in microbiology Table IV M76I 0 4 34194404 Host Adaptive Evolution of Avian-Origin H3N2 Canine Influenza Virus. N188D 2021 Frontiers in microbiology Table IV N188D 0 5 34194404 Host Adaptive Evolution of Avian-Origin H3N2 Canine Influenza Virus. N347D 2021 Frontiers in microbiology Table IV N347D 0 5 34194404 Host Adaptive Evolution of Avian-Origin H3N2 Canine Influenza Virus. P212S 2021 Frontiers in microbiology Table IV P212S 0 5 34194404 Host Adaptive Evolution of Avian-Origin H3N2 Canine Influenza Virus. R187K 2021 Frontiers in microbiology Table IV R187K 0 5 34194404 Host Adaptive Evolution of Avian-Origin H3N2 Canine Influenza Virus. R18K 2021 Frontiers in microbiology Table IV R18K 0 4 34194404 Host Adaptive Evolution of Avian-Origin H3N2 Canine Influenza Virus. R261H 2021 Frontiers in microbiology Table IV R261H 0 5 34194404 Host Adaptive Evolution of Avian-Origin H3N2 Canine Influenza Virus. R283Q 2021 Frontiers in microbiology Table IV R283Q 0 5 34194404 Host Adaptive Evolution of Avian-Origin H3N2 Canine Influenza Virus. R338K 2021 Frontiers in microbiology Table IV R338K 0 5 34194404 Host Adaptive Evolution of Avian-Origin H3N2 Canine Influenza Virus. R401K 2021 Frontiers in microbiology Table IV R401K 0 5 34194404 Host Adaptive Evolution of Avian-Origin H3N2 Canine Influenza Virus. R95K 2021 Frontiers in microbiology Table IV R95K 0 4 34194404 Host Adaptive Evolution of Avian-Origin H3N2 Canine Influenza Virus. S146G 2021 Frontiers in microbiology Table IV S146G 0 5 34194404 Host Adaptive Evolution of Avian-Origin H3N2 Canine Influenza Virus. S188N 2021 Frontiers in microbiology Table IV S188N 0 5 34194404 Host Adaptive Evolution of Avian-Origin H3N2 Canine Influenza Virus. S207N 2021 Frontiers in microbiology Table IV S207N 0 5 34194404 Host Adaptive Evolution of Avian-Origin H3N2 Canine Influenza Virus. S216N 2021 Frontiers in microbiology Table IV S216N 0 5 34194404 Host Adaptive Evolution of Avian-Origin H3N2 Canine Influenza Virus. S311N 2021 Frontiers in microbiology Table IV S311N 0 5 34194404 Host Adaptive Evolution of Avian-Origin H3N2 Canine Influenza Virus. S334N 2021 Frontiers in microbiology Table IV S334N 0 5 34194404 Host Adaptive Evolution of Avian-Origin H3N2 Canine Influenza Virus. S388G 2021 Frontiers in microbiology Table IV S388G 0 5 34194404 Host Adaptive Evolution of Avian-Origin H3N2 Canine Influenza Virus. S714I 2021 Frontiers in microbiology Table IV S714I 0 5 34194404 Host Adaptive Evolution of Avian-Origin H3N2 Canine Influenza Virus. S714R 2021 Frontiers in microbiology Table IV S714R 0 5 34194404 Host Adaptive Evolution of Avian-Origin H3N2 Canine Influenza Virus. T16A 2021 Frontiers in microbiology Table IV T16A 0 4 34194404 Host Adaptive Evolution of Avian-Origin H3N2 Canine Influenza Virus. T197I 2021 Frontiers in microbiology Table IV T197I 0 5 34194404 Host Adaptive Evolution of Avian-Origin H3N2 Canine Influenza Virus. T434S 2021 Frontiers in microbiology Table IV T434S 0 5 34194404 Host Adaptive Evolution of Avian-Origin H3N2 Canine Influenza Virus. T598A 2021 Frontiers in microbiology Table IV T598A 0 5 34194404 Host Adaptive Evolution of Avian-Origin H3N2 Canine Influenza Virus. V15I 2021 Frontiers in microbiology Table IV V15I 0 4 34194404 Host Adaptive Evolution of Avian-Origin H3N2 Canine Influenza Virus. V200I 2021 Frontiers in microbiology Table IV V200I 0 5 34194404 Host Adaptive Evolution of Avian-Origin H3N2 Canine Influenza Virus. V218I 2021 Frontiers in microbiology Table IV V218I 0 5 34194404 Host Adaptive Evolution of Avian-Origin H3N2 Canine Influenza Virus. V242I 2021 Frontiers in microbiology Table IV V242I 0 5 34194404 Host Adaptive Evolution of Avian-Origin H3N2 Canine Influenza Virus. V263T 2021 Frontiers in microbiology Table IV V263T 0 5 34194404 Host Adaptive Evolution of Avian-Origin H3N2 Canine Influenza Virus. V27I 2021 Frontiers in microbiology Table IV V27I 0 4 34194404 Host Adaptive Evolution of Avian-Origin H3N2 Canine Influenza Virus. V338I 2021 Frontiers in microbiology Table IV V338I 0 5 34194404 Host Adaptive Evolution of Avian-Origin H3N2 Canine Influenza Virus. V418I 2021 Frontiers in microbiology Table IV V418I 0 5 34194404 Host Adaptive Evolution of Avian-Origin H3N2 Canine Influenza Virus. V50I 2021 Frontiers in microbiology Table IV V50I 0 4 34194404 Host Adaptive Evolution of Avian-Origin H3N2 Canine Influenza Virus. V511I 2021 Frontiers in microbiology Table IV V511I 0 5 34194404 Host Adaptive Evolution of Avian-Origin H3N2 Canine Influenza Virus. Y65H 2021 Frontiers in microbiology Table IV Y65H 0 4 34194404 Host Adaptive Evolution of Avian-Origin H3N2 Canine Influenza Virus. Y67H 2021 Frontiers in microbiology Table IV Y67H 0 4 17922571 A single mutation in the PB1-F2 of H5N1 (HK/97) and 1918 influenza A viruses contributes to increased virulence. (A) MDCK cells were inoculated at an MOI of 0.1 and 0.001, and virus growth of WH and WH N66S was assessed at the time points indicated. 2007 PLoS pathogens Figure IV N66S 89 93 17922571 A single mutation in the PB1-F2 of H5N1 (HK/97) and 1918 influenza A viruses contributes to increased virulence. (B) Eight mice were inoculated with recombinant 1918 S66N virus at 102,103, 104, 105, or 106 PFU, and their weights were measured every other day. 2007 PLoS pathogens Figure IV S66N 53 57 17922571 A single mutation in the PB1-F2 of H5N1 (HK/97) and 1918 influenza A viruses contributes to increased virulence. (B) MDCK cells were inoculated at an MOI of .01 and .001, and virus growth of r1918 and r1918 S66N was assessed at the time points indicated. 2007 PLoS pathogens Figure IV S66N 94 98 17922571 A single mutation in the PB1-F2 of H5N1 (HK/97) and 1918 influenza A viruses contributes to increased virulence. (B) Virus titers from lung homogenates were measured from mice infected with WH or WH N66S virus at days 1, 2, 3, 5, 7, and 8 after inoculation. 2007 PLoS pathogens Figure IV N66S 86 90 17922571 A single mutation in the PB1-F2 of H5N1 (HK/97) and 1918 influenza A viruses contributes to increased virulence. (C) Effect of S66N mutation on mouse lung titers in r1918 virus. 2007 PLoS pathogens Figure IV S66N 14 18 17922571 A single mutation in the PB1-F2 of H5N1 (HK/97) and 1918 influenza A viruses contributes to increased virulence. Alignment and Location of N66S Mutation in the PB1-F2 Protein. 2007 PLoS pathogens Figure IV N66S 26 30 PB1F2 47 53 17922571 A single mutation in the PB1-F2 of H5N1 (HK/97) and 1918 influenza A viruses contributes to increased virulence. Contribution of PB1-F2 N66S Mutation to Pathogenicity of Recombinant Virus. 2007 PLoS pathogens Figure IV N66S 23 27 PB1F2 16 22 17922571 A single mutation in the PB1-F2 of H5N1 (HK/97) and 1918 influenza A viruses contributes to increased virulence. The Effect of the S66N Mutation on Pathogenicity in Mice. 2007 PLoS pathogens Figure IV S66N 18 22 17922571 A single mutation in the PB1-F2 of H5N1 (HK/97) and 1918 influenza A viruses contributes to increased virulence. Virus titers from lung homogenates were measured from 3 mice infected per time point with r1918 or r1918 S66N virus at days 1, 2, 3, 6, 7, and 8 after inoculation. 2007 PLoS pathogens Figure IV S66N 105 109 18248089 Interaction of polymerase subunit PB2 and NP with importin alpha1 is a determinant of host range of influenza A virus. 293T cells were transfected with plasmids encoding SC35-PB2 (30 mug), SC35M-PB2 (30 mug), and SC35-PB2 D701N (30 mug) (A) and SC35-NP (10 mug) and SC35M-NP (10 mug) (B) proteins. 2008 PLoS pathogens Figure IV D701N 103 108 NP;NP;PB2;PB2;PB2 131;153;56;76;99 133;155;59;79;102 18248089 Interaction of polymerase subunit PB2 and NP with importin alpha1 is a determinant of host range of influenza A virus. CEC-32 cells were transfected with plasmids encoding SC35-PB2 (30 mug), SC35M-PB2 (30 mug), and SC35-PB2 D701N (30 mug) (A) and SC35-NP (10 mug) and SC35M-NP (10 mug) (B) proteins. 2008 PLoS pathogens Figure IV D701N 105 110 NP;NP;PB2;PB2;PB2 133;155;58;78;101 135;157;61;81;104 18404209 Human-like receptor specificity does not affect the neuraminidase-inhibitor susceptibility of H5N1 influenza viruses. * P<0.01 compared to wild-type rgVN1203 virus (one-way ANOVA performed for all viruses); P<0.01 compared to virus carrying only the NA H274Y substitution (one-way ANOVA performed for viruses carrying the H274Y NA mutation). 2008 PLoS pathogens Figure IV H274Y;H274Y 136;205 141;210 NA;NA 133;211 135;213 18404209 Human-like receptor specificity does not affect the neuraminidase-inhibitor susceptibility of H5N1 influenza viruses. * P<0.01 compared to wild-type rgVN1203 virus, one-way ANOVA test performed for all viruses; P<0.01 compared to H274Y virus, one-way ANOVA test performed for viruses carrying the H274Y NA mutation. 2008 PLoS pathogens Figure IV H274Y;H274Y 113;180 118;185 186 188 18601954 Treatment of influenza A (H1N1) virus infections in mice and ferrets with cyanovirin-N. treatment with CV-N and ribavirin on mean body weights during a lethal influenza A/WSN/33 HAnc-Asp225Gly (H1N1) virus infection in mice. 2008 Antiviral research Figure IV D225G;H225G;A225G;N225G;C225G 95;95;95;95;95 104;104;104;104;104 18769709 Host determinant residue lysine 627 lies on the surface of a discrete, folded domain of influenza virus polymerase PB2 subunit. Effect of the K627E mutation on the electrostatic surface of the 627-domain. 2008 PLoS pathogens Figure IV K627E 14 19 18769709 Host determinant residue lysine 627 lies on the surface of a discrete, folded domain of influenza virus polymerase PB2 subunit. The maps reveal that the K627E substitution disrupts a prominent basic surface patch which also includes residues Lys586, Arg589, Arg597, Arg630 and Arg646. 2008 PLoS pathogens Figure IV K627E 25 30 19014974 Aurintricarboxylic acid inhibits influenza virus neuraminidase. Effects of ATA on wild-type and mutant H274Y NA activity. 2009 Antiviral research Figure IV H274Y 39 44 45 47 19331731 Oseltamivir-resistant influenza virus A (H1N1), Europe, 2007-08 season. Sequences of oseltamivir-resistant viruses, possessing the H275Y (H274Y in N2 numbering) mutation are in boldface; vaccine strains are in italics. 2009 Emerging infectious diseases Figure IV H275Y;H274Y 59;66 64;71 19394063 The origin and global emergence of adamantane resistant A/H3N2 influenza viruses. In addition, isolates bearing the S31N mutation are shaded in red. 2009 Virology Figure IV S31N 34 38 19394063 The origin and global emergence of adamantane resistant A/H3N2 influenza viruses. Independent introductions of the S31N replacement are numbered #1 - #11. 2009 Virology Figure IV S31N 33 37 19436701 Avian Influenza virus glycoproteins restrict virus replication and spread through human airway epithelium at temperatures of the proximal airways. Multi-step growth kinetics in HAE inoculated with (Ai) PB2 polymerase mutant (K627E), (Bi) HA (L226Q, S228G) mutant, (Ci) Vic+Chick N1 reassortant virus, (Di) Vic (226-228)HA+Chick N1 at 32 C (solid line, closed circles) or 37 C (solid line, open circles). 2009 PLoS pathogens Figure IV K627E;L226Q;S228G 78;95;102 83;100;107 HA;HA;PB2 91;172;55 93;174;58 19454348 Influenza A virus NS1 targets the ubiquitin ligase TRIM25 to evade recognition by the host viral RNA sensor RIG-I. (A)At 48 h post-transfection of HEK293T with vector, V5-TRIM25 or TRIM25-B-boxes/CCD together with NS1 WT, R38A/K41A, or E96A/E97A, WCLs were subjected to IP with alpha-V5 followed by IB with alpha-NS1 or alpha-V5. 2009 Cell host & microbe Figure IV R38A;K41A;E96A;E97A 107;112;121;126 111;116;125;130 NS1;NS1 99;198 102;201 19454348 Influenza A virus NS1 targets the ubiquitin ligase TRIM25 to evade recognition by the host viral RNA sensor RIG-I. (A)Whole cell lysates (WCLs) of HEK293T cells transfected with GST-RIG-I 2CARD together with vector, NS1, V5-VP35 or V5-E3L were subjected to GST-pulldown (GST-PD) followed by immunoblotting (IB) with alpha-GST or alpha-Ub. 2009 Cell host & microbe Figure IV E3L 120 123 NS1 101 104 19454348 Influenza A virus NS1 targets the ubiquitin ligase TRIM25 to evade recognition by the host viral RNA sensor RIG-I. (B) After transfection with GST or GST-RIG-I 2CARD together with vector, NS1 WT, R38A/K41A, or E96A/E97A, WCLs were used for GST-PD followed by IB with alpha-GST or alpha-Ub (upper two panels). 2009 Cell host & microbe Figure IV R38A;K41A;E96A;E97A 81;86;95;100 85;90;99;104 NS1 73 76 19454348 Influenza A virus NS1 targets the ubiquitin ligase TRIM25 to evade recognition by the host viral RNA sensor RIG-I. (D) HEK293T were transfected with GST or GST-RIG-I 2CARD together with vector or increasing amount of NS1 WT, R38A/K41A, or E96A/E97A as well as IFN-beta-luciferase and pGK-beta-gal. 2009 Cell host & microbe Figure IV R38A;K41A;E96A;E97A 110;115;124;129 114;119;128;133 NS1 102 105 19454348 Influenza A virus NS1 targets the ubiquitin ligase TRIM25 to evade recognition by the host viral RNA sensor RIG-I. (E) At 48 h post-transfection with vector, TRIM25-Flag, TRIM25-V5 and increasing amount NS1 WT, R38A/K41A, or E96A/E97A, HEK293T WCLs were subjected to IP with alpha-Flag followed by IB with alpha-V5 or alpha-Flag. 2009 Cell host & microbe Figure IV R38A;K41A;E96A;E97A 96;101;110;115 100;105;114;119 NS1 88 91 19454348 Influenza A virus NS1 targets the ubiquitin ligase TRIM25 to evade recognition by the host viral RNA sensor RIG-I. Inhibition of TRIM25-mediated RIG-I signaling by WT NS1 but not E96A/E97A and R38A/K41A NS1 mutants. 2009 Cell host & microbe Figure IV E96A;E97A;R38A;K41A 64;69;78;83 68;73;82;87 NS1;NS1 52;88 55;91 19857993 Evaluation of a rapid molecular algorithm for detection of pandemic influenza A (H1N1) 2009 virus and screening for a key oseltamivir resistance (H275Y) substitution in neuraminidase. H275Y endpoint fluorescence scatter plot. 2010 Journal of clinical virology Figure IV H275Y 0 5 19857993 Evaluation of a rapid molecular algorithm for detection of pandemic influenza A (H1N1) 2009 virus and screening for a key oseltamivir resistance (H275Y) substitution in neuraminidase. Mixtures of in vitro transcribed wild type and mutant RNA (total input 1.0 x 105 vp/ml) were analyzed using the H275Y discrimination assay (black dots). 2010 Journal of clinical virology Figure IV H275Y 112 117 19905033 Design and pharmacological characterization of inhibitors of amantadine-resistant mutants of the M2 ion channel of influenza A virus. A/M2- S31N with amantadine IC50=237.01+-22.14; with BL-1743 IC50>10 mM; with spiran amine 8 IC50>10 mM. 2009 Biochemistry Figure IV S31N 6 10 M2 2 4 19905033 Design and pharmacological characterization of inhibitors of amantadine-resistant mutants of the M2 ion channel of influenza A virus. A/M2-L26F with amantadine IC50=164.46+-14.40; with BL-1743 IC50>10 mM; with spiran amine 8 IC50=30.62+-8.13. 2009 Biochemistry Figure IV L26F 5 9 M2 2 4 19905033 Design and pharmacological characterization of inhibitors of amantadine-resistant mutants of the M2 ion channel of influenza A virus. A/M2-V27A with amantadine IC50=1840; with BL-1743 IC50>10 mM; with spiran amine 8 IC50=84.92+-13.61. 2009 Biochemistry Figure IV V27A 5 9 M2 2 4 19905033 Design and pharmacological characterization of inhibitors of amantadine-resistant mutants of the M2 ion channel of influenza A virus. Effects of amantadine, BL-1743 and spiran amine 8 (50 muM) on influenza mutant virus V27A/L38F plaque formation. 2009 Biochemistry Figure IV L38F;V27A 90;85 94;89 19905033 Design and pharmacological characterization of inhibitors of amantadine-resistant mutants of the M2 ion channel of influenza A virus. Inhibition efficiency of amantadine, BL-1743 and spiran amine 8 on wt A/M2 channels and A/M2 L26F, V27A and S31N mutants. 2009 Biochemistry Figure IV L26F;V27A;S31N 93;99;108 97;103;112 M2;M2 72;90 74;92 19905033 Design and pharmacological characterization of inhibitors of amantadine-resistant mutants of the M2 ion channel of influenza A virus. Wt influenza virus (A/Udorn/72) and influenza virus containing mutations in the M2 TM domain (V27A/L38F) were recovered from cloned DNA and assayed for plaque formation on MDCK cells in the presence or absence of drugs as described in Materials and Methods. 2009 Biochemistry Figure IV V27A;L38F 94;99 98;103 M2 80 82 19958488 Prediction of avian influenza A binding preference to human receptor using conformational analysis of receptor bound to hemagglutinin. M226T, K189G, K218S and L190P binding to human receptor alpha(2,6) analog. 2009 BMC genomics Figure IV M226T;K189G;K218S;L190P 0;7;14;24 5;12;19;29 19958488 Prediction of avian influenza A binding preference to human receptor using conformational analysis of receptor bound to hemagglutinin. non-mutated Puerto-34 (black), G224S (green), Q222L(red) and Q222L/G224S (blue) binding to alpha(2,3) receptor (top) and alpha(2,6) receptor (bottom). 2009 BMC genomics Figure IV G224S;Q222L;G224S;Q222L 31;46;67;61 36;51;72;66 19958488 Prediction of avian influenza A binding preference to human receptor using conformational analysis of receptor bound to hemagglutinin. Six nanosecond RMSD plots of three simulated HA systems: Sing-97 (black), L129V/A143V Kan-1(red), and Puerto-34 (green). 2009 BMC genomics Figure IV L129V;A143V 74;80 79;85 HA 45 47 19995550 X-ray structures of NS1 effector domain mutants. A detailed view of Trp 187 and Tyr 187 in the superposition of wild type effector domain with W187Y mutant effector domain. 2010 Archives of biochemistry and biophysics Figure IV W187Y 94 99 19995550 X-ray structures of NS1 effector domain mutants. Calorimetry data for titration of NS1-ED (a) wild type, (b) W187A and (c) W187Y into CPSF30 (F1F3). 2010 Archives of biochemistry and biophysics Figure IV W187A;W187Y 60;74 65;79 NS1 34 37 19995550 X-ray structures of NS1 effector domain mutants. Electron density for the (a) W187A and (b) W187Y mutant of NS1A effector domain. 2010 Archives of biochemistry and biophysics Figure IV W187A;W187Y 29;43 34;48 NS 59 61 19995550 X-ray structures of NS1 effector domain mutants. Superposition of wild type effector domain with W187Y and W187A mutant effector domains. 2010 Archives of biochemistry and biophysics Figure IV W187Y;W187A 48;58 53;63 19995550 X-ray structures of NS1 effector domain mutants. The Calpha trace of wild type effector domain is shown in red bonds, the Calpha trace of W187Y mutant effector domain is shown in blue bonds, and that of W187A mutant effector domain is shown in grey bonds. 2010 Archives of biochemistry and biophysics Figure IV W187Y;W187A 89;154 94;159 19995550 X-ray structures of NS1 effector domain mutants. The crystallographic dimer interface for (a) W187Y and (b) W187A mutant NS1-effector domain. 2010 Archives of biochemistry and biophysics Figure IV W187Y;W187A 45;59 50;64 NS1 72 75 19995550 X-ray structures of NS1 effector domain mutants. The pocket is unoccupied and exposed to solvent in the W187A mutant. 2010 Archives of biochemistry and biophysics Figure IV W187A 55 60 19995550 X-ray structures of NS1 effector domain mutants. The wild type elution profile is shown as a red line, the W187A mutant is shown in green, and the W187Y mutant is shown in blue. 2010 Archives of biochemistry and biophysics Figure IV W187A;W187Y 58;98 63;103 19995550 X-ray structures of NS1 effector domain mutants. This pocket is filled by the Y187 of crystallographic monomer B of W187Y mutant. 2010 Archives of biochemistry and biophysics Figure IV W187Y 67 72 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. (B) The images shown are hematoxylin-and-eosin-stained sections of lung tissue from ferrets inoculated with the WT, E119A, and N294S viruses obtained on day 4 post-inoculation. 2010 PLoS pathogens Figure IV E119A;N294S 116;127 121;132 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. Lung alveoli of the N294S-infected ferrets are filled with inflammatory cells and hyperplastic pneumocytes obscuring interstitial septa. 2010 PLoS pathogens Figure IV N294S 20 25 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. Replication of recombinant WT, E119A, and N294S viruses in internal organs and histologic changes in the lungs morphology of ferrets infected with these H5N1 viruses. 2010 PLoS pathogens Figure IV E119A;N294S 31;42 36;47 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. The lung alveolar architecture of the ferrets inoculated with the E119A mutant is lost due to necrosis of alveolar pneumocytes and the interstitial septa. 2010 PLoS pathogens Figure IV E119A 66 71 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. In the mutant, HA-E391K, the intra-molecular salt bridge of E38/31 to R336/321could be replaced by an inter-molecular salt bridge between E38/31 from one monomer to K391/47 in the other which weakens stability of the region within the monomer while it strengthens the interaction between the monomers. 2010 PLoS currents Figure IV E391K 18 23 HA 15 17 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. Rise of the HA-E391K mutation globally and in Singapore. 2010 PLoS currents Figure IV E391K 15 20 HA 12 14 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. Strains with HA-E391K are colored green, all non-Singaporean sequences are in bold letters. 2010 PLoS currents Figure IV E391K 16 21 HA 13 15 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. Subtrees are only shown in detail if they contain at least one HA-E391K sample. 2010 PLoS currents Figure IV E391K 66 71 HA 63 65 20535229 A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. The residues involving mutations E391K (position 47 in HA2 in alternative numbering) and V47A (position 40 in HA1 in alternative numbering) are shown as balls and colored red or magenta, respectively. 2010 PLoS currents Figure IV E391K;V47A 33;89 38;93 HA;HA1 55;110 57;113 20661429 Oseltamivir-resistant pandemic A/H1N1 virus is as virulent as its wild-type counterpart in mice and ferrets. Body temperature of ferrets infected with wild-type (WT) or H274Y mutant isolates of pH1N1. 2010 PLoS pathogens Figure IV H274Y 60 65 20661429 Oseltamivir-resistant pandemic A/H1N1 virus is as virulent as its wild-type counterpart in mice and ferrets. Body temperatures were recorded by implanted thermometers during 14 days post-inoculation in groups of 4-5 ferrets infected with WT (A/Quebec/147023/2009) or oseltamivir-resistant H274Y mutant (A/Quebec/147365/2009) pH1N1 isolates. 2010 PLoS pathogens Figure IV H274Y 180 185 20661429 Oseltamivir-resistant pandemic A/H1N1 virus is as virulent as its wild-type counterpart in mice and ferrets. Lung histopathology of mice infected with wild-type (WT) or H274Y mutant isolates of pH1N1. 2010 PLoS pathogens Figure IV H274Y 60 65 20661429 Oseltamivir-resistant pandemic A/H1N1 virus is as virulent as its wild-type counterpart in mice and ferrets. Lung IL-6 and KC expression in mice infected with wild-type (WT) or H274Y mutant isolates of pH1N1. 2010 PLoS pathogens Figure IV H274Y 68 73 20661429 Oseltamivir-resistant pandemic A/H1N1 virus is as virulent as its wild-type counterpart in mice and ferrets. Lung viral titers of mice infected with wild-type (WT) or H274Y mutant isolates of pH1N1. 2010 PLoS pathogens Figure IV H274Y 58 63 20661429 Oseltamivir-resistant pandemic A/H1N1 virus is as virulent as its wild-type counterpart in mice and ferrets. Mice were infected intranasally with 5x105 PFUs of either WT pH1N1 (A/Quebec/147023/2009) or oseltamivir-resistant H274Y mutant (A/Quebec/147365/2009) isolate. 2010 PLoS pathogens Figure IV H274Y 115 120 20661429 Oseltamivir-resistant pandemic A/H1N1 virus is as virulent as its wild-type counterpart in mice and ferrets. Mice were infected intranasally with 5x105 PFUs of either WT pH1N1 isolate (A/Quebec/147023/2009) or oseltamivir-resistant H274Y mutant (A/Quebec/147365/2009). 2010 PLoS pathogens Figure IV H274Y 123 128 20661429 Oseltamivir-resistant pandemic A/H1N1 virus is as virulent as its wild-type counterpart in mice and ferrets. Nasal wash viral titers of ferrets infected with wild-type (WT) or H274Y mutant isolates of pH1N1. 2010 PLoS pathogens Figure IV H274Y 67 72 20661429 Oseltamivir-resistant pandemic A/H1N1 virus is as virulent as its wild-type counterpart in mice and ferrets. Replicative capacities of wild-type (WT) and H274Y mutant isolates of pH1N1 and seasonal A/H1N1 viruses. 2010 PLoS pathogens Figure IV H274Y 45 50 20661429 Oseltamivir-resistant pandemic A/H1N1 virus is as virulent as its wild-type counterpart in mice and ferrets. The weight loss of mice was evaluated in two groups of 15 mice (infected with the WT and H274Y mutant isolate) over a period of 14 days. 2010 PLoS pathogens Figure IV H274Y 89 94 20661429 Oseltamivir-resistant pandemic A/H1N1 virus is as virulent as its wild-type counterpart in mice and ferrets. Viral titers were determined at the indicated time points from supernatants of ST6Gal I-expressing MDCK cells infected with pH1N1 A/Quebec/147023/2009 (WT), pH1N1 A/Quebec/147365/2009 (H274Y mutant), A/Brisbane/59/07-like (WT) and A/Brisbane/59/07-like (H274Y mutant) isolates at a multiplicity of infection (MOI) of 0.001. 2010 PLoS pathogens Figure IV H274Y;H274Y 185;254 190;259 20661429 Oseltamivir-resistant pandemic A/H1N1 virus is as virulent as its wild-type counterpart in mice and ferrets. Viral titers were determined daily over 14 days post-inoculation from nasal washes of ferrets infected with WT (A/Quebec/147023/2009) or oseltamivir-resistant H274Y mutant (A/Quebec/147365/2009) pH1N1 isolates. 2010 PLoS pathogens Figure IV H274Y 159 164 20661429 Oseltamivir-resistant pandemic A/H1N1 virus is as virulent as its wild-type counterpart in mice and ferrets. Weight loss of mice infected with wild-type (WT) or H274Y mutant isolates of pH1N1. 2010 PLoS pathogens Figure IV H274Y 52 57 20689744 The PB2-E627K mutation attenuates viruses containing the 2009 H1N1 influenza pandemic polymerase. (G, H) Sections from an animal infected with the 1918RNP-K627E virus showing no pathological changes in the lung but some viral antigen staining in bronchiolar epithelial cells (arrow) in the absence of inflammation (original magnifications, x100). 2010 mBio Figure IV K627E 57 62 20689744 The PB2-E627K mutation attenuates viruses containing the 2009 H1N1 influenza pandemic polymerase. (G, H) Sections from an animal infected with the CA09RNP-E627K virus showing no pathological changes in the lung and no viral antigen (original magnifications, x100). 2010 mBio Figure IV E627K 57 62 20689744 The PB2-E627K mutation attenuates viruses containing the 2009 H1N1 influenza pandemic polymerase. (I, J) Sections from an animal infected with the CA09RNP-D701N virus showing no pathological changes in the lung and no viral antigen (original magnification, x100). 2010 mBio Figure IV D701N 57 62 20689744 The PB2-E627K mutation attenuates viruses containing the 2009 H1N1 influenza pandemic polymerase. Sections from an animal infected with the S09RNP-E627K virus showing necrotizing bronchiolitis with a transmural inflammatory cell infiltrate. 2010 mBio Figure IV E627K 49 54 Bronchiolitis 81 94 20920297 Characterization of an H3N2 triple reassortant influenza virus with a mutation at the receptor binding domain (D190A) that occurred upon virus transmission from turkeys to pigs. A strain with Glu627Lys mutation in the PB2 gene was included in the kinetic study to serve as control, since such mutation was shown to affect host range specificity of influenza A viruses. 2010 Virology journal Figure IV E627K 14 23 PB2 40 43 20920297 Characterization of an H3N2 triple reassortant influenza virus with a mutation at the receptor binding domain (D190A) that occurred upon virus transmission from turkeys to pigs. HA structure with Asp to Ala mutation at residue 190 of the RBD. 2010 Virology journal Figure IV D190A 18 52 HA 0 2 21172786 Pandemic H1N1 2009 influenza virus with the H275Y oseltamivir resistance neuraminidase mutation shows a small compromise in enzyme activity and viral fitness. Recombinant A/England/195/09 viruses containing wild-type or mutated H275Y NA segments were inoculated onto cells. 2011 The Journal of antimicrobial chemotherapy Figure IV H275Y 69 74 75 77 21226922 Influenza A virus NS1 gene mutations F103L and M106I increase replication and virulence. BALB/c mice were infected intransally with 105 pfu of rWSN-Ck/Bj-NS-L103F + I106M and lungs were collected 2 dpi. 2011 Virology journal Figure IV L103F;I106M 68;76 73;81 NS 65 67 21226922 Influenza A virus NS1 gene mutations F103L and M106I increase replication and virulence. Effect of F103L, M106I, and F103L + M106I NS1 mutations on the rate of viral protein synthesis in MDCK. 2011 Virology journal Figure IV F103L;M106I;F103L;M106I 10;17;28;36 15;22;33;41 NS1 42 45 21226922 Influenza A virus NS1 gene mutations F103L and M106I increase replication and virulence. rPR8-HK-NS-F103L + M106I infected lungs. 2011 Virology journal Figure IV F103L;M106I 11;19 16;24 NS 8 10 21226922 Influenza A virus NS1 gene mutations F103L and M106I increase replication and virulence. rPR8-HK-NS-F103L infected lungs D. 2011 Virology journal Figure IV F103L 11 16 NS 8 10 21226922 Influenza A virus NS1 gene mutations F103L and M106I increase replication and virulence. rPR8-HK-NS-M106I infected lungs E. 2011 Virology journal Figure IV M106I 11 16 NS 8 10 21249207 Nationwide molecular surveillance of pandemic H1N1 influenza A virus genomes: Canada, 2009. Phylogenetic trees were inferred using the neighbour-joining distance method, with genetic distances calculated by maximum likelihood using Kimura's two-parameter model (K2P) in MEGA 4.0. 2011 PloS one Figure IV K2P 170 173 21349290 Development of a real-time RT-PCR assay for detection of resistance to oseltamivir in influenza A pandemic (H1N1) 2009 virus using single nucleotide polymorphism probes. Amplification curves for templates containing sensitive (C823), resistant (C823T) and mixed alleles (C823 and C823T). 2011 Journal of virological methods Figure IV C823T;C823T 75;110 80;115 21349290 Development of a real-time RT-PCR assay for detection of resistance to oseltamivir in influenza A pandemic (H1N1) 2009 virus using single nucleotide polymorphism probes. log10 concentration) for serial dilutions of the plasmid with C823T nucleotide. 2011 Journal of virological methods Figure IV C823T 62 67 21407805 A single base-pair change in 2009 H1N1 hemagglutinin increases human receptor affinity and leads to efficient airborne viral transmission in ferrets. Respiratory droplet transmissibility of rgCA04/09 and rgCA04/09 HA Ile219Lys mutant virus. 2011 PloS one Figure IV I219K 67 76 HA 64 66 21407805 A single base-pair change in 2009 H1N1 hemagglutinin increases human receptor affinity and leads to efficient airborne viral transmission in ferrets. Three ferrets were intranasally inoculated with 106 PFU of rgCA04/09 (A) or rgCA04/09 HA Ile219Lys mutant virus (B). 2011 PloS one Figure IV I219K 89 98 HA 86 88 21455300 Assessing the in vitro fitness of an oseltamivir-resistant seasonal A/H1N1 influenza strain using a mathematical model. Fit of the mathematical model to the combined data for the WT (solid line fitted to filled circles) and H275Y mutant strains (dashed line fitted to empty circles). 2011 PloS one Figure IV H275Y 104 109 21455300 Assessing the in vitro fitness of an oseltamivir-resistant seasonal A/H1N1 influenza strain using a mathematical model. Linear fits on the log-linear graph determine the rates of exponential growth, , for the WT (solid line) and H275Y mutant (dashed) strains, as well as the rates of viral titer decay (dotted). 2011 PloS one Figure IV H275Y 109 114 21455300 Assessing the in vitro fitness of an oseltamivir-resistant seasonal A/H1N1 influenza strain using a mathematical model. Linear fits to the first three time points are shown for the WT (solid line) and H275Y (dashed line). 2011 PloS one Figure IV H275Y 81 86 21455300 Assessing the in vitro fitness of an oseltamivir-resistant seasonal A/H1N1 influenza strain using a mathematical model. Parameter region where the parameter values are most consistent with the experimentally-measured values of the plaque velocity (A and D), the exponential viral titer growth rate (B and E), and with both measures (C and F), for the A/Brisbane/59/2007 (H1N1) WT (first row) and H275Y mutant (second row) strains. 2011 PloS one Figure IV H275Y 276 281 21455300 Assessing the in vitro fitness of an oseltamivir-resistant seasonal A/H1N1 influenza strain using a mathematical model. Plaque radius as a function of time for the WT (filled circles) and H275Y mutant (open circles) A/Brisbane/59/2007 (H1N1) pair. 2011 PloS one Figure IV H275Y 68 73 21455300 Assessing the in vitro fitness of an oseltamivir-resistant seasonal A/H1N1 influenza strain using a mathematical model. Single-cycle viral yield assay confirming delayed growth of the A/Brisbane/59/2007 (H1N1) H275Y mutant strain. 2011 PloS one Figure IV H275Y 90 95 21455300 Assessing the in vitro fitness of an oseltamivir-resistant seasonal A/H1N1 influenza strain using a mathematical model. The growth of the H275Y mutant virus titer is delayed by 2-3 h with respect to the WT. 2011 PloS one Figure IV H275Y 18 23 21455300 Assessing the in vitro fitness of an oseltamivir-resistant seasonal A/H1N1 influenza strain using a mathematical model. The plaques of the A/Brisbane/59/2007 (H1N1) wild-type (WT) and H275Y NA mutant in ST6GalI-MDCK cells are shown over a period of 96 h. 2011 PloS one Figure IV H275Y 64 69 70 72 21455300 Assessing the in vitro fitness of an oseltamivir-resistant seasonal A/H1N1 influenza strain using a mathematical model. Viral yield in time for the A/Brisbane/59/2007 (H1N1) WT (filled circles) and H275Y mutant (open circle) strains. 2011 PloS one Figure IV H275Y 78 83 21572517 Mutation analysis of 2009 pandemic influenza A(H1N1) viruses collected in Japan during the peak phase of the pandemic. (A) The left panel depicts the three-dimensional structure of an HA trimer complex deduced from the crystal structure of the H1N1 hemagglutinin of the 2009 A(H1N1) virus (PDB entry: 3LZG) to highlight one HA monomer with the amino acid substitutions (A156T and D185N) found in our severe cases. 2011 PloS one Figure IV A156T;D185N 251;261 256;266 HA;HA;HA 65;205;130 67;207;143 21572517 Mutation analysis of 2009 pandemic influenza A(H1N1) viruses collected in Japan during the peak phase of the pandemic. Also represented on this alignment are the major substitution (N248D) between samples "I" and "II," H275Y and N295S causing oseltamivir resistance, and the stalk region (underlined). 2011 PloS one Figure IV N248D;H275Y;N295S 63;100;110 68;105;115 21572517 Mutation analysis of 2009 pandemic influenza A(H1N1) viruses collected in Japan during the peak phase of the pandemic. Also represented on this alignment are the major substitution (S220T) between samples "I" and "II"; A156T and D185N observed in fatal or severe cases; the antigenic sites Sa (*), Sb , and Ca ; the receptor binding site (highlighted in grey); and the cleavage site (underlined). 2011 PloS one Figure IV S220T;A156T;D185N 63;100;110 68;105;115 21572517 Mutation analysis of 2009 pandemic influenza A(H1N1) viruses collected in Japan during the peak phase of the pandemic. Both A156T and D185N substitutions appear to occur in the Ca antigenic site and to head outside the receptor-binding site. 2011 PloS one Figure IV A156T;D185N 5;15 10;20 21572517 Mutation analysis of 2009 pandemic influenza A(H1N1) viruses collected in Japan during the peak phase of the pandemic. The left panel shows the NA protein with the N248D substitution, representing locations of the amino acid substitution as well as H275 and E277. 2011 PloS one Figure IV N248D 45 50 25 27 21572517 Mutation analysis of 2009 pandemic influenza A(H1N1) viruses collected in Japan during the peak phase of the pandemic. The right panel shows the NA protein with the H275Y substitution, revealing that the side chain of E277 is shifted by 1.62 A in the oseltamivir-resistant variant found in samples "II." 2011 PloS one Figure IV H275Y 46 51 26 28 21572517 Mutation analysis of 2009 pandemic influenza A(H1N1) viruses collected in Japan during the peak phase of the pandemic. The right panel shows the NA protein with the H275Y substitution, revealing that the side chain of E277 is shifted by 1.62 A in the oseltamivir-resistant variant found in samples "II.". 2011 PloS one Figure IV H275Y 46 51 26 28 21572517 Mutation analysis of 2009 pandemic influenza A(H1N1) viruses collected in Japan during the peak phase of the pandemic. The right panels represent close-up views of the head part of the HA monomer with an amino acid substitution of A156T (top) or D185N (bottom). 2011 PloS one Figure IV A156T;D185N 112;127 117;132 HA 66 68 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. Calu-3 (circles), HMVEC-LBI (triangles), or HCEpiC (squares) cells were infected at a MOI of 0.01 with the indicated viruses (CA/4, closed symbols; D222G, open symbols). 2011 PloS one Figure IV D222G 148 153 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. Dose-dependent binding of CA/04 D222G (A) or wild-type CA/04 (B) virus to representative alpha2-3 and alpha2-6 sialylated glycans on the glycan array. 2011 PloS one Figure IV D222G 32 37 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. Dose-dependent glycan array-binding of CA/04 D222G virus. 2011 PloS one Figure IV D222G 45 50 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. Replication kinetics of CA/04 and D222G viruses in human ocular and respiratory cells. 2011 PloS one Figure IV D222G 34 39 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. Respiratory droplet transmissibility of D222G virus. 2011 PloS one Figure IV D222G 40 45 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. Three ferrets were inoculated with 106 PFU of reverse-genetics CA/04 (published previously in) (A) or D222G (B) virus. 2011 PloS one Figure IV D222G 102 107 21980293 Multidrug resistant 2009 A/H1N1 influenza clinical isolate with a neuraminidase I223R mutation retains its virulence and transmissibility in ferrets. MDCK (panel A) or MDCK-SIAT1 (panel B) cells were inoculated with 0.001 TCID50 virus per cell of recNL/602 (black circles), isolate NL/2631-R223 (black triangles) and recNL/602-I223R (open circles). 2011 PLoS pathogens Figure IV I223R 177 182 21980293 Multidrug resistant 2009 A/H1N1 influenza clinical isolate with a neuraminidase I223R mutation retains its virulence and transmissibility in ferrets. Transmission of recNL/602 and recNL/602-I223R by aerosol or respiratory droplets in ferrets. 2011 PLoS pathogens Figure IV I223R 40 45 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. Body temperatures were recorded by rectal thermometer during 10 days post-inoculation in groups of 4 index ferrets infected with 1.25x105 PFU of recombinant A/Brisbane/59/2007-like wild-type (WT) virus as well as H275Y and H275Y/Q222R mutants (A) and in groups of 4 naive ferrets that were placed in direct contact with index ferrets 24 h later (B). 2011 PLoS pathogens Figure IV H275Y;H275Y;Q222R 213;223;229 218;228;234 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. Mean viral titers +- standard deviations were determined in nasal washes by using standard plaque assays in groups of 4 index ferrets infected with 1.25x105 PFU of recombinant A/Brisbane/59/2007-like wild-type (WT) virus as well as H275Y and H275Y/Q222R mutants (A) and in groups of 4 naive ferrets that were placed in direct contact with index ferrets 24 h later (B).*P<0.05 and **P<0.01 for differences in viral titers when compared to the recombinant WT virus. 2011 PLoS pathogens Figure IV H275Y;H275Y;Q222R 232;242;248 237;247;253 22238617 Mutational analyses of the influenza A virus polymerase subunit PA reveal distinct functions related and unrelated to RNA polymerase activity. (B) Plaque formation on MDCK cells by wild-type (WT), recombinant mutant L1 (K497A, T498A), and L8 (N513A, D514A). 2012 PloS one Figure IV K497A;T498A;N513A;D514A 77;84;100;107 82;89;105;112 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. A - Size distribution of monomeric wt NP (5 microM) alone (black, 6.8 nm, 93%, 5.0 micro, 7%) and 1 hour (dotted blue, 13.8 nm 91%, 760 nm 9%) or 3 hours after addition of 1.8 microM RNA (16.3 nm, 100%); B- Size distribution of monomeric R361A (5 microM) alone (black, 7.8 nm, 100%) and 4 hours after addition of 1.8 microM RNA (dashed green, 9.85 nm, 75%, 279 nm, 25%) C: Comparison of the oligomerization kinetics of R361A (violet squares) and R361A-E80A-E81A (green stars) (10 microM) after addition of RNA (3 microM). 2012 PloS one Figure IV R361A;R361A;R361A;E80A;E81A;R361A;R361A;R361A;E80A;E81A 239;420;447;453;458;238;419;446;452;457 244;425;452;457;462;243;424;451;456;461 NP 38 40 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. A: Comparison of the association to and dissociation from RNA of R361A-R204A-R208A (full triangles) and wt-R204A-R208A (open triangles); B: Comparison of the oligomerization kinetics of 10 microM proteins after addition of RNA (3 microM): wt NP (full squares), R361A (open squares), wt-R204A-R208A (open circles) and R361A-R204A-R208A (full triangles) (10 microM). 2012 PloS one Figure IV R361A;R204A;R208A;R204A;R208A;R361A;R204A;R208A;R361A;R204A;R208A;R361A;R204A;R208A;R204A;R208A;R361A;R204A;R208A;R361A;R204A;R208A 66;72;78;108;114;262;287;293;318;324;330;65;71;77;107;113;261;286;292;317;323;329 71;77;83;113;119;267;292;298;323;329;335;70;76;82;112;118;266;291;297;322;328;334 NP 242 244 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. A: Effect of the mutations R361A (green circles) and R361A-E80A-E81A (blue squares) compared to wt NP (black triangles) binding to RNA; Inset: comparison of the SPR signals obtained in the presence of Flu1-RNA with 300 nM C-terminal His-tagged NP, R361A or R361A-E80A-E81A. 2012 PloS one Figure IV R361A;R361A;E80A;E81A;R361A;R361A;E80A;E81A;R361A;R361A;E81A;E80A;R361A;R361A;E81A;E80A 28;54;60;65;249;258;264;269;27;53;64;59;248;257;268;263 33;59;64;69;254;263;268;273;32;58;68;63;253;262;272;267 NP;NP 99;244 101;246 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. B: Binding to Flu1-RNA of the double and triple mutants, wt-E80A-E81A (blue squares), R361A-E80A-E81A (red circles) respectively. 2012 PloS one Figure IV E81A;E80A;R361A;E81A;E80A 65;60;86;97;92 69;64;91;101;96 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. B: Root-mean-square fluctuations of the NP (red) and R361A (green) monomers during the simulated trajectories: one can see a reduced flexibility in loop 2 and a small increase of the flexibility of loop 1 of the R361A mutant. 2012 PloS one Figure IV R361A;R361A 53;212 58;217 NP 40 42 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. Comparison of representative structures of NP (red) and the R361A mutant (green) proteins. 2012 PloS one Figure IV R361A 60 65 NP 43 45 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. Comparison of the NP and R361A proteins by molecular modelling. 2012 PloS one Figure IV R361A 25 30 NP 18 20 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. Distribution of the minimal distance between loops 1 and 2 in NP and the R361A mutant. 2012 PloS one Figure IV R361A 73 78 NP 62 64 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. Due to its low affinity for RNA, the signal of the R361A-RNA complex (green) is ca four times smaller than NP-RNA (black), while the signal of the triple mutant (blue) is intermediate between them. 2012 PloS one Figure IV R361A 51 56 NP 107 109 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. It characterized the differences in loops interactions between wt NP and R361A. 2012 PloS one Figure IV R361A 73 78 NP 66 68 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. Note the large difference in the final size of the protein-RNA oligomers being 10+-1 nm and 16+-1 nm for R361A and R361A-E80A-E81A, the latter resembling the size of oligomeric NP-RNA complexes. 2012 PloS one Figure IV R361A;R361A;E81A;E80A 105;115;126;121 110;120;130;125 NP 177 179 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. The position of the mutated residue R361 is highlighted in CPK representation; the salt bridge between residues E80 and R208 and hydrophobic interactions between L79 and W207 stabilized the relative positions of the two loops at shorter distance in R361A than in NP (insert). 2012 PloS one Figure IV R361A 249 254 NP 263 265 22363521 Frequency of D222G and Q223R hemagglutinin mutants of pandemic (H1N1) 2009 influenza virus in Japan between 2009 and 2010. Alignment of the amino acid sequences including D187E, D222G, and Q223R mutants within the receptor binding site of H1N1pdm hemagglutinin. 2012 PloS one Figure IV D187E;D222G;Q223R 48;55;66 53;60;71 HA 124 137 22438920 Mutations in polymerase genes enhanced the virulence of 2009 pandemic H1N1 influenza virus in mice. (B) Mortality associated with infection with the recombinant viruses SC_WT, SC_PA-A36T, and SC_PB2-H357N was also examined. 2012 PloS one Figure IV A36T;H357N 82;99 86;104 22438920 Mutations in polymerase genes enhanced the virulence of 2009 pandemic H1N1 influenza virus in mice. *, , p<0.05, when comparing SC_PA-A36T and SC_PB2-H357N with SC_WT respectively, as determined by a t-test of TCID50 values. 2012 PloS one Figure IV A36T;H357N 35;51 39;56 22438920 Mutations in polymerase genes enhanced the virulence of 2009 pandemic H1N1 influenza virus in mice. Cells were co-transfected with Gluc reporter plasmid and expression plasmids PB1 and NP, PA, and PB2 (WT or PA-A36T, PB2-H357N mutants) to generate different viral RNPs. 2012 PloS one Figure IV A36T;H357N 111;121 115;126 NP;PA;PA;PB1;PB2;PB2;RNP 85;89;108;77;97;117;164 87;91;110;80;100;120;168 22438920 Mutations in polymerase genes enhanced the virulence of 2009 pandemic H1N1 influenza virus in mice. Confluent monolayer of A549, PK15 and LA-4 cell lines were inoculated with SC_WT, SC_PA-A36T or SC_PB2-H357N virus at MOI of 0.0001. 2012 PloS one Figure IV A36T;H357N 88;103 92;108 22438920 Mutations in polymerase genes enhanced the virulence of 2009 pandemic H1N1 influenza virus in mice. Pathogenicity of SC_WT, SC_PA-A36T, and SC_PB2-H357N viruses in mice. 2012 PloS one Figure IV A36T;H357N 30;47 34;52 22438920 Mutations in polymerase genes enhanced the virulence of 2009 pandemic H1N1 influenza virus in mice. Six-week-old female BALB/c mice (n = 3/group/time-point) were inoculated intranasally with 50 microl containing 104 TCID50 of SC_WT, SC_PA-A36T, and SC_PB2-H357N. 2012 PloS one Figure IV A36T;H357N 139;156 143;161 22438920 Mutations in polymerase genes enhanced the virulence of 2009 pandemic H1N1 influenza virus in mice. Six-week-old female BALB/c mice (n = 5/group) were inoculated intranasally with 50 microl containing 104 TCID50 of the recombinant viruses SC_WT, SC_PA-A36T, and SC_PB2-H357N, or PBS (mock). 2012 PloS one Figure IV A36T;H357N 152;169 156;174 22438920 Mutations in polymerase genes enhanced the virulence of 2009 pandemic H1N1 influenza virus in mice. Viral RNA polymerase activity of SC_WT, SC_PA-A36T and SC_PB2-H357N in 293T cells cultured at different temperatures. 2012 PloS one Figure IV A36T;H357N 46;62 50;67 22615752 Functional analysis of conserved motifs in influenza virus PB1 protein. Effects of PB1 mutation K480R on influenza polymerase activity in human and avian cells. 2012 PloS one Figure IV K480R 24 29 PB1 11 14 22615752 Functional analysis of conserved motifs in influenza virus PB1 protein. Growth characteristics of wild-type virus and virus possessing the PB1 K480R mutation. 2012 PloS one Figure IV K480R 71 76 PB1 67 70 22615752 Functional analysis of conserved motifs in influenza virus PB1 protein. The effects of PB1 mutation K480R were evaluated in the background of the A/California/04/09 (H1N1) virus replication complex in human 293T and chicken DF-1 cells. 2012 PloS one Figure IV K480R 28 33 PB1 15 18 22615752 Functional analysis of conserved motifs in influenza virus PB1 protein. Wild-type A/California/04/09 virus and recombinant virus possessing the K480R mutation were used for infection of human Calu-3 cells (MOI = 0.001). 2012 PloS one Figure IV K480R 72 77 22788742 Comprehensive global amino acid sequence analysis of PB1F2 protein of influenza A H5N1 viruses and the influenza A virus subtypes responsible for the 20th-century pandemics. - A/Goose/Guangdong/1/96, A/Chicken/Hong Kong/258/97, and A/Hong Kong/156/97 strains harboring N84S mutation and grouping with the aforementioned five Indian strains. 2013 Influenza and other respiratory viruses Figure IV N84S;N84S 96;95 100;99 22788742 Comprehensive global amino acid sequence analysis of PB1F2 protein of influenza A H5N1 viruses and the influenza A virus subtypes responsible for the 20th-century pandemics. 2013 Influenza and other respiratory viruses Figure IV N84S;N84S 69;68 73;72 22808250 Mouse-adapted H9N2 influenza A virus PB2 protein M147L and E627K mutations are critical for high virulence. Five-week-old BALB/c mice (five/group) were inoculated intranasally with different H9N2 viruses, SD16 (A), SD16-MA (B), SD16:MA PB2 (C), or SD16-M147L/E627K (D). 2012 PloS one Figure IV M147L;E627K 145;151 150;156 PB2 128 131 22851656 Emergence of fatal avian influenza in New England harbor seals. The mutation G151E causes a conformational shift and interrupts H bonding between seal H3 S152 and SAalpha2,3, which suggests a reduction in SAalpha2,3 binding efficiency. 2012 mBio Figure IV G151E 13 18 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. Antiviral resistance mechanism of the I223R mutant. 2012 PLoS pathogens Figure IV I223R 38 43 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. Both the open and closed neuraminidase structures lack a smaller cavity near position 223, due to an isoleucine to arginine change (I223R). 2012 PLoS pathogens Figure IV I223R 132 137 25 38 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. Further narrowing of the active site by the I223R change causes antiviral resistance to both oseltamivir and zanamivir. 2012 PLoS pathogens Figure IV I223R 44 49 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. In panel A, an overlay of three pandemic neuraminidase structures is presented: I223R mutant ligand-free structure (blue, NL2631, PDB ID code 4B7M) and both wild type (green, Cal07, PDB ID code 4B7R) and I223R mutant (white, Cal07, PDB ID code 4B7J) oseltamivir complexes. 2012 PLoS pathogens Figure IV I223R;I223R 80;204 85;209 41 54 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. In panel A, hydrogen bond contacts are presented (dotted lines), which are formed between zanamivir and active site residues in the I223R mutant (purple, PDB ID code 4B7N). 2012 PLoS pathogens Figure IV I223R 132 137 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. In panel B, an overlay is presented of an H275Y mutant neuraminidase structure in complex with oseltamivir (yellow, VN04, PDB ID code 2CL0) with two I223R mutant neuraminidase crystal structures: The ligand-free structure (blue, NL2631, PDB ID code 4B7M) and the structure in complex with oseltamivir (green, NL2631, PDB ID code 4B7J). 2012 PLoS pathogens Figure IV H275Y;I223R 42;149 47;154 NA;NA 55;162 68;175 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. Oseltamivir binding to the I223R mutant involves reorientation of both R223 and S247 residues. 2012 PLoS pathogens Figure IV I223R 27 32 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. The insert displays the interactions between the same residues in the I223R mutant ligand-free structure (blue, PDB ID code 4B7M). 2012 PLoS pathogens Figure IV I223R 70 75 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. The key amino acid residues involved in I223R antiviral resistance pattern are displayed. 2012 PLoS pathogens Figure IV I223R 40 45 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. The polarity of zanamivir enables inhibition of the I223R mutant. 2012 PLoS pathogens Figure IV I223R 52 57 23028314 H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis. The resistance mechanisms of the H275Y and I223R mutants act synergistically to gain enhanced levels of oseltamivir resistance. 2012 PLoS pathogens Figure IV H275Y;I223R 33;43 38;48 23326573 An assay suitable for high throughput screening of anti-influenza drugs. (C) Expression of AcGFP-M2 (V27A) fusion protein in the presence of a group of compounds to be screened as described in (A). 2013 PloS one Figure IV V27A 28 32 M2 24 26 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. (A) A549 cells were infected with the S9A NP mutant and WT NP viruses at a multiplicity of infection of 1. 2013 PloS one Figure IV S9A 38 41 NP;NP 42;59 44;61 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. (B) Mini-genome assay using the S9A NP mutant. 2013 PloS one Figure IV S9A 32 35 NP 36 38 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. (B) Qip1-silenced HEK-293 cells were transfected with plasmids encoding PB2, PB1, PA, WT or S9A NP and vNP-luc, and luciferase activity was measured after 48 h. 2013 PloS one Figure IV S9A 92 95 NP;PA;PB1;PB2 96;82;77;72 98;84;80;75 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. (D) Competition binding assay of importin alpha to WT and S9A NP110aa-binding beads. 2013 PloS one Figure IV S9A 58 61 NP 62 64 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. (D) Qip1-silenced A549 cells were transfected with pCAGGS encoding mRFP-Flag-tagged WT or S9A NP110aa. 2013 PloS one Figure IV S9A 90 93 NP 94 96 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. (E) Binding of WT full length NP, WT and S9A NP110aa to the three importin alpha isoforms in HEK-293T cells. 2013 PloS one Figure IV S9A 41 44 NP;NP 30;45 32;47 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. (E) The Qip1-silenced A549 cells were infected with A/WSN/33 virus containing WT or S9A NP at an MOI of 0.01. 2013 PloS one Figure IV S9A 84 87 NP 88 90 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. After washing with buffer, the binding of importin alpha to WT and S9A NP110aa was detected by Western blotting with anti-Rch1, -Qip1 and -NPI-1 mAbs. 2013 PloS one Figure IV S9A 67 70 NP 71 73 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. All three importin alpha proteins (50 microM) were incubated with WT and S9A NP110aa-binding Flag beads at 4 C for 1 day. 2013 PloS one Figure IV S9A 73 76 NP 77 79 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. Both GST beads bound to Rch1, Qip1, NPI-1 and non-bound GST beads were incubated with the WT, 14-110aa, R8A or S9A NP110aa proteins. 2013 PloS one Figure IV R8A;S9A 104;111 107;114 NP 115 117 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. Data represent the relative growth of the S9A mutant compared with that of the WT. 2013 PloS one Figure IV S9A 42 45 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. HEK-293T cells were transfected with pCAGGS encoding mRFP-Flag-tagged WT full length NP, WT or S9A NP110aa, cells were lysed and proteins were purified using ANTI-FLAG M2 Agarose beads and the 3x Flag peptide. 2013 PloS one Figure IV S9A 95 98 M2;NP;NP 168;85;99 170;87;101 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. The amount of importin alpha proteins which bound to WT NP110aa and S9A NP110aa were calculated by analyzing the standard curves as shown in C right panel. 2013 PloS one Figure IV S9A 68 71 NP;NP 56;72 58;74 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. The amounts of importin alpha proteins which bound to WT NP, WT NP110aa and S9A NP110aa were calculated by analyzing the standard curves as shown in C right panel. 2013 PloS one Figure IV S9A 76 79 NP;NP;NP 57;64;80 59;66;82 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. The effect of the S9A mutation on viral transcription was determined using a mini-genome assay with the plasmid encoding the S9A NP mutant. 2013 PloS one Figure IV S9A;S9A 18;125 21;128 NP 129 131 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. To analyze the effect of the S9A mutation on vRNA transcription, luciferase activity was compared with that generated by the WT. 2013 PloS one Figure IV S9A 29 32 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. To generate the R8A NP and S9A NP mutant viruses, plasmids expressing mutant NP proteins and genomes were used as a substitute for the WT plasmid. 2013 PloS one Figure IV R8A;S9A 16;27 19;30 NP;NP;NP 20;31;77 22;33;79 23383318 Inhibitors of the influenza A virus M2 proton channel discovered using a high-throughput yeast growth restoration assay. Yeast strains containing an empty plasmid (A) or plasmid bearing WT M2 (B), S31N M2 (C) or V27A M2 (D) were distributed into 96-well plates and their growth was measured over time following transfer at 0h to medium containing galactose and addition of the indicated concentrations of amantadine. 2013 PloS one Figure IV S31N;V27A 76;91 80;95 M2;M2;M2 68;81;96 70;83;98 23437033 Quantitative description of glycan-receptor binding of influenza A virus H7 hemagglutinin. D, shows dose-dependent direct glycan array binding of mutant mNY/107:A135T HA. 2013 PloS one Figure IV A135T 70 75 HA 76 78 23437033 Quantitative description of glycan-receptor binding of influenza A virus H7 hemagglutinin. Glycan receptor-binding specificity of FC, CC, NY/107 and mNY/107:A135T HA. 2013 PloS one Figure IV A135T 66 71 HA 72 74 23437217 Parallel screening of wild-type and drug-resistant targets for anti-resistance neuraminidase inhibitors. (C) Fold changes in IC50 of RB19, zanamivir, and GS4071 when the dual H275Y/I223R mutation arises. 2013 PloS one Figure IV H275Y;I223R 70;76 75;81 23555270 Monomeric nucleoprotein of influenza A virus. Comparison of the kinetics of the formation of NP-RNA complexes using a 24 nt ribonucleotide by wt monomeric NP and the S165D mutant monitored by dynamic light scattering. 2013 PLoS pathogens Figure IV S165D 120 125 NP;NP 47;109 49;111 23555270 Monomeric nucleoprotein of influenza A virus. Comparison of the R416A monomer structure with the H1N1 and H5N1 wt trimer structures. 2013 PLoS pathogens Figure IV R416A 18 23 23555270 Monomeric nucleoprotein of influenza A virus. Kinetics of formation of NP-RNA rings by the S165D mutant using a 51 nt ribonucleotide as followed by negative staining EM. 2013 PLoS pathogens Figure IV S165D 45 50 NP 25 27 23555270 Monomeric nucleoprotein of influenza A virus. Monomeric wt and R416A NP. 2013 PLoS pathogens Figure IV R416A 17 22 NP 23 25 23555270 Monomeric nucleoprotein of influenza A virus. Monomeric wt and S165D NP. 2013 PLoS pathogens Figure IV S165D 17 22 NP 23 25 23555270 Monomeric nucleoprotein of influenza A virus. Trimeric wt and obligate trimeric Y148A mutant NP. 2013 PLoS pathogens Figure IV Y148A 34 39 NP 47 49 23593230 Effect of cysteine mutations in the extracellular domain of CM2 on the influenza C virus replication. (A) (B) WT-, CM2-deficient (DeltaCM2)- or C1620A-VLPs were generated and purified as described in Materials and Methods. 2013 PloS one Figure IV C1620A 42 48 CM2 13 16 23593230 Effect of cysteine mutations in the extracellular domain of CM2 on the influenza C virus replication. (C) (D) HMV-II cells infected with mock, WT-VLPs or C1620A-VLPs, followed by superinfection with AA/50, were incubated. 2013 PloS one Figure IV C1620A 52 58 23593230 Effect of cysteine mutations in the extracellular domain of CM2 on the influenza C virus replication. (E) HMV-II cells infected with WT- or C1620A-VLPs were incubated at 4 C for 30 min and then transferred to 33 C, followed by incubation for a further 60 min. 2013 PloS one Figure IV C1620A 38 44 23593230 Effect of cysteine mutations in the extracellular domain of CM2 on the influenza C virus replication. HMV-II cells infected with WT- or C1620A-VLPs containing Luc-vRNA were lysed at the indicated periods (hrs) after infection, and the Luc activities in the respective lysates were quantified (D). 2013 PloS one Figure IV C1620A 34 40 23626667 Quantitative characterization of glycan-receptor binding of H9N2 influenza A virus hemagglutinin. A, Dose-dependent direct glycan array binding of mWF10:T189A HA (left) shows increased specificity to the human receptor 6'SLN-LN when compared to WF10 ( Figure 1A, left panel). 2013 PloS one Figure IV T189A;T189A 56;55 61;60 HA 61 63 23626667 Quantitative characterization of glycan-receptor binding of H9N2 influenza A virus hemagglutinin. A, shows dose-dependent direct glycan array binding of mQa88:Q226L. 2013 PloS one Figure IV Q226L;Q226L 62;61 67;66 23626667 Quantitative characterization of glycan-receptor binding of H9N2 influenza A virus hemagglutinin. B, Dose-dependent direct glycan array binding of mWF10:L226Q HA (left) shows a complete reversal in binding from human (6' SLN-LN) to avian receptors (3'SLN-LN and 3'SLN-LN-LN). 2013 PloS one Figure IV L226Q 55 60 HA 61 63 23626667 Quantitative characterization of glycan-receptor binding of H9N2 influenza A virus hemagglutinin. B, shows dose-dependent direct glycan array binding of mQa88:Q226L/T189A. 2013 PloS one Figure IV Q226L;T189A 61;67 66;72 23626667 Quantitative characterization of glycan-receptor binding of H9N2 influenza A virus hemagglutinin. C, Dose-dependent direct binding of mQa88:T189A shows that this mutant retains avian receptor-binding but specificity for avian receptors is higher when compared to mQa88 HA in Figure 1B. 2013 PloS one Figure IV T189A 42 47 HA 171 173 23626667 Quantitative characterization of glycan-receptor binding of H9N2 influenza A virus hemagglutinin. D, Consistent with glycan array-binding mQa88:Q226L/T189A HA shows extensive staining of apical surface of human tracheal epithelium and mQa88:T189A HA shows extensive staining of human alveolar section. 2013 PloS one Figure IV Q226L;T189A;T189A 46;52;143 51;57;148 HA;HA 58;149 60;151 23626667 Quantitative characterization of glycan-receptor binding of H9N2 influenza A virus hemagglutinin. Glycan receptor-binding properties of mWF10:T189A and mWF10:L226Q. 2013 PloS one Figure IV T189A;L226Q 44;60 49;65 23626667 Quantitative characterization of glycan-receptor binding of H9N2 influenza A virus hemagglutinin. Glycan receptor-binding specificity of mQa88:Q226L, mQa88:T189A and double mutant mQa88:Q226L/T189A HA. 2013 PloS one Figure IV Q226L;T189A;Q226L;T189A 45;58;88;94 50;63;93;99 HA 100 102 23626667 Quantitative characterization of glycan-receptor binding of H9N2 influenza A virus hemagglutinin. The additional T189A mutation increases binding specificity for human receptor (6'SLN-LN). 2013 PloS one Figure IV T189A 15 20 23626667 Quantitative characterization of glycan-receptor binding of H9N2 influenza A virus hemagglutinin. The single Q226L mutation shows binding exclusively to human receptors (6' SLN-LN) on the array. 2013 PloS one Figure IV Q226L 11 16 23626667 Quantitative characterization of glycan-receptor binding of H9N2 influenza A virus hemagglutinin. Tissue staining (right) shows poor staining of apical surface of human tracheal epithelia and extensive staining of human alveolar sections by mWF10:L226Q HA (in green) shown against propidium iodide staining (in red). 2013 PloS one Figure IV L226Q 149 154 HA 155 157 23626667 Quantitative characterization of glycan-receptor binding of H9N2 influenza A virus hemagglutinin. Tissue-binding of mWF10:T189A HA (right) shows extensive staining of apical surface of human tracheal section and minimal staining of human alveolar section mWF10: T189A HA in green against propidium iodide in red). 2013 PloS one Figure IV T189A;T189A 24;164 29;169 HA;HA 30;170 32;172 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. (B) To control for differences in infection rate between wildtype and N156K viruses, antibody binding is expressed as the proportion relative to K142N+N156K antiserum (% positive for test antiserum/% positive K142N+N156K antiserum). 2013 PLoS pathogens Figure IV N156K;N156K;K142N;N156K;K142N 70;151;145;215;209 75;156;150;220;214 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. (D-E) The proportion of N156 wildtype (black) and N156K (white) viruses in peak day nasal wash samples from all ferrets from the MIV+IFA (D) and N156K naive (E) passage lines quantified by pyrosequencing. 2013 PLoS pathogens Figure IV N156K;N156K 50;145 55;150 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. (E) Model of N156 wildtype (green HA/yellow ligand), N156K (cyan HA/red ligand) and N156E (blue HA/purple ligand) shown with alpha-2,3 host receptor analogue. 2013 PLoS pathogens Figure IV N156K;N156E 53;84 58;89 HA;HA;HA 34;65;96 36;67;98 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. (F-G) Mixtures of (F) N156 wildtype and N156K or (G) N156K and K142N+N156K viruses were passaged by contact transmission through naive ferrets. 2013 PLoS pathogens Figure IV N156K;N156K;N156K;K142N 40;53;69;63 45;58;74;68 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. (F) Comparison of N156 wildtype (green HA/yellow ligand) and N156K (cyan HA/red ligand) with double mutant K153E+N156K (light blue HA/orange ligand). 2013 PLoS pathogens Figure IV N156K;N156K;K153E 61;113;107 66;118;112 HA;HA;HA 39;73;131 41;75;133 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. 3-D modeling of HA containing N156K and cell culture adaptations. 2013 PLoS pathogens Figure IV N156K 30 35 HA 16 18 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. After 48 h, cells were analysed for binding of (A) anti-HA mAbs, (B) post-immunization ferret antisera (MIV or MIV+IFA) or post-infection ferret antisera (wildtype A/Tasmania/2004/2009, N156K or K142N+N156K virus) or (C) synthetic glycans. 2013 PLoS pathogens Figure IV N156K;N156K;K142N 186;201;195 191;206;200 HA 56 58 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. Growth, detection and adaptation of N156K virus in cell cultures. 2013 PLoS pathogens Figure IV N156K 36 41 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. The proportion of N156 wildtype (black), N156K (white) or K142N+N156K (striped) in peak day nasal wash samples was quantified by pyrosequencing. 2013 PLoS pathogens Figure IV N156K;N156K;K142N 41;64;58 46;69;63 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. Virus replication and transmission kinetics in ferret passage lines and emergence and persistence of the N156K mutant. 2013 PLoS pathogens Figure IV N156K 105 110 23717200 Prolonged influenza virus shedding and emergence of antiviral resistance in immunocompromised patients and ferrets. (a) Schematic of the experimental setup in which 6 groups of ferrets (n = 6) were infected on day 0 with wild type (WT; groups 1-3; green) or oseltamivir resistant (H275Y) mutant virus (groups 4-6; magenta). 2013 PLoS pathogens Figure IV H275Y 165 170 23717200 Prolonged influenza virus shedding and emergence of antiviral resistance in immunocompromised patients and ferrets. Bar colours indicate the absence (green) or presence (magenta) of the H275Y oseltamivir resistance mutation as detected by RT-PCR. 2013 PLoS pathogens Figure IV H275Y 70 75 23717200 Prolonged influenza virus shedding and emergence of antiviral resistance in immunocompromised patients and ferrets. Bar colours indicate the absence (green) or presence (magenta) of the oseltamivir resistance mutation H275Y as detected by RT-PCR. 2013 PLoS pathogens Figure IV H275Y 102 107 23717200 Prolonged influenza virus shedding and emergence of antiviral resistance in immunocompromised patients and ferrets. Bars are coloured white for those respiratory samples in which the H275Y genotype could not be determined or in cases when genotyping was not performed. 2013 PLoS pathogens Figure IV H275Y 67 72 23717200 Prolonged influenza virus shedding and emergence of antiviral resistance in immunocompromised patients and ferrets. Emergence of oseltamivir resistance mutation H275Y in influenza virus quasispecies from ferrets infected with wild type virus. 2013 PLoS pathogens Figure IV H275Y 45 50 23717200 Prolonged influenza virus shedding and emergence of antiviral resistance in immunocompromised patients and ferrets. Groups of ferrets were infected with wild type (green;a;c) or oseltamivir resistant (H275Y) mutant virus (magenta;b;d). 2013 PLoS pathogens Figure IV H275Y 85 90 23717200 Prolonged influenza virus shedding and emergence of antiviral resistance in immunocompromised patients and ferrets. The animals were infected either with wild type (WT; green; a, b) or mutant virus (H275Y; magenta; c, d). 2013 PLoS pathogens Figure IV H275Y 83 88 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. (A) Confluent monolayers of Madin-Darby canine kidney (MDCK) cells were inoculated with the rNY1682-WT (WT) or rNY1682-D701N (D701N) viruses at 0.01 TCID50/cell. 2013 PloS one Figure IV D701N;D701N 119;126 124;131 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. (B) Confluent mouse rectal epithelial carcinoma cells (CMT-93) were inoculated with rNY1682-WT (WT) or rNY1682-D701N (D701N) viruses at 0.01 TCID50/cell and supernatants were harvested at 12, 24, 48, 72 and 96 hpi. 2013 PloS one Figure IV D701N;D701N 111;118 116;123 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. (B) Mortality associated with infection by the recombinant viruses (rNY1682-WT (WT) or rNY1682-D701N (D701N)) was also examined. 2013 PloS one Figure IV D701N;D701N 95;102 100;107 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. (C, D, E) Confluent human lung epithelial cells (Calu-3) were inoculated with rNY1682-WT (WT) or rNY1682-D701N (D701N) viruses at 0.02 TCID50/cell and supernatants were harvested at 2, 24, 48, 72 and 96 hpi. 2013 PloS one Figure IV D701N;D701N 105;112 110;117 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. * Indicates that the difference between the PB2-WT and PB2-D701N was statistically significant (p<0.05, t-test). 2013 PloS one Figure IV D701N 59 64 PB2;PB2 44;55 47;58 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. Due to the variation in cytokine responses among different donors, for each donor, cytokine/chemokine induced by WT was set as 100% and cytokine/chemokine induced by D701N or Mock was presented as a percentage of WT. 2013 PloS one Figure IV D701N 166 171 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. Five-week-old female BALB/cJ mice (n=5/group) were inoculated intranasally with 50 microl containing 1x103, 104, 105, or 106 TCID50 of rNY1682-D701N or they were mock inoculated. 2013 PloS one Figure IV D701N 143 148 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. Horizontal bar in each group indicates the average value from seven donors and * indicates a statistical difference between WT and D701N (p<0.05, ANOVA). 2013 PloS one Figure IV D701N 131 136 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. Human alveolar type I-like cells were infected at 37 C with MOI of 0.01 PFU/cell of the rNY1682-WT (WT) or rNY1682-D701N (D701N) virus, or were mock infected (Mock). 2013 PloS one Figure IV D701N;D701N 115;122 120;127 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. Pathogenicity of rNY1682-WT, rNY1682-E158G, rNY1682-E627K, and rNY1682-D701N viruses in mice. 2013 PloS one Figure IV E158G;E627K;D701N 37;52;71 42;57;76 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. PB2-D701N substitution enhances viral RNA polymerase activity in human cells. 2013 PloS one Figure IV D701N 4 9 PB2 0 3 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. Replication kinetics of rNY1682-WT and rNY1682-D701N in vitro. 2013 PloS one Figure IV D701N 47 52 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. Representative growth kinetics of the WT and D701N viruses in one donor cells are shown. 2013 PloS one Figure IV D701N 45 50 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. Respiratory droplet transmissibility of rNY1682-WT and rNY1682-D701N viruses in ferrets. 2013 PloS one Figure IV D701N 63 68 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. Six-week-old female BALB/cJ mice (n=3/group/time-point) were inoculated intranasally with 50 microl containing 103 TCID50 of rNY1682-WT (WT) or rNY1682-D701N (D701N). 2013 PloS one Figure IV D701N;D701N 152;159 157;164 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. Six-week-old female BALB/cJ mice (n=5/group) were inoculated intranasally with 50 microl containing 105 TCID50 of different recombinant viruses (rNY1682-WT (WT), rNY1682-E158G (E158G), rNY1682-E627K (E627K), or rNY1682-D701N (D701N)) or they were mock inoculated (Mock). 2013 PloS one Figure IV E158G;E158G;E627K;E627K;D701N;D701N 170;177;193;200;219;226 175;182;198;205;224;231 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. The average body weight of each group is shown with error bars representing SD (+/-), and a significant difference between D701N and WT or E627K was evident as early as 4 d.p.i (*, p<0.01, ANOVA). 2013 PloS one Figure IV D701N;E627K 123;139 128;144 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. The average of each group is shown with error bars representing SD(+/-), and * indicates a statistical difference between WT and D701N (p<0.05, ANOVA). 2013 PloS one Figure IV D701N 129 134 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. The HEK-293T cells were also co-transfected with plasmids expressing the NY1682 PB1, PA and NP, and one of the PB2 clones (WT, or D701N) to generate different viral RdRp. 2013 PloS one Figure IV D701N 130 135 NP;PA;PB1;PB2 92;85;80;111 94;87;83;114 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. Three ferrets were inoculated with 106 PFU of (A) rNY1682-WT or (B) rNY1682-D701N virus. 2013 PloS one Figure IV D701N 76 81 23894575 Analysis of adaptation mutants in the hemagglutinin of the influenza A(H1N1)pdm09 virus. A, interactions of S143 in wild-type HA; B, interactions of S143G in variant 1; C, S185 in wild-type HA; D, S185T in variant 1. 2013 PloS one Figure IV S143G;S185T 60;108 65;113 HA;HA 37;101 39;103 23894575 Analysis of adaptation mutants in the hemagglutinin of the influenza A(H1N1)pdm09 virus. Destabilizing effect of mutation E374K. 2013 PloS one Figure IV E374K 33 38 23894575 Analysis of adaptation mutants in the hemagglutinin of the influenza A(H1N1)pdm09 virus. Effect of D222E in receptor binding. 2013 PloS one Figure IV D222E 10 15 23894575 Analysis of adaptation mutants in the hemagglutinin of the influenza A(H1N1)pdm09 virus. Effect of mutation S134T on receptor binding. 2013 PloS one Figure IV S134T 19 24 23894575 Analysis of adaptation mutants in the hemagglutinin of the influenza A(H1N1)pdm09 virus. In D222E, only K219 and E224 interact with galactose, while E222 interacts through water-mediated hydrogen bonds with nearby glycosylations originating at N87. 2013 PloS one Figure IV D222E 3 8 23894575 Analysis of adaptation mutants in the hemagglutinin of the influenza A(H1N1)pdm09 virus. In E374K, the lysine residue interacts only with the oxygen from the amide group of N366. 2013 PloS one Figure IV E374K 3 8 23894575 Analysis of adaptation mutants in the hemagglutinin of the influenza A(H1N1)pdm09 virus. Mutation S134T modifies interactions of HA with the receptor by establishing hydrogen bonds between T134 and sialic acid, and by losing interactions between galactose and D222; instead, D222 in mutant S134T interacts with glycosylations originating at N87. 2013 PloS one Figure IV S134T;S134T 9;201 14;206 HA 40 42 23894575 Analysis of adaptation mutants in the hemagglutinin of the influenza A(H1N1)pdm09 virus. Mutation S185T does not change interactions within the protein (D). 2013 PloS one Figure IV S185T 9 14 23894575 Analysis of adaptation mutants in the hemagglutinin of the influenza A(H1N1)pdm09 virus. Surface electrostatic potential in wild-type and E374K HA. 2013 PloS one Figure IV E374K 49 54 HA 55 57 23894575 Analysis of adaptation mutants in the hemagglutinin of the influenza A(H1N1)pdm09 virus. The E374K mutant exhibits a decrement in negative charge distribution in the stem portion of HA because the carboxyl group from glutamic acid is replaced by an amino group from lysine and interactions with N366 changed, thus exposing the amino group of N366 to the solvent. 2013 PloS one Figure IV E374K 4 9 HA 93 95 23951116 Resistance mutation R292K is induced in influenza A(H6N2) virus by exposure of infected mallards to low levels of oseltamivir. Red (R292K) = mixed genotype R292 and K292. 2013 PloS one Figure IV R292K 5 10 24312396 Conformational polymorphism of m7GTP in crystal structure of the PB2 middle domain from human influenza A virus. Secondary structures are labeled in black and two mutations P453H and I471T are indicated by arrows with blue and red labels, respectively. 2013 PloS one Figure IV P453H;I471T 60;70 65;75 24391498 A single amino acid in the stalk region of the H1N1pdm influenza virus HA protein affects viral fusion, stability and infectivity. (B) Structure modeling of residues HA1-21 and HA2-47, salt bridges between HA1-E21 and HA2-K47 (Bris/10), or HA1-K21 and HA2-E47 (Cal/09 E21K) are indicated. 2014 PLoS pathogens Figure IV E21K 137 141 HA;HA;HA;HA1;HA1;HA1 46;87;121;35;75;109 48;89;123;38;78;112 24558492 Study of oseltamivir and zanamivir resistance-related mutations in influenza viruses isolated from wild mallards in Sweden. (3) - H1N1 R118K mutant; (4) - H1N1 R118K/D151N mutant; (14) - H6N1 R118K/D151N/D198N mutant. 2014 PloS one Figure IV R118K;R118K;D151N;R118K;D151N;D198N 11;36;42;68;74;80 16;41;47;73;79;85 24569063 An investigational antiviral drug, DAS181, effectively inhibits replication of zoonotic influenza A virus subtype H7N9 and protects mice from lethality. Animals (16/group) were intranasally inoculated with 5 50% mouse lethal doses of plaque-purified influenza A virus subtype H7N9, equivalent to 5 x 103 50% tissue culture infective doses (TCID50) of Shanghai/1 wild-type (A, F, K), 104 TCID50 of Shanghai/1 R292K (B, G, L), 1.6 x 105 TCID50 of Taiwan/1 wild-type (C, H, M), or 1.6 x 105 TCID50 of Taiwan/1 R292K (D, I, N). 2014 The Journal of infectious diseases Figure IV R292K;R292K 255;354 260;359 24569063 An investigational antiviral drug, DAS181, effectively inhibits replication of zoonotic influenza A virus subtype H7N9 and protects mice from lethality. Animals (8/group) were intranasally inoculated with 5 50% mouse lethal doses of plaque-purified influenza A virus subtype H7N9, equivalent to 1.6 x 105 50% tissue culture infective doses (TCID50) of Taiwan/1 wild-type (A, B) or 1.6 x 105 TCID50 of Taiwan/1 R292K (C, D). 2014 The Journal of infectious diseases Figure IV R292K 257 262 24569063 An investigational antiviral drug, DAS181, effectively inhibits replication of zoonotic influenza A virus subtype H7N9 and protects mice from lethality. In oseltamivir control groups, mice (n = 8) were infected with 104 TCID50 of Taiwan/1 wild-type (G, H) or R292K (G, I) virus and received twice-daily treatment for 5 days, starting 24 hours after infection. 2014 The Journal of infectious diseases Figure IV R292K 106 111 24667168 Low 2012-13 influenza vaccine effectiveness associated with mutation in the egg-adapted H3N2 vaccine strain not antigenic drift in circulating viruses. Three amino acid differences (Q156H, V186G and Y219S) are owing to mutation in the egg-adapted IVR-165 vaccine strain rather than circulating viruses which instead share identity with the MDCK-passaged WHO reference prototype at these positions. 2014 PloS one Figure IV Q156H;V186G;Y219S 30;37;47 35;42;52 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. Addition of NA V241I and N369K enhances the fitness of earlier H275Y A(H1N1)pdm09 viruses. 2014 PLoS pathogens Figure IV V241I;N369K;H275Y 15;25;63 20;30;68 12 14 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. Donor ferrets were infected with pure populations or virus mixtures of reverse genetics derived A/Perth/261/2009 oseltamivir resistant (rgPerth261 OR) and rgPerth261 V241I, N369K OR. 2014 PLoS pathogens Figure IV V241I;N369K 166;173 171;178 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. Donor ferrets were infected with pure populations or virus mixtures of reverse genetics derived New17 OR (rgNew17 OR) and rgNew17 I241V, K369N OR. 2014 PLoS pathogens Figure IV I241V;K369N 130;137 135;142 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. NA V241I and N369K enhance the expression and activity of A(H1N1)pdm09 NA proteins. 2014 PLoS pathogens Figure IV V241I;N369K 3;13 8;18 NA;NA 0;71 2;73 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. Removal of NA V241I and N369K decreases the fitness of recent H275Y A(H1N1)pdm09 viruses. 2014 PLoS pathogens Figure IV V241I;N369K;H275Y 14;24;62 19;29;67 11 13 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. The H275Y mutation does not compromise the fitness of HNE2011 A(H1N1)pdm09 viruses. 2014 PLoS pathogens Figure IV H275Y 4 9 24795482 A novel I221L substitution in neuraminidase confers high-level resistance to oseltamivir in influenza B viruses. Overlaid structures of the active sites of wild-type (purple; B/Brisbane/60/2008) and mutant (I221L; green; B/Lyon/CHU/15.216/2011) neuraminidase with bound inhibitors oseltamivir (A) and zanamivir (B). 2014 The Journal of infectious diseases Figure IV I221L 94 99 132 145 24941437 Easily accessible polycyclic amines that inhibit the wild-type and amantadine-resistant mutants of the M2 channel of influenza A virus. Representation of compound 18 bound to (left) the wild-type M2 channel and its V27A variant (down and up orientations shown in middle and right panels, respectively). 2014 Journal of medicinal chemistry Figure IV V27A 79 83 M2 60 62 24941437 Easily accessible polycyclic amines that inhibit the wild-type and amantadine-resistant mutants of the M2 channel of influenza A virus. Structures of Amt, Rmt, and Recently Developed Compounds with Potent Activity against A/M2-V27A Mutant Channelsa. 2014 Journal of medicinal chemistry Figure IV V27A 91 95 M2 88 90 24941437 Easily accessible polycyclic amines that inhibit the wild-type and amantadine-resistant mutants of the M2 channel of influenza A virus. The IC50 values denote the reported 50% inhibitory concentrations on A/M2 wt, S31N, and V27A proton channel function. 2014 Journal of medicinal chemistry Figure IV S31N;V27A 78;88 82;92 25078692 A single amino acid substitution in the novel H7N9 influenza A virus NS1 protein increases CPSF30 binding and virulence. 293T cell lysate overexpressing FLAG-CPSF30 was mixed with the indicated bacterially expressed 6His-NS1 protein (WT, L103F, I106M, or L103F/I106M [DM] or the 6His multiple cloning site [6His-MCS] negative control) and pulled down (PD) using Ni-nitrilotriacetic acid (NTA) beads. 2014 Journal of virology Figure IV L103F;I106M;I106M;L103F 117;124;140;134 122;129;145;139 NS1 100 103 25078692 A single amino acid substitution in the novel H7N9 influenza A virus NS1 protein increases CPSF30 binding and virulence. A single I106M substitution in the H7N9 NS1 protein specifically restores efficient CPSF30 binding and inhibition of host cell gene expression. 2014 Journal of virology Figure IV I106M 9 14 NS1 40 43 25078692 A single amino acid substitution in the novel H7N9 influenza A virus NS1 protein increases CPSF30 binding and virulence. Characterization of H7N9-based NS1-WT and NS1-I106M viruses in vitro and in vivo. 2014 Journal of virology Figure IV I106M 46 51 NS1;NS1 31;42 34;45 25078692 A single amino acid substitution in the novel H7N9 influenza A virus NS1 protein increases CPSF30 binding and virulence. Multicycle growth analysis of rSh/1 (6+2) WT and rSh/1 (6+2) NS1-I106M viruses in primary differentiated human airway epithelial (HTBE) cells. 2014 Journal of virology Figure IV I106M 65 70 NS1 61 64 25191344 Prevalence of Oseltamivir-Resistant 2009 H1N1 Influenza Virus among Patients with Pandemic 2009 H1N1 Influenza infection in NRITLD, Tehran, Iran. Allelic discrimination of pandemic 2009 H1N1 influenza virus for H275Y mutation (oseltamivir-resistant genotype) 2011 Tanaffos Figure IV H275Y 65 70 25191344 Prevalence of Oseltamivir-Resistant 2009 H1N1 Influenza Virus among Patients with Pandemic 2009 H1N1 Influenza infection in NRITLD, Tehran, Iran. Allelic discrimination of pandemic 2009 H1N1 influenza virus for H275Y mutation (oseltamivir-resistant genotype). 2011 Tanaffos Figure IV H275Y 65 70 25210166 Accumulation of human-adapting mutations during circulation of A(H1N1)pdm09 influenza virus in humans in the United Kingdom. (b) Human nasal MucilAir cell cultures (HAE; Epithelix) were infected in triplicate with RG viruses based on A/195 that differed only in PA at N321K. 2014 Journal of virology Figure IV N321K 143 148 PA 137 139 25470189 Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel. (A) 2D 13C-1H NOESY (150 ms) experiment for S31N (19-49) VANIG sample in the presence of 11. 2014 Journal of the American Chemical Society Figure IV S31N 44 48 25470189 Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel. (B) The solution NMR structure of M2WJ332 (2)-bound A/M2-S31N (PDB: 2LY0). 2014 Journal of the American Chemical Society Figure IV S31N 57 61 M2 54 56 25470189 Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel. (C) Illustration of relative position of 11 in S31N and WT, based on intermolecular peptide-drug NOEs. 2014 Journal of the American Chemical Society Figure IV S31N 47 51 25470189 Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel. (D) Models calculated with the same peptide-drug NOEs in addition to distance constraints for the peptide obtained for S31N-WJ332 structure. 2014 Journal of the American Chemical Society Figure IV S31N 119 123 25470189 Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel. Design of Dual Inhibitors Targeting Both WT and S31N. 2014 Journal of the American Chemical Society Figure IV S31N 48 52 25470189 Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel. Drug binding orientations in M2-WT and M2-S31N channels. 2014 Journal of the American Chemical Society Figure IV S31N 42 46 M2;M2 29;39 31;41 25470189 Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel. Final MD snapshots of compound 11 bound to the transmembrane segment of WT and S31N M2 in a lipid bilayer. 2014 Journal of the American Chemical Society Figure IV S31N 79 83 M2 84 86 25470189 Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel. Left is for S31N, and right is for WT in both parts C and D. 2014 Journal of the American Chemical Society Figure IV S31N 12 16 25470189 Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel. Models generated using the drug-M2 NOEs were deposited in PDB with codes of 2MUW and 2MUV for drug-bound WT-M2 and the S31N mutant, respectively. 2014 Journal of the American Chemical Society Figure IV S31N 119 123 M2;M2 32;108 34;110 25470189 Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel. Positions of the dual inhibitor 11 in S31N and WT are flipped and mirrored along residue 31, providing a direction to design an inhibitor for all M2 mutants. 2014 Journal of the American Chemical Society Figure IV S31N 38 42 M2 146 148 25470189 Flipping in the pore: discovery of dual inhibitors that bind in different orientations to the wild-type versus the amantadine-resistant S31N mutant of the influenza A virus M2 proton channel. Right: 11 bound within S31N M2 after 100 ns. 2014 Journal of the American Chemical Society Figure IV S31N 23 27 M2 28 30 25742269 Oseltamivir-resistant influenza A(H1N1)pdm2009 strains found in Brazil are endowed with permissive mutations, which compensate the loss of fitness imposed by antiviral resistance. Sequences with the mutation H275Y are shown in red. 2015 Memorias do Instituto Oswaldo Cruz Figure IV H275Y 28 33 25939747 Two polar residues within C-terminal domain of M1 are critical for the formation of influenza A Virions. MDCK cells uninfected (A) and infected with WSN viruses (B) or WSN-S183A virus (C) or WSN-T185A virus (D) at an MOI = 0.5 were examined by transmission electron microscopy at 16 h post-infection. 2015 Cellular microbiology Figure IV S183A;T185A 67;90 72;95 25939747 Two polar residues within C-terminal domain of M1 are critical for the formation of influenza A Virions. Negative staining electron microscopy was used to examine the oligomerization pattern of M1-S183A (D), M1-T185A (E) and the M1-S183A/T185A double-point mutant (F). 2015 Cellular microbiology Figure IV S183A;T185A;S183A;T185A 92;106;127;133 97;111;132;138 M1;M1;M1 89;103;124 91;105;126 25939747 Two polar residues within C-terminal domain of M1 are critical for the formation of influenza A Virions. The viral particles generated by WSN (A) or WSN-S183A virus (B) or WSN-T185A virus (C) infecting MDCK cells were purified by ultracentrifugation and investigated by negative staining electron microscopy. 2015 Cellular microbiology Figure IV S183A;T185A 48;71 53;76 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. (A) Without therapy, the fitness of the WT and MUT-H275Y strains is comparable. 2015 PloS one Figure IV H275Y 51 56 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. (B) In the presence of oseltamivir, the WT has a replicative disadvantage over the MUT-H275Y. 2015 PloS one Figure IV H275Y 87 92 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. (B) Infections with either the MUT-H275Y or the MUT-I223V single mutants over two separate experiments. 2015 PloS one Figure IV H275Y;I223V 35;52 40;57 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. (C) Without therapy, the MUT-H275Y strain already has a fitness advantage over the MUT-I223V strain. 2015 PloS one Figure IV H275Y;I223V 29;87 34;92 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. Impact of the H275Y and I223V NA mutations in the H1N1pdm09 background. 2015 PloS one Figure IV H275Y;I223V 14;24 19;29 30 32 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. Measured H1N1pdm09 WT-I223 (blue circles) and MUT-I223V (green triangles) viral load concentrations for the (A) multiple-cycle, (B) single-cycle, and (C) mock-yield assays. 2015 PloS one Figure IV I223V 50 55 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. Simulated competition between the wild-type, MUT-H275Y and MUT-I223V strains. 2015 PloS one Figure IV H275Y;I223V 49;63 54;68 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. Simulated competition between the WT-I223 and MUT-I223V strains. 2015 PloS one Figure IV I223V 50 55 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. The probability density functions of the key viral replication parameters characterizing the fitness of the WT-H275 and MUT-H275Y H1N1pdm09 strains (from earlier work,), and that of the WT-I223 and MUT-I223V strains are presented side-by-side for comparison. 2015 PloS one Figure IV H275Y;I223V 124;202 129;207 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. To facilitate the comparison across the two separate experiments, the WT distributions have been centred at one (100) and the H275Y and I223V mutants' parameters are shown relative to their respective WT parameters. 2015 PloS one Figure IV H275Y;I223V 126;136 131;141 26056814 Molecular Characterisation of the Haemagglutinin Glycan-Binding Specificity of Egg-Adapted Vaccine Strains of the Pandemic 2009 H1N1 Swine Influenza A Virus. (A) Docked and superimposed confirmations of LSTc (alpha2,6) & LSTa (alpha2,3) in the RBS of A/California/07/09 HA and in the mutated models; (B) The D225G mutant with the docked LSTc (alpha2,6) & LSTa (alpha2,3); (C) LSTc (alpha2,6) docked in the D225G/Q226R double mutant; and (D) Q226R (in orange) superimposed on the D225G/Q226R (in blue) mutant and the docked LSTc (alpha2,6). 2015 Molecules (Basel, Switzerland) Figure IV D225G;D225G;Q226R;Q226R;D225G;Q226R 150;248;254;283;321;327 155;253;259;288;326;332 HA 112 114 26056814 Molecular Characterisation of the Haemagglutinin Glycan-Binding Specificity of Egg-Adapted Vaccine Strains of the Pandemic 2009 H1N1 Swine Influenza A Virus. The binding cavity of the Q226R is narrower than the wild type A/California/07/09 pocket making it more suited to accommodating the extended conformation of the LSTa (alpha2,3) avian receptor analog. 2015 Molecules (Basel, Switzerland) Figure IV Q226R 26 31 26754751 Coupling high-throughput genetics with phylogenetic information reveals an epistatic interaction on the influenza A virus M segment. A209T as a compensatory substitution for Q214H. 2016 BMC genomics Figure IV A209T;Q214H 0;41 5;46 26974849 Effects of egg-adaptation on receptor-binding and antigenic properties of recent influenza A (H3N2) vaccine viruses. Binding curves for egg-propagated Switz13e, CVV X-223 and RG /Vic361e viruses with AA substitutions S219F or I226N to 3-SLN (2a) analogue compared with Vic361e; binding curves for Switz13e, its CVVs X-247 and NIB-88, and RG/Vic361e viruses with AA substitutions S219F or I226N to 6-SLN (2b) receptor-analogue compared with Vic361e; binding curves for exclusively cell culture680 propagated Vic361c and Switz13c, and RG/Vic361c virus bearing AA substitution H156R to 6-SLN receptor-analogue (2c). 2016 The Journal of general virology Figure IV S219F;I226N;S219F;I226N;H156R 100;109;262;271;457 105;114;267;276;462 26974849 Effects of egg-adaptation on receptor-binding and antigenic properties of recent influenza A (H3N2) vaccine viruses. Binding curves for egg-propagated Vic361e and CVV IVR-165, X-217, and NIB-79 to 3-SLN analogue (a) and 6-SLN analogue (d); binding curves for egg-propagated RG viruses bearing AA substitutions R156Q or S219Y or with the combined R156Q+S219Y substitutions compared to egg-propagated Vic361e for 3-SLN (b) and 6-SLN (e); binding curves for egg-propagated RG viruses bearing AA substitutions D190E or R156H or V186G compared to egg-propagated Vic361e for 3-SLN (c) and 6-SLN (f). 2016 The Journal of general virology Figure IV R156Q;S219Y;R156Q;S219Y;D190E;R156H;V186G 193;202;229;235;389;398;407 198;207;234;240;394;403;412 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. (A) 293T cells expressing the WT or G234E A/Perth/16/2009 HA were incubated with a positive control antibody (left panel) or 39.29 (middle and right panels) at pH 7 (left and middle panels) or 4.8 (right panel). 2016 PLoS pathogens Figure IV G234E 36 41 HA 58 60 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. (B) Hela cells expressing the WT or G234E A/Perth/16/2009 HA were treated with trypsin to activate HA0 and then incubated with either 39.29 or a negative control antibody before pH drop to 5.4 to induce maximal cell-cell fusion. 2016 PLoS pathogens Figure IV G234E 36 41 HA 58 60 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. 293T cells expressing the Q387K, D391Y, F175Y/D391G or WT A/Perth/16/2009 HA were collected before (Stage 1) or after (Stage 2) trypsin treatment to activate HA0. 2016 PLoS pathogens Figure IV Q387K;D391Y;F175Y;D391G 26;33;40;46 31;38;45;51 HA 74 76 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. 39.29 was able to block the fusion mediated by the G234E mutant HA. 2016 PLoS pathogens Figure IV G234E 51 56 HA 64 66 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. Binding and fusion properties of the Q386K, D390Y and D390G mutant HAs of A/California/7/2009. 2016 PLoS pathogens Figure IV Q386K;D390Y;D390G 37;44;54 42;49;59 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. The G234E mutant HA of A/Perth/16/2009 binds and is blocked by 39.29 as well as the WT HA. 2016 PLoS pathogens Figure IV G234E 4 9 HA;HA 17;87 19;89 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. The Q387K, D391Y and D391G mutations of the A/Perth/16/2009 resistant viruses were introduced into the corresponding residues of the A/California/7/2009 HA to generate the Q386K, D390Y and D390G mutant HAs. 2016 PLoS pathogens Figure IV Q387K;D391Y;D391G;Q386K;D390Y;D390G 4;11;21;172;179;189 9;16;26;177;184;194 HA 153 155 27405392 G45R mutation in the nonstructural protein 1 of A/Puerto Rico/8/1934 (H1N1) enhances viral replication independent of dsRNA-binding activity and type I interferon biology. a The expression levels of IFNalpha, IFNbeta and NS1 in A549 cells infected with rX31 virus encoding WT or G45R NS1 at 8 h post infection. 2016 Virology journal Figure IV G45R 107 111 NS1;NS1 49;112 52;115 27405392 G45R mutation in the nonstructural protein 1 of A/Puerto Rico/8/1934 (H1N1) enhances viral replication independent of dsRNA-binding activity and type I interferon biology. b Growth of rX31 viruses encoding PR8 NS1 (WT and G45R). 2016 Virology journal Figure IV G45R 50 54 NS1 38 41 27405392 G45R mutation in the nonstructural protein 1 of A/Puerto Rico/8/1934 (H1N1) enhances viral replication independent of dsRNA-binding activity and type I interferon biology. b The viruses containing PR8 NS1, IA30 NS1, chimera 1 or chimera 2, and c PR8 NS1 with a single amino acid mutation (G45R, K55E, I68V and K70E) were infected in triplicate in A549 cells at an MOI of 0.01. 2016 Virology journal Figure IV G45R;K55E;I68V;K70E 117;123;129;138 121;127;133;142 NS1;NS1;NS1 29;39;78 32;42;81 27405392 G45R mutation in the nonstructural protein 1 of A/Puerto Rico/8/1934 (H1N1) enhances viral replication independent of dsRNA-binding activity and type I interferon biology. Replication kinetics of the rX31 virus encoding PR8 NS1s (WT, G45R or R38AK41A (AA)) in wild type (WT) and type I IFN receptor null (IFNARnull) Let1 cells. 2016 Virology journal Figure IV G45R 62 66 NS1 52 56 27405392 G45R mutation in the nonstructural protein 1 of A/Puerto Rico/8/1934 (H1N1) enhances viral replication independent of dsRNA-binding activity and type I interferon biology. RIG-I mediated IFNbeta-promoter activity in 293 T cells expressing PR8 NS1 (wild type; WT, G45R and R38AK41A; AA), RIG I and IFNbeta-promoter luciferase reporter at 24 h post infection. 2016 Virology journal Figure IV G45R 91 95 NS1 71 74 27405392 G45R mutation in the nonstructural protein 1 of A/Puerto Rico/8/1934 (H1N1) enhances viral replication independent of dsRNA-binding activity and type I interferon biology. rX31 virus with G45R NS1 also replicated to significantly high titer compared to the WT virus early in infection. 2016 Virology journal Figure IV G45R 16 20 NS1 21 24 27405392 G45R mutation in the nonstructural protein 1 of A/Puerto Rico/8/1934 (H1N1) enhances viral replication independent of dsRNA-binding activity and type I interferon biology. rX31 with G45R NS1 induced significantly high level of IFNalpha, IFNbeta and NS1 expression compared to the WT virus. 2016 Virology journal Figure IV G45R 10 14 NS1;NS1 15;77 18;80 27405392 G45R mutation in the nonstructural protein 1 of A/Puerto Rico/8/1934 (H1N1) enhances viral replication independent of dsRNA-binding activity and type I interferon biology. rX31 with G45R replicated to significantly higher titer that WT in both a WT and b IFNARnull Let1 cells. 2016 Virology journal Figure IV G45R 10 14 27405392 G45R mutation in the nonstructural protein 1 of A/Puerto Rico/8/1934 (H1N1) enhances viral replication independent of dsRNA-binding activity and type I interferon biology. The G45R/NS1 bound to dsRNA with lower affinity than the wild type (WT). 2016 Virology journal Figure IV G45R 4 8 NS1 9 12 27405392 G45R mutation in the nonstructural protein 1 of A/Puerto Rico/8/1934 (H1N1) enhances viral replication independent of dsRNA-binding activity and type I interferon biology. WT and G45R NS1s decreased the luciferase expression in dose-dependent manner by inhibition of RIG-I mediated IFNbeta-promoter activity. 2016 Virology journal Figure IV G45R 7 11 NS1 12 16 27535054 NS1 Protein Mutation I64T Affects Interferon Responses and Virulence of Circulating H3N2 Human Influenza A Viruses. IAV H3N2 NS1 protein I64T mutation decreases the binding to CPSF30 without significantly affecting the binding to dsRNA. 2016 Journal of virology Figure IV I64T 21 25 NS1 9 12 27535054 NS1 Protein Mutation I64T Affects Interferon Responses and Virulence of Circulating H3N2 Human Influenza A Viruses. Mutation I64T in IAV 1918 H1N1 NS1 affects its ability to inhibit general gene expression and innate immune responses. 2016 Journal of virology Figure IV I64T 9 13 NS1 31 34 27630240 Human Monoclonal Antibody 81.39a Effectively Neutralizes Emerging Influenza A Viruses of Group 1 and 2 Hemagglutinins. Viral titers in lungs (A, D, G, J, and M), change in body weight (B, E, H, K, and N), and survival (C, F, I, L, and O) of mice inoculated with 105.6 EID50 of H5N2 (A to C), 106.6 EID50 of H5N8 (D to F), 105.1 TCID50 of H6N1 (G to I), 105.2 TCID50 of A(H7N9) wild-type (J to L), or 105.2 TCID50 of A(H7N9) HA2-Asp19Gly (M to O) virus and treated at 24 hpi for A(H5N2), A(H5N8), and A(H6N1) or 48 hpi for A(H7N9) with 81.39a at the indicated dose. 2016 Journal of virology Figure IV D19G 309 317 HA 305 307 27714496 Community- and hospital-acquired infections with oseltamivir- and peramivir-resistant influenza A(H1N1)pdm09 viruses during the 2015-2016 season in Japan. Phylogenetic analysis of the hemagglutinin (a) and neuraminidase gene (b) of the five H275Y mutant influenza A(H1N1)pdm09 strains isolated in Niigata and Nagasaki, Japan in January to February 2016. 2017 Virus genes Figure IV H275Y 86 91 HA;NA 29;51 42;64 27714496 Community- and hospital-acquired infections with oseltamivir- and peramivir-resistant influenza A(H1N1)pdm09 viruses during the 2015-2016 season in Japan. The H275Y mutant strains are shown in red, and those detected in the 2015/2016 season are indicated in closed circle. 2017 Virus genes Figure IV H275Y 4 9 27741319 Cross-Neutralising Nanobodies Bind to a Conserved Pocket in the Hemagglutinin Stem Region Identified Using Yeast Display and Deep Mutational Scanning. Absence of binding for D19A,Y34M, I45F and D46N mutation are indicated with a black arrow. 2016 PloS one Figure IV D19A;Y34M;I45F;D46N 23;28;34;43 27;32;38;47 27741319 Cross-Neutralising Nanobodies Bind to a Conserved Pocket in the Hemagglutinin Stem Region Identified Using Yeast Display and Deep Mutational Scanning. The epitope map shows mutational hotspots and coldspots within the region Ile6 and Glu68 spanning the HA2 domain (region HA1-Gly303 to HA2-Ala5, which gave only 'coldspots' except R329G for R1a-B6, is not included in Fig 4A. 2016 PloS one Figure IV R329G 180 185 HA;HA;HA1 102;135;121 104;137;124 27849220 Surveillance of antiviral resistance markers in Argentina: detection of E119V neuraminidase mutation in a post-treatment immunocompromised patient. (A) a quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) amplification plot corresponding to the wild-type E119 virus; (B) a qRT-PCR amplification plot corresponding to the mixture of E119 and V119 viral subpopulations; (C) a Sanger sequencing chromatogram showing base substitutions in the codon for residue 119 of the neuraminidase gene in the pre-treatment sample; and (D) Sanger sequencing chromatogram of the post-treatment sample; sensitive/resistant E119E/V subpopulations. 2016 Memorias do Instituto Oswaldo Cruz Figure IV E119E;E119V 477;477 484;484 340 353 27869615 Highly Pathogenic Influenza A(H5Nx) Viruses with Altered H5 Receptor-Binding Specificity. A) mutant H5N12.3.4 K222Q (QS); B) mutant H5N12.3.4 S227R (KR); C) mutant H5N12.3.4 K222Q/S227R (QR); D) H5N8 Q222K (KR); E) R227S (QS); F) Q227R/R227S (KS). 2017 Emerging infectious diseases Figure IV K222Q;S227R;K222Q;S227R;Q222K;R227S;R227S;Q227R 20;52;84;90;110;125;146;140 25;57;89;95;115;130;151;145 28282440 H1N1 influenza viruses varying widely in hemagglutinin stability transmit efficiently from swine to swine and to ferrets. (C) Heat map of major amino-acid changes occurring in pigs and ferrets in the Y17H group. 2017 PLoS pathogens Figure IV Y17H 78 82 28282440 H1N1 influenza viruses varying widely in hemagglutinin stability transmit efficiently from swine to swine and to ferrets. HA2-V192A is located in the transmembrane domain and cannot be shown here. 2017 PLoS pathogens Figure IV V192A 4 9 HA 0 2 28282440 H1N1 influenza viruses varying widely in hemagglutinin stability transmit efficiently from swine to swine and to ferrets. Residues HA1-17, HA2-V55I, HA2-106, and HA2-K153E are at positions 24, 399, 450, and 497, respectively, after the initiating methionine in the H1N1 HA protein (H1 numbering). 2017 PLoS pathogens Figure IV V55I;K153E 21;44 25;49 HA;HA;HA;HA;HA1 17;27;40;148;9 19;29;42;150;12 28282440 H1N1 influenza viruses varying widely in hemagglutinin stability transmit efficiently from swine to swine and to ferrets. Significant differences between the WT and Y17H groups are indicated as follows: **P < 0.01, ***P < 0.001, ****P < 0.0001. 2017 PLoS pathogens Figure IV Y17H 43 47 28282440 H1N1 influenza viruses varying widely in hemagglutinin stability transmit efficiently from swine to swine and to ferrets. There was no significant difference between the WT and R106K groups. 2017 PLoS pathogens Figure IV R106K 55 60 28282440 H1N1 influenza viruses varying widely in hemagglutinin stability transmit efficiently from swine to swine and to ferrets. Three-week-old piglets were inoculated intranasally with 1.4 x 106 PFU of WT, Y17H, or R106K viruses in PBS. 2017 PLoS pathogens Figure IV Y17H;R106K 78;87 82;92 28282440 H1N1 influenza viruses varying widely in hemagglutinin stability transmit efficiently from swine to swine and to ferrets. Two-way ANOVA with Bonferroni multiple comparisons was performed, and significant differences between the WT and Y17H groups at time points (*) and at the peak of infection (#) are shown as follows:*,#P < 0.05, ***P < 0.001, ****P < 0.0001. 2017 PLoS pathogens Figure IV Y17H 113 117 28744280 Amino Acid Substitution K470R in the Nucleoprotein Increases the Virulence of H5N1 Influenza A Virus in Mammals. (A) The localization of WT NP and its mutants (K91R/K198R) was determined using IFAs. 2017 Frontiers in microbiology Figure IV K91R;K198R 47;52 51;57 NP 27 29 28744280 Amino Acid Substitution K470R in the Nucleoprotein Increases the Virulence of H5N1 Influenza A Virus in Mammals. (C) 293T cells were transfected with a plasmid expressing WT NP, K91R or K198R mutant and harvested at 30 h p.t. 2017 Frontiers in microbiology Figure IV K91R;K198R 65;73 69;78 NP 61 63 28744280 Amino Acid Substitution K470R in the Nucleoprotein Increases the Virulence of H5N1 Influenza A Virus in Mammals. K91R and K198R mutants disrupted the cell distribution of NP. 2017 Frontiers in microbiology Figure IV K91R;K198R 0;9 4;14 NP 58 60 28744280 Amino Acid Substitution K470R in the Nucleoprotein Increases the Virulence of H5N1 Influenza A Virus in Mammals. The characteristics of the K227R, K229R and K470R mutant recombinant viruses in vitro. 2017 Frontiers in microbiology Figure IV K470R;K227R;K229R 44;27;34 49;32;39 28744280 Amino Acid Substitution K470R in the Nucleoprotein Increases the Virulence of H5N1 Influenza A Virus in Mammals. The characteristics of the K227R, K229R, and K470R mutant recombinant viruses in vivo. 2017 Frontiers in microbiology Figure IV K470R;K227R;K229R 45;27;34 50;32;39 28790432 Conformational modulation of influenza virus hemagglutinin: characterization and in vivo efficacy of monomeric form. (C) Characterization of the single mutant, F88E and V91W, and the double mutant F88E/V91W using size exclusion chromatography (upper and lower panels, respectively). 2017 Scientific reports Figure IV F88E;V91W;V91W;F88E 43;52;85;80 47;56;89;84 28790432 Conformational modulation of influenza virus hemagglutinin: characterization and in vivo efficacy of monomeric form. F88E and V91W mutants were eluted as a monomer, whereas other mutants were eluted as the wild-type HA trimer. 2017 Scientific reports Figure IV F88E;V91W 0;9 4;13 HA 99 101 28790432 Conformational modulation of influenza virus hemagglutinin: characterization and in vivo efficacy of monomeric form. Native PAGE is shown in inset for the pre- and post-thrombin F88E mutant HA. 2017 Scientific reports Figure IV F88E 61 65 HA 73 75 28790432 Conformational modulation of influenza virus hemagglutinin: characterization and in vivo efficacy of monomeric form. The CU44 wild-type HA in this study showed 3 mutations different from the original CU44 HA: HA1 M116I and HA2 I91V and N169S. 2017 Scientific reports Figure IV M116I;I91V;N169S 96;110;119 101;114;124 HA;HA;HA;HA1 19;88;106;92 21;90;108;95 28790432 Conformational modulation of influenza virus hemagglutinin: characterization and in vivo efficacy of monomeric form. The mutation sites are highlighted in red on the crystal structure of CU44 HA at the center with cross-section views along the dashed lines at the left (S199F, V91W and F88E) and right (R75K, R106E and G47E) (middle panel). 2017 Scientific reports Figure IV S199F;V91W;F88E;R75K;R106E;G47E 153;160;169;186;192;202 158;164;173;190;197;206 HA 75 77 28814737 Susceptibility of influenza A(H1N1)/pdm2009, seasonal A(H3N2) and B viruses to Oseltamivir in Guangdong, China between 2009 and 2014. Alignment of the N369K and K432E mutations. 2017 Scientific reports Figure IV N369K;K432E 17;27 22;32 28814737 Susceptibility of influenza A(H1N1)/pdm2009, seasonal A(H3N2) and B viruses to Oseltamivir in Guangdong, China between 2009 and 2014. Alignment of V241I with H275Y. 2017 Scientific reports Figure IV V241I;H275Y 13;24 18;29 28814737 Susceptibility of influenza A(H1N1)/pdm2009, seasonal A(H3N2) and B viruses to Oseltamivir in Guangdong, China between 2009 and 2014. Loop rearrangement of NA resulting from the N386K mutation. 2017 Scientific reports Figure IV N386K 44 49 22 24 28814737 Susceptibility of influenza A(H1N1)/pdm2009, seasonal A(H3N2) and B viruses to Oseltamivir in Guangdong, China between 2009 and 2014. Magenta: NA with V241I alone. 2017 Scientific reports Figure IV V241I 17 22 9 11 28814737 Susceptibility of influenza A(H1N1)/pdm2009, seasonal A(H3N2) and B viruses to Oseltamivir in Guangdong, China between 2009 and 2014. Slate: both V241I and H275Y. 2017 Scientific reports Figure IV V241I;H275Y 12;22 17;27 28814737 Susceptibility of influenza A(H1N1)/pdm2009, seasonal A(H3N2) and B viruses to Oseltamivir in Guangdong, China between 2009 and 2014. Wild-type NA is denoted in violet, and the N369K/K432E NA is in white. 2017 Scientific reports Figure IV N369K;K432E 43;49 48;54 NA;NA 10;55 12;57 28815216 Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity. (D) Competition assays were performed as described above for the PB1 T123A, PA T97I, and PB1 T123A PA T97I mutants in the presence of 5-fluorouracil. 2017 mSphere Figure IV T123A;T97I;T123A;T97I 69;79;93;102 74;83;98;106 PA;PA;PB1;PB1 76;99;65;89 78;101;68;92 28815216 Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity. MDCK cells were infected with wild-type, PB1 T123A, PA T97I, or PB1 T123A PA T97I viruses at an MOI of 0.1 in either 0 muM (solid lines) or 100 muM (dashed lines) 5-fluorouracil. 2017 mSphere Figure IV T123A;T97I;T123A;T97I 45;55;68;77 50;59;73;81 PA;PA;PB1;PB1 52;74;41;64 54;76;44;67 28837667 Influenza NS1 directly modulates Hedgehog signaling during infection. (A) NL20 cells transfected with plasmids expressing GFP (top row), NS1-WT (middle row) or NS1-A122V (bottom row) were stained with anti-NS1 (green) and anti-BMP2 (red) antibodies. 2017 PLoS pathogens Figure IV A122V 94 99 NS1;NS1;NS1 67;90;136 70;93;139 28837667 Influenza NS1 directly modulates Hedgehog signaling during infection. (A) Viral titers were measured for mouse lungs infected with the PR8-WT (blue) and PR8-A122V (red) viruses at 2, 4, and 7 days post infection. 2017 PLoS pathogens Figure IV A122V 87 92 28837667 Influenza NS1 directly modulates Hedgehog signaling during infection. (B) 25 mice per group compiled from three independent experiments were infected with either the PR8-WT (blue) or PR8-A122V viruses (red) at 1x104 pfu and monitored daily for survival (p = 0.0001). 2017 PLoS pathogens Figure IV A122V 117 122 28837667 Influenza NS1 directly modulates Hedgehog signaling during infection. (C) IL6 levels in lung extracts were higher in PR8-A122V infected lungs compared to PR8-WT (n = 4-5, p = 0.005). 2017 PLoS pathogens Figure IV A122V 51 56 28837667 Influenza NS1 directly modulates Hedgehog signaling during infection. (D) PR8-A122V infected cells in mouse lung tissue had higher intensity values of IL6 compared to PR8-WT infected cells. 2017 PLoS pathogens Figure IV A122V 8 13 28837667 Influenza NS1 directly modulates Hedgehog signaling during infection. (E) Uninfected, PR8-WT, or PR8-A122V infected mouse lungs were stained 2 days post infection with anti-NS1 (red) and anti-IL6 (green) antibodies. 2017 PLoS pathogens Figure IV A122V 31 36 NS1 103 106 28837667 Influenza NS1 directly modulates Hedgehog signaling during infection. (M) Equivalent protein levels of the NS1(Vn) and NS1(Vn)-A122V were detected on Western blots of fly extracts using an antibody to C-terminal Myc tags. 2017 PLoS pathogens Figure IV A122V 57 62 NS1;NS1 37;49 40;52 28837667 Influenza NS1 directly modulates Hedgehog signaling during infection. In contrast, Gli1-dependent activation of dpp-lacZEP was not disrupted when co-expressed with NS1 A122V (U vs. 2017 PLoS pathogens Figure IV A122V 98 103 NS1 94 97 28837667 Influenza NS1 directly modulates Hedgehog signaling during infection. NS1-WT (J) produces, on average, lower lifetime values of Alexa 488 compared to discs with no transgene (E) or those expressing the NS1-A122V transgene (O). 2017 PLoS pathogens Figure IV A122V 136 141 NS1;NS1 0;132 3;135 28837667 Influenza NS1 directly modulates Hedgehog signaling during infection. The NS1(PR8) phenotype is significantly rescued by the A122V mutation (K,L). 2017 PLoS pathogens Figure IV A122V 55 60 NS1 4 7 28837667 Influenza NS1 directly modulates Hedgehog signaling during infection. The NS1(Vn) phenotype (A,B) was greatly reduced by the A122V mutation (C,D). 2017 PLoS pathogens Figure IV A122V 55 60 NS1 4 7 28837667 Influenza NS1 directly modulates Hedgehog signaling during infection. Uninfected, PR8-WT, or PR8-A122V infected mouse lungs were stained 2 days post infection with anti-NS1 (red in A and C), anti-Ptch1 (green in A), and anti-BMP2 (green in C) antibodies Asterisks in C denote neighboring uninfected cells that show an upregulation of BMP2. 2017 PLoS pathogens Figure IV A122V 27 32 NS1 99 102 28837667 Influenza NS1 directly modulates Hedgehog signaling during infection. Wing discs with no transgene (no tg) or those ubiquitously expressing NS1(Vn)-WT or NS1(Vn)-A122V from a MS1096 wing-GAL4 driver were co-stained with Ci-155 and NS1 primaries and Alexa-488 (green) and Alexa-555 (red) secondaries, respectively. 2017 PLoS pathogens Figure IV A122V 92 97 NS1;NS1;NS1 70;84;161 73;87;164 28860593 Prerequisites for the acquisition of mammalian pathogenicity by influenza A virus with a prototypic avian PB2 gene. Mixtures (1:1) of wild-type rPB2(01310) and rPB2(01310)-MVV (top) or rPB2(01310) and rPB2(01310)-E627K (bottom) were inoculated in ECEs (a), EDEs (b), and MDCK cells (c). 2017 Scientific reports Figure IV E627K 97 102 28860593 Prerequisites for the acquisition of mammalian pathogenicity by influenza A virus with a prototypic avian PB2 gene. Statistical significance was analysed by two-way analysis of variance with Bonferroni post-test correction (compared to PR8, *P < 0.05; compared to rPB2(01310)-K627E, **P < 0.05). 2017 Scientific reports Figure IV K627E 160 165 28860593 Prerequisites for the acquisition of mammalian pathogenicity by influenza A virus with a prototypic avian PB2 gene. Statistical significance was analysed by two-way analysis of variance with Bonferroni post-test correction (compared to rPB2(01310), *P < 0.05; compared to rPB2(01310)-E627K, **P < 0.05). 2017 Scientific reports Figure IV E627K 168 173 28860593 Prerequisites for the acquisition of mammalian pathogenicity by influenza A virus with a prototypic avian PB2 gene. Statistical significance was analysed using Student's t-test (compared to the polymerase activity of PR8 PB2 gene, *P < 0.05; compared to the polymerase activity of PB2(PR8)-K627E, **P < 0.05). 2017 Scientific reports Figure IV K627E 174 179 PB2;PB2 105;165 108;168 28860593 Prerequisites for the acquisition of mammalian pathogenicity by influenza A virus with a prototypic avian PB2 gene. Statistical significance was calculated using Student's t-test (compared to PB2(01310), *P < 0.05; compared to PB2(01310)-I133V, **P < 0.05; compared to PB2(01310)-MVV, ***P < 0.05). 2017 Scientific reports Figure IV I133V 122 127 PB2;PB2;PB2 76;111;153 79;114;156 28951584 Identification of neuraminidase inhibitors against dual H274Y/I222R mutant strains. (H) The fold change in IC50 values of the inhibitors for H274Y, I222R, and H274 and I222R mutant strains. 2017 Scientific reports Figure IV H274Y;I222R;I222R 57;64;84 62;69;89 29023600 Reduced accumulation of defective viral genomes contributes to severe outcome in influenza virus infected patients. M mut bearing M1 S30N and M2 V86S mutations; M-PA mut, recombinant virus bearing M1 S30N, M2 V86S and PA 529N mutations. 2017 PLoS pathogens Figure IV S30N;V86S;S30N;V86S 17;29;84;93 21;33;88;97 M;M;M1;M1;M2;M2;PA;PA 0;45;14;81;26;90;47;102 1;46;16;83;28;92;49;104 29023600 Reduced accumulation of defective viral genomes contributes to severe outcome in influenza virus infected patients. Mutation PA D529N present in a virus from a fatal case increases mortality in vivo. 2017 PLoS pathogens Figure IV D529N 12 17 PA 9 11 29023600 Reduced accumulation of defective viral genomes contributes to severe outcome in influenza virus infected patients. Mutation PA D529N present in a virus from a fatal case increases pathogenicity and induces altered immune response in vivo. 2017 PLoS pathogens Figure IV D529N 12 17 PA 9 11 29023600 Reduced accumulation of defective viral genomes contributes to severe outcome in influenza virus infected patients. Mutation PA D529N present in a virus from a fatal case reduces DVGs levels in virions of recombinant viruses with two different genetic backgrounds. 2017 PLoS pathogens Figure IV D529N 12 17 PA 9 11 29097654 Role of influenza A virus NP acetylation on viral growth and replication. Titers for rK77Q,K229Q were determined at 72 h.p.i. 2017 Nature communications Figure IV K229Q 17 22 29145498 Antigenicity of the 2015-2016 seasonal H1N1 human influenza virus HA and NA proteins. The approximate location of HA mutation S220T, situated in the Ca1 antigenic site at the subunit interface, is indicated. 2017 PloS one Figure IV S220T 40 45 HA 28 30 29299533 Cooperating H3N2 Influenza Virus Variants Are Not Detectable in Primary Clinical Samples. D151G does not exceed the frequency of library preparation and sequencing errors in unpassaged clinical samples. 2018 mSphere Figure IV D151G 0 5 29299533 Cooperating H3N2 Influenza Virus Variants Are Not Detectable in Primary Clinical Samples. The red vertical line shows the proportion of A-to-G mutations at codon position 2 of amino acid site 151 of NA, which corresponds to the frequency of D151G. 2018 mSphere Figure IV D151G;A2G 151;46 156;82 109 111 29299533 Cooperating H3N2 Influenza Virus Variants Are Not Detectable in Primary Clinical Samples. Typically, the D151 viral variant is encoded by the nucleotides GAT, and the G151 variant is encoded by GGT, meaning that D151G arises as the result of an A-to-G mutation. 2018 mSphere Figure IV D151G 122 127 29312300 Histone Deacetylase 1 Plays an Acetylation-Independent Role in Influenza A Virus Replication. Two K103 NP mutants, K103A and K103R, lacked of regulation by HDAC1, enhanced NP nuclear localization and replication efficiency of the recombinant viruses in vitro. 2017 Frontiers in immunology Figure IV K103A;K103R 21;31 26;36 NP;NP 9;78 11;80 29409570 Early season co-circulation of influenza A(H3N2) and B(Yamagata): interim estimates of 2017/18 vaccine effectiveness, Canada, January 2018. Among Australian 2017 A(H3N2) viruses, 128 (62%) belonged to clade 3C.2a and 15 (7%) of A(H3N2) viruses overall belonged to the clade 3C.2a subgroup bearing T131K + R142K + R261Q substitutions (nextflu subgroup 3). 2018 Euro surveillance Figure IV T131K;R142K;R261Q 157;165;173 162;170;178 29409570 Early season co-circulation of influenza A(H3N2) and B(Yamagata): interim estimates of 2017/18 vaccine effectiveness, Canada, January 2018. Among Canadian 2016/17 A(H3N2) viruses, 43 (19%) belonged to clade 3C.2a and 32 (14%) of A(H3N2) viruses overall belonged to the clade 3C.2a subgroup bearing T131K + R142K + R261Q substitutions (nextflu subgroup 3). 2018 Euro surveillance Figure IV T131K;R142K;R261Q 158;166;174 163;171;179 29409570 Early season co-circulation of influenza A(H3N2) and B(Yamagata): interim estimates of 2017/18 vaccine effectiveness, Canada, January 2018. Of these 228 A(H3N2) viruses, 199 (87%) belonged to clade 3C.2a, and 189 (83%) overall belonged to the clade 3C.2a subgroup bearing T131K + R142K + R261Q substitutions (nextflu subgroup 3). 2018 Euro surveillance Figure IV T131K;R142K;R261Q 132;140;148 137;145;153 29587786 Effects of the S42 residue of the H1N1 swine influenza virus NS1 protein on interferon responses and virus replication. Lane 1, 10,000 bp marker; Lane 2, WT; Lane 3, NS1 S42P; Lane 4, NS1 D92E; and Lane 5, NS1 S42P/D92E. 2018 Virology journal Figure IV S42P;D92E;D92E;S42P 50;68;95;90 54;72;99;94 NS1;NS1;NS1 46;64;86 49;67;89 29587786 Effects of the S42 residue of the H1N1 swine influenza virus NS1 protein on interferon responses and virus replication. MDCK cells were infected with a wt or mutated virus (rSIV NS1 S42P, rSIV NS1 D92E and rSIV NS1 S42P/ D92E) at an MOI of 0.001. 2018 Virology journal Figure IV S42P;D92E;S42P;D92E 62;77;95;101 66;81;99;105 NS1;NS1;NS1 58;73;91 61;76;94 29587786 Effects of the S42 residue of the H1N1 swine influenza virus NS1 protein on interferon responses and virus replication. MDCK cells were infected with the WT and mutated virus (S42P, D92E, S42P/D92E) at an MOI of 0.001. 2018 Virology journal Figure IV S42P;D92E;S42P;D92E 56;62;68;73 60;66;72;77 29587786 Effects of the S42 residue of the H1N1 swine influenza virus NS1 protein on interferon responses and virus replication. NS1 mutations S42P alter virus replication on MDCK cells. 2018 Virology journal Figure IV S42P 14 18 NS1 0 3 29587786 Effects of the S42 residue of the H1N1 swine influenza virus NS1 protein on interferon responses and virus replication. Whole cell lysates obtained from MDCK cells infected with mutants (rSIV NS1 S42P, rSIV NS1 D92E and rSIV NS1 S42P/ D92E) and wild-type viruses at an MOI of 0.001 for 24 h were subjected to SDS-PAGE and western blot analysis. 2018 Virology journal Figure IV S42P;D92E;S42P;D92E 76;91;109;115 80;95;113;119 NS1;NS1;NS1 72;87;105 75;90;108 29587792 Major contribution of the RNA-binding domain of NS1 in the pathogenicity and replication potential of an avian H7N1 influenza virus in chickens. Wt, filled circles; 3841AA, open squares; A149V, black triangles. 2018 Virology journal Figure IV A149V 42 47 29643248 A Single Amino Acid in the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses. Five mice per group were infected with 103 to 106 PFU of Vc_BR60 backbone recombinant viruses rVc_BR60 (A), rVc_BR60PA:K338R (B), rVc_BR60/WI01PA (C), and rVc_BR60/WI01PA:K338R (D). 2018 Journal of virology Figure IV K338R;K338R 119;171 124;176 29643248 A Single Amino Acid in the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses. Five mice per group were infected with 103 to 106 PFU of Ym_WI01 backbone recombinant viruses rYm_WI01 (A), rYm_WI01PA:K338R (B), rYm_WI01/BR60PA (C), and rYm_WI01/BR60PA:K338R (D). 2018 Journal of virology Figure IV K338R;K338R 119;171 124;176 29643248 A Single Amino Acid in the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses. Pathogenicity of rVc_BR60 and PA K338R mutants in mice. 2018 Journal of virology Figure IV K338R 33 38 PA 30 32 29643248 A Single Amino Acid in the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses. Pathogenicity of rVc_BR60, rYm_WI01, and their PA K338R mutants in ferrets. 2018 Journal of virology Figure IV K338R 50 55 PA 47 49 29643248 A Single Amino Acid in the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses. Pathogenicity of rYm_WI01 and PA K338R mutants in mice. 2018 Journal of virology Figure IV K338R 33 38 PA 30 32 29643248 A Single Amino Acid in the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses. Relative activity of IBV polymerase complexes harboring WT PA and the K338R mutant. 2018 Journal of virology Figure IV K338R 70 75 PA 59 61 29688498 Dynamic Variation and Reversion in the Signature Amino Acids of H7N9 Virus During Human Infection. The kinetics of R292K and E627K mutations in sequential samples obtained from patients during disease development. 2018 The Journal of infectious diseases Figure IV R292K;E627K 16;26 21;31 29691337 Identification of the I38T PA Substitution as a Resistance Marker for Next-Generation Influenza Virus Endonuclease Inhibitors. Crystal structures of WT and I38T PAN in complex with RO-7. 2018 mBio Figure IV I38T 29 33 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. IFN-alpha and IFN-beta mRNA levels in lung tissues (E) of mice (n = 3) infected with WT or NS1 R38A/K41A virus for 0, 12, and 24 h p.i. 2018 Frontiers in cellular and infection microbiology Figure IV K41A;R38A 100;95 104;99 NS1 91 94 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. Immunogenicity and protective efficiency of the NS1 R38A/K41A virus. 2018 Frontiers in cellular and infection microbiology Figure IV R38A;K41A 52;57 56;61 NS1 48 51 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. Mice (n = 6) pre-inoculated with PBS or NS1 R38A/K41A virus in the previous experiments were infected with 103.88 PFU of WT WSN virus at 17 d p.i. 2018 Frontiers in cellular and infection microbiology Figure IV R38A;K41A 44;49 48;53 NS1 40 43 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. Mice (n = 6) were intranasally infected with 103 PFU of the third passage NS1 R38A/K41A virus from the Tet-on NS1-expressing Vero cells, WT virus, or PBS, and then monitored daily for survival for 14 days. 2018 Frontiers in cellular and infection microbiology Figure IV R38A;K41A 78;83 82;87 NS1;NS1 74;110 77;113 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. Sera of WT or NS1 R38A/K41A virus infected mice (n = 6) was collected at 3, 7, and 14 d p.i. 2018 Frontiers in cellular and infection microbiology Figure IV R38A;K41A 18;23 22;27 NS1 14 17 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. The 12-plasmid reverse genetics system was used to rescue recombinant influenza viruses A/WSN/33 (WSN) expressing WT or mutant NS1 (R38A, K41A, or R38A/K41A) in 293T and RIG-I-knockout 293T cells. 2018 Frontiers in cellular and infection microbiology Figure IV R38A;K41A;R38A;K41A 132;138;147;152 136;142;151;156 NS1 127 130 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. The 293T cells were transfected with 0, 4, or 8 mug of FLAG-NS1 plasmid and then infected with NS1 R38A/K41A virus at MOI of 0.01. 2018 Frontiers in cellular and infection microbiology Figure IV R38A;K41A 99;104 103;108 NS1;NS1 60;95 63;98 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. The NS1 R38A/K41A and WT viruses from each passage of were obtained from the Tet-On 3G NS1-expressing Vero cells and subjected to plaque assays using MDCK cells to measure the virus titers (D). 2018 Frontiers in cellular and infection microbiology Figure IV R38A;K41A 8;13 12;17 NS1;NS1 4;87 7;90 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. The NS1 R38A/K41A virus exerted full infectivity but its replication is limited in mice. 2018 Frontiers in cellular and infection microbiology Figure IV R38A;K41A 8;13 12;17 NS1 4 7 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. The NS1 R38A/K41A virus loses IFN antagonist activity. 2018 Frontiers in cellular and infection microbiology Figure IV R38A;K41A 8;13 12;17 NS1 4 7 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. The replication of NS1 R38A/K41A virus is limited in IFN-competent cells during successive passaging. 2018 Frontiers in cellular and infection microbiology Figure IV K41A;R38A 28;23 32;27 NS1 19 22 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. The rescued WT and NS1 R38A/K41A virus of F1 were blindly passaged in Vero cells. 2018 Frontiers in cellular and infection microbiology Figure IV R38A;K41A 23;28 27;32 NS1 19 22 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. The survival rate (C) of mice (n = 6) pre-inoculated with PBS or the NS1 R38A/K41A virus against the WT WSN virus was calculated. 2018 Frontiers in cellular and infection microbiology Figure IV R38A;K41A 73;78 77;82 NS1 69 72 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. The Tet-On 3G NS1-expressing Vero cell line facilitates the propagation of the NS1 R38A/K41A virus. 2018 Frontiers in cellular and infection microbiology Figure IV R38A;K41A 83;88 87;92 NS1;NS1 14;79 17;82 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. Virus titers (A) of F2 to F5 WT and NS1 R38A/K41A virus in Vero cells were measured in MDCK cells by plaque assays. 2018 Frontiers in cellular and infection microbiology Figure IV R38A;K41A 40;45 44;49 NS1 36 39 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. (A) For endonuclease activity (lane marked - in all panels), FAM-RNA was incubated with either 0.5-5 muM PA-A-WT, 5-50 muM PA-A-I38T, 5-50 microM PA-B-WT or 50-500 microM PA-B-I38T. 2018 Scientific reports Figure IV I38T;I38T 128;176 132;180 PA;PA;PA;PA 105;123;146;171 107;125;148;173 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. (B) BXA binding stabilizes PA WT (blue, green) and PA I38T (red, purple) for both influenza A (left) and influenza B (right). 2018 Scientific reports Figure IV I38T 54 58 PA;PA 27;51 29;53 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. (B) Superposition of ligand-free (forest green) and BXA-bound PA-B I38T (light magenta sticks for BXA, orange sticks/cartoon for PA). 2018 Scientific reports Figure IV I38T 67 71 PA;PA 62;129 64;131 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. Black triangles compare the RNase activity of WT and I38T forms at equal protein concentration for FluA (5 microM, left) and FluB (50 microM right). 2018 Scientific reports Figure IV I38T 54 58 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. Both BXA (in green for PA WT and light magenta for PA I38T) and the interacting side chains (in teal for WT and orange for I38T) are represented as sticks, Mn ions (purple) and water molecules (red) as spheres. 2018 Scientific reports Figure IV I38T;I38T 54;123 58;127 PA;PA 23;51 25;53 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. BXA interacts with (A) PA-A WT and (B) PA-A I38T by chelating the two manganese ions in the active site. 2018 Scientific reports Figure IV I38T 44 48 PA;PA 23;39 25;41 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. Comparison of PA endonuclease from Flu A and Flu B bound to BXA in either WT or I38T form. 2018 Scientific reports Figure IV I38T 80 84 PA 14 16 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. Complexes PA/BXA are represented in sticks and coloured in chartreuse/TV red for A WT, TV blue/yellow for A I38T, teal/green for B WT, orange/light magenta for B I38T. 2018 Scientific reports Figure IV I38T;I38T 108;162 112;166 PA 10 12 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. For the I38T mutant, both side-chains change rotamer and the contacts with both the main chain and the compound hydrophobic pocket are altered. 2018 Scientific reports Figure IV I38T 8 12 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. Green and purple curves represent the stabilization effect induced by BXA at concentration >=36 muM in complex with WT and I38T constructs, respectively. 2018 Scientific reports Figure IV I38T 123 127 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. In all cases, four compound concentrations were tested, maintaining the molar ratio to protein equal to 0.1-0.2-0.5-1 (in all panels, WT: lanes 4-7, I38T: lanes 9-12). 2018 Scientific reports Figure IV I38T 149 153 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. In the structures, both BXA (in TV red for PA WT and yellow for PA I38T) and the interacting side chains (in chartreuse green for WT and TV blue for I38T) are represented as sticks, Mn ions (purple) and water molecules (red) as spheres. 2018 Scientific reports Figure IV I38T;I38T 67;149 71;153 PA;PA 43;64 45;66 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. Superposition of PA-BXA complexes: (A) PA-A WT and PA-A I38T, (B) PA-B WT and PA-B I38T, (C) PA-A WT and PA-B WT, (D) PA-A I38T and PA-B I38T. 2018 Scientific reports Figure IV I38T;I38T;I38T;I38T 56;83;123;137 60;87;127;141 PA;PA;PA;PA;PA;PA;PA;PA;PA 17;39;51;66;78;93;105;118;132 19;41;53;68;80;95;107;120;134 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. The emergence of Oseltamivir resistant viruses was monitored in throat and nose samples from untreated immunocompetent ferrets (A), untreated immunocompromised ferrets (B) and Oseltamivir treated immunocompromised ferrets (C) by mutation-specific RT-PCR for the Oseltamivir-resistance mutation R292K. 2018 PloS one Figure IV R292K 294 299 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. The frequency of the R292K mutation as determined by Illumina NGS in Oseltamivir treated immunocompromised ferrets. 2018 PloS one Figure IV R292K 21 26 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. The graph depicts the frequency of the R292K mutation over time for each ferret separately, with circles, squares, triangles, down triangles, diamonds and open circles representing ferrets 1-6 respectively. 2018 PloS one Figure IV R292K 39 44 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. The percentage of the R292K variant was determined in pooled throat/nose samples collected at 2, 4, 6, 8 and 10 dpi from immunocompromised ferrets that received Oseltamivir treatment. 2018 PloS one Figure IV R292K 22 27 30050898 Structurally Diverse Polyketides From the Mangrove-Derived Fungus Diaporthe sp. SCSIO 41011 With Their Anti-influenza A Virus Activities. The inhibitory activities of compounds 14, 15, 26, and 5-chloroisorotiorin against influenza A viruses, including A/Puerto Rico/8/34 H274Y (H1N1) (A), A/FM-1/1/47 (H1N1) (B), and A/Aichi/2/68 (H3N2) (C). 2018 Frontiers in chemistry Figure IV H274Y 133 138 30111290 Development of a quadruple qRT-PCR assay for simultaneous identification of highly and low pathogenic H7N9 avian influenza viruses and characterization against oseltamivir resistance. H7-W: detection target for universal H7; H7-M: detection target for highly pathogenic H7; N9-W: detection target for universal N9; N9-M: detection target for R292K mutation of N9. 2018 BMC infectious diseases Figure IV R292K 158 163 N9;N9;N9;N9 90;127;131;176 92;129;133;178 30186261 Acquisition of Innate Inhibitor Resistance and Mammalian Pathogenicity During Egg Adaptation by the H9N2 Avian Influenza Virus. (A) Growth kinetics of rH20N20 and rH20N20-N133T in MDCK cells. 2018 Frontiers in microbiology Figure IV N133T 43 48 30186261 Acquisition of Innate Inhibitor Resistance and Mammalian Pathogenicity During Egg Adaptation by the H9N2 Avian Influenza Virus. Effects of N133T mutation on viral replication and resistance to innate inhibitors. 2018 Frontiers in microbiology Figure IV N133T 11 16 30186261 Acquisition of Innate Inhibitor Resistance and Mammalian Pathogenicity During Egg Adaptation by the H9N2 Avian Influenza Virus. The resistance of rH20N20-N133T in (B) mouse lung extracts and (C) mouse sera was measured by the hemagglutination inhibition assay. 2018 Frontiers in microbiology Figure IV N133T 26 31 30202644 Molecular identification of avian influenza virus subtypes H5N1 and H9N2 in birds from farms and live bird markets and in respiratory patients. Deduced amino acid sequences of the HA protein of our isolates (isolates from farms are marked by an asterisk) in comparison to parent (A/chicken/Egypt/06207-NLQP/2006), classic (A/chicken/Egypt/NLQP-0918/2009), variant (A/chicken/Egypt/0879/2008), vaccinal H5N1 (A/chicken/Egypt/Q1995D/2010), H5N2 (A/duck/Potsdam/1402-6/1986) strains and latest duck in Sharkia (A/duck/Egypt/1435CAS/2014), latest duck in Egypt (A/duck/Egypt/2/2015), latest pigeon in Sharkia (A/pigeon/Egypt/Sharkia-22/2014) and latest quail strains in Egypt (A/quail/Egypt/14102TCP/2014 and A/quail/Egypt/1171SG/2011). 2018 PeerJ Figure IV Q1995D 280 286 HA 36 38 30245911 The 2015 Outbreak of Severe Influenza in Kashmir, North India: Emergence of a New Clade of A/H1n1 Influenza Virus. 2015 isolates belong to Clade 6B.1 with clade specific S203T or A203T, and D97N signature mutations. 2018 PLoS currents Figure IV S203T;A203T;D97N 55;64;75 60;69;79 30282714 Amino Acid Residue 217 in the Hemagglutinin Glycoprotein Is a Key Mediator of Avian Influenza H7N9 Virus Antigenicity. The mutations A125T, A151T, and L217Q (mature H7 HA numbering) are indicated in green, blue, and red, respectively. 2019 Journal of virology Figure IV A125T;A151T;L217Q 14;21;32 19;26;37 HA 49 51 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. 293T cells transfected with plasmids expressing H7N9 NS1-WT (WT), NS1-S212P (S212P) or EV were infected with WSN (C) or PR8 delNS1 virus (D) as described in (A, B), then cells were harvested and cell extracts were prepared for Western blotting using indicated antibodies. 2018 Veterinary research Figure IV S212P;S212P 70;77 75;82 NS1;NS1 53;66 56;69 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. 293T cells were transfected with plasmids expressing H7N9 NS1-WT (WT) or NS1-I178V (I178V) as described in (A), then the cells were treated with CHX (100 mug/mL). 2018 Veterinary research Figure IV I178V;I178V 77;84 82;89 NS1;NS1 58;73 61;76 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. A 293T cells transfected with plasmids expressing H7N9 NS1 or empty vector (EV) were infected with WSN virus (MOI = 1) for 12 h, followed by quantitative real-time PCR to detect the mRNA levels of the indicated genes. 2018 Veterinary research Figure IV A293T 0 6 NS1 55 58 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. A 293T cells transfected with plasmids expressing H7N9 NS1-WT (WT), NS1-S212P (S212P) or EV were infected with WSN (MOI = 1) for 12 h, followed by Western blotting to detect viral NP expression. 2018 Veterinary research Figure IV A293T;S212P;S212P 0;72;79 6;77;84 NP;NS1;NS1 180;55;68 182;58;71 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. A 293T cells were transfected with plasmids expressing H7N9 NS1-WT (WT) or NS1 mutants (R55E, H63Q, E70K, P87S, S114P, A143T, I178V, S212P) for 24 h, followed by Western blotting to detect the NS1 protein levels. 2018 Veterinary research Figure IV A293T;R55E;H63Q;E70K;P87S;S114P;A143T;I178V;S212P 0;88;94;100;106;112;119;126;133 6;92;98;104;110;117;124;131;138 NS1;NS1;NS1 60;75;193 63;78;196 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. A 293T cells were transfected with plasmids expressing H7N9 NS1-WT (WT), NS1 mutants (R55E, H63Q, E70K, P87S, S114P, A143T, I178V, S212P) or EV for 24 h, then the cells were infected with WSN virus (MOI = 1) for 12 h, followed by quantitative real-time PCR to detect IFN-beta mRNA expression levels. 2018 Veterinary research Figure IV A293T;R55E;H63Q;E70K;P87S;S114P;A143T;I178V;S212P 0;86;92;98;104;110;117;124;131 6;90;96;102;108;115;122;129;136 NS1;NS1 60;73 63;76 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. A-C 293T cells transfected with plasmids expressing H7N9 NS1-WT (WT) or NS1-I178V (I178V) were treated with CHX (100 mug/mL), then were either mock treated or treated with MG132 (10 muM) (A), NH4Cl (20 mM) (B) or chloroquine (50 muM) (C). 2018 Veterinary research Figure IV C293T;I178V;I178V 2;76;83 8;81;88 NS1;NS1 57;72 60;75 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. A, B 293T cells transfected with plasmids expressing H7N9 NS1-WT (WT), NS1-S212P (S212P) or EV were infected with WSN (A) or PR8 delNS1 virus (B) (MOI = 1) for 12 h, followed by quantitative real-time PCR to detect RIG-I mRNA levels. 2018 Veterinary research Figure IV S212P;S212P 75;82 80;87 NS1;NS1 58;71 61;74 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. B 293T cells were transfected with plasmids expressing H7N9 NS1-WT (WT) or NS1-I178V (I178V) as described in (A). 2018 Veterinary research Figure IV I178V;I178V 79;86 84;91 NS1;NS1 60;75 63;78 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. B-D 293T cells transfected with plasmids expressing H7N9 NS1 or EV were infected with WSN virus as described in (A). 2018 Veterinary research Figure IV D293T 2 8 NS1 57 60 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. B-G After 293T cells were transfected with plasmids expressing H7N9 NS1-WT (WT), NS1-S212P (S212P) or EV for 24 h, the cells were then infected with WSN or PR8 delNS1 virus (MOI = 1) for 12 h, followed by quantitative real-time PCR to detect IFN-alpha (B), IFN-beta (C), IL-28 (D), OASL (E), MxA (F) and IL-6 (G) mRNA levels. 2018 Veterinary research Figure IV S212P;S212P 85;92 90;97 NS1;NS1 68;81 71;84 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. C 293T cells transfected with plasmids expressing H7N9 NS1-WT (WT), NS1-S212P (S212P) or EV were infected with PR8 delNS1 virus (MOI = 1) for 12 h, followed by Western blotting to detect viral NP expression. 2018 Veterinary research Figure IV C293T;S212P;S212P 0;72;79 6;77;84 NP;NS1;NS1 193;55;68 195;58;71 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. C Half-lives of NS1-WT (WT) and NS1-I178V (I178V) were examined. 2018 Veterinary research Figure IV I178V;I178V 36;43 41;48 NS1;NS1 16;32 19;35 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. E 293T cells transfected with plasmids expressing H7N9 NS1 or EV were treated as described in (A), and viral titers in the supernatants of the cells were examined by plaque assay. 2018 Veterinary research Figure IV E293T 0 6 NS1 55 58 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. E, F 293T cells transfected with plasmids expressing H7N9 NS1-WT (WT), NS1-S212P (S212P) or EV were infected with WSN (E) or PR8 delNS1 virus (F) (MOI = 1) for 12 h, and viral titers in the supernatants of the cells were examined by plaque assay. 2018 Veterinary research Figure IV F293T;S212P;S212P 3;75;82 9;80;87 NS1;NS1 58;71 61;74 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. H7N9 NS1 S212P mutation causes a decrease of its ability to suppress RIG-I expression and STAT1 activation. 2018 Veterinary research Figure IV S212P 9 14 NS1 5 8 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. H7N9 NS1-S212P mutation reduces its capacity to inhibit WSN and PR8 delNS1 virus-induced host antiviral response. 2018 Veterinary research Figure IV S212P 9 14 NS1 5 8 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. I178V mutation decreases stability of H7N9 NS1 protein. 2018 Veterinary research Figure IV I178V 0 5 NS1 43 46 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. I178V mutation induces proteasome degradation of NS1 protein. 2018 Veterinary research Figure IV I178V 0 5 NS1 49 52 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. P212S and V178I mutation in NS1 of PR8 virus enhances its virulence in vivo. 2018 Veterinary research Figure IV P212S;V178I 0;10 5;15 NS1 28 31 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. S212P mutation of H7N9 NS1 results in a reduction in the viral replication. 2018 Veterinary research Figure IV S212P 0 5 NS1 23 26 30301950 Tree shrew as a new animal model to study the pathogenesis of avian influenza (H9N2) virus infection. Asterisks indicate a significant difference between the Y280-wt and Y280-PB2-E627K viruses. 2018 Emerging microbes & infections Figure IV E627K 77 82 PB2 73 76 30301950 Tree shrew as a new animal model to study the pathogenesis of avian influenza (H9N2) virus infection. The mRNA expression levels of TNF-alpha (a), IFN-beta (b), IL-4 (c), IL-6 (d), CXCL8 (e), IL-10 (f), IL-13 (g), CXCL10 (h), CCL5 (i), CXCL9 (j), and CCL2 (k) were determined by quantitative PCR in the nasal turbinate, throat, trachea, and lung tissue of tree shrews (n = 4 per time point) that were infected with H9N2 viruses (Y280-wt or Y280-PB2-E627K). 2018 Emerging microbes & infections Figure IV E627K 347 352 PB2 343 346 30301950 Tree shrew as a new animal model to study the pathogenesis of avian influenza (H9N2) virus infection. Tissues isolated from different parts of the respiratory tract were infected with 106 TCID50/mL of H9N2 viruses (Y280-wt or Y280-PB2-E627K) at 37 C. 2018 Emerging microbes & infections Figure IV E627K 133 138 PB2 129 132 30301950 Tree shrew as a new animal model to study the pathogenesis of avian influenza (H9N2) virus infection. Tissues isolated from different sites of the respiratory tract were infected with 106 TCID50/mL of H9N2 viruses (Y280-wt or Y280-PB2-E627K) at 37 C. 2018 Emerging microbes & infections Figure IV E627K 133 138 PB2 129 132 30301950 Tree shrew as a new animal model to study the pathogenesis of avian influenza (H9N2) virus infection. Tree shrews (n = 4 per group) were infected with 106 TCID50 of one of two H9N2 viruses (Y280-wt or Y280-PB2-E627K). 2018 Emerging microbes & infections Figure IV E627K 108 113 PB2 104 107 30301950 Tree shrew as a new animal model to study the pathogenesis of avian influenza (H9N2) virus infection. Tree shrews (n = 4 per group) were infected with 106 TCID50 of Y280-wt or Y280-PB2-E627K virus. 2018 Emerging microbes & infections Figure IV E627K 83 88 PB2 79 82 30301950 Tree shrew as a new animal model to study the pathogenesis of avian influenza (H9N2) virus infection. Tree shrews (n = 4 per group) were inoculated with 106 TCID50 of H9N2 viruses (Y280-wt or Y280-PB2-E627K). 2018 Emerging microbes & infections Figure IV E627K 99 104 PB2 95 98 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. (C) Venn diagram analysis comparing the 29 chimpanzee-biased genes to the RNA-Seq data for all IFNs (GFP versus IFN) and for HsIFNlambda4 K154E versus wt specifically. 2018 PLoS pathogens Figure IV K154E 138 143 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. (E) Comparison of differentially-expressed genes (significant and at least 2-fold difference) stimulated by the HsIFNlambda4 variants (HsIFNlambda4 wt in green, HsIFNlambda4 P70S in cyan and HsIFNlambda4 K154E in purple) illustrated by a Venn diagram showing shared and unique genes. 2018 PLoS pathogens Figure IV P70S;K154E 174;204 178;209 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. (F) Raw gene expression values (FKPM+1) for representative genes from core, shared and K154E-'specific' groups for the different treatments. 2018 PLoS pathogens Figure IV K154E 87 92 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. CM was obtained from cells transfected with HsIFNlambda3op (red); HsIFNlambda4 wt (green); HsIFNlambda4 P70S (cyan), and HsIFNlambda4 K154E (purple). 2018 PLoS pathogens Figure IV P70S;K154E 104;134 108;139 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. Common variants include: wt (orange), C17Y (light green), R60P (dark blue) and P70S (cyan). 2018 PLoS pathogens Figure IV C17Y;R60P;P70S 38;58;79 42;62;83 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. Comparing wt and K154E RLU at 72h by two-tailed Student's T-test gave a significant difference ** = <0.01. 2018 PLoS pathogens Figure IV K154E 17 22 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. Exemplary genes selected were: ISG15 and MX1 (core), UBA7 (not significantly induced by P70S), and ISG20 and IDO1 (apparently specific for K154E). 2018 PLoS pathogens Figure IV P70S;K154E 88;139 92;144 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. Mechanism of action of the IFNlambda4 K154E variant. 2018 PLoS pathogens Figure IV K154E 38 43 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. Note that there are 2 non-synonymous changes at C17 (C17R and C17Y). 2018 PLoS pathogens Figure IV C17R;C17Y 53;62 57;66 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. Rare variants (purple) include: A8S, C17R, R25Q, S56R, P73S, L79F, K133M, V134A, R151P, K154E, S156N, and V158I. 2018 PLoS pathogens Figure IV A8S;C17R;R25Q;S56R;P73S;L79F;K133M;V134A;R151P;K154E;S156N;V158I 32;37;43;49;55;61;67;74;81;88;95;106 35;41;47;53;59;65;72;79;86;93;100;111 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. Those variants with >2-fold change are highlighted with colours: purple (K154E,), cyan (P70S) and yellow (L79F). 2018 PLoS pathogens Figure IV K154E;P70S;L79F 73;88;106 78;92;110 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. Variants K133M and S156N (black) did not have an associated ethnicity but were found in the dataset from the Netherlands (Genome of the Netherlands cohort). 2018 PLoS pathogens Figure IV K133M;S156N 9;19 14;24 30352857 The mechanism of resistance to favipiravir in influenza. (A) Minigenome assay showing relative polymerase activity for Eng195 and K229R + P653L in presence of increasing concentrations of ribavirin. 2018 Proc Natl Acad Sci U S A Figure IV K229R;P653L 73;81 78;86 30352857 The mechanism of resistance to favipiravir in influenza. (A) Minigenome assay with Eng195, PB1 K229R, PA P653L, and PB1 K229R + PA P653L in presence of increasing concentrations of favipiravir. 2018 Proc Natl Acad Sci U S A Figure IV K229R;P653L;K229R;P653L 38;48;63;74 43;53;68;79 PA;PA;PB1;PB1 45;71;34;59 47;73;37;62 30352857 The mechanism of resistance to favipiravir in influenza. (A) Minigenome assay with H3N2 A/Victoria/3/1975, PB1 K229R, PA P653L, and PB1 K229R + PA P653L in presence of increasing concentrations of favipiravir. 2018 Proc Natl Acad Sci U S A Figure IV K229R;P653L;K229R;P653L 54;64;79;90 59;69;84;95 PA;PA;PB1;PB1 61;87;50;75 63;89;53;78 30352857 The mechanism of resistance to favipiravir in influenza. (A) Viral growth curves on MDCKs at MOI = 0.002 for Eng195, PB1 K229R, PA P653L, and PB1 K229R + PA P653L. 2018 Proc Natl Acad Sci U S A Figure IV K229R;P653L;K229R;P653L 64;74;89;100 69;79;94;105 PA;PA;PB1;PB1 71;97;60;85 73;99;63;88 30352857 The mechanism of resistance to favipiravir in influenza. (B) Individual mutations per 10,000 sequenced nucleotides above the control (0 microM, Eng195) measured by primer ID at 0, 10, and 100 microM favipiravir from RNA expressed in a minigenome assay with Eng195, PB1 K229R, PA P653L, or PB1 K229R + PA P653L polymerase. 2018 Proc Natl Acad Sci U S A Figure IV K229R;P653L;K229R;P653L 212;222;236;247 217;227;241;252 PA;PA;PB1;PB1 219;244;208;232 221;246;211;235 30352857 The mechanism of resistance to favipiravir in influenza. (B) Minigenome assay with H7N9 A/Anhui/1/2013, PB1 K229R, PA P653L, and PB1 K229R + PA P653L in presence of increasing concentrations of favipiravir. 2018 Proc Natl Acad Sci U S A Figure IV K229R;P653L;K229R;P653L 51;61;76;87 56;66;81;92 PA;PA;PB1;PB1 58;84;47;72 60;86;50;75 30352857 The mechanism of resistance to favipiravir in influenza. (B) Virus inhibition assay for Eng195 and PB1 K229R + PA P653L in presence of increasing concentrations of favipiravir. 2018 Proc Natl Acad Sci U S A Figure IV K229R;P653L 46;57 51;62 PA;PB1 54;42 56;45 30352857 The mechanism of resistance to favipiravir in influenza. (C and D) Gel analysis and quantitation of the activity of the wild type or PB1 K229R mutant influenza A virus RNA polymerase on the 3' 4C template provided with CTP and either GTP or 500 muM F-RTP. 2018 Proc Natl Acad Sci U S A Figure IV K229R 80 85 PB1 76 79 30352857 The mechanism of resistance to favipiravir in influenza. (C) Surface models of F-RTP binding by the wild-type influenza A virus and by the K229R mutant. 2018 Proc Natl Acad Sci U S A Figure IV K229R 82 87 30352857 The mechanism of resistance to favipiravir in influenza. (F) Gel analysis of the replication activity of the wild type or PB1 K229R mutant polymerase on the promoter up template in the absence or presence of 500 muM F-RTP. 2018 Proc Natl Acad Sci U S A Figure IV K229R 69 74 PB1 65 68 30352857 The mechanism of resistance to favipiravir in influenza. (G) Quantitation of the replication assay performed with wild type, K229R, P653L, or double mutant polymerase. 2018 Proc Natl Acad Sci U S A Figure IV K229R;P653L 68;75 73;80 30352857 The mechanism of resistance to favipiravir in influenza. Alignment and structural modeling of the PB1 K229R mutation. 2018 Proc Natl Acad Sci U S A Figure IV K229R 45 50 PB1 41 44 30352857 The mechanism of resistance to favipiravir in influenza. K229R and P653L combine to give resistance to favipiravir in a minigenome assay. 2018 Proc Natl Acad Sci U S A Figure IV K229R;P653L 0;10 5;15 30352857 The mechanism of resistance to favipiravir in influenza. PB1 K229R confers resistance to favipiravir in other influenza A polymerases. 2018 Proc Natl Acad Sci U S A Figure IV K229R 4 9 PB1 0 3 30352857 The mechanism of resistance to favipiravir in influenza. PB1 K229R does not confer resistance to ribavirin but prevents mutations caused by favipiravir. 2018 Proc Natl Acad Sci U S A Figure IV K229R 4 9 PB1 0 3 30352857 The mechanism of resistance to favipiravir in influenza. PB1 K229R has a cost to viral growth that is rescued by PA P653L. 2018 Proc Natl Acad Sci U S A Figure IV K229R;P653L 4;59 9;64 PA;PB1 56;0 58;3 30405591 Identification of Amino Acid Residues Responsible for Inhibition of Host Gene Expression by Influenza A H9N2 NS1 Targeting of CPSF30. Amino acid changes L103F, I106IM, P114S, G125D and N139D in H9N2 NS1 are required for interaction with CPSF30. 2018 Frontiers in microbiology Figure IV L103F;P114S;G125D;N139D 19;34;41;51 24;39;46;56 NS1 65 68 30405591 Identification of Amino Acid Residues Responsible for Inhibition of Host Gene Expression by Influenza A H9N2 NS1 Targeting of CPSF30. Five amino acid changes (L103F, I106IM, P114S, G125D, and N139D) in HK/97 NS1 restores its ability to block host gene expression. 2018 Frontiers in microbiology Figure IV L103F;P114S;G125D;N139D 25;40;47;58 30;45;52;63 NS1 74 77 30509291 Conserved methionine 165 of matrix protein contributes to the nuclear import and is essential for influenza A virus replication. After 24 h, the cells were fixed and M1 and M165A were detected using a primary anti-M1 antibody and a secondary antibody coupled to Alexa488 (in green) and NP protein was labelled with anti- NP antibody and a secondary antibody coupled with Alexa555 (in red). 2018 Virology journal Figure IV M165A 44 49 M1;M1;NP;NP 37;85;157;192 39;87;159;194 30509291 Conserved methionine 165 of matrix protein contributes to the nuclear import and is essential for influenza A virus replication. After 24 h, the cells were fixed and M1 and M165A were detected using a primary anti-M1 antibody and a secondary antibody coupled to Alexa488 (in green). 2018 Virology journal Figure IV M165A 44 49 M1;M1 37;85 39;87 30509291 Conserved methionine 165 of matrix protein contributes to the nuclear import and is essential for influenza A virus replication. Cellular co-localization and quantification of NP with M1 and M165A mutant using immunofluorescence confocal microscopy. 2018 Virology journal Figure IV M165A 62 67 M1;NP 55;47 57;49 30509291 Conserved methionine 165 of matrix protein contributes to the nuclear import and is essential for influenza A virus replication. Cellular co-localization of CLUH with M1 and M165A mutant using immunofluorescence confocal microscopy. 2018 Virology journal Figure IV M165A 45 50 M1 38 40 30509291 Conserved methionine 165 of matrix protein contributes to the nuclear import and is essential for influenza A virus replication. Cellular co-localization of CRM1 with M1 and M165A mutant using immunofluorescence confocal microscopy. 2018 Virology journal Figure IV M165A 45 50 M1 38 40 30509291 Conserved methionine 165 of matrix protein contributes to the nuclear import and is essential for influenza A virus replication. Cellular co-localization of plasma membrane with M1 and M165A mutant using immunofluorescence confocal microscopy. 2018 Virology journal Figure IV M165A 56 61 M1 49 51 30509291 Conserved methionine 165 of matrix protein contributes to the nuclear import and is essential for influenza A virus replication. M1 and M165A were detected using a primary anti-M1 antibody and a secondary antibody coupled to Alexa555 (in red). 2018 Virology journal Figure IV M165A 7 12 M1;M1 0;48 2;50 30509291 Conserved methionine 165 of matrix protein contributes to the nuclear import and is essential for influenza A virus replication. NP(M1) is NP in the cells transfected with M1, NP(M165) is NP in the cells transfected with M165A mutant. 2018 Virology journal Figure IV M165A 92 97 M1;M1;NP;NP;NP;NP 3;43;0;10;47;59 5;45;2;12;49;61 30509291 Conserved methionine 165 of matrix protein contributes to the nuclear import and is essential for influenza A virus replication. The virus production was determined in multistep growth curve (MOI = 0,01) of control virus (VC) and virus-containing R163A, Q164A, and V166A mutation. 2018 Virology journal Figure IV R163A;Q164A;V166A 118;125;136 123;130;141 30518648 HDAC6 Restricts Influenza A Virus by Deacetylation of the RNA Polymerase PA Subunit. (D) Calculated relative half-lives of PA, PA-K664R, and PA-K664Q, using the data from panel C. 2019 Journal of virology Figure IV K664R;K664Q 45;59 50;64 PA;PA;PA 38;42;56 40;44;58 30533399 Potential Pandemic of H7N9 Avian Influenza A Virus in Human. (A) Sites A118T, S123N, A131V, R136K, L173I, and M232I in HA1 (H5 numbering). 2018 Frontiers in cellular and infection microbiology Figure IV A118T;S123N;A131V;R136K;L173I;M232I 10;17;24;31;38;49 15;22;29;36;43;54 HA1 58 61 30533399 Potential Pandemic of H7N9 Avian Influenza A Virus in Human. (B) Sites E383A, V426I, and S486R in HA2 (H5 numbering). 2018 Frontiers in cellular and infection microbiology Figure IV E383A;V426I;S486R 10;17;28 15;22;33 HA 37 39 30533399 Potential Pandemic of H7N9 Avian Influenza A Virus in Human. (C) Sites I16T, S247P, and N327S in NA (N9 numbering). 2018 Frontiers in cellular and infection microbiology Figure IV I16T;S247P;N327S 10;16;27 14;21;32 N9;NA 40;36 42;38 30533399 Potential Pandemic of H7N9 Avian Influenza A Virus in Human. (D) Sites K191E, N559T, and A588V in PB2 (N9 numbering). 2018 Frontiers in cellular and infection microbiology Figure IV K191E;N559T;A588V 10;17;28 15;22;33 N9;PB2 42;37 44;40 30533399 Potential Pandemic of H7N9 Avian Influenza A Virus in Human. (E) Site N394D in PA (N9 numbering). 2018 Frontiers in cellular and infection microbiology Figure IV N394D 9 14 N9;PA 22;18 24;20 30533399 Potential Pandemic of H7N9 Avian Influenza A Virus in Human. (F) Site E24D in M2 (N9 numbering). 2018 Frontiers in cellular and infection microbiology Figure IV E24D 9 13 M2;N9 17;21 19;23 30533399 Potential Pandemic of H7N9 Avian Influenza A Virus in Human. All amino acid changes occurring in HA1 (A118T, S123N, A131V, R136K, L173I, and M232I) locate in the receptor-binding region and in close proximity to the antigenic site. 2018 Frontiers in cellular and infection microbiology Figure IV A118T;S123N;A131V;R136K;L173I;M232I 41;48;55;62;69;80 46;53;60;67;74;85 HA1 36 39 30619194 Influenza A Virus NS1 Protein Suppresses JNK1-Dependent Autophagosome Formation Mediated by Rab11a Recycling Endosomes. (E) HeLa cells were infected with Wt, R38AK41A, or Y89F virus at MOI of 3. 2018 Frontiers in microbiology Figure IV Y89F 51 55 30619194 Influenza A Virus NS1 Protein Suppresses JNK1-Dependent Autophagosome Formation Mediated by Rab11a Recycling Endosomes. (F) HeLa cells were infected with Wt, R38AK41A or Y89F virus at MOI of 3. 2018 Frontiers in microbiology Figure IV Y89F 50 54 30619194 Influenza A Virus NS1 Protein Suppresses JNK1-Dependent Autophagosome Formation Mediated by Rab11a Recycling Endosomes. (G,H) HeLa cells expressing GFP-LAMP2 (shown in magenta) were infected with M2-N31S delNS1 virus at MOI of 3 with or without 50 muM amantadine (Amt). 2018 Frontiers in microbiology Figure IV N31S 79 83 M2 76 78 30619194 Influenza A Virus NS1 Protein Suppresses JNK1-Dependent Autophagosome Formation Mediated by Rab11a Recycling Endosomes. HeLa cells (A) and A549 cells (C) were infected with either Wt, R38AK41A, or Y89F virus at MOI of 3. 2018 Frontiers in microbiology Figure IV Y89F 77 81 30996301 Bacterial glycosyltransferase-mediated cell-surface chemoenzymatic glycan modification. a Modification of glycocalyx of MDCK cells using Pm2,3ST-M144D, Pd2,6ST, or Hp1,3ST and the corresponding donor substrate conjugated with biotin. 2019 Nature communications Figure IV M144D 57 62 30996301 Bacterial glycosyltransferase-mediated cell-surface chemoenzymatic glycan modification. b Modification of glycocalyx of MDCK cells using a combination of Pm2,3ST-M144D and Hp1,3ST. 2019 Nature communications Figure IV M144D 74 79 30996301 Bacterial glycosyltransferase-mediated cell-surface chemoenzymatic glycan modification. NeuAcalpha2-6-(Fucalpha1-2)-LacNAc was formed by combining Hm1,2FT and Pm2,3ST-M144D (e). 2019 Nature communications Figure IV M144D 79 84 30996301 Bacterial glycosyltransferase-mediated cell-surface chemoenzymatic glycan modification. Recombinant bacterial glycosyltransferases (FTs and STs) used in this study include Hm1,2FT, Hp1,3FT, Pm2,3ST-M144D, and Pd2,6ST. 2019 Nature communications Figure IV M144D 110 115 30996301 Bacterial glycosyltransferase-mediated cell-surface chemoenzymatic glycan modification. sLeX was formed by combining Hp1,3FT and Pm2,3ST-M144D (d). 2019 Nature communications Figure IV M144D 49 54 30996301 Bacterial glycosyltransferase-mediated cell-surface chemoenzymatic glycan modification. The embryonic frozen sections from E16 mouse were incubated with STs (Pm2,3ST-M144D or Pd2,6ST) or without STs, and CMP-SiaNAz-biotin, followed by Alexa Fluor 594-streptavidin conjugate staining. 2019 Nature communications Figure IV M144D 78 83 30996301 Bacterial glycosyltransferase-mediated cell-surface chemoenzymatic glycan modification. The Pm2,3ST-M144D, Pd2,6ST, or Hp1,3ST-mediated incorporation of unnatural sugars conjugated to a fluorescent dye (Cy3) or an affinity tag (biotin), enabled a One-step cell-surface glycan labeling. 2019 Nature communications Figure IV M144D 12 17 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. (B) Biolayer interferometry (BLI) was used to measure the binding kinetics of anti-RBS C05 IgG against recombinant HAs of Bris07 WT, G186V mutant, and L194P mutant. 2019 Cell host & microbe Figure IV G186V;L194P 133;151 138;156 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. (C and D) Bris07 HA G186V mutant virus (C) and Bris07 HA L194P mutant virus (D) were passaged for five rounds in eggs. 2019 Cell host & microbe Figure IV G186V;L194P 20;57 25;62 HA;HA 17;54 19;56 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. (C) The distances between the phenolic oxygen of Tyr 98 (OH98) and the Calpha of residue 190 (Calpha190) in different H3 strains were measured: Wy03: PDB 6BKN, Fin04: PDB 2YP2, HK05: PDB 2YP7, Bris07: PDB 6AOR, Bris07 (L194P): PDB 6AOP, Vic11: PDB 4O5N, and Mich14: PDB 6BKP. 2019 Cell host & microbe Figure IV L194P 219 224 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. (C) The HA RBS conformations of IVR-165 HA and Bris07-L194P HA in complex with 3'SLNLN are compared. 2019 Cell host & microbe Figure IV L194P 54 59 HA;HA;HA 8;40;60 10;42;62 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. (D) The RBS conformations of IVR-165 HA and Bris07 HA-L194P in complex with 6'SLNLN are compared. 2019 Cell host & microbe Figure IV L194P 54 59 HA;HA 37;51 39;53 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. (E) The distance between equivalent Calphas of IVR-165 and Calphas of Bris07-L194P for each residue in the receptor-binding subdomain (HA1 residues 117-265) is shown. 2019 Cell host & microbe Figure IV L194P 77 82 HA1 135 138 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. Antigenic Characterization of G186V and L194P. 2019 Cell host & microbe Figure IV G186V;L194P 30;40 35;45 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. Final 2Fo-Fc electron density maps and coordinates for L194P mutant were retrieved from PDB 6AOP (apo form), PDB 6AOS (in complex with 3'SLNLN), and PDB 6AOT (in complex with 6'SLNLN). 2019 Cell host & microbe Figure IV L194P 55 60 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. Final 2Fo-Fc electron density maps for the HA receptor-binding site of the L194P mutant (top) and G186V/L194P double mutant (bottom) are represented in a blue mesh and contoured at 0.8 sigma. 2019 Cell host & microbe Figure IV L194P;L194P;G186V 75;104;98 80;109;103 HA 43 45 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. Incompatibility of Egg-Adaptive Mutations HA L194P and G186V. 2019 Cell host & microbe Figure IV L194P;G186V 45;55 50;60 HA 42 44 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. Of note, the egg-adaptive mutation G186E in A/South Australia/55/2014 (IVR-175) was seldom observed during egg adaptation. 2019 Cell host & microbe Figure IV G186E 35 40 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. Sera from immunized mice were tested for binding to WT, G186V mutant, and L194P mutant of recombinant Bris07 HA using ELISA. 2019 Cell host & microbe Figure IV G186V;L194P 56;74 61;79 HA 109 111 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. The HA of the Bris07 G186V/L194P double mutant was expressed recombinantly in insect cells (see STAR Methods). 2019 Cell host & microbe Figure IV L194P;G186V 27;21 32;26 HA 4 6 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. This analysis was performed on the structural alignment of IVR-165 and Bris07-L194P in complex with 3'SLNLN (upper panel) and in complex with 6'SLNLN (bottom panel). 2019 Cell host & microbe Figure IV L194P 78 83 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. Three independent passaging experiments were performed for the Bris07 HA G186V mutant virus in (C) and one passaging experiment was performed for the Bris07 HA L194P mutant virus in (D). 2019 Cell host & microbe Figure IV G186V;L194P 73;160 78;165 HA;HA 70;157 72;159 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. Four residues in the N-terminal PA domain mediate the acquisition of the H7N9 PB2 E627K mutation in mice. 2019 mBio Figure IV E627K 82 87 PA;PB2 32;78 34;81 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. NA, virus was not recovered; red arrows indicate the appearance of the PB2 E627K mutation. 2019 mBio Figure IV E627K 75 80 NA;PB2 0;71 2;74 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. PA drives the emergence of the PB2 E627K mutation during the replication of PG/S1421(H7N9) virus in mice. 2019 mBio Figure IV E627K 35 40 PA;PB2 0;31 2;34 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. PG/S1421(H7N9) virus replication is impaired by ANP32A depletion in Anp32a-/- mice, driving the emergence of the PB2 D701N mutation instead of E627K. 2019 mBio Figure IV D701N;E627K 117;143 122;148 PB2 113 116 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. The polymerase activity of PG/S1421(H7N9) bearing the PB2 E627K mutation was also included as a control. 2019 mBio Figure IV E627K 58 63 PB2 54 57 31266524 Highly pathogenic avian influenza H7N9 viruses with reduced susceptibility to neuraminidase inhibitors showed comparable replication capacity to their sensitive counterparts. Crystal structure model of NA monomer of A/ Anhui1/2013/H7N9 virus (PDB ID: 4MWJ) was used to display and label the four drug resistance mutations (292 K, E119V, A246T or H274Y) by DeepView v4.1.0 software. 2019 Virology journal Figure IV E119V;A246T;H274Y 155;162;171 160;167;176 27 29 31267843 Mammalian-adaptive mutation NP-Q357K in Eurasian H1N1 Swine Influenza viruses determines the virulence phenotype in mice. Conceptual model of the generalized inferred evolutionary pathways and virulence outcomes of NP-Q357K in influenza A viruses. 2019 Emerging microbes & infections Figure IV Q357K 96 101 NP 93 95 31267843 Mammalian-adaptive mutation NP-Q357K in Eurasian H1N1 Swine Influenza viruses determines the virulence phenotype in mice. The Q357K substitution alters the viral phenotype in mice. 2019 Emerging microbes & infections Figure IV Q357K 4 9 31267843 Mammalian-adaptive mutation NP-Q357K in Eurasian H1N1 Swine Influenza viruses determines the virulence phenotype in mice. The Q357K substitution was introduced into the NP protein during the adaptation of the avian influenza virus to swine. 2019 Emerging microbes & infections Figure IV Q357K 4 9 NP 47 49 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. (A and B) Representative BLI recordings of the rgSH2 (blue) and rgSH2-G218E (red) binding with immobilized 3'SLN (A) and 6'SLN (B) in the presence of NAi (dashed line) or NAi-free (solid line) through the entire association phase. 2019 Journal of virology Figure IV G218E 70 75 NAI;NAI 150;171 153;174 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. (A to F) Representative SEM images of MDCK monolayers after 2 and 10 h of infection with NL12WT (A and B) or NL12ad (D and E) and at 10 h postinfection with rgSH2WT (C) and rgSH2-G218E (F). 2019 Journal of virology Figure IV G218E 179 184 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. (A) Location of G218E in H7 HA. 2019 Journal of virology Figure IV G218E 16 21 HA 28 30 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. (B) Relative infectivity of rgSH2WT and rgSH2-G218E in the MDCK cells with reduced SA receptor density by cholera filtrate pretreatment. 2019 Journal of virology Figure IV G218E 46 51 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. (C to E) BLI equilibrium binding to the immobilized 3'SLN or 6'SLN by NL12WT and NL12ad (C), rgSH2WT and rgSH2-G218E (D), and rgGD17 and rgGD-G218E (E). 2019 Journal of virology Figure IV G218E;G218E 111;142 116;147 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. (C) The (AUCNAi - AUCNAi-free)/AUCNAi ratio was calculated for comparison of the apparent NA activities of rgSH2WT and rgSH2-G218E (means +- the SD from three independent experiments). 2019 Journal of virology Figure IV G218E 125 130 90 92 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. (C) Virus titers from nasal wash samples after rgGD17 or rgGD17-G218E immunization, followed by GD17WT challenge. 2019 Journal of virology Figure IV G218E 64 69 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. (D) Relative total viral protein yield from purified MDCK-grown NL12ad, rgSH2-G218E, and rgGD-G218E to the wild-type counterparts, respectively. 2019 Journal of virology Figure IV G218E;G218E 78;94 83;99 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. (D) Separation of total viral proteins, with or without deglycosylation, from rgSH2WT and rgSH2-G218E in reduced SDS-PAGE gel (10% NuPAGE Bis-Tris gel, 5 mug of protein per sample, colloidal blue staining). 2019 Journal of virology Figure IV G218E 96 101 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. (E) NA activities of rgSH2WT (blue) and rgSH2-G218E (red) measured by the 4-MU-NANA method. 2019 Journal of virology Figure IV G218E 46 51 4 6 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. Comparison of plaque morphology and multistep growth curves (after infection with each virus at an MOI of 0.01) of NL12ad with NL12WT (A), rgSH2-G218E with rgSH2WT (B), and rgGD-G218E with rgGD17 (C). 2019 Journal of virology Figure IV G218E;G218E 145;178 150;183 31305236 Prevailing I292V PB2 mutation in avian influenza H9N2 virus increases viral polymerase function and attenuates IFN-beta induction in human cells. PB2-I292V mutation in avian H9N2 virus strongly attenuated IFN-beta induction. 2019 The Journal of general virology Figure IV I292V 4 9 PB2 0 3 31305236 Prevailing I292V PB2 mutation in avian influenza H9N2 virus increases viral polymerase function and attenuates IFN-beta induction in human cells. PB2-I292V mutation in H9N2 virus raised pathogenicity and viral replication in mice. 2019 The Journal of general virology Figure IV I292V 4 9 PB2 0 3 31305236 Prevailing I292V PB2 mutation in avian influenza H9N2 virus increases viral polymerase function and attenuates IFN-beta induction in human cells. Prevalence of PB2-I292V in multiple subtypes of influenza viruses. 2019 The Journal of general virology Figure IV I292V 18 23 PB2 14 17 31436527 Human-to-Human Transmission of Influenza A(H3N2) Virus with Reduced Susceptibility to Baloxavir, Japan, February 2019. Clinical timeline of 2 siblings infected with mutant influenza A(H3N2) viruses encoding the polymerase acidic I38T substitution, Japan, February 2019. 2019 Emerging infectious diseases Figure IV I38T 110 114 PA 92 109 31538644 Baloxavir Marboxil in Japanese Pediatric Patients With Influenza: Safety and Clinical and Virologic Outcomes. A, Time courses of % proportion of PA/I38 T/M-substituted viruses in the swabs and B, viral titer (log10TCID50/mL) in the swabs were represented. 2020 Clinical infectious diseases Figure IV I38T 38 45 PA 35 37 31538644 Baloxavir Marboxil in Japanese Pediatric Patients With Influenza: Safety and Clinical and Virologic Outcomes. Abbreviations: BXA, baloxavir acid; LLoQ, lower limit of quantification; NA, not applicable; ND, below detection limit of 2.05 log10 RNA copies/mL, or no PCR amplification observed, or no variant profiles obtained due to low coverage (<100); NGS, next-generation sequencing; PA/I38T, isoleucine substituted by threonine at position 38 of virus polymerase acidic protein; PA/I38M, isoleucine substituted by methionine at position 38 of virus polymerase acidic protein; WT, wild-type virus. 2020 Clinical infectious diseases Figure IV I38T;I38M;I38T;I38M 278;374;284;380 282;378;334;431 NA;PA;PA;PA;PA 73;275;371;344;441 75;277;373;361;458 31538644 Baloxavir Marboxil in Japanese Pediatric Patients With Influenza: Safety and Clinical and Virologic Outcomes. Abbreviations: HAI, hemagglutinin inhibition; PA/I38T, isoleucine substituted by threonine at position 38 of virus polymerase acidic protein; PA/I38M, isoleucine substituted by methionine at position 38 of virus polymerase acidic protein; TTIA, time to illness alleviation. 2020 Clinical infectious diseases Figure IV I38T;I38M;I38T;I38M 49;145;55;151 53;149;105;202 HA;PA;PA;PA;PA 20;46;142;115;212 33;48;144;132;229 31538644 Baloxavir Marboxil in Japanese Pediatric Patients With Influenza: Safety and Clinical and Virologic Outcomes. Abbreviations: HAI, hemagglutinin inhibition; PA/I38T, isoleucine substituted by threonine at position 38 of virus polymerase acidic protein; PA/I38M, isoleucine substituted by methionine at position 38 of virus polymerase acidic protein. 2020 Clinical infectious diseases Figure IV I38T;I38M;I38T;I38M 49;145;55;151 53;149;105;202 HA;PA;PA;PA;PA 20;46;142;115;212 33;48;144;132;229 31538644 Baloxavir Marboxil in Japanese Pediatric Patients With Influenza: Safety and Clinical and Virologic Outcomes. Abbreviations: PA/I38T, isoleucine substituted by threonine at position 38 of virus polymerase acidic protein; PA/I38M, isoleucine substituted by methionine at position 38 of virus polymerase acidic protein; SD, standard deviation; TCID50, 50% tissue culture infective dose. 2020 Clinical infectious diseases Figure IV I38T;I38M;I38T;I38M 18;114;24;120 22;118;74;171 PA;PA;PA;PA 15;111;84;181 17;113;101;198 31538644 Baloxavir Marboxil in Japanese Pediatric Patients With Influenza: Safety and Clinical and Virologic Outcomes. Abbreviations: PA/I38T, isoleucine substituted by threonine at position 38 of virus polymerase acidic protein; PA/I38M, isoleucine substituted by methionine at position 38 of virus polymerase acidic protein; TTIA, time to illness alleviation. 2020 Clinical infectious diseases Figure IV I38T;I38M;I38T;I38M 18;114;24;120 22;118;74;171 PA;PA;PA;PA 15;111;84;181 17;113;101;198 31538644 Baloxavir Marboxil in Japanese Pediatric Patients With Influenza: Safety and Clinical and Virologic Outcomes. B, Individual influenza virus titer in patients with PA/I38T/M-substituted viruses (red line) and without PA/I38T/M-substituted viruses (black line). 2020 Clinical infectious diseases Figure IV I38M;I38M;I38T;I38T 56;109;56;109 62;115;62;115 PA;PA 53;106 55;108 31538644 Baloxavir Marboxil in Japanese Pediatric Patients With Influenza: Safety and Clinical and Virologic Outcomes. Comparison between proportion (A) of PA/I38T/M-substituted viruses with viral titer (B) and plasma BXA concentration (C). 2020 Clinical infectious diseases Figure IV I38M;I38T 40;40 46;46 PA 37 39 31538644 Baloxavir Marboxil in Japanese Pediatric Patients With Influenza: Safety and Clinical and Virologic Outcomes. Kaplan-Meier analysis of the alleviation of the symptoms of influenza illness after treatment with baloxavir marboxil in patients with and without PA/I38T/M-substituted viruses by HAI virus antibody titer at baseline. 2020 Clinical infectious diseases Figure IV I38M;I38T 150;150 156;156 PA 147 149 31538644 Baloxavir Marboxil in Japanese Pediatric Patients With Influenza: Safety and Clinical and Virologic Outcomes. Kaplan-Meier analysis of the illness alleviation after treatment with baloxavir marboxil in patients with and without PA/I38T/M-substituted viruses. 2020 Clinical infectious diseases Figure IV I38M;I38T 121;121 127;127 PA 118 120 31538644 Baloxavir Marboxil in Japanese Pediatric Patients With Influenza: Safety and Clinical and Virologic Outcomes. Kaplan-Meier analysis of the time to sustained cessation of viral shedding by virus titer after treatment with baloxavir marboxil in patients with and without PA/I38T/M-substituted viruses by HAI antibody titer at baseline. 2020 Clinical infectious diseases Figure IV I38M;I38T 162;162 168;168 PA 159 161 31538644 Baloxavir Marboxil in Japanese Pediatric Patients With Influenza: Safety and Clinical and Virologic Outcomes. The median times to sustained cessation of viral shedding: 216.0 hours (antibody <40 with PA/I38T/M-substituted viruses [n = 11]), 24.0 hours (antibody <40 without PA/I38T/M-substituted viruses [n = 15]), 168.0 hours (antibody >=40 with PA/I38T/M-substituted viruses [n = 7]), and 24.0 hours (antibody >=40 without PA/I38T/M-substituted viruses [n = 34]). 2020 Clinical infectious diseases Figure IV I38M;I38M;I38M;I38M;I38T;I38T;I38T;I38T 93;167;240;318;93;167;240;318 99;173;246;324;99;173;246;324 PA;PA;PA;PA 90;164;237;315 92;166;239;317 31538644 Baloxavir Marboxil in Japanese Pediatric Patients With Influenza: Safety and Clinical and Virologic Outcomes. The median TTIA was 79.6 hours in patients with PA/I38T/M-substituted viruses (n = 18) and was 42.8 hours in patients without PA/I38T/M-substituted viruses (n = 59). 2020 Clinical infectious diseases Figure IV I38M;I38M;I38T;I38T 51;129;51;129 57;135;57;135 PA;PA 48;126 50;128 31538644 Baloxavir Marboxil in Japanese Pediatric Patients With Influenza: Safety and Clinical and Virologic Outcomes. The median TTIA was 85.4 hours (antibody <40 with PA/I38T/M-substituted viruses [n = 11]), 29.9 hours (antibody <40 without PA/I38T/M-substituted viruses [n = 15]), 56.0 hours (antibody >=40 with PA/I38T/M-substituted viruses [n = 6]), and 44.7 hours (antibody >=40 without PA/I38T/M-substituted viruses [n = 34]). 2020 Clinical infectious diseases Figure IV I38M;I38M;I38M;I38M;I38T;I38T;I38T;I38T 53;127;199;277;53;127;199;277 59;133;205;283;59;133;205;283 PA;PA;PA;PA 50;124;196;274 52;126;198;276 31575766 Influenza Virus Polymerase Mutation Stabilizes a Foreign Gene Inserted into the Virus Genome by Enhancing the Transcription/Replication Efficiency of the Modified Segment. (E) MDCK cells were infected with WT-Venus-PR8 (WT) or Venus-PR8-PB2-E712D (712) at an MOI of 1. 2019 mBio Figure IV E712D 69 74 PB2 65 68 31575766 Influenza Virus Polymerase Mutation Stabilizes a Foreign Gene Inserted into the Virus Genome by Enhancing the Transcription/Replication Efficiency of the Modified Segment. Effect of PB2-E712D on the mutation rate. 2019 mBio Figure IV E712D 14 19 PB2 10 13 31575766 Influenza Virus Polymerase Mutation Stabilizes a Foreign Gene Inserted into the Virus Genome by Enhancing the Transcription/Replication Efficiency of the Modified Segment. Means +- the standard deviations of triplicate experiments, taking each value in Venus-PR8-PB2-E712D-infected cells as 1, are shown in panels A, B, C, D, and F. 2019 mBio Figure IV E712D 95 100 PB2 91 94 31581279 Influenza virus polymerase subunits co-evolve to ensure proper levels of dimerization of the heterotrimer. (A) Titers and plaque phenotype of recombinant viruses bearing one or several reversion mutations in the att-PxW genetic background, as follows: PB2-D701N (d), PB1-M195T (e), PA-L28R (f), PA-E349K (g), PA-L28R/E349K (h) PB2-D701N+PA-L28R/E349K (i) and PB2-D701N+PB1-M195T+PA-L28R/E349K (j). 2019 PLoS pathogens Figure IV D701N;M195T;L28R;E349K;L28R;E349K;L28R;E349K;D701N;D701N;M195T;L28R;E349K 149;164;178;191;205;210;233;238;224;256;266;275;280 154;169;182;196;209;215;237;243;229;261;271;279;285 PA;PA;PA;PA;PA;PB1;PB1;PB2;PB2;PB2 175;188;202;230;272;160;262;145;220;252 177;190;204;232;274;163;265;148;223;255 31581279 Influenza virus polymerase subunits co-evolve to ensure proper levels of dimerization of the heterotrimer. Where indicated, plasmids encoding a transcription-deficient (PB2-E361A, R+/T-) or replication-deficient (PB2-R142A, R-/T+) PB2 protein were co-transfected to trans-complement the att-PxW polymerase (b-e). 2019 PLoS pathogens Figure IV E361A;R142A 66;110 71;115 PB2;PB2;PB2 62;106;124 65;109;127 31600274 Adaptation of H3N2 canine influenza virus to feline cell culture. CRFK cells were infected with recombinant viruses possessing (A) single mutation (rHA1-K299R, rHA2-T107I, rNA-L35R, or rM2-W41C), (B) multiple mutations (rHA1-K299R/NA-L35R, rHA1-K299R/M2-W41C, or rHA1-K299R/NA-L35R/M2-W41C), or recombinant wild-type (rWT) virus at an moi of 0.01. 2019 PloS one Figure IV K299R;T107I;L35R;W41C;K299R;L35R;K299R;W41C;K299R;L35R;W41C 87;99;110;123;159;168;179;188;202;211;219 92;104;114;127;164;172;184;192;207;215;223 M2;M2;NA;NA;NA 185;216;165;208;106 187;218;167;210;109 31600274 Adaptation of H3N2 canine influenza virus to feline cell culture. Fcwf-4 cells were infected with recombinant viruses possessing (A) single mutation (rHA1-K299R, rHA2-T107I, rNA-L35R, or rM2-W41C), (B) multiple mutations (rHA1-K299R/NA-L35R, rHA1-K299R/M2-W41C, or rHA1-K299R/NA-L35R/M2-W41C), or recombinant wild-type (rWT) virus at an moi of 0.01. 2019 PloS one Figure IV K299R;T107I;L35R;W41C;K299R;L35R;K299R;W41C;K299R;L35R;W41C 89;101;112;125;161;170;181;190;204;213;221 94;106;116;129;166;174;186;194;209;217;225 M2;M2;NA;NA;NA 187;218;167;210;108 189;220;169;212;111 31600274 Adaptation of H3N2 canine influenza virus to feline cell culture. MDCK cells were co-transfected with a mutant (HA1-K299R or HA2-T107I) or wild-type (HA-WT) HA expression plasmid and a Venus expression plasmid. 2019 PloS one Figure IV K299R;T107I 50;63 55;68 HA;HA;HA;HA1 59;84;91;46 61;86;93;49 31600274 Adaptation of H3N2 canine influenza virus to feline cell culture. MDCK cells were infected with recombinant viruses possessing (A) single mutation (rHA1-K299R, rHA2-T107I, rNA-L35R, or rM2-W41C), (B) multiple mutations (rHA1-K299R/NA-L35R, rHA1-K299R/M2-W41C, or rHA1-K299R/NA-L35R/M2-W41C), or recombinant wild-type (rWT) virus at an moi of 0.001. 2019 PloS one Figure IV K299R;T107I;L35R;W41C;K299R;L35R;K299R;W41C;K299R;L35R;W41C 87;99;110;123;159;168;179;188;202;211;219 92;104;114;127;164;172;184;192;207;215;223 M2;M2;NA;NA;NA 185;216;165;208;106 187;218;167;210;109 31600274 Adaptation of H3N2 canine influenza virus to feline cell culture. The mutant (rHA1-K299R and rHA1-T107I) and wild-type (rWT) viruses were diluted to 4x106 PFU/mL and aliquoted. 2019 PloS one Figure IV K299R;T107I 17;32 22;37 31608791 Insights into species-specific regulation of ANP32A on the mammalian-restricted influenza virus polymerase activity. (A) 293T cells were transfected with PR8 Myc-PB2 K627E or 627K, PB1, PA, and NP as well as ANP32A with or without cNA-Luc. 2019 Emerging microbes & infections Figure IV K627E 49 54 NP;PA;PB1;PB2 77;69;64;45 79;71;67;48 31608791 Insights into species-specific regulation of ANP32A on the mammalian-restricted influenza virus polymerase activity. (A) Schematic representation of wild-type and mutant influenza cRNA promoter structures (5' promoter C3U + G8A mutations and 3' promoter A3G + U8C mutations) according to the panhandle model. 2019 Emerging microbes & infections Figure IV A3G;G8A 137;107 140;110 31608791 Insights into species-specific regulation of ANP32A on the mammalian-restricted influenza virus polymerase activity. (A) The viral titres of PR8-PB2 K627E and PR8-PB2 627K in 293T cells. 2019 Emerging microbes & infections Figure IV K627E 32 37 PB2;PB2 28;46 31;49 31608791 Insights into species-specific regulation of ANP32A on the mammalian-restricted influenza virus polymerase activity. (B) 293T cells were transfected with PR8 Myc-PB2 K627E or 627K, PB1(D446Y), PA, and NP as well as ANP32A with cNA-Luc. 2019 Emerging microbes & infections Figure IV K627E;D446Y 49;68 54;73 NP;PA;PB1;PB2 84;76;64;45 86;78;67;48 31608791 Insights into species-specific regulation of ANP32A on the mammalian-restricted influenza virus polymerase activity. (B) Effect of PB2 mutations on the regulation of ANP32A in PR8 PB2 K627E polymerase activity. 2019 Emerging microbes & infections Figure IV K627E 67 72 PB2;PB2 14;63 17;66 31608791 Insights into species-specific regulation of ANP32A on the mammalian-restricted influenza virus polymerase activity. (C) The effects of different expression levels of chANP32A-X1 and chANP32A-X2 on the activity of PR8 PB2 K627E polymerase in 293T cells. 2019 Emerging microbes & infections Figure IV K627E 105 110 PB2 101 104 31608791 Insights into species-specific regulation of ANP32A on the mammalian-restricted influenza virus polymerase activity. 293T cells infected with either PR8-K627E or PR8-627K virus with or without 100 mug/mL cycloheximide (CHX) at an MOI of 5. 2019 Emerging microbes & infections Figure IV K627E 36 41 31608791 Insights into species-specific regulation of ANP32A on the mammalian-restricted influenza virus polymerase activity. 293T cells were transfected with PB1, PB2 627E or 627K, PA and NP (0.1 mug/well) as well as ANP32A (0.5 mug/well) at 37 C for 24 h, subsequently infected with the PR8-627K virus or PR8-K627E virus at an MOI of 5 and treated with CHX (100 mug/ml) for 4 h. 2019 Emerging microbes & infections Figure IV K627E 185 190 NP;PA;PB1;PB2 63;56;33;38 65;58;36;41 31608791 Insights into species-specific regulation of ANP32A on the mammalian-restricted influenza virus polymerase activity. Effect of PB2 mutations on PR8 PB2 K627E polymerase and the regulation of ANP32A in PR8 PB2 K627E polymerase activity. 2019 Emerging microbes & infections Figure IV K627E;K627E 35;92 40;97 PB2;PB2;PB2 10;31;88 13;34;91 31608791 Insights into species-specific regulation of ANP32A on the mammalian-restricted influenza virus polymerase activity. Wild-type or chANP32A-X1-expressed 293T cells were infected with PR8-PB2 K627E and PR8-PB2 627K (MOI = 0.01). 2019 Emerging microbes & infections Figure IV K627E 73 78 PB2;PB2 69;87 72;90 31719554 Synergistic PA and HA mutations confer mouse adaptation of a contemporary A/H3N2 influenza virus. (C,D) Body weight loss and survival curve of mice infected with 1 x 105 PFU of recombinant viruses containing a single substitution (K615E) in MA-H3N2-PA segment and various substitutions in MA-H3N2-HA segment (N144E, N246K, and A304T). 2019 Scientific reports Figure IV K615E;N144E;N246K;A304T 133;211;218;229 138;216;223;234 HA;PA 199;151 201;153 31749796 Enhanced Antiviral Activity of Human Surfactant Protein D by Site-Specific Engineering of the Carbohydrate Recognition Domain. Modifications of hSP-D present in iSP-D are highlighted with deviating colors: the 326GSS-insertion (magenta), and the Asp324Asn and Asp330Asn mutations (blue; also indicated with blue arrows). 2019 Frontiers in immunology Figure IV D324N;D330N 119;133 128;142 31805964 The tyrosine 73 and serine 83 dephosphorylation of H1N1 swine influenza virus NS1 protein attenuates virus replication and induces high levels of beta interferon. a 293 T cells transfected with plasmid pCAGGS-NS1 or pCAGGS-NS1 mutant Y73F, S76A, S83A, T151A, S161A, and S195A were lysed 48 h after transfection. 2019 Virology journal Figure IV Y73F;S76A;S83A;T151A;S161A;S195A 71;77;83;89;96;107 75;81;87;94;101;112 NS1;NS1 46;60 49;63 31805964 The tyrosine 73 and serine 83 dephosphorylation of H1N1 swine influenza virus NS1 protein attenuates virus replication and induces high levels of beta interferon. MDCK cells were infected with rSIV or mutated virus (rSIV NS1 Y73F and rSIV NS1 S83A) at an MOI of 0.001. 2019 Virology journal Figure IV Y73F;S83A 62;80 66;84 NS1;NS1 58;76 61;79 31805964 The tyrosine 73 and serine 83 dephosphorylation of H1N1 swine influenza virus NS1 protein attenuates virus replication and induces high levels of beta interferon. NS1 protein localization is not affected by Y73F or S83A dephosphorylation. 2019 Virology journal Figure IV Y73F;S83A 44;52 48;56 NS1 0 3 31805964 The tyrosine 73 and serine 83 dephosphorylation of H1N1 swine influenza virus NS1 protein attenuates virus replication and induces high levels of beta interferon. Recombinant viruses possessing wild-type NS1, NS1 Y73F and NS1 S83A were generated by reverse genetics, as described in the Materials and Methods. 2019 Virology journal Figure IV Y73F;S83A 50;63 54;67 NS1;NS1;NS1 41;46;59 44;49;62 31805964 The tyrosine 73 and serine 83 dephosphorylation of H1N1 swine influenza virus NS1 protein attenuates virus replication and induces high levels of beta interferon. RIG-I contributes to IFN-beta production during infection with Y73F and S83A mutants. 2019 Virology journal Figure IV Y73F;S83A 63;72 67;76 31805964 The tyrosine 73 and serine 83 dephosphorylation of H1N1 swine influenza virus NS1 protein attenuates virus replication and induces high levels of beta interferon. Y73F and S83A substitution affects IFN-beta antagonistic properties of NS1. 2019 Virology journal Figure IV Y73F;S83A 0;9 4;13 NS1 71 74 31864377 Changes in RNA secondary structure affect NS1 protein expression during early stage influenza virus infection. Predicted secondary structures of NS gene segment RNA regions 82-148 and 497-564 without and with mutations (a) 82-148 original sequence of A/Brevig Mission/1/1918 (H1N1) (hairpin), (b) 82-148 mutated sequence featuring G123A and A132G substitutions, (c)497-564 original sequence of A/Vietnam/1194/2004 (H5N1) (hairpin), (d) 497-564 mutated sequence featuring G511A, G512A and C537G substitutions. 2019 Virology journal Figure IV G123A;A132G;G511A;G512A;C537G 220;230;360;367;377 225;235;365;372;382 NS 34 36 31906790 Contribution of Fc-dependent cell-mediated activity of a vestigial esterase-targeting antibody against H5N6 virus infection. (C) Binding of human C1q to 9F4-K322A is abolished. 2020 Emerging microbes & infections Figure IV K322A 32 37 31906790 Contribution of Fc-dependent cell-mediated activity of a vestigial esterase-targeting antibody against H5N6 virus infection. Balb/c mice were infected with 100 PFU of rgPR8 H5N6 and received a single therapeutic dose of 9F4-WT, 9F4-K322A or the isotype control 1A4 at 10 mg/kg via intraperitoneal injections 24 hpi. 2020 Emerging microbes & infections Figure IV K322A 107 112 31906790 Contribution of Fc-dependent cell-mediated activity of a vestigial esterase-targeting antibody against H5N6 virus infection. ELISA was performed to compare the binding affinity of 9F4-WT with (A) 9F4-LALA or (B) 9F4-K322A to H5N6-HA. 2020 Emerging microbes & infections Figure IV K322A 91 96 HA 105 107 31906790 Contribution of Fc-dependent cell-mediated activity of a vestigial esterase-targeting antibody against H5N6 virus infection. mFcgammaRIV activation is induced by 9F4-WT and 9F4-K322A but not 9F4-LALA. 2020 Emerging microbes & infections Figure IV K322A 52 57 31906790 Contribution of Fc-dependent cell-mediated activity of a vestigial esterase-targeting antibody against H5N6 virus infection. Mouse FcgammaRIV-based ADCC reporter assay was performed for 9F4-WT, (A) 9F4-LALA and (B) 9F4-K322A as described in materials and methods. 2020 Emerging microbes & infections Figure IV K322A 94 99 31906790 Contribution of Fc-dependent cell-mediated activity of a vestigial esterase-targeting antibody against H5N6 virus infection. Pseudotyped lentiviral particles harbouring the HA proteins of H5N6 IAV were incubated with 10-fold serially diluted 9F4-WT, (C) 9F4-LALA or (D) 9F4-K322A for 1 h at RT before inoculation onto MDCK cells. 2020 Emerging microbes & infections Figure IV K322A 149 154 HA 48 50 31932446 A molecularly engineered antiviral banana lectin inhibits fusion and is efficacious against influenza virus infection in vivo. (D) Therapeutic efficacy of H84T administered subcutaneously in BALB/c mice challenged intranasally with a lethal dose of A/WSN/HA(NC/2099-N225G)/1933 (H1N1). 2020 Proc Natl Acad Sci U S A Figure IV N225G 139 144 HA 128 130 31932446 A molecularly engineered antiviral banana lectin inhibits fusion and is efficacious against influenza virus infection in vivo. BALB/c mice were injected intraperitoneally with two 50-mg/kg doses of WT, H84T, or D133G BanLec administered 1 mo apart (n = 10 per group). 2020 Proc Natl Acad Sci U S A Figure IV D133G 84 89 31932446 A molecularly engineered antiviral banana lectin inhibits fusion and is efficacious against influenza virus infection in vivo. Blots were incubated with 100 nM H84T or D133G BanLec. 2020 Proc Natl Acad Sci U S A Figure IV D133G 41 46 31932446 A molecularly engineered antiviral banana lectin inhibits fusion and is efficacious against influenza virus infection in vivo. MDCK cells were pretreated for 1 h with 0.1, 1, or 10 muM H84T, 10 muM D133G, or 40 muM of the fusion inhibitor ARB and infected with A/WSN/1933 (MOI 0.5) for 2.5 h at 37 C. 2020 Proc Natl Acad Sci U S A Figure IV D133G 71 76 31932446 A molecularly engineered antiviral banana lectin inhibits fusion and is efficacious against influenza virus infection in vivo. MDCK cells were pretreated for 1 h with H84T (0.1, 1, or 10 muM in A; 0.05, 0.1, or 1 muM in C), 10 muM D133G, or 40 muM of the fusion inhibitor ARB and infected with A/WSN/1933 (H1N1) (A) or A/Colorado/15/2014 (H3N2) (C) (MOI = 0.5) for 5 h at 37 C. 2020 Proc Natl Acad Sci U S A Figure IV D133G 104 109 31932446 A molecularly engineered antiviral banana lectin inhibits fusion and is efficacious against influenza virus infection in vivo. Therapeutic efficacy of H84T administered intraperitoneally in BALB/c mice challenged intranasally with two times the 50% mouse lethal dose of A/WSN/HA(NC/2099-N225G)/1933 (H1N1). 2020 Proc Natl Acad Sci U S A Figure IV N225G 160 165 HA 149 151 32064779 Rapid detection of an I38T amino acid substitution in influenza polymerase acidic subunit associated with reduced susceptibility to baloxavir marboxil. Endpoint fluorescence plot of A/H1pdm PA_I38T rhPCR, A/H3 PA_I38T rhPCR, and B PA_I38T rhPCR. 2020 Influenza and other respiratory viruses Figure IV I38T;I38T;I38T 41;61;82 45;65;86 PA;PA;PA 38;58;79 40;60;81 32064779 Rapid detection of an I38T amino acid substitution in influenza polymerase acidic subunit associated with reduced susceptibility to baloxavir marboxil. Endpoint fluorescence plots of A/H1pdm PA_I38T rhPCR and A/H3 PA_I38T rhPCR using cDNA synthesized from RNAs of clinical strains and clinical specimens. 2020 Influenza and other respiratory viruses Figure IV I38T;I38T 42;65 46;69 PA;PA 39;62 41;64 32064779 Rapid detection of an I38T amino acid substitution in influenza polymerase acidic subunit associated with reduced susceptibility to baloxavir marboxil. Endpoint fluorescence plots of A/H1pdm PA_I38T rhPCR, A/H3 PA_I38T rhPCR, and B PA_I38T rhPCR. 2020 Influenza and other respiratory viruses Figure IV I38T;I38T;I38T 42;62;83 46;66;87 PA;PA;PA 39;59;80 41;61;82 32130243 Epidemic of influenza A(H1N1)pdm09 analyzed by full genome sequences and the first case of oseltamivir-resistant strain in Myanmar 2017. Red circle represents oseltamivir- and peramivir-resistant strain exhibiting NA H275Y substitution. 2020 PloS one Figure IV H275Y 81 86 78 80 32159230 Antigenic drift of hemagglutinin and neuraminidase in seasonal H1N1 influenza viruses from Saudi Arabia in 2014 to 2015. B, S179N amino acid change present in the antigenic site Sa of HA1 of H1N1 circulating strains compared to that of the H1N1 vaccine strain is shown in ribbon in red. 2020 Journal of medical virology Figure IV S179N 3 8 HA1 63 66 32159230 Antigenic drift of hemagglutinin and neuraminidase in seasonal H1N1 influenza viruses from Saudi Arabia in 2014 to 2015. C, The approximate location of HA amino acid change S220T, situated in the Ca1 antigenic site at the subunit interface, is indicated. 2020 Journal of medical virology Figure IV S220T 52 57 HA 31 33 32415096 mRNA display with library of even-distribution reveals cellular interactors of influenza virus NS1. A lower ratio represented a stronger loss of binding for D92Y mutant. 2020 Nature communications Figure IV D92Y 57 61 32415096 mRNA display with library of even-distribution reveals cellular interactors of influenza virus NS1. a Ratio of average enrichment scores of indicated proteins binding to NS1 versus D92Y mutant (N = 6 for NS1 protein and N = 2 for D92Y mutant, biologically independent samples). 2020 Nature communications Figure IV D92Y;D92Y 81;130 85;134 NS1;NS1 70;104 73;107 32415096 mRNA display with library of even-distribution reveals cellular interactors of influenza virus NS1. b Interactions between CPSF1 and NS1 proteins (WT and D92Y mutant) were examined by immunoprecipitation. 2020 Nature communications Figure IV D92Y 54 58 NS1 33 36 32415096 mRNA display with library of even-distribution reveals cellular interactors of influenza virus NS1. c Inhibition of protein expression by WT or D92Y NS1 proteins using GFP reporter. 2020 Nature communications Figure IV D92Y 44 48 NS1 49 52 32415096 mRNA display with library of even-distribution reveals cellular interactors of influenza virus NS1. e Effect of CPSF1 overexpression on the replication of WT or D92Y mutant viruses (N = 3 biologically independent samples). 2020 Nature communications Figure IV D92Y 61 65 32415096 mRNA display with library of even-distribution reveals cellular interactors of influenza virus NS1. f Interactions between WT and mutant (R38A/K41A) NS1 protein with FASN were examined by Co-immunoprecipitation assay, using Strep-tagged NS1 and FLAG-tagged FASN in 293T cells. 2020 Nature communications Figure IV R38A;K41A 38;43 42;47 NS1;NS1 49;137 52;140 32415096 mRNA display with library of even-distribution reveals cellular interactors of influenza virus NS1. GFP reporter was transfected in 293T cells together with WT or D92Y NS1 expression plasmid. 2020 Nature communications Figure IV D92Y 63 67 NS1 68 71 32415096 mRNA display with library of even-distribution reveals cellular interactors of influenza virus NS1. h The levels of newly synthesized fatty acids upon WT or mutant (R38A/K41A) NS1 protein expression were examined by GC/MS (N = 4 for NS1 WT and mutant, N = 3 for NP, biologically independent samples). 2020 Nature communications Figure IV R38A;K41A 65;70 69;74 NP;NS1;NS1 162;76;133 164;79;136 32415096 mRNA display with library of even-distribution reveals cellular interactors of influenza virus NS1. Mechanistic characterization of an NS1 IFN-sensitive mutation D92Y. 2020 Nature communications Figure IV D92Y 62 66 NS1 35 38 32601336 Pre-existing immunity to influenza virus hemagglutinin stalk might drive selection for antibody-escape mutant viruses in a human challenge model. 24 hours after infection, cells were harvested, and the expression of wild-type and mutant HA was measured by flow cytometry to evaluate the effect of the A388V mutation on the HA stalk epitopes. 2020 Nature medicine Figure IV A388V 155 160 HA;HA 91;177 93;179 32601336 Pre-existing immunity to influenza virus hemagglutinin stalk might drive selection for antibody-escape mutant viruses in a human challenge model. A significant conformational change to the HA stalk region induced by A388V mutation. 2020 Nature medicine Figure IV A388V 70 75 HA 43 45 32601336 Pre-existing immunity to influenza virus hemagglutinin stalk might drive selection for antibody-escape mutant viruses in a human challenge model. A388V mutation, HA trimerization domain, and StrepTag II sequence are highlighted. 2020 Nature medicine Figure IV A388V 0 5 HA 16 18 32601336 Pre-existing immunity to influenza virus hemagglutinin stalk might drive selection for antibody-escape mutant viruses in a human challenge model. Amino acid sequences of (a) full-length HA and (b) stalk-only proteins with or without A388V mutation are shown. 2020 Nature medicine Figure IV A388V 87 92 HA 40 42 32601336 Pre-existing immunity to influenza virus hemagglutinin stalk might drive selection for antibody-escape mutant viruses in a human challenge model. Stalk-only constructs with or without the A388V mutation (See Extended Data. 2020 Nature medicine Figure IV A388V 42 47 32601336 Pre-existing immunity to influenza virus hemagglutinin stalk might drive selection for antibody-escape mutant viruses in a human challenge model. The comparison result (summarized in the table) shows that the A388V stalk-only construct closely represents the natural stalk structure of the full-length A388V HA. 2020 Nature medicine Figure IV A388V;A388V 63;156 68;161 HA 162 164 32601336 Pre-existing immunity to influenza virus hemagglutinin stalk might drive selection for antibody-escape mutant viruses in a human challenge model. To confirm that the stalk-only construct with A388V mutation appropriately represents the natural A388V stalk structure, the level of decrease in broadly neutralizing monoclonal antibodies (bNAbs) binding was compared between the stalk-only construct and the full-length HA. 2020 Nature medicine Figure IV A388V;A388V 46;98 51;103 HA 271 273 32601336 Pre-existing immunity to influenza virus hemagglutinin stalk might drive selection for antibody-escape mutant viruses in a human challenge model. To find potential loss in viral fitness in humans caused by the A388V mutation, (f) days of symptoms, (g) number of symptoms, and (h) duration of shedding after the challenge infection were compared between groups. 2020 Nature medicine Figure IV A388V 64 69 32631240 Successful treatment with baloxavir marboxil of a patient with peramivir-resistant influenza A/H3N2 with a dual E119D/R292K substitution after allogeneic hematopoietic cell transplantation: a case report. Clinical course in a severely immunosuppressed patient with peramivir-resistant dual E119D/R292K neuraminidase mutated-influenza A/H3N2 after allo-HCT allo-HCT, allogeneic hematopoietic cell transplantation; A-VVV, cytosine arabinoside, etoposide, vincristine, and vinblastine; CsA, cyclosporine A; HU, hydroxyurea; Lym, lymphocyte; PSL, prednisolone. 2020 BMC infectious diseases Figure IV E119D;R292K 85;91 90;96 97 110 32631440 Characterization of neuraminidase inhibitor-resistant influenza virus isolates from immunocompromised patients in the Republic of Korea. A/Korea/S0002/2019 harbored Q51K, F74S, T152I and D416N mutation and A/Korea/S0003/2019 harbored I29M, P93S, I99V, G298A, V321I and V394I mutation compared to A/Brisbane/02/2018. 2020 Virology journal Figure IV Q51K;F74S;T152I;D416N;I29M;P93S;I99V;G298A;V321I;V394I 28;34;40;50;97;103;109;115;122;132 32;38;45;55;101;107;113;120;127;137 32631440 Characterization of neuraminidase inhibitor-resistant influenza virus isolates from immunocompromised patients in the Republic of Korea. A/Korea/S0002/2019 virus belonged to 6B.1A5 harboring T202I, N277D and K521R mutations compared to A/Brisbane/02/2018 and clustered with isolated viruses in 2019 year, Republic of Korea (ROK), whereas A/Korea/S0003/2019 virus belonged to 6B.1A4 harboring A158E mutation and clustered with isolated viruses in previous year. 2020 Virology journal Figure IV T202I;N277D;K521R;A158E 54;61;71;255 59;66;76;260 32631440 Characterization of neuraminidase inhibitor-resistant influenza virus isolates from immunocompromised patients in the Republic of Korea. The H275Y mutated viruses (A/Korea/S0002/2019 and A/Korea/S0003/2019) were not identical in phylogenetic tree of NA. 2020 Virology journal Figure IV H275Y 4 9 113 115 32636820 Enhanced Potency of a Broad H7N9-Neutralizing Antibody HNIgGA6 Through Structure-Based Design. (B) S28H neutralized 11 out of the total 12 strains tested. 2020 Frontiers in microbiology Figure IV S28H 4 8 32636820 Enhanced Potency of a Broad H7N9-Neutralizing Antibody HNIgGA6 Through Structure-Based Design. Enhancement of in vitro neutralizing potency for the S28H variant. 2020 Frontiers in microbiology Figure IV S28H 53 57 32636820 Enhanced Potency of a Broad H7N9-Neutralizing Antibody HNIgGA6 Through Structure-Based Design. Enhancement of viral HA binding affinity for the S28H mutant. 2020 Frontiers in microbiology Figure IV S28H 49 53 HA 21 23 32636820 Enhanced Potency of a Broad H7N9-Neutralizing Antibody HNIgGA6 Through Structure-Based Design. Increased in vivo neutralization potency of the S28H variant. 2020 Frontiers in microbiology Figure IV S28H 48 52 32636820 Enhanced Potency of a Broad H7N9-Neutralizing Antibody HNIgGA6 Through Structure-Based Design. Less dramatic pathological changes in the lungs of the S28H-treated mice were detected One-way ANOVA was used to analyze the data (ANOVA, F = 70.52, p = 2.32E-07). 2020 Frontiers in microbiology Figure IV S28H 55 59 32636820 Enhanced Potency of a Broad H7N9-Neutralizing Antibody HNIgGA6 Through Structure-Based Design. Mice received HNIgGA6 or S28H mAb 24 h before H7N9 infection and were monitored daily for 14 days. 2020 Frontiers in microbiology Figure IV S28H 25 29 32636820 Enhanced Potency of a Broad H7N9-Neutralizing Antibody HNIgGA6 Through Structure-Based Design. Mice were passively immunized with HNIgGA6 or S28H variant 24 h and then challenged with a lethal dose of H7N9 virus. 2020 Frontiers in microbiology Figure IV S28H 46 50 32636820 Enhanced Potency of a Broad H7N9-Neutralizing Antibody HNIgGA6 Through Structure-Based Design. The S28H mAb protected mice from H7N9 infection. 2020 Frontiers in microbiology Figure IV S28H 4 8 Influenza A virus H7N9 infection 33 47 32636820 Enhanced Potency of a Broad H7N9-Neutralizing Antibody HNIgGA6 Through Structure-Based Design. Virus titres were substantially reduced in the S28H-treated group compared to HNIgGA6-treated and the control mice. 2020 Frontiers in microbiology Figure IV S28H 47 51 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. a Optical images of A4-Au NPs in the presence of I223R/H275Y pH1N1 (upper panel) and wt pH1N1 (lower panel). 2020 Nature communications Figure IV I223R;H275Y 49;55 54;60 NP 26 29 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. a Optical images of A4-based lateral flow systems after detection of I223R/H275Y pH1N1, wt pH1N1, and control sample. 2020 Nature communications Figure IV I223R;H275Y 69;75 74;80 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. a SERS spectra of MGITC obtained from NPs-on-plate structures in the presence of I223R/H275Y pH1N1 and wt pH1N1. 2020 Nature communications Figure IV I223R;H275Y 81;87 86;92 NP 38 41 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. A4 was applied to wt NA and I223R/H275Y NA dotted in a twofold dilution series (0.78-100 ng mL-1), and HRP-conjugated anti-human IgG Fc was applied for detection. 2020 Nature communications Figure IV I223R;H275Y 28;34 33;39 NA;NA 21;40 23;42 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. Application of A4 to I223R/H275Y virus detection. 2020 Nature communications Figure IV I223R;H275Y 21;27 26;32 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. b Optical images of A4-based lateral flow systems after detection of I223R/H275Y and wt pH1N1 mixture in nasal fluid and control sample. 2020 Nature communications Figure IV I223R;H275Y 69;75 74;80 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. Calculated binding modes of the model epitopes for c wt NA and d I223R/H275Y NA in CDR of A4. 2020 Nature communications Figure IV I223R;H275Y 65;71 70;76 NA;NA 56;77 58;79 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. Docked poses of the model epitopes for a wt NA and b I223R/H275Y NA in CDR of A4. 2020 Nature communications Figure IV I223R;H275Y 53;59 58;64 NA;NA 44;65 46;67 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. LFA of I223R/H275Y influenza viruses in human nasal fluid samples using A4. 2020 Nature communications Figure IV I223R;H275Y 7;13 12;18 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. LFA of I223R/H275Y pH1N1 in human nasal fluid samples using A4. 2020 Nature communications Figure IV I223R;H275Y 7;13 12;18 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. Optical images of A4-based lateral flow systems after detection of influenza-positive nasopharyngeal swab samples a in the absence or b presence of I223R/H275Y pH1N1 (103 PFU). 2020 Nature communications Figure IV I223R;H275Y 148;154 153;159 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. Optical images of A4-based lateral flow systems after detection of influenza-positive nasopharyngeal swab samples in the absence or presence of I223R/H275Y influenza viruses (A/Puerto Rico/8/1934 (H1N1), A/Brisbane/10/2007 (H3N2), A/swine/Korea/GC0503/2005 (H1N1), and A/canine/Korea/MV1/2012 (H3N2)). 2020 Nature communications Figure IV I223R;H275Y 144;150 149;155 32647286 Development of A4 antibody for detection of neuraminidase I223R/H275Y-associated antiviral multidrug-resistant influenza virus. Selection of I223R/H275Y NA-specific monoclonal antibody. 2020 Nature communications Figure IV I223R;H275Y 13;19 18;24 25 27 32677963 Influenza A virus NS1 optimises virus infectivity by enhancing genome packaging in a dsRNA-binding dependent manner. 3a in the absence of NS1 or NS1 WT or NS1 R38A. 2020 Virology journal Figure IV R38A 42 46 NS1;NS1;NS1 21;28;38 24;31;41 32677963 Influenza A virus NS1 optimises virus infectivity by enhancing genome packaging in a dsRNA-binding dependent manner. a 293 T RIG-I KO cells were infected with PR8 delNS1 at MOI 0.01 and transfected with empty vector (E.C.), NS1 WT or NS1 R38A as described in. 2020 Virology journal Figure IV R38A 121 125 NS1;NS1 107;117 110;120 32714761 Structural Basis of Human Helicase DDX21 in RNA Binding, Unwinding, and Antiviral Signal Activation. D339H forms a new salt bridge (purple) with ATP phosphate and new cooperative bond (purple) with Mg2+ ion by the His substitution, while E340G mutation lacks the inter-domain interactions with Arg499 and His523. 2020 Advanced science (Weinheim, Baden-Wurttemberg, Germany) Figure IV D339H;E340G 0;137 5;142 32714761 Structural Basis of Human Helicase DDX21 in RNA Binding, Unwinding, and Antiviral Signal Activation. F) Superimposition of D339H and E340G mutants. 2020 Advanced science (Weinheim, Baden-Wurttemberg, Germany) Figure IV D339H;E340G 22;32 27;37 32746754 A single N342D substitution in Influenza B Virus NA protein determines viral pathogenicity in mice. The N342D substitution is shown in red, previously described mutations are shown in green. 2020 Emerging microbes & infections Figure IV N342D 4 9 32750468 Functional neuraminidase inhibitor resistance motifs in avian influenza A(H5Nx) viruses. (A) Amino acid substitutions found in HA genes of H5N6_R292K and N294S viruses. 2020 Antiviral research Figure IV N294S;R292K 65;55 70;60 HA 38 40 32750468 Functional neuraminidase inhibitor resistance motifs in avian influenza A(H5Nx) viruses. (J-O) Susceptibility profile of H5N6 carrying R292K NA substitution to NAIs as determined by plaque reduction assay. 2020 Antiviral research Figure IV R292K 46 51 NA;NAI 52;71 54;75 32750468 Functional neuraminidase inhibitor resistance motifs in avian influenza A(H5Nx) viruses. Each panel of viruses (R292K only for H5N2) alongside with the PR8 strain were tested for their susceptibility to OSE (left column), ZAN (middle column) and PER (right column). 2020 Antiviral research Figure IV R292K 23 28 32750468 Functional neuraminidase inhibitor resistance motifs in avian influenza A(H5Nx) viruses. FLAG-tagged NAs (wt, E119V, H274Y, R292K and N294S) were expressed in HEK 293T cells, the NA activities were determined by MUNANA assay and normalised to protein expression levels. 2020 Antiviral research Figure IV E119V;H274Y;R292K;N294S 21;28;35;45 26;33;40;50 NA;NA 90;12 92;15 32750468 Functional neuraminidase inhibitor resistance motifs in avian influenza A(H5Nx) viruses. MDCK cells were infected with H5N6 viruses bearing either wt (blue) or R292K (orange) NA variants. 2020 Antiviral research Figure IV R292K 71 76 86 88 32873642 Dynamic PB2-E627K substitution of influenza H7N9 virus indicates the in vivo genetic tuning and rapid host adaptation. (B) Early adaptation of E627K (indicated by Lys ratios/days after disease onset) in the upper respiratory tract of deceased patients compared with recovered patients (n = 34). 2020 Proc Natl Acad Sci U S A Figure IV E627K 24 29 32929001 RNA-seq accuracy and reproducibility for the mapping and quantification of influenza defective viral genomes. (A) RNA-seq data corresponding to RT-seq and RT-PCR-seq on the WT, PA-K635A, and PA-R638A viral stocks from Expt 1 were analyzed using the ViReMa pipeline. 2020 RNA (New York, N.Y.) Figure IV K635A;R638A 70;84 75;89 PA;PA 67;81 69;83 32929001 RNA-seq accuracy and reproducibility for the mapping and quantification of influenza defective viral genomes. The DVGs identified upon DG-seq analysis of vRNAs purified from the WT, PA-K635A and PA-R638A viral stocks in Expt 1 were characterized separately for each virus (while they were analyzed all together in. 2020 RNA (New York, N.Y.) Figure IV K635A;R638A 75;88 80;93 PA;PA 72;85 74;87 33024040 Structure-Based Modification of an Anti-neuraminidase Human Antibody Restores Protection Efficacy against the Drifted Influenza Virus. (A and D) Gel filtration survival analysis of Z2B3-D102R Fab with Serbia N1 (A) and 18N1 (D). 2020 mBio Figure IV D102R 51 56 33024040 Structure-Based Modification of an Anti-neuraminidase Human Antibody Restores Protection Efficacy against the Drifted Influenza Virus. (B and E) An SPR assay characterizing the specific binding between Z2B3-D102R and specific NAs, including Serbia N1 (B) and 18N1 (E). 2020 mBio Figure IV D102R 72 77 91 94 33024040 Structure-Based Modification of an Anti-neuraminidase Human Antibody Restores Protection Efficacy against the Drifted Influenza Virus. (C and F) NA inhibition activity of Z2B3 and Z2B3-D102R for Serbia N1 (C) and 18N1 proteins (F). 2020 mBio Figure IV D102R 50 55 10 12 33024040 Structure-Based Modification of an Anti-neuraminidase Human Antibody Restores Protection Efficacy against the Drifted Influenza Virus. (I and J) The prophylactic (I) and therapeutic (J) efficacy of Z2B3 or Z2B3-D102R against A/Serbia/NS-601/2014 (H1N1) infection were tested in DBA/2 mice (n = 5 per group). 2020 mBio Figure IV D102R 76 81 NS 99 101 Influenza A virus H1N1 infection 112 127 33024040 Structure-Based Modification of an Anti-neuraminidase Human Antibody Restores Protection Efficacy against the Drifted Influenza Virus. A D102R substitution in Z2B3 can restore the reactivity to Serbia N1. 2020 mBio Figure IV D102R 2 7 33024040 Structure-Based Modification of an Anti-neuraminidase Human Antibody Restores Protection Efficacy against the Drifted Influenza Virus. Protection efficacy of Z2B3 or Z2B3-D102R against lethal infection with influenza viruses in mice. 2020 mBio Figure IV D102R 36 41 33024040 Structure-Based Modification of an Anti-neuraminidase Human Antibody Restores Protection Efficacy against the Drifted Influenza Virus. Z2B3-D102R (magenta), NA (cyan), or Z2B3-D102R-NA (blue) mixtures were analyzed by a Superdex 200 gel filtration column. 2020 mBio Figure IV D102R;D102R 5;41 10;46 NA;NA 22;47 24;49 33028722 PA Mutations Inherited during Viral Evolution Act Cooperatively To Increase Replication of Contemporary H5N1 Influenza Virus with an Expanded Host Range. (A and C) Transparent surface diagrams of the D1/PA polymerase complex composed of PB2 (blue), PB1 (pink), and PA (green) with the A448E, S388R, and E18G mutations (red). 2020 Journal of virology Figure IV A448E;S388R;E18G 131;138;149 136;143;153 PA;PA;PB1;PB2 49;111;95;83 51;113;98;86 33063654 Detection and discrimination of influenza B Victoria lineage deletion variant viruses by real-time RT-PCR. HA (coding sequence) phylogenetic tree with representative viruses of the genetic groups of B/Victoria and B/Yamagata lineages of related viruses; V1A, V1A-2DEL, V1A-3DEL and YAM are indicated by the bars on the right. 2020 Euro surveillance Figure IV V1A;V1A;V1A 147;152;162 150;155;165 HA 0 2 33270431 Colorimetric Detection of SARS-CoV-2 and Drug-Resistant pH1N1 Using CRISPR/dCas9. (a, b) Sequence of gRNA, pH1N1/H275Y N1, pH1N1 WT N1, and biotin-PAMmer. 2020 ACS sensors Figure IV H275Y 31 36 33270431 Colorimetric Detection of SARS-CoV-2 and Drug-Resistant pH1N1 Using CRISPR/dCas9. (d) Photograph of the microplate and corresponding heat map after the detection of pH1N1-spiked, pH1N1/H275Y-spiked, and control human fluid samples using CRISPR/dCas9. 2020 ACS sensors Figure IV H275Y 103 108 33270431 Colorimetric Detection of SARS-CoV-2 and Drug-Resistant pH1N1 Using CRISPR/dCas9. In the presence of pH1N1/H275Y, the color of all dCas9/gRNA (H1 and H275Y N1)-attached wells turns yellow. 2020 ACS sensors Figure IV H275Y;H275Y 25;68 30;73 33270431 Colorimetric Detection of SARS-CoV-2 and Drug-Resistant pH1N1 Using CRISPR/dCas9. Only in the presence of pH1N1 H1 and pH1N1/H275Y N1 RNAs, the color of both wells turns yellow. 2020 ACS sensors Figure IV H275Y 43 48 33281788 Altering Intracellular Localization of the RNA Interference Factors by Influenza A Virus Non-structural Protein 1. (A) Influenza viral titers were determined by qPCR in the lungs of BALB/c mice infected with PR8 WT and PR8 D101H viruses. 2020 Frontiers in microbiology Figure IV D101H 108 113 33281788 Altering Intracellular Localization of the RNA Interference Factors by Influenza A Virus Non-structural Protein 1. (A) Western and northern blotting detection of RNAi protein components and miR-16 in nuclear and cytoplasmic extracts isolated from 293T cells 12 h after inoculation with buffer (Mock), PR8 7 + 1, PR8 D101H, PR8 A155T, or PR8 D189N viruses. 2020 Frontiers in microbiology Figure IV D101H;A155T;D189N 201;212;226 206;217;231 33281788 Altering Intracellular Localization of the RNA Interference Factors by Influenza A Virus Non-structural Protein 1. (B) Representative lung H&E slice images of BALB/c mice after intranasal inoculation with Mock (left panel), PR8 WT (middle panel), or PR8 D101H virus (right panel). 2020 Frontiers in microbiology Figure IV D101H 139 144 33281788 Altering Intracellular Localization of the RNA Interference Factors by Influenza A Virus Non-structural Protein 1. (B) Representative lung IHC slice images of BALB/c mice intranasally inoculated with Mock (left panel), PR8 WT virus (middle panel), or PR8 D101H virus (right panel). 2020 Frontiers in microbiology Figure IV D101H 140 145 33281788 Altering Intracellular Localization of the RNA Interference Factors by Influenza A Virus Non-structural Protein 1. Mock infected (n = 5); PR8 WT infected (n = 10); PR8 D101H infected (n = 10). 2020 Frontiers in microbiology Figure IV D101H 53 58 33281788 Altering Intracellular Localization of the RNA Interference Factors by Influenza A Virus Non-structural Protein 1. Weight loss of BALB/c mice was measured daily after intranasal inoculation with Mock, PR8 WT, or PR8 D101H virus (**p < 0.01; log rank). 2020 Frontiers in microbiology Figure IV D101H 101 106 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. (A) PB1/K612R mutation does not affect the PB1-PB2 interaction. 2021 PLoS pathogens Figure IV K612R 8 13 PB1;PB1;PB2 4;43;47 7;46;50 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. (B-D) HEK293T cells were transfected with plasmids expressing the Flag-tagged 494-757 region of wild-type PB1 or a K612R mutant PB1 of WSN (H1N1) (B), VN/1180 (H5N1) (C), or AH/1 (H7N9) (D) virus; plasmid expression was verified by western blotting. 2021 PLoS pathogens Figure IV K612R 115 120 PB1;PB1 106;128 109;131 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. (B) HEK293T cells were transfected with plasmids encoding Flag-tagged WSN-H1PB1 or its potential SUMOylation site mutant WSN-H1PB1/K379R, WSN-H1PB1/K612R, or WSN-H1PB1/K736R, together with or without SUMO1 and Ubc9. 2021 PLoS pathogens Figure IV K379R;K612R;K736R 131;148;168 136;153;173 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. (C) PB1/K612R mutation does not affect the PB1-PA interaction. 2021 PLoS pathogens Figure IV K612R 8 13 PA;PB1;PB1 47;4;43 49;7;46 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. (G-I) Growth curves of WSN (H1N1) or WSN-PB1K612R (H1N1) (G), VN/1180 (H5N1) or VN/1180-PB1K612R (H5N1) (H), and AH/1 (H7N9) or AH/1-PB1K612R (H7N9) (I). 2021 PLoS pathogens Figure IV K612R 136 141 PB1;PB1;PB1 41;88;133 44;91;136 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. Four vRNP protein expression plasmids (PB2, PA, NP, and PB1 or a PB1/K612R mutant) derived from WSN (H1N1) (A), VN/1180 (H5N1) (B), or AH/1 (H7N9) (C), together with a luciferase reporter, pHH21-SC09NS F-Luc, and an internal control reporter, pRL-TK, were cotransfected into HEK293T cells. 2021 PLoS pathogens Figure IV K612R 69 74 NP;PA;PB1;PB1;PB2 48;44;56;65;39 50;46;59;68;42 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. HEK293T cells were transfected individually or in combination as indicated with plasmids expressing WSN-H1PB1 or WSN-H1PB1/K612R mutant, and WSN-H1PA. 2021 PLoS pathogens Figure IV K612R 123 128 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. HEK293T cells were transfected individually or in combination as indicated with plasmids expressing WSN-H1PB1 or WSN-H1PB1/K612R mutant, and WSN-H1PB2. 2021 PLoS pathogens Figure IV K612R 123 128 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. HEK293T cells were transfected with plasmids encoding Flag-tagged VN/1180-H5PB1 (D) or AH/1-H7PB1 (E), or their corresponding K612R mutant, together with SUMO1 or SUMO1mut, and Ubc9. 2021 PLoS pathogens Figure IV K612R 126 131 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. HEK293T cells were transfected with plasmids encoding Flag-tagged WSN-H1PB1 or WSN-H1PB1/K612R (B), VN/1180-H5PB1 or VN1180-H5PB1/K612R (D), or AH/1-H7PB1 or AH/1-H7PB1/K612R (F), together with SUMO1 and Ubc9. 2021 PLoS pathogens Figure IV K612R;K612R;K612R 89;130;169 94;135;174 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. HEK293T cells were transfected with plasmids encoding WSN-H1PB1 or WSN-H1PB1/K612R (A), VN/1180-H5PB1 or VN/1180-H5PB1/K612R (C), or AH/1-H7PB1 or AH/1-H7PB1/K612R (E). 2021 PLoS pathogens Figure IV K612R;K612R;K612R 77;119;158 82;124;163 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. K612R mutation impairs the ability of PB1 to bind to vRNA. 2021 PLoS pathogens Figure IV K612R 0 5 PB1 38 41 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. PB1/K612R mutation compromises the replication and respiratory droplet transmission of IAVs in ferrets. 2021 PLoS pathogens Figure IV K612R 4 9 PB1 0 3 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. SUMOylation-defective PB1/K612R mutation attenuates the replication and pathogenicity of IAVs in mice. 2021 PLoS pathogens Figure IV K612R 26 31 PB1 22 25 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. The amount of truncated PB1 protein WSN-H1PB1494-757 or WSN-H1PB1494-757/K612R (K), VN/1180-H5PB1494-757 or VN/1180-H5PB1494-757/K612R (L), or AH/1-H7PB1494-757 or AH/1-H7PB1494-757/K612R (M) bound and unbound by the model vRNA was detected by western blotting. 2021 PLoS pathogens Figure IV K612R;K612R;K612R 73;129;182 78;134;187 PB1 24 27 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. The amount of vRNA bound by WSN-H1PB1494-757 or WSN-H1PB1494-757/K612R (H), VN/1180-H5PB1494-757 or VN/1180-H5PB1494-757/K612R (I), or AH/1-H7PB1494-757 or AH/1-H7PB1494-757/K612R (J) was quantified by use of qRT-PCR. 2021 PLoS pathogens Figure IV K612R;K612R;K612R 65;121;174 70;126;179 33647314 The active form of the influenza cap-snatching endonuclease inhibitor baloxavir marboxil is a tight binding inhibitor. B, inhibition of WT FluB-ht by BXA increases with the duration of BXA preincubation (C) Inhibition of PA I38T FluB-ht by BXA is time-independent. 2021 The Journal of biological chemistry Figure IV I38T 105 109 PA 102 104 33647314 The active form of the influenza cap-snatching endonuclease inhibitor baloxavir marboxil is a tight binding inhibitor. C, endonuclease activity of WT, PA I38T, or endonuclease-deficient (PA E81Q/D109N/E120Q) FluB-ht on PAGE. 2021 The Journal of biological chemistry Figure IV I38T;E81Q;D109N;E120Q 35;71;76;82 39;75;81;87 PA;PA 32;68 34;70 33647314 The active form of the influenza cap-snatching endonuclease inhibitor baloxavir marboxil is a tight binding inhibitor. Differential inhibition of WT and PA I38T FluB-ht by BXA.A, 165 nM of WT or PA I38T was mixed with increasing concentrations of BXA and inhibition quantified. 2021 The Journal of biological chemistry Figure IV I38T;I38T 37;79 41;83 PA;PA 34;76 36;78 33647314 The active form of the influenza cap-snatching endonuclease inhibitor baloxavir marboxil is a tight binding inhibitor. Effects of the order of addition of FluB-ht (E), substrate (S), BXA (I), and MgCl2on the endonuclease activity of WT and PA I38T FluB-ht.A, order of addition of reaction components in the absence of BXA has negligible effects on reaction progress for both WT (top) and PA I38T (bottom) FluB-ht. 2021 The Journal of biological chemistry Figure IV I38T;I38T 124;272 128;276 PA;PA 121;269 123;271 33647314 The active form of the influenza cap-snatching endonuclease inhibitor baloxavir marboxil is a tight binding inhibitor. Inhibition of PA I38T (bottom) is not observed regardless of the order of addition the reaction components. 2021 The Journal of biological chemistry Figure IV I38T 17 21 PA 14 16 33647314 The active form of the influenza cap-snatching endonuclease inhibitor baloxavir marboxil is a tight binding inhibitor. Percent error for WT IC50 measurements was 27% while percent error for PA I38T was 36%. 2021 The Journal of biological chemistry Figure IV I38T 74 78 PA 71 73 33647314 The active form of the influenza cap-snatching endonuclease inhibitor baloxavir marboxil is a tight binding inhibitor. Plots of IC50 versus enzyme concentration for both WT and PA I38T yield a linear relationship with a slope of approximately 0.5 (WT = 0.56, PA I38T = 0.58.) (C) Close-up of the Y-axis from panel B emphasizing the apparent inhibition constant (Kiapp) of BXA for WT and PA I38T FluB-ht. 2021 The Journal of biological chemistry Figure IV I38T;I38T;I38T 61;143;271 65;147;275 PA;PA;PA 58;140;268 60;142;270 33647314 The active form of the influenza cap-snatching endonuclease inhibitor baloxavir marboxil is a tight binding inhibitor. Purification and biochemical characterization of the Influenza B polymerase heterotrimer (FluB-ht).A, SDS-PAGE migration patterns of the purified WT FluB-ht, baloxavir resistance mutant (PA I38T), or endonuclease-deficient mutant (PA E81Q/D109N/E120Q). 2021 The Journal of biological chemistry Figure IV I38T;E81Q;D109N;E120Q 190;234;239;245 194;238;244;250 PA;PA 187;231 189;233 33679636 Improved in vitro Efficacy of Baloxavir Marboxil Against Influenza A Virus Infection by Combination Treatment With the MEK Inhibitor ATR-002. MDCK cells were infected (MOI = 0.001) with either wild type or PA-I38T mutant influenza virus (A) rgA/Giessen/6/2009 (H1N1) or (B) rgA/Victoria/3/75 (H3N2). 2021 Frontiers in microbiology Figure IV I38T 67 71 PA 64 66 33782012 Discovery of a Novel Respiratory Syncytial Virus Replication Inhibitor. Effect of triazole-1 on RSV minigenome transcription mediated by wild-type L protein or the T1684A mutant. 2021 Antimicrobial agents and chemotherapy Figure IV T1684A 92 98 33782012 Discovery of a Novel Respiratory Syncytial Virus Replication Inhibitor. Identification of the T1684A mutation on L polymerase in the triazole-1-resistant variant. 2021 Antimicrobial agents and chemotherapy Figure IV T1684A 22 28 33782012 Discovery of a Novel Respiratory Syncytial Virus Replication Inhibitor. Luciferase assays were performed on HEp-2 cells transfected with a minigenome construct (Minigenome-Luc) or T7 promoter construct (T7pro-Luc) together with pcDNA constructs expressing N, P, L (wild-type or T1684A mutant), and M2-1 proteins and treated with 0.316 muM to 10 muM triazole-1. 2021 Antimicrobial agents and chemotherapy Figure IV T1684A 206 212 M2 226 228 33975931 Analysis of the Evolution of Pandemic Influenza A(H1N1) Virus Neuraminidase Reveals Entanglement of Different Phenotypic Characteristics. K432E and N369K are located in the 2SBS. 2021 mBio Figure IV K432E;N369K 0;10 5;15 33975931 Analysis of the Evolution of Pandemic Influenza A(H1N1) Virus Neuraminidase Reveals Entanglement of Different Phenotypic Characteristics. V241I is located underneath the active site but does not belong to the catalytic or framework residues. 2021 mBio Figure IV V241I 0 5 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. (D-E) Changes from starting body weight and percent survival of DBA/2 mice after inoculation with 750 PFU of WT and 750 or 375000 PFU of Y17H. 2021 PloS one Figure IV Y17H 137 141 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. Mice were inoculated intranasally with PBS, WT virus (750 PFU), or Y17H virus (750 or 375,000 PFU). 2021 PloS one Figure IV Y17H 67 71 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. Mice were intranasally inoculated with PBS, 750 PFU of WT virus, 750 PFU of Y17H virus, or 375,000 PFU of Y17H virus. 2021 PloS one Figure IV Y17H;Y17H 76;106 80;110 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. Mice were intranasally inoculated with PBS, WT virus (750 PFU), or Y17H virus (750 or 375,000 PFU). 2021 PloS one Figure IV Y17H 67 71 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. Symbols used in all panels as follows: PBS (green hexagon), WT 750 (black squares), Y17H 750 (red circles), and Y17H 375 (blue triangles). 2021 PloS one Figure IV Y17H;Y17H 84;112 88;116 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. The bars for each group are colored as follows: PBS (white with black outline), WT (solid black), Y17H750-PFU (solid red), and Y17H 375-PFU (solid blue). 2021 PloS one Figure IV Y17H;Y17H 127;98 131;102 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. The inoculated doses were 750 PFU for WT and 750 or 375,000 PFU for Y17H. 2021 PloS one Figure IV Y17H 68 72 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. 4 donor ferrets were infected with 10^4 PFU of a virus mix of wildtype Eng195 and K229R+P653L. 2021 PLoS pathogens Figure IV K229R;P653L 82;88 87;93 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. B) As A but the strain fitness for Wild type, K229R, P653L and K229R + P653L were set at 1, 0.01, 1 and 1 respectively. 2021 PLoS pathogens Figure IV K229R;P653L;K229R;P653L 46;53;63;71 51;58;68;76 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. C) As A but the strain fitness for Wild type, K229R, P653L and K229R + P653L were set at 1, 1, 1.25 and 1 respectively. 2021 PLoS pathogens Figure IV K229R;P653L;K229R;P653L 46;53;63;71 51;58;68;76 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. Large pie charts show the percentage of PB1 K229R + PA P653L mutant (purple) and wild-type viruses (black). 2021 PLoS pathogens Figure IV K229R;P653L 44;55 49;60 PA;PB1 52;40 54;43 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. Reassortment leads to the generation of the single mutant PA P653L (blue) in the donor which is transmitted to the direct contact. 2021 PLoS pathogens Figure IV P653L 61 66 PA 58 60 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. Strain fitness for Wild type, K229R, P653L and K229R + P653L were set at 1, 0.01, 1.25 and 1 respectively. 2021 PLoS pathogens Figure IV K229R;P653L;K229R;P653L 30;37;47;55 35;42;52;60 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. Targeted sequencing of PA and PB1 using NGS showed the percentage of PB1 K229R and PA P653L mutations for donor, contact and indirect contact ferrets. 2021 PLoS pathogens Figure IV K229R;P653L 73;86 78;91 PA;PA;PB1;PB1 23;83;30;69 25;85;33;72 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. The starting proportions are 5% Wild type and 95% K229R + P653L. 2021 PLoS pathogens Figure IV K229R;P653L 50;58 55;63 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. (A) Occupancies of residue interactions for the wild-type (WT) and H274Y mutant within the oseltamivir (OTV) binding site and mutation site. 2021 PeerJ Figure IV H274Y 67 72 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. (B) Changes in the decomposed binding free energy due to H274Y mutation. 2021 PeerJ Figure IV H274Y 57 62 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. (B) Changes in the occupancy of residue interactions due to H274Y mutation. 2021 PeerJ Figure IV H274Y 60 65 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. dRINs for (A) the wild-type (WT) and (B) H274Y mutant influenza neuraminidase, showing the oseltamivir (OTV) binding site and mutation site. 2021 PeerJ Figure IV H274Y 41 46 64 77 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. RMSDs for the backbone atoms in the WT and H274Y mutant NA with respect to the initial structure along the simulation time. 2021 PeerJ Figure IV H274Y 43 48 56 58 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. Snapshot images obtained from the MD simulations for (A) the wild-type (WT) and (B) H274Y mutant influenza neuraminidase, showing the 150-loop region (residues 147-152) and oseltamivir (OTV). 2021 PeerJ Figure IV H274Y 84 89 107 120 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. Snapshot images obtained from the MD simulations for (A) the wild-type (WT) and (B) H274Y mutant influenza neuraminidase, showing the oseltamivir (OTV) binding site and the mutation site. 2021 PeerJ Figure IV H274Y 84 89 107 120 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. The structural fluctuations of each residue in the WT and H274Y mutant NA are shown as the B-factor values. 2021 PeerJ Figure IV H274Y 58 63 71 73 34194404 Host Adaptive Evolution of Avian-Origin H3N2 Canine Influenza Virus. The G146S, N188D and V242I substitutions are shown as red spheres that are located at the antigenic epitopes A, B, and D, respectively. 2021 Frontiers in microbiology Figure IV G146S;N188D;V242I 4;11;21 9;16;26 34194404 Host Adaptive Evolution of Avian-Origin H3N2 Canine Influenza Virus. The I153T (represented as a red sphere) and H155Y (represented as an orange sphere) substitutions are located close to the active site (highlighted in yellow) on the head region (shown as gray cartoon) of the NA protein. 2021 Frontiers in microbiology Figure IV I153T;H155Y 4;44 9;49 209 211 34194404 Host Adaptive Evolution of Avian-Origin H3N2 Canine Influenza Virus. The T16A (shown as green cartoon) substitution is located in the transmembrane region (shown as a purple cartoon) of the NA protein. 2021 Frontiers in microbiology Figure IV T16A 4 8 121 123 34240696 Nanopore metagenomic sequencing of influenza virus directly from respiratory samples: diagnosis, drug resistance and nosocomial transmission, United Kingdom, 2018/19 influenza season. Green boxes in different shades indicate sequences that carry the S331R mutation in the NA segment: the light green box represent sequences from the 2018/19 season, and two darker green boxes represent sequences from the 2017/18 season. 2021 Euro surveillance Figure IV S331R 66 71 88 90 34253060 In Vivo Therapy with M2e-Specific IgG Selects for an Influenza A Virus Mutant with Delayed Matrix Protein 2 Expression. Changes in M2e associated with treatment with M2e-specific MAbs is limited to P10H, P10L, and I11T. 2021 mBio Figure IV P10H;P10L;I11T 78;84;94 82;88;98 34253060 In Vivo Therapy with M2e-Specific IgG Selects for an Influenza A Virus Mutant with Delayed Matrix Protein 2 Expression. Five mutations were present above 50% in the viral population of one of the MAb 37-treated mice (EXP1; mouse 5; dpi 33): K443R in PB2, I550T and a silent mutation (G679A) in PA, A231S in HA1, and I18M in HA2. 2021 mBio Figure IV K443R;I550T;G679A;A231S;I18M 121;135;164;178;196 126;140;169;183;200 HA;HA1;PA;PB2 204;187;174;130 206;190;176;133 34253060 In Vivo Therapy with M2e-Specific IgG Selects for an Influenza A Virus Mutant with Delayed Matrix Protein 2 Expression. MDCK cells were infected with A/Puerto Rico/8/34 (PR8) virus or a PR8 virus that carries a P10L, P10H, or I11T M2 mutation. 2021 mBio Figure IV P10L;P10H;I11T 91;97;106 95;101;110 M2 111 113 34253060 In Vivo Therapy with M2e-Specific IgG Selects for an Influenza A Virus Mutant with Delayed Matrix Protein 2 Expression. The frequency of each M2e variant (white, P10H; black, P10L; gray, I11T) is shown by the bars and in the grid above the graph. 2021 mBio Figure IV P10H;P10L;I11T 42;55;67 46;59;71 34253060 In Vivo Therapy with M2e-Specific IgG Selects for an Influenza A Virus Mutant with Delayed Matrix Protein 2 Expression. The latter virus was generated by reverse genetics and carries the mutations K443R in PB2, I550T in PA, silent mutation G679A in HA, A231S in HA1, I18M in HA2, and V115M in HA2. 2021 mBio Figure IV K443R;I550T;G679A;A231S;I18M;V115M 77;91;120;133;147;164 82;96;125;138;151;169 HA;HA;HA;HA1;PA;PB2 129;155;173;142;100;86 131;157;175;145;102;89 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. (A) Plaque assay of P3 wild-type and K235R recombinant IAV. 2021 Nucleic acids research Figure IV K235R 37 42 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. (A) Polymerization rates (kpol) for cognate CTP and noncognate CTP in wild-type and K235R mutant RdRps. 2021 Nucleic acids research Figure IV K235R 84 89 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. (A) The observed incorporation rates obtained from the fast phase against various CTP, and (B) UTP concentrations were fitted into hyperbolic equations to derive the kpol and Kd,app values for wild-type (WT) and K235R mutant RdRps. 2021 Nucleic acids research Figure IV K235R 212 217 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. (B) Diagram showing the R239 and K235R mutant residues interact (shown in dashed lines) with the beta-phosphate group of the NTP. 2021 Nucleic acids research Figure IV K235R 33 38 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. (B) The genome-wide depth distribution of sequencing reads from P3 wild-type and K235R viral genome. 2021 Nucleic acids research Figure IV K235R 81 86 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. (C) The contour plot of the distance between the Pbeta atom of NTP and K235/K235R versus that between the beta-phosphate (Pbeta) atom of NTP and R239 when CTP is in the active site. 2021 Nucleic acids research Figure IV K235R 76 81 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. (C) The specificity for WT and K235R RdRps in CTP and UTP incorporation was determined by kcat/Km = kpol/Kd,app. 2021 Nucleic acids research Figure IV K235R 31 36 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. (C) The Supplementary Table Summary of SNV counts screened from each gene segment of the extracted P3 wild-type and K235R mutant IAV genome RNA. 2021 Nucleic acids research Figure IV K235R 116 121 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. (D) The discrimination of CTP:G(template) over UTP:G(template) for WT and K235R RdRps. 2021 Nucleic acids research Figure IV K235R 74 79 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. (D) WT and K235R live virus rescue and growth kinetics measurement. 2021 Nucleic acids research Figure IV K235R 11 16 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. (D) WT and R239K live virus rescue and growth kinetics measurement. 2021 Nucleic acids research Figure IV R239K 11 16 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. Full confluent MDCK cells were inoculated by diluted P3 wild-type and K235R recombinant viruses with agar overlay for 3 days. 2021 Nucleic acids research Figure IV K235R 70 75 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. K235R mutation accelerates the incorporation of the cognate CTP. 2021 Nucleic acids research Figure IV K235R 0 5 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. Lys 235 Arg mutation increases the IAV polymerase activity. 2021 Nucleic acids research Figure IV K235R 0 11 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. NGS sequencing on wild-type and K235R mutant virus genome. 2021 Nucleic acids research Figure IV K235R 32 37 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. R239K mutant cannot be rescued by recombinant virus from plasmids. 2021 Nucleic acids research Figure IV R239K 0 5 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. The average sequencing depths of both wild-type and K235R are ~105 per replicate. 2021 Nucleic acids research Figure IV K235R 52 57 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. The K235R mutant exhibited similar growth kinetics to WT. 2021 Nucleic acids research Figure IV K235R 4 9 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. The single-turnover NTP incorporation assay of wild-type and K235R mutant RdRps on CTP:G(template) and UTP:G(template) pairings. 2021 Nucleic acids research Figure IV K235R 61 66 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. The TCID50 titer concentration was measured and plotted against hours post infection (h.p.i) for WT (blue) and K235R (red). 2021 Nucleic acids research Figure IV K235R 111 116 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. The TCID50 titer concentration was measured and plotted against hours post infection (h.p.i) for WT (blue) and R239K (green). 2021 Nucleic acids research Figure IV R239K 111 116 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. WT and K235R recombinant viruses were rescued by co-transfecting cells with the eight plasmids coding each gene of A/WSN/1933 strain and inoculated to MDCK cells at MOI = 0.01. 2021 Nucleic acids research Figure IV K235R 7 12 34379778 A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. WT and R239K recombinant viruses were rescued by co-transfecting cells with the eight plasmids coding each gene of A/WSN/1933 strain and inoculated to MDCK cells at MOI = 0.01. 2021 Nucleic acids research Figure IV R239K 7 12 35044215 N-Glycolylneuraminic Acid Binding of Avian and Equine H7 Influenza A Viruses. (A) A hemagglutination assay (n = 3, mean + standard deviation [SD] shown) with chicken and horse erythrocytes was performed using H7tu WT and mutant HAs (A135E, A135E+S128T, A135E+I130V, and A135E+T189A+K193R). 2022 Journal of virology Figure IV A135E;S128T;A135E;A135E;I130V;A135E;T189A;K193R 155;168;162;175;181;192;198;204 160;173;167;180;186;197;203;209 35044215 N-Glycolylneuraminic Acid Binding of Avian and Equine H7 Influenza A Viruses. (B) The binding specificities of WT HA of A/Chicken/Jalisco/12283/12 H7N3 and A135E, S128T+A135E, I130V+A135E, and A135E+T189A+K193R mutant HAs were evaluated on the glycan microarray as described in the legend to. 2022 Journal of virology Figure IV A135E;S128T;A135E;A135E;I130V;A135E;T189A;K193R 78;85;91;104;98;115;121;127 83;90;96;109;103;120;126;132 HA 36 38 35044215 N-Glycolylneuraminic Acid Binding of Avian and Equine H7 Influenza A Viruses. (B) The binding specificities of WT HA of A/Duck/Australia/341/1983 H15N8 and A135E, S128T+I130V+A135E, A135E+T189A+K193R, and S128T+I130V+A135E+T189A+K193R mutant Has were evaluated on the glycan microarray as described in the legend to. 2022 Journal of virology Figure IV A135E;A135E;S128T;I130V;A135E;T189A;K193R;A135E;S128T;I130V;T189A;K193R 78;97;85;91;104;110;116;139;127;133;145;151 83;102;90;96;109;115;121;144;132;138;150;156 HA 36 38 35044215 N-Glycolylneuraminic Acid Binding of Avian and Equine H7 Influenza A Viruses. for H7tu A135T and A135V mutants are shown. 2022 Journal of virology Figure IV A135T;A135V 9;19 14;24 35044215 N-Glycolylneuraminic Acid Binding of Avian and Equine H7 Influenza A Viruses. Hemagglutination assay with Y161A HA mutants on equine and canine erythrocytes. 2022 Journal of virology Figure IV Y161A 28 33 HA 34 36 35044215 N-Glycolylneuraminic Acid Binding of Avian and Equine H7 Influenza A Viruses. Likewise, the binding specificities of the WT and mutant (T128S, V130I, E135A, A189T, R189K) HAs of A/Equine/New York/43/73 H7N7 were evaluated by using the glycan microarray in which the WT had been previously investigated (D), the hemagglutination assay (E), and tissue staining (F). 2022 Journal of virology Figure IV T128S;V130I;E135A;A189T;R189K 58;65;72;79;86 63;70;77;84;91 35044215 N-Glycolylneuraminic Acid Binding of Avian and Equine H7 Influenza A Viruses. Recombinantly expressed HAs of wild-type (WT) and Y161A mutants of H1 (A/Duck/Hokkaido/111/2009 H1N5), H2 (A/Duck/Hokkaido/95/2001 H2N2), H4 (A/Duck/Hokkaido/138/2007 H4N6), and H5 (A/Vietnam/1203/2004 H5N1) were investigated. 2022 Journal of virology Figure IV Y161A 50 55 35044215 N-Glycolylneuraminic Acid Binding of Avian and Equine H7 Influenza A Viruses. Representative binding specificities for two independent assays for mutant HAs containing mutation A135E and an additional mutation (S128T, I130V, G144R, A159G+A160V, T189A, K193, or A219P) (A) and mutant HAs containing mutations A135E, K193R, and an additional mutation (G144R, A159G+A160V, T189A, or A219P) (B) are shown. 2022 Journal of virology Figure IV G144R;G144R;A135E;S128T;I130V;A159G;A160V;T189A;A219P;A135E;K193R;A159G;A160V;T189A;A219P 147;272;99;133;140;154;160;167;183;230;237;279;285;292;302 152;277;104;138;145;159;165;172;188;235;242;284;290;297;307 35044215 N-Glycolylneuraminic Acid Binding of Avian and Equine H7 Influenza A Viruses. The binding specificity of the mutant HA (S128T, I130V, A135E, T189A, K193R) of A/Turkey/Italy/214845/02 H7N3 was evaluated by using the glycan microarray as described in the legend to. 2022 Journal of virology Figure IV S128T;I130V;A135E;T189A;K193R 42;49;56;63;70 47;54;61;68;75 HA 38 40 35044215 N-Glycolylneuraminic Acid Binding of Avian and Equine H7 Influenza A Viruses. The glycan microarray, which is representative of two independent assays, was used to determine the receptor specificity of recombinantly expressed HA of the H7tu wild type (WT) (B) and S128T (C), I130V (D), A135E (E), G144R (F), A159G+A160V (G), T189A (H), K193R (I), and A219P (J) mutants. 2022 Journal of virology Figure IV G144R;S128T;I130V;A135E;A159G;A160V;T189A;K193R;A219P 219;186;197;208;230;236;247;258;273 224;191;202;213;235;241;252;263;278 HA 148 150 35044215 N-Glycolylneuraminic Acid Binding of Avian and Equine H7 Influenza A Viruses. Tissue staining of chicken and horse tracheal epithelium was performed with WT and Y161A mutant HA of A/Vietnam/1203/2004 H5N1 as a positive and negative control (B) and H7tu WT or mutant HAs as described for panel A (C). 2022 Journal of virology Figure IV Y161A 83 88 HA 96 98 17922571 A single mutation in the PB1-F2 of H5N1 (HK/97) and 1918 influenza A viruses contributes to increased virulence. In addition, the 1918 wt virus showed higher lung titers and slower viral clearance when compared with the 1918 S66N virus. 2007 PLoS pathogens Discussion IV S66N 112 116 17922571 A single mutation in the PB1-F2 of H5N1 (HK/97) and 1918 influenza A viruses contributes to increased virulence. In support of this, we observed that the WH N66S and wt 1918 viruses caused a significant increase in IFN-gamma and TNF-alpha cytokine production over the WH and 1918 S66N viruses, respectively. 2007 PLoS pathogens Discussion IV N66S;S66N 44;167 48;171 17922571 A single mutation in the PB1-F2 of H5N1 (HK/97) and 1918 influenza A viruses contributes to increased virulence. In this study, we provide evidence that PB1-F2 does contribute to the high pathogenicity phenotype and that the N66S mutation, also found in the 1918 H1N1 virus, contributes to virulence in highly pathogenic viruses. 2007 PLoS pathogens Discussion IV N66S 112 116 PB1F2 40 46 17922571 A single mutation in the PB1-F2 of H5N1 (HK/97) and 1918 influenza A viruses contributes to increased virulence. Recombinant A/WSN/33 viruses were created to specifically examine the effects of the N66S mutation during viral infection. 2007 PLoS pathogens Discussion IV N66S 85 89 17922571 A single mutation in the PB1-F2 of H5N1 (HK/97) and 1918 influenza A viruses contributes to increased virulence. The location of the N66S mutation also made it an excellent candidate for affecting the proapoptotic function of PB1-F2. 2007 PLoS pathogens Discussion IV N66S 20 24 PB1F2 113 119 17922571 A single mutation in the PB1-F2 of H5N1 (HK/97) and 1918 influenza A viruses contributes to increased virulence. The mutation we investigate here is not currently found in recent H5N1 isolates; however, it is possible for those viruses to acquire the mutation either through the error-prone RNA polymerase or through reassortment with a virus that contains the N66S mutation. 2007 PLoS pathogens Discussion IV N66S 248 252 17922571 A single mutation in the PB1-F2 of H5N1 (HK/97) and 1918 influenza A viruses contributes to increased virulence. The N66S mutation within the PB1-F2 protein partially reversed this attenuating effect. 2007 PLoS pathogens Discussion IV N66S 4 8 PB1F2 29 35 17922571 A single mutation in the PB1-F2 of H5N1 (HK/97) and 1918 influenza A viruses contributes to increased virulence. The observation that the WH N66S virus grew to higher titers in the lung and persisted at high titers for a longer time than the WH virus supports the role of PB1-F2 in allowing for increased replication. 2007 PLoS pathogens Discussion IV N66S 28 32 PB1F2 159 165 17922571 A single mutation in the PB1-F2 of H5N1 (HK/97) and 1918 influenza A viruses contributes to increased virulence. This may also explain the impairment of viral clearance in the mice infected with WH N66S. 2007 PLoS pathogens Discussion IV N66S 85 89 18188421 Identification of a casein kinase II phosphorylation domain in NS1 protein of H5N1 influenza virus. As it was found in A/chicken/Vietnam/27/2003, G148E mutation, glutamic acid that is hydrophilic AA was replaced by hydrophobic glycine and the secondary structure was altered from helix to coil (Table 1 in supplementary material). 2007 Bioinformation Discussion IV G148E;G148E 48;46 53;51 18188421 Identification of a casein kinase II phosphorylation domain in NS1 protein of H5N1 influenza virus. Mutation at P223S might play a role in folding properties of the protein since proline is an uncharged amino acid that helps in protein folding while serine is a hydrophilic, polar amino acid and it has no role in protein folding. 2007 Bioinformation Discussion IV P223S 12 17 18188421 Identification of a casein kinase II phosphorylation domain in NS1 protein of H5N1 influenza virus. The mutation at I171N changed amino acid from hydrophilic to hydrophobic and hence secondary structure was changed from helix to strand. 2007 Bioinformation Discussion IV I171N 16 21 18188421 Identification of a casein kinase II phosphorylation domain in NS1 protein of H5N1 influenza virus. This domain was formed in A/Hatay/2004 due to the mutation from ILE151 to THR151. 2007 Bioinformation Discussion IV I151T 65 81 18248089 Interaction of polymerase subunit PB2 and NP with importin alpha1 is a determinant of host range of influenza A virus. Considerably less is known about the mechanism by which mutation N319K improves importin alpha1 binding and nuclear transport of NP in mammalian cells. 2008 PLoS pathogens Discussion IV N319K 65 70 NP 129 131 18248089 Interaction of polymerase subunit PB2 and NP with importin alpha1 is a determinant of host range of influenza A virus. It has to be pointed out, however, that adaptive mutations different from PB2 D701N and NP N319K have been described in SC35M as well as numerous other viruses. 2008 PLoS pathogens Discussion IV D701N;N319K 78;91 83;96 NP;PB2 88;74 90;77 18248089 Interaction of polymerase subunit PB2 and NP with importin alpha1 is a determinant of host range of influenza A virus. More detailed structural analysis of PB2 binding to importin alpha1 may also help to explain why adaptive PB2 mutation S714R did not affect in our study importin alpha1 binding and nuclear transport, even though it has also been implicated in PB2 binding to importin alpha5. 2008 PLoS pathogens Discussion IV S714R 119 124 PB2;PB2;PB2 37;106;243 40;109;246 18248089 Interaction of polymerase subunit PB2 and NP with importin alpha1 is a determinant of host range of influenza A virus. NLSs have also been identified in PB1 and PA, but there is no apparent link between these signals and adaptation mutations L13P and S678N in PB1 and K615N in PA. 2008 PLoS pathogens Discussion IV L13P;S678N;K615N 123;132;149 127;137;154 PA;PA;PB1;PB1 42;158;34;141 44;160;37;144 18248089 Interaction of polymerase subunit PB2 and NP with importin alpha1 is a determinant of host range of influenza A virus. These authors also suggested that the adaptive mutation D701N observed in PB2 of SC35M might affect binding to importin alpha5 in different species. 2008 PLoS pathogens Discussion IV D701N 56 61 PB2 74 77 18248089 Interaction of polymerase subunit PB2 and NP with importin alpha1 is a determinant of host range of influenza A virus. We show here that mutations D701N in PB2 and N319K in NP responsible for mouse adaptation of the avian influenza virus SC35 enhance binding of these proteins to importin alpha1 of mammalian origin and, thus, improve the efficiency of their transport into the nucleus of mammalian cells. 2008 PLoS pathogens Discussion IV D701N;N319K 28;45 33;50 NP;PB2 54;37 56;40 18404209 Human-like receptor specificity does not affect the neuraminidase-inhibitor susceptibility of H5N1 influenza viruses. Additionally, our finding that A/Vietnam/1203/04 virus carrying the Q226L HA mutation, which is known to switch the receptor specificity in the H3 HA subtype, and the H274Y NA mutation was not genetically stable, could provide evidence that some HA mutations have the potential impact on the acquisition of mutations in NA, including those that can lead to decreased drug susceptibility. 2008 PLoS pathogens Discussion IV Q226L;H274Y 68;167 73;172 HA;HA;HA;NA;NA 74;147;246;173;320 76;149;248;175;322 18769709 Host determinant residue lysine 627 lies on the surface of a discrete, folded domain of influenza virus polymerase PB2 subunit. By contrast the similar sized PB2 cap-binding domain (residues 318-483) has only two host determinant sites (K368R and M475L). 2008 PLoS pathogens Discussion IV K368R;M475L 109;119 114;124 PB2 30 33 18769709 Host determinant residue lysine 627 lies on the surface of a discrete, folded domain of influenza virus polymerase PB2 subunit. From an analysis of H5N1 viruses isolated from infected humans in Vietnam it was observed that in 5/8 fatal and 3/4 non-fatal cases the E627K mutation had occurred. 2008 PLoS pathogens Discussion IV E627K 136 141 18769709 Host determinant residue lysine 627 lies on the surface of a discrete, folded domain of influenza virus polymerase PB2 subunit. In addition, the residues 701 and 714, whose mutation (respectively D701N and S714R) have been shown to affect polymerase activity in a laboratory model of adaptation of virulent strains from birds to mice, are located on the surface of the NLS-domain. 2008 PLoS pathogens Discussion IV D701N;S714R 68;78 73;83 18769709 Host determinant residue lysine 627 lies on the surface of a discrete, folded domain of influenza virus polymerase PB2 subunit. Interestingly, in 3/4 cases retaining Glu627, but none of those with E627K, the D701N mutation was also found, leading to the suggestion that the latter mutation may compensate for the lack of change at position 627. 2008 PLoS pathogens Discussion IV E627K;D701N 69;80 74;85 18769709 Host determinant residue lysine 627 lies on the surface of a discrete, folded domain of influenza virus polymerase PB2 subunit. The 156 amino acid 627-domain is located between the cap-binding and NLS-domains and contains six of the seventeen host species determining sites described within the PB2 subunit: N567D/E, I588A/V, T613V/A, K627E, T661A, T674A/S (Figure S4) where for each position the consensus human and then avian residues are given. 2008 PLoS pathogens Discussion IV N567D;N567E;I588A;I588V;T613V;T613A;K627E;T661A;T674A;T674S 180;180;189;189;198;198;207;214;221;221 187;187;196;196;205;205;212;219;228;228 PB2 167 170 18769709 Host determinant residue lysine 627 lies on the surface of a discrete, folded domain of influenza virus polymerase PB2 subunit. The complete C-terminal region, comprising both the 627-domain and NLS-domain, also includes the host variable residue R702K and, in the inter-domain linker, the HxN2 subtype host determinants S682G and S684A. 2008 PLoS pathogens Discussion IV R702K;S682G;S684A 119;193;203 124;198;208 19008377 The human H5N1 influenza A virus polymerase complex is active in vitro over a broad range of temperatures, in contrast to the WSN complex, and this property can be attributed to the PB2 subunit. The E627K mutation in the avian PB2 led to only a slight increase in thermotolerance. 2008 The Journal of general virology Discussion IV E627K 4 9 PB2 32 35 19119420 Transmission of influenza virus in a mammalian host is increased by PB2 amino acids 627K or 627E/701N. In terms of viral growth in vitro and in vivo as well as transmission between guinea pigs, the introduction of N at position 701 was found to at least partially reverse the phenotype of the K627E mutant viruses in both virus backgrounds tested. 2009 PLoS pathogens Discussion IV K627E 190 195 19119420 Transmission of influenza virus in a mammalian host is increased by PB2 amino acids 627K or 627E/701N. In the rPan99 background, the reduction in plaque size observed with the K627E mutation was again seen at both temperatures and was more subtle than for rVN1203. 2009 PLoS pathogens Discussion IV K627E 73 78 19119420 Transmission of influenza virus in a mammalian host is increased by PB2 amino acids 627K or 627E/701N. that, with respect to adaptation of an avian virus to a mammalian host, D701N can functionally replace E627K. 2009 PLoS pathogens Discussion IV D701N;E627K 72;103 77;108 19119420 Transmission of influenza virus in a mammalian host is increased by PB2 amino acids 627K or 627E/701N. The observation that the fully human-adapted virus rPan99 was better able to tolerate the PB2 K627E mutation and maintain plaque formation at 33 C than the more avian-like rVN1203 virus may indicate that Pan99 has developed degenerate mechanisms to permit growth at the lower temperature of 33 C. 2009 PLoS pathogens Discussion IV K627E 94 99 PA;PB2 204;90 206;93 19119420 Transmission of influenza virus in a mammalian host is increased by PB2 amino acids 627K or 627E/701N. Using minigenome systems and infected cell cultures, the introduction of the E627K mutation into an avian PB2 gene has previously been shown to increase polymerase activity and viral growth at 33 C. 2009 PLoS pathogens Discussion IV E627K 77 82 PB2 106 109 19119420 Transmission of influenza virus in a mammalian host is increased by PB2 amino acids 627K or 627E/701N. We found that, when PB2 627 is a glutamic acid residue, the D701N mutation not only improves viral growth in mammalian cells, but enhances transmission between guinea pigs. 2009 PLoS pathogens Discussion IV D701N 60 65 PB2 20 23 19249874 Recognition of mannosylated ligands and influenza A virus by human surfactant protein D: contributions of an extended site and residue 343. Because R343V also shows enhanced recognition of alpha-linked GlcNAc, it is possible that contributions of more complex glycans also may influence binding. 2009 Biochemistry Discussion IV R343V 8 13 19249874 Recognition of mannosylated ligands and influenza A virus by human surfactant protein D: contributions of an extended site and residue 343. Comparison crystallographic complexes of wild type and R343V with alpha1-2 DM showed that the sugar ring conformations and geometry of the saccharide linkage were highly similar in the two complexes (Figure 6) and consistent with the preferred solution conformation. 2009 Biochemistry Discussion IV R343V 55 60 19249874 Recognition of mannosylated ligands and influenza A virus by human surfactant protein D: contributions of an extended site and residue 343. For example, a mutant that combines the RAK insertion with isoleucine at 343, resembling CL-43, shows a greater apparent affinity for mannan relative to R343V, but is less active in viral neutralization (Hartshorn and coworkers, unpublished data). 2009 Biochemistry Discussion IV R343V 153 158 19249874 Recognition of mannosylated ligands and influenza A virus by human surfactant protein D: contributions of an extended site and residue 343. For example, the rat NCRD resembles R343V in its high affinity for alpha1-2 DM, but resembles the wild-type hNCRD with respect to viral binding and neutralization (Hartshorn and coworkers, data not shown). 2009 Biochemistry Discussion IV R343V 36 41 19249874 Recognition of mannosylated ligands and influenza A virus by human surfactant protein D: contributions of an extended site and residue 343. Given that R343V shows enhanced viral binding and blocks the viral neutralizing activity of 246-05, our data effectively localize the 246-05 epitope and the primary site of viral interaction to the carbohydrate binding face of the trimer. 2009 Biochemistry Discussion IV R343V 11 16 19249874 Recognition of mannosylated ligands and influenza A virus by human surfactant protein D: contributions of an extended site and residue 343. However, the alternate orientation, which is selected by R343V, should permit interactions with non-terminal mannoses of more complex glycans. 2009 Biochemistry Discussion IV R343V 57 62 19249874 Recognition of mannosylated ligands and influenza A virus by human surfactant protein D: contributions of an extended site and residue 343. In particular, the SP-D mutants R343A and R343I showed significantly lower viral binding, HAI, and neutralizing activity than R343V. 2009 Biochemistry Discussion IV R343A;R343I;R343V 32;42;126 37;47;131 19249874 Recognition of mannosylated ligands and influenza A virus by human surfactant protein D: contributions of an extended site and residue 343. Mechanism of enhanced antiviral activity of R343V. 2009 Biochemistry Discussion IV R343V 44 49 19249874 Recognition of mannosylated ligands and influenza A virus by human surfactant protein D: contributions of an extended site and residue 343. Our data suggest that the enhanced antiviral activity of R343V results from its capacity to recognize non-terminal sugars of more complex glycans. 2009 Biochemistry Discussion IV R343V 57 62 19249874 Recognition of mannosylated ligands and influenza A virus by human surfactant protein D: contributions of an extended site and residue 343. R343K also showed no detectable binding to IAV. 2009 Biochemistry Discussion IV R343K 0 5 19249874 Recognition of mannosylated ligands and influenza A virus by human surfactant protein D: contributions of an extended site and residue 343. R343V shows greatly enhanced interactions with SP-D reactive strains of IAV. 2009 Biochemistry Discussion IV R343V 0 5 19249874 Recognition of mannosylated ligands and influenza A virus by human surfactant protein D: contributions of an extended site and residue 343. R343V utilizes an alternative extended binding site for alpha1-2 dimannose. 2009 Biochemistry Discussion IV R343V 0 5 19249874 Recognition of mannosylated ligands and influenza A virus by human surfactant protein D: contributions of an extended site and residue 343. Studies designed to examine the antiviral properties of R343V in vivo are in progress. 2009 Biochemistry Discussion IV R343V 56 61 19249874 Recognition of mannosylated ligands and influenza A virus by human surfactant protein D: contributions of an extended site and residue 343. Substitution of Arg343 with valine greatly enhanced binding to alpha1-2 DM in competition assays. 2009 Biochemistry Discussion IV R343V 16 34 19249874 Recognition of mannosylated ligands and influenza A virus by human surfactant protein D: contributions of an extended site and residue 343. This suggestion is consistent with the crystallographic analysis of R343V. 2009 Biochemistry Discussion IV R343V 68 73 19249874 Recognition of mannosylated ligands and influenza A virus by human surfactant protein D: contributions of an extended site and residue 343. Thus, these observations offer a possible structural basis for the distinct binding preferences and enhanced interactions with high-mannose oligosaccharides exhibited by R343V as compared with wild-type SP-D. 2009 Biochemistry Discussion IV R343V 170 175 19249874 Recognition of mannosylated ligands and influenza A virus by human surfactant protein D: contributions of an extended site and residue 343. Whereas the wild-type protein bound alpha1-2 DM in the more typical orientation, i.e., with the non-reducing terminal sugar bound to calcium, the binding orientation of the dimannose was flipped in R343V. 2009 Biochemistry Discussion IV R343V 198 203 19331731 Oseltamivir-resistant influenza virus A (H1N1), Europe, 2007-08 season. Furthermore, other previously analyzed influenza viruses A (H1N1) with the H275Y mutation showed impaired replicative ability in cell culture and reduced infectivity and substantially compromised pathogenicity in animal models, compared with the corresponding wild-type virus. 2009 Emerging infectious diseases Discussion IV H275Y 75 80 19331731 Oseltamivir-resistant influenza virus A (H1N1), Europe, 2007-08 season. Sporadically occurring A/New Caledonia/20/99-like ORVs with H275Y were detected during the 2006-07 season in the United Kingdom and United States but did not become epidemiologically important. 2009 Emerging infectious diseases Discussion IV H275Y 60 65 19331731 Oseltamivir-resistant influenza virus A (H1N1), Europe, 2007-08 season. The coincidental emergence of H275Y with the circulation of the A/Brisbane/59/2007 drift variant may have favored the emergence of fit transmissible ORVs. 2009 Emerging infectious diseases Discussion IV H275Y 30 35 19331731 Oseltamivir-resistant influenza virus A (H1N1), Europe, 2007-08 season. The finding of a high prevalence of ORVs in the community and the overall temporal increase in resistance demonstrates that the previously documented reduced fitness of viruses bearing the H275Y mutation, ostensibly caused by structural and functional constraints, has been overcome in currently circulating influenza viruses A (H1N1). 2009 Emerging infectious diseases Discussion IV H275Y 189 194 19331731 Oseltamivir-resistant influenza virus A (H1N1), Europe, 2007-08 season. Unexpectedly, influenza viruses A (H1N1) with a single amino acid substitution H275Y in the NA, which caused a several hundred-fold selective reduction in susceptibility to oseltamivir, emerged and were sustained in circulation in Europe during 2007-08, despite low antivirual drug use (Figure 1). 2009 Emerging infectious diseases Discussion IV H275Y 79 84 92 94 19394063 The origin and global emergence of adamantane resistant A/H3N2 influenza viruses. As several introductions of the resistant S31N mutation were detected in elderly patients in temperate regions where adamantane is more frequently administered to seniors, it is possible that intra-host selection was involved in a number of these introductions. 2009 Virology Discussion IV S31N 42 46 19394063 The origin and global emergence of adamantane resistant A/H3N2 influenza viruses. Finally, the processes of local evolution, reassortment, and global spread through genomic hitchhiking we observe in the spread of S31N among A/H3N2 viruses are also likely to be involved in the recent global proliferation of A/H1N1 influenza viruses that are resistant to adamantanes, as well as in the unexpected proliferation of the H274Y substitution conferring resistance to NA inhibitors (oseltamivir). 2009 Virology Discussion IV S31N;H274Y 131;336 135;341 380 382 19394063 The origin and global emergence of adamantane resistant A/H3N2 influenza viruses. However, 10/11 of these introductions were represented by no more than three isolates in each case, suggesting that these introductions experienced only limited in spread in our studied population, and that drug selection pressure alone was insufficient to increase the prevalence of S31N. 2009 Virology Discussion IV S31N 284 288 19454348 Influenza A virus NS1 targets the ubiquitin ligase TRIM25 to evade recognition by the host viral RNA sensor RIG-I. Interestingly, the NS1 R38A/K41A mutant virus, impaired in both NS1 binding to dsRNA and TRIM25, also shows reduced IFN production in TRIM25-/- cells. 2009 Cell host & microbe Discussion IV K41A;R38A 28;23 32;27 NS1;NS1 19;64 22;67 19454348 Influenza A virus NS1 targets the ubiquitin ligase TRIM25 to evade recognition by the host viral RNA sensor RIG-I. It is plausible that the R38A/K41A mutations have created conformational changes that have resulted in the unanticipated loss of binding to TRIM25. 2009 Cell host & microbe Discussion IV R38A;K41A 25;30 29;34 19454348 Influenza A virus NS1 targets the ubiquitin ligase TRIM25 to evade recognition by the host viral RNA sensor RIG-I. Nevertheless, the use of a recombinant influenza virus bearing the NS1 E96A/E97A mutations and of TRIM25 knockout cells allowed us to conclude that NS1 binding to TRIM25 is needed for optimal inhibition of IFN production in virus-infected cells. 2009 Cell host & microbe Discussion IV E96A;E97A 71;76 75;80 NS1;NS1 67;148 70;151 19857993 Evaluation of a rapid molecular algorithm for detection of pandemic influenza A (H1N1) 2009 virus and screening for a key oseltamivir resistance (H275Y) substitution in neuraminidase. For validation of the H275Y discrimination assay, virus isolates were chosen that were derived from pandemic influenza A/H1N1 2009 infected patients before oseltamivir treatment. 2010 Journal of clinical virology Discussion IV H275Y 22 27 19857993 Evaluation of a rapid molecular algorithm for detection of pandemic influenza A (H1N1) 2009 virus and screening for a key oseltamivir resistance (H275Y) substitution in neuraminidase. Recently, a pandemic influenza sequence was uploaded to the influenza sequence database that encoded for a H275Y variant. 2010 Journal of clinical virology Discussion IV H275Y 107 112 19857993 Evaluation of a rapid molecular algorithm for detection of pandemic influenza A (H1N1) 2009 virus and screening for a key oseltamivir resistance (H275Y) substitution in neuraminidase. Taken these samples as a baseline, up to 5% for the H275Y oseltamivir resistant mutants could be detected in mixed virus populations using the H275Y discrimination assay. 2010 Journal of clinical virology Discussion IV H275Y;H275Y 52;143 57;148 19857993 Evaluation of a rapid molecular algorithm for detection of pandemic influenza A (H1N1) 2009 virus and screening for a key oseltamivir resistance (H275Y) substitution in neuraminidase. These patients respond well to oseltamivir treatment in general, therefore we assume that no H275Y minor variants were present in these samples. 2010 Journal of clinical virology Discussion IV H275Y 93 98 19857993 Evaluation of a rapid molecular algorithm for detection of pandemic influenza A (H1N1) 2009 virus and screening for a key oseltamivir resistance (H275Y) substitution in neuraminidase. Using the H275Y discrimination RT-PCR, pandemic influenza A/H1N1 viruses can be screened for oseltamivir susceptibility within 4-6 h time, which makes it useful for surveillance and valuable in clinical patient management. 2010 Journal of clinical virology Discussion IV H275Y 10 15 19893747 Novel pandemic influenza A(H1N1) viruses are potently inhibited by DAS181, a sialidase fusion protein. Because the pandemic influenza A(H1N1) virus, or any other emerging strain of influenza, could potentially gain the oseltamivir-resistance mutation (H274Y) it is critical to continue to develop anti-influenza compounds with alternative mechanisms of action. 2009 PloS one Discussion IV H274Y 149 154 19893747 Novel pandemic influenza A(H1N1) viruses are potently inhibited by DAS181, a sialidase fusion protein. The most common mutation conferring oseltamivir-resistance involves H274Y (H275Y in N1 numbering) substitution in the neuraminidase of viruses of N1 antigenic subtype (H1N1 and H5N1). 2009 PloS one Discussion IV H274Y;H275Y 68;75 73;80 118 131 19893747 Novel pandemic influenza A(H1N1) viruses are potently inhibited by DAS181, a sialidase fusion protein. This in vitro finding indicates that DAS181 may be active against currently circulating oseltamivir-resistant IFV and further suggests that if novel strains, such as the pandemic influenza A(H1N1) viruses, attain the H274Y mutation, DAS181 may be active against these new isolates as well. 2009 PloS one Discussion IV H274Y 217 222 19893749 Inhibition of neuraminidase inhibitor-resistant influenza virus by DAS181, a novel sialidase fusion protein. An NA mutation (I222V) was observed in two of the zanamivir-resistant 2009 seasonal IFV strains, in addition to the well described H274Y mutation. 2009 PloS one Discussion IV I222V;H274Y 16;131 21;136 3 5 19893749 Inhibition of neuraminidase inhibitor-resistant influenza virus by DAS181, a novel sialidase fusion protein. Drug sensitivity analysis was not performed on these viral isolates, therefore the significance of the I222V mutation in patients is unclear. 2009 PloS one Discussion IV I222V 103 108 19893749 Inhibition of neuraminidase inhibitor-resistant influenza virus by DAS181, a novel sialidase fusion protein. Examination of the HA sequence of pandemic 2009 IFV finds that nearly all isolates have a lysine (K) at amino acid 163, yet exhibit normal zanamivir sensitivity. 2009 PloS one Discussion IV K163K 89 119 HA 19 21 19893749 Inhibition of neuraminidase inhibitor-resistant influenza virus by DAS181, a novel sialidase fusion protein. Finally, an IFV A/Victoria/3/75 passaged with peramivir and found to be strongly pan-NAI resistant (oseltamivir, zanamivir, peramivir) in vitro , correlating with a single HA mutation (K186E), has been subsequently shown to be highly sensitive to DAS181 in MDCK cells and mice (unpublished data). 2009 PloS one Discussion IV K186E 185 190 HA;NAI 172;85 174;88 19893749 Inhibition of neuraminidase inhibitor-resistant influenza virus by DAS181, a novel sialidase fusion protein. For seasonal influenza H1N1 an alignment of 2009 sequences prior to the swine flu outbreak (01/2009 to 03/2009) reveals that 85/89 have an N and 2/89 have K/H/T at amino acid 163, indicating that the N163K/H/T mutation is rare, but does exist at some low level in seasonal influenza (Influenza Virus Resources,). 2009 PloS one Discussion IV N163K;N163H;N163T 200;200;200 209;209;209 19893749 Inhibition of neuraminidase inhibitor-resistant influenza virus by DAS181, a novel sialidase fusion protein. Hence, N163K/H/T-mediated reduction in NAI sensitivity in humans is unlikely to have been observed as yet. 2009 PloS one Discussion IV N163K;N163H;N163T 7;7;7 16;16;16 NAI 39 42 19893749 Inhibition of neuraminidase inhibitor-resistant influenza virus by DAS181, a novel sialidase fusion protein. However in our analysis, the N163H/K/T mutation was primarily observed in isolates with reduced zanamivir sensitivity, which seems to indicate an opposite effect of mutation involving N163. 2009 PloS one Discussion IV N163H;N163K;N163T 29;29;29 38;38;38 19893749 Inhibition of neuraminidase inhibitor-resistant influenza virus by DAS181, a novel sialidase fusion protein. In the first case, a combination of A28T(HA) and R292K(NA) mutations resulted in 3230-fold and 60-fold resistance by A/Victoria/3/75 (H3N2) to oseltamivir and zanamivir, respectively. 2009 PloS one Discussion IV A28T;R292K 36;49 40;54 HA;NA 41;55 43;57 19893749 Inhibition of neuraminidase inhibitor-resistant influenza virus by DAS181, a novel sialidase fusion protein. In the second case, B/Yamagata/16/88 acquired 100 to 700-fold resistance to oseltamivir, zanamivir, and peramivir due to a H274Y mutation in NA in combination with six HA mutations (G141E, D195N, T197N, T139N, R162M, and Y319H). 2009 PloS one Discussion IV H274Y;G141E;D195N;T197N;T139N;R162M;Y319H 123;182;189;196;203;210;221 128;187;194;201;208;215;226 HA;NA 168;141 170;143 19893749 Inhibition of neuraminidase inhibitor-resistant influenza virus by DAS181, a novel sialidase fusion protein. Interestingly this mutation has recently been observed, in tandem with the H274Y mutation, in 2 patients with pandemic 2009 IFV. 2009 PloS one Discussion IV H274Y 75 80 19893749 Inhibition of neuraminidase inhibitor-resistant influenza virus by DAS181, a novel sialidase fusion protein. It has been well established that IFV develops resistance to NAIs through two mechanisms: one, mutations in NA that decrease binding affinity to NAI drugs, such as the H274Y mutation in the current seasonal IFV; two, mutations in HA which decrease virus receptor binding affinity, thereby reducing dependence on NA. 2009 PloS one Discussion IV H274Y 168 173 HA;NA;NA;NAI;NAI 230;108;312;145;61 232;110;314;148;65 19893749 Inhibition of neuraminidase inhibitor-resistant influenza virus by DAS181, a novel sialidase fusion protein. Previous in vitro selection studies have indicated that the I222V mutation exacerbates oseltamivir- and peramivir-resistance caused by H274Y, but has only modest affect on zanamivir sensitivity. 2009 PloS one Discussion IV I222V;H274Y 60;135 65;140 19893749 Inhibition of neuraminidase inhibitor-resistant influenza virus by DAS181, a novel sialidase fusion protein. reported that introduction of an N163G mutation made a recombinant laboratory IFV strain more sensitive to NAIs in MDCK cells. 2009 PloS one Discussion IV N163G 33 38 NAI 107 111 19893749 Inhibition of neuraminidase inhibitor-resistant influenza virus by DAS181, a novel sialidase fusion protein. Similarly in our study, the 2007 and 2009 isolates that are resistant to oseltamivir and have reduced sensitivity to zanamivir carry mutations in both NA (H274Y) and HA (N163K/T/H and D225G), but the observed HA mutations have not been reported previously in drug-resistant IFV strains. 2009 PloS one Discussion IV H274Y;N163K;N163T;N163H;D225G 155;170;170;170;184 160;179;179;179;189 HA;HA;NA 166;209;151 168;211;153 19893749 Inhibition of neuraminidase inhibitor-resistant influenza virus by DAS181, a novel sialidase fusion protein. The high frequency of observed oseltamivir resistance and H274Y mutation in our 2009 H1N1 isolates correlates with worldwide reports of resistance in this season (http://www.cdc.gov/flu/weekly/weeklyarchives2008-2009/weekly15.htm). 2009 PloS one Discussion IV H274Y 58 63 19893749 Inhibition of neuraminidase inhibitor-resistant influenza virus by DAS181, a novel sialidase fusion protein. There is no reduction in DAS181 sensitivity amongst all the tested IFV clinical isolates from 2004, 2007 and 2009, demonstrating that the H274Y mutation does not reduce DAS181 sensitivity. 2009 PloS one Discussion IV H274Y 138 143 19893749 Inhibition of neuraminidase inhibitor-resistant influenza virus by DAS181, a novel sialidase fusion protein. When HA sequence analysis was performed on viruses recovered from oseltamivir treated children, an HA S262N mutation was found in 1 out of 50 cases, but NA mutations were detected in 18% of the cases. 2009 PloS one Discussion IV S262N 102 107 HA;HA;NA 5;99;153 7;101;155 19905033 Design and pharmacological characterization of inhibitors of amantadine-resistant mutants of the M2 ion channel of influenza A virus. Compound 8 from this series shows promising inhibitory activity against two of the naturally occurring A/M2 point mutants: A/M2-L26F and A/M2-V27A (Figure 2). 2009 Biochemistry Discussion IV L26F;V27A 128;142 132;146 M2;M2;M2 105;125;139 107;127;141 19905033 Design and pharmacological characterization of inhibitors of amantadine-resistant mutants of the M2 ion channel of influenza A virus. However, it is inviting to speculate that the decrease in hydrophobicity and steric bulk associated with the V27A mutation might increase the polarity and pore radius near the N-terminal region of the binding site. 2009 Biochemistry Discussion IV V27A 109 113 19905033 Design and pharmacological characterization of inhibitors of amantadine-resistant mutants of the M2 ion channel of influenza A virus. However, of these, only S31N poses a significant clinical threat. 2009 Biochemistry Discussion IV S31N 24 28 19905033 Design and pharmacological characterization of inhibitors of amantadine-resistant mutants of the M2 ion channel of influenza A virus. It is interesting to note that, although these L26F and V27A were inhibited by 8, none of the amantadine insensitive mutants located deeper in the pore was sensitive to spirane amine 8 (Table 2). 2009 Biochemistry Discussion IV L26F;V27A 47;56 51;60 19905033 Design and pharmacological characterization of inhibitors of amantadine-resistant mutants of the M2 ion channel of influenza A virus. Relatively modest modifications to BL-1743 have now resulted in a potent inhibitor of two naturally occurring A/M2 amantadine insensitive mutants: A/M2-L26F and A/M2-V27A. 2009 Biochemistry Discussion IV L26F;V27A 152;166 156;170 M2;M2;M2 112;149;163 114;151;165 19958488 Prediction of avian influenza A binding preference to human receptor using conformational analysis of receptor bound to hemagglutinin. (ii) L129V/A134V Kan-1 could bind to both receptor types, since the trans conformation was predominant for alpha(2,3) binding and the cis conformation for alpha(2,6) binding. 2009 BMC genomics Discussion IV L129V;A134V 5;11 10;16 19958488 Prediction of avian influenza A binding preference to human receptor using conformational analysis of receptor bound to hemagglutinin. (iii) Q222L, G224S, Q222L/G224S Sing-97 mutants appear to have a weaker preference for alpha(2,3) than non-mutated Sing-97 because fluctuations from the trans to cis conformation were observed. 2009 BMC genomics Discussion IV Q222L;G224S;G224S;Q222L 6;13;26;20 11;18;31;25 19958488 Prediction of avian influenza A binding preference to human receptor using conformational analysis of receptor bound to hemagglutinin. According to our prediction scheme, the L129V/A134V Kan-1 variants. 2009 BMC genomics Discussion IV L129V;A134V 40;46 45;51 19958488 Prediction of avian influenza A binding preference to human receptor using conformational analysis of receptor bound to hemagglutinin. For the alpha(2,3) receptor, all the Puerto-34 systems except for G224S appear to interact weakly since the receptor is in the cis-conformation. 2009 BMC genomics Discussion IV G224S 66 71 19958488 Prediction of avian influenza A binding preference to human receptor using conformational analysis of receptor bound to hemagglutinin. mutations M226T, K189G, K218S, and L190P, may have increased the selectivity slightly toward human receptor, since the receptor was present in cis conformation for some of the simulation (Figure 4). 2009 BMC genomics Discussion IV M226T;K189G;K218S;L190P 10;17;24;35 15;22;29;40 19958488 Prediction of avian influenza A binding preference to human receptor using conformational analysis of receptor bound to hemagglutinin. The alpha(2,6) simulation of mutated Sing-97 implied that the Q222L/G224L variant had markedly greater binding affinity toward human cell receptor as it bound in cis with alpha(2,6) all the time. 2009 BMC genomics Discussion IV Q222L;G224L 62;68 67;73 19958488 Prediction of avian influenza A binding preference to human receptor using conformational analysis of receptor bound to hemagglutinin. The order of selectivity toward Siaalpha(2,6)Gal binding was Puerto-34 > L129V/A134V Kan-1 Q222L/G224S Sing-97 > Sing-97 HA Kan-1. 2009 BMC genomics Discussion IV L129V;A134V;Q222L;G224S 73;79;93;99 78;84;98;104 HA 123 125 19958488 Prediction of avian influenza A binding preference to human receptor using conformational analysis of receptor bound to hemagglutinin. The trans conformation is observed for G224S, although the average torsion angle is increased from -50 to -30 degrees, suggesting that it may not be optimal for binding. 2009 BMC genomics Discussion IV G224S 39 44 19958488 Prediction of avian influenza A binding preference to human receptor using conformational analysis of receptor bound to hemagglutinin. The two single mutations, Q222L and G224S cause a loss in human receptor affinity as shown by fluctuations to the trans-conformation, while the double mutation Q222L/G224S maintained its preference for human receptor as the bound alpha(2,6) glycosides were in the cis conformation. 2009 BMC genomics Discussion IV Q222L;G224S;Q222L;G224S 26;36;160;166 31;41;165;171 20303563 Substitution of lysine at 627 position in PB2 protein does not change virulence of the 2009 pandemic H1N1 virus in mice. Genetic analysis revealed that the pandemic (H1N 1) 2009 contained all six "compensating" residues in PB2 gene. 2010 Virology Discussion IV H1N 45 48 PB2 102 105 20303563 Substitution of lysine at 627 position in PB2 protein does not change virulence of the 2009 pandemic H1N1 virus in mice. In this study, we demonstrated that the single amino acid substitution of PB2 E627K, in the context of the current influenza pandemic stain, rendered neither increased pathogenecity in mice, nor improved viral replication in MDCK cells under 33-39 C. 2010 Virology Discussion IV E627K 78 83 PB2 74 77 20303563 Substitution of lysine at 627 position in PB2 protein does not change virulence of the 2009 pandemic H1N1 virus in mice. It was reported that increased virulence in mice caused by the E627K mutation in H5N1 avian influenza virus could be compensated by multiple mutations at other sites of PB2 gene (L89V, G309D, T339K, R477G, I495V and A676T), suggesting that E627K substitution may not be an indispensable determinant for virulence. 2010 Virology Discussion IV E627K;L89V;G309D;T339K;R477G;I495V;A676T;E627K 63;179;185;192;199;206;216;240 68;183;190;197;204;211;221;245 PB2 169 172 20303563 Substitution of lysine at 627 position in PB2 protein does not change virulence of the 2009 pandemic H1N1 virus in mice. Most strikingly, a single passage in mice was reported to be sufficient for the avian H5N1 virus to acquire the E627K substitution, and all recovered viruses from the brains of dead mice turned out to have a 627K. 2010 Virology Discussion IV E627K 112 117 20303563 Substitution of lysine at 627 position in PB2 protein does not change virulence of the 2009 pandemic H1N1 virus in mice. Studies on viral pathogenecity revealed that a single amino acid substitution of E627K in PB2 would remarkably enhance the virulence of avian H5N1 and equine H7N7 influenza viruses in mammalian species (Hatto et al., 2001). 2010 Virology Discussion IV E627K 81 86 PB2 90 93 20303563 Substitution of lysine at 627 position in PB2 protein does not change virulence of the 2009 pandemic H1N1 virus in mice. Whether current pandemic H1N1 virus may evolve to obtain E627K substitution remains to be seen. 2010 Virology Discussion IV E627K 57 62 20459681 Oseltamivir-resistant pandemic (H1N1)2009 in Yemen - case report. H274Y jumped from clade2C (Hong Kong/2562/2006-like) to clade 1 (New Caledonia/20/1999-like) to clade 2B (Brisbane/59/2007-like) which included multiple introductions. 2010 Virology journal Discussion IV H274Y 0 5 20459681 Oseltamivir-resistant pandemic (H1N1)2009 in Yemen - case report. Moreover, this isolate, and others collected over the summer in Hong Kong have a clade 2C HA and M2 which has H274Y in NA (both clade 2B and clade C) as well as S31N on M2, signaling additional exchanges of polymorphisms6 leading to the emergence of H1N1 which is resistant to oseltamivir and the adamantanes. 2010 Virology journal Discussion IV H274Y;S31N 110;161 115;165 HA;M2;M2;NA 90;97;169;119 92;99;171;121 20459681 Oseltamivir-resistant pandemic (H1N1)2009 in Yemen - case report. Prior studies also supported a fitness penalty for the acquisition of H274Y, which predicted that the change would be limited to patients receiving oseltamivir. 2010 Virology journal Discussion IV H274Y 70 75 20459681 Oseltamivir-resistant pandemic (H1N1)2009 in Yemen - case report. Prior studies of oseltamivir resistance in Japan5 were linked to sub-optimal dosing and resistance was found in both current influenza A subtypes, H1N1 and H3N2, and included, but was not limited to H274Y. 2010 Virology journal Discussion IV H274Y 199 204 20459681 Oseltamivir-resistant pandemic (H1N1)2009 in Yemen - case report. Sub-clades that had acquired key changes on the neuraminidase and hemagglutinin genes expanded and fixed of H274Y on H1N1. 2010 Virology journal Discussion IV H274Y 108 113 HA;NA 66;48 79;61 20459681 Oseltamivir-resistant pandemic (H1N1)2009 in Yemen - case report. The dramatic rise of oseltamivir resistance in the H1N1 serotype in the 2007/2008 season3, and the fixing of H274Y in the 2008/2009 season have raised concerns regarding individuals at risk for seasonal influenza, as well as development of similar resistance in the H5N1 serotype3. 2010 Virology journal Discussion IV H274Y 109 114 20459681 Oseltamivir-resistant pandemic (H1N1)2009 in Yemen - case report. These changes led to the spread of adamantane resistance on clade 2C outside of Asia, followed by the spread of oseltamivir resistance in 2007/2008 and the fixing of H274Y in 2008/2009. 2010 Virology journal Discussion IV H274Y 166 171 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. Conversely, A/WSN/33 (H1N1) virus with the I117V change was susceptible to both NA inhibitors. 2010 PLoS pathogens Discussion IV I117V 43 48 80 82 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. E119G/A/D/V NA mutations are commonly reported to be associated with NA inhibitor resistance and were identified in influenza viruses of the N2 NA subtype. 2010 PLoS pathogens Discussion IV E119G;E119A;E119D;E119V 0;0;0;0 11;11;11;11 NA;NA;NA 12;69;144 14;71;146 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. Five of these 7 NA mutations (all but K150N and Y252H) reduced H5N1 virus susceptibility either to oseltamivir carboxylate or to both NA inhibitors. 2010 PLoS pathogens Discussion IV K150N;Y252H 38;48 43;53 NA;NA 16;134 18;136 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. Further, the E119A NA substitution has been selected in several strains of influenza A (H4N2) and B viruses after in vitro passages in the presence of zanamivir and has resulted in reduced NA activity. 2010 PLoS pathogens Discussion IV E119A 13 18 NA;NA 19;189 21;191 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. However, recombinant H5N1 viruses carrying I117V and Y252H NA mutations possessed the highest relative NA activity, but ferrets infected with these viruses experienced a mild, brief illness. 2010 PLoS pathogens Discussion IV I117V;Y252H 43;53 48;58 NA;NA 59;103 61;105 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. However, the possibility that after exposure to one NA inhibitor the chance exists that occurring drug-resistant H5N1 mutant could be cross resistant to both antiviral drugs and will be more virulent that the WT virus (like E119A H5N1 recombinant virus) should prompt to re-assess the suitability of single-drug usage. 2010 PLoS pathogens Discussion IV E119A 224 229 52 54 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. Importantly, recombinant H5N1 viruses carrying framework NA mutations (E119A and N294S) were more virulent and were associated with significantly higher virus titers in the lungs and liver than WT virus (P<0.01). 2010 PLoS pathogens Discussion IV E119A;N294S 71;81 76;86 57 59 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. In a previous study, the E119A mutant in an A/WSN/33 (H1N1)-virus background could not be rescued, suggesting that this mutation may impede the growth of H1N1 viruses more than that of H4N2 viruses. 2010 PLoS pathogens Discussion IV E119A 25 30 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. In contrast, we recently found that in mice, E119A mutation is stably maintained in the NA of clade 2 H5N1 virus during oseltamivir therapy and is associated with resistance to both NA inhibitors. 2010 PLoS pathogens Discussion IV E119A 45 50 NA;NA 88;182 90;184 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. In the present study, V116A and I117V mutants showed a low (~6-fold greater than WT) level of resistance to oseltamivir carboxylate. 2010 PLoS pathogens Discussion IV V116A;I117V 22;32 27;37 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. It is noteworthy that alignment of the NA genes of currently circulating highly pathogenic H5N1 influenza A viruses identified the NA mutations studied here in ~0.1%-1.4% of isolates (namely, I117V was found in 1.4% and V116A and I119A were found in 0.1% isolates), raising concern about the drug sensitivity of a possible pandemic strain. 2010 PLoS pathogens Discussion IV I117V;V116A;I119A 192;220;230 197;225;235 NA;NA 39;131 41;133 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. Moreover, the E119G NA mutation significantly compromised viral growth and was genetically unstable in a clade 1 A/Vietnam/1203/04 (H5N1)-virus background. 2010 PLoS pathogens Discussion IV E119G 14 19 20 22 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. Of 11 NA mutations studied, seven located within (E119A, H274Y, and N294S) or near (V116A, I117V, K150N, and Y252H) the enzyme active site were stably maintained and grew to titers comparable to WT virus in MDCK cells. 2010 PLoS pathogens Discussion IV E119A;H274Y;N294S;V116A;I117V;K150N;Y252H 50;57;68;84;91;98;109 55;62;73;89;96;103;114 6 8 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. Our finding that E119A reduced the NA activity of H5N1 virus 10-fold without compromising viral yield in MDCK cells suggests that these changes in NA activity do not compromise the infectivity of these viruses due to their high replication ability. 2010 PLoS pathogens Discussion IV E119A 17 22 NA;NA 35;147 37;149 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. Our most important finding is that the E119A NA substitution in the clade 2.2 A/Turkey/15/06 (H5N1)-virus background is viable and genetically stable and confers cross-resistance to oseltamivir carboxylate and zanamivir. 2010 PLoS pathogens Discussion IV E119A 39 44 45 47 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. Our study is the first to our knowledge to fully elucidate the role of the V116A and I117V NA amino acid substitutions in NA inhibitor resistance in a genetically homogeneous H5N1-virus background in the absence of concomitant HA and/or NA mutations. 2010 PLoS pathogens Discussion IV V116A;I117V 75;85 80;90 HA;NA;NA;NA 227;91;122;237 229;93;124;239 20523902 Effect of neuraminidase inhibitor-resistant mutations on pathogenicity of clade 2.2 A/Turkey/15/06 (H5N1) influenza virus in ferrets. The resistance of the E119A NA mutant to both zanamivir and oseltamivir carboxylate suggests that they interact similarly with the conserved framework residues of viral NA. 2010 PLoS pathogens Discussion IV E119A 22 27 NA;NA 28;169 30;171 20591072 Increasing antiviral activity of surfactant protein d trimers by introducing residues from bovine serum collectins: dissociation of mannan-binding and antiviral activity. Although the combined mutations greatly increased mannan binding activity, antiviral activity was decreased as compared to R343V (or R343I). 2010 Scandinavian journal of immunology Discussion IV R343V;R343I 123;133 128;138 20591072 Increasing antiviral activity of surfactant protein d trimers by introducing residues from bovine serum collectins: dissociation of mannan-binding and antiviral activity. Although the RAK+R343V (or I) double mutants did not result in increased antiviral activity compared to single mutants, we are pursuing other strategies including substitutions for D325 in combination with the R343V substitution and have found increased activity (unpublished data). 2010 Scandinavian journal of immunology Discussion IV R343V;R343V 17;210 22;215 20591072 Increasing antiviral activity of surfactant protein d trimers by introducing residues from bovine serum collectins: dissociation of mannan-binding and antiviral activity. It is of interest that binding of mAbs 246-02 and 3C3-C-20, which is reduced to RAK, is partially or fully restored for RAK+R343V, implying that the combination of the insertion and substitution restore a structural feature in hSP-D-NCRD that is recognized by these mAbs. 2010 Scandinavian journal of immunology Discussion IV R343V 124 129 20591072 Increasing antiviral activity of surfactant protein d trimers by introducing residues from bovine serum collectins: dissociation of mannan-binding and antiviral activity. Note that cross-linking of the R343V variant of hSP-D-NCRD with either mAb 246-08 or 6B2 results in very potent antiviral activity, which approaches the activity of native dodecamers (see Table 3). 2010 Scandinavian journal of immunology Discussion IV R343V 31 36 20591072 Increasing antiviral activity of surfactant protein d trimers by introducing residues from bovine serum collectins: dissociation of mannan-binding and antiviral activity. Since CL-43 had particularly strong mannan binding and antiviral activity, for this paper we produced and tested addition of the RAK sequence to the R343V (or R343I) mutant of hSP-D-NCRD. 2010 Scandinavian journal of immunology Discussion IV R343V;R343I 149;159 154;164 20591072 Increasing antiviral activity of surfactant protein d trimers by introducing residues from bovine serum collectins: dissociation of mannan-binding and antiviral activity. We have shown that the R343V or R343I mutants of hSP-D-NCRD have greatly increased antiviral activity compared to the wild type hSP-D-NCRD; hence, this is one important difference accounting for the increased antiviral activity of bovine serum collectin NCRDs. 2010 Scandinavian journal of immunology Discussion IV R343V;R343I 23;32 28;37 20661429 Oseltamivir-resistant pandemic A/H1N1 virus is as virulent as its wild-type counterpart in mice and ferrets. Additional studies are required to assess the mechanism leading to increased IL-6 levels in animals infected with the H274Y NA mutant. 2010 PLoS pathogens Discussion IV H274Y 118 123 124 126 20661429 Oseltamivir-resistant pandemic A/H1N1 virus is as virulent as its wild-type counterpart in mice and ferrets. Although preexisting antibody levels against an heterologous strain could have an effect on pathogenicity and transmission of pH1N1, the geometrical mean antibody titers were similar for our two groups of ferrets, which should not change our conclusion about the relative pathogenicity of the H274Y mutant compared to the WT strain. 2010 PLoS pathogens Discussion IV H274Y 293 298 20661429 Oseltamivir-resistant pandemic A/H1N1 virus is as virulent as its wild-type counterpart in mice and ferrets. Altogether, those results suggest that the H274Y pH1N1 mutant isolate stimulated a more important inflammatory response in mice compared to WT virus, which could be due to rapid induction of IL-6 and KC in the former. 2010 PLoS pathogens Discussion IV H274Y 43 48 20661429 Oseltamivir-resistant pandemic A/H1N1 virus is as virulent as its wild-type counterpart in mice and ferrets. However, transmission of the H274Y mutant strain was documented in ferrets. 2010 PLoS pathogens Discussion IV H274Y 29 34 20661429 Oseltamivir-resistant pandemic A/H1N1 virus is as virulent as its wild-type counterpart in mice and ferrets. In agreement with previously-described seasonal A/H1N1 viruses containing the H274Y NA mutation, our oseltamivir-resistant pH1N1 mutant showed cross-resistance to peramivir, a parenteral NAI that is in phase 3 clinical trials and also readily available through an emergency access program. 2010 PLoS pathogens Discussion IV H274Y 78 83 NA;NAI 84;187 86;190 20661429 Oseltamivir-resistant pandemic A/H1N1 virus is as virulent as its wild-type counterpart in mice and ferrets. In fact, more weight loss was induced by the H274Y mutant compared to the WT virus during the first 7-8 days post-infection although all mice eventually returned to their initial weight. 2010 PLoS pathogens Discussion IV H274Y 45 50 20661429 Oseltamivir-resistant pandemic A/H1N1 virus is as virulent as its wild-type counterpart in mice and ferrets. In influenza viruses of the N1 subtype, including seasonal A/H1N1 viruses and avian A/H5N1 strains, oseltamivir resistance is mainly conferred by the H274Y (N2 numbering) mutation. 2010 PLoS pathogens Discussion IV H274Y 150 155 20661429 Oseltamivir-resistant pandemic A/H1N1 virus is as virulent as its wild-type counterpart in mice and ferrets. In summary, although some slight differences were observed in the two animal models, we can conclude that the H274Y pH1N1 mutant seems as virulent as the WT isolate with no obvious impairment in viral fitness. 2010 PLoS pathogens Discussion IV H274Y 110 115 20661429 Oseltamivir-resistant pandemic A/H1N1 virus is as virulent as its wild-type counterpart in mice and ferrets. In the meantime, careful monitoring of the H274Y mutation during pH1N1 outbreaks is mandatory to rapidly identify transmission events that could lead to large-scale dissemination of an oseltamivir-resistant pH1N1 strain. 2010 PLoS pathogens Discussion IV H274Y 43 48 20661429 Oseltamivir-resistant pandemic A/H1N1 virus is as virulent as its wild-type counterpart in mice and ferrets. In the N1 subtype, the H274Y mutation has been initially reported as impairing the viral fitness of older seasonal strains such as A/New Caledonia/20/99-like and A/Texas/36/91 when evaluated in the ferret model. 2010 PLoS pathogens Discussion IV H274Y 23 28 20661429 Oseltamivir-resistant pandemic A/H1N1 virus is as virulent as its wild-type counterpart in mice and ferrets. In the present study, the replication of the pH1N1 H274Y mutant was initially impaired in vitro compared to the WT virus but viral titers were virtually identical on days 2 and 3 post-infection. 2010 PLoS pathogens Discussion IV H274Y 51 56 20661429 Oseltamivir-resistant pandemic A/H1N1 virus is as virulent as its wild-type counterpart in mice and ferrets. Interestingly, the H274Y mutant also induced preferential expression of IL-6, IL-12 and IFN-gamma in the retropharyngeal lymph nodes of ferrets compared to the WT virus. 2010 PLoS pathogens Discussion IV H274Y 19 24 20661429 Oseltamivir-resistant pandemic A/H1N1 virus is as virulent as its wild-type counterpart in mice and ferrets. Interestingly, the H274Y NA mutant induced a slightly more pronounced weight loss than the WT virus in mice, and this observation correlated with increased production of IL-6 and KC and a more important pulmonary inflammation involving the perivascular (day 6) and pleural (days 6 and 12) compartments. 2010 PLoS pathogens Discussion IV H274Y 19 24 25 27 20661429 Oseltamivir-resistant pandemic A/H1N1 virus is as virulent as its wild-type counterpart in mice and ferrets. Moreover, we now report that the H274Y pH1N1 mutant virus is clearly as fit as the WT virus in this animal model. 2010 PLoS pathogens Discussion IV H274Y 33 38 20661429 Oseltamivir-resistant pandemic A/H1N1 virus is as virulent as its wild-type counterpart in mice and ferrets. Other H274Y pH1N1 mutants (with different genetic backgrounds) should be studied in terms of virulence and efficiency of transmission to confirm our conclusions. 2010 PLoS pathogens Discussion IV H274Y 6 11 20661429 Oseltamivir-resistant pandemic A/H1N1 virus is as virulent as its wild-type counterpart in mice and ferrets. The two pH1N1 isolates replicated less efficiently (lower titers and reduced plaque formation) than the recent WT and H274Y mutant A/Brisbane/59/2007 strains in ST6Gal I-expressing MDCK cells, which may indicate a greater affinity of the seasonal strain for alpha2,6 sialic acid receptors. 2010 PLoS pathogens Discussion IV H274Y 118 123 20661429 Oseltamivir-resistant pandemic A/H1N1 virus is as virulent as its wild-type counterpart in mice and ferrets. We have recently described the rapid emergence of oseltamivir resistance in a family cluster of pH1N1 infection due to the H274Y NA mutation, and now report on the viral fitness of this mutant in vitro and in vivo. 2010 PLoS pathogens Discussion IV H274Y 123 128 129 131 Influenza A virus H1N1 infection 96 111 20661429 Oseltamivir-resistant pandemic A/H1N1 virus is as virulent as its wild-type counterpart in mice and ferrets. We report here that the H274Y mutant could be transmitted by contact to uninfected ferrets but did not compare the efficiency of transmission with the WT strain and neither evaluated aerosol transmission. 2010 PLoS pathogens Discussion IV H274Y 24 29 20686654 Oseltamivir-resistant pandemic H1N1/2009 influenza virus possesses lower transmissibility and fitness in ferrets. Although the transmissibility of the oseltamivir-resistant H1N1/2009 virus was reduced by the H275Y NA mutation, the severity and course of disease was similar to that caused by oseltamivir-sensitive H1N1/2009 virus in both inoculated and direct-contact ferrets, with no apparent attenuation of clinical signs. 2010 PLoS pathogens Discussion IV H275Y 94 99 100 102 20686654 Oseltamivir-resistant pandemic H1N1/2009 influenza virus possesses lower transmissibility and fitness in ferrets. As this study was undertaken, additional H275Y mutants of H1N1/2009 viruses have emerged in the absence of oseltamivir use. 2010 PLoS pathogens Discussion IV H275Y 41 46 20686654 Oseltamivir-resistant pandemic H1N1/2009 influenza virus possesses lower transmissibility and fitness in ferrets. Further studies of these newly isolated H275Y mutants of H1N1/2009 viruses are warranted to determine whether they have acquired additional changes. 2010 PLoS pathogens Discussion IV H275Y 40 45 20686654 Oseltamivir-resistant pandemic H1N1/2009 influenza virus possesses lower transmissibility and fitness in ferrets. In a subsequent study, an R292K mutant of H3N2 virus was not transmitted by direct contact among ferrets. 2010 PLoS pathogens Discussion IV R292K 26 31 20686654 Oseltamivir-resistant pandemic H1N1/2009 influenza virus possesses lower transmissibility and fitness in ferrets. In the earliest studies, oseltamivir-resistant H3N2 (R292K NA mutant) and H1N1 (H275Y NA mutant) variants exhibited severely compromised replication and virulence both in vitro and in vivo and were therefore thought unlikely to be of clinical consequence. 2010 PLoS pathogens Discussion IV R292K;H275Y 53;80 58;85 NA;NA 59;86 61;88 20686654 Oseltamivir-resistant pandemic H1N1/2009 influenza virus possesses lower transmissibility and fitness in ferrets. The H275Y mutant of H1N1/2009 used in this study was the first oseltamivir-resistant H1N1/2009 isolate from a patient on oseltamivir prophylaxis. 2010 PLoS pathogens Discussion IV H275Y 4 9 20686654 Oseltamivir-resistant pandemic H1N1/2009 influenza virus possesses lower transmissibility and fitness in ferrets. The only study to date that has evaluated both routes of transmission of oseltamivir-resistant virus showed that recombinant resistant H3N2 viruses with either the E119V or the E119V+I222V NA mutation were transmitted efficiently by direct contact but not by respiratory droplets among guinea pigs. 2010 PLoS pathogens Discussion IV E119V;E119V;I222V 164;177;183 169;182;188 189 191 20686654 Oseltamivir-resistant pandemic H1N1/2009 influenza virus possesses lower transmissibility and fitness in ferrets. The slightly reduced (not severely impaired) NA enzyme function and delayed viral growth of the H275Y mutant may have been more crucial in recipient ferrets that acquired virus from environment via natural routes than in donor ferrets inoculated with a high dose of virus, as we observed delayed viral shedding or inefficient transmission in the recipient ferrets, but not in the inoculated donor ferret. 2010 PLoS pathogens Discussion IV H275Y 96 101 45 47 20686654 Oseltamivir-resistant pandemic H1N1/2009 influenza virus possesses lower transmissibility and fitness in ferrets. Therefore, the H275Y mutant of pandemic H1N1/2009 virus is likely to be of clinical consequence in humans. 2010 PLoS pathogens Discussion IV H275Y 15 20 20686654 Oseltamivir-resistant pandemic H1N1/2009 influenza virus possesses lower transmissibility and fitness in ferrets. This study is the first, to our knowledge, to demonstrate the inefficient respiratory droplet transmission of an oseltamivir-resistant H275Y mutant of H1N1/2009 in ferrets, which are an established animal model of the pathogenesis and transmission of human influenza viruses. 2010 PLoS pathogens Discussion IV H275Y 135 140 20686654 Oseltamivir-resistant pandemic H1N1/2009 influenza virus possesses lower transmissibility and fitness in ferrets. Under similar conditions, the transmission of an E119V mutant of H3N2 virus and an H275Y mutant of A/New Caledonia/20/99-like (H1N1) virus by direct contact required a higher dose of inoculum than transmission of the wild-type viruses, and it occurred more slowly. 2010 PLoS pathogens Discussion IV E119V;H275Y 49;83 54;88 20686654 Oseltamivir-resistant pandemic H1N1/2009 influenza virus possesses lower transmissibility and fitness in ferrets. We suggest that the lower fitness of oseltamivir-resistant variant within the host along with its reduced NA enzyme efficiency and delayed growth of the H275Y mutant virus in vitro may at least in part explain its impaired transmission among ferrets. 2010 PLoS pathogens Discussion IV H275Y 153 158 106 108 20689744 The PB2-E627K mutation attenuates viruses containing the 2009 H1N1 influenza pandemic polymerase. A recently published study likewise demonstrated neither any potentiation of viral replication or pathogenicity in 2009 H1N1 pandemic viruses due to PB2-E627K or -D701N in mice or ferrets nor any potentiation of transmission in ferrets. 2010 mBio Discussion IV E627K;D701N 153;163 158;168 PB2 149 152 20689744 The PB2-E627K mutation attenuates viruses containing the 2009 H1N1 influenza pandemic polymerase. In yet another context, that of the avian S09 RNP, the PB2-E627K mutation changed the dominant histopathology from an alveolitis to a bronchiolitis, while the identical mutation was detrimental to pathogenicity in the setting of the CA09 RNP. 2010 mBio Discussion IV E627K 59 64 PB2;RNP;RNP 55;46;238 58;49;241 Bronchiolitis 134 147 20689744 The PB2-E627K mutation attenuates viruses containing the 2009 H1N1 influenza pandemic polymerase. Interestingly, when Mehle and Doudna introduced the SR mutations alongside E627K in the avian S09 RNP background, no detriment to viral replication was observed in tissue culture, in contrast to the impaired replication that we observed for viruses containing the 2009 H1N1 RNP. 2010 mBio Discussion IV E627K 75 80 RNP;RNP 98;274 101;277 20689744 The PB2-E627K mutation attenuates viruses containing the 2009 H1N1 influenza pandemic polymerase. Perhaps most intriguingly, in the case of the virus pair comprising 1918RNP and 1918RNP-K627E, a disconnect is observed between the clinical disease and histopathology and viral replication: 1918RNP-K627E is only mildly attenuated in mouse lung replication compared to 1918RNP, yet the 1918RNP-K627E virus causes no clinical illness and virtually no histopathology. 2010 mBio Discussion IV K627E;K627E;K627E 88;199;294 93;204;299 20689744 The PB2-E627K mutation attenuates viruses containing the 2009 H1N1 influenza pandemic polymerase. Similarly, the K627E back-mutation in the context of rNY312 did not decrease its replication competence in vitro or in vivo. 2010 mBio Discussion IV K627E 15 20 20689744 The PB2-E627K mutation attenuates viruses containing the 2009 H1N1 influenza pandemic polymerase. Thus, while it is unexpected that the PB2-E627K and -D701N mutations, shown to be beneficial to viral replication in mammalian models in other contexts, attenuate viruses containing the 2009 H1N1 pandemic RNP, it is becoming clear that viral RNP adaptation to humans can be achieved through routes other than PB2-627K or -701N. 2010 mBio Discussion IV E627K;D701N 42;53 47;58 PB2;PB2;RNP;RNP 38;309;205;242 41;312;208;245 20689744 The PB2-E627K mutation attenuates viruses containing the 2009 H1N1 influenza pandemic polymerase. We show that in both A549 cell culture and a mouse model of influenza infection, two of these changes, PB2-E627K and -D701N, do not potentiate the replication or virulence of a virus containing the 2009 pandemic RNP. 2010 mBio Discussion IV E627K;D701N 107;118 112;123 PB2;RNP 103;212 106;215 IV infections 60 79 20689744 The PB2-E627K mutation attenuates viruses containing the 2009 H1N1 influenza pandemic polymerase. While the PB2-E627K mutation clearly carries great significance, it was insufficient to increase replication of an avian RNP-containing virus in human cell culture. 2010 mBio Discussion IV E627K 14 19 PB2;RNP 10;121 13;124 20836794 Oseltamivir-resistant influenza A 2009 H1N1 virus in immunocompromised patients. Our finding of patients with 2009 H1N1 influenza virus harboring the H275Y mutation with apparently low suspicion for developing resistance is concerning. 2010 Influenza and other respiratory viruses Discussion IV H275Y 69 74 20836794 Oseltamivir-resistant influenza A 2009 H1N1 virus in immunocompromised patients. We focused on the H275Y neuraminidase mutation, which is currently of greatest concern. 2010 Influenza and other respiratory viruses Discussion IV H275Y 18 23 24 37 20970464 Structure-based design of NS2 mutants for attenuated influenza A virus vaccines. Amino acid substitution E67S or E74S in NS2/NEP was accompanied by G224V/T225A mutations or disruption of the stop codon by adding seven amino acid residues (231FGNKMVD237) to NS1, due to gene overlapping. 2011 Virus research Discussion IV E67S;E74S;G224V;T225A 24;32;67;73 28;36;72;78 NEP;NS1;NS2 44;176;40 47;179;43 20970464 Structure-based design of NS2 mutants for attenuated influenza A virus vaccines. It is likely that the additional C-terminal amino acids of NS1 alter its function, since this region contains the PABII-binding domain and a possible PDZ element, although several natural isolates, such as A/Udorn/72 (H3N2), possess extended NS1s (237 amino compared to 230 in WSN NS1), which are the same size as those of the mutants containing E74S. 2011 Virus research Discussion IV E74S 346 350 NS1;NS1;NS1 59;281;242 62;284;246 21048522 Oseltamivir-resistant influenza A and B viruses pre- and postantiviral therapy in children and young adults with cancer. Additional amino acid substitutions in the NA (I194V, K199E, and L372S) were detected in 1 patient with influenza A (H3N2) virus (patient 2). 2011 The Pediatric infectious disease journal Discussion IV I194V;K199E;L372S 47;54;65 52;59;70 43 45 21048522 Oseltamivir-resistant influenza A and B viruses pre- and postantiviral therapy in children and young adults with cancer. The influenza A (H3N2) virus harbored an E119V NA mutation, which has been reported in oseltamivir-treated patients, but this is the first report of this mutation arising prior to oseltamivir exposure. 2011 The Pediatric infectious disease journal Discussion IV E119V 41 46 47 49 21048522 Oseltamivir-resistant influenza A and B viruses pre- and postantiviral therapy in children and young adults with cancer. The resistant influenza B harbored an N294S NA mutation. 2011 The Pediatric infectious disease journal Discussion IV N294S 38 43 44 46 21116343 Does pandemic A/H1N1 virus have the potential to become more pathogenic? In contrast, the HA K154Q substitution identified in G1 was not present in any contemporary pandemic A/H1N1 influenza virus examined. 2010 mBio Discussion IV K154Q 20 25 HA 17 19 21116343 Does pandemic A/H1N1 virus have the potential to become more pathogenic? In this study, a single mutation, PB2 D87N, was responsible for increased G2 RNP polymerase activity at the lower temperature (33 C) found in the mammalian airway and, therefore, probably contributed to better replication in the nose, significantly elevated inflammation, or more efficient transmission. 2010 mBio Discussion IV D87N 38 42 PB2;RNP 34;77 37;80 21116343 Does pandemic A/H1N1 virus have the potential to become more pathogenic? It is noteworthy that alignment of full PB2 proteins showed the D87N mutation only in 0.06% of sequenced isolates. 2010 mBio Discussion IV D87N 64 68 PB2 40 43 21116343 Does pandemic A/H1N1 virus have the potential to become more pathogenic? Located next to the HA receptor-binding site, the K154Q mutation affected the protein structure such that binding to the 6'-SL receptor became impossible, probably because of an increase of the negative charge of the HA molecule. 2010 mBio Discussion IV K154Q 50 55 HA;HA 20;217 22;219 21116343 Does pandemic A/H1N1 virus have the potential to become more pathogenic? Our data showed that the acquisition of two nonsynonymous mutations in the HA (K154Q) and PA (L295P) genes resulted in rapid selection of the pandemic virus with improved replication and virulence. 2010 mBio Discussion IV K154Q;L295P 79;94 84;99 HA;PA 75;90 77;92 21172786 Pandemic H1N1 2009 influenza virus with the H275Y oseltamivir resistance neuraminidase mutation shows a small compromise in enzyme activity and viral fitness. Examples of such mutations are D344N, and V235M and/or R223Q. 2011 The Journal of antimicrobial chemotherapy Discussion IV D344N;V235M;R223Q 31;42;55 36;47;60 21172786 Pandemic H1N1 2009 influenza virus with the H275Y oseltamivir resistance neuraminidase mutation shows a small compromise in enzyme activity and viral fitness. In this background, the small compromise in enzyme affinity for sialic acid substrate (observed by a 1.3-fold increase in the NA Km value) and the decrease in cell surface expression that results from the H275Y mutation, had no effect on virus growth in MDCK cell culture. 2011 The Journal of antimicrobial chemotherapy Discussion IV H275Y 205 210 126 128 21172786 Pandemic H1N1 2009 influenza virus with the H275Y oseltamivir resistance neuraminidase mutation shows a small compromise in enzyme activity and viral fitness. Neither of the latter two mutations currently exist in the NA protein of pH1N1 isolates, but further circulation of the pH1N1 virus in humans may select for these or other NA or haemagglutinin (HA) mutations that better prime the virus to accommodate or even select for the H275Y mutation. 2011 The Journal of antimicrobial chemotherapy Discussion IV H275Y 274 279 HA;HA;NA;NA 194;178;59;172 196;192;61;174 21172786 Pandemic H1N1 2009 influenza virus with the H275Y oseltamivir resistance neuraminidase mutation shows a small compromise in enzyme activity and viral fitness. Similarly, in the manuscript from Kiso et al., the conclusion is again that the H275Y mutant transmits through the air between ferrets, but there is a 2 day delay in transmission of one of the mutant strains of virus studied. 2011 The Journal of antimicrobial chemotherapy Discussion IV H275Y 80 85 21172786 Pandemic H1N1 2009 influenza virus with the H275Y oseltamivir resistance neuraminidase mutation shows a small compromise in enzyme activity and viral fitness. The biological consequences of the H275Y mutation in the NA gene of pH1N1 influenza virus, which confers resistance to oseltamivir, are important because the drug is a first-line treatment for patients who present with pandemic influenza infection. 2011 The Journal of antimicrobial chemotherapy Discussion IV H275Y 35 40 57 59 21172786 Pandemic H1N1 2009 influenza virus with the H275Y oseltamivir resistance neuraminidase mutation shows a small compromise in enzyme activity and viral fitness. To probe this, we tested the NA activity of the mutated virus in assays that presented large sialylated substrates: in a red cell elution assay we detected a 4-fold compromise in the ability of the virus with H275Y mutation to mediate desialylation of chicken erythrocytes, although the biological significance of this assay is not entirely clear. 2011 The Journal of antimicrobial chemotherapy Discussion IV H275Y 209 214 29 31 21226922 Influenza A virus NS1 gene mutations F103L and M106I increase replication and virulence. Both HK-NS1 F103L and M106I mutations enhanced the level and duration of replication resulting in increased virulence in the mouse lung where viral titers were 104 to 105 fold higher at 5 dpi in infected lungs, in contrast to rPR8-HK-NS-wt, which had viral titers below the level of detection. 2011 Virology journal Discussion IV F103L;M106I 12;22 17;27 NS;NS1 234;8 236;11 21226922 Influenza A virus NS1 gene mutations F103L and M106I increase replication and virulence. F103L and M106I Mutations enhance protein synthesis. 2011 Virology journal Discussion IV F103L;M106I 0;10 5;15 21226922 Influenza A virus NS1 gene mutations F103L and M106I increase replication and virulence. Given that the 103 and 106 amino acids also map to regions of interaction between NS1 and cellular translational initiation factors eIF4GI and PABPI, leads to the hypothesis of increased NS1-mediated initiation complex formation on IAV mRNA for enhanced viral gene expression due to mutations F103L and M106I. 2011 Virology journal Discussion IV F103L;M106I 293;303 298;308 NS1;NS1 82;187 85;190 21226922 Influenza A virus NS1 gene mutations F103L and M106I increase replication and virulence. Here we demonstrated that both the IAV NS1 F103L and M106I mutations were adaptive mutations that increased replicative abilities in cells of multiple species as well as virulence in the mouse lung. 2011 Virology journal Discussion IV F103L;M106I 43;53 48;58 NS1 39 42 21226922 Influenza A virus NS1 gene mutations F103L and M106I increase replication and virulence. In our experiments, the F103L and M106I mutations enhanced IFN-beta induction only when transferred onto the foreign, A/PR/8/34, genetic background. 2011 Virology journal Discussion IV F103L;M106I 24;34 29;39 21226922 Influenza A virus NS1 gene mutations F103L and M106I increase replication and virulence. Increased IFN-beta induction was also suppressed for the H9N2 NS gene on the WSN backbone, and the H5N1 NS gene on the PR8 backbone where it was demonstrated that in the absence of increased IFN-beta induction the F103L and M106I mutations mediated a large increase in extent of lung infection and virulence. 2011 Virology journal Discussion IV F103L;M106I 214;224 219;229 NS;NS 62;104 64;106 21226922 Influenza A virus NS1 gene mutations F103L and M106I increase replication and virulence. It has been reported that the A/HK/156/97(H5N1) was able to suppress IFN-beta induction in the context of its NS1 gene, possessing F103L and M106I mutations, due to properties of its NP and PA genes. 2011 Virology journal Discussion IV F103L;M106I 131;141 136;146 NP;NS1;PA 183;110;190 185;113;192 21226922 Influenza A virus NS1 gene mutations F103L and M106I increase replication and virulence. The extent of infection as monitored by virus yield suggested that more cells were infected in the lung for all the mutant viruses but that both mutations in combination were not more effective in the PR8 backbone than the F103L mutation alone, presumably because of the increased amount of induced IFN-beta by this mutant. 2011 Virology journal Discussion IV F103L 223 228 21226922 Influenza A virus NS1 gene mutations F103L and M106I increase replication and virulence. The F103L and M106I mutations increased virulence of human and avian NS1 genes. 2011 Virology journal Discussion IV F103L;M106I 4;14 9;19 NS1 69 72 21226922 Influenza A virus NS1 gene mutations F103L and M106I increase replication and virulence. The increased protein synthesis of the F103L NS1 mutant was clearly seen for the M1 and NS1 proteins at all times in MDCK cells whereas the M106I mutation increased protein synthesis at 2 hpi but not at later times, and where the double mutant was not significantly enhanced relative to rPR8-HK-NS-wt (Figure 3). 2011 Virology journal Discussion IV F103L;M106I 39;140 44;145 M1;NS;NS1;NS1 81;295;45;88 83;297;48;91 21226922 Influenza A virus NS1 gene mutations F103L and M106I increase replication and virulence. The NS1 F103L and M106I mutations mediated a large expansion of cell tropism for rWSN-Ck/Bj-NS-103L + 106I where the virus infected a much larger proportion of the lung. 2011 Virology journal Discussion IV F103L;M106I 8;18 13;23 NS;NS1 92;4 94;7 21226922 Influenza A virus NS1 gene mutations F103L and M106I increase replication and virulence. The observation that both the NS1 F103L and M106I mutations were under positive selection and were therefore adaptive mutations was evident by their increased prevalence in mouse adapted populations; where they were found in 3 of 6 and 3 of 3 virus clones in independent mouse-adapted populations (Table 1). 2011 Virology journal Discussion IV F103L;M106I 34;44 39;49 NS1 30 33 21226922 Influenza A virus NS1 gene mutations F103L and M106I increase replication and virulence. Thus the F103L and M106I mutations were not associated with increased IFN-beta induction either in A/HK/156/97(H5N1) virus or for the MA20c and MA51 mouse-adapted viruses in which these mutations were selected, indicating that these mutations were selected in a genetic context that maintains suppression of IFN-beta induction. 2011 Virology journal Discussion IV F103L;M106I 9;19 14;24 21226922 Influenza A virus NS1 gene mutations F103L and M106I increase replication and virulence. Thus there was an enhancement of protein synthesis due to each mutation alone but that this was being suppressed by the increased amounts of IFN-beta that were simultaneously expressed for F103L and M106I in combination, thus indicating the critical role of NS1 in inhibition of IFN-beta induction. 2011 Virology journal Discussion IV F103L;M106I 189;199 194;204 NS1 258 261 21226922 Influenza A virus NS1 gene mutations F103L and M106I increase replication and virulence. We also demonstrated that these mutations were critical for the enhanced virulence of the HK/156/97 and Ck/Bj/95 NS1 genes such that reversion to L103F and I106M resulted in an IAV that was very restricted in its ability to infect lung tissues. 2011 Virology journal Discussion IV L103F;I106M 146;156 151;161 NS1 113 116 21226922 Influenza A virus NS1 gene mutations F103L and M106I increase replication and virulence. We have therefore demonstrated that both F103L and M106I mutations were multifunctional, including loss of ability to suppress IFN-beta in some contexts but also including gain-of-function that increased replicative abilities and virulence. 2011 Virology journal Discussion IV F103L;M106I 41;51 46;56 21249207 Nationwide molecular surveillance of pandemic H1N1 influenza A virus genomes: Canada, 2009. All sampled Canadian viruses encoded the A/H1N1pdm signature S31N (M2) allele that conveys antiviral resistance to Amantadine. 2011 PloS one Discussion IV S31N 61 65 M2 67 69 21249207 Nationwide molecular surveillance of pandemic H1N1 influenza A virus genomes: Canada, 2009. Among the Canadian sampled viruses, we observed elevated diversity in the PB1 segment, encoding RNA polymerase, that can only be partially explained by variants that circulated regionally [e.g., N158S (clade 7 - AB: 14 sequences); V157A (clade 2 - NS: 7 sequences); I181V and I535V (clade 2 - SK: 6 sequences); A587V (clade 2 - NS: 13 sequences)]. 2011 PloS one Discussion IV N158S;V157A;I181V;I535V;A587V 195;231;266;276;311 200;236;271;281;316 NS;NS;PB1 248;328;74 250;330;77 21249207 Nationwide molecular surveillance of pandemic H1N1 influenza A virus genomes: Canada, 2009. And despite the fact that A/H1N1pdm HA D222E/G (and N) variant viruses have been detected in fatal cases, the same mutation also has been detected globally in mild A/H1N1pdm cases; conversely, viruses from numerous fatal cases lack the mutation. 2011 PloS one Discussion IV D222E;D222G 39;39 46;46 HA 36 38 21249207 Nationwide molecular surveillance of pandemic H1N1 influenza A virus genomes: Canada, 2009. For example, HA D222E/G/N (also called 239) and HA Q293H (also called 310) mutant viruses have been isolated worldwide from fatal laboratory-confirmed A/H1N1pdm cases. 2011 PloS one Discussion IV D222E;D222G;D222N;Q293H 16;16;16;51 25;25;25;56 HA;HA 13;48 15;50 21249207 Nationwide molecular surveillance of pandemic H1N1 influenza A virus genomes: Canada, 2009. Genetic variation was highest in the segments encoding HA, NA and NP; however, most observed variation is explained by the fixed clade 2, 5, 6, and 7- defining marker variations (relative to ancestor sequences) in these three genes (up to 5 per virus), namely HA (K-15E [K2E], Q293H [Q310H]), and S203T [S220T]), NA (V106I and N248D), and NP (V100I); (residue positions within square-brackets for HA represent the H1 propeptide numbering scheme). 2011 PloS one Discussion IV K2E;Q293H;Q310H;S203T;S220T;V106I;N248D;V100I 271;277;284;297;304;317;327;343 274;282;289;302;309;322;332;348 HA;HA;HA;NA;NA;NP;NP 55;260;397;59;313;66;339 57;262;399;61;315;68;341 21249207 Nationwide molecular surveillance of pandemic H1N1 influenza A virus genomes: Canada, 2009. The clade 7 marker variation S203T (S220T in H1 propeptide), observed in 81 of the 235 sampled Canadian viruses, is located near the HA monomer-monomer interface. 2011 PloS one Discussion IV S203T;S220T 29;36 34;41 HA 133 135 21249207 Nationwide molecular surveillance of pandemic H1N1 influenza A virus genomes: Canada, 2009. The neuraminidase H275Y (H274Y in N2 numbering) mutation known to confer resistance to oseltamivir (Tamiflu ) and to peramivir, a drug used intravenously under an emergency use authorization, also was detected but only sporadically (n = 5) in 3 distinct clades/regions: namely clade 7 - AB (3); clade 3 - PQ (1) and clade 6 - ON (1). 2011 PloS one Discussion IV H275Y;H274Y 18;25 23;30 4 17 21249207 Nationwide molecular surveillance of pandemic H1N1 influenza A virus genomes: Canada, 2009. This H275Y mutation does not cause resistance to zanamivir (Relenza ). 2011 PloS one Discussion IV H275Y 5 10 21306576 Influenza and other respiratory viruses in three Central American countries. Our previous findings 8 showed that the mutation H274Y conferring resistance to oseltamivir began to be detected in influenza A/H1N1 strains circulating in Central America (Honduras) at the beginning of 2008. 2011 Influenza and other respiratory viruses Discussion IV H274Y 50 55 21349290 Development of a real-time RT-PCR assay for detection of resistance to oseltamivir in influenza A pandemic (H1N1) 2009 virus using single nucleotide polymorphism probes. As there are still some questions as to whether or not this H275Y polymorphism impairs viral fitness and transmission, we must be prepared for the possibility that oseltamivir-resistant isolates of the pandemic (H1N1) 2009 virus could expand in a manner similar to that seen in the previous seasonal H1N1 viruses. 2011 Journal of virological methods Discussion IV H275Y 60 65 21349290 Development of a real-time RT-PCR assay for detection of resistance to oseltamivir in influenza A pandemic (H1N1) 2009 virus using single nucleotide polymorphism probes. Given the concerns about how H275Y SNP assays perform in the context of mixed viral populations and mutations in the probe-binding region, the authors feel that the results of a SNP assay should be interpreted with caution and ambiguous results should be confirmed by sequencing. 2011 Journal of virological methods Discussion IV H275Y 29 34 21349290 Development of a real-time RT-PCR assay for detection of resistance to oseltamivir in influenza A pandemic (H1N1) 2009 virus using single nucleotide polymorphism probes. In conclusion, this manuscript describes the development and validation of a SNP assay for the detection of H275Y mutations associated with oseltamivir resistance in pandemic (H1N1) 2009 virus. 2011 Journal of virological methods Discussion IV H275Y 108 113 21349290 Development of a real-time RT-PCR assay for detection of resistance to oseltamivir in influenza A pandemic (H1N1) 2009 virus using single nucleotide polymorphism probes. Resistance to oseltamivir in seasonal and pandemic influenza A (H1N1) has been linked primarily to an H275Y polymorphism in NA glycoprotein. 2011 Journal of virological methods Discussion IV H275Y 102 107 124 126 Influenza A virus H1N1 infection 51 70 21349290 Development of a real-time RT-PCR assay for detection of resistance to oseltamivir in influenza A pandemic (H1N1) 2009 virus using single nucleotide polymorphism probes. SNP assays may also be unable to detect minor populations in heterogenous mixtures of H275 and H275Y alleles within some specimens. 2011 Journal of virological methods Discussion IV H275Y 95 100 21349290 Development of a real-time RT-PCR assay for detection of resistance to oseltamivir in influenza A pandemic (H1N1) 2009 virus using single nucleotide polymorphism probes. The H275Y amino acid change was first reported in pandemic (H1N1) virus in June 2009 in an immuno-compromised patient treated with oseltamivir, and more cases have since been reported sporadically worldwide. 2011 Journal of virological methods Discussion IV H275Y 4 9 21349290 Development of a real-time RT-PCR assay for detection of resistance to oseltamivir in influenza A pandemic (H1N1) 2009 virus using single nucleotide polymorphism probes. The possible caveats of using SNP probes to detect H275 and H275Y include the presence of mutations in the probe region adjacent to the SNP positions. 2011 Journal of virological methods Discussion IV H275Y 60 65 21349290 Development of a real-time RT-PCR assay for detection of resistance to oseltamivir in influenza A pandemic (H1N1) 2009 virus using single nucleotide polymorphism probes. The strength of this assay is its ability to identify H275Y mutations rapidly without specialized sequencing equipment. 2011 Journal of virological methods Discussion IV H275Y 54 59 21349290 Development of a real-time RT-PCR assay for detection of resistance to oseltamivir in influenza A pandemic (H1N1) 2009 virus using single nucleotide polymorphism probes. This approach has been reported previously for the detection of the C823T mutation in seasonal H1N1 and pandemic (H1N1) 2009 viruses. 2011 Journal of virological methods Discussion IV C823T 68 73 21364825 Identification of sequence mutations affecting hemagglutinin specificity to sialic acid receptor in influenza A virus subtypes. In this study, we have analyzed the sequences of the hemagglutinin protein across influenza A subtypes and identified mutation patterns occurring in positions 190 and 225 (E190 D and G225D) and positions 226 and 228 (Q226L and G228S) respectively, which can cause a change in chemical properties in the protein, ultimately affecting its binding specificity to sialic acid. 2010 Bioinformation Discussion IV E190D;G225D;Q226L;G228S 174;185;220;230 180;190;225;235 HA 53 66 21407805 A single base-pair change in 2009 H1N1 hemagglutinin increases human receptor affinity and leads to efficient airborne viral transmission in ferrets. In the present study we demonstrate that a single Ile219 Lys amino acid change stabilizes the ionic molecular interaction network involving residues 219, 227 and 186 in the RBS of 2009 H1N1 HA that in turn substantially increases its human receptor affinity in comparison with wild-type HA. 2011 PloS one Discussion IV I219K 50 60 HA;HA 190;287 192;289 21407805 A single base-pair change in 2009 H1N1 hemagglutinin increases human receptor affinity and leads to efficient airborne viral transmission in ferrets. Moreover, the Ile219->Lys mutation requires a single nucleotide change, which also increases the probability of such a mutation to occur. 2011 PloS one Discussion IV I219K 14 25 21455300 Assessing the in vitro fitness of an oseltamivir-resistant seasonal A/H1N1 influenza strain using a mathematical model. Specifically, we have found that the latent infection period of the H275Y mutant strain : equal to the time elapsed between the successful infection of a cell by a virion and the significant release of virus progeny by the newly infected cell : is much longer than that of the WT strain (by 4-10 h). 2011 PloS one Discussion IV H275Y 68 73 21455300 Assessing the in vitro fitness of an oseltamivir-resistant seasonal A/H1N1 influenza strain using a mathematical model. These results are consistent with the larger NA activity of the susceptible (WT) strain compared to the H275Y mutant, reported here and by others, and its increased NA surface expression. 2011 PloS one Discussion IV H275Y 104 109 NA;NA 45;165 47;167 21455300 Assessing the in vitro fitness of an oseltamivir-resistant seasonal A/H1N1 influenza strain using a mathematical model. Two substitutions, G189V and L264F, do not involve interaction with the receptor, but the third, A193T, lies within the receptor-binding site. 2011 PloS one Discussion IV G189V;L264F;A193T 19;29;97 24;34;102 21455300 Assessing the in vitro fitness of an oseltamivir-resistant seasonal A/H1N1 influenza strain using a mathematical model. We are currently designing competition experiments for the A/Brisbane/59/2007 WT and H275Y mutant strains in which the predictions which follow from the parameters extracted here can be tested directly. 2011 PloS one Discussion IV H275Y 85 90 21455300 Assessing the in vitro fitness of an oseltamivir-resistant seasonal A/H1N1 influenza strain using a mathematical model. We have recently sequenced the entire genomes of our A/Brisbane/59/2007 strains, and found three amino acid substitutions in the HA gene for the H275Y mutant compared to the WT strain. 2011 PloS one Discussion IV H275Y 145 150 HA 129 131 21504394 Oseltamivir-resistant influenza viruses get by with a little help from permissive mutations. Although it is difficult to directly test, it will be important to try to understand if viruses possessing H274Y were directly selected based on oseltamivir resistance in the human population or whether these viruses were selected based on something else. 2011 Expert review of anti-infective therapy Discussion IV H274Y 107 112 21504394 Oseltamivir-resistant influenza viruses get by with a little help from permissive mutations. An oseltamivir resistance mutation in neuraminidase (NA), H274Y, attenuates older strains of H1N1 influenza A viruses (IAVs) by preventing normal incorporation of NA into virions. 2011 Expert review of anti-infective therapy Discussion IV H274Y 58 63 NA;NA;NA 53;163;38 55;165;51 21504394 Oseltamivir-resistant influenza viruses get by with a little help from permissive mutations. Compensatory NA mutations arising in response to HA antigenic mutations can be located at NA residue 274, supporting the hypothesis that H274Y may have arisen due to selective pressures unrelated to oseltamivir usage. 2011 Expert review of anti-infective therapy Discussion IV H274Y 137 142 HA;NA;NA 49;13;90 51;15;92 21504394 Oseltamivir-resistant influenza viruses get by with a little help from permissive mutations. First, these studies show that the biochemical basis of H274Y attenuation in earlier H1N1 strains is at the level of NA surface expression rather than enzymatic activity. 2011 Expert review of anti-infective therapy Discussion IV H274Y 56 61 117 119 21504394 Oseltamivir-resistant influenza viruses get by with a little help from permissive mutations. More recent strains of H1N1 IAVs possessing H274Y are not attenuated and normal amounts of NA are incorporated in these virions. 2011 Expert review of anti-infective therapy Discussion IV H274Y 44 49 91 93 21504394 Oseltamivir-resistant influenza viruses get by with a little help from permissive mutations. Permissive mutations in more recent strains of H1N1 IAVs allow for toleration of H274Y. 2011 Expert review of anti-infective therapy Discussion IV H274Y 81 86 21504394 Oseltamivir-resistant influenza viruses get by with a little help from permissive mutations. Recent studies have shown that HA antigenic mutations can promote the generation of NA mutations and it will be important to determine if an interplay between HA and NA was involved during the emergence of V234M and R222Q in H1N1 IAVs as they circulated in humans in the 2000s. 2011 Expert review of anti-infective therapy Discussion IV V234M;R222Q 206;216 211;221 HA;HA;NA;NA 31;159;84;166 33;161;86;168 21504394 Oseltamivir-resistant influenza viruses get by with a little help from permissive mutations. study, initial H274Y circulation did not correlate with oseltamivir usage, however, it is difficult to definitively assign geographic locations with distinct selective pressures. 2011 Expert review of anti-infective therapy Discussion IV H274Y 15 20 21504394 Oseltamivir-resistant influenza viruses get by with a little help from permissive mutations. study, the V234M and R222Q NA permissive mutations were found to increase NA cell surface expression of infected cells when expressed in the absence of H274Y. 2011 Expert review of anti-infective therapy Discussion IV V234M;R222Q;H274Y 11;21;152 16;26;157 NA;NA 27;74 29;76 21504394 Oseltamivir-resistant influenza viruses get by with a little help from permissive mutations. This may explain, in part, why it has been difficult to elucidate the mechanisms by which modern seasonal H1N1 viruses are able to tolerate H274Y. 2011 Expert review of anti-infective therapy Discussion IV H274Y 140 145 21504394 Oseltamivir-resistant influenza viruses get by with a little help from permissive mutations. When introduced into older H1N1 IAVs, these permissive mutations rescue the negative effects of H274Y. 2011 Expert review of anti-infective therapy Discussion IV H274Y 96 101 21555520 Biophysical analysis of influenza A virus RNA promoter at physiological temperatures. Indeed, both the nonfunctional G3U and functional G3U/C8A 3' sequences interacted with the 5'-vRNA sequence with similar rates. 2011 The Journal of biological chemistry Discussion IV C8A 54 57 21572517 Mutation analysis of 2009 pandemic influenza A(H1N1) viruses collected in Japan during the peak phase of the pandemic. Among these NA substitutions, a His-to-Tyr (H274Y) substitution at position 274 is one of the best characterized oseltamivir-resistance markers. 2011 PloS one Discussion IV H274Y 44 49 12 14 21572517 Mutation analysis of 2009 pandemic influenza A(H1N1) viruses collected in Japan during the peak phase of the pandemic. As compared with the notable effect of the NA-H275Y mutation, the substitution of N248 to D248 in our model caused little conformational change in the side chain of E277 (Figure 5B), which is consistent with hitherto available clinical data. 2011 PloS one Discussion IV H275Y 46 51 43 45 21572517 Mutation analysis of 2009 pandemic influenza A(H1N1) viruses collected in Japan during the peak phase of the pandemic. have suggested that NA-N248D may be associated with oseltamivir resistance, since N248 is located closely to H275 (N1 numbering). 2011 PloS one Discussion IV N248D;N248D 24;23 29;28 20 22 21572517 Mutation analysis of 2009 pandemic influenza A(H1N1) viruses collected in Japan during the peak phase of the pandemic. In this study, phylogenic analysis has revealed that HA-S220T and NA-N248D are the major non-synonymous mutations that clearly discriminate between the 2009 pdm influenza viruses identified in samples "I" and those found in samples "II" collected in Japan (Figure 2). 2011 PloS one Discussion IV S220T;N248D 56;69 61;74 HA;NA 53;66 55;68 21572517 Mutation analysis of 2009 pandemic influenza A(H1N1) viruses collected in Japan during the peak phase of the pandemic. In this study, sequence analysis has revealed that, among a variety of mutations, the HA-S220T and NA-N248D mutations are specific for the dominant variant(s) of the 2009 pdm influenza A(H1N1) viruses. 2011 PloS one Discussion IV S220T;N248D 89;102 94;107 HA;NA 86;99 88;101 21572517 Mutation analysis of 2009 pandemic influenza A(H1N1) viruses collected in Japan during the peak phase of the pandemic. In this study, three patients were identified as being infected with oseltamivir-resistant mutant variants (two with NA-H275Y and one with NA-N295S) (Figure 2). 2011 PloS one Discussion IV H275Y;N295S 120;142 125;147 NA;NA 117;139 119;141 21572517 Mutation analysis of 2009 pandemic influenza A(H1N1) viruses collected in Japan during the peak phase of the pandemic. Instead, a D239E mutation was found in three samples (Table 2). 2011 PloS one Discussion IV D239E 11 16 21572517 Mutation analysis of 2009 pandemic influenza A(H1N1) viruses collected in Japan during the peak phase of the pandemic. Mutations of D239G/N (in H1 numbering) have reportedly been associated with severe cases. 2011 PloS one Discussion IV D239G;D239N 13;13 20;20 21572517 Mutation analysis of 2009 pandemic influenza A(H1N1) viruses collected in Japan during the peak phase of the pandemic. Sequence analyses of these two clinical isolates identified HA-A156T and HA-D185N, which are both located in the Ca antigenic site. 2011 PloS one Discussion IV A156T;D185N 63;76 68;81 HA;HA 60;73 62;75 21572517 Mutation analysis of 2009 pandemic influenza A(H1N1) viruses collected in Japan during the peak phase of the pandemic. The above-mentioned mutation, HA-S220T, is located in the Ca antigenic site. 2011 PloS one Discussion IV S220T 33 38 HA 30 32 21572517 Mutation analysis of 2009 pandemic influenza A(H1N1) viruses collected in Japan during the peak phase of the pandemic. The models based on the crystal structure of H1 hemagglutinin from the 2009 pdm H1N1 virus (PDB entry: 3LZG) demonstrate that the amino acid substitutions of A156T and D185N are not located in the receptor-binding site, but rather in the Ca antigenic site (Figure 5A). 2011 PloS one Discussion IV A156T;D185N 158;168 163;173 HA 48 61 21572517 Mutation analysis of 2009 pandemic influenza A(H1N1) viruses collected in Japan during the peak phase of the pandemic. The NA-H275Y mutation is known to cause oseltamivir resistance mainly because of its ability to reposition the carboxy side chains of E277, a critical residue for hydrogen bond formation with the drug molecule. 2011 PloS one Discussion IV H275Y 7 12 4 6 21572517 Mutation analysis of 2009 pandemic influenza A(H1N1) viruses collected in Japan during the peak phase of the pandemic. The NA-H275Y substitution was detected in sporadic cases of oseltamivir-treated and -untreated patients infected with 2009 pdm A(H1N1) viruses. 2011 PloS one Discussion IV H275Y 7 12 4 6 21572517 Mutation analysis of 2009 pandemic influenza A(H1N1) viruses collected in Japan during the peak phase of the pandemic. Thus, we examined the potential effect of the NA-N248D (Figure 5B) by utilizing the crystal structure of the H5N1 neuraminidase (PDB entry: 2HU4) as a structural template. 2011 PloS one Discussion IV N248D 49 54 NA;NA 46;114 48;127 21935413 Genetic structure of human A/H1N1 and A/H3N2 influenza virus on Corsica Island: phylogenetic analysis and vaccine strain match, 2006-2010. All Corsican A/H1N1pdm strains analyzed were characterized by the S203T mutation specific to clade 7 isolates. 2011 PloS one Discussion IV S203T 66 71 21935413 Genetic structure of human A/H1N1 and A/H3N2 influenza virus on Corsica Island: phylogenetic analysis and vaccine strain match, 2006-2010. Few mutations in the A/H1N1 seasonal isolates during the 2007-2008 season that differentiate them from the A/SalomonIslands/3/2006 (S125N at antigenic site B) and A/Brisbane/59/2007-like (S189D fixed at antigenic site B) lineages were located at the antigenic sites (Table 2). 2011 PloS one Discussion IV S125N;S189D 132;188 137;193 21935413 Genetic structure of human A/H1N1 and A/H3N2 influenza virus on Corsica Island: phylogenetic analysis and vaccine strain match, 2006-2010. Key residues in the RBD predicted to have a role in binding to human receptors (T98Y, S136T, 153W and 183H) were found to be Y98, S136, W153 and H183 in the Corsican isolates as in other A/H1N1pdm viruses isolated elsewhere. 2011 PloS one Discussion IV T98Y;S136T 80;86 84;91 21935413 Genetic structure of human A/H1N1 and A/H3N2 influenza virus on Corsica Island: phylogenetic analysis and vaccine strain match, 2006-2010. Overrepresentation of certain mutations among geographically and temporally related samples needs to be carefully controlled for possible founder effects which could be identified as homogenous clusters in phylogenetic analyses, as was observed to be the case for the D222E mutation. 2011 PloS one Discussion IV D222E 268 273 21935413 Genetic structure of human A/H1N1 and A/H3N2 influenza virus on Corsica Island: phylogenetic analysis and vaccine strain match, 2006-2010. Phylogenetic analysis of A/H1N1pdm influenza viruses showed that viruses isolated in Corsica Island formed a separate sub-clade of clade 7 as a consequence of the presence of the D222E substitution. 2011 PloS one Discussion IV D222E 179 184 21935413 Genetic structure of human A/H1N1 and A/H3N2 influenza virus on Corsica Island: phylogenetic analysis and vaccine strain match, 2006-2010. Recently, a cluster of D222E viruses among school children was isolated in Italy, confirming human-to-human transmission of viruses mutated at amino acid position 222. 2011 PloS one Discussion IV D222E 23 28 21935413 Genetic structure of human A/H1N1 and A/H3N2 influenza virus on Corsica Island: phylogenetic analysis and vaccine strain match, 2006-2010. The clade 7 marker variation S203T, observed in all sampled Corsican viruses, is a A/H1N1pdm virus site under positive selection and also involved in antigenicity. 2011 PloS one Discussion IV S203T 29 34 21935413 Genetic structure of human A/H1N1 and A/H3N2 influenza virus on Corsica Island: phylogenetic analysis and vaccine strain match, 2006-2010. The D222G mutation was not observed among A/H1N1pdm isolated on Corsica Island. 2011 PloS one Discussion IV D222G 4 9 21935413 Genetic structure of human A/H1N1 and A/H3N2 influenza virus on Corsica Island: phylogenetic analysis and vaccine strain match, 2006-2010. These strains, which were characterized by two fixed mutations located at site E (K264E and K265E) compared to the vaccine strain A/Brisbane/10/2007, were closely related to the A/Brisbane/10/2007-like lineage (vaccine strain for the 2008-2009 season in the Northern Hemisphere). 2011 PloS one Discussion IV K264E;K265E 82;92 87;97 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. A previous study found that the D222G mutation on the CA/04 background conferred greater morbidity, mortality, and heightened virus replication in the lungs of mice compared with a wild-type virus, which is in agreement with our results. 2011 PloS one Discussion IV D222G 32 37 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. Along with these previously published studies, our data suggests that the presence of D222G can enhance viral replication in some cell types, but this contribution is modest and is only apparent at later stages of infection. 2011 PloS one Discussion IV D222G 86 91 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. Although a single base-pair change (leading to the I216K mutation) in CA/04 HA can lead to efficient transmission in ferrets, we found that the D222G mutation did not appear to significantly enhance or diminish transmission (4 of 6 naive contact ferrets had detectable virus in nasal washes) of the 2009 H1N1 virus. 2011 PloS one Discussion IV I216K;D222G 51;144 56;149 HA 76 78 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. An additional study performed a similar assessment of virulence with this mutation, but the use of a parental strain which is lethal for mice may have masked subtle differences conferred by the D222G mutation. 2011 PloS one Discussion IV D222G 194 199 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. but higher D222G virus titers in this tissue at day 6 p.i. 2011 PloS one Discussion IV D222G 11 16 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. Compared with wild-type virus, a D222G-bearing virus replicated to higher titers in human alveolar basal epithelial A549 cells, although generally similar kinetics between D222G and wild-type viruses were observed in the human placental cell line JEG-3 and MDCK cells. 2011 PloS one Discussion IV D222G;D222G 33;172 38;177 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. Extrapulmonary spread of virus to the intestinal tract was detected following infection with both CA/04 and D222G viruses, a feature shared by numerous wild-type 2009 H1N1 viruses. 2011 PloS one Discussion IV D222G 108 113 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. However, D222G virus failed to spread to other tissues following infection in either mice or ferrets. 2011 PloS one Discussion IV D222G 9 14 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. However, differences in receptor binding specificity between CA/04 and D222G did not preclude efficient replication of both viruses in ferret nasal wash samples. 2011 PloS one Discussion IV D222G 71 76 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. However, the enhanced ability of D222G virus to bind to alpha2-3 linked sialic acids did not confer the ability to replicate efficiently in respiratory endothelial cells. 2011 PloS one Discussion IV D222G 33 38 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. However, these viruses are capable of acquiring a lethal phenotype in mice following acquisition of key mutations, one of which is D222G. 2011 PloS one Discussion IV D222G 131 136 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. In addition, subtle differences in viruses, experimental conditions and other factors may result in somewhat different results from different laboratories; nevertheless, the association of the D222G mutation with more severe human infections highlights the need to continue research in this area. 2011 PloS one Discussion IV D222G 193 198 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. in Calu-3 cells, in agreement with a previous study using MDCK cells which also noted reduced viral titers with a virus bearing this mutation at this time p.i.; however, significantly higher titers of D222G virus compared with wild-type virus were detected in Calu-3 cells at 48 and 72 hrs p.i. 2011 PloS one Discussion IV D222G 201 206 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. In fact, molecular epidemiologic studies revealed that the majority of 2009 H1N1 viruses circulating during the pandemic did not bear the D222G mutation, further suggesting that this mutation is not a determinant of virus transmissibility. 2011 PloS one Discussion IV D222G 138 143 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. In the ferret model, the D222G mutation on the CA/04 background did not confer enhanced virulence, in accordance with previous results. 2011 PloS one Discussion IV D222G 25 30 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. In the present study, the presence of D222G did not confer the ability of this virus to infect mice by the ocular route or the ability to replicate more efficiently compared with wild-type CA/04 virus in human corneal epithelial cells. 2011 PloS one Discussion IV D222G 38 43 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. Interestingly, similar viral replication kinetics were observed in our murine model, with comparable titers between CA/04 and D222G viruses in the lungs of mice on day 3 p.i. 2011 PloS one Discussion IV D222G 126 131 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. Nonetheless, the lack of productive replication of D222G virus in human ocular cells indicates that the enhanced cell tropism present with this virus, observed in the ability to bind both ciliated and non-ciliated cells in HTBE cell cultures, does not translate to all cell types. 2011 PloS one Discussion IV D222G 51 56 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. Previous studies have investigated the effect of D222G HA mutation on glycan-binding using binding assays such as red blood cell agglutination and binding to glycan arrays at saturating viral titers. 2011 PloS one Discussion IV D222G 49 54 HA 55 57 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. The consequence of the D222G mutation on viral replication kinetics has been assessed previously in several relevant cell lines. 2011 PloS one Discussion IV D222G 23 28 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. The detection of D222G among severe and fatal cases of human infection has resulted in analyses to determine if this mutation represents the first virulence marker associated with 2009 H1N1 pandemic viruses. 2011 PloS one Discussion IV D222G 17 22 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. The detection of macroscopic ocular symptoms in mice infected with a virus bearing the D222G mutation in a previous study may be due to strain-specific differences between parental viruses used or laboratory-specific conditions, but does not appear to be a universal property of 2009 H1N1 viruses possessing this mutation. 2011 PloS one Discussion IV D222G 87 92 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. The enhanced replication and morbidity in mice, but not ferrets following D222G virus infection, is consistent with augmented binding to alpha2-3 sialylated glycans and the known predominance of alpha2-3 sialic acids in the mouse model. 2011 PloS one Discussion IV D222G 74 79 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. The enhanced transmission observed with the HA (Ile219 Lys) may be due, at least in part, to its increased human receptor-(alpha2-6) binding affinity (particularly to the 6'SLN-LN glycan) by several-fold in comparison with wild-type. 2011 PloS one Discussion IV I219K 48 58 HA 44 46 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. The inability of D222G virus to confer efficient respiratory droplet transmission may be related to the findings that this particular HA mutation does not substantially improve alpha2-6 binding avidity of the virus. 2011 PloS one Discussion IV D222G 17 22 HA 134 136 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. The relatively rapid emergence of D222G during serial passage in mice, cells, or eggs indicates the ability of 2009 H1N1 viruses to acquire this mutation under the right conditions, and the lack of reversion observed in this study suggests that this mutation is stably maintained. 2011 PloS one Discussion IV D222G 34 39 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. This work underscores the importance of studying the contribution of virulence markers such as D222G on parental strains that do not themselves possess heightened virulence to avoid masking subtle differences which, while minor, nonetheless result in a detectable increase in virus pathogenicity in mammals. 2011 PloS one Discussion IV D222G 95 100 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. Thus, results in the ferret model have not supported a role of D222G in enhancing 2009 H1N1 virus virulence. 2011 PloS one Discussion IV D222G 63 68 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. We demonstrate that a single D222G amino acid change augments binding to alpha2-3 linked sialic acids and results in higher overall titers of infectious virus in human airway cells and mouse lungs compared with wild-type virus. 2011 PloS one Discussion IV D222G 29 34 21966421 Effect of D222G mutation in the hemagglutinin protein on receptor binding, pathogenesis and transmissibility of the 2009 pandemic H1N1 influenza virus. We observed lower viral titers of D222G virus compared with CA/04 virus 24 hrs p.i. 2011 PloS one Discussion IV D222G 34 39 21980293 Multidrug resistant 2009 A/H1N1 influenza clinical isolate with a neuraminidase I223R mutation retains its virulence and transmissibility in ferrets. A I223V/H275Y double mutant was detected in two closely residing patients who were treated with OS. 2011 PLoS pathogens Discussion IV I223V;H275Y 2;8 7;13 21980293 Multidrug resistant 2009 A/H1N1 influenza clinical isolate with a neuraminidase I223R mutation retains its virulence and transmissibility in ferrets. Although these results suggest that introduction of the I223R does not attenuate the virus, it cannot be ruled out that other mutations than 223R in NL/2631-R223 may have compensated for the initial loss of fitness due to the I223R mutation. 2011 PLoS pathogens Discussion IV I223R;I223R 56;226 61;231 21980293 Multidrug resistant 2009 A/H1N1 influenza clinical isolate with a neuraminidase I223R mutation retains its virulence and transmissibility in ferrets. Besides the I223R single mutant virus studied here, an I223R/H275Y double mutant was detected in an immune suppressed patient treated with OS and ZA. 2011 PLoS pathogens Discussion IV I223R;I223R;H275Y 12;55;61 17;60;66 21980293 Multidrug resistant 2009 A/H1N1 influenza clinical isolate with a neuraminidase I223R mutation retains its virulence and transmissibility in ferrets. Further research is needed to study the I223R resistance mechanism in competitive mixture experiments and potential co-mutations on a molecular level. 2011 PLoS pathogens Discussion IV I223R 40 45 21980293 Multidrug resistant 2009 A/H1N1 influenza clinical isolate with a neuraminidase I223R mutation retains its virulence and transmissibility in ferrets. Furthermore, it was demonstrated here that compensatory mutations for the I223R mutation are not required, since recombinant NL/602 with a single I223R change transmitted as efficiently as its parental virus in ferrets. 2011 PLoS pathogens Discussion IV I223R;I223R 74;146 79;151 21980293 Multidrug resistant 2009 A/H1N1 influenza clinical isolate with a neuraminidase I223R mutation retains its virulence and transmissibility in ferrets. Here, a 2009 pandemic influenza A/H1N1 virus isolate, harboring an I223R multidrug resistance mutation, was characterized by studying its replication capacity in MDCK cells and its pathogenicity and transmissibility in the ferret model. 2011 PLoS pathogens Discussion IV I223R 67 72 21980293 Multidrug resistant 2009 A/H1N1 influenza clinical isolate with a neuraminidase I223R mutation retains its virulence and transmissibility in ferrets. However, when recNL/602-I223R was tested in the ferret transmission model, the virus transmitted to 2 out of 2 exposed animals (Figure 5B). 2011 PLoS pathogens Discussion IV I223R 24 29 21980293 Multidrug resistant 2009 A/H1N1 influenza clinical isolate with a neuraminidase I223R mutation retains its virulence and transmissibility in ferrets. In addition, the initial virus replication of NL/602-I223R on MDCK-SIAT1 cells started 6 to 12 hours later as compared to its parental virus (Figure 1B). 2011 PLoS pathogens Discussion IV I223R 53 58 21980293 Multidrug resistant 2009 A/H1N1 influenza clinical isolate with a neuraminidase I223R mutation retains its virulence and transmissibility in ferrets. In combination with the H275Y change, these viruses demonstrated resistance patterns similar to the I223R/H275Y mutant. 2011 PLoS pathogens Discussion IV H275Y;H275Y;I223R 24;106;100 29;111;105 21980293 Multidrug resistant 2009 A/H1N1 influenza clinical isolate with a neuraminidase I223R mutation retains its virulence and transmissibility in ferrets. Interestingly, neighboring residue 247 has been linked to NAI resistance in combination with the H275Y mutation. 2011 PLoS pathogens Discussion IV H275Y 97 102 NAI 58 61 21980293 Multidrug resistant 2009 A/H1N1 influenza clinical isolate with a neuraminidase I223R mutation retains its virulence and transmissibility in ferrets. Notably, 2009 pandemic viruses were reported with a serine to asparagine change at position 247. 2011 PLoS pathogens Discussion IV S247N 52 95 21980293 Multidrug resistant 2009 A/H1N1 influenza clinical isolate with a neuraminidase I223R mutation retains its virulence and transmissibility in ferrets. The virus secretion pattern, which is the combination of the amount of virus secreted and the duration of virus shedding from the upper respiratory tract, of animals exposed to recNL/602 and rec/NL602-I223R are similar. 2011 PLoS pathogens Discussion IV I223R 201 206 21980293 Multidrug resistant 2009 A/H1N1 influenza clinical isolate with a neuraminidase I223R mutation retains its virulence and transmissibility in ferrets. These results suggested that compensatory mutations may be required to accommodate the isoleucine to arginine substitution at position 223 in NA and emphasizes the importance of the viral backbone used to study resistance-associated mutations. 2011 PLoS pathogens Discussion IV I223R 87 138 142 144 21980293 Multidrug resistant 2009 A/H1N1 influenza clinical isolate with a neuraminidase I223R mutation retains its virulence and transmissibility in ferrets. This I223R mutant virus is not attenuated for replication in the ferret respiratory tract and transmitted as well as NAI susceptible reference virus NL/602. 2011 PLoS pathogens Discussion IV I223R 5 10 NAI 117 120 21980293 Multidrug resistant 2009 A/H1N1 influenza clinical isolate with a neuraminidase I223R mutation retains its virulence and transmissibility in ferrets. This observation demonstrates that the transmissibility of recNL/602-I223R is not significantly diminished or can at least not be studied using a ferret transmission model. 2011 PLoS pathogens Discussion IV I223R 69 74 21980293 Multidrug resistant 2009 A/H1N1 influenza clinical isolate with a neuraminidase I223R mutation retains its virulence and transmissibility in ferrets. This suggests that no marked differences in viral fitness are introduced by the single I223R mutation. 2011 PLoS pathogens Discussion IV I223R 87 92 21980293 Multidrug resistant 2009 A/H1N1 influenza clinical isolate with a neuraminidase I223R mutation retains its virulence and transmissibility in ferrets. When the impact of the single I223R mutation in the recombinant NL/602 backbone on in vitro replication kinetics was evaluated, a reduction in virus replication in MDCK cells was noticed (Figure 1). 2011 PLoS pathogens Discussion IV I223R 30 35 22022458 Minor changes in the hemagglutinin of influenza A(H1N1)2009 virus alter its antigenic properties. An interesting observation in the present study was that three out of four 2010-2011 season viruses had an E374K mutation in the HA2 region (A/Finland/19/2010, A/Finland/20/10, and A/Finland/22/10). 2011 PloS one Discussion IV E374K 107 112 HA 129 131 22022458 Minor changes in the hemagglutinin of influenza A(H1N1)2009 virus alter its antigenic properties. Barr and coworkers also reported that viruses carrying the N125D and E374K mutations were found in vaccine breakthrough cases in teenagers and adults, who had been vaccinated with the monovalent pandemic influenza A(H1N1)2009 vaccine and the same mutant viruses were also found in a number of fatal cases. 2011 PloS one Discussion IV N125D;E374K 59;69 64;74 22022458 Minor changes in the hemagglutinin of influenza A(H1N1)2009 virus alter its antigenic properties. However, our results showed that only one amino acid change in the antigenic site Sa (N125D) compromised antibody recognition, which could be seen as reduced antibody titers in the HI test. 2011 PloS one Discussion IV N125D 86 91 22022458 Minor changes in the hemagglutinin of influenza A(H1N1)2009 virus alter its antigenic properties. If there was another amino acid change (N156K) in the Sa epitope, as was the case in the A/Finland/694/2009 virus (Figure 2 and Figure S2), the antibody titers were even lower. 2011 PloS one Discussion IV N156K 40 45 22022458 Minor changes in the hemagglutinin of influenza A(H1N1)2009 virus alter its antigenic properties. In addition, post-vaccination anti sera showed reduced recognition of epidemic season 2010-2011 viruses A/Finland/19/2010 and A/Finland/22/2010, which showed point mutations in antigenic sites Sa (N125D) and Ca1 (S203T). 2011 PloS one Discussion IV N125D;S203T 197;213 202;218 22022458 Minor changes in the hemagglutinin of influenza A(H1N1)2009 virus alter its antigenic properties. Viruses isolated later during the epidemic, such as the strains A/Finland/694/2009 (changes at positions N125D, N156K and S203T), A/Finland/618/2009 (changes at positions S162R and S203T) and A/Finland/698/2009 (changes at positions S74N and S203T), which showed dual or triple mutations in antigenic sites (Figure 2 and S2) showed impaired recognition by patient convalescent sera. 2011 PloS one Discussion IV N125D;N156K;S203T;S162R;S203T;S74N;S203T 105;112;122;171;181;233;242 110;117;127;176;186;237;247 22138712 The 2008-2009 H1N1 influenza virus exhibits reduced susceptibility to antibody inhibition: Implications for the prevalence of oseltamivir resistant variant viruses. Another study found that permissive mutations at V234M and R222Q, outside of the active enzyme site, significantly increase the amount of NA protein that reaches the cell surface, while the activity per enzyme molecule is either unaffected or slightly decreased. 2012 Antiviral research Discussion IV V234M;R222Q 49;59 54;64 138 140 22138712 The 2008-2009 H1N1 influenza virus exhibits reduced susceptibility to antibody inhibition: Implications for the prevalence of oseltamivir resistant variant viruses. Assessment of the fitness of resistant strains in animal models suggests that the H275Y variant of pandemic 2009 H1N1 virus may not be less transmissible or virulent than wild type. 2012 Antiviral research Discussion IV H275Y 82 87 22138712 The 2008-2009 H1N1 influenza virus exhibits reduced susceptibility to antibody inhibition: Implications for the prevalence of oseltamivir resistant variant viruses. Consistent with this observation, the D344N substitution is present in all of the oseltamivir resistant isolates included in this study (Supplementary Table 1). 2012 Antiviral research Discussion IV D344N 38 43 22138712 The 2008-2009 H1N1 influenza virus exhibits reduced susceptibility to antibody inhibition: Implications for the prevalence of oseltamivir resistant variant viruses. Examination of the HA gene also revealed exclusive association of the A189T substitution with oseltamivir resistant (H275Y) 2008-2009 H1N1 viruses, as well as variations at positions 141, 185 and 186 in some resistant variants. 2012 Antiviral research Discussion IV A189T;H275Y 70;117 75;122 HA 19 21 22138712 The 2008-2009 H1N1 influenza virus exhibits reduced susceptibility to antibody inhibition: Implications for the prevalence of oseltamivir resistant variant viruses. It appears the H275Y substitution alone is insufficient to account for the altered immunogenic properties of 2008-2009 oseltamivir resistant H1N1 viruses. 2012 Antiviral research Discussion IV H275Y 15 20 22138712 The 2008-2009 H1N1 influenza virus exhibits reduced susceptibility to antibody inhibition: Implications for the prevalence of oseltamivir resistant variant viruses. It is likely that the adaptive changes that allow H275Y variation in the NA of the pandemic H1N1 virus may be different to those which occur in the 2008-2009 H1N1 viruses. 2012 Antiviral research Discussion IV H275Y 50 55 73 75 22138712 The 2008-2009 H1N1 influenza virus exhibits reduced susceptibility to antibody inhibition: Implications for the prevalence of oseltamivir resistant variant viruses. It is notable that all oseltamivir resistant strains of seasonal H1N1 virus examined in this study also contain a D354G substitution in the NA gene that is not seen in any of the susceptible isolates (Supplementary Table 1). 2012 Antiviral research Discussion IV D354G 114 119 140 142 22138712 The 2008-2009 H1N1 influenza virus exhibits reduced susceptibility to antibody inhibition: Implications for the prevalence of oseltamivir resistant variant viruses. It remains to be investigated whether these H275Y-coupled mutations in the NA protein provide the capacity to re-balance HA and NA functions, restoring the H275Y mutation-associated defects in protein folding, substrate interaction, and transport of NA, and possibly reinstating fitness of the virus. 2012 Antiviral research Discussion IV H275Y;H275Y 44;156 49;161 HA;NA;NA;NA 121;75;128;250 123;77;130;252 22138712 The 2008-2009 H1N1 influenza virus exhibits reduced susceptibility to antibody inhibition: Implications for the prevalence of oseltamivir resistant variant viruses. Our data using recombinant viruses varying only by the H275Y substitution suggests that molecular changes caused by H275Y substitution in the NA of the 2008-2009 oseltamivir resistant H1N1 virus can cause reduced reactivity to antibodies raised against the susceptible H1N1 strain in the in vitro HI assay (Figure 4 and Table 6). 2012 Antiviral research Discussion IV H275Y;H275Y 55;116 60;121 142 144 22138712 The 2008-2009 H1N1 influenza virus exhibits reduced susceptibility to antibody inhibition: Implications for the prevalence of oseltamivir resistant variant viruses. Sequence and structural analyses found that the H275Y resistant strains are predominantly clade 2B lineage H1N1 viruses which carry an additional NA substitution, D344N. 2012 Antiviral research Discussion IV H275Y;D344N 48;163 53;168 146 148 22138712 The 2008-2009 H1N1 influenza virus exhibits reduced susceptibility to antibody inhibition: Implications for the prevalence of oseltamivir resistant variant viruses. The D354G substitution is also observed in some other clade 2B H1N1 viruses, however, there is no known structural basis to support this mutation having a major impact on the enzymatic characteristics of NA. 2012 Antiviral research Discussion IV D354G 4 9 204 206 22138712 The 2008-2009 H1N1 influenza virus exhibits reduced susceptibility to antibody inhibition: Implications for the prevalence of oseltamivir resistant variant viruses. The rapid rise to prevalence of the naturally occurring H275Y resistant of the H1N1 virus since its emergence in late 2007 suggested a possible adaptation mechanism involving restoration of fitness and/or gain of an epidemic advantage. 2012 Antiviral research Discussion IV H275Y 56 61 22138712 The 2008-2009 H1N1 influenza virus exhibits reduced susceptibility to antibody inhibition: Implications for the prevalence of oseltamivir resistant variant viruses. We found that antisera obtained from vaccine immunized or naturally infected people, and monoclonal antibodies raised against HA of vaccine strains reacted less strongly with H275Y resistant strains of seasonal 2008-2009 H1N1 viruses. 2012 Antiviral research Discussion IV H275Y 175 180 HA 126 128 22138712 The 2008-2009 H1N1 influenza virus exhibits reduced susceptibility to antibody inhibition: Implications for the prevalence of oseltamivir resistant variant viruses. While resistant variants of the 2009 H1N1 virus carrying the H275Y substitution have been detected, current circulating strains remain mostly susceptible to oseltamivir. 2012 Antiviral research Discussion IV H275Y 61 66 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. Alternatively, the Q222R mutation could affect airborne transmission which has not been evaluated in our study. 2011 PLoS pathogens Discussion IV Q222R 19 24 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. Although clinical 2009 pandemic H1N1 variants containing such permissive mutations have not been reported, a computational approach had recently led to the identification of R257K and T289M as potential secondary mutations in that context. 2011 PLoS pathogens Discussion IV R257K;T289M 174;184 179;189 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. As a result, the H275Y/Q222R mutant virus was significantly compromised in vitro based on plaque size and replication kinetics patterns. 2011 PLoS pathogens Discussion IV Q222R;H275Y 23;17 28;22 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. Besides its effect on NA affinity, the Q222R reversion mutation was also associated with a significant decrease in relative NA activity (Table 1 and. 2011 PLoS pathogens Discussion IV Q222R 39 44 NA;NA 22;124 24;126 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. By contrast, the appearance of the R222Q and D344N mutations in H1N1 viruses isolated after 2007 was associated with a significant increase in NA affinity (decreased Km values) in both 275H and 275Y strains. 2011 PLoS pathogens Discussion IV R222Q;D344N 35;45 40;50 143 145 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. Despite the fact that the secondary mutations described here were not investigated individually but in conjunction with H275Y, our study provides a comprehensive analysis of relevant permissive NA mutations in the contemporarily seasonal H1N1 background. 2011 PLoS pathogens Discussion IV H275Y 120 125 194 196 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. For instance, Yang and colleagues recently demonstrated that the dominant H275Y variant that emerged in Taiwan in 2007-2008 was a result of intra-subtypic reassortments between HA, NA, PB2 and PA genes from one clade (clade 2B) and the remaining 4 genes from another one (clade 1). 2011 PLoS pathogens Discussion IV H275Y 74 79 HA;NA;PA;PB2 177;181;193;185 179;183;195;188 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. Furthermore, the H275Y NA substitution and other changes in NA, HA, PB1 and PB2 proteins occurred in that background. 2011 PLoS pathogens Discussion IV H275Y 17 22 HA;NA;NA;PB1;PB2 64;23;60;68;76 66;25;62;71;79 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. However, the H275Y/Q222R mutant was transmitted to all naive ferrets by direct contact meaning that the combination of several permissive NA mutations and/or mutations elsewhere in the viral genome may be necessary to recapitulate the epidemiological observations showing increased transmission of the oseltamivir-resistant Bris07 virus. 2011 PLoS pathogens Discussion IV Q222R;H275Y 19;13 24;18 138 140 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. In accordance with these observations, we demonstrated a sharp impact for the Q222R and N344D reversion mutations on Km values using our Bris07 recombinants (Table 1). 2011 PLoS pathogens Discussion IV Q222R;N344D 78;88 83;93 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. In addition to the R222Q mutation, a permissive role was also suggested for V234M and D344N substitutions. 2011 PLoS pathogens Discussion IV R222Q;V234M;D344N 19;76;86 24;81;91 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. In our study, although the M234V and N344D reversions were associated with decreased relative NA activity and affinity, respectively (Table 1 and. 2011 PLoS pathogens Discussion IV M234V;N344D 27;37 32;42 94 96 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. In this study, we used recombinant viruses derived from a clinical WT Bris07 strain to demonstrate using both in vitro and ferret experiments that the R222Q NA mutation was the main but possibly not the only permissive mutation that allowed the widespread dissemination of the oseltamivir-resistant H275Y mutant during the 2007-09 influenza seasons. 2011 PLoS pathogens Discussion IV R222Q;H275Y 151;299 156;304 157 159 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. Indeed, the recombinant WT virus and its H275Y variant demonstrated similar replication kinetics during in vitro experiments. 2011 PLoS pathogens Discussion IV H275Y 41 46 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. Nevertheless, a possible synergy between these mutations and Q222R cannot be completely excluded. 2011 PLoS pathogens Discussion IV Q222R 61 66 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. Of interest, only one NA substitution (R194G) was sufficient to restore the viral fitness of an influenza A/WSN/33 (H1N1) virus containing the compromising H275Y NA mutation. 2011 PLoS pathogens Discussion IV R194G;H275Y 39;156 44;161 NA;NA 22;162 24;164 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. Of note, possibly due to the lower affinity of Q222R for MUNANA, less NAIs were required for competitive inhibition of the H275Y/Q222R mutant compared to the H275Y mutant. 2011 PLoS pathogens Discussion IV Q222R;Q222R;H275Y;H275Y 47;129;123;158 52;134;128;163 NAI 70 74 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. Our study revealed that the H275Y NA mutation was not deleterious to fitness in the Bris07 genetic context in contrast to older H1N1 strains. 2011 PLoS pathogens Discussion IV H275Y 28 33 34 36 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. Phylogenetic analyses previously demonstrated that the V234M mutation was already present in oseltamivir-susceptible A/Solomon Islands/3/2006 (SI06) viruses. 2011 PLoS pathogens Discussion IV V234M 55 60 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. R222Q) in conjunction with the oseltamivir resistance H275Y mutation on enzymatic properties and viral fitness of the Bris07 H1N1 strain. 2011 PLoS pathogens Discussion IV R222Q;H275Y 0;54 5;59 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. Such decreased viral replication of the H275Y/Q222R mutant was also evident in vivo, resulting in lower viral titers in nasal wash samples and an absence of febrile response in contact ferrets. 2011 PLoS pathogens Discussion IV Q222R;H275Y 46;40 51;45 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. Therefore, we believe that changes in the NA gene alone may not provide a complete explanation for the emergence and spread of the oseltamivir-resistant H275Y Bris07 variant. 2011 PLoS pathogens Discussion IV H275Y 153 158 42 44 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. These changes included the well-known framework H275Y mutation, responsible for the resistance phenotype to oseltamivir and peramivir, as well as other substitutions (V234M, R222Q and D344N) that may have contributed to the emergence and dissemination of resistance by acting as permissive/compensatory mutations. 2011 PLoS pathogens Discussion IV H275Y;V234M;R222Q;D344N 48;167;174;184 53;172;179;189 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. Thus, it would be also interesting to assess the effect of HA and particularly polymerase mutations that differed between WT and H275Y mutant clinical Bris07 isolates on replicative capacities and transmissibility. 2011 PLoS pathogens Discussion IV H275Y 129 134 HA 59 61 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. Thus, the presence of the permissive mutations (R222Q, V234M and D344N) in the NA protein of our WT strain was apparently not sufficient to alter the viral fitness to the level that a compensatory change, such as the H275Y mutation, would be necessary. 2011 PLoS pathogens Discussion IV R222Q;V234M;D344N;H275Y 48;55;65;217 53;60;70;222 79 81 22174688 Role of permissive neuraminidase mutations in influenza A/Brisbane/59/2007-like (H1N1) viruses. Whether the Q222R mutation is also deleterious in the absence of H275Y was not investigated here; however, in a previous work, influenza A/Paris/497/2007 (222Q/275H) and A/Solomon Islands/3/2006 (222R/275H) seasonal H1N1 isolates grew to comparable titers in in vitro kinetics experiments. 2011 PLoS pathogens Discussion IV Q222R;H275Y 12;65 17;70 22194944 Adaption of seasonal H1N1 influenza virus in mice. Analysis of the potential molecular mechanism underlying the high virulence of the adapted viruses revealed that there were three mutations incrementally acquired at passage 2 (T89I), passage 3 (N125T), and passage 6 (D221G). 2011 PloS one Discussion IV T89I;N125T;D221G 177;195;218 181;200;223 22194944 Adaption of seasonal H1N1 influenza virus in mice. However, it is still uncertain whether the increased virulence is caused by the T89I substitution only or the combinations of the three mutations. 2011 PloS one Discussion IV T89I 80 84 22194944 Adaption of seasonal H1N1 influenza virus in mice. The T89I mutation exists in another mouse lung adapted virus from A/USSR/90/77(H1N1), but not in natural strains of the human and animal influenza viruses. 2011 PloS one Discussion IV T89I 4 8 22217077 Surveillance in Eastern India (2007-2009) revealed reassortment event involving NS and PB1-F2 gene segments among co-circulating influenza A subtypes. In addition, these five strains contained G63E substitution in NEP, similar to the highly pathogenic avian influenza H5N1 viruses, which may confer higher pathogenicity. 2012 Virology journal Discussion IV G63E 42 46 NEP 63 66 22230322 Highly pathogenic avian influenza virus H5N1 controls type I IFN induction in chicken macrophage HD-11 cells: a polygenic trait that involves NS1 and the polymerase complex. The fact that the A144V mutation within NS1 of the Yama virus results in strong induction of type I IFN indicates that NS1 functions as an inhibitor of the Yama virus-mediated type I IFN induction. 2012 Virology journal Discussion IV A144V 18 23 NS1;NS1 40;119 43;122 22235288 Acute respiratory distress syndrome induced by a swine 2009 H1N1 variant in mice. It has been shown that 2009 H1N1 virus possessing a D222G mutation in hemagglutinin (HA) could increase the pathogenicity in mice and binding to the alpha-2,3 SA receptor. 2012 PloS one Discussion IV D222G 52 57 HA;HA 85;70 87;83 22235288 Acute respiratory distress syndrome induced by a swine 2009 H1N1 variant in mice. Notably, the swine isolate, SD/09, had a D222G mutation in HA. 2012 PloS one Discussion IV D222G 41 46 HA 59 61 22235288 Acute respiratory distress syndrome induced by a swine 2009 H1N1 variant in mice. Therefore, we suggest that the variant possessing the D222G mutation in HA can induce ARDS in a mouse model. 2012 PloS one Discussion IV D222G 54 59 HA 72 74 Acute respiratory distress syndrome 86 90 22238617 Mutational analyses of the influenza A virus polymerase subunit PA reveal distinct functions related and unrelated to RNA polymerase activity. Our previous discovery of a novel, lethal phenotype for mutant J10 (G507A-R508A) in the C-terminal half of PA raised the possibility that PA protein plays another essential role in influenza biology that is unrelated to viral RNA synthesis. 2012 PloS one Discussion IV G507A;R508A 68;74 73;79 PA;PA 107;138 109;140 22238617 Mutational analyses of the influenza A virus polymerase subunit PA reveal distinct functions related and unrelated to RNA polymerase activity. The L6 mutant (S509A, H510A), by contrast, localizes normally but profoundly impairs viral RNA synthesis, suggesting an effect on polymerase activity per se. 2012 PloS one Discussion IV H510A;S509A 22;15 27;20 22252168 Susceptibility of avian influenza viruses of the N6 subtype to the neuraminidase inhibitor oseltamivir. Among 5490 avian NA sequences from the NCBI database and from a European bird observatory, 6 of 55 influenza viruses analyzed of the N6 NA subtype (10.91%) had the NA catalytic residue change R152K, and 2 viruses (4%) had the I222V NA framework mutation. 2012 Antiviral research Discussion IV R152K;I222V 192;226 197;231 NA;NA;NA;NA 17;136;164;232 19;138;166;234 22252168 Susceptibility of avian influenza viruses of the N6 subtype to the neuraminidase inhibitor oseltamivir. Interestingly, substitutions of I to R, K or V, at the 222 NA residue of human H1N1 2009 viruses confer moderately reduced susceptibilities to both zanamivir and oseltamivir but, when combined with the H275Y NA substitution, cause even higher levels of resistance to oseltamivir and peramivir than the H275Y substitution alone. 2012 Antiviral research Discussion IV H275Y;H275Y 202;302 207;307 NA;NA 59;208 61;210 22252168 Susceptibility of avian influenza viruses of the N6 subtype to the neuraminidase inhibitor oseltamivir. Our sequence analysis verified an I222V NA residue change in two virus isolates (A/Herring Gull/Delaware/660/1988 and A/Herring Gull/Delaware/665/1988). 2012 Antiviral research Discussion IV I222V 34 39 40 42 22252168 Susceptibility of avian influenza viruses of the N6 subtype to the neuraminidase inhibitor oseltamivir. The R292K NA mutation in H3N2 influenza viruses is the only NA mutation that has been shown to cause cross-resistance to oseltamivir, zanamivir, and peramivir. 2012 Antiviral research Discussion IV R292K 4 9 NA;NA 10;60 12;62 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. Altogether, the drastic increase of the Kd for RNA and the subsequent altered oligomerization of R361A relative to NP may be mediated by a reduced flexibility of loop 2 and hindrance to access to its RNA binding groove and its vicinity. 2012 PloS one Discussion IV R361A 97 102 NP 115 117 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. As expected, this triple mutant had a Kd of 240 nM for RNA as compared to 565 nM for R361A (Figure 5). 2012 PloS one Discussion IV R361A 85 90 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. eight fold compared to the Kd of wt NP, similarly to the affinity loss of wt-E80A-E81A. 2012 PloS one Discussion IV E81A;E80A 82;77 86;81 NP 36 38 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. However in R361A-R204A-R208A, the protein-RNA interactions were weaker than in R361A. 2012 PloS one Discussion IV R204A;R208A;R361A;R361A 17;23;11;79 22;28;16;84 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. In addition, the Kd of the triple mutant and the double mutant wt-E80A-E81A were similar. 2012 PloS one Discussion IV E80A;E81A 66;71 70;75 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. In loop 2, a marked decrease of the flexibility as compared to that of NP was observed in R361A (Figure 1A). 2012 PloS one Discussion IV R361A 90 95 NP 71 73 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. In R361A, loop 1 elongated as compared to that in NP and the interactions of K113 with loop 1 were weaker (Table 1). 2012 PloS one Discussion IV R361A 3 8 NP 50 52 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. Interestingly, the wt-R204A-R208A mutant was unable to generate oligomeric species of the same size as NP and the wt-E80A-E81A did. 2012 PloS one Discussion IV E80A;R204A;R208A;E81A 117;22;28;122 121;27;33;126 NP 103 105 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. K113A did not induce significant change in RNP function and the mutant K90A, K91A, K113A, R117A, R121A had the same affinity for RNA than wt NP, suggesting compensation of the K113A mutation (by other charged residues) for RNA binding. 2012 PloS one Discussion IV K113A;K90A;K91A;K113A;R117A;R121A;K113A 0;71;77;83;90;97;176 5;75;81;88;95;102;181 NP;RNP 141;43 143;46 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. R361A had a markedly decreased affinity for RNA compared to that of NP, Kd = 565 nM and 41 nM respectively. 2012 PloS one Discussion IV R361A 0 5 NP 68 70 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. six fold affinity loss compared to wt NP corresponded to the effect of the E80A-E81A mutation in loop 1, supporting the hypothesis that loop 1 was involved in RNA sampling and/or capture. 2012 PloS one Discussion IV E80A;E81A 75;80 79;84 NP 38 40 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. The double mutation R204A-R208A aimed at avoiding a compensating salt bridge formation between R204 and E80 or E81. 2012 PloS one Discussion IV R208A;R204A 26;20 31;25 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. The importance of K113 was previously suggested by the inability of the K113A mutant to rescue viral growth. 2012 PloS one Discussion IV K113A 72 77 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. The oligomerization process of the double mutant wt-E80A-E81A was similar to that of the wt, suggesting that loop 1 was not involved in NP oligomerization. 2012 PloS one Discussion IV E81A;E80A 57;52 61;56 NP 136 138 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. The R361A mutation did not alter RNA polymerase activity although the virus could not be rescued which suggested that the RNP compensated the effect of the R361A mutation: for example, NP oligomerization rate could be enhanced by one or more protein of the polymerase complex. 2012 PloS one Discussion IV R361A;R361A 4;156 9;161 NP;RNP 185;122 187;125 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. The R361A-R204A-R208A protein formed oligomers of significantly larger size than those observed with R361A, while R361A-E80A-E81A oligomers were as large as to wt ones within experimental error, Figures 6C and 7B. 2012 PloS one Discussion IV R361A;R204A;R208A;R361A;R361A;E81A;E80A 4;10;16;101;114;125;120 9;15;21;106;119;129;124 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. The reduction of the electrostatic interactions by mutation of R208A and R204A at the tip of loop 2 likely will enhance hydrophobic contacts between L79 and W207 (Figure 2 and Table 1). 2012 PloS one Discussion IV R208A;R204A 63;73 68;78 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. The wt-R204A-R208A mutant exhibited a decrease of ca. 2012 PloS one Discussion IV R204A;R208A 7;13 12;18 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. These data clearly suggested a role of loop 2 in NP oligomerization, in agreement with the largely decreased transcription/replication efficiency of the RNP complex and loss of function by the R208A mutation. 2012 PloS one Discussion IV R208A 193 198 NP;RNP 49;153 51;156 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. This suggests that the double mutation may affect RNA dissociation from NP, in agreement with the dissociation rate constants calculated from the SPR data, being koff = 0.004 s-1 for the NP-RNA complex as compared to koff = 0.007 s-1 for the wt-E801-E81A-RNA complex. 2012 PloS one Discussion IV E81A 250 254 NP;NP 72;187 74;189 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. Thus, the expected rupture of the E80 - R208 salt bridge by mutation improved RNA-induced oligomerization as compared to that observed in R361A. 2012 PloS one Discussion IV R361A 138 143 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. We assume that the reduced flexibility of loop 2 (Figure 1B) and its increased hydrophobicity helped maintaining transient contacts with loop 1 in R361A-R204A-R208A despite the rupture of the E80-R208 salt bridge, explaining its low affinity for RNA. 2012 PloS one Discussion IV R204A;R208A;R361A 153;159;147 158;164;152 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. We assumed that the affinity drop of R361A compared to wt NP was due to the formation of a salt bridge between loop 1 (E80) and loop 2 (R208) and expressed the mutant R361A-E80A-E81A in an attempt to disrupt the putative salt bridge E80-R208. 2012 PloS one Discussion IV R361A;R361A;E80A;E81A 37;167;173;178 42;172;177;182 NP 58 60 22272272 Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding. We further tested loops flexibility in the R361A protein, the mutated residue being located in the RNA binding groove and carried by a linker (360-373). 2012 PloS one Discussion IV R361A 43 48 22363521 Frequency of D222G and Q223R hemagglutinin mutants of pandemic (H1N1) 2009 influenza virus in Japan between 2009 and 2010. Also, the homology modeling results showed that the double mutations, D187E and Q223R, would decrease virus affinity for the alpha2,6-linked receptor because the salt-bridge between E187 and R223 would lead to narrowing of the receptor binding pocket (data not shown). 2012 PloS one Discussion IV D187E;Q223R 70;80 75;85 22363521 Frequency of D222G and Q223R hemagglutinin mutants of pandemic (H1N1) 2009 influenza virus in Japan between 2009 and 2010. D222G mutants were detected as a minor population even in mild cases; thus, every patient may have been exposed to D222G mutant viruses. 2012 PloS one Discussion IV D222G;D222G 0;115 5;120 22363521 Frequency of D222G and Q223R hemagglutinin mutants of pandemic (H1N1) 2009 influenza virus in Japan between 2009 and 2010. However, these substitutions nearly disappeared in the samples from five mild cases in Dec 2010, suggesting that the D222G and/or Q223R mutants showed low rates of human-to-human transmission. 2012 PloS one Discussion IV D222G;Q223R 117;130 122;135 22363521 Frequency of D222G and Q223R hemagglutinin mutants of pandemic (H1N1) 2009 influenza virus in Japan between 2009 and 2010. In the present study, the D187E substitution was not striking, suggesting that E187 had already disappeared in humans, or the original swine lineages, by May 2009. 2012 PloS one Discussion IV D187E 26 31 22363521 Frequency of D222G and Q223R hemagglutinin mutants of pandemic (H1N1) 2009 influenza virus in Japan between 2009 and 2010. In this study, D222E, D222N, and D222V variants were not detected, even when deep sequencing was performed (Table S1). 2012 PloS one Discussion IV D222E;D222N;D222V 15;22;33 20;27;38 22363521 Frequency of D222G and Q223R hemagglutinin mutants of pandemic (H1N1) 2009 influenza virus in Japan between 2009 and 2010. No conclusions can be drawn regarding the relationship between the D222G substitution and pathogenesis from the present study. 2012 PloS one Discussion IV D222G 67 72 22363521 Frequency of D222G and Q223R hemagglutinin mutants of pandemic (H1N1) 2009 influenza virus in Japan between 2009 and 2010. Sequencing analysis using next-generation technology is necessary to reveal H1N1pdm genetic diversity in detail; our preliminary sequencing analysis using a conventional cloning approach failed to detect the D222G mutation in specimen #1 (Figure 1 and Table 2). 2012 PloS one Discussion IV D222G 208 213 22363521 Frequency of D222G and Q223R hemagglutinin mutants of pandemic (H1N1) 2009 influenza virus in Japan between 2009 and 2010. Several reports have shown that the D222G substitution was associated with severe, and sometimes fatal, cases of H1N1pdm. 2012 PloS one Discussion IV D222G 36 41 22363521 Frequency of D222G and Q223R hemagglutinin mutants of pandemic (H1N1) 2009 influenza virus in Japan between 2009 and 2010. The D222G mutation would result in a loss of interaction between galactose and K219 (Figure S4) because of the loss of charge and the side-chain. 2012 PloS one Discussion IV D222G 4 9 22363521 Frequency of D222G and Q223R hemagglutinin mutants of pandemic (H1N1) 2009 influenza virus in Japan between 2009 and 2010. The frequency of mutations such as D187E in specimens #1 and #2 and D222G in specimen #2 was not the same between GS-Junior technology and conventional Sanger sequencing (Figures 1, S1, S2, and S3, Tables 1 and 2). 2012 PloS one Discussion IV D187E;D222G 35;68 40;73 22363521 Frequency of D222G and Q223R hemagglutinin mutants of pandemic (H1N1) 2009 influenza virus in Japan between 2009 and 2010. The K119N mutation was also significantly detected in one specimen (3.1%) from a patient who had similar clinical symptoms as those of other patients during the second wave of the outbreak (Table 2). 2012 PloS one Discussion IV K119N 4 9 22363521 Frequency of D222G and Q223R hemagglutinin mutants of pandemic (H1N1) 2009 influenza virus in Japan between 2009 and 2010. The N125D mutation, however, was detected (0.66-2.15%), even in the second wave of the outbreak (Table 2). 2012 PloS one Discussion IV N125D 4 9 22363521 Frequency of D222G and Q223R hemagglutinin mutants of pandemic (H1N1) 2009 influenza virus in Japan between 2009 and 2010. The present study did not confirm whether viruses with the D222G and/or Q223R substitutions actually replicated in humans; however, the D222G and Q223R mutant viruses formed the dominant population when specimens were inoculated into embryonic chicken eggs (Table 3), indicating that the G222 and R223 mutants may be able to replicate in humans. 2012 PloS one Discussion IV D222G;Q223R;D222G;Q223R 59;72;136;146 64;77;141;151 22363521 Frequency of D222G and Q223R hemagglutinin mutants of pandemic (H1N1) 2009 influenza virus in Japan between 2009 and 2010. The proportion of HA sequences observed with D222G and Q223R in the #1 and #2 P6 and in the #3 P5 PCR products (Table 3) was consistent with results obtained by direct sequencing analysis using the ABI Sanger sequencer (Figure S6), suggesting that high-throughput amplicon sequencing analysis was highly quantitative. 2012 PloS one Discussion IV D222G;Q223R 45;55 50;60 HA 18 20 22363521 Frequency of D222G and Q223R hemagglutinin mutants of pandemic (H1N1) 2009 influenza virus in Japan between 2009 and 2010. The results showed that alpha2,3 sialic acid-specific viruses containing D222G and/or Q223R substitutions within the HA molecule were present in the upper respiratory tract as a minor population in patients with mild H1N1pdm infections in the early phase (May 2009) of the pandemic in Japan. 2012 PloS one Discussion IV D222G;Q223R 73;86 78;91 HA 117 119 Influenza A virus H1N1 infection 217 235 22438920 Mutations in polymerase genes enhanced the virulence of 2009 pandemic H1N1 influenza virus in mice. A synergistic effect on polymerase activity rendered by dual PA-36T and PB2-357N substitutions was observed (data not shown) and the mutant containing PA-A36T and PB2-H357N accompanied with HA-D222G was detected in our mice-adaptive experiments. 2012 PloS one Discussion IV A36T;H357N;D222G 154;167;193 158;172;198 HA;PA;PA;PB2;PB2 190;61;151;72;163 192;63;153;75;166 22438920 Mutations in polymerase genes enhanced the virulence of 2009 pandemic H1N1 influenza virus in mice. Although the A36T in PA in our study did not remarkably alter viral pathogenicity in mice, it contributed significantly to RNP activity and viral replication in mammalian cells, especially in PK15 cells. 2012 PloS one Discussion IV A36T 13 17 PA;RNP 21;123 23;126 22438920 Mutations in polymerase genes enhanced the virulence of 2009 pandemic H1N1 influenza virus in mice. H357A mutation could decrease PB2's cap binding activity and thus reduce mRNA transcription while H357W showed an enhanced binding to m7GTP. 2012 PloS one Discussion IV H357A;H357W 0;98 5;103 PB2 30 33 22438920 Mutations in polymerase genes enhanced the virulence of 2009 pandemic H1N1 influenza virus in mice. Of note, it was recently identified that synergistic actions of HA D222G, K163E and PA F35L in pH1N1 result in an enhanced pathogenicity in mice model. 2012 PloS one Discussion IV D222G;K163E;F35L 67;74;87 72;79;91 HA;PA 64;84 66;86 22438920 Mutations in polymerase genes enhanced the virulence of 2009 pandemic H1N1 influenza virus in mice. Since pig is the hypothesized 'mixing vessel' for generating novel reassortants or pandemic flu viruses, the superior growth properties of SC_PA-A36T in PK15 cells implies a potential threat of the variants carrying this mutation and required its monitoring in future work. 2012 PloS one Discussion IV A36T 145 149 22438920 Mutations in polymerase genes enhanced the virulence of 2009 pandemic H1N1 influenza virus in mice. The mutations, particularly PA A36T, exhibited the strongest up-regulation effect at 39 C than that of either 33 C or 37 C. 2012 PloS one Discussion IV A36T 31 35 PA 28 30 22438920 Mutations in polymerase genes enhanced the virulence of 2009 pandemic H1N1 influenza virus in mice. Thus, substitution of A36T in PA may affect viral transcription and replication. 2012 PloS one Discussion IV A36T 22 26 PA 30 32 22438920 Mutations in polymerase genes enhanced the virulence of 2009 pandemic H1N1 influenza virus in mice. To decode the factors contributing to adaptation and virulence of pH1N1 and to assess its potential risk to human health, an experimental evolutionary study was conducted and the polymerase mutations PA-A36T and PB2-H357N, were observed in the mouse-adapted descendants of pH1N1 virus-A/Sichuan/1/2009 (SC). 2012 PloS one Discussion IV A36T;H357N 203;216 207;221 PA;PB2 200;212 202;215 22449422 Engineering temperature sensitive live attenuated influenza vaccines from emerging viruses. Previously, it was shown that five ts mutations from ca A/AA/6/60 (PB1-K391E, D581G, A661T; PB2-N265S, and NP-D34G) were sufficient to impart strong temperature sensitivity to A/PR/8/34. 2012 Vaccine Discussion IV K391E;D581G;A661T;N265S;D34G 71;78;85;96;110 76;83;90;101;114 NP;PB1;PB2 107;67;92 109;70;95 22449422 Engineering temperature sensitive live attenuated influenza vaccines from emerging viruses. So we also generated the rNY1682-TS2 LAIV candidate, in which the three mutations (K391E, D581G, A661T) in the PB1 gene were based upon the ca A/AA/6/60 master donor strain and the four mutations in the PB2 gene were from ca A/AA/6/60 (N265S), ts A/Ud/307/72 (P112S, N556D) and a reassortant ts virus containing an A/GL/0389/65 PB2 (Y658H) . 2012 Vaccine Discussion IV K391E;D581G;A661T;N265S;P112S;N556D;Y658H 83;90;97;236;260;267;333 88;95;102;241;265;272;338 PB1;PB2;PB2 111;203;328 114;206;331 22449422 Engineering temperature sensitive live attenuated influenza vaccines from emerging viruses. The results of the TS1 LAIVs also suggest that N265S does not have the same impact on avian lineage PB2's as it does on human lineage PB2's. 2012 Vaccine Discussion IV N265S 47 52 PB2;PB2 100;134 103;137 22449422 Engineering temperature sensitive live attenuated influenza vaccines from emerging viruses. The three additional ts mutations (P112S, N556D, and Y658H) transferred from the other two ts mutant viruses played an important role in further attenuating the H1N1pdm virus. 2012 Vaccine Discussion IV P112S;N556D;Y658H 35;42;53 40;47;58 22449422 Engineering temperature sensitive live attenuated influenza vaccines from emerging viruses. Whether or not all eight ts mutations (PB1-K391E, D581G, A661T; PB2-P112S, N265S, N556D, Y658H; NP-D34G) are required to achieve the degree of attenuation of rNY1682-TS2 remains to be determined. 2012 Vaccine Discussion IV K391E;D581G;A661T;P112S;N265S;N556D;Y658H;D34G 43;50;57;68;75;82;89;99 48;55;62;73;80;87;94;103 NP;PB1;PB2 96;39;64 98;42;67 22564359 Effect of receptor specificity of A/Hong Kong/1/68 (H3N2) influenza virus variants on replication and transmission in pigs. 21 showed that A/Victoria/3/75 with L226Q and S228G mutations in the HA was not significantly less fit than its wild-type counterpart as both viruses infected similar numbers of human ciliated airway epithelium cells and replicated to comparable peak titers when incubated at 37 C. 2013 Influenza and other respiratory viruses Discussion IV L226Q;S228G;L226Q;S228G 38;48;37;47 43;53;42;52 HA 70 72 22564359 Effect of receptor specificity of A/Hong Kong/1/68 (H3N2) influenza virus variants on replication and transmission in pigs. A Q226L mutant with human-virus-like receptor specificity, which emerged during the course of their experiment, was transmissible even through respiratory droplets. 2013 Influenza and other respiratory viruses Discussion IV Q226L 2 7 22615752 Functional analysis of conserved motifs in influenza virus PB1 protein. Although the K480R mutation yielded increased amounts of replication products . 2012 PloS one Discussion IV K480R 13 18 22615752 Functional analysis of conserved motifs in influenza virus PB1 protein. As this mutation has been found in several early pandemic (H1N1) 2009 virus isolates, we used reverse genetics to introduce the K480R mutation into the PB1 subunit of the A/California/04/09 (H1N1; CA04) virus strain to assess viral growth characteristics. 2012 PloS one Discussion IV K480R 128 133 PB1 152 155 22615752 Functional analysis of conserved motifs in influenza virus PB1 protein. Interestingly, mutation K480R in motif IV of the PB1 subunit consistently demonstrated slightly increased polymerase activity in H5N1 and H1N1 polymerase complexes relative to wild-type ( Table 3 , and Figs. 2012 PloS one Discussion IV K480R 24 29 PB1 49 52 22615752 Functional analysis of conserved motifs in influenza virus PB1 protein. Our analysis of publicly available PB1 sequences suggests that mutations in PB1 motifs I - IV occur more often in avian virus PB1 proteins than in human or swine virus PB1 sequences (with the exception of the K480R mutation which is frequently found in swine virus PB1 proteins). 2012 PloS one Discussion IV K480R 209 214 PB1;PB1;PB1;PB1;PB1 35;76;126;168;265 38;79;129;171;268 22615752 Functional analysis of conserved motifs in influenza virus PB1 protein. We found that mutations S444P and D445G rendered the protein unstable . 2012 PloS one Discussion IV S444P;D445G 24;34 29;39 22615752 Functional analysis of conserved motifs in influenza virus PB1 protein. While the K480R mutation reproducibly enhanced transcription/replication in two different polymerase backgrounds and in two different cell lines, the observed increase (see Table 3 and Figs. 2012 PloS one Discussion IV K480R 10 15 22661221 Intrahost emergent dynamics of oseltamivir-resistant virus of pandemic influenza A (H1N1) 2009 in a fatally immunocompromised patient. Considering the route of virus spread from upper respiratory tract to lower respiratory tract, it is likely that the H275Y mutant is generated primarily in the nasopharynx, then spreads to the right and left lungs. 2012 Journal of infection and chemotherapy Discussion IV H275Y 117 122 22661221 Intrahost emergent dynamics of oseltamivir-resistant virus of pandemic influenza A (H1N1) 2009 in a fatally immunocompromised patient. Further analysis of intrahost variation of the virus in the left lung demonstrated that a part of the population was H275Y mutant and was predicted to be derived from oseltamivir-sensitive clone L1. 2012 Journal of infection and chemotherapy Discussion IV H275Y 117 122 22661221 Intrahost emergent dynamics of oseltamivir-resistant virus of pandemic influenza A (H1N1) 2009 in a fatally immunocompromised patient. In this study, we first detected the H275Y mutation in the right lung but not in the left lung. 2012 Journal of infection and chemotherapy Discussion IV H275Y 37 42 22661221 Intrahost emergent dynamics of oseltamivir-resistant virus of pandemic influenza A (H1N1) 2009 in a fatally immunocompromised patient. It is likely that case 1 might have been infected primarily with the oseltamivir-sensitive virus and that long-term administration of oseltamivir seems to have induced the generation of the H275Y mutant. 2012 Journal of infection and chemotherapy Discussion IV H275Y 190 195 22661221 Intrahost emergent dynamics of oseltamivir-resistant virus of pandemic influenza A (H1N1) 2009 in a fatally immunocompromised patient. Unfortunately, specimens were not available at the early phase of oseltamivir therapy, and we could not determine when the H275Y mutant was generated during therapy. 2012 Journal of infection and chemotherapy Discussion IV H275Y 123 128 22788742 Comprehensive global amino acid sequence analysis of PB1F2 protein of influenza A H5N1 viruses and the influenza A virus subtypes responsible for the 20th-century pandemics. Analysis for the N66S mutation in the strains belonging to the H2N2 and H3N2 subtypes revealed that this mutation is enriched in the avian strains. 2013 Influenza and other respiratory viruses Discussion IV N66S 17 21 22788742 Comprehensive global amino acid sequence analysis of PB1F2 protein of influenza A H5N1 viruses and the influenza A virus subtypes responsible for the 20th-century pandemics. Analysis of the pathogenic mutation N66S revealed that it was present only in 35 (3 8%) of 919 H5N1 strains. 2013 Influenza and other respiratory viruses Discussion IV N66S 36 40 22788742 Comprehensive global amino acid sequence analysis of PB1F2 protein of influenza A H5N1 viruses and the influenza A virus subtypes responsible for the 20th-century pandemics. In search of the pathogenic marker for H5N1 viruses, we identified a mutation (N84S) at the C-terminal end of the PB1F2 protein. 2013 Influenza and other respiratory viruses Discussion IV N84S 79 83 PB1F2 114 119 22808250 Mouse-adapted H9N2 influenza A virus PB2 protein M147L and E627K mutations are critical for high virulence. After adaptation, SD16-MA virus gained higher virulence and replicative fitness in mice with major roles shown for M147L/E627K mutations that possessed higher virulence than SD16, accompanied by greater virus titers in lungs of mice. 2012 PloS one Discussion IV M147L;E627K 115;121 120;126 22808250 Mouse-adapted H9N2 influenza A virus PB2 protein M147L and E627K mutations are critical for high virulence. All these data suggested that the virulence function of PB2 E627K seemed to be strain-specific or needed to interact with residue at other positions. 2012 PloS one Discussion IV E627K 60 65 PB2 56 59 22808250 Mouse-adapted H9N2 influenza A virus PB2 protein M147L and E627K mutations are critical for high virulence. Although the E627K mutation on its own enhanced replication and polymerase activity, it did not significantly increase pathogenicity of virus in mice. 2012 PloS one Discussion IV E627K 13 18 22808250 Mouse-adapted H9N2 influenza A virus PB2 protein M147L and E627K mutations are critical for high virulence. Another report showed that PB2 E158G could increase the morbidity and mortality of the H1N1 pandemic virus, which was much stronger than the effect of PB2 E627K. 2012 PloS one Discussion IV E158G;E627K 31;155 36;160 PB2;PB2 27;151 30;154 22808250 Mouse-adapted H9N2 influenza A virus PB2 protein M147L and E627K mutations are critical for high virulence. Here, PB2 E627K increased the polymerase activity and replication of virus, but did not significantly increase morbidity, as did the combination of V250G and E627K. 2012 PloS one Discussion IV E627K;V250G;E627K 10;148;158 15;153;163 PB2 6 9 22808250 Mouse-adapted H9N2 influenza A virus PB2 protein M147L and E627K mutations are critical for high virulence. Herfst et al also found that introduction of E627K mutation to H1N1/2009 virus had no major impact on virus replication in the respiratory tracts of mice and ferrets or on pathogenesis. 2012 PloS one Discussion IV E627K 45 50 22808250 Mouse-adapted H9N2 influenza A virus PB2 protein M147L and E627K mutations are critical for high virulence. However, in our study, PB2 E627K mutation did not significantly increase pathogenicity though it could increase viral replication in lungs of mice, indicating that the viral genomic backbone affects the phenotype of mutations at position 627. 2012 PloS one Discussion IV E627K 27 32 PB2 23 26 22808250 Mouse-adapted H9N2 influenza A virus PB2 protein M147L and E627K mutations are critical for high virulence. In the present study, introducing single mutation of M147L, V250G or E627K to SD16 PB2 protein did not significantly increase the pathogenicity of virus in mice, nevertheless, substitution of two amino acid residues could increase the virulence, among which the 147L/627K combination caused significant mortality. 2012 PloS one Discussion IV M147L;V250G;E627K 53;60;69 58;65;74 PB2 83 86 22808250 Mouse-adapted H9N2 influenza A virus PB2 protein M147L and E627K mutations are critical for high virulence. Most of the previous studies found major contributions of single amino acid mutations to viral adaptation and virulence, such as PB2 E158G, I504V, E627K, D710N, here, we demonstrated the importance of synergism of two or more amino acid substitutions in combination with E627K. 2012 PloS one Discussion IV E158G;I504V;E627K;D710N;E627K 133;140;147;154;271 138;145;152;159;276 PB2 129 132 22808250 Mouse-adapted H9N2 influenza A virus PB2 protein M147L and E627K mutations are critical for high virulence. Song et al reported that PA N383D contributed to the difference in the polymerase activities of two H5N1 viruses, but could not increase viral virulence, which may be affected by high level of polymerase accumulation in the nucleus of influenza virus-infected cells. 2012 PloS one Discussion IV N383D 28 33 PA 25 27 IV infections 235 259 22808250 Mouse-adapted H9N2 influenza A virus PB2 protein M147L and E627K mutations are critical for high virulence. The adapted viruses were readily infect mice and resulted in a quick selection of PB2 E627K mutation. 2012 PloS one Discussion IV E627K 86 91 PB2 82 85 22808250 Mouse-adapted H9N2 influenza A virus PB2 protein M147L and E627K mutations are critical for high virulence. The amino acid at position 627 of the PB2 protein has been described as a host range determinant, and the mutation E627K has been shown to be a key factor in the adaptation of H5N1 or other avian subtypes influenza viruses to mammals. 2012 PloS one Discussion IV E627K 115 120 PB2 38 41 22808250 Mouse-adapted H9N2 influenza A virus PB2 protein M147L and E627K mutations are critical for high virulence. The combination of M147L and E627K in PB2 was critical for the high virulence of mouse-adapted H9N2 virus. 2012 PloS one Discussion IV M147L;E627K 19;29 24;34 PB2 38 41 22808250 Mouse-adapted H9N2 influenza A virus PB2 protein M147L and E627K mutations are critical for high virulence. The present results showed that adapted virus could be obtained by serial passages and PB2 gene of SD16-MA is critical for the virulence of mouse-adapted H9N2 influenza virus, especially, the combination of PB2 M147L and E627K contribute to the highly lethality of mouse-adapted H9N2 influenza virus. 2012 PloS one Discussion IV M147L;E627K 211;221 216;226 PB2;PB2 87;207 90;210 22808250 Mouse-adapted H9N2 influenza A virus PB2 protein M147L and E627K mutations are critical for high virulence. The SD16-M147L, SD16-E627K, SD16-V250G/E627K mutants also replicated efficiently in vivo and in vitro, but were not lethal for mice. 2012 PloS one Discussion IV M147L;E627K;E627K;V250G 9;21;39;33 14;26;44;38 22809862 Treatment of oseltamivir-resistant influenza A (H1N1) virus infections in mice with antiviral agents. Amantadine's 100% protective activity at the highest dose against the A/MS-H275Y virus infection was similar to that seen previously. 2012 Antiviral research Discussion IV H275Y 75 80 22809862 Treatment of oseltamivir-resistant influenza A (H1N1) virus infections in mice with antiviral agents. An example of this was a study of children infected with oseltamivir-resistant influenza A H1N1 H275Y virus who showed reduced benefit from treatment compared to children infected with sensitive virus. 2012 Antiviral research Discussion IV H275Y 96 101 22809862 Treatment of oseltamivir-resistant influenza A (H1N1) virus infections in mice with antiviral agents. At this dose in mice, oseltamivir provided no benefit against the A/MS-H275Y and A/HK-H275Y virus infections. 2012 Antiviral research Discussion IV H275Y;H275Y 86;71 91;76 22809862 Treatment of oseltamivir-resistant influenza A (H1N1) virus infections in mice with antiviral agents. Because antiviral protection was seen with oseltamivir at high (100 and 300 mg/kg/day) doses in the mouse models of A/MS-H275Y and A/HK-H275Y virus infections, we are not suggesting that this could translate into protection against oseltamivir-resistant virus infections in humans. 2012 Antiviral research Discussion IV H275Y;H275Y 136;121 141;126 22809862 Treatment of oseltamivir-resistant influenza A (H1N1) virus infections in mice with antiviral agents. From the results of these studies, the infection of mice with mouse-adapted influenza A/MS-H275Y virus appears to represent a useful model for studying the treatment of oseltamivir-resistant virus infections with newly discovered antiviral substances and compounds used in combination. 2012 Antiviral research Discussion IV H275Y 91 96 22809862 Treatment of oseltamivir-resistant influenza A (H1N1) virus infections in mice with antiviral agents. In addition, we found the older A/MS-H275Y virus isolated in 2001 was also adapted and found lethal to mice. 2012 Antiviral research Discussion IV H275Y 37 42 22809862 Treatment of oseltamivir-resistant influenza A (H1N1) virus infections in mice with antiviral agents. In this report we demonstrated that two different influenza A viruses possessing the H275Y mutation in the neuraminidase gene could be mouse adapted to cause fatal infections in mice. 2012 Antiviral research Discussion IV H275Y 85 90 107 120 22809862 Treatment of oseltamivir-resistant influenza A (H1N1) virus infections in mice with antiviral agents. In this report we indicate that the A/HK-H275Y 2009 virus described by Chen et al. 2012 Antiviral research Discussion IV H275Y 41 46 22809862 Treatment of oseltamivir-resistant influenza A (H1N1) virus infections in mice with antiviral agents. It is not known whether the A/WSN/33 (H1N1) H275Y virus reported by would perform the same as our viruses in infected mice if treated with higher doses of oseltamivir. 2012 Antiviral research Discussion IV H275Y 44 49 22809862 Treatment of oseltamivir-resistant influenza A (H1N1) virus infections in mice with antiviral agents. One of the HA mutations, D225G, was associated with increased virulence in mice. 2012 Antiviral research Discussion IV D225G 25 30 HA 11 13 22809862 Treatment of oseltamivir-resistant influenza A (H1N1) virus infections in mice with antiviral agents. Prior to this, only the genetically engineered A/WSN/33 (H1N1) and A/Vietnam/1203/2004 (H5N1) H275Y viruses had been reported to lethally infect mice. 2012 Antiviral research Discussion IV H275Y 94 99 22809862 Treatment of oseltamivir-resistant influenza A (H1N1) virus infections in mice with antiviral agents. Resistance of the pandemic 2009 H1N1 viruses to adamantanes has been previously described, and is attributable to an S31N mutation in the M2 gene. 2012 Antiviral research Discussion IV S31N 117 121 M2 138 140 22809862 Treatment of oseltamivir-resistant influenza A (H1N1) virus infections in mice with antiviral agents. Since the A/HK-H275Y virus is resistant to oseltamivir and to adamantanes, it offers more limited possibilities for combination treatment than the A/MS-H275Y virus. 2012 Antiviral research Discussion IV H275Y;H275Y 15;152 20;157 22809862 Treatment of oseltamivir-resistant influenza A (H1N1) virus infections in mice with antiviral agents. tested the same strain of influenza A/HK-H275Y virus that we used with the NA-Star assay, and reported IC50 values of 78, 9.2, and 0.43 muM for oseltamivir carboxylate, peramivir, and zanamivir, respectively. 2012 Antiviral research Discussion IV H275Y 41 46 75 77 22809862 Treatment of oseltamivir-resistant influenza A (H1N1) virus infections in mice with antiviral agents. The A/HK-H275Y model is also useful but we found that variable mortality occurred from experiment to experiment (the studies presented here were acceptable, but other unreported experiments where we tested different inhibitors had too few deaths in placebo groups for adequate statistical interpretation). 2012 Antiviral research Discussion IV H275Y 9 14 22809862 Treatment of oseltamivir-resistant influenza A (H1N1) virus infections in mice with antiviral agents. The A/MS-H275Y virus has already shown to be synergistically inhibited in vitro by the combination of oseltamivir carboxylate, amantadine, and ribavirin. 2012 Antiviral research Discussion IV H275Y 9 14 22809862 Treatment of oseltamivir-resistant influenza A (H1N1) virus infections in mice with antiviral agents. The A/MS-H275Y virus was also inhibited by amantadine and rimantadine whereas the A/HK-H275Y was resistant to the adamantanes. 2012 Antiviral research Discussion IV H275Y;H275Y 9;87 14;92 22809862 Treatment of oseltamivir-resistant influenza A (H1N1) virus infections in mice with antiviral agents. The cell culture studies demonstrated that the A/MS-H275Y and A/HK-H275Y viruses were resistant to oseltamivir, showed decreased sensitivity to peramivir, and were highly sensitive to zanamivir. 2012 Antiviral research Discussion IV H275Y;H275Y 52;67 57;72 22809862 Treatment of oseltamivir-resistant influenza A (H1N1) virus infections in mice with antiviral agents. The first study that we are aware of was that of using a recombinant influenza A/WSN/33 (H1N1) H275Y virus. 2012 Antiviral research Discussion IV H275Y 95 100 22809862 Treatment of oseltamivir-resistant influenza A (H1N1) virus infections in mice with antiviral agents. The H275Y mutation was stable during the mouse passages, as determined by genetic analysis of the relevant region of the neuraminidase gene. 2012 Antiviral research Discussion IV H275Y 4 9 121 134 22809862 Treatment of oseltamivir-resistant influenza A (H1N1) virus infections in mice with antiviral agents. The same pattern of antiviral potency exhibited by the compounds (i.e., zanamivir > peramivir > oseltamivir) was evident for both the A/MS-H275Y and A/HK-H275Y viruses. 2012 Antiviral research Discussion IV H275Y;H275Y 139;154 144;159 22809862 Treatment of oseltamivir-resistant influenza A (H1N1) virus infections in mice with antiviral agents. The wild type neuraminidases for the A/HK-H275Y and A/MS-275Y viruses were sequenced and reported in GenBank. 2012 Antiviral research Discussion IV H275Y 42 47 14 28 22809862 Treatment of oseltamivir-resistant influenza A (H1N1) virus infections in mice with antiviral agents. Treatment of influenza H3N2 and H5N1 virus infections did not provide sufficient protection with even a one-day delay of treatment initiation, as occurs with the A/MS-H275Y and A/HK-H275Y virus infections. 2012 Antiviral research Discussion IV H275Y;H275Y 182;167 187;172 Influenza A virus H5N1 infection 32 53 22952752 Molecular evolutionary analysis of pH1N1 2009 influenza virus in Reunion Island, South West Indian Ocean region: a cohort study. In addition, clade RUN was characterized by 2 mutations that were systematically found in all local HA and NA sequences, respectively, the D239E mutation and the silent g873a mutation (Table 3). 2012 PloS one Discussion IV D239E 139 144 HA;NA 100;107 102;109 22952752 Molecular evolutionary analysis of pH1N1 2009 influenza virus in Reunion Island, South West Indian Ocean region: a cohort study. Moreover, the D239E variant was found to preferentially colonize the upper respiratory tract, while D239G/N mutants also colonize the lower respiratory tract, hence causing severe acute respiratory syndromes, as is often observed in H5N1 Influenza . 2012 PloS one Discussion IV D239N;D239E;D239G 100;14;100 107;19;107 Acute respiratory distress syndrome 180 207 22952752 Molecular evolutionary analysis of pH1N1 2009 influenza virus in Reunion Island, South West Indian Ocean region: a cohort study. Recent studies in hospitalized patients suffering pH1N1 infection have shown that the D239G, D239N and D239E mutations were associated with severe. 2012 PloS one Discussion IV D239G;D239N;D239E 86;93;103 91;98;108 22952752 Molecular evolutionary analysis of pH1N1 2009 influenza virus in Reunion Island, South West Indian Ocean region: a cohort study. There have been many descriptions of the HA D239E mutation including predictive structural studies. 2012 PloS one Discussion IV D239E 44 49 HA 41 43 22952752 Molecular evolutionary analysis of pH1N1 2009 influenza virus in Reunion Island, South West Indian Ocean region: a cohort study. This observation is in keeping with reports showing that infections with [D239E]-HA variants have generally speaking, been less severe than the one provoked by other variants. 2012 PloS one Discussion IV D239E 74 79 HA 81 83 22952752 Molecular evolutionary analysis of pH1N1 2009 influenza virus in Reunion Island, South West Indian Ocean region: a cohort study. Viral sequences from Reunion Island have fixed all the mutations that had previously been identified as being specific to clade 7, including the [V100I]-NP and [N248D]-NA mutations which were not fixed among all clade 7 isolates. 2012 PloS one Discussion IV V100I;N248D 146;161 151;166 NA;NP 168;153 170;155 22958470 Molecular and phylogenetic analysis of matrix gene of avian influenza viruses isolated from wild birds and live bird markets in the USA. High prevalence of S31N substitution in this study is in line with those observed earlier, as this substitution is considered to be the most common mutation conferring resistance to adamentanes 20 , whereas V27A mutation is rare in frequency (1 6%). 2013 Influenza and other respiratory viruses Discussion IV S31N;V27A 19;207 23;211 22958470 Molecular and phylogenetic analysis of matrix gene of avian influenza viruses isolated from wild birds and live bird markets in the USA. Substitution at position 31 (S31N) in M2 protein was the most commonly observed substitution with 16 of the 17 isolate having this mutation, whereas only one isolate had V27A change. 2013 Influenza and other respiratory viruses Discussion IV S31N;V27A 29;170 33;174 M2 38 40 23029425 Multiple distinct forms of CD8+ T cell cross-reactivity and specificities revealed after 2009 H1N1 influenza A virus infection in mice. Interestingly, the virus carrying M371A mutation maintained NP366 immunodominance during infection. 2012 PloS one Discussion IV M371A 34 39 NP 60 62 23029425 Multiple distinct forms of CD8+ T cell cross-reactivity and specificities revealed after 2009 H1N1 influenza A virus infection in mice. It has been shown that M6 residue on NP366 epitope of PR8 or X31 virus is critical for TCR recognition, as single M6A mutations results in complete loss of peptide-induced cytokine production and cytotoxicity. 2012 PloS one Discussion IV M6A 114 117 NP 37 39 23029425 Multiple distinct forms of CD8+ T cell cross-reactivity and specificities revealed after 2009 H1N1 influenza A virus infection in mice. Similar to the laboratory M371A mutation, the M371V substitution on CA/E3/09 NP protein also dramatically changed the antigen specificity of the native epitope, yet the CANP366 epitope is still dominant among other epitopes identified. 2012 PloS one Discussion IV M371A;M371V 26;46 31;51 NP 77 79 23029425 Multiple distinct forms of CD8+ T cell cross-reactivity and specificities revealed after 2009 H1N1 influenza A virus infection in mice. Thus, S224P substitution does not affect the antigenicity of peptide PA224, but abolishes its immunogenicity during CA/E3/09 infection. 2012 PloS one Discussion IV S224P 6 11 PA 69 71 23280098 Genetic characterization of influenza virus circulating in Brazilian pigs during 2009 and 2010 reveals a high prevalence of the pandemic H1N1 subtype. Interestingly, isolate 14/2009, which did not have the N248D NA mutation, cannot be clustered within any of the seven clades. 2013 Influenza and other respiratory viruses Discussion IV N248D 55 60 61 63 23280098 Genetic characterization of influenza virus circulating in Brazilian pigs during 2009 and 2010 reveals a high prevalence of the pandemic H1N1 subtype. It has been demonstrated that pandemic H1N1 2009 evolved and shifted from an initial mixed clade pattern to a clade 7-predominant pattern.34 The subsequent selection and evolution of clade 7 resulted in the circulation of variants D222G/N or E.35 Mutation D222G in the hemagglutinin protein has been correlated with the clinical onset of disease, and it was frequently found in severe/fatal cases of the pandemic influenza in humans.36 Likewise, the substitution D222N, which was observed in isolates 19/2010 and 20/2010, is more frequent among fatal cases of the disease in humans.37 However, the animals from which those viruses were isolated did not show signs of severe disease. 2013 Influenza and other respiratory viruses Discussion IV D222G;D222N;D222G;D222N 231;231;256;463 238;238;261;468 HA 269 282 23280098 Genetic characterization of influenza virus circulating in Brazilian pigs during 2009 and 2010 reveals a high prevalence of the pandemic H1N1 subtype. Seven distinct clades of pandemic H1N1 viruses were identified globally circulating in the beginning of the pandemic.33 The HA substitution S203T combined with NA V106I and N248D found in 18 of the 20 swine isolates and in the human isolate described here suggests that these Brazilian isolates might be members of clade 7 of pH1N1.33 Isolate 7/2009 could be clustered with clade 6 because it did not show the HA substitution. 2013 Influenza and other respiratory viruses Discussion IV S203T;V106I;N248D 140;163;173 145;168;178 HA;HA;NA 124;410;160 126;412;162 23289789 Genetic analysis of influenza B viruses isolated in Uganda during the 2009-2010 seasons. The 2009 viruses could be clearly differentiated from the 2010 viruses by a D35G substitution in the neuraminidase protein. 2013 Virology journal Discussion IV D35G 76 80 101 114 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. Binding of Rch1 or NPI-1 to S9A NP110aa was markedly reduced compared with that shown by WT NP110aa. 2013 PloS one Discussion IV S9A 28 31 NP;NP 32;92 34;94 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. Furthermore, nuclear localization of WT and S9A NP110aa was unaffected by Qip1 silencing. 2013 PloS one Discussion IV S9A 44 47 NP 48 50 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. Furthermore, Qip1 out-competed Rch1 and NPI-1 for binding to WT NP110aa and S9A NP110aa. 2013 PloS one Discussion IV S9A 76 79 NP;NP 64;80 66;82 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. Furthermore, we showed that, although S9A NP110aa mainly localized to the nucleus, viral growth and vRNA transcription was reduced by the S9A mutation, indicating that the unconventional NLS of NP is involved in vRNA transcription and nuclear transport via two distinct pathways. 2013 PloS one Discussion IV S9A;S9A 38;138 41;141 NP;NP 42;194 44;196 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. However, although nuclear localization of R8A NP110aa was still almost 50% of analyzed cells, viruses with the R8A mutation were not rescued by reverse-genetics. 2013 PloS one Discussion IV R8A;R8A 42;111 45;114 NP 46 48 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. However, the percentage of cells showing cytoplasmic localization was clearly higher in R8A NP110aa-transfected cells than in K7A NP110aa-transfected cells. 2013 PloS one Discussion IV R8A;K7A 88;126 91;129 NP;NP 92;130 94;132 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. However, the reduction in viral titers of S9A mutant was not detected in. 2013 PloS one Discussion IV S9A 42 45 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. However, viral replication and vRNA transcription were reduced by Qip1 silencing only in S9A NP. 2013 PloS one Discussion IV S9A 89 92 NP 93 95 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. However, vRNA transcription by S9A NP WSN in Qip1-silenced cells decreased to around 70% of that in control cells. 2013 PloS one Discussion IV S9A 31 34 NP 35 37 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. In addition, binding of all three importin alpha isoforms to R8A NP110aa was markedly reduced in a similar manner. 2013 PloS one Discussion IV R8A 61 64 NP 65 67 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. In conclusion, the results of the present study show for the first time that importin alpha3/Qip1 contribute to the proper function of the unconventional NLS of S9A NP, including up-regulation of transcription and/or replication of vRNA, and viral multiplication in a nuclear localization independent manner. 2013 PloS one Discussion IV S9A 161 164 NP 165 167 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. In contrast to Rch1 and NPI-1, binding of Qip1 to S9A NP110aa was almost the same as that observed for WT NP110aa. 2013 PloS one Discussion IV S9A 50 53 NP;NP 54;106 56;108 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. In this case of virus-plasmids-transfected cells, many cells died by viral cytopathic effect in both WT and S9A viruses when we cultured over 72 hours. 2013 PloS one Discussion IV S9A 108 111 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. Indeed, transcription and viral growth were reduced using S9A mutant NP, which was attenuated the binding activity of NP to Rch1 and NPI-1. 2013 PloS one Discussion IV S9A 58 61 NP;NP 69;118 71;120 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. Indeed, we obtained differences the titer of mutant virus with S9A when we evaluated the production of progeny virus at 24 hours post infection. 2013 PloS one Discussion IV S9A 63 66 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. Interestingly, we also found that S9A NP110aa had a preference binding to Qip1. 2013 PloS one Discussion IV S9A 34 37 NP 38 40 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. Lastly, we showed that, although binding of Rch1 and NPI-1 was reduced in WT NP110aa and S9A NP110aa compare to full-length WT NP, Qip1 bound to WT NP110aa and S9A NP110aa as well as full-length WT NP. 2013 PloS one Discussion IV S9A;S9A 89;160 92;163 NP;NP;NP;NP;NP;NP 77;93;127;148;164;198 79;95;129;150;166;200 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. On the other hand, Qip1 bound to WT NP110aa and S9A NP110aa as well as full length WT NP. 2013 PloS one Discussion IV S9A 48 51 NP;NP;NP 36;52;86 38;54;88 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. On the other hand, viral growth of the S9A mutant was notably reduced at 72 h post-infection in Qip1-silenced A549 cells compared to that in control cells. 2013 PloS one Discussion IV S9A 39 42 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. Second, the mutant S9A NP110aa, which mainly localized to the nucleus, showed reduced viral growth and vRNA transcription. 2013 PloS one Discussion IV S9A 19 22 NP 23 25 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. Therefore, suppression of nuclear localization, vRNA transcription, and packaging of vRNA by the R8A mutation may result in the inability to rescue R8A mutant viruses. 2013 PloS one Discussion IV R8A;R8A 97;148 100;151 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. These differences may contribute to the binding of Qip1 to S9A NP110aa. 2013 PloS one Discussion IV S9A 59 62 NP 63 65 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. This indicates that the replication of S9A mutant virus requires Qip1. 2013 PloS one Discussion IV S9A 39 42 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. This is supported by data showing that R8A NP110aa, which lost nearly 50% of its nuclear localization activity, had decreased binding for Qip1, NPI-1 and Rch1. 2013 PloS one Discussion IV R8A 39 42 NP 43 45 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. This study also shows that, although S9A NP110aa mainly localized to the nucleus, viral growth and vRNA transcription were reduced by the S9A mutation, indicating that the amino acid at position 9 within the unconventional NLS may have an important function during viral multiplication aside from nuclear localization. 2013 PloS one Discussion IV S9A;S9A 37;138 40;141 NP 41 43 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. Thus, Qip1 appears to contribute to S9A NP virus multiplication through the unconventional NLS independently of nuclear localization of NP, whereas it is not essential for multiplication of WT virus because it may hide under interaction of many importin isoforms to WT NP. 2013 PloS one Discussion IV S9A 36 39 NP;NP;NP 40;136;269 42;138;271 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. Thus, the generation of progeny viruses may saturate at 72 hours post transfection, thereby resulting in equivalent titer between WT and S9A mutant viruses. 2013 PloS one Discussion IV S9A 137 140 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. To examine the effect of the mutation at S9A to viral growth in. 2013 PloS one Discussion IV S9A 41 44 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. Using the signal in lysate detected by western blot as the baseline, the binding of WT NP110aa and S9A NP110aa to Rch1 and NPI-1 was reduced compare to full-length WT NP. 2013 PloS one Discussion IV S9A 99 102 NP;NP;NP 87;103;167 89;105;169 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. We also examined the importance of Qip1 binding to NP for viral transcription and growth using WT or S9A NP mutant and Qip1-silenced A549 cells. 2013 PloS one Discussion IV S9A 101 104 NP;NP 51;105 53;107 23383277 Importin alpha3/Qip1 is involved in multiplication of mutant influenza virus with alanine mutation at amino acid 9 independently of nuclear transport function. we determined whether R8A and S9A mutant viruses are able to rescue by reverse-genetics. 2013 PloS one Discussion IV R8A;S9A 22;30 25;33 23383318 Inhibitors of the influenza A virus M2 proton channel discovered using a high-throughput yeast growth restoration assay. 2 is not only highly potent against the amantadine-resistant V27A mutant as reported, but that it is a 3-fold more potent inhibitor of the WT M2 channel than amantadine and rimantadine, and may therefore be a candidate for drug development. 2013 PloS one Discussion IV V27A 61 65 M2 142 144 23383318 Inhibitors of the influenza A virus M2 proton channel discovered using a high-throughput yeast growth restoration assay. 2 that is active against WT, L26F and V27A M2. 2013 PloS one Discussion IV L26F;V27A 29;38 33;42 M2 43 45 23397331 Influenza virus A(H1N1)pdm09 hemagglutinin polymorphism and associated disease in southern Germany during the 2010/11 influenza season. All viruses analysed here had the amino acid changes P83S and S203T in the HA1 region and I321V and E374K in the HA2 region. 2013 Archives of virology Discussion IV P83S;S203T;I321V;E374K 53;62;90;100 57;67;95;105 HA;HA1 113;75 115;78 23397331 Influenza virus A(H1N1)pdm09 hemagglutinin polymorphism and associated disease in southern Germany during the 2010/11 influenza season. Also, other mutations, such as the double mutation N125D and E374K, have been associated with a more virulent phenotype. 2013 Archives of virology Discussion IV N125D;E374K 51;61 56;66 23397331 Influenza virus A(H1N1)pdm09 hemagglutinin polymorphism and associated disease in southern Germany during the 2010/11 influenza season. Although it is clear that influenza virus tropism depends on several viral and host factors and not only on HA specificity, the presence of the K119N mutation exclusively in the virus isolated from the LRT might indicate a more efficient binding/replication of viruses carrying this mutation to/in cells expressing 2,3-SA. 2013 Archives of virology Discussion IV K119N 144 149 HA 108 110 23397331 Influenza virus A(H1N1)pdm09 hemagglutinin polymorphism and associated disease in southern Germany during the 2010/11 influenza season. Clinically, the mutations D222G and N have been associated with a more virulent phenotype. 2013 Archives of virology Discussion IV D222G 26 31 23397331 Influenza virus A(H1N1)pdm09 hemagglutinin polymorphism and associated disease in southern Germany during the 2010/11 influenza season. Finally, the oseltamivir-resistance-associated mutation H275Y was detected only once in our study population. 2013 Archives of virology Discussion IV H275Y 56 61 23397331 Influenza virus A(H1N1)pdm09 hemagglutinin polymorphism and associated disease in southern Germany during the 2010/11 influenza season. Group 6, characterized by mutations D97N and S185T, was the dominant H1N1 lineage (48 %), followed by group 5 (33 %; D97N, R205K, I216V), group 4 (12 %; N125D) and group 7 (9 %; S185T, S143G, A197T). 2013 Archives of virology Discussion IV D97N;S185T;D97N;R205K;I216V;N125D;S185T;S143G;A197T 36;45;117;123;130;153;178;185;192 40;50;121;128;135;158;183;190;197 23397331 Influenza virus A(H1N1)pdm09 hemagglutinin polymorphism and associated disease in southern Germany during the 2010/11 influenza season. Human influenza viruses carrying the K119N mutation show improved growth in eggs and appear to exhibit enhanced virulence in the mouse model. 2013 Archives of virology Discussion IV K119N 37 42 23397331 Influenza virus A(H1N1)pdm09 hemagglutinin polymorphism and associated disease in southern Germany during the 2010/11 influenza season. In particular, two additional mutations (K130R-M344L in one case and K119N- I216K in the other case) were identified only in the LRT. 2013 Archives of virology Discussion IV K130R;M344L;K119N;I216K 41;47;69;76 46;52;74;81 23397331 Influenza virus A(H1N1)pdm09 hemagglutinin polymorphism and associated disease in southern Germany during the 2010/11 influenza season. Moreover, analysis of potential glycosylation sites revealed that the K119N mutation provides an additional potential glycosylation site. 2013 Archives of virology Discussion IV K119N 70 75 23397331 Influenza virus A(H1N1)pdm09 hemagglutinin polymorphism and associated disease in southern Germany during the 2010/11 influenza season. No D222G change was observed here. 2013 Archives of virology Discussion IV D222G 3 8 23418535 Evolutionary characterization of the pandemic H1N1/2009 influenza virus in humans based on non-structural genes. Future studies are necessary to elucidate the effects of the V123I mutation on the binding capabilities of the NS and M proteins and on transmission between humans. 2013 PloS one Discussion IV V123I 61 66 M;NS 118;111 119;113 23437033 Quantitative description of glycan-receptor binding of influenza A virus H7 hemagglutinin. Furthermore the Gln-226 Leu mutation has been observed in the H9 avian isolates. 2013 PloS one Discussion IV Q226L 16 27 23437217 Parallel screening of wild-type and drug-resistant targets for anti-resistance neuraminidase inhibitors. For example, H275Y, which is a frequent resistance mutation, changes the orientation of E277 and alters the hydrophobic pocket of the S4 subsite, which forms interactions with the 3-pentyloxy moiety of GS4071. 2013 PloS one Discussion IV H275Y 13 18 23437217 Parallel screening of wild-type and drug-resistant targets for anti-resistance neuraminidase inhibitors. For the dual mutation I223R and H275Y, the volume of the S4 subsite is reduced because of the long side-chain of arginine and tyrosine. 2013 PloS one Discussion IV I223R;H275Y 22;32 27;37 23437217 Parallel screening of wild-type and drug-resistant targets for anti-resistance neuraminidase inhibitors. In contrast, RB19 is not affected by some drug-resistant mutations such as I223R, H275Y, and I223R/H275Y NA mutants because RB19 contains a flexible chain with a large polar moiety. 2013 PloS one Discussion IV I223R;H275Y;I223R;H275Y 75;82;93;99 80;87;98;104 105 107 23437217 Parallel screening of wild-type and drug-resistant targets for anti-resistance neuraminidase inhibitors. Many mutations of NAs have been reported including E119V, D151E, H275Y, R293K, and N295S. 2013 PloS one Discussion IV E119V;D151E;H275Y;R293K;N295S 51;58;65;72;83 56;63;70;77;88 18 21 23437217 Parallel screening of wild-type and drug-resistant targets for anti-resistance neuraminidase inhibitors. The dual I223R/H275Y mutant NA discussed here was relatively impervious to the three traditional NA drugs. 2013 PloS one Discussion IV H275Y;I223R 15;9 20;14 NA;NA 28;97 30;99 23437217 Parallel screening of wild-type and drug-resistant targets for anti-resistance neuraminidase inhibitors. Through this strategy, a novel scaffold (RB19) was identified as a good starting lead for designing more effective NA inhibitors that combat oseltamivir-resistant (H275Y), zanamivir-resistant (I223R), and multidrug-resistant (I223R and H275Y) influenza viruses. 2013 PloS one Discussion IV H275Y;I223R;I223R;H275Y 164;193;226;236 169;198;231;241 115 117 23451169 Simultaneous detection of oseltamivir- and amantadine-resistant influenza by oligonucleotide microarray visualization. For instance, I117V, I117M, S247N, I223R, N294S, and R292K of NA have been reported to be associated with NA inhibitor resistance, and some of them had combinatorial, compensatory, or synergistic effects. 2013 PloS one Discussion IV I117V;I117M;S247N;I223R;N294S;R292K 14;21;28;35;42;53 19;26;33;40;47;58 NA;NA 62;106 64;108 23555270 Monomeric nucleoprotein of influenza A virus. A flexible loop formed by residues 392-407 and the C-terminus point towards the RNA binding surface which may be the reason for the lowered affinity for RNA, in particular for the obligate monomeric mutant R416A. 2013 PLoS pathogens Discussion IV R416A 206 211 23555270 Monomeric nucleoprotein of influenza A virus. Recombinant virus with a S165A mutation could not be recovered indicating the importance of this phosphorylation site for the activity of the protein. 2013 PLoS pathogens Discussion IV S165A 25 30 23555270 Monomeric nucleoprotein of influenza A virus. The biochemical behaviour of the monomeric S165D mutant is different with a lowered affinity for RNA but with an enhanced polymerisation at RNA concentrations above the Kd compared to wt monomeric NP. 2013 PLoS pathogens Discussion IV S165D 43 48 NP 197 199 23555270 Monomeric nucleoprotein of influenza A virus. This could imply that the insertion of the exchange domain into a neighbouring NP protomer in the RNP is not equivalent to that in the RNA-free trimer and this may be related to our findings that the S165D mutant does not form trimers but can polymerize onto RNA and that trimers can bind RNA but do not form NP-RNA rings. 2013 PLoS pathogens Discussion IV S165D 200 205 NP;NP;RNP 79;309;98 81;311;101 23555270 Monomeric nucleoprotein of influenza A virus. Using RNP reconstitution experiments in 293 T cells they could measure transcription and replication for the S165A but not for a S165E mutant. 2013 PLoS pathogens Discussion IV S165A;S165E 109;129 114;134 RNP 6 9 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. A similar influenza A(H1N1)pdm09 virus S247N variant with mildly reduced oseltamivir and zanamivir sensitivity was detected in more than 10% of community specimens in Singapore and more than 30% of samples from northern Australia during the early months of 2011.42 This variant was also detected in other regions of the Asia-Pacific. 2013 Influenza and other respiratory viruses Discussion IV S247N 39 44 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. An important limitation of this study was the unavailability of original clinical specimens matching virus isolates with previously unreported changes in the NA, such as A/Santiago/14689/2011 with N325K substitution and B/Ontario/1256/2011 with G140R and N144K substitutions. 2013 Influenza and other respiratory viruses Discussion IV N325K;G140R;N144K 197;245;255 202;250;260 158 160 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. Despite the low incidence of oseltamivir resistance observed during the 2011 Southern Hemisphere season, the spread of oseltamivir-resistant A(H1N1)pdm09 viruses is still a concern and may develop as a result of selective pressure or spontaneous mutation, such as the cluster of oseltamivir-resistant H275Y variants detected in the Hunter New England region of New South Wales, Australia.18, 19 Therefore, it remains prudent to continue conducting NAI sensitivity testing of viruses to monitor emergence of H275Y and other NAI-resistant virus variants, particularly if the use of NAIs increases in the community. 2013 Influenza and other respiratory viruses Discussion IV H275Y;H275Y 301;507 306;512 NAI;NAI;NAI 448;523;580 451;526;584 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. In addition, monitoring could be enhanced by detection of H275Y directly on clinical specimens using molecular methods, including pyrosequencing25, 26, 27 or real-time RT-PCR techniques.28, 29 . 2013 Influenza and other respiratory viruses Discussion IV H275Y 58 63 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. In addition, monitoring could be enhanced by detection of H275Y directly on clinical specimens using molecular methods, including pyrosequencing25, 26, 27 or real-time RT-PCR techniques.28, 29. 2013 Influenza and other respiratory viruses Discussion IV H275Y 58 63 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. In addition, we detected a novel amino acid substitution N325K in the NA of one A(H1N1)pdm09 isolate, A/Santiago/14689/2011, which exhibited significantly reduced susceptibility to oseltamivir (19-fold), and mildly reduced sensitivity to zanamivir and peramivir. 2013 Influenza and other respiratory viruses Discussion IV N325K 57 62 70 72 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. In this study, the H275Y substitution was detected in only 2 (0 6%) of the 326 influenza A(H1N1)pdm09 viruses, one of which contained a mix of H275Y and H275 wild-type viruses, in addition to a mix of D199N and D199 wild-type viruses, and was three times less resistant to oseltamivir and peramivir than the other resistant virus, which was predominantly H275Y. 2013 Influenza and other respiratory viruses Discussion IV H275Y;H275Y;D199N;H275Y 19;143;201;355 24;148;206;360 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. Novel NA substitutions were also detected in one influenza B isolate, B/Ontario/1256/2011, with G140R and N144K, which showed significantly reduced susceptibility to zanamivir and peramivir, but only mildly reduced sensitivity to oseltamivir. 2013 Influenza and other respiratory viruses Discussion IV G140R;N144K 96;106 101;111 6 8 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. Of note, the fluorescent NI assay has been shown to provide the greater discrimination between IC50 values of oseltamivir-susceptible and oseltamivir-resistant H275Y variants compared with the chemiluminescent assay.48 The NA-Fluor Kit comes with the manufacturer's protocol, which facilitates harmonization of the testing in laboratories worldwide. 2013 Influenza and other respiratory viruses Discussion IV H275Y 160 165 223 225 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. Of note, the N325K lies outside the NA enzyme active site. 2013 Influenza and other respiratory viruses Discussion IV N325K 13 18 36 38 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. One of these H273Y variants, B/Ontario/006876/2011, was previously detected by Public Health Ontario surveillance46 using the chemiluminescent NI assay, where it exhibited reduced susceptibility to oseltamivir and peramivir, as it did in the present study. 2013 Influenza and other respiratory viruses Discussion IV H273Y 13 18 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. The main goal of antiviral susceptibility surveillance is to detect the emergence/spread of drug resistant variants (such as H275Y) and to recognize a change in the drug susceptibility of viruses compared with those circulating in the previous season. 2013 Influenza and other respiratory viruses Discussion IV H275Y 125 130 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. The NI method used in this study has been shown to be well suited for the surveillance of drug resistance, particularly as it has been reported to be more predictive of in vivo susceptibility than cell based assays.47 While detection of H275Y variants can be readily performed using the fluorescent NI assay, especially when all three NAIs used in this study provide a clearly recognized IC50 pattern, the detection of H275Y variants present in mixed populations or that of novel amino acid substitutions which may alter NAI susceptibility may not be as apparent in such a functional assay; hence, additional genetic testing of potentially resistant viruses is vital. 2013 Influenza and other respiratory viruses Discussion IV H275Y;H275Y 237;419 242;424 NAI;NAI 521;335 524;339 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. This low trend is similar to that seen in previous seasons, since the emergence of the 2009 H1N1 pandemic virus.16, 17 Among influenza B viruses, the corresponding H273Y mutation, associated with reduced susceptibility to oseltamivir and peramivir in this virus type, was detected in only two (0 6%) viruses. 2013 Influenza and other respiratory viruses Discussion IV H273Y 164 169 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. We also detected two A(H1N1)pdm09 viruses with S247N substitution in the NA, both showing mildly reduced susceptibility to oseltamivir and peramivir. 2013 Influenza and other respiratory viruses Discussion IV S247N 47 52 73 75 23575174 Neuraminidase inhibitor susceptibility surveillance of influenza viruses circulating worldwide during the 2011 Southern Hemisphere season. When combined with the H275Y substitution, as detected in an oseltamivir-treated patient, the dual S247N+H275Y mutant exhibited extremely high oseltamivir resistance.42 This finding emphasizes a need to monitor for NA changes such as the S247N substitution, which by itself causes only a mild decrease in susceptibility to NAIs, but when present in combination with substitutions, such as H275Y, has the potential to dramatically augment resistance to NAIs. 2013 Influenza and other respiratory viruses Discussion IV H275Y;S247N;H275Y;S247N;H275Y 23;99;105;238;389 28;104;110;243;394 NA;NAI;NAI 215;323;452 217;327;456 23593230 Effect of cysteine mutations in the extracellular domain of CM2 on the influenza C virus replication. 2B) forms tetramers via non-covalent linkage on the rC1620A-infected cell surface and contributes to genome packaging through its channel function. 2013 PloS one Discussion IV C1620A 52 59 23593230 Effect of cysteine mutations in the extracellular domain of CM2 on the influenza C virus replication. 4C) and VLPs (WT-VLP:C1620A-VLP = 1.0:0.3. 2013 PloS one Discussion IV C1620A 21 27 23593230 Effect of cysteine mutations in the extracellular domain of CM2 on the influenza C virus replication. Alternatively, it may also be proposed that the dimers of CM2-C1620A exist as tetramers in the virions, but they are not stable under the conditions used in our analysis, like a recombinant influenza A virus lacking M2 oligomerization. 2013 PloS one Discussion IV C1620A 62 68 CM2;M2 58;216 61;218 23593230 Effect of cysteine mutations in the extracellular domain of CM2 on the influenza C virus replication. B), and the tetramer form of the mutant protein CM2-C1620A synthesized in the rC1620A-infected cells was present at less than trace amounts. 2013 PloS one Discussion IV C1620A;C1620A 52;78 58;85 CM2 48 51 23593230 Effect of cysteine mutations in the extracellular domain of CM2 on the influenza C virus replication. there was a statistical difference in the amount of GFP-vRNA between WT- and C1620A-VLPs. 2013 PloS one Discussion IV C1620A 77 83 23593230 Effect of cysteine mutations in the extracellular domain of CM2 on the influenza C virus replication. Therefore, it may be speculated that dimeric CM2-C1620A. 2013 PloS one Discussion IV C1620A 49 55 CM2 45 48 23626667 Quantitative characterization of glycan-receptor binding of H9N2 influenza A virus hemagglutinin. Based on the calculated Kd', the mQa88:Q226L mutant shows 5-fold higher affinity to human receptor than WF10. 2013 PloS one Discussion IV Q226L 39 44 23626667 Quantitative characterization of glycan-receptor binding of H9N2 influenza A virus hemagglutinin. One of the mutations Thr-189 Ala is in the RBS of H9 HA while the other mutation is in HA2 close to the transmembrane region (unlikely to impact RBS features and hence receptor binding). 2013 PloS one Discussion IV T189A 21 32 HA;HA 53;87 55;89 23626667 Quantitative characterization of glycan-receptor binding of H9N2 influenza A virus hemagglutinin. The contribution of Gln-226 to avian receptor binding and Leu-226 to human receptor binding was corroborated by the preferential avian receptor binding of mWF10:L226Q and human receptor-binding of mQa88:Q226L mutants respectively. 2013 PloS one Discussion IV L226Q;Q226L 161;203 166;208 23626667 Quantitative characterization of glycan-receptor binding of H9N2 influenza A virus hemagglutinin. The fact that the Thr-189 Ala mutation is needed for respiratory droplet transmission highlights the role of improving human receptor specificity in the context of other genes in a reassorted virus in conferring airborne transmissibility. 2013 PloS one Discussion IV T189A 18 29 23626667 Quantitative characterization of glycan-receptor binding of H9N2 influenza A virus hemagglutinin. Therefore, this study provides an important framework to understand key mutations such as Gln226 Leu in the context of the entire RBS in different H9 HAs to appropriately monitor the evolution of H9 viruses. 2013 PloS one Discussion IV Q226L 90 100 23626667 Quantitative characterization of glycan-receptor binding of H9N2 influenza A virus hemagglutinin. Unlike H2 and H3 subtypes where change in receptor binding preference from avian to human receptor has been associated with at least two mutations Q226L and G228S, it appears that in the case of H9 HA a single mutation Q226L might be sufficient to alter its glycan-receptor binding properties. 2013 PloS one Discussion IV Q226L;G228S;Q226L 147;157;219 152;162;224 HA 198 200 23626667 Quantitative characterization of glycan-receptor binding of H9N2 influenza A virus hemagglutinin. We demonstrated that Thr189 Ala mutation in WF10, mQ88:Q226L and Qa88 HAs increases binding specificity. 2013 PloS one Discussion IV Q226L;T189A 55;21 60;31 23626667 Quantitative characterization of glycan-receptor binding of H9N2 influenza A virus hemagglutinin. While H9N2 subtype is yet to adapt to the human host, reassorted strains with H9 HA and NA have acquired as few as 2 amino acid changes in HA and a single Ile-28 Val change in NA to confer respiratory droplet transmission in ferrets (characteristic trait of human-adapted viruses). 2013 PloS one Discussion IV I28V 155 165 HA;HA;NA;NA 81;139;88;176 83;141;90;178 23646055 Occurrence and characterization of oseltamivir-resistant influenza virus in children between 2007-2008 and 2008-2009 seasons. However, phenotypic analysis showed that oseltamivir IC50 ranged within high-level drug resistance, H275Y of NA gene and partial variation of HA gene does not affect antigenicity to HA vaccine, even though oseltamivir treatment group had shorter admisson duration and fewer lower respiratory tract complications compared to the oseltamivir nontreatment group. 2013 Korean journal of pediatrics Discussion IV H275Y 100 105 HA;HA;NA 142;182;109 144;184;111 23646055 Occurrence and characterization of oseltamivir-resistant influenza virus in children between 2007-2008 and 2008-2009 seasons. In addition, unlike the 2007-2008 season, the influenza A/H1N1 isolated during 2008-2009 season had high oseltamivir IC50 in the phenotypic analysis, and had H275Y (N1 numbering) mutation in the genotypic analysis, showing that NI-resistant virus was prevalent. 2013 Korean journal of pediatrics Discussion IV H275Y 158 163 23646055 Occurrence and characterization of oseltamivir-resistant influenza virus in children between 2007-2008 and 2008-2009 seasons. In conclusion, based on the our knowledge, this study was the first study to investigate Korean pediatric patients infected influenza virus (two groups based on the oseltamivir treament), their oseltamivir resistance, NA H275Y protein variation, partial variation of HA in the influenza A/H1N1 virus isolated from both oseltamivir treatment and non-treatment groups, during the progression from the first study period to the second study period even though oseltamivir treatment group had shorter admission duration and fewer lower respiratory tract complications compared to the oseltamivir nontreatment group. 2013 Korean journal of pediatrics Discussion IV H275Y 221 226 HA;NA 267;218 269;220 23646055 Occurrence and characterization of oseltamivir-resistant influenza virus in children between 2007-2008 and 2008-2009 seasons. In this study, oseltamivir-resistant influenza A/H1N1 type during 2008-2009 seasons had H275Y mutation of NA gene and D354G mutation, which was genetically close to oseltamivir-resistant A/H1N1 that was prevalent in Europe and North America during 2007-2008 season. 2013 Korean journal of pediatrics Discussion IV H275Y;D354G 88;118 93;123 106 108 23646055 Occurrence and characterization of oseltamivir-resistant influenza virus in children between 2007-2008 and 2008-2009 seasons. studied pediatric patients who were infected with influenza during 2007-2008 and 2008-2009 seasons, and reported that the H275Y mutation rate of influenza A/H1N1 was 1.6% during 2007-2008 influenza season, and 100% during 2008-2009 influenza season, and they also reported that no difference in the patient's characteristics and hospitalization duration was found between pediatric patients infected with oseltamivir-resistant influenza A/H1N1 and those infected with wild-type seasonal A/H1N1 in compatible with this study . 2013 Korean journal of pediatrics Discussion IV H275Y 122 127 23646055 Occurrence and characterization of oseltamivir-resistant influenza virus in children between 2007-2008 and 2008-2009 seasons. The results of genotype analysis revealed H275Y (N1 numbering) mutation, which was consistent with those of previous studies. 2013 Korean journal of pediatrics Discussion IV H275Y 42 47 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. Alternate mutations at this position, N156E and N156D, have been shown to cause antigenic changes. 2013 PLoS pathogens Discussion IV N156E;N156D 38;48 43;53 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. Although a pure population of the N156K mutant virus could not be efficiently isolated, either from ferret nasal washes or by reverse genetics, flow cytometry antibody binding assays demonstrated that the N156K mutation causes antigenic escape. 2013 PLoS pathogens Discussion IV N156K;N156K 34;205 39;210 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. Although this double mutant outgrew the N156K mutant in a competitive mixture in vivo, the K142N mutation was not acquired in both lines of passaging suggesting it is not essential for transmission in naive ferrets. 2013 PLoS pathogens Discussion IV N156K;K142N 40;91 45;96 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. As antiserum from a wildtype virus-infected ferret appeared directed to the N156 region and could no longer recognise the N156K mutant virus, and antiserum from a N156K virus-infected ferret appeared directed to a different region of the HA common to wildtype and N156K mutant virus, we hypothesize that immunity is directional and drives antigenic drift in this contact transmission model. 2013 PLoS pathogens Discussion IV N156K;N156K;N156K 122;163;264 127;168;269 HA 238 240 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. Attempts to assess the avidity of the N156K and K142N+N156K mutants were unsuccessful due to virus isolation difficulties and the inability of the viruses to bind RBC. 2013 PLoS pathogens Discussion IV N156K;K142N;N156K 38;48;54 43;53;59 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. In vitro and/or in vivo passage of the 2012/2013 A(H1N1)pdm09 viruses under immune pressure would indicate whether N156K is permissive in the presence of additional mutations or whether other regions of the HA globular head are now under greater selective pressure. 2013 PLoS pathogens Discussion IV N156K 115 120 HA 207 209 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. Interestingly subsequent passage of the N156K mutant virus in naive ferrets did result in an additional mutation in the HA protein, K142N, in one passage line. 2013 PLoS pathogens Discussion IV N156K;K142N 40;132 45;137 HA 120 122 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. K142N did not alter receptor binding specificity in the assays used in this study, but whether changes in avidity have occurred is unknown. 2013 PLoS pathogens Discussion IV K142N 0 5 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. N156K is computationally predicted to be structurally significant by introduction of a longer charged side chain that changes the distribution of the charge of the HA. 2013 PLoS pathogens Discussion IV N156K 0 5 HA 164 166 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. Overall, these data suggest that selection of the N156K mutant, maintained through contact transmission in ferrets, drives emergence of a virus with altered, but effective, binding to receptors of the ferret respiratory tract, and is capable of extensive replication in vivo. 2013 PLoS pathogens Discussion IV N156K 50 55 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. The cell culture adaptations, K153E and G155E, are predicted to induce structural changes in the HA head that reduce the positive electrostatic potential of the HA head domain. 2013 PLoS pathogens Discussion IV K153E;G155E 30;40 35;45 HA;HA 97;161 99;163 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. The emergence of the N156K virus did not alter the virus kinetics in the MIV+IFA-immunised ferrets. 2013 PLoS pathogens Discussion IV N156K 21 26 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. The low HA titre in the initial passage, and negative association with cell culture, may prevent identification of original clinical samples containing N156K alone, hence laboratories may exclude these viruses from surveillance studies. 2013 PLoS pathogens Discussion IV N156K 152 157 HA 8 10 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. The N156K mutant virus could not be recognized by a monoclonal antibody (mAb174) which drives escape in the Sa/Sb antigenic site of wildtype virus. 2013 PLoS pathogens Discussion IV N156K 4 9 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. The N156K mutation also increases the positive charge potential, which may be important for surface interactions of the HA protein with antibodies or more remote carbohydrate moieties extending from the natural host receptor structure. 2013 PLoS pathogens Discussion IV N156K 4 9 HA 120 122 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. The N156K virus outgrew the wildtype virus in both naive and immunized ferrets when in direct competition, suggesting that the N156K mutant is fitter than the wildtype virus in both the presence and absence of immune pressure. 2013 PLoS pathogens Discussion IV N156K;N156K 4;127 9;132 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. The N156K virus transmitted between immunized ferrets for up to four passages, although a break in transmission occurred in both lines. 2013 PLoS pathogens Discussion IV N156K 4 9 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. This is supported by the following additional evidence: The N156K mutant arose only in ferrets with specific antibodies, and was present in both passage lines. 2013 PLoS pathogens Discussion IV N156K 60 65 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. This N156K mutation was generated in two independent lines of MIV+IFA-immunized ferrets, but was not detected in the virus used to infect ferrets, nor did it appear in unimmunized ferrets, suggesting that the N156K mutation had a selective advantage when placed under non-sterilizing immune pressure. 2013 PLoS pathogens Discussion IV N156K;N156K 5;209 10;214 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. Thus, we hypothesize that the N156K mutation increases receptor binding avidity compared to wildtype virus. 2013 PLoS pathogens Discussion IV N156K 30 35 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. We anticipate that further passage of the N156K mutant virus in homologous vaccinated ferrets (i.e vaccinated with the N156K mutant) would drive further drift of the A(H1N1)pdm09 N156K virus that would be again accompanied by changes in the receptor binding properties. 2013 PLoS pathogens Discussion IV N156K;N156K;N156K 42;119;179 47;124;184 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. We have demonstrated that the N156K mutation produced structural changes that altered receptor specificity, including the loss of ability to agglutinate RBC from a variety of species. 2013 PLoS pathogens Discussion IV N156K 30 35 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. When cultured in vitro, the cell culture adaptations negate the significant effects of the N156K mutation on the charge distribution and alter the receptor binding preference of the HA protein (and possibly the avidity), which facilitates hemagglutination. 2013 PLoS pathogens Discussion IV N156K 91 96 HA 182 184 23671418 Antigenic drift of the pandemic 2009 A(H1N1) influenza virus in A ferret model. When passaged in naive ferrets, the growth kinetics and transmission potential of the N156K virus was equivalent to the wildtype virus, indicating that the N156K mutation was not deleterious in non-immune ferrets. 2013 PLoS pathogens Discussion IV N156K;N156K 86;156 91;161 23717200 Prolonged influenza virus shedding and emergence of antiviral resistance in immunocompromised patients and ferrets. Early studies on H275Y pH1N1 viral fitness were performed on viruses isolated shortly after the start of the 2009 pandemic. 2013 PLoS pathogens Discussion IV H275Y 17 22 23717200 Prolonged influenza virus shedding and emergence of antiviral resistance in immunocompromised patients and ferrets. In the 2007/2008 H1N1 virus season an H275Y oseltamivir resistant mutant emerged, which had completely overtaken the circulating virus population by the end of 2008. 2013 PLoS pathogens Discussion IV H275Y 38 43 23717200 Prolonged influenza virus shedding and emergence of antiviral resistance in immunocompromised patients and ferrets. It is therefore plausible that oseltamivir therapy reduced H275Y mutant virus titer in the lungs, but not in the upper respiratory tract. 2013 PLoS pathogens Discussion IV H275Y 59 64 23717200 Prolonged influenza virus shedding and emergence of antiviral resistance in immunocompromised patients and ferrets. It might happen again with pH1N1 virus if it would also harbour the H275Y mutation without loss of viral fitness. 2013 PLoS pathogens Discussion IV H275Y 68 73 23717200 Prolonged influenza virus shedding and emergence of antiviral resistance in immunocompromised patients and ferrets. Priority should now be given to study the overall fitness of these recent pH1N1 viruses that appear not to be affected by the H275Y change. 2013 PLoS pathogens Discussion IV H275Y 126 131 23717200 Prolonged influenza virus shedding and emergence of antiviral resistance in immunocompromised patients and ferrets. Recent reports on clusters of transmitted pH1N1 H275Y mutant viruses are the first indication that this may not be an unlikely scenario. 2013 PLoS pathogens Discussion IV H275Y 48 53 23717200 Prolonged influenza virus shedding and emergence of antiviral resistance in immunocompromised patients and ferrets. These levels were still about 100 and 30 times higher than the 50% inhibitor concentration of an H275Y mutant virus, which is roughly 30 ng/ml (~100 nM). 2013 PLoS pathogens Discussion IV H275Y 97 102 23717200 Prolonged influenza virus shedding and emergence of antiviral resistance in immunocompromised patients and ferrets. This introduction of the H275Y mutation disqualified oseltamivir as the first line antiviral drug. 2013 PLoS pathogens Discussion IV H275Y 25 30 23717200 Prolonged influenza virus shedding and emergence of antiviral resistance in immunocompromised patients and ferrets. We also used an early H275Y virus isolate in our experiment. 2013 PLoS pathogens Discussion IV H275Y 22 27 23717200 Prolonged influenza virus shedding and emergence of antiviral resistance in immunocompromised patients and ferrets. We observed lower mortality in the treated animals infected with H275Y mutant virus without an observed difference in virus titers in the upper respiratory tract. 2013 PLoS pathogens Discussion IV H275Y 65 70 23717200 Prolonged influenza virus shedding and emergence of antiviral resistance in immunocompromised patients and ferrets. We observed that, for animals infected with either wild type or H275Y mutant virus, high dose oseltamivir treatment was still beneficial. 2013 PLoS pathogens Discussion IV H275Y 64 69 23759670 Virological self-sampling to monitor influenza antiviral susceptibility in a community cohort. Emergence of the influenza A(H1N1)pdm09 virus with the H275Y mutation, which confers oseltamivir resistance, did occur under drug pressure in a low percentage of community patients (four patients; 0.3%) and in two patients who were not receiving drug treatment (0.1%), although none contained >30% of resistant virus. 2013 The Journal of antimicrobial chemotherapy Discussion IV H275Y 55 60 23759670 Virological self-sampling to monitor influenza antiviral susceptibility in a community cohort. Influenza A(H1N1)pdm09 virus with the H275Y substitution does not cause more severe disease than the susceptible virus. 2013 The Journal of antimicrobial chemotherapy Discussion IV H275Y 38 43 23759670 Virological self-sampling to monitor influenza antiviral susceptibility in a community cohort. One limitation of this study is that we screened for only the H275Y mutation, and other amino acid substitutions that have been shown to cause a reduced susceptibility of the influenza A(H1N1)pdm09 virus to one or more NIs, such as at position 223, were not screened for, due to their comparatively infrequent incidence in global surveillance. 2013 The Journal of antimicrobial chemotherapy Discussion IV H275Y 62 67 23759670 Virological self-sampling to monitor influenza antiviral susceptibility in a community cohort. There have, however, been documented episodes of transmission involving the H275Y-containing A(H1HN1)pdm09 viruses in both immunocompromised and immunocompetent patients. 2013 The Journal of antimicrobial chemotherapy Discussion IV H275Y 76 81 23759670 Virological self-sampling to monitor influenza antiviral susceptibility in a community cohort. While the level of transmissibility of the H275Y oseltamivir-resistant A(H1N1)pdm09 strain varies in different in vivo transmission models, none to date has indicated that the resistant strains are any more transmissible than the susceptible strains. 2013 The Journal of antimicrobial chemotherapy Discussion IV H275Y 43 48 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. However, considering the estimated large number of infections worldwide, additional viruses with the PB2-D701N mutation may exist in the population. 2013 PloS one Discussion IV D701N 105 110 PB2 101 104 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. However, the supplemental data published by Yamada et al., showed the PB2-D701N substitution in rA/California/04/2009 H1N1pdm enhanced morbidity in BALB/cJ mice, which is consistent with our findings. 2013 PloS one Discussion IV D701N 74 79 PB2 70 73 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. However, the tissue titers of the rA/California/04/2009 PB2-701N virus were comparable with those of the PB2-701D virus at 3 dpi and 6 dpi, and the authors did not remark that PB2-D701N actually showed enhanced virulence as their supplemental data suggested. 2013 PloS one Discussion IV D701N 180 185 PB2;PB2;PB2 56;105;176 59;108;179 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. In summary, our findings support a role for the asparagine residue at PB2-701 in contributing to the virulence of influenza A viruses and show that PB2-D701N in the H1N1pdm virus increases its viral RNA polymerase activity in human and other mammalian cells, confers more efficient replication in cell lines and in primary human alveolar epithelial cells, and results in increased pathogenicity in mice and increased transmissibility in ferrets. 2013 PloS one Discussion IV D701N 152 157 PB2;PB2 70;148 73;151 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. Notably, this is the first demonstration that PB2-D701N substitution enhances the transmissibility of influenza A viruses in the ferret transmission model. 2013 PloS one Discussion IV D701N 50 55 PB2 46 49 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. Surprisingly, of the approximate 4,000 H1N1pdm PB2 sequences available in the major influenza virus databases (Influenza Research Database, NIH/NCBI Influenza Virus Resource, EpiFlu Database), there is only one H1N1pdm virus (A/Wisconsin/51/2009) containing the PB2-D701N mutation (GISAID EpiFlu, accession#EPI273622, accessed 08-15-2012). 2013 PloS one Discussion IV D701N 266 271 PB2 262 265 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. The data from Herfst et al., suggested that the PB2-D701N substitution didn't increase the transmission efficiency of the rA/Netherlands/602/2009 virus in their ferret transmission model. 2013 PloS one Discussion IV D701N 52 57 PB2 48 51 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. The data presented in this study demonstrate that the PB2-D701N substitution also increased the H1N1pdm virus replication in primary human cells, pathogenicity in the mouse model, and transmission in the ferret model. 2013 PloS one Discussion IV D701N 58 63 PB2 54 57 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. The rarity of PB2 sequences with D701N mutation indicates that so far the mutation has not conferred better fitness to the H1N1pdm virus for transmission in humans, which is plausible since fitness and evolution in the human population is a polygenic trait. 2013 PloS one Discussion IV D701N 33 38 PB2 14 17 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. The true threat of the PB2-D701N substitution to humans is unknown; however, if H1N1pdm viruses containing PB2-701N do emerge as this unique virus continues to evolve in human populations, it may pave the way to a more severe disease burden. 2013 PloS one Discussion IV D701N 27 32 PB2;PB2 23;107 26;110 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. Therefore, we speculate that H1N1pdm viruses containing a PB2-D701N substitution may be more virulent and/or transmissible in humans than the viruses that circulated in the early years of the pandemic. 2013 PloS one Discussion IV D701N 62 67 PB2 58 61 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. This more stringent transmission model allows one to detect the increased transmission rate upon introduction of the PB2-D701N substitution into the H1N1pdm virus and the data also clearly shows increased transmission kinetics (Figure 6). 2013 PloS one Discussion IV D701N 121 126 PB2 117 120 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. Those virulence factors alone, or in combination with the PB2-D701N mutation, may increase the replication and pathogenicity of H1N1pdm viruses. 2013 PloS one Discussion IV D701N 62 67 PB2 58 61 23799150 Asparagine substitution at PB2 residue 701 enhances the replication, pathogenicity, and transmission of the 2009 pandemic H1N1 influenza A virus. Two other studies that examined the PB2-D701N and other PB2 mutations in the context of rA/Netherlands/602/2009 and rA/California/04/2009 H1N1pdm viruses concluded that both the PB2-E627K and PB2-D701N mutations had little impact on pathogenicity and transmissibility. 2013 PloS one Discussion IV D701N;E627K;D701N 40;182;196 45;187;201 PB2;PB2;PB2;PB2 36;56;178;192 39;59;181;195 23860768 Resistance to neuraminidase inhibitors conferred by an R292K mutation in a human influenza virus H7N9 isolate can be masked by a mixed R/K viral population. A reduced HA binding affinity would allow the virus to tolerate the low NA activity caused by the NA R292K mutation and allow the virus to form large plaques and to replicate efficiently in vitro. 2013 mBio Discussion IV R292K 101 106 HA;NA;NA 10;72;98 12;74;100 23860768 Resistance to neuraminidase inhibitors conferred by an R292K mutation in a human influenza virus H7N9 isolate can be masked by a mixed R/K viral population. Changes in hydrogen bonding in the R292K mutant lead to a reduced interaction between the inhibitor carboxylate and the protein. 2013 mBio Discussion IV R292K 35 40 23860768 Resistance to neuraminidase inhibitors conferred by an R292K mutation in a human influenza virus H7N9 isolate can be masked by a mixed R/K viral population. In summary, we confirm that the R292K mutation in the novel H7N9 virus confers resistance to zanamivir, peramivir, and oseltamivir carboxylate. 2013 mBio Discussion IV R292K 32 37 23860768 Resistance to neuraminidase inhibitors conferred by an R292K mutation in a human influenza virus H7N9 isolate can be masked by a mixed R/K viral population. It is crucial to monitor the emergence of the R292K mutation among H7N9 patients by genotypic methods. 2013 mBio Discussion IV R292K 46 51 23860768 Resistance to neuraminidase inhibitors conferred by an R292K mutation in a human influenza virus H7N9 isolate can be masked by a mixed R/K viral population. It is not clear if balanced HA-NA activity would be maintained in vivo during ferret transmission experiments, including the transmissibility of the resistant strain carrying the R292K mutation and the potential of a wild-type revertant to arise in vivo over time. 2013 mBio Discussion IV R292K 179 184 HA;NA 28;31 30;33 23860768 Resistance to neuraminidase inhibitors conferred by an R292K mutation in a human influenza virus H7N9 isolate can be masked by a mixed R/K viral population. It is therefore recommended that the emergence of the R292K mutation in H7N9 patients undergoing NA inhibitor treatment should be monitored using genotypic methods in combination with the phenotypic characterization of the virus. 2013 mBio Discussion IV R292K 54 59 97 99 23860768 Resistance to neuraminidase inhibitors conferred by an R292K mutation in a human influenza virus H7N9 isolate can be masked by a mixed R/K viral population. It remains to be investigated whether the R292K mutation would exhibit similar plaque morphology or replication characteristics in the other novel H7N9 viruses. 2013 mBio Discussion IV R292K 42 47 23860768 Resistance to neuraminidase inhibitors conferred by an R292K mutation in a human influenza virus H7N9 isolate can be masked by a mixed R/K viral population. It was observed previously that the seasonal H3N2 virus carrying the R292K mutation showed compromised replication efficiency in MDCK-SIAT1 cells and possessed inefficient transmissibility to naive direct-contact ferrets. 2013 mBio Discussion IV R292K 69 74 23860768 Resistance to neuraminidase inhibitors conferred by an R292K mutation in a human influenza virus H7N9 isolate can be masked by a mixed R/K viral population. It was reported that the R292K mutation reduced the NA activity to 20% of the wild-type virus activity and that the virus carrying this mutation alone formed plaques significantly smaller than those formed by the parent strain. 2013 mBio Discussion IV R292K 25 30 52 54 23860768 Resistance to neuraminidase inhibitors conferred by an R292K mutation in a human influenza virus H7N9 isolate can be masked by a mixed R/K viral population. One major molecular difference between the A/Shanghai/1/2013 and A/Shanghai/2/2013 viruses in the HA protein is the absence of the avian-to-human-adaptation Q226L change in the A/Shanghai/1/2013 virus. 2013 mBio Discussion IV Q226L 157 162 HA 98 100 23860768 Resistance to neuraminidase inhibitors conferred by an R292K mutation in a human influenza virus H7N9 isolate can be masked by a mixed R/K viral population. Subsequent passage yielded variants with additional HA (G143E or N199S) in combination with the NA R292K mutation. 2013 mBio Discussion IV G143E;N199S;R292K 56;65;99 61;70;104 HA;NA 52;96 54;98 23860768 Resistance to neuraminidase inhibitors conferred by an R292K mutation in a human influenza virus H7N9 isolate can be masked by a mixed R/K viral population. Surveillance studies suggest that the emergence of NA mutations conferring resistance to NA inhibitors has reportedly been low, with the exception of the naturally emergent H274Y NA mutation in H1N1 seasonal influenza viruses during the influenza season of 2007 to 2008. 2013 mBio Discussion IV H274Y 173 178 NA;NA;NA 51;89;179 53;91;181 23860768 Resistance to neuraminidase inhibitors conferred by an R292K mutation in a human influenza virus H7N9 isolate can be masked by a mixed R/K viral population. The HA mutations were observed to increase the plaque size of the H1N9 virus carrying the R292K mutation. 2013 mBio Discussion IV R292K 90 95 HA 4 6 23860768 Resistance to neuraminidase inhibitors conferred by an R292K mutation in a human influenza virus H7N9 isolate can be masked by a mixed R/K viral population. The mechanism by which the R292K confers higher resistance to oseltamivir is through preventing rotation of the E276 to form the salt link to R224, which is required for the formation of a hydrophobic pocket to accommodate the bulky pentyl ether group of the oseltamivir carboxylate. 2013 mBio Discussion IV R292K 27 32 23860768 Resistance to neuraminidase inhibitors conferred by an R292K mutation in a human influenza virus H7N9 isolate can be masked by a mixed R/K viral population. The R292K mutants were serially passaged in the absence of NA inhibitors 10 times, and no reversion in the HA or NA mutation was observed previously. 2013 mBio Discussion IV R292K 4 9 HA;NA;NA 107;59;113 109;61;115 23860768 Resistance to neuraminidase inhibitors conferred by an R292K mutation in a human influenza virus H7N9 isolate can be masked by a mixed R/K viral population. The R292K mutation is one of the most commonly identified mutations among seasonal H3N2 isolates with significantly reduced sensitivity to oseltamivir carboxylate, intermediate resistance to peramivir, and slightly reduced sensitivity to zanamivir. 2013 mBio Discussion IV R292K 4 9 23860768 Resistance to neuraminidase inhibitors conferred by an R292K mutation in a human influenza virus H7N9 isolate can be masked by a mixed R/K viral population. The R292K mutation that confers resistance to both zanamivir and oseltamivir carboxylate in a reassortant H1N9 virus was selected in vitro after 8 passages in the presence of the 6-carboximide derivative of zanamivir. 2013 mBio Discussion IV R292K 4 9 23860768 Resistance to neuraminidase inhibitors conferred by an R292K mutation in a human influenza virus H7N9 isolate can be masked by a mixed R/K viral population. The stability of the R292K mutation in the novel H7N9 viruses also needs to be further characterized. 2013 mBio Discussion IV R292K 21 26 23860768 Resistance to neuraminidase inhibitors conferred by an R292K mutation in a human influenza virus H7N9 isolate can be masked by a mixed R/K viral population. This could have been due to the low NA activity (25%) possessed by the R292K mutant virus relative to the A/Shanghai/1/2013 wild-type virus, comparable to the previously reported results that the R292K mutation reduced the enzyme activity in an H1N9 virus to only 20% of the wild-type level. 2013 mBio Discussion IV R292K;R292K 71;196 76;201 36 38 23860768 Resistance to neuraminidase inhibitors conferred by an R292K mutation in a human influenza virus H7N9 isolate can be masked by a mixed R/K viral population. Using the enzyme-based NA inhibition assay, it was shown that the R292K mutation in the H1N9 virus conferred reduced sensitivity to zanamivir (by 55-fold), peramivir (by 1,000-fold), and oseltamivir carboxylate (by 6,500-fold), comparable to the results we observed with the novel H7N9 influenza viruses. 2013 mBio Discussion IV R292K 66 71 23 25 23860768 Resistance to neuraminidase inhibitors conferred by an R292K mutation in a human influenza virus H7N9 isolate can be masked by a mixed R/K viral population. We report here that the R292K NA mutation confers resistance to zanamivir, peramivir, and oseltamivir carboxylate in the novel H7N9 virus. 2013 mBio Discussion IV R292K 24 29 30 32 23894575 Analysis of adaptation mutants in the hemagglutinin of the influenza A(H1N1)pdm09 virus. 2012 (doi:10.1128/mBio.00120-12) in which the escape mutant K157N had characteristics similar to the wild type HA, although it was no longer recognized by antibodies. 2013 PloS one Discussion IV K157N;K157N 61;60 66;65 HA 111 113 23894575 Analysis of adaptation mutants in the hemagglutinin of the influenza A(H1N1)pdm09 virus. Consistent with our results, mutation D222G possesses increased affinity for alpha2,6 receptors compared with D222. 2013 PloS one Discussion IV D222G 38 43 23894575 Analysis of adaptation mutants in the hemagglutinin of the influenza A(H1N1)pdm09 virus. Contrary to what happened with other mutations, S185T caused no change in interactions with nearby amino acids. 2013 PloS one Discussion IV S185T 48 53 23894575 Analysis of adaptation mutants in the hemagglutinin of the influenza A(H1N1)pdm09 virus. In the case of variant 3, polymorphism at position 222 has been extensively studied due mainly to mutation D222G, which has been associated with severe influenza as a consequence of change in the preference of sialic acid receptors. 2013 PloS one Discussion IV D222G 107 112 Influenza 145 161 23894575 Analysis of adaptation mutants in the hemagglutinin of the influenza A(H1N1)pdm09 virus. Mutation E374K is located in a pocket harboring the fusion peptide. 2013 PloS one Discussion IV E374K 9 14 23894575 Analysis of adaptation mutants in the hemagglutinin of the influenza A(H1N1)pdm09 virus. Mutation S143G created a rearrangement in loop 130-140, altering the conformation and charge distribution of antigenic site Ca2 by hindering a histidine residue located at the tip of the loop. 2013 PloS one Discussion IV S143G 9 14 23894575 Analysis of adaptation mutants in the hemagglutinin of the influenza A(H1N1)pdm09 virus. Thus, we assumed that a likely cause that would positively select mutation S185T was immune recognition avoidance. 2013 PloS one Discussion IV S185T 75 80 23894575 Analysis of adaptation mutants in the hemagglutinin of the influenza A(H1N1)pdm09 virus. Thus, we propose that the E374K mutation may yield a more unstable HA, with an increased pH of activation, and hence an increased capability to infect cells. 2013 PloS one Discussion IV E374K 26 31 HA 67 69 23902660 Frequency of D222G haemagglutinin mutant of pandemic (H1N1) pdm09 influenza virus in Tunisia between 2009 and 2011. (2010) and, since then, different studies in several countries have found the D222G substitution to be more frequently associated with patients with severe pandemic influenza than in non-severe control cases. 2013 Diagnostic pathology Discussion IV D222G 78 83 23902660 Frequency of D222G haemagglutinin mutant of pandemic (H1N1) pdm09 influenza virus in Tunisia between 2009 and 2011. Although most of studies demonstrated the presence of D222G substitution in severe cases, it was also reported in mild cases. 2013 Diagnostic pathology Discussion IV D222G 54 59 23902660 Frequency of D222G haemagglutinin mutant of pandemic (H1N1) pdm09 influenza virus in Tunisia between 2009 and 2011. Although, 7% of them, found in severe cases in the present study, had the D222G substitution. 2013 Diagnostic pathology Discussion IV D222G 74 79 23902660 Frequency of D222G haemagglutinin mutant of pandemic (H1N1) pdm09 influenza virus in Tunisia between 2009 and 2011. An association between D222G and severity was initially proposed by Kilander et al. 2013 Diagnostic pathology Discussion IV D222G 23 28 23902660 Frequency of D222G haemagglutinin mutant of pandemic (H1N1) pdm09 influenza virus in Tunisia between 2009 and 2011. Despite the available virological, epidemiological and clinical information, the D222E substitution could confer more severity to the disease. 2013 Diagnostic pathology Discussion IV D222E 81 86 23902660 Frequency of D222G haemagglutinin mutant of pandemic (H1N1) pdm09 influenza virus in Tunisia between 2009 and 2011. Further study is warranted to elucidate the intriguing relationship between D222G substitution and severe disease. 2013 Diagnostic pathology Discussion IV D222G 76 81 23902660 Frequency of D222G haemagglutinin mutant of pandemic (H1N1) pdm09 influenza virus in Tunisia between 2009 and 2011. It is worth noting that although the Asp222Gly mutation currently has not been associated with severe pandemic in humans. 2013 Diagnostic pathology Discussion IV D222G 37 46 23902660 Frequency of D222G haemagglutinin mutant of pandemic (H1N1) pdm09 influenza virus in Tunisia between 2009 and 2011. Many retrospective analyses have found that cases bearing the D222G mutation were more likely to be associated with severe pneumonia, admission to intensive care facilities, and death. 2013 Diagnostic pathology Discussion IV D222G 62 67 Pneumonia 123 132 23902660 Frequency of D222G haemagglutinin mutant of pandemic (H1N1) pdm09 influenza virus in Tunisia between 2009 and 2011. Moreover, D222G substitution had been present in the Tunisian virus strain since pandemic season and throughout 2010-2011 season. 2013 Diagnostic pathology Discussion IV D222G 10 15 23902660 Frequency of D222G haemagglutinin mutant of pandemic (H1N1) pdm09 influenza virus in Tunisia between 2009 and 2011. Other groups have not observed substantial differences between wild-type and D222G viruses in mouse or ferret models, indicating the need for further investigation into the role of D222G in virulence of influenza A (H1N1)pdm09. 2013 Diagnostic pathology Discussion IV D222G;D222G 77;181 82;186 23902660 Frequency of D222G haemagglutinin mutant of pandemic (H1N1) pdm09 influenza virus in Tunisia between 2009 and 2011. The D222E was detected with less frequency than the D222G and only found in severe case patient. 2013 Diagnostic pathology Discussion IV D222E;D222G 4;52 9;57 23902660 Frequency of D222G haemagglutinin mutant of pandemic (H1N1) pdm09 influenza virus in Tunisia between 2009 and 2011. The frequency of D222G substitution is higher in severe cases than mild cases. 2013 Diagnostic pathology Discussion IV D222G 17 22 23902660 Frequency of D222G haemagglutinin mutant of pandemic (H1N1) pdm09 influenza virus in Tunisia between 2009 and 2011. The majority of studies have reported that presence of D222G is sufficient to enhance virus replication and lethality in mouse models, with this effect ranging from modest to pronounced. 2013 Diagnostic pathology Discussion IV D222G 55 60 23902660 Frequency of D222G haemagglutinin mutant of pandemic (H1N1) pdm09 influenza virus in Tunisia between 2009 and 2011. Viruses with D222G substitution in HA protein have appeared sporadically and spontaneously in Tunisia since July 2009. 2013 Diagnostic pathology Discussion IV D222G 13 18 HA 35 37 23951116 Resistance mutation R292K is induced in influenza A(H6N2) virus by exposure of infected mallards to low levels of oseltamivir. Although no proper kinetic assay of the NA enzyme was performed, we observed an approximately 70% reduction in NA-activity of the R292K isolates while preparing our viral samples for NAI inhibition analysis. 2013 PloS one Discussion IV R292K 130 135 NA;NA;NAI 40;111;183 42;113;186 23951116 Resistance mutation R292K is induced in influenza A(H6N2) virus by exposure of infected mallards to low levels of oseltamivir. Both D113N and D141N are frequently occurring variants in avian N2 strains and the residues are closely located to each other. 2013 PloS one Discussion IV D113N;D141N 5;15 10;20 23951116 Resistance mutation R292K is induced in influenza A(H6N2) virus by exposure of infected mallards to low levels of oseltamivir. Despite the low increase in IC50 to ZA (<10-fold) by the R292K mutation, it still raises concern as it indicates that overuse of one NAI might harm also other members of this drug class. 2013 PloS one Discussion IV R292K 57 62 NAI 133 136 23951116 Resistance mutation R292K is induced in influenza A(H6N2) virus by exposure of infected mallards to low levels of oseltamivir. Further investigations are needed in this regard, as well as whether the R292K mutation can be retained in mallards also without drug pressure. 2013 PloS one Discussion IV R292K 73 78 23951116 Resistance mutation R292K is induced in influenza A(H6N2) virus by exposure of infected mallards to low levels of oseltamivir. It does however demonstrate that fecal-oral infection with a R292K-mutated virus resulted in IHC positivity in the intestine 5 days pi which was not seen in any of the two birds fecal-orally infected with wild-type A(H6N2) virus. 2013 PloS one Discussion IV R292K 61 66 23951116 Resistance mutation R292K is induced in influenza A(H6N2) virus by exposure of infected mallards to low levels of oseltamivir. It is possible that the additional mutations D113N or D141N in NA and/or E216K in HA might have influenced such an adaptation, like permissive mutations have been demonstrated in N1 virus that can compensate for the resistance mutation H274Y. 2013 PloS one Discussion IV D113N;D141N;E216K;H274Y 45;54;73;236 50;59;78;241 HA;NA 82;63 84;65 23951116 Resistance mutation R292K is induced in influenza A(H6N2) virus by exposure of infected mallards to low levels of oseltamivir. No difference in shedding pattern was observed when comparing wild-type virus from the 120 ng/L and 1.2 microg/L OC levels and R292K-mutated virus from the 12 microg/L OC level suggesting a retained replicative capacity for the mutant. 2013 PloS one Discussion IV R292K 127 132 23951116 Resistance mutation R292K is induced in influenza A(H6N2) virus by exposure of infected mallards to low levels of oseltamivir. One of the birds from which sections of intestine were evaluated by IHC, was infected with R292K-mutated virus. 2013 PloS one Discussion IV R292K 91 96 23951116 Resistance mutation R292K is induced in influenza A(H6N2) virus by exposure of infected mallards to low levels of oseltamivir. Our findings of additional mutations D113N or D141N in the NA and E216K in the HA together with R292K in the last isolates of the high-dose experiment, co-varied with the persistence of R292K through the egg propagation process. 2013 PloS one Discussion IV D113N;D141N;E216K;R292K;R292K 37;46;66;96;186 42;51;71;101;191 HA;NA 79;59 81;61 23951116 Resistance mutation R292K is induced in influenza A(H6N2) virus by exposure of infected mallards to low levels of oseltamivir. Persistence of R292K without drug pressure has been shown in vitro but not in vivo in a ferret model or in a treated patient. 2013 PloS one Discussion IV R292K 15 20 23951116 Resistance mutation R292K is induced in influenza A(H6N2) virus by exposure of infected mallards to low levels of oseltamivir. Studies in mammal models have previously shown reduced infectivity in mice and ferrets and no or reduced transmissibility in ferrets of R292K-mutated virus. 2013 PloS one Discussion IV R292K 136 141 23951116 Resistance mutation R292K is induced in influenza A(H6N2) virus by exposure of infected mallards to low levels of oseltamivir. The difference in sensitivity decrease to OC and ZA caused by R292K can be explained by the protein structure of N2 NAs. 2013 PloS one Discussion IV R292K 62 67 116 119 23951116 Resistance mutation R292K is induced in influenza A(H6N2) virus by exposure of infected mallards to low levels of oseltamivir. The E216K substitution in HA has not been reported in relation to NAI-resistance mutations in the NA. 2013 PloS one Discussion IV E216K 4 9 HA;NA;NAI 26;98;66 28;100;69 23951116 Resistance mutation R292K is induced in influenza A(H6N2) virus by exposure of infected mallards to low levels of oseltamivir. The occurrence and relevance of the R292K mutation has been described already during the development phase of oseltamivir both in vitro and in humans treated with the substance during clinical trials. 2013 PloS one Discussion IV R292K 36 41 23951116 Resistance mutation R292K is induced in influenza A(H6N2) virus by exposure of infected mallards to low levels of oseltamivir. The R292K mutation has previously been shown to decrease NA activity and to decrease replication capacity in cell cultures and in embryonated hen eggs, although conflicting results have been found in replication studies. 2013 PloS one Discussion IV R292K 4 9 57 59 23951116 Resistance mutation R292K is induced in influenza A(H6N2) virus by exposure of infected mallards to low levels of oseltamivir. The residue is however close to the 220 loop of the HA binding site and residues essential for binding specificity and might possibly compensate for the R292K NA mutation. 2013 PloS one Discussion IV R292K 153 158 HA;NA 52;159 54;161 23951116 Resistance mutation R292K is induced in influenza A(H6N2) virus by exposure of infected mallards to low levels of oseltamivir. The resistance was caused by acquisition of the mutation R292K in the NA. 2013 PloS one Discussion IV R292K 57 62 70 72 23951116 Resistance mutation R292K is induced in influenza A(H6N2) virus by exposure of infected mallards to low levels of oseltamivir. The unchanged viral shedding pattern of the two last generations of mallards in the 12 microg/L experiment (shedding R292K mutated virus) furthermore indicates that the transmissibility was not reduced for the mutant virus (Figure 2). 2013 PloS one Discussion IV R292K 117 122 23951116 Resistance mutation R292K is induced in influenza A(H6N2) virus by exposure of infected mallards to low levels of oseltamivir. This suggests similar infectivity of the R292K mutant compared to wild-type virus in the mallard gut. 2013 PloS one Discussion IV R292K 41 46 23951116 Resistance mutation R292K is induced in influenza A(H6N2) virus by exposure of infected mallards to low levels of oseltamivir. We do however argue that there are reasons to take our results into environmental account as the threshold for resistance development could lie anywhere between 1.2 and 12 microg/L and as seen in our previous experiment with an A(H1N1) virus the resistance mutation (H274Y) was detected at 1 microg/L in only two samples; a similar resistance development could have been missed in the present, shorter experiment. 2013 PloS one Discussion IV H274Y 267 272 23951116 Resistance mutation R292K is induced in influenza A(H6N2) virus by exposure of infected mallards to low levels of oseltamivir. We observed a decrease in recoverable virus after propagation in embryonated hen eggs when comparing R292K to wild-type, suggesting a decreased replication capacity in embryonated hen eggs. 2013 PloS one Discussion IV R292K 101 106 23951116 Resistance mutation R292K is induced in influenza A(H6N2) virus by exposure of infected mallards to low levels of oseltamivir. When the NCBI database was screened, no R292K-carrying avian influenza A/N2 virus was found. 2013 PloS one Discussion IV R292K 40 45 23951116 Resistance mutation R292K is induced in influenza A(H6N2) virus by exposure of infected mallards to low levels of oseltamivir. ZA binding does not require a conformational change in the active site and the slight decrease in binding to the R292K mutant is due to a lower ability to penetrate the active site. 2013 PloS one Discussion IV R292K 113 118 24147093 Emerging antigenic variants at the antigenic site Sb in pandemic A(H1N1)2009 influenza virus in Japan detected by a human monoclonal antibody. By contrast, the incidence of S188T at Sb increased markedly and completely replaced the original sequence during Period 6 (Table S7). 2013 PloS one Discussion IV S188T 30 35 24147093 Emerging antigenic variants at the antigenic site Sb in pandemic A(H1N1)2009 influenza virus in Japan detected by a human monoclonal antibody. First in Singapore, and subsequently in Australia and New Zealand, the genetic variants with dual HA (N128D and E377K) and NA (M15I and N189S) mutations predominated in H1N1pdm by June 2010, although at that point there were no major antigenic differences in any of the variant viruses. 2013 PloS one Discussion IV N128D;E377K;M15I;N189S 102;112;127;136 107;117;131;141 HA;NA 98;123 100;125 24147093 Emerging antigenic variants at the antigenic site Sb in pandemic A(H1N1)2009 influenza virus in Japan detected by a human monoclonal antibody. In addition, a mutant with dual HA substitutions, at S188T and E377K, became the predominant strain in Hong Kong in 2010. 2013 PloS one Discussion IV S188T;E377K 53;63 58;68 HA 32 34 24147093 Emerging antigenic variants at the antigenic site Sb in pandemic A(H1N1)2009 influenza virus in Japan detected by a human monoclonal antibody. In addition, the incidence of E/G225 at Ca2 and N128D at Sa increased during Periods 2 and 3, respectively; however, these mutations did not predominate, implying that they might have been associated with a disadvantage during A(H1N1)pdm09 replication. 2013 PloS one Discussion IV N128D 48 53 24147093 Emerging antigenic variants at the antigenic site Sb in pandemic A(H1N1)2009 influenza virus in Japan detected by a human monoclonal antibody. It is difficult to determine whether the S188T substitution arose from antigenic selection or from adaptation using genetic analyses techniques alone. 2013 PloS one Discussion IV S188T 41 46 24162312 Adaptation of novel H7N9 influenza A virus to human receptors. H2N2 viruses isolated from humans during the first year (1957) of the "Asian" pandemic had not yet obtained the G228S substitution and show lower avidity towards human-like receptors. 2013 Scientific reports Discussion IV G228S 112 117 24162312 Adaptation of novel H7N9 influenza A virus to human receptors. Introduction of the Q226L mutation resulted in severely reduced fetuin binding and in decreased or increased binding of alpha2-3 and alpha2-6 sialosides, respectively. 2013 Scientific reports Discussion IV Q226L 20 25 24162312 Adaptation of novel H7N9 influenza A virus to human receptors. Strikingly, almost all novel avian H7N9 viruses already carry the Q226L and G186V mutations, indicating that mutations that increase binding to human-like receptors may be obtained by IAVs in an avian host. 2013 Scientific reports Discussion IV Q226L;G186V 66;76 71;81 24162312 Adaptation of novel H7N9 influenza A virus to human receptors. The reduced binding to fetuin was compensated by G186V. 2013 Scientific reports Discussion IV G186V 49 54 24162312 Adaptation of novel H7N9 influenza A virus to human receptors. While human H2 and H3 viruses have obtained the G228S substitution, for H5 an alternative mutation (N224K) may also suffice. 2013 Scientific reports Discussion IV G228S;N224K 48;100 53;105 24165891 Characterization of two distinct neuraminidases from avian-origin human-infecting H7N9 influenza viruses. In these cases, oseltamivir should be used with caution, as it is > 100 000 times less effective against the R294K-containing H7N9. 2013 Cell research Discussion IV R294K 109 114 24165891 Characterization of two distinct neuraminidases from avian-origin human-infecting H7N9 influenza viruses. It is reported that in some clinical cases of H7N9 infection treated with oseltamivir, viruses carrying an R294K multidrug-resistant substitution in their N9 proteins have been isolated. 2013 Cell research Discussion IV R294K 107 112 N9 155 157 Influenza A virus H7N9 infection 46 60 24165891 Characterization of two distinct neuraminidases from avian-origin human-infecting H7N9 influenza viruses. Of the 4 reported patients with the R294K substitution, 2 have died and 1 has remained hospitalized. 2013 Cell research Discussion IV R294K 36 41 24165891 Characterization of two distinct neuraminidases from avian-origin human-infecting H7N9 influenza viruses. The knowledge that the Shanghai H7N9 viruses may contain an R294K substitution in their NA protein is critical for directing future drug administration in H7N9 patients. 2013 Cell research Discussion IV R294K 60 65 88 90 24165891 Characterization of two distinct neuraminidases from avian-origin human-infecting H7N9 influenza viruses. Therefore, it is not surprising that N9 from A/Shanghai/1/2013 H7N9 has much lower NA activity and that R294K has never been found before in a wild-type N9 variant, though laboratory artificial drug-present passages yielded an R294K N9. 2013 Cell research Discussion IV R294K;R294K 104;227 109;232 N9;N9;N9;NA 37;153;233;83 39;155;235;85 24165891 Characterization of two distinct neuraminidases from avian-origin human-infecting H7N9 influenza viruses. This is at a level much higher than even the prevalent H274Y oseltamivir-resistant substitution found in N1 viruses, which results in up to 1 200-fold resistance. 2013 Cell research Discussion IV H274Y 55 60 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. A decrease in interaction energy at MAN503A suggests that the Asp325 to Ala mutation stabilizes the binding of the Man9 chain on SP-D. 2013 Biochemistry Discussion IV D325A 62 75 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. After subtracting the interactions between SP-D and the Man9 chain, it is observed that D325A+R343V still interacts more strongly with HA by an average of 9 kcal/mol. 2013 Biochemistry Discussion IV D325A;R343V 88;94 93;99 HA 135 137 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. Ala325 is in close proximity to MAN503A suggesting loss of a steric constraint due to the Asp325 to Ala mutation. 2013 Biochemistry Discussion IV D325A 90 103 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. Although the interaction energies for residues on the short loop fluctuate, the importance of the short loop for D325A+R343V could still be harnessed by averaging the energies over three independent trajectories. 2013 Biochemistry Discussion IV D325A;R343V 113;119 118;124 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. As a result, D325A+R343V binds more strongly to HA than does WT by more than 19kcal/mol. 2013 Biochemistry Discussion IV D325A;R343V 13;19 18;24 HA 48 50 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. As shown in Figure 5, D325A+R343V forms hydrophobic contacts with HA, but WT does not. 2013 Biochemistry Discussion IV D325A;R343V 22;28 27;33 HA 66 68 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. Based on experimental and computational evidence, we speculate that altered binding orientation and increased viral aggregation, perhaps coupled with the increased binding to HA by the mutant, enhance the ability of D325A+R343V to neutralize IAV. 2013 Biochemistry Discussion IV D325A;R343V 216;222 221;227 HA 175 177 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. Experimental evidence from that study shows that trimeric D325A+R343V NCRD is nearly as effective at aggregating IAV as is native dodecameric SP-D, whereas the WT NCRD trimer does not aggregate or neutralize the virus . 2013 Biochemistry Discussion IV D325A;R343V 58;64 63;69 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. Formation of hydrogen bonds between Glu333/Arg349 and MAN505 (labeled in Figure 8) is potentiated by the Arg343 to Val mutation, which removes the steric hindrance caused by Arg343. 2013 Biochemistry Discussion IV R343V 105 118 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. From the interaction energies calculated from simulations WTS and DMS, D325A+R343V binds more strongly than WT to HA by approximately 19 kcal/mol. 2013 Biochemistry Discussion IV R343V;D325A 77;71 82;76 HA 114 116 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. However, in contrast to WT and pig SP-D, the long loop of D325A+R343V contributes less to the overall stabilization of the complex; instead, in the D325A+R343V complex, short loop residues 300-304 interact primarily with HA at the SA binding site. 2013 Biochemistry Discussion IV D325A;R343V;D325A;R343V 58;64;148;154 63;69;153;159 HA 221 223 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. However, simulation SMS with the single mutant R343V does not support this hypothesis as it shows that Asp325 interacts strongly with MAN503A due to the formation of hydrogen bonds. 2013 Biochemistry Discussion IV R343V 47 52 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. In addition to using different loops, WT and D325A+R343V exhibit different modes of glycan binding that impact their interactions with the HA trimer. 2013 Biochemistry Discussion IV D325A;R343V 45;51 50;56 HA 139 141 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. In crystallographic studies of alpha-1,2-dimannose complexes with WT or R343V, a reversed mode of dimannose binding is observed between the two proteins . 2013 Biochemistry Discussion IV R343V 72 77 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. In prior SPR experiments with Phil82 HA, D325A+R343V was found to bind more tightly than WT, with mean apparent Kd values of 0.04 nM versus 0.231 nM, respectively . 2013 Biochemistry Discussion IV D325A;R343V 41;47 46;52 HA 37 39 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. In the present liganded D325A+R343V crystal structure, the double mutant binds to the dimannose moiety of Man9 in a manner similar to the binding of dimannose to R343V, providing further evidence that the Arg343 to Val mutation is responsible for the altered binding mode. 2013 Biochemistry Discussion IV D325A;R343V;R343V;R343V 24;30;162;205 29;35;167;218 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. Interestingly, for pig SP-D, there is an insertion of three amino acid residues between residues 328 and 329 . 2013 Biochemistry Discussion IV ins aa328 41 100 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. It is important to note that the interaction energies do not account for hydrophobic contributions and that D325A+R343V/HA has higher interaction energy than WT/HA if one takes only electrostatic interactions into account. 2013 Biochemistry Discussion IV D325A;R343V 108;114 113;119 HA;HA 120;161 122;163 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. MAN504A in R343V is rotated 180 such that its O3 and O4 atoms are swapped compared to MAN505A in WT (Figure 8). 2013 Biochemistry Discussion IV R343V 11 16 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. Mannose interactions are not the only component of D325A+R343V binding to HA. 2013 Biochemistry Discussion IV R343V;D325A 57;51 62;56 HA 74 76 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. Our previous studies of SP-D have shown that mutating these residues greatly influences antiviral activities, with D325A+R343V gaining significant functional capabilities compared with WT. 2013 Biochemistry Discussion IV D325A;R343V 115;121 120;126 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. Significant differences in spatial orientation adopted by WT and D325A+R343V, such as those seen in Figure 9, could provide such a mechanism by altering the ability to cross-link HA and promoting viral aggregation and neutralization. 2013 Biochemistry Discussion IV D325A;R343V 65;71 70;76 HA 179 181 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. Table 3 shows a difference in interaction energies for two neighboring mannose residues, namely MAN505A/MAN503A for D325A+R343V, and MAN504A/MAN503A for WT. 2013 Biochemistry Discussion IV D325A;R343V 116;122 121;127 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. Table 3 shows that compared with WT, D325A+R343V binds more strongly to the Man9 chain by approximately 10 kcal/mol. 2013 Biochemistry Discussion IV D325A;R343V 37;43 42;48 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. The computational results further suggest that the greater HA binding by D325A+R343V may be due, in part, to higher glycan binding affinity. 2013 Biochemistry Discussion IV D325A;R343V 73;79 78;84 HA 59 61 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. The computational results with Aichi HA are consistent with the experimental Phil82 HA data in that while WT and D325A+R343V both bind to the viral glycoprotein, D325A+R343V binds with higher affinity (Table 4). 2013 Biochemistry Discussion IV D325A;R343V;D325A;R343V 113;119;162;168 118;124;167;173 HA;HA 37;84 39;86 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. The critical importance of the lectin activity in the interaction is underscored in two sets of simulations, WTNS and DMNS, in which both WT/HA and D325A+R343V/HA complexes exhibit significant fluctuation and drifting in 100ns when the Man9 chain is absent (Figure 7). 2013 Biochemistry Discussion IV D325A;R343V 148;154 153;159 HA;HA 141;160 143;162 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. The key loop interactions with the SA binding site of HA are different for WT and D325A+R343V. 2013 Biochemistry Discussion IV D325A;R343V 82;88 87;93 HA 54 56 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. The nature of the mutations appears to play a role in the differences between WT and D325A+R343V in binding Man9. 2013 Biochemistry Discussion IV D325A;R343V 85;91 90;96 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. These data suggest that an increase in interaction energy at MAN505A is due to the Arg343 to Val mutation, consistent with structural evidence . 2013 Biochemistry Discussion IV R343V 83 96 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. These observations suggest that D325A+R343V is able to utilize a mechanism that circumvents the need for an extended oligomer to aggregate viral particles. 2013 Biochemistry Discussion IV D325A;R343V 32;38 37;43 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. These results are consistent with carbohydrate microarray experiments in which R343V, which shares the same arginine mutation as D325A+R343V, binds more strongly to branched mannose oligosaccharides than does WT . 2013 Biochemistry Discussion IV R343V;D325A;R343V 79;129;135 84;134;140 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. We additionally have suggested means through which binding of HA glycans by D325A+R343V could lead to increased viral neutralization. 2013 Biochemistry Discussion IV D325A;R343V 76;82 81;87 HA 62 64 24224757 Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. We have proposed previously that in D325A+R343V, viral aggregation can be achieved by SP-D-mediated cross-linking of HA on neighboring viral particles. 2013 Biochemistry Discussion IV D325A;R343V 36;42 41;47 HA 117 119 24224816 Swine influenza in Norway: a distinct lineage of influenza A(H1N1)pdm09 virus. One of the substitutions, S164F, is located in the HA globular head subunit (HA1) and has not been reported elsewhere. 2013 Influenza and other respiratory viruses Discussion IV S164F 26 31 HA;HA1 51;77 53;80 24224816 Swine influenza in Norway: a distinct lineage of influenza A(H1N1)pdm09 virus. The N473D substitution, located in the HA2 stalk subunit (position 146), has subsequently been found in another A(H1N1)pdm09 genetic lineage. 2013 Influenza and other respiratory viruses Discussion IV N473D 4 9 HA 39 41 24312396 Conformational polymorphism of m7GTP in crystal structure of the PB2 middle domain from human influenza A virus. Among these four sites, the mutation at position 453 is particularly interesting because it is so drastic, going from proline (H1N1) to histidine (H3N2), though other mutations occur within similar character such as basic (R368K) or hydrophobic (I382V). 2013 PloS one Discussion IV R368K;I382V 223;246 228;251 24312396 Conformational polymorphism of m7GTP in crystal structure of the PB2 middle domain from human influenza A virus. E627K mutation dramatically increased basic charge on the surface. 2013 PloS one Discussion IV E627K 0 5 24312396 Conformational polymorphism of m7GTP in crystal structure of the PB2 middle domain from human influenza A virus. In this report, we observed that the PB2 middle domain with two mutations (P453H and I471T) change the solubility and finally we obtained good diffraction crystals by these mutations. 2013 PloS one Discussion IV P453H;I471T 75;85 80;90 PB2 37 40 24312396 Conformational polymorphism of m7GTP in crystal structure of the PB2 middle domain from human influenza A virus. It has been well known that the electrostatic surface change by the single E627K mutation enhanced the virulence, though it is still open question what is the role of K627 in the RNP complex. 2013 PloS one Discussion IV E627K 75 80 RNP 179 182 24312396 Conformational polymorphism of m7GTP in crystal structure of the PB2 middle domain from human influenza A virus. It should be noticed again that two mutations (P453H and I471T) we introduced are totally opposite surface against cap-binding site, thus they does not influence the conformational polymorphism of m7GTP (original (2VQZ) and novel site (this report)). 2013 PloS one Discussion IV P453H;I471T 47;57 52;62 24312396 Conformational polymorphism of m7GTP in crystal structure of the PB2 middle domain from human influenza A virus. P453H mutation increased the surface basic electrostatic potential drastically. 2013 PloS one Discussion IV P453H 0 5 24312396 Conformational polymorphism of m7GTP in crystal structure of the PB2 middle domain from human influenza A virus. The P453H mutation first appeared in 1940. 2013 PloS one Discussion IV P453H 4 9 24312396 Conformational polymorphism of m7GTP in crystal structure of the PB2 middle domain from human influenza A virus. Thus, based on the characteristic features of P453H mutation, it might be more possible candidate than the others for an adaptive mutation from avian to human HxN2. 2013 PloS one Discussion IV P453H 46 51 24312396 Conformational polymorphism of m7GTP in crystal structure of the PB2 middle domain from human influenza A virus. Whether the P453H mutation is linked to the viral specific feature of H2N2 or H3N2 is an important issue to be addressed. 2013 PloS one Discussion IV P453H 12 17 24391498 A single amino acid in the stalk region of the H1N1pdm influenza virus HA protein affects viral fusion, stability and infectivity. A K58I mutation in the HA2 of H5N1 that decreased the activation pH for fusion reduced viral pathogenicity in ducks, but increased the virulence and the infectivity and immunogenicity of an intranasal H5N1 vaccine virus in mice, showing the species specific impact of the fusion activation pH. 2014 PLoS pathogens Discussion IV K58I 2 6 HA 23 25 24391498 A single amino acid in the stalk region of the H1N1pdm influenza virus HA protein affects viral fusion, stability and infectivity. A mouse-adapted H1N1 virus that acquires an HA2-W47G change was reported to lower both the fusion pH and lethal dose in mice. 2014 PLoS pathogens Discussion IV W47G 48 52 HA 44 46 24391498 A single amino acid in the stalk region of the H1N1pdm influenza virus HA protein affects viral fusion, stability and infectivity. For avian H5N1 viruses to transmit among ferrets, sequence changes are required in both the HA head region to alter receptor binding specificity and the stalk region, in which a single residue change (T318I) near the fusion peptide lowers the pH for fusion and increases virus stability. 2014 PLoS pathogens Discussion IV T318I 201 206 HA 92 94 24391498 A single amino acid in the stalk region of the H1N1pdm influenza virus HA protein affects viral fusion, stability and infectivity. Since July 2009, an E47K mutation emerged and rapidly became predominant worldwide. 2014 PLoS pathogens Discussion IV E47K 20 24 24391498 A single amino acid in the stalk region of the H1N1pdm influenza virus HA protein affects viral fusion, stability and infectivity. The E47K change at the same HA2 position in the H1N1pdm viruses resulted in a similar biological phenotype for fusion activation pH and infectivity in ferrets. 2014 PLoS pathogens Discussion IV E47K 4 8 HA 28 30 24391498 A single amino acid in the stalk region of the H1N1pdm influenza virus HA protein affects viral fusion, stability and infectivity. The HA2 Q47R and Q47K changes in the H3 and H7 viruses, respectively, have been previously reported to affect virus fusion pH. 2014 PLoS pathogens Discussion IV Q47R;Q47K 8;17 12;21 HA 4 6 24503069 The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus. A single Phe95 Tyr mutation was able to promote the binding affinity of influenza B/Yamagata/73 HA to a comparable level as that of influenza A virus HA, regardless of human or avian-like receptors, thus enabling its efficient binding to three cultured cell lines containing a varied range of glycan composition for which the wild-type HA binds very poorly. 2014 Virology Discussion IV F95Y 9 18 HA;HA;HA 96;150;336 98;152;338 24503069 The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus. Here, by using recombinant B/Yamagata/73 HA proteins, we demonstrated that Phe95 Tyr is able to enhance the binding affinity to synthetic glycans by up to 107 times. 2014 Virology Discussion IV F95Y 75 84 HA 41 43 24503069 The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus. However, in the case B/Lee/40 HA, although the loss of the glycosylation at HA1 194 results in a picomolar dissociation constant for Neu5Acalpha(2,3)Gal receptors, the introduction of Phe95 Tyr into this background reduces the binding affinity for Neu5Acalpha(2,3)Gal receptors. 2014 Virology Discussion IV F95Y 184 193 HA;HA1 30;76 32;79 24503069 The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus. In sharp contrast, the large-to-small mutation of Tyr98 Phe on influenza A/H3 HA almost abolished the binding of the virus to red blood cells, and the recombinant Tyr98 Phe virus can not infect mutant MDCK cells with a reduced level of cell-surface sialic acids and replicates poorly in mice. 2014 Virology Discussion IV Y98F;Y98F 50;163 59;172 HA 78 80 24503069 The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus. It is interesting to note that the small-to-large mutation of Phe95 Tyr in our study can be accommodated in the receptor-binding site of influenza B virus HA easily and enhances the receptor-binding affinity. 2014 Virology Discussion IV F95Y 62 71 HA 155 157 24503069 The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus. Phe95 Tyr increases the receptor-binding affinity of recombinant influenza B virus HA proteins. 2014 Virology Discussion IV F95Y 0 9 24503069 The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus. Similarly, in the background of B/Lee/40 HA Asn194 Asp, the Phe95 Tyr mutation also increases the binding affinity for 6'SLN-LN by ~2,000 times (Table 1). 2014 Virology Discussion IV N194D;F95Y 44;60 54;69 HA 41 43 24503069 The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus. Since the hydroxyl oxygen atom on the side chain of Tyr-98 makes one hydrogen bond within the receptor-binding site and two additional ones with the sialic acid receptors, it is likely that Tyr98 Phe somehow distorts the receptor-binding site and/or substantially weakens the receptor binding in influenza A/H3 HA. 2014 Virology Discussion IV Y98F 190 199 HA 311 313 24503069 The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus. The different paths that LSTa and LSTc exit from the receptor-binding site provide a plausible explanation for the mutational effects of Asn194 Asp and Phe95 Tyr in this study. 2014 Virology Discussion IV N194D;F95Y 137;152 147;161 24503069 The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus. The enhanced receptor binding affinity of influenza B virus HA upon a single Phe95 Tyr mutation at the receptor-binding site provides a plausible explanation for the very limited host range displayed by influenza B virus. 2014 Virology Discussion IV F95Y 77 86 HA 60 62 24503069 The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus. The interference may be responsible for the only modest increase in binding to Neu5Acalpha(2,3)Gal receptors by the Phe95 Tyr mutation that introduces two strong hydrogen bonds with the Sia-1 moiety, while the corresponding increase for Neu5Acalpha(2,6)Gal receptors is 107 folds. 2014 Virology Discussion IV F95Y 116 125 24503069 The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus. Therefore, the removal of the glycosylation at HA1 194 in B/Yamagata/73 HA containing either Asn194 Asp or Phe95 Tyr/Asn194 Asp relieves this interference and yields picomolar dissociation constants for both Neu5Acalpha(2,3)Gal and Neu5Acalpha(2,6)Gal receptors (Table 1). 2014 Virology Discussion IV N194D 93 103 HA;HA1 72;47 74;50 24503069 The roles of hemagglutinin Phe-95 in receptor binding and pathogenicity of influenza B virus. While it is not known when, how and why influenza B virus HA acquired Tyr95 Phe mutation in the course of evolution, it is likely that some or all of the other viral proteins of influenza B virus have undergone concomitant changes, including a delicate balance between HA and NA. 2014 Virology Discussion IV Y95F 70 79 HA;HA;NA 58;269;276 60;271;278 24524021 Generation and Characterization of Recombinant Influenza A(H1N1) Viruses Resistant to Neuraminidase Inhibitors. A previous study has reported that I117V has a synergistic effect of increasing resistance with H275Y, whereas the I117M mutation does not alter oseltamivir sensitivity in the recombinant viruses with NA from the pandemic (H1N1) 2009 virus and the remaining genes from A/PR/8/34. 2013 Osong public health and research perspectives Discussion IV I117V;H275Y;I117M 35;96;115 40;101;120 201 203 24524021 Generation and Characterization of Recombinant Influenza A(H1N1) Viruses Resistant to Neuraminidase Inhibitors. Addition of the N295S mutation to the Y275H mutation has a synergistic effect on oseltamivir resistance, increasing the IC50 value of oseltamivir to 40.3-fold of that of the Y275H mutation alone, whereas the addition of the N295S mutation to the Y275 has an antagonistic effect on oseltamivir resistance, decreasing the IC50 value of oseltamivir to 0.2-fold of that of the Y275 alone. 2013 Osong public health and research perspectives Discussion IV N295S;Y275H;Y275H;N295S 16;38;174;224 21;43;179;229 24524021 Generation and Characterization of Recombinant Influenza A(H1N1) Viruses Resistant to Neuraminidase Inhibitors. In combination with Y275, the I117V or I223V mutation has a synergistic effect on oseltamivir resistance, increasing IC50 values of oseltamivir by 1.3-fold and 1.1-fold, respectively, compared to the values caused by the Y275 mutation alone. 2013 Osong public health and research perspectives Discussion IV I117V;I223V 30;39 35;44 24524021 Generation and Characterization of Recombinant Influenza A(H1N1) Viruses Resistant to Neuraminidase Inhibitors. In summary, I117V or I223V mutation has increased the resistance to oseltamivir in combination with Y275 virus, whereas N295S mutation has decreased resistance to oseltamivir in combination with Y275 virus. 2013 Osong public health and research perspectives Discussion IV I117V;I223V;N295S 12;21;120 17;26;125 24524021 Generation and Characterization of Recombinant Influenza A(H1N1) Viruses Resistant to Neuraminidase Inhibitors. NA-inhibition assays showed that all the single and double mutants containing the Y275, except the single Y275-E119V mutant, conferred important levels of resistance to oseltamivir, whereas all the single, double, and triple mutants containing the E119V mutation were associated with the resistance to zanamivir (Table 2). 2013 Osong public health and research perspectives Discussion IV E119V;E119V 111;248 116;253 0 2 24524021 Generation and Characterization of Recombinant Influenza A(H1N1) Viruses Resistant to Neuraminidase Inhibitors. The I117M mutation was detected in a pandemic (H1N1) 2009 virus from South Korea that was isolated from a patient during oseltamivir treatment. 2013 Osong public health and research perspectives Discussion IV I117M 4 9 24524021 Generation and Characterization of Recombinant Influenza A(H1N1) Viruses Resistant to Neuraminidase Inhibitors. The I117V mutation was detected in influenza A(H5N1) virus. 2013 Osong public health and research perspectives Discussion IV I117V 4 9 24558492 Study of oseltamivir and zanamivir resistance-related mutations in influenza viruses isolated from wild mallards in Sweden. A similar effect was observed in the R118K mutants of the N9 subtype in comparison with one of the WTs. 2014 PloS one Discussion IV R118K 37 42 N9 58 60 24558492 Study of oseltamivir and zanamivir resistance-related mutations in influenza viruses isolated from wild mallards in Sweden. Effect of R118K mutation in different subtypes. 2014 PloS one Discussion IV R118K 10 15 24558492 Study of oseltamivir and zanamivir resistance-related mutations in influenza viruses isolated from wild mallards in Sweden. For example, the OC resistance-related mutation H274Y (N2 numbering) in pandemic H1N1 A/Osaka/180/2009 resulted in IC50 of 93.9, 1,048.2 and 1,333.8 nM analyzed by CL, FL or CM assay respectively. 2014 PloS one Discussion IV H274Y 48 53 24558492 Study of oseltamivir and zanamivir resistance-related mutations in influenza viruses isolated from wild mallards in Sweden. Hence, the mutants showed the same groupings into N1 and N2 divisions previously observed in WTs, with the exception of I222V and D151K mutants belonging to N1 subtype. 2014 PloS one Discussion IV I222V;D151K 120;130 125;135 24558492 Study of oseltamivir and zanamivir resistance-related mutations in influenza viruses isolated from wild mallards in Sweden. In the case of H5N1 2.2 A/Turkey/15/06 recombinant virus and inhibition by OC the IC50 for E119A, H274Y and N294S were 236.5, 6308.0 and 424.2 nM respectively (FL assay). 2014 PloS one Discussion IV E119A;H274Y;N294S 91;98;108 96;103;113 24558492 Study of oseltamivir and zanamivir resistance-related mutations in influenza viruses isolated from wild mallards in Sweden. In the N6 subtype, the R152K mutation appeared to increase the sensitivity to both inhibitors in all mutants compared to both WTs (Table 2). 2014 PloS one Discussion IV R152K 23 28 24558492 Study of oseltamivir and zanamivir resistance-related mutations in influenza viruses isolated from wild mallards in Sweden. Previously, the R118K mutation had been introduced into the H3N2 A/Wuhan/359/95-like virus strain using reverse genetics and this mutant was able to proliferate only in the presence of exogenous (bacterial) NA. 2014 PloS one Discussion IV R118K 16 21 207 209 24558492 Study of oseltamivir and zanamivir resistance-related mutations in influenza viruses isolated from wild mallards in Sweden. The inhibition by ZA of the same recombinant virus that has V116A or E119A mutation resulted in IC50 of 32.8 and 1253.8 nM respectively. 2014 PloS one Discussion IV V116A;E119A 60;69 65;74 24558492 Study of oseltamivir and zanamivir resistance-related mutations in influenza viruses isolated from wild mallards in Sweden. The mutation R118K inhibited replication of the human strain but did not appear to affect the fitness. 2014 PloS one Discussion IV R118K 13 18 24563658 Synergistic combinations of favipiravir and oseltamivir against wild-type pandemic and oseltamivir-resistant influenza A virus infections in mice. Further work with the A/Mississippi/3/2001 (H1N1) H275Y mouse model will continue as novel inhibitors are discovered and used in combination with oseltamivir. 2013 Future virology Discussion IV H275Y 50 55 24563658 Synergistic combinations of favipiravir and oseltamivir against wild-type pandemic and oseltamivir-resistant influenza A virus infections in mice. In addition, H275Y-carrying viruses that are resistant to oseltamivir were effectively treated in mice with the combination of oseltamivir and favipiravir. 2013 Future virology Discussion IV H275Y 13 18 24563658 Synergistic combinations of favipiravir and oseltamivir against wild-type pandemic and oseltamivir-resistant influenza A virus infections in mice. In the case of the present research, there is no guarantee that the mouse-adapted wild-type influenza A/California/04/2009 (H1N1pdm) virus can be converted to an H275Y virus by genetic manipulation and still retain its virulence in mice. 2013 Future virology Discussion IV H275Y 162 167 24563658 Synergistic combinations of favipiravir and oseltamivir against wild-type pandemic and oseltamivir-resistant influenza A virus infections in mice. In the infection of mice with the oseltamivir-resistant influenza A/Mississippi/3/2001 (H1N1) H275Y virus, the dose of oseltamivir had to be increased (relative to the doses used for the H1N1pdm virus infection) to higher levels to provide even a weak (30% survival) benefit, as was done previously. 2013 Future virology Discussion IV H275Y 94 99 Influenza A virus H1N1 infection 187 210 24563658 Synergistic combinations of favipiravir and oseltamivir against wild-type pandemic and oseltamivir-resistant influenza A virus infections in mice. In this report we used a wild-type (oseltamivirsensitive) pandemic H1N1 and oseltamivir-resistant H274Y seasonal H1N1 virus infections in mice for evaluating drug combination efficacy. 2013 Future virology Discussion IV H274Y 98 103 Influenza A virus H1N1 infection 113 134 24563658 Synergistic combinations of favipiravir and oseltamivir against wild-type pandemic and oseltamivir-resistant influenza A virus infections in mice. Previously, we reported the adaptation of a pandemic influenza A/Hong Kong/2369/2009 (H1N1pdm) H275Y virus in mice. 2013 Future virology Discussion IV H275Y 95 100 24563658 Synergistic combinations of favipiravir and oseltamivir against wild-type pandemic and oseltamivir-resistant influenza A virus infections in mice. Regarding our selection of the A/Mississippi/3/2001 (H1N1) H275Y virus for the current studies, infection with this virus gives more consistent mortality from experiment to experiment compared with the A/Hong Kong/2369/2009 (H1N1pdm) H275Y virus. 2013 Future virology Discussion IV H275Y;H275Y 59;234 64;239 24563658 Synergistic combinations of favipiravir and oseltamivir against wild-type pandemic and oseltamivir-resistant influenza A virus infections in mice. Regarding the present work, this represents the first reports of drug combination studies of oseltamivir and favipiravir against H1N1pdm and oseltamivir-resistant H275Y virus infections in mice. 2013 Future virology Discussion IV H275Y 163 168 24563658 Synergistic combinations of favipiravir and oseltamivir against wild-type pandemic and oseltamivir-resistant influenza A virus infections in mice. The A/Hong Kong/2369/2009 (H1N1pdm) H275Y virus infection in mice was weakly treatable with high doses of oseltamivir in a manner very similar to what was found with the A/Mississippi/3/2001 (H1N1) H275Y virus infection in mice. 2013 Future virology Discussion IV H275Y;H275Y 36;198 41;203 24563658 Synergistic combinations of favipiravir and oseltamivir against wild-type pandemic and oseltamivir-resistant influenza A virus infections in mice. There may be no benefit from treatment of H275Y virus infections in humans with oseltamivir when used alone or in combination, unless the dosage is increased. 2013 Future virology Discussion IV H275Y 42 47 24569063 An investigational antiviral drug, DAS181, effectively inhibits replication of zoonotic influenza A virus subtype H7N9 and protects mice from lethality. Although there are no established criteria for clinically relevant resistance of influenza viruses to the NAI class of drugs, the laboratory NA inhibition assay data for viruses carrying R292K may be interpreted as resistance to oseltamivir and, possibly, to 1 or more other NAIs, making it imperative to assess antiviral drugs with alternative mechanisms of action. 2014 The Journal of infectious diseases Discussion IV R292K 187 192 NA;NAI;NAI 141;106;275 143;109;279 24569063 An investigational antiviral drug, DAS181, effectively inhibits replication of zoonotic influenza A virus subtype H7N9 and protects mice from lethality. As anticipated, the presence of R292K was accompanied by an increase in IC50 values to Food and Drug Administration-approved (oseltamivir and zanamivir) and investigational (peramivir and laninamivir) NAIs in the NA inhibition assay, consistent with the previous reports. 2014 The Journal of infectious diseases Discussion IV R292K 32 37 NA;NAI 213;201 215;205 24569063 An investigational antiviral drug, DAS181, effectively inhibits replication of zoonotic influenza A virus subtype H7N9 and protects mice from lethality. Lower survival rates were observed in R292K virus-infected animals given DAS181 48-72 hours after infection. 2014 The Journal of infectious diseases Discussion IV R292K 38 43 24569063 An investigational antiviral drug, DAS181, effectively inhibits replication of zoonotic influenza A virus subtype H7N9 and protects mice from lethality. Moreover, wild-type (R292) viruses and R292K virus variants maintained their NA sequence at residue 292, based on the data from a pyrosequencing assay for lungs collected on days 3 and 6 after infection. 2014 The Journal of infectious diseases Discussion IV R292K 39 44 77 79 24569063 An investigational antiviral drug, DAS181, effectively inhibits replication of zoonotic influenza A virus subtype H7N9 and protects mice from lethality. Of note, oseltamivir treatment did not result in acquisition of R292K by wild-type virus at both analyzed days. 2014 The Journal of infectious diseases Discussion IV R292K 64 69 24569063 An investigational antiviral drug, DAS181, effectively inhibits replication of zoonotic influenza A virus subtype H7N9 and protects mice from lethality. Our data show that the influenza A(H7N9) isolates replicated very efficiently in mouse lungs, regardless of the R292K presence. 2014 The Journal of infectious diseases Discussion IV R292K 112 117 24569063 An investigational antiviral drug, DAS181, effectively inhibits replication of zoonotic influenza A virus subtype H7N9 and protects mice from lethality. Remarkably, treatment with DAS181 dramatically reduced the number of foci in cultured cells and lung virus titers in mice infected with the lethal dose of influenza A(H7N9), regardless of the presence of R292K. 2014 The Journal of infectious diseases Discussion IV R292K 204 209 24569063 An investigational antiviral drug, DAS181, effectively inhibits replication of zoonotic influenza A virus subtype H7N9 and protects mice from lethality. Similarly, Watanabe et al detected reduction in lung virus titers of wild-type Anhui/1 in mice (inoculation dose, 103 and 104 plaque-forming units) after high-dose oseltamivir treatment (started at 2 hours after infection) and little or no effect on the replication of R292K virus variant (reassortant Anhui/1). 2014 The Journal of infectious diseases Discussion IV R292K 269 274 24569063 An investigational antiviral drug, DAS181, effectively inhibits replication of zoonotic influenza A virus subtype H7N9 and protects mice from lethality. This result is in agreement with the report on a different influenza A(H7N9) pair, the wild-type A/Anhui/1/2013 (Anhui/1) and reassortant Anhui/1 virus carrying NA with R292K from Shanghai/1 virus. 2014 The Journal of infectious diseases Discussion IV R292K 169 174 161 163 24569063 An investigational antiviral drug, DAS181, effectively inhibits replication of zoonotic influenza A virus subtype H7N9 and protects mice from lethality. We found that replication of the R292K virus was not affected by treatment with oseltamivir in mice. 2014 The Journal of infectious diseases Discussion IV R292K 33 38 24569063 An investigational antiviral drug, DAS181, effectively inhibits replication of zoonotic influenza A virus subtype H7N9 and protects mice from lethality. We used 2 wild-type influenza A(H7N9) isolates (Shanghai/1 and Taiwan/1) and their counterparts carrying the NA R292K substitution. 2014 The Journal of infectious diseases Discussion IV R292K 112 117 109 111 24576826 Unique reassortant of influenza A(H7N9) virus associated with severe disease emerging in Hong Kong. A previous study has also shown that V139I was enriched in human A(H7N7) viruses when compared to avian A(H7N7) viruses. 2014 The Journal of infection Discussion IV V139I 37 42 24576826 Unique reassortant of influenza A(H7N9) virus associated with severe disease emerging in Hong Kong. Another substitution, PB2 V139I, was identified only in the A/Hong Kong/470129/2013 and A/Guangdong/1/2013 strains, but not in other human or avian A(H7N9) strains. 2014 The Journal of infection Discussion IV V139I 26 31 PB2 22 25 24576826 Unique reassortant of influenza A(H7N9) virus associated with severe disease emerging in Hong Kong. However, R289K mutation was not found in the A/Hong Kong/470129/2013 strain, suggesting that this strain remain susceptible to neuraminidase inhibitors. 2014 The Journal of infection Discussion IV R289K 9 14 127 140 24576826 Unique reassortant of influenza A(H7N9) virus associated with severe disease emerging in Hong Kong. In fact, L336M substitution is conserved among the 2009 pandemic A(H1N1)pdm09 virus isolates but rarely found in other human or avian influenza viruses. 2014 The Journal of infection Discussion IV L336M 9 14 24576826 Unique reassortant of influenza A(H7N9) virus associated with severe disease emerging in Hong Kong. In the PA protein, the L336M was only present in the A/Hong Kong/470129/2013 but not A/Guangdong/1/2013 strains or other human or avian A(H7N9) strains. 2014 The Journal of infection Discussion IV L336M 23 28 PA 7 9 24576826 Unique reassortant of influenza A(H7N9) virus associated with severe disease emerging in Hong Kong. Mice challenged with recombinant A(H1N1) virus containing PA L336M substitution had more body weight loss and higher lung viral titres than those infected with the wild type virus, suggesting that PA L336M substitution is associated with higher pathogenicity in mammals. 2014 The Journal of infection Discussion IV L336M;L336M 61;200 66;205 PA;PA 58;197 60;199 24576826 Unique reassortant of influenza A(H7N9) virus associated with severe disease emerging in Hong Kong. PA L336M substitution has been shown to increase the polymerase activity. 2014 The Journal of infection Discussion IV L336M 3 8 PA 0 2 24576826 Unique reassortant of influenza A(H7N9) virus associated with severe disease emerging in Hong Kong. Previous studies have shown that R289K mutant, which confers reduced susceptibility to neuraminidase inhibitors, could emerge quickly after treatment with neuraminidase inhibitors. 2014 The Journal of infection Discussion IV R289K 33 38 NA;NA 87;155 100;168 24667168 Low 2012-13 influenza vaccine effectiveness associated with mutation in the egg-adapted H3N2 vaccine strain not antigenic drift in circulating viruses. X-223 manifests additional antigenic site B (T128N, S198P) and D (I226N) mutations relative to A/Victoria/361/2011 and IVR-165, different also from our circulating viruses. 2014 PloS one Discussion IV T128N;S198P;I226N 45;52;66 50;57;71 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. also noted that introduction of a T289M NA mutation (which was identified as a PPM by computational analyses, but has not yet been detected in circulating strains) into an early H275Y A(H1N1)pdm09 virus resulted in greater weight loss, enhanced mortality and higher lung viral titres in mice. 2014 PLoS pathogens Discussion IV T289M;H275Y 34;178 39;183 40 42 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. Given the apparent robust fitness of the H275Y HNE2011 viruses in this study, the obvious question is why have they not yet re-emerged? One explanation is that a high level of circulating A(H1N1)pdm09 viruses may be required for a A(H1N1)pdm09 OR virus to become established and spread. 2014 PLoS pathogens Discussion IV H275Y 41 46 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. Hence, the risk that H275Y A(H1N1)pdm09 viruses will spread globally, in a similar manner to OR seasonal A(H1N1) viruses in 2007-2008, now appears greater than at any time since the A(H1N1)pdm09 lineage emerged in 2009. 2014 PLoS pathogens Discussion IV H275Y 21 26 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. Here we demonstrate that contemporary A(H1N1)pdm09 viruses have acquired NA mutations which permit the acquisition of NA H275Y without compromising viral fitness. 2014 PLoS pathogens Discussion IV H275Y 121 126 NA;NA 73;118 75;120 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. In 2007-2008, the H275Y NA mutation became fixed in a new seasonal A(H1N1) antigenic variant (A/Brisbane/59/2007-like), suggesting that the antigenic novelty of the OR virus assisted its prolific spread. 2014 PLoS pathogens Discussion IV H275Y 18 23 24 26 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. In most of these studies, the viruses used did not contain the PPMs V241I and N369K which were shown here to improve the fitness of the OR viruses. 2014 PLoS pathogens Discussion IV V241I;N369K 68;78 73;83 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. In the most recent 2013/14 Northern Hemisphere influenza season, a cluster of A(H1N1)pdm09 H275Y OR viruses that contained both the V241I and N369K PPMs plus an additional N386K NA mutation, was detected in Sapporo, Japan, during a period of the season where A(H1N1)pdm09 viruses contributed approximately 50% of the circulating influenza strains. 2014 PLoS pathogens Discussion IV H275Y;V241I;N369K;N386K 91;132;142;172 96;137;147;177 178 180 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. In this way it was possible to investigate whether the presence or absence of the NA V241I and/or the N369K permissive mutations enabled the OR viruses to replicate more efficiently within ferrets, and/or be more efficiently transmitted between ferrets. 2014 PLoS pathogens Discussion IV V241I;N369K 85;102 90;107 82 84 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. It is notable that the majority of OR viruses (including those containing the NA H275Y mutation) retain sensitivity to zanamivir and laninamivir. 2014 PLoS pathogens Discussion IV H275Y 81 86 78 80 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. Most recently in 2013 two other NA mutations (N44S and N200S) have become almost universally observed in A(H1N1)pdm09 viruses, whilst at the same time an NA V106I mutation, which was rapidly acquired at the beginning of the A(H1N1)pdm09 pandemic, has been lost (Figure S1). 2014 PLoS pathogens Discussion IV N44S;N200S;V106I 46;55;157 50;60;162 NA;NA 32;154 34;156 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. Previous studies in ferrets, guinea pigs and mice revealed broadly equivalent, or lower fitness of early H275Y OR A(H1N1)pdm09 viruses compared to genetically similar OS (NA 275H) strains. 2014 PLoS pathogens Discussion IV H275Y 105 110 171 173 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. showed that the introduction of the V241I and N369K PPMs into an early H275Y A(H1N1)pdm09 virus resulted in higher virus titres in ferret nasal washes. 2014 PLoS pathogens Discussion IV V241I;N369K;H275Y 36;46;71 41;51;76 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. The computational analysis reported previously, in conjunction with the in vitro experiments presented here, demonstrate that NA V241I and N369K are indeed permissive mutations that act by enhancing both the surface expression and total activity of H275Y A(H1N1)pdm09 NA proteins, similar to the effect that the R222Q and V234M mutations had on the NA of H275Y seasonal A(H1N1) viruses. 2014 PLoS pathogens Discussion IV V241I;N369K;H275Y;R222Q;V234M;H275Y 129;139;249;312;322;355 134;144;254;317;327;360 NA;NA;NA 126;268;349 128;270;351 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. The experiments and accompanying mathematical analysis presented in this study demonstrate that these mutations enable A(H1N1)pdm09 viruses to maintain robust viral fitness when they acquire the NA H275Y oseltamivir resistance mutation. 2014 PLoS pathogens Discussion IV H275Y 198 203 195 197 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. The PPMs NA V241I and N369K are now present in >99% of circulating A(H1N1)pdm09 viruses (Figure S1). 2014 PLoS pathogens Discussion IV V241I;N369K 12;22 17;27 9 11 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. The results of this study show that A(H1N1)pdm09 viruses have now acquired permissive NA mutations which allow them to retain viral fitness when the H275Y NA mutation is present, raising the possibility of rapid global spread of an OR A(H1N1)pdm09 virus if H275Y were to arise in an antigenically drifted virus. 2014 PLoS pathogens Discussion IV H275Y;H275Y 149;257 154;262 NA;NA 86;155 88;157 24699865 Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. These mutations, which are now present in virtually all circulating A(H1N1)pdm09 viruses, enhance the surface expression and enzymatic activity of the A(H1N1)pdm09 H275Y NA protein in vitro and result in enhanced viral fitness in vivo. 2014 PLoS pathogens Discussion IV H275Y 164 169 170 172 24790833 Isolation and characterization of H9N2 influenza virus isolates from poultry respiratory disease outbreak. Additionally, both viruses have a L13P substitution frequently observed in human associated H9 viruses, but it is important to note that this change is commonly observed in H9N2 strains. 2014 SpringerPlus Discussion IV L13P 34 38 24790833 Isolation and characterization of H9N2 influenza virus isolates from poultry respiratory disease outbreak. Analyses of additional host range signatures for M2 gene in both isolates revealed I28F, E16G and L55F substitutions commonly observed in human associated H9 viruses. 2014 SpringerPlus Discussion IV I28F;E16G;L55F 83;89;98 87;93;102 M2 49 51 24790833 Isolation and characterization of H9N2 influenza virus isolates from poultry respiratory disease outbreak. Considering the PA gene, isolate1 revealed R57Q and C241Y substitutions, which are associated with human adaptation. 2014 SpringerPlus Discussion IV R57Q;C241Y 43;52 47;57 PA 16 18 24790833 Isolation and characterization of H9N2 influenza virus isolates from poultry respiratory disease outbreak. E227K substitution is observed in some of the H5N1 viruses isolated from Indonesia and Saudi Arabia (Obenauer et al.; Monne et al.). 2014 SpringerPlus Discussion IV E227K 0 5 24790833 Isolation and characterization of H9N2 influenza virus isolates from poultry respiratory disease outbreak. However, it remains to be investigated whether E227K substitution results in increased virulence of H9N2 viruses in avian species. 2014 SpringerPlus Discussion IV E227K 47 52 24790833 Isolation and characterization of H9N2 influenza virus isolates from poultry respiratory disease outbreak. In particular the amino acids glutamine (Q) or leucine (L) at position 226 (H3 numbering, 234H9 numbering) plays a key role in avian and human virus-like receptor specificity respectively. 2014 SpringerPlus Discussion IV L226L 46 75 24790833 Isolation and characterization of H9N2 influenza virus isolates from poultry respiratory disease outbreak. Isolate 1 from this study has the S31N substitution, which has also been identified in H9N2 viruses from Iran, UAE and Qatar (Fusaro et al.). 2014 SpringerPlus Discussion IV S31N 34 38 24790833 Isolation and characterization of H9N2 influenza virus isolates from poultry respiratory disease outbreak. Our analysis found that since 2003 Q226L substitution is prevailing in the H9N2 viruses predominantly of G1 like lineage isolated from the India. 2014 SpringerPlus Discussion IV Q226L 35 40 24790833 Isolation and characterization of H9N2 influenza virus isolates from poultry respiratory disease outbreak. Our analysis of the NS1 protein revealed E227K substitution in both the isolates, a substitution that confers increased pathogenicity and virulence in mice (Jackson et al.). 2014 SpringerPlus Discussion IV E227K 41 46 NS1 20 23 24790833 Isolation and characterization of H9N2 influenza virus isolates from poultry respiratory disease outbreak. Similar type of observations were also reported for HA gene of H9N2 viruses prevalent in Israel after detailed molecular analysis and it was found that H9N2 viruses circulating in the Israel are predominantly of G1 lineage and harbors Q226L substitution in HA gene (Davidson et al.). 2014 SpringerPlus Discussion IV Q226L 235 240 HA;HA 52;257 54;259 24790833 Isolation and characterization of H9N2 influenza virus isolates from poultry respiratory disease outbreak. The M1 protein revealed V15I substitution in both isolates which is common in all the H9N2 lineages. 2014 SpringerPlus Discussion IV V15I 24 28 M1 4 6 24790833 Isolation and characterization of H9N2 influenza virus isolates from poultry respiratory disease outbreak. The M2 gene has been extensively studied for drug resistance several mutations are known to confer drug resistance; L26F, V27A, A30T, S31N, G34E, L38F (Schnell and Chou). 2014 SpringerPlus Discussion IV L26F;V27A;A30T;S31N;G34E;L38F 116;122;128;134;140;146 120;126;132;138;144;150 M2 4 6 24790833 Isolation and characterization of H9N2 influenza virus isolates from poultry respiratory disease outbreak. The NP gene revealed D34G, L136I and E372D substitutions frequently seen in human associated H9 viruses. 2014 SpringerPlus Discussion IV D34G;L136I;E372D 21;27;37 25;32;42 NP 4 6 24790833 Isolation and characterization of H9N2 influenza virus isolates from poultry respiratory disease outbreak. The PB2 gene in both isolates revealed K355R and A588V substitutions which are not associated with human associated H9 viruses. 2014 SpringerPlus Discussion IV K355R;A588V 39;49 44;54 PB2 4 7 24790833 Isolation and characterization of H9N2 influenza virus isolates from poultry respiratory disease outbreak. The presence of leucine (L) at position 226 is associated with mammalian adaptation avian influenza virus. 2014 SpringerPlus Discussion IV L226L 15 44 24790833 Isolation and characterization of H9N2 influenza virus isolates from poultry respiratory disease outbreak. The Q226L substitution seen in RBS of H9N2 avian isolates is important as it confers human virus like receptor specificity and binds more strongly with 2-6-linked sialic acid receptors as seen in human H3N2 viruses (Matrosovich et al.) in contrast to viruses lacking this substitution which binds more strongly with 2-3 linked sialic acid receptors. 2014 SpringerPlus Discussion IV Q226L 4 9 24790833 Isolation and characterization of H9N2 influenza virus isolates from poultry respiratory disease outbreak. Thereafter again it was detected in 2003 from Chandigarh and Haryana state of India and we found that these viruses which introduced after 2003 contained Q226L substitution. 2014 SpringerPlus Discussion IV Q226L 154 159 24795482 A novel I221L substitution in neuraminidase confers high-level resistance to oseltamivir in influenza B viruses. As for the I223V/R and H275Y substitutions in N1, the N2-I222V substitution alone confers a slight increase in oseltamivir IC50 but acts in synergy with E119V (in N2) to yield highly reduced inhibition by oseltamivir. 2014 The Journal of infectious diseases Discussion IV I223V;I223R;H275Y;I222V;E119V 11;11;23;57;153 18;18;28;62;158 24795482 A novel I221L substitution in neuraminidase confers high-level resistance to oseltamivir in influenza B viruses. Characterization of reassortant A(H1N1)pdm09 viruses showed that the NA I223V substitution alone conferred only a slight increase in oseltamivir IC50 but induced a synergistic increase in oseltamivir IC50 when associated with the H275Y mutation (1733 nM vs 982 nM for H275Y alone). 2014 The Journal of infectious diseases Discussion IV I223V;H275Y;H275Y 72;230;268 77;235;273 69 71 24795482 A novel I221L substitution in neuraminidase confers high-level resistance to oseltamivir in influenza B viruses. Conversely, for reassortant viruses generated by reverse genetics, the NA I223R substitution appears to reduce virus titers. 2014 The Journal of infectious diseases Discussion IV I223R 74 79 71 73 24795482 A novel I221L substitution in neuraminidase confers high-level resistance to oseltamivir in influenza B viruses. For clade 2.1 A(H5N1) viruses, the oseltamivir IC50 values ranged from 43 nM to 75 nM for the I223T/V substitutions and from 268 nM to 349 nM for the I223M substitution. 2014 The Journal of infectious diseases Discussion IV I223V;I223T;I223M 94;94;150 101;101;155 24795482 A novel I221L substitution in neuraminidase confers high-level resistance to oseltamivir in influenza B viruses. In comparison to the I221T or I221V substitutions, the I221L substitution emerged in an immunocompromised patient who underwent prolonged oseltamivir treatment and conferred an increase of >100-fold in the oseltamivir IC50, a much higher fold increase than those seen for the other substitutions. 2014 The Journal of infectious diseases Discussion IV I221T;I221V;I221L 21;30;55 26;35;60 24795482 A novel I221L substitution in neuraminidase confers high-level resistance to oseltamivir in influenza B viruses. In experimental infections of ferrets with influenza A(H5N1) viruses, the I223L substitution emerged spontaneously without any drug pressure. 2014 The Journal of infectious diseases Discussion IV I223L 74 79 24795482 A novel I221L substitution in neuraminidase confers high-level resistance to oseltamivir in influenza B viruses. In our case, I221L substitution in NA of influenza B virus isolates induced highly reduced inhibition by oseltamivir, with IC50 values greater than concentrations of oseltamivir achievable in body fluids (ie, sinus fluid, middle ear fluid, and plasma) under single and multiple dosing regimens. 2014 The Journal of infectious diseases Discussion IV I221L 13 18 35 37 24795482 A novel I221L substitution in neuraminidase confers high-level resistance to oseltamivir in influenza B viruses. In the present study, influenza B viruses bearing a wild-type or I221L-substituted NA showed similar in vitro replicative fitness. 2014 The Journal of infectious diseases Discussion IV I221L 65 70 83 85 24795482 A novel I221L substitution in neuraminidase confers high-level resistance to oseltamivir in influenza B viruses. Influenza A(H1N1) viruses with an I223V substitution alone have been detected during global influenza surveillance (eg, A/Hamamatsu/92/2002) and associated with the H275Y substitution during the 2009 influenza A(H1N1) pandemic in immunocompetent patients under oseltamivir prophylaxis. 2014 The Journal of infectious diseases Discussion IV I223V;H275Y 34;165 39;170 24795482 A novel I221L substitution in neuraminidase confers high-level resistance to oseltamivir in influenza B viruses. Influenza A(H1N1)pdm09 isolates carrying both I223R and H275Y substitutions were isolated from immunocompromised patients after prolonged oseltamivir and/or zanamivir treatment and were highly resistant to oseltamivir. 2014 The Journal of infectious diseases Discussion IV I223R;H275Y 46;56 51;61 24795482 A novel I221L substitution in neuraminidase confers high-level resistance to oseltamivir in influenza B viruses. Influenza A(H1N1)pdm09 viruses carrying a NA I223R substitution conferring a 46-fold increase in oseltamivir IC50 (9.1 nM) were isolated from an immunocompromised patient treated with intravenous zanamivir. 2014 The Journal of infectious diseases Discussion IV I223R 45 50 42 44 24795482 A novel I221L substitution in neuraminidase confers high-level resistance to oseltamivir in influenza B viruses. Influenza B viruses carrying the NA I221T substitution have been previously isolated in the course of global surveillance studies and in patients before treatment. 2014 The Journal of infectious diseases Discussion IV I221T 36 41 33 35 24795482 A novel I221L substitution in neuraminidase confers high-level resistance to oseltamivir in influenza B viruses. Interestingly, viruses carrying the NA I223V substitution propagated to significantly higher titers than wild-type virus and could restore virus fitness and partially compensate for the loss of NA activity due to the H275Y substitution. 2014 The Journal of infectious diseases Discussion IV I223V;H275Y 39;217 44;222 NA;NA 36;194 38;196 24795482 A novel I221L substitution in neuraminidase confers high-level resistance to oseltamivir in influenza B viruses. More recently, a cluster of 14 influenza B viruses carrying the NA I221V substitution, present as a mixed population, were isolated in North Carolina (from November 2010 through February 2011) in untreated patients. 2014 The Journal of infectious diseases Discussion IV I221V 67 72 64 66 24795482 A novel I221L substitution in neuraminidase confers high-level resistance to oseltamivir in influenza B viruses. Moreover, the NA I221L substitution does not impair virus replicative fitness. 2014 The Journal of infectious diseases Discussion IV I221L 17 22 14 16 24795482 A novel I221L substitution in neuraminidase confers high-level resistance to oseltamivir in influenza B viruses. Of 782 NA sequences from influenza A(H5N1) viruses, 24 had substitutions at NA 223: I223T (15 strains), I223V (4 strains), I223L (2 strains), and I223K/F/M (1 each). 2014 The Journal of infectious diseases Discussion IV I223T;I223V;I223L;I223K;I223F;I223M 84;104;123;146;146;146 89;109;128;155;155;155 NA;NA 7;76 9;78 24795482 A novel I221L substitution in neuraminidase confers high-level resistance to oseltamivir in influenza B viruses. Substitutions at position I222V (N2 numbering) have also been described in patients undergoing treatment for influenza A(H3N2) virus infections. 2014 The Journal of infectious diseases Discussion IV I222V 26 31 Influenza A virus H3N2 infection 109 143 24795482 A novel I221L substitution in neuraminidase confers high-level resistance to oseltamivir in influenza B viruses. Taken together, influenza B viruses carrying the I221L substitution in NA can be considered clinically resistant, thereby presenting significant difficulties in the management of infection. 2014 The Journal of infectious diseases Discussion IV I221L 49 54 71 73 24795482 A novel I221L substitution in neuraminidase confers high-level resistance to oseltamivir in influenza B viruses. The I223L substitution identified in A/chicken/Laos/P0020/2007 was associated with K150N and S246N substitutions and contributed to a 77-fold increase in the mean oseltamivir IC50 (84.3 nM). 2014 The Journal of infectious diseases Discussion IV I223L;K150N;S246N 4;83;93 9;88;98 24795482 A novel I221L substitution in neuraminidase confers high-level resistance to oseltamivir in influenza B viruses. The level of resistance of the I221V substitution might be higher because the wild-type virus propagated in tissue culture more readily than the I221V mutant, as assessed by pyrosequencing of clinical specimens and virus isolates. 2014 The Journal of infectious diseases Discussion IV I221V;I221V 31;145 36;150 24795482 A novel I221L substitution in neuraminidase confers high-level resistance to oseltamivir in influenza B viruses. The mean oseltamivir IC50 of the influenza B viruses bearing an NA I221V/I polymorphism was 19.86 nM (a 2-fold increase, compared with corresponding wild-type influenza B viruses). 2014 The Journal of infectious diseases Discussion IV I221V;I221I 67;67 74;74 64 66 24795482 A novel I221L substitution in neuraminidase confers high-level resistance to oseltamivir in influenza B viruses. This article contains the first description of an I221L substitution in the NA gene of influenza B viruses. 2014 The Journal of infectious diseases Discussion IV I221L 50 55 76 78 24889237 Enhanced human receptor binding by H5 haemagglutinins. In the HA of the H1 pandemic virus, for example, a Glu190Asp substitution disrupts a hydrogen bond network required for avian receptor binding and in H2 and H3 pandemic virus HAs, and dramatically in the HA of experimentally transmitted H5 virus, Gln226Leu substitutions also decrease affinity for avian receptors. 2014 Virology Discussion IV E190D;Q226L 51;247 60;256 HA;HA 7;204 9;206 24889237 Enhanced human receptor binding by H5 haemagglutinins. In this regard, our binding and structural data suggest that the Delta133/Ile155Thr mutant is a plausible intermediate since it has the ability to bind avian receptors tightly while at the same time displaying enhanced affinity for human receptor. 2014 Virology Discussion IV I155T 74 83 24889237 Enhanced human receptor binding by H5 haemagglutinins. Indeed surveillance data show that H5 viruses with HAs containing the Delta133/Ile155Thr mutations have been isolated from both poultry and humans in Egypt. 2014 Virology Discussion IV I155T 79 88 24889237 Enhanced human receptor binding by H5 haemagglutinins. Indeed, together with Asn186Lys, which also increases the net-charge of HA but is closer to bound receptor, the basic substitutions Gly143Arg and Gln196Arg appear to alter the avidity for human and avian receptor to similar extents. 2014 Virology Discussion IV N186K;G143R;Q196R 22;132;146 31;141;155 HA 72 74 24889237 Enhanced human receptor binding by H5 haemagglutinins. Our results show that mutant VN1194 viruses with HAs containing Ser227Asn or Asn186Lys substitutions, have lower avidity than wild-type virus for avian receptor. 2014 Virology Discussion IV S227N;N186K 64;77 73;86 24889237 Enhanced human receptor binding by H5 haemagglutinins. Recently also the Delta133/Ile155Thr mutations have been identified in clade 2.1 isolates in Indonesia. 2014 Virology Discussion IV I155T 27 36 24889237 Enhanced human receptor binding by H5 haemagglutinins. The double mutants - Ser227Asn/Gln196Arg and Asn186Lys/Gly143Arg identified in human isolates of H5 in Southeast Asia both have mutations (Ser227Asn or Asn186Lys) that compromise avian receptor binding. 2014 Virology Discussion IV Q196R;G143R;S227N;N186K;S227N;N186K;S227Q 31;55;21;45;139;152;21 40;64;30;54;148;161;30 24889237 Enhanced human receptor binding by H5 haemagglutinins. The structural studies with the Delta133/Ile155Thr mutant of tyTy HA reveal a more polar environment near the 130-and 150-loops. 2014 Virology Discussion IV I155T 41 50 HA 66 68 24889237 Enhanced human receptor binding by H5 haemagglutinins. The widespread distribution of H5 clade 2.2 viruses with Delta133/Ile155Thr mutations many of which also lack glycosylation at residue 158, which is known to be important in aerosol transmission studies in ferrets, is a concerning feature of the current stage of evolution of highly pathogenic avian H5 viruses. 2014 Virology Discussion IV I155T 66 75 24889237 Enhanced human receptor binding by H5 haemagglutinins. Thus, VN1194 Gln196Arg, Gly143Arg and tyTy Delta133/Ile155Thr gain avidity for human receptor but have little effect on avian receptor binding. 2014 Virology Discussion IV I155T;Q196R;G143R 52;13;24 61;22;33 24889237 Enhanced human receptor binding by H5 haemagglutinins. Two of the substitutions Gly143Arg and Gln196Arg are distant from bound receptor (see Supplementary. 2014 Virology Discussion IV G143R;Q196R 25;39 34;48 24928037 The R35 residue of the influenza A virus NS1 protein has minimal effects on nuclear localization but alters virus replication through disrupting protein dimerization. Changes at NS1 positions 37 and 41 did not significantly affect virus replication and had minimal effects on NS1 localization, including loss of nucleolar localization in the virus with the NS1 K41A mutation. 2014 Virology Discussion IV K41A 194 198 NS1;NS1;NS1 11;109;190 14;112;193 24928037 The R35 residue of the influenza A virus NS1 protein has minimal effects on nuclear localization but alters virus replication through disrupting protein dimerization. If the R35A viruses were not viable or strongly outcompeted by low frequency D39X mutations, this indicates that blocking dimerization can have a dramatic affect on virus replication. 2014 Virology Discussion IV R35A;D39X 7;77 11;81 24928037 The R35 residue of the influenza A virus NS1 protein has minimal effects on nuclear localization but alters virus replication through disrupting protein dimerization. In this study, we demonstrated that the NS1 R38A virus, which has a loss of RNA binding in addition to disrupting NLS1, has reduced virus replication and changes in NS1 protein localization, consistent with our previous results. 2014 Virology Discussion IV R38A 44 48 NS1;NS1 40;165 43;168 24928037 The R35 residue of the influenza A virus NS1 protein has minimal effects on nuclear localization but alters virus replication through disrupting protein dimerization. It may be that the NS1 R35A mutation not only disrupts NS1 dimerization, but it may also adversely affect other aspects of virus replication and thus prevent recombinant virus rescue. 2014 Virology Discussion IV R35A 23 27 NS1;NS1 19;55 22;58 24928037 The R35 residue of the influenza A virus NS1 protein has minimal effects on nuclear localization but alters virus replication through disrupting protein dimerization. Replication of a virus encoding NS1 R38A K41A was enhanced by a mutation in NS1 (S42G). 2014 Virology Discussion IV R38A;K41A;S42G 36;41;81 40;45;85 NS1;NS1 32;76 35;79 24928037 The R35 residue of the influenza A virus NS1 protein has minimal effects on nuclear localization but alters virus replication through disrupting protein dimerization. Similar to the viruses with NS1 R38A or K41A, no nucleolar localization of NS1 was seen in cells infected with viruses expressing the NS1 R35A D39X proteins. 2014 Virology Discussion IV R38A;K41A;R35A;D39X 32;40;138;143 36;44;142;147 NS1;NS1;NS1 28;75;134 31;78;137 24928037 The R35 residue of the influenza A virus NS1 protein has minimal effects on nuclear localization but alters virus replication through disrupting protein dimerization. The BiFC assays indicate that the ability of NS1 to interact is dramatically decreased with an R35A mutation. 2014 Virology Discussion IV R35A 95 99 NS1 45 48 24928037 The R35 residue of the influenza A virus NS1 protein has minimal effects on nuclear localization but alters virus replication through disrupting protein dimerization. The NS1 R35A D39X viruses were able to replicate in MDCK and Vero cells, though viruses with NS1 D39N and D39Y replicated less efficiently than wild type virus in MDCK but not Vero cells. 2014 Virology Discussion IV R35A;D39X;D39N;D39Y 8;13;97;106 12;17;101;110 NS1;NS1 4;93 7;96 24928037 The R35 residue of the influenza A virus NS1 protein has minimal effects on nuclear localization but alters virus replication through disrupting protein dimerization. This mutation did not alter NS1 RNA binding activity but we speculate that perhaps it improved NS1 dimer formation, analogous to the D39X mutations we identified. 2014 Virology Discussion IV D39X 133 137 NS1;NS1 28;95 31;98 24928037 The R35 residue of the influenza A virus NS1 protein has minimal effects on nuclear localization but alters virus replication through disrupting protein dimerization. When NS1 R35A interacts with wild type NS1, the interaction between R35 on the wild type protein and the D39 on the NS1 R35A mutant may be enough to stabilize the dimer even though the other 35-39 pair interaction might have a weak repulsion. 2014 Virology Discussion IV R35A;R35A 9;120 13;124 NS1;NS1;NS1 5;39;116 8;42;119 24928037 The R35 residue of the influenza A virus NS1 protein has minimal effects on nuclear localization but alters virus replication through disrupting protein dimerization. When protein dimerization was assessed with the BiFC system, the NS1 R35A proteins were not able to dimerize to the same extent as NS1 wild type. 2014 Virology Discussion IV R35A 69 73 NS1;NS1 65;131 68;134 24928037 The R35 residue of the influenza A virus NS1 protein has minimal effects on nuclear localization but alters virus replication through disrupting protein dimerization. When the NS1 amino acid mutation R35A was introduced into the NS segment, recombinant virus was produced, but every characterized isolate presented an additional mutation at the aspartic acid at position 39. 2014 Virology Discussion IV R35A 33 37 NS;NS1 62;9 64;12 24928037 The R35 residue of the influenza A virus NS1 protein has minimal effects on nuclear localization but alters virus replication through disrupting protein dimerization. While the localization of the NS1 protein was similar between the three NS1 R35A D39X viruses, it was different from wild type virus, most obviously through the appearance of cytoplasmic puncta of NS1. 2014 Virology Discussion IV R35A;D39X 76;81 80;85 NS1;NS1;NS1 30;72;197 33;75;200 24940441 Analysis of the full-length genome of a novel strain of the H7N9 avian influenza virus. Although no E627K and D701N mutations were detected in the PB2 protein of A/Changsha/2/2013, the E627K mutation and D701N mutation occurred in eight human H7N9 virus strains and one human H7N9 virus strain among the 51 new H7N9 viruses, respectively. 2014 Experimental and therapeutic medicine Discussion IV E627K;D701N;E627K;D701N 12;22;97;116 17;27;102;121 PB2 59 62 24940441 Analysis of the full-length genome of a novel strain of the H7N9 avian influenza virus. However avian and environmental H7N9 viruses had no E627K and D701N mutations. 2014 Experimental and therapeutic medicine Discussion IV E627K;D701N 52;62 57;67 24940441 Analysis of the full-length genome of a novel strain of the H7N9 avian influenza virus. In addition, 52 H7N9 viruses harbored the G186V and G228S mutations in the receptor binding site of the HA protein. 2014 Experimental and therapeutic medicine Discussion IV G186V;G228S 42;52 47;57 HA 104 106 24940441 Analysis of the full-length genome of a novel strain of the H7N9 avian influenza virus. Resistance gene loci analysis demonstrated that the R294K mutations of the NA coding protein only occurred in one H7N9 virus strain isolated in Taiwan (A/Taiwan/S02076/2013), suggesting that A/Changsha/2/2013 and 50 other new H7N9 viruses isolated in 2013 were sensitive to neuraminidase inhibitors (e.g. 2014 Experimental and therapeutic medicine Discussion IV R294K 52 57 NA;NA 75;274 77;287 24940441 Analysis of the full-length genome of a novel strain of the H7N9 avian influenza virus. The E627K and D701N mutations favor the efficient replication and dissemination of avian influenza viruses in mammals. 2014 Experimental and therapeutic medicine Discussion IV E627K;D701N 4;14 9;19 24940441 Analysis of the full-length genome of a novel strain of the H7N9 avian influenza virus. The E627K mutation of the PB2 polymerase protein was identified in H5N1 and H7N7 avian influenza viruses isolated from several cases of mortality. 2014 Experimental and therapeutic medicine Discussion IV E627K 4 9 PB2 26 29 24940441 Analysis of the full-length genome of a novel strain of the H7N9 avian influenza virus. The HA protein of A/Changsha/2/2013 and other 45 other new human, avian and environmental H7N9 viruses harbored the Q226L mutation (with a mutation rate of 88.5%) in the receptor binding site. 2014 Experimental and therapeutic medicine Discussion IV Q226L 116 121 HA 4 6 25066276 Development and clinical testing of a simple, low-density gel element array for influenza identification, subtyping, and H275Y detection. 5.3 Detection of H275Y variants. 2014 Journal of virological methods Discussion IV H275Y 17 22 25066276 Development and clinical testing of a simple, low-density gel element array for influenza identification, subtyping, and H275Y detection. In this context, not only was the H275Y portion of the microarray test the most sensitive (< 10 gc per reaction), the development and use of SNR ratios : which is conceptually similar to resequencing microarray data analysis methods : enabled us to positively identify H275Y variants when present at 5% of a mixed population. 2014 Journal of virological methods Discussion IV H275Y;H275Y 34;269 39;274 25066276 Development and clinical testing of a simple, low-density gel element array for influenza identification, subtyping, and H275Y detection. It is therefore important to test patient samples for H275Y variants in both clinical and public health/epidemiology laboratories, and use a diagnostic test that can detect the variant in the presence of excess wild type sequences. 2014 Journal of virological methods Discussion IV H275Y 54 59 25066276 Development and clinical testing of a simple, low-density gel element array for influenza identification, subtyping, and H275Y detection. The LoD for all probes on the microarray test is therefore consistent with anticipated viral loads in a majority of clinical specimens, and the overall microarray work-flow described here represents a significant advance over using multiple real-time PCR assays and sequencing methods for influenza typing, sub-typing, and H275Y genotyping. 2014 Journal of virological methods Discussion IV H275Y 323 328 25066276 Development and clinical testing of a simple, low-density gel element array for influenza identification, subtyping, and H275Y detection. The presence of the H275Y variant in A/H1N1 subtypes is associated with oseltamivir resistance. 2014 Journal of virological methods Discussion IV H275Y 20 25 25119465 Functional balance between the hemagglutinin and neuraminidase of influenza A(H1N1)pdm09 HA D222 variants. The HA D222G/E/N substitution increases the intensity of binding for SAalpha-2,6 and alters the HA-NA balance which may decrease viral fitness in a SAalpha-2,6 environment. 2014 PloS one Discussion IV D222G;D222E;D222N 7;7;7 16;16;16 HA;HA;NA 4;96;99 6;98;101 25119465 Functional balance between the hemagglutinin and neuraminidase of influenza A(H1N1)pdm09 HA D222 variants. The limited number of isolated strains did not allow us to conclude on the potential impact of the D222G or HA-NA balance in human pathogenicity. 2014 PloS one Discussion IV D222G 99 104 HA;NA 108;111 110;113 25119465 Functional balance between the hemagglutinin and neuraminidase of influenza A(H1N1)pdm09 HA D222 variants. The NA activity of the Ste10D virus was higher compared with the other viruses studied, yet differed from the Lyon09D and Ste09G NA by only the M15I substitution. 2014 PloS one Discussion IV M15I 144 148 NA;NA 4;129 6;131 25119465 Functional balance between the hemagglutinin and neuraminidase of influenza A(H1N1)pdm09 HA D222 variants. This is the first report, to our knowledge, that has studied the functional balance of HA-NA in human strains regarding the impact of the D222G/N/E substitution on SAalpha-2,6 HA binding. 2014 PloS one Discussion IV D222G;D222N;D222E 138;138;138 147;147;147 HA;HA;NA 87;176;90 89;178;92 25119465 Functional balance between the hemagglutinin and neuraminidase of influenza A(H1N1)pdm09 HA D222 variants. This may explain why D222G and also D222E/N viruses are not able to be transmitted efficiently and are isolated only sporadically. 2014 PloS one Discussion IV D222G;D222E;D222N 21;36;36 26;43;43 25119465 Functional balance between the hemagglutinin and neuraminidase of influenza A(H1N1)pdm09 HA D222 variants. While acquisition of a lethal phenotype has been shown in viruses affecting mice following the acquisition of key mutations, one of which is D222G, we found no such differences in human influenza viruses and D222G did not appear as a main virulence factor in mice. 2014 PloS one Discussion IV D222G;D222G 141;208 146;213 25124927 Characterization of drug-resistant influenza A(H7N9) variants isolated from an oseltamivir-treated patient in Taiwan. Although the role of NS1-K126R in the virulence of influenza A(H7N9) has not been demonstrated, introduction of NS1-K126R in the A/Puerto Rico/8/34(H1N1) virus led to increased viral yields in cell culture and virulence in mice. 2015 The Journal of infectious diseases Discussion IV K126R;K126R 25;116 30;121 NS1;NS1 21;112 24;115 25124927 Characterization of drug-resistant influenza A(H7N9) variants isolated from an oseltamivir-treated patient in Taiwan. In our study, NS1-K126R had no apparent effect on influenza A(H7N9) replication in ferrets, indicating its host-specific nature. 2015 The Journal of infectious diseases Discussion IV K126R 18 23 NS1 14 17 25124927 Characterization of drug-resistant influenza A(H7N9) variants isolated from an oseltamivir-treated patient in Taiwan. In this study, the NA-R292K virus replicated to similarly high titers as the NA-WT virus in MDCK cells but showed less efficient replication in MDCK-SIAT1 cells modified to overexpress alpha2,6-NeuAc-receptors. 2015 The Journal of infectious diseases Discussion IV R292K 22 27 NA;NA 19;77 21;79 25124927 Characterization of drug-resistant influenza A(H7N9) variants isolated from an oseltamivir-treated patient in Taiwan. Laboratory data for virus with NA-R292K, the most commonly detected substitution in the influenza A(H7N9) subtype, indicate clinically relevant resistance to oseltamivir and, possibly, peramivir. 2015 The Journal of infectious diseases Discussion IV R292K 34 39 31 33 25124927 Characterization of drug-resistant influenza A(H7N9) variants isolated from an oseltamivir-treated patient in Taiwan. Moreover, NA-WT virus required a much greater dose to produce lethality in mice, when compared to the 3 NA variants (E119V, I222R, and, especially, I222K). 2015 The Journal of infectious diseases Discussion IV E119V;I222R;I222K 117;124;148 122;129;153 NA;NA 10;104 12;106 25124927 Characterization of drug-resistant influenza A(H7N9) variants isolated from an oseltamivir-treated patient in Taiwan. Notably, nasal wash titers of the NA-R292K virus were significantly lower than those of the NA-WT virus in the first 3 days after inoculation, suggesting impaired replicative fitness. 2015 The Journal of infectious diseases Discussion IV R292K 37 42 NA;NA 34;92 36;94 25124927 Characterization of drug-resistant influenza A(H7N9) variants isolated from an oseltamivir-treated patient in Taiwan. Peculiarly, the NA-R292K virus possessed a mixture of R/K in NS1-126 and it also exhibited reduced virulence in mice. 2015 The Journal of infectious diseases Discussion IV R292K 19 24 NA;NS1 16;61 18;64 25124927 Characterization of drug-resistant influenza A(H7N9) variants isolated from an oseltamivir-treated patient in Taiwan. Similarly, Yen et al demonstrate that NA-R292K virus (Shanghai/1 background) showed competitive fitness loss in ferrets; this virus, however, transmitted at comparable efficiency as WT virus to animals via direct or respiratory droplet contact. 2015 The Journal of infectious diseases Discussion IV R292K 41 46 38 40 25124927 Characterization of drug-resistant influenza A(H7N9) variants isolated from an oseltamivir-treated patient in Taiwan. The identified HA substitutions (HA-S281N and HA-D340G) are located in positions not known to affect receptor binding or antigenicity; the role of other identified internal gene mutations is also unknown at this time. 2015 The Journal of infectious diseases Discussion IV S281N;D340G 36;49 41;54 HA;HA;HA 15;33;46 17;35;48 25124927 Characterization of drug-resistant influenza A(H7N9) variants isolated from an oseltamivir-treated patient in Taiwan. The NA-I222K virus showed the highest virulence in mice and contained a substitution at PB2-S714N, which was not found among influenza A(H7N9) sequences in GISAID. 2015 The Journal of infectious diseases Discussion IV I222K;S714N 7;92 12;97 NA;PB2 4;88 6;91 25124927 Characterization of drug-resistant influenza A(H7N9) variants isolated from an oseltamivir-treated patient in Taiwan. The NA-R292K virus appeared to be the most attenuated, based on fewer counts of inflammatory cells and lower protein levels in nasal washes and a steady increase in body weights. 2015 The Journal of infectious diseases Discussion IV R292K 7 12 4 6 25124927 Characterization of drug-resistant influenza A(H7N9) variants isolated from an oseltamivir-treated patient in Taiwan. The NA-R292K virus showed an MLD50 similar to that of the NA-WT virus, consistent with a recent report indicating comparable virulence of recombinant Shanghai/1 viruses, with or without NA-R292K. 2015 The Journal of infectious diseases Discussion IV R292K;R292K 7;189 12;194 NA;NA;NA 4;58;186 6;60;188 25124927 Characterization of drug-resistant influenza A(H7N9) variants isolated from an oseltamivir-treated patient in Taiwan. Therefore, NA-R292K is likely to cause a greater functional loss of NA enzymatic activity than the framework substitutions, potentially leading to a greater deficit of virus replicative fitness. 2015 The Journal of infectious diseases Discussion IV R292K 14 19 NA;NA 11;68 13;70 25124927 Characterization of drug-resistant influenza A(H7N9) variants isolated from an oseltamivir-treated patient in Taiwan. This virus contained 2 substitutions PB2-V227M and NS1-K126R, not seen in any other influenza A(H7N9), including the published Taiwan/1 sequence. 2015 The Journal of infectious diseases Discussion IV V227M;K126R 41;55 46;60 NS1;PB2 51;37 54;40 25124927 Characterization of drug-resistant influenza A(H7N9) variants isolated from an oseltamivir-treated patient in Taiwan. Thus, R292K may reduce the effectiveness of treatment and prophylaxis with these drugs. 2015 The Journal of infectious diseases Discussion IV R292K 6 11 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. A blast search among available influenza PB1 sequences at the NCBI Influenza Virus Source identified a total five isolates possessing the PB1-V43I mutation. 2014 Nature communications Discussion IV V43I 142 146 PB1;PB1 41;138 44;141 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. Applying expressed polymerase proteins in enzyme-based assays to determine the binding affinity of the PB1 protein with V43I mutation to ribavirin and NTP will further clarify the molecular mechanism of fidelity. 2014 Nature communications Discussion IV V43I 120 124 PB1 103 106 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. Because ribavirin and favipiravir are both purine analogs, we then assessed the effect of guanosine on wild-type PB1 and PB1-V43I proteins to investigate the potential molecular mechanisms of V43I mutation on RdRP fidelity. 2014 Nature communications Discussion IV V43I;V43I 125;192 129;196 PB1;PB1 113;121 116;124 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. Further studies would be needed to elucidate the precise mechanism leading to differences in lethality observed with the VN1203 wild-type and PB1-V43I mutants. 2014 Nature communications Discussion IV V43I 146 150 PB1 142 145 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. Furthermore, with the Wuhan wild-type and PB1-V43I viruses we demonstrated that they differed in the ability in generating monoclonal antibody escape mutants. 2014 Nature communications Discussion IV V43I 46 50 PB1 42 45 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. In addition to ribavirin, we have evaluated the sensitivity of the PB1-V43I mutation with a panel of nucleoside analogues using the mini-genome assay: tubercidin (adenosine analog), 6-azauridine (uridine), 8-hydroxy-2'-deoxyguanosine (guanosine), acycloguanosine (guanosine), 5-fluorouracil (uridine), favipiravir (guanosine and adenosine), and N4-aminocytidine (cytidine); the V43I mutation only exhibited reduced sensitivity to ribavirin and favipiravir. 2014 Nature communications Discussion IV V43I;V43I 71;378 75;382 PB1 67 70 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. It was noted that the PB1-V43I VN04 virus showed reduced neuro-tropism while compared to the VN1203 wild-type virus. 2014 Nature communications Discussion IV V43I 26 30 PB1 22 25 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. Our results suggest that the PB1-V43I mutation reduced PB1 binding affinity for ribavirin and confer to increased selectivity for NTP, which likely serves as the mechanism for the altered RdRP fidelity and reduced mutational frequency. 2014 Nature communications Discussion IV V43I 33 37 PB1;PB1 29;55 32;58 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. Overall, a single PB1-V43I mutation was identified to confer resistance to ribavirin and altered selectivity to guanosine for the polymerase complex derived from both human seasonal H3N2 and the avian-origin H5N1 highly pathogenic influenza viruses. 2014 Nature communications Discussion IV V43I 22 26 PB1 18 21 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. The lung titers between mice inoculated with the VN1203 wild-type or the PB1-V43I mutant viruses were comparable suggesting that the difference in lethality was not due to differences in the replication capability between these two viruses. 2014 Nature communications Discussion IV V43I 77 81 PB1 73 76 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. The V43I mutation lies within the putative viral RNA binding domain in the N-terminus of PB1 and is generally quite conserved. 2014 Nature communications Discussion IV V43I 4 8 PB1 89 92 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. This was shown to be the case with enterovirus, where both the G64S and A372V mutations were reported to confer the high fidelity phenotype . 2014 Nature communications Discussion IV G64S;A372V 63;72 67;77 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. We demonstrate that a single V43I mutation in PB1 protein confers resistance to ribavirin and increased selectivity to nucleoside, leading to a RdRP with increased fidelity and a reduction in population genetic diversity of both seasonal H3N2 (Wuhan95) and highly pathogenic H5N1 (VN04) viruses. 2014 Nature communications Discussion IV V43I 29 33 PB1 46 49 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. We have selected the PB1-V43I mutation for further characterization because of its most significantly decreased sensitivity to ribavirin in the mini-genome system. 2014 Nature communications Discussion IV V43I 25 29 PB1 21 24 25183443 Generation and characterization of influenza A viruses with altered polymerase fidelity. While we did not directly measure the intracellular NTP concentration under increasing guanosine treatment, we observed that the PB1-V43I protein is more sensitive than that of the wild-type PB1 protein under high concentrations of guanosine (> 40 muM), leading to a reduced firefly luciferase mRNA synthesis, suggesting that the V43I mutation would increase RdRP selectivity for nucleoside under biased NTP concentrations. 2014 Nature communications Discussion IV V43I;V43I 133;330 137;334 PB1;PB1 129;191 132;194 25191344 Prevalence of Oseltamivir-Resistant 2009 H1N1 Influenza Virus among Patients with Pandemic 2009 H1N1 Influenza infection in NRITLD, Tehran, Iran. This study showed the H275Y mutation (oseltamivir-resistant genotype) could appear in the absence or presence of selective drug pressure. 2011 Tanaffos Discussion IV H275Y 22 27 25210166 Accumulation of human-adapting mutations during circulation of A(H1N1)pdm09 influenza virus in humans in the United Kingdom. All of the second- and third-wave viruses in our cohort had NA mutations V106I and N248D compared to first-wave A/195. 2014 Journal of virology Discussion IV V106I;N248D 73;83 78;88 60 62 25210166 Accumulation of human-adapting mutations during circulation of A(H1N1)pdm09 influenza virus in humans in the United Kingdom. already predicted some mutations in A/California/04/2009 virus by which this could be achieved, one of which is common to the A/687 NS1, G189D. 2014 Journal of virology Discussion IV G189D 137 142 NS1 132 135 25210166 Accumulation of human-adapting mutations during circulation of A(H1N1)pdm09 influenza virus in humans in the United Kingdom. In our MOSAIC hospitalized cohort, we did not detect the specific HA mutations described by others to affect A(H1N1)pdm09 virulence, for example, HA D222G, which purportedly facilitates better binding to alpha-2,3-sialic acid-linked receptors in the lower respiratory tract, changes in glycosylation, or antigenicity were not present. 2014 Journal of virology Discussion IV D222G 149 154 HA;HA 66;146 68;148 25210166 Accumulation of human-adapting mutations during circulation of A(H1N1)pdm09 influenza virus in humans in the United Kingdom. indicated a change in receptor binding caused by an S185T mutation. 2014 Journal of virology Discussion IV S185T 52 57 25210166 Accumulation of human-adapting mutations during circulation of A(H1N1)pdm09 influenza virus in humans in the United Kingdom. Other groups have suggested that HA D222G is relatively common in severe cases.The D222G mutation has been suggested to sometimes arise during virus culture as an artifact and may also only be present as a minority variant in samples taken at certain times during the infection. 2014 Journal of virology Discussion IV D222G;D222G 36;83 41;88 HA 33 35 25210166 Accumulation of human-adapting mutations during circulation of A(H1N1)pdm09 influenza virus in humans in the United Kingdom. Previously, we showed that the NA mutation H275Y in first-wave virus conferred a replicative cost that was not detected by growth curve analysis but only by competition assay. 2014 Journal of virology Discussion IV H275Y 43 48 31 33 25210166 Accumulation of human-adapting mutations during circulation of A(H1N1)pdm09 influenza virus in humans in the United Kingdom. That the lost affinity for the alpha-2,3-sialic acids is observed in both second- and third-wave isolates would implicate one or more of the previously reported variations in the HA I32L, D97N, S185T, E374K, and S451N. 2014 Journal of virology Discussion IV I32L;D97N;S185T;E374K;S451N 182;188;194;201;212 186;192;199;206;217 HA 179 181 25210166 Accumulation of human-adapting mutations during circulation of A(H1N1)pdm09 influenza virus in humans in the United Kingdom. These previously described mutations may contribute to some of the enhanced polymerase activity we measured for the A/687 third-wave virus polymerase, but our in vitro polymerase reporter system also indicated that the N321K amino acid change in the PA protein, not previously reported, drove enhancement of viral polymerase activity. 2014 Journal of virology Discussion IV N321K 219 224 PA 250 252 25210166 Accumulation of human-adapting mutations during circulation of A(H1N1)pdm09 influenza virus in humans in the United Kingdom. This mutation at HA residue E374K (H1 numbering) is present in 5 of 6 third-wave viruses in our subset (Table 1) and may also have contributed to the increased replication in HAE cultures we observed. 2014 Journal of virology Discussion IV E374K 28 33 HA 17 19 25409547 The K526R substitution in viral protein PB2 enhances the effects of E627K on influenza virus replication. A distinct substitution, K526R, was found among some of the human isolates, in conjunction with 627K or 701N markers. 2014 Nature communications Discussion IV K526R 25 30 25409547 The K526R substitution in viral protein PB2 enhances the effects of E627K on influenza virus replication. Full evaluation of the transmission and replication abilities of H7N9 and other avian influenza A viruses, such as H5N1-(Indonesia), bearing K526R PB2 will provide valuable information for understanding the adaptation process and establish the importance of this new marker in surveillance of zoonotic influenza A viruses. 2014 Nature communications Discussion IV K526R 141 146 PB2 147 150 25409547 The K526R substitution in viral protein PB2 enhances the effects of E627K on influenza virus replication. Importantly, we found that the H3N2 virus has also gained the PB2-K526R substitution, in addition to 627K; this occurred around 1970, based on available sequence data, and this genotype has become prevalent in humans since then (Table 1. 2014 Nature communications Discussion IV K526R 66 71 25409547 The K526R substitution in viral protein PB2 enhances the effects of E627K on influenza virus replication. In addition to the Q226L substitution in the HA, which may provide the virus with some ability to bind to human type receptors, what other distinct properties has this virus gained to make it different from other avian influenza viruses? This study found that isolates from human H7N9 cases carried one or more adaptation markers in the PB2 polymerase gene (Table 1). 2014 Nature communications Discussion IV Q226L 19 24 HA;PB2 45;337 47;340 25409547 The K526R substitution in viral protein PB2 enhances the effects of E627K on influenza virus replication. It remains to be tested whether the frequently higher seasonal activity of H3N2 virus in humans, compared with H1N1, may be due to its more optimal replication properties and if gaining K526R has contributed to the fitness of H3N2 virus. 2014 Nature communications Discussion IV K526R 186 191 25409547 The K526R substitution in viral protein PB2 enhances the effects of E627K on influenza virus replication. Taken together, these results support the notion that K526R is a new adaptation marker for H7N9 and H5N1-(Indonesia) avian influenza A virus in humans and also provides an extra advantage for H3N2 virus replication. 2014 Nature communications Discussion IV K526R 54 59 25409547 The K526R substitution in viral protein PB2 enhances the effects of E627K on influenza virus replication. The K526R substitution has not been recognized as a mammalian adaptation marker previously. 2014 Nature communications Discussion IV K526R 4 9 25409547 The K526R substitution in viral protein PB2 enhances the effects of E627K on influenza virus replication. The PB2 E627K substitution is recognized as a dominant adaptation marker in the majority of human-adapted influenza A viruses, facilitating replication in mammalian cells, however, the 590S/591R motif was found to complement the function of 627K in the PB2 of 2009 H1N1 virus to allow replication in humans. 2014 Nature communications Discussion IV E627K 8 13 PB2;PB2 4;253 7;256 25505461 D701N mutation in the PB2 protein contributes to the pathogenicity of H5N1 avian influenza viruses but not transmissibility in guinea pigs. found that when PB2 627 holds a glutamic acid residue, the D701N mutation not only improves viral growth in mammalian cells but enhances transmission of both human influenza viruses and AIVs among guinea pigs. 2014 Frontiers in microbiology Discussion IV D701N 59 64 PB2 16 19 25505461 D701N mutation in the PB2 protein contributes to the pathogenicity of H5N1 avian influenza viruses but not transmissibility in guinea pigs. However, an amino acid change in the HA protein (T160A), resulting in the loss of glycosylation at 158-160, was responsible for HA binding to sialylated glycans and was critical for H5N1 virus transmission in guinea pigs. 2014 Frontiers in microbiology Discussion IV T160A 49 54 HA;HA 37;128 39;130 25505461 D701N mutation in the PB2 protein contributes to the pathogenicity of H5N1 avian influenza viruses but not transmissibility in guinea pigs. In our study, the D701N mutation in PB2 protein did not enhance the virus's transmission ability among guinea pigs which suggest other genes may affect virus's ability to transmission among the guinea pigs. 2014 Frontiers in microbiology Discussion IV D701N 18 23 PB2 36 39 25505461 D701N mutation in the PB2 protein contributes to the pathogenicity of H5N1 avian influenza viruses but not transmissibility in guinea pigs. Interestingly, the viruses isolated from the co-caged guinea pigs had a D701N mutation in the PB2 protein. 2014 Frontiers in microbiology Discussion IV D701N 72 77 PB2 94 97 25505461 D701N mutation in the PB2 protein contributes to the pathogenicity of H5N1 avian influenza viruses but not transmissibility in guinea pigs. Previous researches have reported that V96I in the PB2 protein and N417S in the NP protein also existed in low pathogenic human and/or AIV, and these mutations did not enhance their pathogencity to mice. 2014 Frontiers in microbiology Discussion IV V96I;N417S 39;67 43;72 NP;PB2 80;51 82;54 25505461 D701N mutation in the PB2 protein contributes to the pathogenicity of H5N1 avian influenza viruses but not transmissibility in guinea pigs. reported that mutation D701N led to an increase in polymerase activity and replication efficiency in mammalian cells and in mouse pathogenicity, and this increase was significantly enhanced when mutation D701N was combined with mutation S714R. 2014 Frontiers in microbiology Discussion IV D701N;D701N;S714R 23;204;237 28;209;242 25505461 D701N mutation in the PB2 protein contributes to the pathogenicity of H5N1 avian influenza viruses but not transmissibility in guinea pigs. Sequenced results showed N417S mutation in the NP protein and V96I, D701N mutation in the PB2 protein in these two viruses (Table 2). 2014 Frontiers in microbiology Discussion IV N417S;V96I;D701N 25;62;68 30;66;73 NP;PB2 47;90 49;93 25505461 D701N mutation in the PB2 protein contributes to the pathogenicity of H5N1 avian influenza viruses but not transmissibility in guinea pigs. The D701N mutation in the PB2 protein is known to affect the replicative efficiency of H5N1 influenza A viruses in mice and transmissibility in guinea pigs. 2014 Frontiers in microbiology Discussion IV D701N 4 9 PB2 26 29 25659818 Assessment of transmission, pathogenesis and adaptation of H2 subtype influenza viruses in ferrets. Amino acid changes were restricted to Glu190Val, Gly205Val, Met/Arg212Arg or 212Met and Gln226Leu in all 9 ferrets tested, including the inoculated ferrets used in RD transmission experiments (data not shown). 2015 Virology Discussion IV E190V;G205V;R212R;Q226L;M212R 38;49;64;88;64 47;58;73;97;73 25659818 Assessment of transmission, pathogenesis and adaptation of H2 subtype influenza viruses in ferrets. In addition to the Met/Arg212Arg or 212Met mutations found in the mallMD ferrets, Glu190Val, Gly205Val, and Gln226Leu changes were detected in the nasal washes of both inoculated and contact ferrets, but not all were present in the same virus. 2015 Virology Discussion IV R212R;E190V;G205V;Q226L;M212R 23;82;93;108;23 32;91;102;117;32 25659818 Assessment of transmission, pathogenesis and adaptation of H2 subtype influenza viruses in ferrets. Instead, a mixed virus subpopulation containing Thr206Pro was present. 2015 Virology Discussion IV T206P 48 57 25659818 Assessment of transmission, pathogenesis and adaptation of H2 subtype influenza viruses in ferrets. The detection of viral subpopulations isolated from H2-infected ferrets containing key mutations, such as the Gln226Leu change (associated with increased human-like receptor binding preference) is important for identifying genetic changes of H2 viruses that can potentially increase its transmissibility. 2015 Virology Discussion IV Q226L 110 119 25659818 Assessment of transmission, pathogenesis and adaptation of H2 subtype influenza viruses in ferrets. Two substitutions, Glu190Gly/Asp and Glu216Asp, in the HA of ckPA virus were present in all nasal wash samples collected from the inoculated and contact ferret pairs where transmission occurred. 2015 Virology Discussion IV E190G;E216D;E190D 19;37;19 32;46;32 HA 55 57 25701593 Influenza A viruses of swine circulating in the United States during 2009-2014 are susceptible to neuraminidase inhibitors but show lineage-dependent resistance to adamantanes. acquired the S31N-M2 around 1999, but it was not detected until 2009, providing a 10-year window during which the S31N-M2 was acquired by IAV-S circulating in North America. 2015 Antiviral research Discussion IV S31N;S31N 13;114 17;118 M2;M2 18;119 20;121 25701593 Influenza A viruses of swine circulating in the United States during 2009-2014 are susceptible to neuraminidase inhibitors but show lineage-dependent resistance to adamantanes. Although the overall frequency of NAI-resistance markers among IAV-S was low (0.03%; 1/3396), the vast majority of N1 sequences possessed NA substitutions that compensated for the diminished fitness normally associated with H274Y-NA in human seasonal influenza A (H1N1) viruses. 2015 Antiviral research Discussion IV H274Y 224 229 NA;NA;NAI 138;230;34 140;232;37 25701593 Influenza A viruses of swine circulating in the United States during 2009-2014 are susceptible to neuraminidase inhibitors but show lineage-dependent resistance to adamantanes. Although the susceptibility of the I27T-M2 protein was similar to that of wild-type protein, the I27T-M2 virus showed decreased susceptibility to amantadine in vitro, comparable pathogenicity in mice and transmissibility between chickens. 2015 Antiviral research Discussion IV I27T;I27T 35;97 39;101 M2;M2 40;102 42;104 25701593 Influenza A viruses of swine circulating in the United States during 2009-2014 are susceptible to neuraminidase inhibitors but show lineage-dependent resistance to adamantanes. Despite the widespread amantadine resistance among currently circulating IAV-S, the M2 protein remains an important target for anti-influenza drugs; novel compounds with antiviral activity against amantadine-resistant viruses with the S31N-M2 have been described. 2015 Antiviral research Discussion IV S31N 235 239 M2;M2 84;240 86;242 25701593 Influenza A viruses of swine circulating in the United States during 2009-2014 are susceptible to neuraminidase inhibitors but show lineage-dependent resistance to adamantanes. Even with the worldwide circulation of the oseltamivir-resistant human H1N1 viruses during 2007-2009, the NA gene from human H1N1 viruses with the H274Y-NA were not introduced into the IAV-S populations. 2015 Antiviral research Discussion IV H274Y 147 152 NA;NA 106;153 108;155 25701593 Influenza A viruses of swine circulating in the United States during 2009-2014 are susceptible to neuraminidase inhibitors but show lineage-dependent resistance to adamantanes. In this study, we confirmed that the I27T-M2 causes an intermediate level of resistance to amantadine in IAV-S in vitro and that pigs in the U.S. 2015 Antiviral research Discussion IV I27T 37 41 M2 42 44 25701593 Influenza A viruses of swine circulating in the United States during 2009-2014 are susceptible to neuraminidase inhibitors but show lineage-dependent resistance to adamantanes. Most of the IAV-S analyzed possessed the S31N-M2, which is associated with amantadine resistance in human H1N1, H3N2, H5N1, and H7N9 influenza viruses. 2015 Antiviral research Discussion IV S31N 41 45 M2 46 48 25701593 Influenza A viruses of swine circulating in the United States during 2009-2014 are susceptible to neuraminidase inhibitors but show lineage-dependent resistance to adamantanes. Our extensive screening of the NA IAV-S sequences identified one IAV-S sequence that possesses the H274Y-NA, a known maker of clinically relevant NAI resistance. 2015 Antiviral research Discussion IV H274Y 99 104 NA;NA;NAI 31;105;146 33;107;149 25701593 Influenza A viruses of swine circulating in the United States during 2009-2014 are susceptible to neuraminidase inhibitors but show lineage-dependent resistance to adamantanes. Our phenotypic analysis of H1N1 IAV-S with the I117V-NA showed less than 10-fold decreased inhibition by oseltamivir, suggesting normal inhibition by NAIs using recent WHO criteria. 2015 Antiviral research Discussion IV I117V 47 52 NA;NAI 53;150 55;154 25701593 Influenza A viruses of swine circulating in the United States during 2009-2014 are susceptible to neuraminidase inhibitors but show lineage-dependent resistance to adamantanes. Previous studies described reduction in susceptibility to oseltamivir in human H5N1 and H1N1pdm09 viruses with the I117V-NA. 2015 Antiviral research Discussion IV I117V 115 120 121 123 25701593 Influenza A viruses of swine circulating in the United States during 2009-2014 are susceptible to neuraminidase inhibitors but show lineage-dependent resistance to adamantanes. Recently, two human influenza cases were caused by the IAV-S with the I27T-M2 in the U.S. 2015 Antiviral research Discussion IV I27T 70 74 M2 75 77 Influenza 14 29 25701593 Influenza A viruses of swine circulating in the United States during 2009-2014 are susceptible to neuraminidase inhibitors but show lineage-dependent resistance to adamantanes. The Eurasian avian lineage of IAV-S acquired the S31N-M2 in the mid-1980s, and the emergence and spread of these viruses have been described among IAV-S in Europe. 2015 Antiviral research Discussion IV S31N 49 53 M2 54 56 25701593 Influenza A viruses of swine circulating in the United States during 2009-2014 are susceptible to neuraminidase inhibitors but show lineage-dependent resistance to adamantanes. The I27T-M2 was the second-most commonly identified substitution among IAV-S isolated in the U.S. 2015 Antiviral research Discussion IV I27T 4 8 M2 9 11 25701593 Influenza A viruses of swine circulating in the United States during 2009-2014 are susceptible to neuraminidase inhibitors but show lineage-dependent resistance to adamantanes. The studies are needed to re-evaluate the I117V-NA marker, as well as other markers reported to reduce susceptibility to NAIs (e.g., E119K, Y155H) based on the recent WHO criteria, and to understand whether variants harboring these substitution alone or in combination with the clinically-relevant H274Y-NA would alter antiviral susceptibility and fitness in IAV-S. 2015 Antiviral research Discussion IV I117V;E119K;Y155H;H274Y 42;133;140;298 47;138;145;303 NA;NA;NAI 48;304;121 50;306;125 25701593 Influenza A viruses of swine circulating in the United States during 2009-2014 are susceptible to neuraminidase inhibitors but show lineage-dependent resistance to adamantanes. The temporally structured M-gene phylogenetic tree showed that S31N-M2 and I27T-M2 emerged stochastically but appeared to be fixed in the U.S. 2015 Antiviral research Discussion IV S31N;I27T 63;75 67;79 M;M2;M2 26;68;80 27;70;82 25701593 Influenza A viruses of swine circulating in the United States during 2009-2014 are susceptible to neuraminidase inhibitors but show lineage-dependent resistance to adamantanes. The V27A-M2, which also confers resistance to adamantanes, and S31N-M2 were detected in the IAV-S of Eurasian avian lineage, and IAV-S with dual S31N-M2 and V27A-M2 emerged after the S31N-M2 IAV-S were established in the swine population in the U.S. 2015 Antiviral research Discussion IV V27A;S31N;S31N;V27A;S31N 4;63;145;157;183 8;67;149;161;187 M2;M2;M2;M2;M2 9;68;150;162;188 11;70;152;164;190 25701593 Influenza A viruses of swine circulating in the United States during 2009-2014 are susceptible to neuraminidase inhibitors but show lineage-dependent resistance to adamantanes. Three independent events of the emergence of the S31N-M2 have been documented among IAV-S worldwide. 2015 Antiviral research Discussion IV S31N 49 53 M2 54 56 25701593 Influenza A viruses of swine circulating in the United States during 2009-2014 are susceptible to neuraminidase inhibitors but show lineage-dependent resistance to adamantanes. Together, these data suggest that the possible spread of variant viruses carrying an M gene of classic swine origin, of which 43% possess the I27T-M2 drug-resistant marker, should be taken into consideration. 2015 Antiviral research Discussion IV I27T 142 146 M;M2 85;147 86;149 25701593 Influenza A viruses of swine circulating in the United States during 2009-2014 are susceptible to neuraminidase inhibitors but show lineage-dependent resistance to adamantanes. Two IAV-S with the H274Y-NA were reported from a farm in Canada, where humans were infected with a reassortant influenza A virus (HA/NA from human H1N1 and internal genes from swine TRIG IAV). 2015 Antiviral research Discussion IV H274Y 19 24 HA;NA;NA 130;25;133 132;27;135 25701593 Influenza A viruses of swine circulating in the United States during 2009-2014 are susceptible to neuraminidase inhibitors but show lineage-dependent resistance to adamantanes. We identified the I27T-M2 as the amino acid substitution that confers an intermediate level of resistance to amantadine in IAV-S of classic swine M lineage. 2015 Antiviral research Discussion IV I27T 18 22 M2 23 25 25713566 PB2 segment promotes high-pathogenicity of H5N1 avian influenza viruses in mice. Asn715 Ser mutation made QL90 only able to replicate in the lungs with a lower titer. 2015 Frontiers in microbiology Discussion IV N715S 0 10 25713566 PB2 segment promotes high-pathogenicity of H5N1 avian influenza viruses in mice. In addition, mutation Gln591Lys of PB2 could compensate for the lack of PB2-627Lys and increase the virulence of an avian H5N1 influenza virus in mice (Yamada et al.,). 2015 Frontiers in microbiology Discussion IV Q591K 22 31 PB2;PB2 35;72 38;75 25713566 PB2 segment promotes high-pathogenicity of H5N1 avian influenza viruses in mice. In this study, the different amino acids include Gln39Lys, near the domain of PB2 which binds to PB1; Thr339Lys, Arg340Lys, and Gly368Arg, locate in "cap snatching"; Ile649Val, Thr684Ala, and Ser715Asn, locate in the domain in which PB2 reacts with the host protein. 2015 Frontiers in microbiology Discussion IV Q39K;T339K;R340K;G368R;I649V;T684A;S715N 49;102;113;128;166;177;192 57;111;122;137;175;186;201 PB1;PB2;PB2 97;78;233 100;81;236 25713566 PB2 segment promotes high-pathogenicity of H5N1 avian influenza viruses in mice. Introduction of mutations in the PB2 gene, such as 339 Lys, 271Ala, 627Lys, 591Lys/Arg, 701Asn, and 714Arg enhance polymerase activity in mammalian cells (Gabriel et al.,; Bussey et al.,; Yamada et al.,; Liu et al.,). 2015 Frontiers in microbiology Discussion IV K591R 76 86 PB2 33 36 25713566 PB2 segment promotes high-pathogenicity of H5N1 avian influenza viruses in mice. It is noteworthy that the Ser715Asn mutation dramatically decreased the virulence of DK212 by almost 2710.19-fold. 2015 Frontiers in microbiology Discussion IV S715N 26 35 25713566 PB2 segment promotes high-pathogenicity of H5N1 avian influenza viruses in mice. Likewise, the Ser715Asn single mutation sharply decreased the virulence of DK212, but the Asn715Ser single mutation did not increase the pathogenicity of QL90. 2015 Frontiers in microbiology Discussion IV S715N;N715S 14;90 23;99 25713566 PB2 segment promotes high-pathogenicity of H5N1 avian influenza viruses in mice. Mutation of Glu 627Lys or 701Asn in PB2 increases the pathogenesis of viruses in mammalian hosts (Li et al.,; de Jong et al.,) and transmissibility between mammalian models (Gabriel et al.,; Gao et al.,; Steel et al.,). 2015 Frontiers in microbiology Discussion IV E627K 12 22 PB2 36 39 25713566 PB2 segment promotes high-pathogenicity of H5N1 avian influenza viruses in mice. The H5N1 virus with some mutation, such as Asp92Glu, Pro42Ser, Leu103Phe, and Ile106Met in NS1, could enhance the ability to inhibit the IFN-alpha/beta production and increase viral replication, resulting in high pathogenicity in pigs or mice (Seo et al.,; Twu et al.,; Jiao et al.,). 2015 Frontiers in microbiology Discussion IV D92E;P42S;L103F;I106M 43;53;63;78 51;61;72;87 NS1 91 94 25713566 PB2 segment promotes high-pathogenicity of H5N1 avian influenza viruses in mice. The results support the contribution of the virus without 627Lys or 701Asn or Gln591Lys could be compensated for by other mutations at other sites of PB2. 2015 Frontiers in microbiology Discussion IV Q591K 78 87 PB2 150 153 25713566 PB2 segment promotes high-pathogenicity of H5N1 avian influenza viruses in mice. The Ser714Arg single mutation introduced into SC35 did not increase the virulence of the virus in mice, but 714Arg was essential for SC35M in maintaining high pathogenicity. 2015 Frontiers in microbiology Discussion IV S714R 4 13 25713566 PB2 segment promotes high-pathogenicity of H5N1 avian influenza viruses in mice. The virulence of 212-Gln39Lys, 212-Ile649Val, 212-Thr684Ala, and 212-Ser715Asn showed as being 19.82-2710.19-fold lower than in rgDK212. 2015 Frontiers in microbiology Discussion IV Q39K;I649V;T684A;S715N 21;35;50;69 29;44;59;78 25713566 PB2 segment promotes high-pathogenicity of H5N1 avian influenza viruses in mice. There were 7 amino acids discrepancy in PB2 between DK212 and QL90, which included three discrepancies at PB2 Ile649Val, Thr684Ala, and Ser715Asn located in the nuclear localization domain or host protein binding domain (Brown,), and one discrepancy at Gln39Lys PB2, near the PA binding area (residues 1-35) (He et al.,; Sugiyama et al.,). 2015 Frontiers in microbiology Discussion IV I649V;T684A;S715N;Q39K 110;121;136;253 119;130;145;261 PA;PB2;PB2;PB2 276;40;106;262 278;43;109;265 25766295 Structure and receptor binding of the hemagglutinin from a human H6N1 influenza virus. Although the Gly228Ser mutation was not detected in these isolates, an Ala128Ser substitution, previously associated with human-like receptor binding, was present in a few viruses, but this mutation does not increase binding to human-type receptors. 2015 Cell host & microbe Discussion IV G228S;A128S 13;71 22;80 25768797 Adamantane-resistant influenza a viruses in the world (1902-2013): frequency and distribution of M2 gene mutations. Additionally, the high levels of the dual L26I and S31N resistance mutations mainly detected in H5N1 variants obtained from Thailand, Vietnam, and Cambodia indicate that viruses carrying this dual motif are stably selected (S3 Table). 2015 PloS one Discussion IV L26I;S31N 42;51 46;55 25768797 Adamantane-resistant influenza a viruses in the world (1902-2013): frequency and distribution of M2 gene mutations. Among these mutations, the S31N is the most frequently reported, suggesting that variants containing the S31N substitution might possess a significant advantage on viral replication or transmission, leading to more efficient circulation. 2015 PloS one Discussion IV S31N;S31N 27;105 31;109 25768797 Adamantane-resistant influenza a viruses in the world (1902-2013): frequency and distribution of M2 gene mutations. Drug-resistance mutations at other amino acid positions (L26F, A30T, G34E, and L38F) are extremely rare (their prevalence appeared to be < 0.2%) (Table 2). 2015 PloS one Discussion IV L26F;A30T;G34E;L38F 57;63;69;79 61;67;73;83 25768797 Adamantane-resistant influenza a viruses in the world (1902-2013): frequency and distribution of M2 gene mutations. Given that the dual L26I and S31N motif are identified firstly in China in 2002 in our study, it appears that China might have been the location of introduction or generation of viruses. 2015 PloS one Discussion IV L26I;S31N 20;29 24;33 25768797 Adamantane-resistant influenza a viruses in the world (1902-2013): frequency and distribution of M2 gene mutations. In our study described here, the most common adamantane resistance mutation was S31N in influenza A viruses from human, avian, and swine (Table 4). 2015 PloS one Discussion IV S31N 80 84 25768797 Adamantane-resistant influenza a viruses in the world (1902-2013): frequency and distribution of M2 gene mutations. It was reported that mutated viruses may either lose the ability to bind M2 ion channel blockers, as with the S31N or A30T amino acid substitutions, or bind the blockers but retain M2 function, as with amino acid replacements L26F or V27A at residue 26 or 27. 2015 PloS one Discussion IV S31N;A30T;L26F;V27A 110;118;226;234 114;122;230;238 M2;M2 73;181 75;183 25768797 Adamantane-resistant influenza a viruses in the world (1902-2013): frequency and distribution of M2 gene mutations. The known mutations that confer adamantane resistance are L26F, V27A, A30T (A30V), S31N, G34E, and L38F. 2015 PloS one Discussion IV L26F;V27A;A30T;A30V;S31N;G34E;L38F 58;64;70;76;83;89;99 62;68;74;80;87;93;103 25928577 Amino acid substitutions in the neuraminidase protein of an H9N2 avian influenza virus affect its airborne transmission in chickens. In the present study, SPF chickens inoculated with a recombinant virus r01/NA381 (containing mutations D368E, S370L, E313K and G381D in SD01 virus NA) failed to infect chickens in the aerosol contact group, and airborne virus was not detected in the isolators. 2015 Veterinary research Discussion IV D368E;S370L;E313K;G381D 103;110;117;127 108;115;122;132 NA;NA 75;147 77;149 25928577 Amino acid substitutions in the neuraminidase protein of an H9N2 avian influenza virus affect its airborne transmission in chickens. It was found that the NA activity of A/Moscow/10/99 (H3N2) influenza virus with D198N and E119D mutations in NA was considerably lower than for the parental virus following stable passage in MDCK cells. 2015 Veterinary research Discussion IV D198N;E119D 80;90 85;95 NA;NA 22;109 24;111 25928577 Amino acid substitutions in the neuraminidase protein of an H9N2 avian influenza virus affect its airborne transmission in chickens. reported that D198N, E119D and I222L mutations in NA of H3N2 influenza virus could alter the biological activity of NA. 2015 Veterinary research Discussion IV D198N;E119D;I222L 14;21;31 19;26;36 NA;NA 50;116 52;118 25928577 Amino acid substitutions in the neuraminidase protein of an H9N2 avian influenza virus affect its airborne transmission in chickens. reported that substitution of R292K in the NA of A/Sydney/5/97 weakened virus infectivity and abolished parental airborne transmissibility in ferrets. 2015 Veterinary research Discussion IV R292K 30 35 43 45 25928577 Amino acid substitutions in the neuraminidase protein of an H9N2 avian influenza virus affect its airborne transmission in chickens. The introduction of four mutations, E368D, L370S, K313E and D381G, in NA of r01/NASS conferred transmissibility of the recombinant virus by aerosols in chickens, especially, the amino-acid pair 313-381 had a major effect on airborne transmissibility. 2015 Veterinary research Discussion IV E368D;L370S;K313E;D381G 36;43;50;60 41;48;55;65 70 72 25928577 Amino acid substitutions in the neuraminidase protein of an H9N2 avian influenza virus affect its airborne transmission in chickens. They also demonstrated that substitution H274Y could reduce the transmission ability of H1N1 influenza virus in mammals. 2015 Veterinary research Discussion IV H274Y 41 46 25939747 Two polar residues within C-terminal domain of M1 are critical for the formation of influenza A Virions. As a result, both spherical and filamentous morphological viral particles could be produced in WSN-M1-S183A and WSN-M1-T185A mutant virus. 2015 Cellular microbiology Discussion IV S183A;T185A 102;119 107;124 M1;M1 99;116 101;118 25939747 Two polar residues within C-terminal domain of M1 are critical for the formation of influenza A Virions. But M1-S183A/T185A did not support virus production, maybe due to other functional role of this motif. 2015 Cellular microbiology Discussion IV S183A;T185A 7;13 12;18 M1 4 6 25939747 Two polar residues within C-terminal domain of M1 are critical for the formation of influenza A Virions. found that one C-terminal domain mutation, N231D, could affect the morphology of equine influenza viruses by producing small filamentous structures (Elton et al.,). 2015 Cellular microbiology Discussion IV N231D 43 48 25966032 Virological characterization of influenza H1N1pdm09 in Vietnam, 2010-2013. Comparing amino acid residues in the HA and NA proteins of A/California/07/2009 with those in Vietnamese isolates, we identified some significant substitutions such as P83S, S203T, and R223Q in HA protein or N248D in NA protein that were observed in all study isolates (Table1). 2015 Influenza and other respiratory viruses Discussion IV P83S;S203T;R223Q;N248D 168;174;185;208 172;179;190;213 HA;HA;NA;NA 37;194;44;217 39;196;46;219 25966032 Virological characterization of influenza H1N1pdm09 in Vietnam, 2010-2013. However, in early 2011, the D222N substitution was found in three cases in the United States and may correlate with severe clinical manifestations, similar to D222G. 2015 Influenza and other respiratory viruses Discussion IV D222N;D222G 28;159 33;164 25966032 Virological characterization of influenza H1N1pdm09 in Vietnam, 2010-2013. However, the mutation G155E has been frequently observed in association with propagation in cell culture, while mutation N156K is more common in original specimens than isolates; therefore, further direct sequencing of clinical samples will be required to assess the need to update vaccine virus strains. 2015 Influenza and other respiratory viruses Discussion IV G155E;N156K 22;121 27;126 25966032 Virological characterization of influenza H1N1pdm09 in Vietnam, 2010-2013. Our result provides additional information about the variant D222N in association with enhanced virulence of influenza A/H1N1pdm09 virus. 2015 Influenza and other respiratory viruses Discussion IV D222N 61 66 25966032 Virological characterization of influenza H1N1pdm09 in Vietnam, 2010-2013. Our study reports a variant D222N virus from a fatal case in 2013. 2015 Influenza and other respiratory viruses Discussion IV D222N 28 33 25966032 Virological characterization of influenza H1N1pdm09 in Vietnam, 2010-2013. Similar to the D222G mutation, the variants D222A, D222E, and D222N also result in enhanced binding to receptor (alpha2-3) of epithelial cells in the lower respiratory tract, whereas wild-type seasonal influenza strains bind preferentially to the alpha2-6 receptor of the upper airway cells. 2015 Influenza and other respiratory viruses Discussion IV D222G;D222A;D222E;D222N 15;44;51;62 20;49;56;67 25966032 Virological characterization of influenza H1N1pdm09 in Vietnam, 2010-2013. The association of mutation N156K on the HA1 with both antigenic drift and virus receptor binding of A/H1N1pdm09 was determined in a ferret model and was confirmed by our study as all low-titer isolates possessed both the G155E and the N156K mutations (Table2). 2015 Influenza and other respiratory viruses Discussion IV N156K;G155E;N156K 28;222;236 33;227;241 HA1 41 44 25966032 Virological characterization of influenza H1N1pdm09 in Vietnam, 2010-2013. The D222G mutation in the HA of A/H1N1pdm/09 viruses was first reported in Norway in November 2009, raising a possible link between this mutation and greater virulence. 2015 Influenza and other respiratory viruses Discussion IV D222G 4 9 HA 26 28 25966032 Virological characterization of influenza H1N1pdm09 in Vietnam, 2010-2013. The frequency of D222G-mutated viruses isolated only from severe or fatal cases was documented in Norway, USA, UK, and Spain. 2015 Influenza and other respiratory viruses Discussion IV D222G 17 22 25966032 Virological characterization of influenza H1N1pdm09 in Vietnam, 2010-2013. Two oseltamivir-resistant A/H1N1pdm09 isolates in 2011 and 2013 were detected by neuraminidase inhibition (NAI) test and Sanger sequence NA gene (H275Y); in total, 11 cases of Vietnamese oseltamivir-resistant A/H1N1pdm09 isolates have been identified between 2009 and 2013. 2015 Influenza and other respiratory viruses Discussion IV H275Y 146 151 NA;NAI;NA 137;107;81 139;110;94 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. A simulated competition experiment between WT-I223 and MUT-I223V shows a larger total (1.3 x 107 to 1.9 x 109 RNA copies/mL, p < 0.001) and infectious (4.5 x 104 to 1.3 x 107 PFU/mL, p < 0.001) viral titer, and fraction of infected cells (0.03 to 0.84, p < 0.001) for the MUT-I223V strain in the presence of 15nM oseltamivir. 2015 PloS one Discussion IV I223V;I223V 59;276 64;281 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. Both the I223V and H275Y mutations were introduced into the H1N1pdm09 background via reverse genetics such that the MUT-H275Y and MUT-I223V strains differ from the WT strain only in their single, respective mutation. 2015 PloS one Discussion IV I223V;H275Y;H275Y;I223V 9;19;120;134 14;24;125;139 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. Experimentally, we found that the MUT-I223V strain reached comparable total and infectious viral titers to those seen with the wild-type (WT), but the viral kinetics observed for the MUT-I223V strain was delayed by a few hours compared to that of its WT counterpart. 2015 PloS one Discussion IV I223V;I223V 38;187 43;192 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. In the MUT-H275Y strain, the significant increase in the eclipse phase length (from 6.9h to 9.4h, p < 0.001) was accompanied by a decrease in the total viral production rate (from 7460 to 1770, p < 0.001) compensated by an increase in the infectiousness of the virions produced. 2015 PloS one Discussion IV H275Y 11 16 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. In this work we presented a set of experiments investigating the impact of the introduction of a single isoleucine-to-valine mutation at residue 223 of the N1 neuraminidase (NA) protein of the A/Quebec/144147/09 H1N1pdm09 strain. 2015 PloS one Discussion IV I223V 104 148 NA;NA 174;159 176;172 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. In this work, the two sets of triplicates for the WT and MUT-I223V were all performed exactly in this manner (two sets of plates processed in the same manner, at the same time, by the same individual) so as to virtually eliminate this variability. 2015 PloS one Discussion IV I223V 61 66 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. Mathematical analyses of the experimental data identified that the I223V mutation in the H1N1pdm09 background causes a significant increase in the length of the eclipse phase (tau E, from 6.9h to 11h, p < 0.001), and a significant decrease in the duration of virus production by infected cells (or infectious lifespan, tau I, from 28h to 11h, p = 0.04), both disadvantageous to the fitness of the MUT-I223V strain relative to the WT. 2015 PloS one Discussion IV I223V;I223V 67;401 72;406 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. Our mathematical approach also allowed us to simulate a competition experiment between the MUT-H275Y and MUT-I223V strains. 2015 PloS one Discussion IV H275Y;I223V 95;109 100;114 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. The simulated competition experiment between the WT and MUT-I223V strains in the absence of oseltamivir shows that the total viral load (1.5 x 1010 to 5.2 x 108 RNA copies/mL, p = 0.002), the infectious viral titer (5.4 x 107 to 3.9 x 106 PFU/mL, p < 0.001) and the fraction of cells infected (0.96 to 0.04, p < 0.001) would be dominated by the WT strain, whereas the MUT-H275Y strain somewhat matched the fitness of the WT strain infecting a comparable fraction of cells and producing a comparable amount of infectious virus. 2015 PloS one Discussion IV I223V;H275Y 60;372 65;377 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. These findings explain the observed delay to peak viral titer for the I223 mutants, and are similar to those we previously reported for the changes caused by a histidine-to-tyrosine mutation at residue 275 of the N1 NA protein of the same strain. 2015 PloS one Discussion IV H275Y 160 205 216 218 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. This more advantageous change was not observed in the MUT-I223V strain. 2015 PloS one Discussion IV I223V 58 63 25992792 Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility. We found that these two strains produce similar amounts of total virus (RNA) when in direct competition, but that the MUT-H275Y strain would produce significantly more infectious virus (p = 0.04) and infect a larger fraction of cells (p < 0.001). 2015 PloS one Discussion IV H275Y 122 127 25999284 Egg-adaptive mutations in H3N2v vaccine virus enhance egg-based production without loss of antigenicity or immunogenicity. Although amino acids at positions 183, 194, and 233 were not predicted to reside in any of the five antigenic sites, the close proximity of positions 183 and 194 to the dominant antigenic site (B) may have altered the antigenicity of CVVs RG271 (L1941I/Y2331H) and RG275 (H1831F). 2015 Vaccine Discussion IV Y2331H;H1831F;L1941I 253;272;246 259;278;252 25999284 Egg-adaptive mutations in H3N2v vaccine virus enhance egg-based production without loss of antigenicity or immunogenicity. Although removal of an N-glycosylation site may unmask antigenic sites and may potentially alter antigenicity, we observed no significant change in antigenicity after mutation of any single glycosylation site (N1261K, T1281N, N1651K, and N2461K) or even after the double mutation T1281N + N1651K. 2015 Vaccine Discussion IV N1261K;T1281N;N1651K;N2461K;T1281N;N1651K 210;218;226;238;280;289 216;224;232;244;286;295 25999284 Egg-adaptive mutations in H3N2v vaccine virus enhance egg-based production without loss of antigenicity or immunogenicity. Analysis of viral proteins supported our yield data (hemagglutination and PFU assays), showing an E6-RG269 (G1861V + N2461K) yield almost double that of E6-RG267 (G1861V). 2015 Vaccine Discussion IV G1861V;N2461K;G1861V 108;117;163 114;123;169 25999284 Egg-adaptive mutations in H3N2v vaccine virus enhance egg-based production without loss of antigenicity or immunogenicity. CVV RG269, carrying the combined mutations G1861V + N2461K, produced the greatest virus yield (significantly greater than the RG267 [G1861V] yield) with no detectable change in HA properties after six egg passages (Table 2). 2015 Vaccine Discussion IV G1861V;N2461K;G1861V 43;52;133 49;58;139 HA 177 179 25999284 Egg-adaptive mutations in H3N2v vaccine virus enhance egg-based production without loss of antigenicity or immunogenicity. However, HA-H1831L and HA-L1941I + Y2331H exhibited significantly altered antigenicity (Table 2). 2015 Vaccine Discussion IV H1831L;L1941I;Y2331H 12;26;35 18;32;41 HA;HA 9;23 11;25 25999284 Egg-adaptive mutations in H3N2v vaccine virus enhance egg-based production without loss of antigenicity or immunogenicity. Increased H3N2 CVV growth due to the N2461K HA mutation has not been reported previously, and it will be important to examine the effect of this mutation on H3N2 CVVs that carry the HA-1861V mutation (e.g., influenza A/Victoria/361/2011[H3N2]). 2015 Vaccine Discussion IV N2461K 37 43 HA;HA 44;182 46;184 25999284 Egg-adaptive mutations in H3N2v vaccine virus enhance egg-based production without loss of antigenicity or immunogenicity. Ind08 virus with the combined substitutions G1861V and N2461K produced the greatest HA protein yield and offer the best means of egg-based production of Ind08-like vaccine. 2015 Vaccine Discussion IV G1861V;N2461K 44;55 50;61 HA 84 86 25999284 Egg-adaptive mutations in H3N2v vaccine virus enhance egg-based production without loss of antigenicity or immunogenicity. It is possible that this altered migration pattern of HA2 could be a reflection of differential post-translational modification due to substitution of a charged Arg with neutral Gly at position 76 (R762G). 2015 Vaccine Discussion IV R762G 198 203 HA 54 56 25999284 Egg-adaptive mutations in H3N2v vaccine virus enhance egg-based production without loss of antigenicity or immunogenicity. Notably, although sequence analysis of the E6-RG267 RT-PCR product indicated acquisition of the N2461K HA mutation (creating an RG269-type HA), the yield of RG269 remained substantially greater than that of RG267, possibly reflecting undetected heterogeneity of RG267. 2015 Vaccine Discussion IV N2461K 96 102 HA;HA 103;139 105;141 25999284 Egg-adaptive mutations in H3N2v vaccine virus enhance egg-based production without loss of antigenicity or immunogenicity. Our results indicate that G1861V is a key HA mutation for the adaptation of Ind08 to eggs without significant impairment of antigenicity or immunogenicity. 2015 Vaccine Discussion IV G1861V 26 32 HA 42 44 25999284 Egg-adaptive mutations in H3N2v vaccine virus enhance egg-based production without loss of antigenicity or immunogenicity. Sequence analysis showed that the virus had acquired the HA mutations L1941I + Y2331H, similar to those in RG271, which underwent the greatest change in antigenicity (Table 2). 2015 Vaccine Discussion IV L1941I;Y2331H 70;79 76;85 HA 57 59 25999284 Egg-adaptive mutations in H3N2v vaccine virus enhance egg-based production without loss of antigenicity or immunogenicity. Supporting this possibility is prior work showing a Glu to Gly mutation at position 81 (E812G) of HA2 in an H3N2 virus (X31), which increased activation pH by 0.3, likely destabilized a hydrogen-bonded salt link with Arg 76, which is important for stabilizing the trimeric arrangement of o-helices . 2015 Vaccine Discussion IV E812G 88 93 HA 98 100 25999284 Egg-adaptive mutations in H3N2v vaccine virus enhance egg-based production without loss of antigenicity or immunogenicity. Supporting this possibility is prior work showing a Glu to Gly mutation at position 81 (E812G) of HA2 in an H3N2 virus (X31), which increased activation pH by 0.3, likely destabilized a hydrogen-bonded salt link with Arg 76, which is important for stabilizing the trimeric arrangement of o-helices. 2015 Vaccine Discussion IV E812G;E81G 88;52 93;86 25999284 Egg-adaptive mutations in H3N2v vaccine virus enhance egg-based production without loss of antigenicity or immunogenicity. Taken together, our results show that the egg-adapted H3N2v vaccine virus E6-RG269 (G186V + N246K), which acquired no other detectable HA mutations, retained its original antigenicity and immunogenicity while producing the greatest yield of HA protein. 2015 Vaccine Discussion IV G186V;N246K 84;92 89;97 HA;HA 135;241 137;243 25999284 Egg-adaptive mutations in H3N2v vaccine virus enhance egg-based production without loss of antigenicity or immunogenicity. The egg-adaptive mutation H1831F was previously reported to improve the egg growth of PR8-based A/Fujian/411/2002 (H3N2) CVV. 2015 Vaccine Discussion IV H1831F 26 32 25999284 Egg-adaptive mutations in H3N2v vaccine virus enhance egg-based production without loss of antigenicity or immunogenicity. The egg-adaptive mutation of the highly conserved basic polaramino acid His1831 to the nonpolar Leu (H1831L) dramatically reduced virus growth in MDCK cells and yielded poor to moder-ate growth in eggs, consistent with the previous observation that His1831 interacts directly via hydrogen bond with bound sialic acid in human erythrocytes and that the H1831F mutation severely impairs sialic acid binding. 2015 Vaccine Discussion IV H1831L;H1831F 101;352 107;358 25999284 Egg-adaptive mutations in H3N2v vaccine virus enhance egg-based production without loss of antigenicity or immunogenicity. The I102M, R762G, and D902N HA2 mutations we observed in this study were all accompanied by the N1651K mutation. 2015 Vaccine Discussion IV I102M;R762G;D902N;N1651K 4;11;22;96 9;16;27;102 HA 28 30 25999284 Egg-adaptive mutations in H3N2v vaccine virus enhance egg-based production without loss of antigenicity or immunogenicity. Therefore, it is possible that RG267 HA along with N2461K, acquired some other undetected (lower population) mutation which rendering it growth to reach to the same level of RG269. 2015 Vaccine Discussion IV N2461K 51 57 HA 37 39 25999284 Egg-adaptive mutations in H3N2v vaccine virus enhance egg-based production without loss of antigenicity or immunogenicity. This led us to hypothesize that HA mutation G1861V though play important role in egg adaptation, but may not be sufficient. 2015 Vaccine Discussion IV G1861V 44 50 HA 32 34 25999284 Egg-adaptive mutations in H3N2v vaccine virus enhance egg-based production without loss of antigenicity or immunogenicity. Upon 6 passages in egg, RG269 (G1861V + N2461K) and RG273 (N1651K + G1861V) HA did not acquired any other detectable mutation, whereas additional mutation N2461K was detected in RG267 (G1861V) HA. 2015 Vaccine Discussion IV G1861V;N2461K;N1651K;G1861V;N2461K;G1861V 31;40;59;68;155;185 37;46;65;74;161;191 HA;HA 76;193 78;195 25999284 Egg-adaptive mutations in H3N2v vaccine virus enhance egg-based production without loss of antigenicity or immunogenicity. We found that the double mutation L1941I + Y2331H improved the growth of CVV RG271 in eggs. 2015 Vaccine Discussion IV L1941I;Y2331H 34;43 40;49 25999284 Egg-adaptive mutations in H3N2v vaccine virus enhance egg-based production without loss of antigenicity or immunogenicity. We observed four groups of egg-adaptive HA mutations or combinations of mutations in Ind08: (1) H1831L and L1941I + Y2331H, the only group that significantly altered the antigenicity of CVVs;(2) G1861V, the most common egg-adaptive mutation identified in H3N2 viruses; (3) mutations in the N-linked glycosylation sites 126-NWT-128, 165-NVT-167, and 246-NWT-248, either alone or accompanied by other mutation(s); and (4) I102M, R762G, and D902N in HA2, together with mutations in HA1. 2015 Vaccine Discussion IV H1831L;L1941I;Y2331H;G1861V;I102M;R762G;D902N 96;107;116;195;420;427;438 102;113;122;201;425;432;443 HA;HA;HA1 40;447;479 42;449;482 26038410 Adaptive mutation in influenza A virus non-structural gene is linked to host switching and induces a novel protein by alternative splicing. By comparing growth properties of synthetic viruses with synonymous 125G mutations that were lacking the novel splice site, we were able to demonstrate that the observed increases in viral growth was primarily due to the novel splice product of the NS gene, and not due to the D125G amino acid change in the NS1 protein that resulted in decreased replication in M1 and MDCK cells (Figure 6). 2012 Emerging microbes & infections Discussion IV D125G 277 282 M1;NS;NS1 362;249;308 364;251;311 26038410 Adaptive mutation in influenza A virus non-structural gene is linked to host switching and induces a novel protein by alternative splicing. have also previously shown that the M124I mutation resulted in positive epistasis with the NS1 M106V mutation in mouse cells but negative epistasis in mouse lungs suggesting different types of NS1 gene interactions that are dependent on the host cell environment. 2012 Emerging microbes & infections Discussion IV M124I;M106V 36;95 41;100 NS1;NS1 91;193 94;196 26038410 Adaptive mutation in influenza A virus non-structural gene is linked to host switching and induces a novel protein by alternative splicing. Here, we show that the A374G nucleotide substitution, encoding the D125G(GAT GGT) mutation, selected upon lung serial-passage of human IAV within a mouse host, activates a new donor splice site, hence producing the NS3 mRNA transcript that encodes the novel NS3 protein. 2012 Emerging microbes & infections Discussion IV A374G;D125G 23;67 28;72 NS;NS 215;258 217;260 26038410 Adaptive mutation in influenza A virus non-structural gene is linked to host switching and induces a novel protein by alternative splicing. In this study, we established that the NS1 A374G substitution induced a D125G coding mutation and concomitantly activated a novel donor splice site, hence producing the novel viral transcript and protein, NS3. 2012 Emerging microbes & infections Discussion IV A374G;D125G 43;72 48;77 NS;NS1 205;39 207;42 26038410 Adaptive mutation in influenza A virus non-structural gene is linked to host switching and induces a novel protein by alternative splicing. Likewise, adaptive mutations such as the (A374G)125G did not enhance replication in the MDCK cell line, because the A/HK/1/68 virus possesses the appropriate functions of NS1 that are required to replicate in this cell line which is highly susceptible to infection with IAV from various host sources due, at least in part, to its defective IFN response due a defective Mx1 gene. 2012 Emerging microbes & infections Discussion IV A374G 42 47 NS1 171 174 26038410 Adaptive mutation in influenza A virus non-structural gene is linked to host switching and induces a novel protein by alternative splicing. Taking into consideration that selection of the (A374G)125G mutation occurs when adapting a human IAV into a mouse host, this suggests that the increase in viral fitness due to the novel splice product, NS3, might only be beneficial in viruses that lack optimal functioning because they have not been adapted into a novel host. 2012 Emerging microbes & infections Discussion IV A374G 49 54 NS 203 205 26038410 Adaptive mutation in influenza A virus non-structural gene is linked to host switching and induces a novel protein by alternative splicing. The (A374G)125G mutation in the human A/HK/1/68 virus in the human A549 cell was not required for replication in human cells and therefore did not enhance NS1 replicative functions, possibly because those functions have already been provided by previous human-adaptive mutations. 2012 Emerging microbes & infections Discussion IV A374G 5 10 NS1 155 158 26038410 Adaptive mutation in influenza A virus non-structural gene is linked to host switching and induces a novel protein by alternative splicing. The increase in viral growth due to the (A374G)125G mutation was only detected in mouse, and not in human or canine cells. 2012 Emerging microbes & infections Discussion IV A374G 41 46 26038410 Adaptive mutation in influenza A virus non-structural gene is linked to host switching and induces a novel protein by alternative splicing. The increased viral replication and gene expression due to the new NS splice product and the A374G/D125G mutation, as well as antagonism of IFN-beta production previously reported in mice, provides a functional basis for examining the individual roles for the NS3 and NS1 125G proteins in viral RNA synthesis and IFN-beta antagonism. 2012 Emerging microbes & infections Discussion IV A374G;D125G 93;99 98;104 NS;NS;NS1 67;260;268 69;262;271 26038410 Adaptive mutation in influenza A virus non-structural gene is linked to host switching and induces a novel protein by alternative splicing. The NS1 mutation (A374G)125G and predicted splice site was also independently selected upon mouse adaptation of the human IAV A/Aichi/2/68(H3N2), providing further support that the novel splice product confers an adaptive advantage upon entry into a new host. 2012 Emerging microbes & infections Discussion IV A374G 18 23 NS1 4 7 26038410 Adaptive mutation in influenza A virus non-structural gene is linked to host switching and induces a novel protein by alternative splicing. The NS3 splice site and resultant NS3 protein rather than the NS1 D125G substitution was critical for the adaptive properties due to this mutation. 2012 Emerging microbes & infections Discussion IV D125G 66 71 NS;NS;NS1 4;34;62 6;36;65 26038410 Adaptive mutation in influenza A virus non-structural gene is linked to host switching and induces a novel protein by alternative splicing. We thus demonstrated increased replication of the splice competent NS1 D125G(GGT) mutant versus the splice incompetent D125G(GGC) and D125G(GGG) viruses that both grew to significantly lower yields in MDCK and M1 cells, as well as in mouse lungs. 2012 Emerging microbes & infections Discussion IV D125G;D125G;D125G 71;119;134 76;124;139 M1;NS1 210;67 212;70 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. Although significant synergism is found against the wild-type virus by combining zanamivir/peramivir and non-NAIs, these regimens generally did not exhibit a synergistic effect against the R292K virus. 2014 Emerging microbes & infections Discussion IV R292K 189 194 NAI 109 113 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. Among available NA inhibitors, zanamivir showed the best inhibitory effect against the R292K variant with the lowest IC50 value in enzyme-based or cell-based assays. 2014 Emerging microbes & infections Discussion IV R292K 87 92 16 18 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. Apart from its drug sensitivity profile, the in vivo fitness of the R292K mutant virus is also of scientific importance. 2014 Emerging microbes & infections Discussion IV R292K 68 73 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. Full genome sequencing showed that in addition to the R292K mutation in the NA gene, this variant as only one amino acid substitution (R220G) in the proximity of the HA receptor binding domain. 2014 Emerging microbes & infections Discussion IV R292K;R220G 54;135 59;140 HA;NA 166;76 168;78 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. Further study is needed to clarify the role of the HA R220G mutation on receptor binding activity and in vivo fitness. 2014 Emerging microbes & infections Discussion IV R220G 54 59 HA 51 53 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. However, for NT-300, known as an inhibitor to HA glycoprotein maturation, an over 10-fold increase of IC50 to the R292K variant is speculated to be caused by an HA R220G mutation, although no experimental evidence is available. 2014 Emerging microbes & infections Discussion IV R292K;R220G 114;164 119;169 HA;HA 46;161 48;163 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. However, the R220G mutation, which resides in the proximity of the HA receptor binding domain, might also contribute to compromised fitness in mice. 2014 Emerging microbes & infections Discussion IV R220G 13 18 HA 67 69 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. However, they found the HA of the Shanghai1R292K virus had a mixture of 151A/S and 209G/E (2013 H7 numbering), while that of the Taiwan1 mutant virus possesses a D340G substitution. 2014 Emerging microbes & infections Discussion IV D340G 162 167 HA 24 26 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. In the current study, we observed that, although both viruses exhibited similar growth kinetics in MDCK cells, mice inoculated with the R292K variant showed delayed weight loss, lower viral loads in the lung at day 3 post inoculation, milder pathological changes and greater survival rates. 2014 Emerging microbes & infections Discussion IV R292K 136 141 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. Interestingly, we had difficulty isolating the R292K variant in vitro under oseltamivir carboxylate selection pressure alone (data not shown). 2014 Emerging microbes & infections Discussion IV R292K 47 52 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. It is possible that the mutations in the HA gene, such as R220G, may achieve a balance between the HA and NA protein in the NAI resistant virus. 2014 Emerging microbes & infections Discussion IV R220G 58 63 HA;HA;NA;NAI 41;99;106;124 43;101;108;127 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. It is possible that the reduced NA activity caused by the R292K mutation is responsible for the reduced fitness. 2014 Emerging microbes & infections Discussion IV R292K 58 63 32 34 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. Lastly, in an attempt to evaluate the pathogenicity and transmission potential of the R292K variant in a model closest to human infection, the Shanghai1 MUT-6 virus, which had 94% of 292K and 6% of 292R, was inoculated in ferrets and transmitted via direct and respiratory droplet contact. 2014 Emerging microbes & infections Discussion IV R292K 86 91 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. Nevertheless, the R292K variant that we obtained through plaque purification efficiently replicated in MDCK cells when exogenous NA was withdrawn (Figures 1 and 2). 2014 Emerging microbes & infections Discussion IV R292K 18 23 129 131 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. Notably, non-NAIs, including inhibitors for viral polymerase activity (ribavirin and T705), largely retained their effectiveness against the R292K variant. 2014 Emerging microbes & infections Discussion IV R292K 141 146 NAI 13 17 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. observed similar results using either Shanghai1 wild-type and R292K or Taiwan1 wild-type and R292K viruses. 2014 Emerging microbes & infections Discussion IV R292K;R292K 62;93 67;98 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. Quantitative analysis of the wild-type and the R292K variant during the course of transmission revealed that, although the R292K mutant had transmission potential, the mutant virus was outcompeted by the wild-type in the upper respiratory tract of inoculated donors and transmitted ferrets, which was suggestive of a competitive fitness loss. 2014 Emerging microbes & infections Discussion IV R292K;R292K 47;123 52;128 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. Taken together, we report here the isolation and characterization of the R292K variant from a clinical specimen derived from an H7N9 fatal case of the Anhui1 lineage. 2014 Emerging microbes & infections Discussion IV R292K 73 78 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. The addition of exogenous NA from Clostridium perfringens greatly facilitated this process, possibly because of the low NA activity exhibited by the R292K variants. 2014 Emerging microbes & infections Discussion IV R292K 149 154 NA;NA 26;120 28;122 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. The combination of favipiravir and ribavirin may synergistically restrict the spread of the R292K variant and needs to be tested in animal models. 2014 Emerging microbes & infections Discussion IV R292K 92 97 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. The compromised pathogenicity in vivo is attributed to the combined NA R292K and HA R220G mutations. 2014 Emerging microbes & infections Discussion IV R292K;R220G 71;84 76;89 HA;NA 81;68 83;70 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. The in vivo fitness of the R292K H7N9 variant virus should be further assessed with genetically well-characterized pairs of viruses and most desirably, with competitive fitness experiments. 2014 Emerging microbes & infections Discussion IV R292K 27 32 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. The lack of concordance on the in vivo fitness of the R292K variant is reminiscent of the literature on the fitness of the H274Y mutation in 2009 H1N1 pandemic viruses. 2014 Emerging microbes & infections Discussion IV R292K;H274Y 54;123 59;128 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. The R292K mutant virus exhibited a high level of resistance to oseltamivir with the IC50-fold change >1000, but the replication of the variant can be partially inhibited under a high concentration of zanamivir or peramivir, a finding similar to previous reports. 2014 Emerging microbes & infections Discussion IV R292K 4 9 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. The reduced pathogenicity of the R292K variant suggests that it is partially compromised in vivo, at least in the mouse model. 2014 Emerging microbes & infections Discussion IV R292K 33 38 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. This R292K variant derived from a clinical specimen is critical to confirm the results derived from recombinant viruses and to investigate potential antiviral strategies to inhibit the NAIs-resistant strain. 2014 Emerging microbes & infections Discussion IV R292K 5 10 NAI 185 189 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. Thus, it is of clinical and scientific importance to characterize R292K variants of the dominant Anhui1 lineage (the dominant H7N9 virus lineage) from clinical specimens. 2014 Emerging microbes & infections Discussion IV R292K 66 71 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. To make an NAI-resistant strain, we report here the isolation of the R292K mutant virus of Anhui1 lineage without genetic manipulation. 2014 Emerging microbes & infections Discussion IV R292K 69 74 NAI 11 14 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. We recently reported the emergence of the R292K mutation in the NA segment in two H7N9 fatal cases during NAI treatment. 2014 Emerging microbes & infections Discussion IV R292K 42 47 NA;NAI 64;106 66;109 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. We speculate that the R292K mutation caused subtle changes in the activity of neuraminidase, which may need some compensatory intermediate mutations in the NA and/or HA segment. 2014 Emerging microbes & infections Discussion IV R292K 22 27 HA;NA;NA 166;156;78 168;158;91 26038501 Drug susceptibility profile and pathogenicity of H7N9 influenza virus (Anhui1 lineage) with R292K substitution. We suspect that the high resistance of the R292K virus against NAIs greatly attenuated the synergism of combining zanamivir/peramivir and non-NAIs especially at median IC50. 2014 Emerging microbes & infections Discussion IV R292K 43 48 NAI;NAI 63;142 67;146 26077257 Influenza A(H7N9) virus acquires resistance-related neuraminidase I222T substitution when infected mallards are exposed to low levels of oseltamivir in water. Additionally, in the present study, as 2.5 mug/liter was the lowest level of OC exposure, we cannot exclude the possibility that the I222T substitution could have been acquired at a lower OC concentration. 2015 Antimicrobial agents and chemotherapy Discussion IV I222T 133 138 26077257 Influenza A(H7N9) virus acquires resistance-related neuraminidase I222T substitution when infected mallards are exposed to low levels of oseltamivir in water. At OC exposure levels of 2.5 and 7.2 mug/liter, the NA I222T mutant virus replicated, was excreted, and was transmitted similarly to wild type viruses measured in previous studies in this mallard model. 2015 Antimicrobial agents and chemotherapy Discussion IV I222T 55 60 52 54 26077257 Influenza A(H7N9) virus acquires resistance-related neuraminidase I222T substitution when infected mallards are exposed to low levels of oseltamivir in water. Changes in inhibition by NAIs caused by NA I222T in our study, 8-fold and 2.4-fold increases in IC50s by OC and ZA, respectively (Table 1), are similar to previously described levels for the substitution in other viral subtypes. 2015 Antimicrobial agents and chemotherapy Discussion IV I222T 43 48 NA;NAI 40;25 42;29 26077257 Influenza A(H7N9) virus acquires resistance-related neuraminidase I222T substitution when infected mallards are exposed to low levels of oseltamivir in water. Drug-induced selection of the NA I222T substitution is supported by the absence of circulating avian N9 virus with the 222T genotype (based upon IAV sequence database screening), by previously observed NA I222R and NA I222K variants in A(H7N9) virus following oseltamivir treatment of humans, and by in vivo induction of NA I222T in A(H3N2) by low-dose OC exposure of infected mice. 2015 Antimicrobial agents and chemotherapy Discussion IV I222T;I222R;I222K;I222T 33;205;218;324 38;210;223;329 N9;NA;NA;NA;NA 101;30;202;215;321 103;32;204;217;323 26077257 Influenza A(H7N9) virus acquires resistance-related neuraminidase I222T substitution when infected mallards are exposed to low levels of oseltamivir in water. In conclusion, the acquisition of I222T in a European wild duck LPAI A(H7N9) virus demonstrates that N9 viruses can harbor I222T substitutions and confirms the levels of reduced NAI sensitivity in other NA subtypes. 2015 Antimicrobial agents and chemotherapy Discussion IV I222T;I222T 34;123 39;128 N9;NA;NAI 101;203;178 103;205;181 26077257 Influenza A(H7N9) virus acquires resistance-related neuraminidase I222T substitution when infected mallards are exposed to low levels of oseltamivir in water. In this OC exposure study, in which mallards were infected with an LPAI A(H7N9) that naturally circulates in wild ducks in Europe, the NA I222T substitution was detected after 2 days of 2.5 mug/liter OC exposure in the first mallard generation passage and rapidly became the dominant genotype. 2015 Antimicrobial agents and chemotherapy Discussion IV I222T 138 143 135 137 26077257 Influenza A(H7N9) virus acquires resistance-related neuraminidase I222T substitution when infected mallards are exposed to low levels of oseltamivir in water. NA I222T and several other amino acid substitutions at the 222 NA residue generate reduced sensitivity to NAIs, either as independent resistance substitutions or, perhaps of more concern, by enhancing resistance induced by H274Y in N1 virus or by E119V in N2 virus. 2015 Antimicrobial agents and chemotherapy Discussion IV I222T;H274Y;E119V 3;223;247 8;228;252 NA;NA;NAI 0;63;106 2;65;110 26077257 Influenza A(H7N9) virus acquires resistance-related neuraminidase I222T substitution when infected mallards are exposed to low levels of oseltamivir in water. NA I222T variants are described in human seasonal influenza B, A(H3N2), and A(H1N1)/pdm2009 viruses, as well as in A(H5N1) virus, where the substitution was demonstrated to change the binding kinetics (loss of slow OC binding). 2015 Antimicrobial agents and chemotherapy Discussion IV I222T 3 8 0 2 26077257 Influenza A(H7N9) virus acquires resistance-related neuraminidase I222T substitution when infected mallards are exposed to low levels of oseltamivir in water. Our experiments did not indicate reduced fitness of the NA I222T mutant as excretion and transmission of virus were similar to previous observations with wild-type viruses, nor did propagation of the fecal samples without drug exposure in embryonated chicken eggs select for wild-type virus over I222T variants (including those with a mixed genotype). 2015 Antimicrobial agents and chemotherapy Discussion IV I222T;I222T 59;296 64;301 56 58 26077257 Influenza A(H7N9) virus acquires resistance-related neuraminidase I222T substitution when infected mallards are exposed to low levels of oseltamivir in water. Retained transmission and replication of the I222T mutant virus in our mallard model indicates that it might be sustained in wild migratory waterfowl. 2015 Antimicrobial agents and chemotherapy Discussion IV I222T 45 50 26077257 Influenza A(H7N9) virus acquires resistance-related neuraminidase I222T substitution when infected mallards are exposed to low levels of oseltamivir in water. Sequential evolution of permissive amino acids in a viral population over time, including at the NA 222 position, appears to facilitate acquisition and harboring of new resistance mutations, illustrated by the OC-resistant human seasonal A(H1N1)/H274Y virus that circulated in 2007 to 2009. 2015 Antimicrobial agents and chemotherapy Discussion IV H274Y 246 251 97 99 26077257 Influenza A(H7N9) virus acquires resistance-related neuraminidase I222T substitution when infected mallards are exposed to low levels of oseltamivir in water. Several substitutions also seem to restore reduced fitness: I222T/V/R combined with H274Y in N1 virus and I222V combined with E119V in N2 virus. 2015 Antimicrobial agents and chemotherapy Discussion IV I222V;I222R;I222T;H274Y;I222V;E119V 60;60;60;84;106;126 69;69;69;89;111;131 26263554 Phenotypic and Genetic Characterization of Avian Influenza H5N2 Viruses with Intra- and Inter-Duck Variations in Taiwan. In other words, both p513-L and p513-S show enhanced binding to MDCK cells and the substitution of N170D in HA has the potential to modulate viral binding to MDCK cells. 2015 PloS one Discussion IV N170D 99 104 HA 108 110 26263554 Phenotypic and Genetic Characterization of Avian Influenza H5N2 Viruses with Intra- and Inter-Duck Variations in Taiwan. In PA, the mutation of S224P with other amino acid substitutions has been shown to increase the replication of duck H5N1 viruses in duck primary embryo fibroblast cells, and elevate viral virulence in a mouse model. 2015 PloS one Discussion IV S224P 23 28 PA 3 5 26263554 Phenotypic and Genetic Characterization of Avian Influenza H5N2 Viruses with Intra- and Inter-Duck Variations in Taiwan. It is less likely that I56T mutation in NA would influence the binding of p513-L and p513-S to MDCK cells. 2015 PloS one Discussion IV I56T 23 27 40 42 26263554 Phenotypic and Genetic Characterization of Avian Influenza H5N2 Viruses with Intra- and Inter-Duck Variations in Taiwan. Second, intra-duck variations (shown in p518-L vs p518-S) included three residue substitutions in PA (P224S), PB2 (E72D), and M1 (A128T), whereas inter-duck variations (shown in DV518 vs DV413) contained the other three mutations in HA (N170D), NA (I56T), and NP (Y289H). 2015 PloS one Discussion IV P224S;E72D;A128T;N170D;I56T;Y289H 102;115;130;237;249;264 107;119;135;242;253;269 HA;M1;NA;NP;PA;PB2 233;126;245;260;98;110 235;128;247;262;100;113 26263554 Phenotypic and Genetic Characterization of Avian Influenza H5N2 Viruses with Intra- and Inter-Duck Variations in Taiwan. Several mutations in NP, including Y289H (located in the region predicted to interact with PB2 at the NP-NP interaction site), were recently identified in adaptation of the novel 2009 H1N1 virus to humans. 2015 PloS one Discussion IV Y289H 35 40 NP;NP;NP;PB2 21;102;105;91 23;104;107;94 26263554 Phenotypic and Genetic Characterization of Avian Influenza H5N2 Viruses with Intra- and Inter-Duck Variations in Taiwan. Taken together, these results and findings by others suggest that N170D of HA does not alter the receptor specificity but may enhance its receptor-binding affinity by forming a more stable structure. 2015 PloS one Discussion IV N170D 66 71 HA 75 77 26263554 Phenotypic and Genetic Characterization of Avian Influenza H5N2 Viruses with Intra- and Inter-Duck Variations in Taiwan. These two viruses involved another three amino acid changes (N170D, I56T, and Y289H) in HA, NA, and NP, respectively. 2015 PloS one Discussion IV N170D;I56T;Y289H 61;68;78 66;72;83 HA;NA;NP 88;92;100 90;94;102 26263554 Phenotypic and Genetic Characterization of Avian Influenza H5N2 Viruses with Intra- and Inter-Duck Variations in Taiwan. This N170D (or N158D) mutation in HA has been correlated with better aerosol transmissibility of H5N1 viruses in ferrets and guinea pigs as well as human H5N1 cases in Vietnam and Egypt. 2015 PloS one Discussion IV N170D;N158D 5;15 10;20 HA 34 36 26263554 Phenotypic and Genetic Characterization of Avian Influenza H5N2 Viruses with Intra- and Inter-Duck Variations in Taiwan. Whether HA (N170D), NA (I56T), and NP (Y289H) mutations alone or in combination contribute to the growth advantage of DV518, p518-L, and p513-S in MDCK cells requires further investigation by using reverse genetics method. 2015 PloS one Discussion IV N170D;I56T;Y289H 12;24;39 17;28;44 HA;NA;NP 8;20;35 10;22;37 26263554 Phenotypic and Genetic Characterization of Avian Influenza H5N2 Viruses with Intra- and Inter-Duck Variations in Taiwan. Whether the N170D mutation does contribute to the better binding of p518-L and p518-S to MDCK cells requires further investigation by using reverse genetics methods. 2015 PloS one Discussion IV N170D 12 17 26345289 Influenza virus surveillance in Argentina during the 2012 season: antigenic characterization, genetic analysis and antiviral susceptibility. In terms of influenza antiviral susceptibility surveillance detection of N1 NA-H275Y is screened for routinely. 2016 Epidemiology and infection Discussion IV H275Y 79 84 76 78 26345289 Influenza virus surveillance in Argentina during the 2012 season: antigenic characterization, genetic analysis and antiviral susceptibility. In the course of the present study we detected an A(H1N1)pdm09 virus, A/Salta/1341/2012 showing highly reduced inhibition by oseltamivir and reduced inhibition by zanamivir which carried an NA-N295S substitution. 2016 Epidemiology and infection Discussion IV N295S 193 198 190 192 26345289 Influenza virus surveillance in Argentina during the 2012 season: antigenic characterization, genetic analysis and antiviral susceptibility. NA-H275Y is the most frequent change related to resistance to oseltamivir in A(H1N1) and A(H5N1). 2016 Epidemiology and infection Discussion IV H275Y 3 8 0 2 26345289 Influenza virus surveillance in Argentina during the 2012 season: antigenic characterization, genetic analysis and antiviral susceptibility. The NA-N295S mutation was originally reported in drug-resistant H5N1 viruses. 2016 Epidemiology and infection Discussion IV N295S 7 12 4 6 26391278 Dual E627K and D701N mutations in the PB2 protein of A(H7N9) influenza virus increased its virulence in mammalian models. An Aspartic acid to Asparagine mutation, relative to avian or environmental samples, was observed at position 701 in PB2 (D701N) in 8.5% (11/129) of human isolates. 2015 Scientific reports Discussion IV D701N 122 127 PB2 117 120 26391278 Dual E627K and D701N mutations in the PB2 protein of A(H7N9) influenza virus increased its virulence in mammalian models. As of 4th December 2014, all available H7N9 virus sequences from the poultry and environmental samples were found to exclusively carry PB2-627E while the majority (69.0%, 89/129) of the human isolates had a lysine mutation at this position (E627K), and a tree sparrow virus identified in Shanghai possessed both E and K. 2015 Scientific reports Discussion IV E627K 241 246 PB2 135 138 26391278 Dual E627K and D701N mutations in the PB2 protein of A(H7N9) influenza virus increased its virulence in mammalian models. However, as the E627K and D701N mutations were not found in airborne exposed ferrets, this suggests they may not increase the airborne transmissibility of the viruses. 2015 Scientific reports Discussion IV E627K;D701N 16;26 21;31 26391278 Dual E627K and D701N mutations in the PB2 protein of A(H7N9) influenza virus increased its virulence in mammalian models. In January 2014, an H7N9 virus (A/Shanghai/PD-02/2014) carrying both the E627K and D701N mutations in the PB2 protein (GenBank accession number KJ549801) was isolated from a fatal human case, indicating that such dual mutations can occur naturally. 2015 Scientific reports Discussion IV E627K;D701N 73;83 78;88 PB2 106 109 26391278 Dual E627K and D701N mutations in the PB2 protein of A(H7N9) influenza virus increased its virulence in mammalian models. In this study, by using a ferret transmission model, we demonstrated that both the E627K and D701N mutations could occur within one passage in physical contact ferrets, and these two mutations could co-emerge in the same virus particle. 2015 Scientific reports Discussion IV E627K;D701N 83;93 88;98 26422258 Oseltamivir Resistance in Influenza A(H6N2) Caused by an R292K Substitution in Neuraminidase Is Not Maintained in Mallards without Drug Pressure. Among human IAVs, oseltamivir resistant H1N1/H274Y viruses with a suitable genetic context can circulate without drug pressure, but to date no circulation of resistant human H3N2 viruses has been seen. 2015 PloS one Discussion IV H274Y 45 50 26422258 Oseltamivir Resistance in Influenza A(H6N2) Caused by an R292K Substitution in Neuraminidase Is Not Maintained in Mallards without Drug Pressure. In avian IAVs, it was previously observed in vivo that an H1N1/H274Y virus, which had acquired resistance by OC exposure in Mallards, maintained the resistance substitution without drug pressure. 2015 PloS one Discussion IV H274Y 63 68 26422258 Oseltamivir Resistance in Influenza A(H6N2) Caused by an R292K Substitution in Neuraminidase Is Not Maintained in Mallards without Drug Pressure. In this study, where we aimed to approximate natural infection and transmission of an oseltamivir resistant influenza A(H6N2) virus in the natural wild bird host, we observed that the resistance substitution R292K in NA could not be maintained without drug pressure. 2015 PloS one Discussion IV R292K 208 213 217 219 26422258 Oseltamivir Resistance in Influenza A(H6N2) Caused by an R292K Substitution in Neuraminidase Is Not Maintained in Mallards without Drug Pressure. The D113N and D141N substitutions, which had emerged in parallel to R292K in the previous OC exposure experiment, did not influence the time to reversal to wild type virus, interpreted as having no significant fitness related effects on the resistant virus. 2015 PloS one Discussion IV D113N;D141N;R292K 4;14;68 9;19;73 26422258 Oseltamivir Resistance in Influenza A(H6N2) Caused by an R292K Substitution in Neuraminidase Is Not Maintained in Mallards without Drug Pressure. This contrasts to the results of the present study, in which the resistant H6N2/R292K virus was rapidly outcompeted by wild type virus when drug pressure was removed from infected Mallards. 2015 PloS one Discussion IV R292K 80 85 26609523 Phylogenetic Analysis of Hemagglutinin Genes of H9N2 Avian Influenza Viruses Isolated from Chickens in Shandong, China, between 1998 and 2013. Additionally, 29 out of 35 H9N2 AIVs had leucine (L) at position 226, including all of the isolates between 2005 and 2013. 2015 BioMed research international Discussion IV L226L 40 69 IAV infections 32 36 26609523 Phylogenetic Analysis of Hemagglutinin Genes of H9N2 Avian Influenza Viruses Isolated from Chickens in Shandong, China, between 1998 and 2013. On the left edge of receptor-binding pocket, most isolates (4 out of 6) between 2012 and 2013 had methionine (M) at position 227. 2015 BioMed research international Discussion IV M227M 97 129 26782141 PB2-588 V promotes the mammalian adaptation of H10N8, H7N9 and H9N2 avian influenza viruses. Additionally, previous studies had reported that the mutation T588I or A588T in PB2 could enhance the virulence of 2009 pandemic H1N1 influenza virus or H5N1 avian influenza virus. 2016 Scientific reports Discussion IV T588I;A588T 62;71 67;76 PB2 80 83 26782141 PB2-588 V promotes the mammalian adaptation of H10N8, H7N9 and H9N2 avian influenza viruses. In our study, the mutation A588V in PB2 enhanced the virulence of avian H7N9, H10N8, and H9N2 influenza viruses. 2016 Scientific reports Discussion IV A588V 27 32 PB2 36 39 26782141 PB2-588 V promotes the mammalian adaptation of H10N8, H7N9 and H9N2 avian influenza viruses. Interestingly, among these residues only V292I and V588A substitutions resulted in a significantly lower polymerase activity in human cells. 2016 Scientific reports Discussion IV V292I;V588A 41;51 46;56 26782141 PB2-588 V promotes the mammalian adaptation of H10N8, H7N9 and H9N2 avian influenza viruses. Many adaptive mutations in PB2, such as E627K, D701N, K526R, and T271A have been proven to be important for different avian influenza viruses to break the host species barrier to infect mammals. 2016 Scientific reports Discussion IV E627K;D701N;K526R;T271A 40;47;54;65 45;52;59;70 PB2 27 30 26782141 PB2-588 V promotes the mammalian adaptation of H10N8, H7N9 and H9N2 avian influenza viruses. Previous studies have shown that D701N and E627K may influence the interaction of PB2 with different isoforms of importin-alpha to adapt mammalian hosts and a recent study showed that the PB2-627K resists the signaling-independent antiviral effect of RIG-I by increasing nucleocapsid stability. 2016 Scientific reports Discussion IV D701N;E627K 33;43 38;48 PB2;PB2 82;188 85;191 26782141 PB2-588 V promotes the mammalian adaptation of H10N8, H7N9 and H9N2 avian influenza viruses. These data indicate that i) the effect of the PB2 627K on influenza viruses may be strain-dependent, similar to data previously reported with H5N1; ii) the PB2 627K mutation is not the only key factor for mammalian adaption of the novel H7N9 influenza virus and other adaptive strategies to mammalian hosts may be employed for this virus (many adaption mutations already exist in this virus), such as the A588V identified in our study. 2016 Scientific reports Discussion IV A588V 405 410 PB2;PB2 46;156 49;159 26845764 Genomic Signatures for Avian H7N9 Viruses Adapting to Humans. Conversely, 23 M535L substitutions were observed in all three seasons, signifying its regular presence and potential role in the increasing H7N9 adaptation to humans. 2016 PloS one Discussion IV M535L 15 20 26845764 Genomic Signatures for Avian H7N9 Viruses Adapting to Humans. For example, we found {V139I, S286G, T569A, M676V}, occurring only in season II (November 2013-January 2014), in 12 strains from Shenzhen and Hong Kong, regardless of whether they were accompanied by 627E or K. 2016 PloS one Discussion IV V139I;S286G;T569A;M676V 22;30;37;44 28;35;42;49 26845764 Genomic Signatures for Avian H7N9 Viruses Adapting to Humans. However, the RNP activity assays suggested no correlation between the amino acid changes at these positions with PB2 K627E. 2016 PloS one Discussion IV K627E 117 122 PB2;RNP 113;13 116;16 26845764 Genomic Signatures for Avian H7N9 Viruses Adapting to Humans. In addition, M535L+K627E restored the RNP activity (P < 0.05). 2016 PloS one Discussion IV K627E;M535L 19;13 24;18 RNP 38 41 26845764 Genomic Signatures for Avian H7N9 Viruses Adapting to Humans. In all, 15 D701N substitutions were observed, and none occurred after January 2014. 2016 PloS one Discussion IV D701N 11 16 26845764 Genomic Signatures for Avian H7N9 Viruses Adapting to Humans. In this study, we demonstrated that Q591K and D701N, each accompanied by K627E, restored the RNP activity (P < 0.001). 2016 PloS one Discussion IV Q591K;D701N;K627E 36;46;73 41;51;78 RNP 93 96 26845764 Genomic Signatures for Avian H7N9 Viruses Adapting to Humans. Of the 147 PB2 sequences we analyzed, only five had Q591K, and four of them occurred at an extremely early stage of H7N9 endemic in March and April 2013. 2016 PloS one Discussion IV Q591K 52 57 PB2 11 14 26845764 Genomic Signatures for Avian H7N9 Viruses Adapting to Humans. Other than RNP activity, the mutation K627E and other co-substitutions may affect the mitochondrion localization of PB2 protein. 2016 PloS one Discussion IV K627E 38 43 PB2;RNP 116;11 119;14 26845764 Genomic Signatures for Avian H7N9 Viruses Adapting to Humans. Several other amino acids exhibited covarying patterns with K627E, which were consistent with those exhibited by Q591K, M535L, and D701N. 2016 PloS one Discussion IV K627E;Q591K;M535L;D701N 60;113;120;131 65;118;125;136 26845764 Genomic Signatures for Avian H7N9 Viruses Adapting to Humans. that Q591K and D701N are crucial in compensating for the absence of 627K. 2016 PloS one Discussion IV Q591K;D701N 5;15 10;20 26845764 Genomic Signatures for Avian H7N9 Viruses Adapting to Humans. The mutation Q226L of influenza HA protein was reported to increase binding to receptors in human upper airway. 2016 PloS one Discussion IV Q226L 13 18 HA 32 34 27089319 The Molecular Epidemiology and Evolutionary Dynamics of Influenza B Virus in Two Italian Regions during 2010-2015: The Experience of Sicily and Liguria. In our setting, the most frequent deduced amino-acid substitutions were N116K in the 120-loop of B/Yamagata clade 3 strains and I146V in the 150-loop of Victoria strains; the latter one shared by none of the Yamagata-lineage viruses. 2016 International journal of molecular sciences Discussion IV N116K;I146V 72;128 77;133 27097026 Novel Polymerase Gene Mutations for Human Adaptation in Clinical Isolates of Avian H5N1 Influenza Viruses. A ferret-transmission experiment showed that an H5N1 virus acquired both HA and polymerase mutations during adaptation to a new host, even though the virus used in that study was a recombinant virus intentionally carrying the well-known adaptation mutations PB2-E627K and HA-Q222L/G224S. 2016 PLoS pathogens Discussion IV E627K;Q222L;G224S 262;275;281 267;280;286 HA;HA;PB2 73;272;258 75;274;261 27097026 Novel Polymerase Gene Mutations for Human Adaptation in Clinical Isolates of Avian H5N1 Influenza Viruses. Among these mutations, PB1-K198R, PB1-K198R/D175N, Inter-1, Inter-3 and Inter-4 were detected only in human isolates in clade 2.2.1.2, and PB1-P627L and Inter-2 were detected only in human isolates in clade 2.2.1-B. 2016 PLoS pathogens Discussion IV K198R;K198R;D175N;P627L 27;38;44;143 32;43;49;148 PB1;PB1;PB1 23;34;139 26;37;142 27097026 Novel Polymerase Gene Mutations for Human Adaptation in Clinical Isolates of Avian H5N1 Influenza Viruses. For example, both the PB2-E627K and PB2-D701N mutations increased PB2 binding to host importin-alpha isoforms to indirectly regulate polymerase activity, suggesting that an excessive shift in vRNP transport between the nucleus and cytoplasm may have led to lower progeny vRNA production by the EG/D1 strain with the PB2-E627K/D701N mutations. 2016 PLoS pathogens Discussion IV E627K;D701N;D701N;E627K 26;40;326;320 31;45;331;325 PB2;PB2;PB2;PB2 22;36;66;316 25;39;69;319 27097026 Novel Polymerase Gene Mutations for Human Adaptation in Clinical Isolates of Avian H5N1 Influenza Viruses. For example, PA-E327K increased polymerase activity, but had no appreciable effect on progeny vRNA production by EG/D1 (wt) in human cells. 2016 PLoS pathogens Discussion IV E327K 16 21 PA 13 15 27097026 Novel Polymerase Gene Mutations for Human Adaptation in Clinical Isolates of Avian H5N1 Influenza Viruses. In addition, PB1-T182I/K214R/L384S and PB2-M473V/D195N were detected in both avian and human isolates in clade 2.2.1.2 and clade 2.2.1-B, respectively. 2016 PLoS pathogens Discussion IV T182I;K214R;L384S;M473V;D195N 17;23;29;43;49 22;28;34;48;54 PB1;PB2 13;39 16;42 27097026 Novel Polymerase Gene Mutations for Human Adaptation in Clinical Isolates of Avian H5N1 Influenza Viruses. In addition, PB2-D701N caused no increase in progeny vRNA production in the EG/D1 genetic background carrying PB2-627K, in spite of the strong effect of PB2-D701N in the minigenome assay. 2016 PLoS pathogens Discussion IV D701N;D701N 17;157 22;162 PB2;PB2;PB2 13;110;153 16;113;156 27097026 Novel Polymerase Gene Mutations for Human Adaptation in Clinical Isolates of Avian H5N1 Influenza Viruses. In contrast, introduction of the PB1-K198R and PB1-T182I mutations in EG/D1, which increased progeny vRNA production in human cells, had a complementary role and increased the c/vRNA synthesis that was restricted in human host cells (Figs 2-5, S3, S6 and S7), indicating differences in their mechanism from PB2-E627K and PB2-D701N. 2016 PLoS pathogens Discussion IV K198R;T182I;E627K;D701N 37;51;311;325 42;56;316;330 PB1;PB1;PB2;PB2 33;47;307;321 36;50;310;324 27097026 Novel Polymerase Gene Mutations for Human Adaptation in Clinical Isolates of Avian H5N1 Influenza Viruses. It is possible that mutations such as PA-E327K and PB2-D701N caused the loss of some functional balance in EG/D1 vRNP carrying PB2-627K. 2016 PLoS pathogens Discussion IV E327K;D701N 41;55 46;60 PA;PB2;PB2 38;51;127 40;54;130 27097026 Novel Polymerase Gene Mutations for Human Adaptation in Clinical Isolates of Avian H5N1 Influenza Viruses. Several of the human adaptation polymerase mutations identified in this study (e.g., PB1-K198R and PB1-T182I) have been detected in H5N1 viruses that are circulating in different geographic areas of Asia, with either amino acid E or K at the PB2-627 residue (Table 1). 2016 PLoS pathogens Discussion IV K198R;T182I 89;103 94;108 PB1;PB1;PB2 85;99;242 88;102;245 27097026 Novel Polymerase Gene Mutations for Human Adaptation in Clinical Isolates of Avian H5N1 Influenza Viruses. The polymerase structure models in this study indicated that the PB1-D175N, -T182I, -K198R and -K214R mutations, which had appreciable effects on H5N1 human adaptation, structurally and energetically modified the conformation of the PB1 beta-ribbon that interacts with the vRNA promoter (S10 Fig). 2016 PLoS pathogens Discussion IV D175N;T182I;K198R;K214R 69;77;85;96 74;82;90;101 PB1;PB1 65;233 68;236 27097026 Novel Polymerase Gene Mutations for Human Adaptation in Clinical Isolates of Avian H5N1 Influenza Viruses. While several other adaptation mutations (e.g., PB2-D701N) have also been identified in PB2, the majority of these amino acid substitutions have not previously been detected together with PB2-E627K, implying that they had little or no synergistic effect with PB2-627K. 2016 PLoS pathogens Discussion IV D701N;E627K 52;192 57;197 PB2;PB2;PB2;PB2 48;88;188;259 51;91;191;262 27105450 Residues in the PB2 and PA genes contribute to the pathogenicity of avian H7N3 influenza A virus in DBA/2 mice. In the North American H7N3 virus, a proline to serine substitution at position 190 in the PA protein attenuated the virus in vivo. 2016 Virology Discussion IV P190S 36 82 PA 90 92 27105450 Residues in the PB2 and PA genes contribute to the pathogenicity of avian H7N3 influenza A virus in DBA/2 mice. Interestingly the E358V in H7N3 had a much greater impact than the reciprocal V358E mutation in H7N9. 2016 Virology Discussion IV E358V;V358E 18;78 23;83 27105450 Residues in the PB2 and PA genes contribute to the pathogenicity of avian H7N3 influenza A virus in DBA/2 mice. Interestingly, a H357N change in PB2 was found in 2009 pdmH1N1 influenza virus that was experimentally adapted to the murine host. 2016 Virology Discussion IV H357N 17 22 PB2 33 36 27105450 Residues in the PB2 and PA genes contribute to the pathogenicity of avian H7N3 influenza A virus in DBA/2 mice. Our studies show that a glutamine (Q) at position 400 on the PA protein increases virulence in a mammalian host. 2016 Virology Discussion IV Q400Q 23 54 PA 61 63 27105450 Residues in the PB2 and PA genes contribute to the pathogenicity of avian H7N3 influenza A virus in DBA/2 mice. The amino-acid differences in PB2 (E358V) and PA (P190S) affected replication and inflammation, resulting in reduced disease and death of the infected host. 2016 Virology Discussion IV E358V;P190S 35;50 40;55 PA;PB2 46;30 48;33 27186639 In-Depth Analysis of HA and NS1 Genes in A(H1N1)pdm09 Infected Patients. Besides the predominant HA variants S203T and D222E, we detected a number of minority variants (S203P/A, D222G, Q223R and E224G) within the RBS, all reported at low frequency, in the population database (S1 Table). 2016 PloS one Discussion IV S203T;D222E;S203P;S203A;D222G;Q223R;E224G 36;46;96;96;105;112;122 41;51;103;103;110;117;127 HA 24 26 27186639 In-Depth Analysis of HA and NS1 Genes in A(H1N1)pdm09 Infected Patients. Noteworthy, the global frequency of known polymorphisms (namely HA S203T and NS1 I123V) observed in our patients as dominant variants (>98%), increased from about 70% in 2009 to about 99% thereafter. 2016 PloS one Discussion IV S203T;I123V 67;81 72;86 HA;NS1 64;77 66;80 27186639 In-Depth Analysis of HA and NS1 Genes in A(H1N1)pdm09 Infected Patients. On the whole, with the exception of the HA P271S variant observed in pt7 (43.16%), the distribution of HA and NS1 mutations in individual patient's quasi-species may be assigned to a dichotomic pattern: highly dominant (>90%) and minority (in fact <7%) variants. 2016 PloS one Discussion IV P271S 43 48 HA;HA;NS1 40;103;110 42;105;113 27268229 Detection of reassortant avian influenza A (H11N9) virus in environmental samples from live poultry markets in China. The N30D and T215A mutations observed in the M1 protein might increase the pathogenicity of these viruses in mice. 2016 Infectious diseases of poverty Discussion IV N30D;T215A 4;13 8;18 M1 45 47 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. Although the WT virus harbors a T148K mutation in the neuraminidase (NA) protein that has been associated with reduced sensitivity to NA inhibitors in other H3N2 viruses, the NA activities of the WT and resistant A/Perth/16/2009 viruses are comparable, and are similarly inhibited by oseltamivir acid. 2016 PLoS pathogens Discussion IV T148K 32 37 NA;NA;NA;NA 69;134;175;54 71;136;177;67 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. Another fusion-augmenting variant selected for its ability to grow in amantadine by the same group of authors contains a Gln47Arg mutation in the helix A of HA2. 2016 PLoS pathogens Discussion IV Q47R 121 129 HA 157 159 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. As an example, a Thr32Arg mutation on HA2 of recent H3N2 strains reduced binding to the anti-IAV group 2 antibody CR8043 by ~10 fold, but these viruses were still potently neutralized by CR8043. 2016 PLoS pathogens Discussion IV T32R 17 25 HA 38 40 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. Based on this model, several factors might contribute to the escape of D391Y and F175Y/D391G: (1) the reduced binding affinity of D391Y and F175Y/D391G HAs to 39.29 at low pH might give the HAs an elongated window of antibody-free state during virus trafficking from early to late endosomes, although this alone is probably not sufficient for virus escape; (2) elevated fusion activation pH might give the viruses a larger fusion window in endosomes with higher pH; (3) the faster fusion kinetics might increase the chance of productive semifusion before HA inactivation. 2016 PLoS pathogens Discussion IV D391Y;F175Y;D391G;D391Y;F175Y;D391G 71;81;87;130;140;146 76;86;92;135;145;151 HA 555 557 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. By contrast, the D391Y and F175Y/D391G mutants bind 39.29 as well as the WT at neutral pH, so they are likely internalized into early endosomes with bound antibody. 2016 PLoS pathogens Discussion IV D391Y;F175Y;D391G 17;27;33 22;32;38 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. F175Y is likely an inconsequential random mutation as it is distant from the 39.29 epitope and does not affect antibody binding or the fusion ability of HA. 2016 PLoS pathogens Discussion IV F175Y 0 5 HA 153 155 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. For example, the G234E mutant HA demonstrated significantly increased fusion ability but was still blocked by 39.29 because it did not lose antibody binding at low pH (Fig 7). 2016 PLoS pathogens Discussion IV G234E 17 22 HA 30 32 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. However, our results do not rule out the possibility that F175Y contributes to viral escape indirectly. 2016 PLoS pathogens Discussion IV F175Y 58 63 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. Interestingly, a variant that harbored a His111Leu mutation in a short helix of HA2, which switches from a coiled coil to a reverse turn during fusion, and reduced binding to the anti-IAV group 1 antibody CR6261 by 60% was able to escape neutralization. 2016 PLoS pathogens Discussion IV H111L 41 50 HA 80 82 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. It will be interesting to test whether the His111Leu mutation can enhance membrane fusion in addition to partially reducing antibody binding. 2016 PLoS pathogens Discussion IV H111L 43 52 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. On the other hand, Q387K introduces a positively charged side chain that may form an electrostatic interaction with the negatively charged D391, and thus further stabilize helix A and lower the fusion activation pH (Fig 3). 2016 PLoS pathogens Discussion IV Q387K 19 24 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. On the other hand, reduction of binding at low pH alone is probably not enough for antibody escape because the same mutations when introduced into an H1 HA (Q386K and D390G) were able to reduce 39.29 binding but could not overcome the fusion block by 39.29, likely due to the lack of fusion-augmenting effect of these mutations in H1 HA (Fig 6). 2016 PLoS pathogens Discussion IV Q386K;D390G 157;167 162;172 HA;HA 153;334 155;336 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. Since membrane fusion in the presence of neutralizing antibody is a competition between HA inactivation by antibody binding and the fusion ability of HA, all these factors likely contribute to the eventual escape of D391Y and F175Y/D391G. 2016 PLoS pathogens Discussion IV D391Y;F175Y;D391G 216;226;232 221;231;237 HA;HA 88;150 90;152 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. The D391Y and F175Y/D391G mutations raise the fusion activation pH of HA (Fig 3). 2016 PLoS pathogens Discussion IV D391Y;F175Y;D391G 4;14;20 9;19;25 HA 70 72 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. The I384T mutation can possibly disrupt the hydrogen bond between Q387 and D391 and thus destabilize Helix A and increase the fusion ability of HA. 2016 PLoS pathogens Discussion IV I384T 4 9 HA 144 146 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. The Q387K mutant completely disrupts binding at neutral or low pH; consequently, this virus is likely endocytosed without bound antibody and achieves productive infection despite a slightly decreased fusion ability compared to the WT (Fig 3). 2016 PLoS pathogens Discussion IV Q387K 4 9 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. The Q387K mutation, on the other hand, appears to reduce but not abolish the membrane fusion ability of HA at low pH, and mutant viruses harboring the Q387K mutation escape antibody neutralization simply by abolishing antibody binding. 2016 PLoS pathogens Discussion IV Q387K;Q387K 4;151 9;156 HA 104 106 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. The Q387K, D391Y and D391G mutations do not exist in natural isolates of IAV, indicating reduced fitness of the escape variants in nature. 2016 PLoS pathogens Discussion IV Q387K;D391Y;D391G 4;11;21 9;16;26 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. Two of the mutant viruses escape by abolishing antibody binding whereas the third one harbors a mutation (I384T in H7 numbering) that only partially reduces antibody binding. 2016 PLoS pathogens Discussion IV I384T 106 111 27351973 Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody. Whole genome sequencing revealed an R384G substitution in the NP protein of all three resistant variants compared to the WT virus. 2016 PLoS pathogens Discussion IV R384G 36 41 NP 62 64 27405392 G45R mutation in the nonstructural protein 1 of A/Puerto Rico/8/1934 (H1N1) enhances viral replication independent of dsRNA-binding activity and type I interferon biology. An adaptation of amino acids on NS1, F103L and M106I, of human influenza A/Hong Kong/1/68(H3N2) has been reported to be associated with the increased virus replication and virulence in mice and human thereby the occurrence of G45R mutation on NS1 of pandemic human 2009 H1N1 virus might be one of crucial factors to cause severe disease. 2016 Virology journal Discussion IV F103L;M106I;G45R 37;47;226 42;52;230 NS1;NS1 32;243 35;246 Influenza A virus H3N2 infection 89 94 27405392 G45R mutation in the nonstructural protein 1 of A/Puerto Rico/8/1934 (H1N1) enhances viral replication independent of dsRNA-binding activity and type I interferon biology. As G45R/NS1 did not act as predicted, we speculated that substitution of G45R on PR8 NS1 may impact dsRNA binding by steric hindrance. 2016 Virology journal Discussion IV G45R;G45R 3;73 7;77 NS1;NS1 8;85 11;88 27405392 G45R mutation in the nonstructural protein 1 of A/Puerto Rico/8/1934 (H1N1) enhances viral replication independent of dsRNA-binding activity and type I interferon biology. Even though G45R in NS1 presents in a minor population of the pandemic H1N1 2009 viruses, it has been proposed that G45R mutation might be related to the increased cytokine production observed during infections by these viruses. 2016 Virology journal Discussion IV G45R;G45R 12;116 16;120 NS1 20 23 27405392 G45R mutation in the nonstructural protein 1 of A/Puerto Rico/8/1934 (H1N1) enhances viral replication independent of dsRNA-binding activity and type I interferon biology. G45R/NS1 replicated to higher titers compared to WT virus while AA/NS1 virus was attenuated in both WT and IFNARnull Let1 cells. 2016 Virology journal Discussion IV G45R 0 4 NS1;NS1 5;67 8;70 27405392 G45R mutation in the nonstructural protein 1 of A/Puerto Rico/8/1934 (H1N1) enhances viral replication independent of dsRNA-binding activity and type I interferon biology. G45R/NS1 strongly influenced virus replication in a type I IFN induction-independent manner. 2016 Virology journal Discussion IV G45R 0 4 NS1 5 8 27405392 G45R mutation in the nonstructural protein 1 of A/Puerto Rico/8/1934 (H1N1) enhances viral replication independent of dsRNA-binding activity and type I interferon biology. However, replication of viruses containing the R38A NS1 mutation was improved in RNaseL knockout cells, suggesting that NS1 was involved in the inhibition of the 2'-5' OAS/RNaseL pathway, possibly by sequestering dsRNA and preventing activation of OAS1. 2016 Virology journal Discussion IV R38A 47 51 NS1;NS1 52;120 55;123 27405392 G45R mutation in the nonstructural protein 1 of A/Puerto Rico/8/1934 (H1N1) enhances viral replication independent of dsRNA-binding activity and type I interferon biology. In fact, high replication of G45R/NS1 was accompanied by increased type I IFN and STAT1 phosphorylation. 2016 Virology journal Discussion IV G45R 29 33 NS1 34 37 27405392 G45R mutation in the nonstructural protein 1 of A/Puerto Rico/8/1934 (H1N1) enhances viral replication independent of dsRNA-binding activity and type I interferon biology. In these assays, G45R/NS1 did not show increased dsRNA-binding compared to WT/NS1. 2016 Virology journal Discussion IV G45R 17 21 NS1;NS1 22;78 25;81 27405392 G45R mutation in the nonstructural protein 1 of A/Puerto Rico/8/1934 (H1N1) enhances viral replication independent of dsRNA-binding activity and type I interferon biology. The reporter assay showed that G45R/NS1 suppressed the activation of IFNbeta-promoter comparable to WT/NS1. 2016 Virology journal Discussion IV G45R 31 35 NS1;NS1 36;103 39;106 27405392 G45R mutation in the nonstructural protein 1 of A/Puerto Rico/8/1934 (H1N1) enhances viral replication independent of dsRNA-binding activity and type I interferon biology. Viruses containing the R38A mutation in NS1 were attenuated, lacked dsRNA binding and were sensitive to IFNbeta. 2016 Virology journal Discussion IV R38A 23 27 NS1 40 43 27405392 G45R mutation in the nonstructural protein 1 of A/Puerto Rico/8/1934 (H1N1) enhances viral replication independent of dsRNA-binding activity and type I interferon biology. We confirmed that type I IFNs induction was not relevant to G45R/NS1 virus replication by using IFNARnull Let1 cells. 2016 Virology journal Discussion IV G45R 60 64 NS1 65 68 27405392 G45R mutation in the nonstructural protein 1 of A/Puerto Rico/8/1934 (H1N1) enhances viral replication independent of dsRNA-binding activity and type I interferon biology. We constructed viruses using reverse genetics that contained the HA and NA genes from X31 in a PR8 background and demonstrated that the single amino acids substitution, G45R, in the RBD of PR8 NS1 accelerated viral replication. 2016 Virology journal Discussion IV G45R 169 173 HA;NA;NS1 65;72;193 67;74;196 27405392 G45R mutation in the nonstructural protein 1 of A/Puerto Rico/8/1934 (H1N1) enhances viral replication independent of dsRNA-binding activity and type I interferon biology. We investigated whether G45R/NS1 increased virus replication by inhibiting RIG-I mediated IFNbeta-promoter activation. 2016 Virology journal Discussion IV G45R 24 28 NS1 29 32 27405392 G45R mutation in the nonstructural protein 1 of A/Puerto Rico/8/1934 (H1N1) enhances viral replication independent of dsRNA-binding activity and type I interferon biology. We investigated whether the enhanced viral replication mediated by G45R/NS1 was due to the increased dsRNA binding in vitro using dsRNA-NS1 pull-down assays. 2016 Virology journal Discussion IV G45R 67 71 NS1;NS1 72;136 75;139 27405392 G45R mutation in the nonstructural protein 1 of A/Puerto Rico/8/1934 (H1N1) enhances viral replication independent of dsRNA-binding activity and type I interferon biology. We suggest that the G45R mutation in PR8 NS1 facilitated virus replication independent of dsRNA-binding and RIG-I mediated IFNbeta promoter activation. 2016 Virology journal Discussion IV G45R 20 24 NS1 41 44 27405392 G45R mutation in the nonstructural protein 1 of A/Puerto Rico/8/1934 (H1N1) enhances viral replication independent of dsRNA-binding activity and type I interferon biology. WSN-NS1 with the triple mutations R38A, K41A and S42G could not bind to dsRNA similar to R38A and K41A, though the virus containing R38A, K41A and S42G decreased activation of the IFNbeta promoter and had a higher replication rate compared to the virus containing R38A and K41A. 2016 Virology journal Discussion IV R38A;K41A;S42G;R38A;K41A;R38A;K41A;S42G;R38A;K41A 34;40;49;89;98;132;138;147;264;273 38;44;53;93;102;136;142;151;268;277 NS1 4 7 27413002 Pulmonary changes in Norwegian fatal cases of pandemic influenza H1N1 (2009) infection: a morphologic and molecular genetic study. In conclusion, our results show a possible association in fatal Norwegian cases from the A(H1N1)pdm09 pandemic between mortality and the factors obesity, underlying illness, and the viral mutation HA D222G. 2016 Influenza and other respiratory viruses Discussion IV D222G 200 205 HA 197 199 27413002 Pulmonary changes in Norwegian fatal cases of pandemic influenza H1N1 (2009) infection: a morphologic and molecular genetic study. Since the outbreak of the novel A(H1N1)pdm09, post-pandemic studies have described the clinical aspects of this virus.23, 24, 25 Several host factors and underlying conditions have been associated with disease severity.9, 14, 15, 16, 20, 21, 22 These include pneumonia, obesity, pregnancy, in addition to effects of vaccines and neuraminidase inhibitors that were used during the pandemic.23, 24, 25 Kilander et al.29 reported a novel mutation in the major surface glycoprotein HA) of A(H1N1)pdm09, namely HA D222G, which was associated with a severe clinical outcome in Norwegian patients.30 The mutation was found with considerable frequency in fatal and severe cases (11 of 61 cases), but was not observed in any of the 205 mild cases included in their study. 2016 Influenza and other respiratory viruses Discussion IV D222G 509 514 HA;HA;NA 478;506;329 480;508;342 Pneumonia 259 268 27413002 Pulmonary changes in Norwegian fatal cases of pandemic influenza H1N1 (2009) infection: a morphologic and molecular genetic study. The viral mutation HA D222G was observed in 6 of 15 cases where the genotype in this position could be ascertained, while the other nine patients possessed the wild-type 222D.30, 40, 41 Interestingly, all four subjects who developed DAD and had no pre-existing illness expressed the HA D222G viral mutation in their lung tissue (Table 2). 2016 Influenza and other respiratory viruses Discussion IV D222G;D222G 22;286 27;291 HA;HA 19;283 21;285 Diffused alveolar damage 233 236 27413002 Pulmonary changes in Norwegian fatal cases of pandemic influenza H1N1 (2009) infection: a morphologic and molecular genetic study. Therefore, we further investigated whether there was an association between the genetic viral HA D222G mutation and the expression of the A(H1N1)pdm09 virus locally at the site of inflammation in the lung tissue. 2016 Influenza and other respiratory viruses Discussion IV D222G 97 102 HA 94 96 27413002 Pulmonary changes in Norwegian fatal cases of pandemic influenza H1N1 (2009) infection: a morphologic and molecular genetic study. This suggests that, similar to obesity, the expression of the HA D222G viral mutation at the site of inflammation predisposes to viral pneumonia and development of DAD with an associated increased mortality rate. 2016 Influenza and other respiratory viruses Discussion IV D222G 65 70 HA 62 64 Pneumonia;Diffused alveolar damage 129;164 144;167 27413002 Pulmonary changes in Norwegian fatal cases of pandemic influenza H1N1 (2009) infection: a morphologic and molecular genetic study. Whereas the likelihood of occurrence of this and other mutations may increase the duration of infection, the duration of illness before death was found to be comparably short for these cases of HA D222G in previously healthy individuals. 2016 Influenza and other respiratory viruses Discussion IV D222G 197 202 HA 194 196 27535054 NS1 Protein Mutation I64T Affects Interferon Responses and Virulence of Circulating H3N2 Human Influenza A Viruses. Also, in a study involving random mutagenesis, rescue of replication-proficient mutants in type I IFN response-deficient cells, and subsequent screening for viruses with an enhanced capacity to induce type I IFN after infection, a similar mutation (I68T), pointing in the same direction of the alpha-helix in the NS1 protein crystal structure as the mutation I64T. 2016 Journal of virology Discussion IV I68T;I64T 249;359 253;363 NS1 313 316 27535054 NS1 Protein Mutation I64T Affects Interferon Responses and Virulence of Circulating H3N2 Human Influenza A Viruses. Both of them showed that mutation I64T, which impaired the ability of NS1 to inhibit host gene expression, also impaired the ability of NS1 to counteract host innate immune responses. 2016 Journal of virology Discussion IV I64T 34 38 NS1;NS1 70;136 73;139 27535054 NS1 Protein Mutation I64T Affects Interferon Responses and Virulence of Circulating H3N2 Human Influenza A Viruses. Furthermore, we show for the first time that a particular mutation (I64T) in the dsRNA-binding domain decreases NS1-mediated host gene expression inhibition by affecting the NS1 binding to CPSF30. 2016 Journal of virology Discussion IV I64T 68 72 NS1;NS1 112;174 115;177 27535054 NS1 Protein Mutation I64T Affects Interferon Responses and Virulence of Circulating H3N2 Human Influenza A Viruses. In agreement with our results, increasing the binding of NS1 protein to CPSF30 in H7N9 and in H5N1 NS1 proteins by introducing the mutations L103F and I106M led to decreased type I IFN responses after infection, augmented virus titers in vivo, and increased virulence in mice. 2016 Journal of virology Discussion IV L103F;I106M 141;151 146;156 NS1;NS1 57;99 60;102 27535054 NS1 Protein Mutation I64T Affects Interferon Responses and Virulence of Circulating H3N2 Human Influenza A Viruses. Interestingly, mutation I64T conferred an IFN-hyperinducer phenotype in a screening in which the authors passaged an IAV H3N2 virus in type I IFN-incompetent cells. 2016 Journal of virology Discussion IV I64T 24 28 27535054 NS1 Protein Mutation I64T Affects Interferon Responses and Virulence of Circulating H3N2 Human Influenza A Viruses. Therefore, whether the mutation I64T affects the binding to CPSF30 directly or affects the conformational structure of amino acids relevant for the binding should be further studied. 2016 Journal of virology Discussion IV I64T 32 36 27535054 NS1 Protein Mutation I64T Affects Interferon Responses and Virulence of Circulating H3N2 Human Influenza A Viruses. To analyze the effect of the I64T mutation on virus growth and virulence, viruses encoding the NS1 proteins from patients 85 and 87 (differing only at amino acid position 64) were rescued. 2016 Journal of virology Discussion IV I64T 29 33 NS1 95 98 27535054 NS1 Protein Mutation I64T Affects Interferon Responses and Virulence of Circulating H3N2 Human Influenza A Viruses. To analyze the molecular mechanism by which mutation I64T decreases the ability of NS1 to block gene expression, the binding of NS1 to CPSF30 was analyzed. 2016 Journal of virology Discussion IV I64T 53 57 NS1;NS1 83;128 86;131 27535054 NS1 Protein Mutation I64T Affects Interferon Responses and Virulence of Circulating H3N2 Human Influenza A Viruses. Whereas mutations in positions 26 and 224 had minor effects on the ability of NS1 to suppress gene expression, mutation I64T strongly decreased the ability of NS1 to inhibit general gene expression either in the H3N2. 2016 Journal of virology Discussion IV I64T 120 124 NS1;NS1 78;159 81;162 27630240 Human Monoclonal Antibody 81.39a Effectively Neutralizes Emerging Influenza A Viruses of Group 1 and 2 Hemagglutinins. A single virus from group 2, a drug-resistant A(H7N9) clone, had HA2-Asp19Gly. 2016 Journal of virology Discussion IV D19G 69 77 HA 65 67 27630240 Human Monoclonal Antibody 81.39a Effectively Neutralizes Emerging Influenza A Viruses of Group 1 and 2 Hemagglutinins. Asp19Asn reduced the binding affinity (Kd [dissociation constant] >= 570 nM) in the H3 subtype, while the binding affinity of the H13 (Kd = 6.3 nM) and H16 (Kd = 20 nM) subtypes carrying HA2-Asn19 was similar to that of the H3 subtype carrying HA2-Asp19 (Kd = 33 nM). 2016 Journal of virology Discussion IV D19N 0 8 HA;HA 187;244 189;246 27630240 Human Monoclonal Antibody 81.39a Effectively Neutralizes Emerging Influenza A Viruses of Group 1 and 2 Hemagglutinins. Further, Asp19Asn was demonstrated to abrogate neutralization of A(H3N2) and A(H7N7) viruses by CR8020, where HA2-Asp19Asn is believed to disrupt a possible salt bridge to VL of arginine at position 53, leading to destabilization of the antibody-HA interaction. 2016 Journal of virology Discussion IV D19N;D19N 114;9 122;17 HA;HA 110;246 112;248 27630240 Human Monoclonal Antibody 81.39a Effectively Neutralizes Emerging Influenza A Viruses of Group 1 and 2 Hemagglutinins. In our study, however, the effect of HA2-Asp19Ala on virus neutralization by 81.39a was different, indicating the distinctive features of each stalk-binding MAb, and underscores the importance of actual testing of viruses in neutralization assays. 2016 Journal of virology Discussion IV D19A 41 49 HA 37 39 27630240 Human Monoclonal Antibody 81.39a Effectively Neutralizes Emerging Influenza A Viruses of Group 1 and 2 Hemagglutinins. Interestingly, we observed the therapeutic benefit from 81.39a treatment in mice infected with the A(H7N9) virus carrying HA2-Asp19Gly despite its lack of neutralization in cell culture. 2016 Journal of virology Discussion IV D19G 126 134 HA 122 124 27630240 Human Monoclonal Antibody 81.39a Effectively Neutralizes Emerging Influenza A Viruses of Group 1 and 2 Hemagglutinins. It is worth noting that while group 1-targeting MAbs D8 and F10 effectively neutralized a pseudotyped virus of H11 subtype carrying Asp19Asn, a lack of neutralization of H3 and H7 subtype viruses carrying this change was reported for CR8020, a group 2-neutralizing MAb. 2016 Journal of virology Discussion IV D19N 132 140 27630240 Human Monoclonal Antibody 81.39a Effectively Neutralizes Emerging Influenza A Viruses of Group 1 and 2 Hemagglutinins. Moreover, binding to H9 and H12 subtypes carrying HA2-Asp19Ala was not affected (Kd of 2 and 2.9, respectively), similar to that of the H1 subtype. 2016 Journal of virology Discussion IV D19A 54 62 HA 50 52 27630240 Human Monoclonal Antibody 81.39a Effectively Neutralizes Emerging Influenza A Viruses of Group 1 and 2 Hemagglutinins. Peculiarly, for the group 1- and 2-targeting MAb CR9114, the effect of substitution HA2-Asp19Asn on binding affinity varied among HA subtypes. 2016 Journal of virology Discussion IV D19N 88 96 HA;HA 84;130 86;132 27630240 Human Monoclonal Antibody 81.39a Effectively Neutralizes Emerging Influenza A Viruses of Group 1 and 2 Hemagglutinins. The HA2-Asp19Gly virus escaped neutralization by 81.39a at a concentration of 50 mug/ml. 2016 Journal of virology Discussion IV D19G 8 16 HA 4 6 27658193 Sensitive Detection and Simultaneous Discrimination of Influenza A and B Viruses in Nasopharyngeal Swabs in a Single Assay Using Next-Generation Sequencing-Based Diagnostics. A mammalian-adapting V100A substitution was identified in most A(H3N2) but not in A(pdH1N1) viruses, and S409N was identified in all A(pdH1N1) and some A(H3N2) viruses, indicating their pandemic potential. 2016 PloS one Discussion IV V100A;S409N 21;105 26;110 27658193 Sensitive Detection and Simultaneous Discrimination of Influenza A and B Viruses in Nasopharyngeal Swabs in a Single Assay Using Next-Generation Sequencing-Based Diagnostics. A mutation of PB2 E627K has been reported to confer high virulence to the virus by enhancing replication efficiency, and increasing polymerase activity and disease severity of avian influenza viruses in mammals. 2016 PloS one Discussion IV E627K 18 23 PB2 14 17 27658193 Sensitive Detection and Simultaneous Discrimination of Influenza A and B Viruses in Nasopharyngeal Swabs in a Single Assay Using Next-Generation Sequencing-Based Diagnostics. An amino-acid signature, valine at position NP-100 reported in 2009 pandemic H1N1 strain, was found as V100I mutation in all A(pdH1N1) and five A(H3N2) viruses, suggesting genetic changes of influenza A viruses in the 2012-13 seasons in this region. 2016 PloS one Discussion IV V100I 103 108 NP 44 46 27658193 Sensitive Detection and Simultaneous Discrimination of Influenza A and B Viruses in Nasopharyngeal Swabs in a Single Assay Using Next-Generation Sequencing-Based Diagnostics. An E105K point mutation at the NA tetramer in influenza B virus was reported leading to reduced susceptibility to NA inhibitor drugs. 2016 PloS one Discussion IV E105K 3 8 NA;NA 31;114 33;116 27658193 Sensitive Detection and Simultaneous Discrimination of Influenza A and B Viruses in Nasopharyngeal Swabs in a Single Assay Using Next-Generation Sequencing-Based Diagnostics. Sequence analysis of 123 influenza A viruses revealed that 66.7%(82/123) of A(H3N2) viruses had a single signature mutation of E627K in the PB2 protein, and 88%(108/123) of influenza A(H3N2 and pdH1N1) viruses contained the S31N mutation in the M2 protein. 2016 PloS one Discussion IV E627K;S31N 127;224 132;228 M2;PB2 245;140 247;143 27658193 Sensitive Detection and Simultaneous Discrimination of Influenza A and B Viruses in Nasopharyngeal Swabs in a Single Assay Using Next-Generation Sequencing-Based Diagnostics. Sequence analysis revealed that the E119V signature mutations in these specimens may be susceptible to oseltamivir in A(H3N2) but not in A(pdH1N1) viruses. 2016 PloS one Discussion IV E119V 36 41 27658193 Sensitive Detection and Simultaneous Discrimination of Influenza A and B Viruses in Nasopharyngeal Swabs in a Single Assay Using Next-Generation Sequencing-Based Diagnostics. The emergence of E627K(PB2) and S31N(M2) mutations raise concerns of increased human disease severity. 2016 PloS one Discussion IV E627K;S31N 17;32 22;36 M2;PB2 37;23 39;26 27658193 Sensitive Detection and Simultaneous Discrimination of Influenza A and B Viruses in Nasopharyngeal Swabs in a Single Assay Using Next-Generation Sequencing-Based Diagnostics. The S31N mutation in the transmembrane region of the M2 protein confers resistance to amantadine. 2016 PloS one Discussion IV S31N 4 8 M2 53 55 27713074 An influenza A virus (H7N9) anti-neuraminidase monoclonal antibody with prophylactic and therapeutic activity in vivo. The most thoroughly studied anti-N9 mAb include NC10 and NC41 that were raised against A/tern/Australia/G70C/1975 (H11/N9). 2016 Antiviral research Discussion IV G70C 104 108 N9;N9 33;119 35;121 27741319 Cross-Neutralising Nanobodies Bind to a Conserved Pocket in the Hemagglutinin Stem Region Identified Using Yeast Display and Deep Mutational Scanning. In addition proximity D46 to the E47K substitution known to be associated with improved viral fitness warrants further investigation and the unique specificity of R2b-E8 may be a useful probe for such purposes. 2016 PloS one Discussion IV E47K 33 37 27741319 Cross-Neutralising Nanobodies Bind to a Conserved Pocket in the Hemagglutinin Stem Region Identified Using Yeast Display and Deep Mutational Scanning. The ability to predict antibody binding has been exemplified by correlating the specificity of R2b-E8 with the D46N substitution across different viral strains. 2016 PloS one Discussion IV D46N 111 115 27849220 Surveillance of antiviral resistance markers in Argentina: detection of E119V neuraminidase mutation in a post-treatment immunocompromised patient. Although the frequency of the E119V substitution is low (0.01%), in this study, we have been able to detect a mixture of E119/V119 subpopulations in an influenza A(H3N2) virus isolate recovered from a post-treatment immunocompromised patient. 2016 Memorias do Instituto Oswaldo Cruz Discussion IV E119V 30 35 27849220 Surveillance of antiviral resistance markers in Argentina: detection of E119V neuraminidase mutation in a post-treatment immunocompromised patient. Molecular detection of the E119V SNP cannot alone inform about oseltamivir resistance without complementary studies to confirm the decrease of the susceptibility to antiviral drugs. 2016 Memorias do Instituto Oswaldo Cruz Discussion IV E119V 27 32 27849220 Surveillance of antiviral resistance markers in Argentina: detection of E119V neuraminidase mutation in a post-treatment immunocompromised patient. The absence of the E119V change in the pre-treatment sample suggests that the V119 variant arose as a consequence of the oseltamivir therapy. 2016 Memorias do Instituto Oswaldo Cruz Discussion IV E119V 19 24 27849220 Surveillance of antiviral resistance markers in Argentina: detection of E119V neuraminidase mutation in a post-treatment immunocompromised patient. These samples should be analysed immediately using molecular-based techniques for common resistance-associated mutations [e.g., E119V in A(H3N2) and H275Y in A(H1N1)pdm09 viruses], and prompt feedback must be given to treating clinicians, so that alternative therapies can be initiated. 2016 Memorias do Instituto Oswaldo Cruz Discussion IV E119V;H275Y 128;149 133;154 27849220 Surveillance of antiviral resistance markers in Argentina: detection of E119V neuraminidase mutation in a post-treatment immunocompromised patient. This finding is in agreement with previous reports about the emergence of E119V substitution in oseltamivir-treated immunocompromised patients infected with influenza A(H3N2) virus. 2016 Memorias do Instituto Oswaldo Cruz Discussion IV E119V 74 79 27869615 Highly Pathogenic Influenza A(H5Nx) Viruses with Altered H5 Receptor-Binding Specificity. Consistent with our findings, HAs of the Taiwanese/North American branch of clade 2.3.4.4 viruses, which obtained reverse substitution R227S (Figure 5), also efficiently bind fucosylated receptors. 2017 Emerging infectious diseases Discussion IV R227S 135 140 27869615 Highly Pathogenic Influenza A(H5Nx) Viruses with Altered H5 Receptor-Binding Specificity. HA residues K222 and S227 are extremely conserved among all clades of highly pathogenic H5N1 viruses; the double substitution K222Q/S227R was introduced only at the root of clade 2.3.4.4 (Figure 5). 2017 Emerging infectious diseases Discussion IV K222Q;S227R 126;132 131;137 HA 0 2 27869615 Highly Pathogenic Influenza A(H5Nx) Viruses with Altered H5 Receptor-Binding Specificity. However, additional introduction of an arginine at position 227 (double substitution K222Q/S227R) in H5N12.3.4 HA was sufficient to cause a glycan array binding profile nearly identical to that of H5N8 HA. 2017 Emerging infectious diseases Discussion IV K222Q;S227R 85;91 90;96 HA;HA 111;202 113;204 27869615 Highly Pathogenic Influenza A(H5Nx) Viruses with Altered H5 Receptor-Binding Specificity. Introduction of K222Q into H5N12.3.4 HA, which removes the competition with the fucose-moiety, in itself does not enable binding to fucosylated receptors (Figure 7). 2017 Emerging infectious diseases Discussion IV K222Q 16 21 HA 37 39 27869615 Highly Pathogenic Influenza A(H5Nx) Viruses with Altered H5 Receptor-Binding Specificity. Substitution S227R might result in the 220-loop interacting with the conserved loop at the N terminus of the 190-helix through 2 hydrogen bonds between R227 and N186 (Figure 8, panel C). 2017 Emerging infectious diseases Discussion IV S227R 13 18 27869615 Highly Pathogenic Influenza A(H5Nx) Viruses with Altered H5 Receptor-Binding Specificity. Substitutions K222Q and S227R were present in the earliest H5N5 virus isolates (A/duck/Guangdong/wy24/2008) and have been maintained in all branches except the Taiwanese/North American branch of clade 2.3.4.4 viruses, which obtained reverse substitution R227S. 2017 Emerging infectious diseases Discussion IV K222Q;S227R;R227S 14;24;254 19;29;259 27869615 Highly Pathogenic Influenza A(H5Nx) Viruses with Altered H5 Receptor-Binding Specificity. We have shown that amino acid substitutions K222Q and S227R in the receptor-binding site of early clade 2.3.4.4 HAs are required for this change in receptor-binding specificity. 2017 Emerging infectious diseases Discussion IV K222Q;S227R 44;54 49;59 27933797 Nuclear Magnetic Resonance and Molecular Dynamics Simulation of the Interaction between Recognition Protein H7 of the Novel Influenza Virus H7N9 and Glycan Cell Surface Receptors. The comparison of the MD simulation trajectories between the model complexes, LSTa:H7sm, LSTc:H7sm with LSTa:H7, and LSTc:H7, suggests that the G228S mutation allows H7sm to bind both glycans with a strength greater than that of the wild type version of H7, even if this reinforcement appears to be more efficient for LSTa. 2016 Biochemistry Discussion IV G228S 144 149 27933797 Nuclear Magnetic Resonance and Molecular Dynamics Simulation of the Interaction between Recognition Protein H7 of the Novel Influenza Virus H7N9 and Glycan Cell Surface Receptors. The previously incompletely characterized interaction between glycan receptors and wild type H7 (AH-H7N9 variant) and a biologically relevant mutant (G228S), supposed to switch the H2 and H3 preference from avian (LSTa) to human (LSTc) receptors, was studied. 2016 Biochemistry Discussion IV G228S 150 155 28084423 Single PA mutation as a high yield determinant of avian influenza vaccines. Based on these, we suggest the PA E31K mutation as a feasible growth determinant of avian influenza CVVs. 2017 Scientific reports Discussion IV E31K 34 38 PA 31 33 28084423 Single PA mutation as a high yield determinant of avian influenza vaccines. Compared with rIETR, the four single mutant viruses (rIETR/PB2:R136K, rIETR/PA:E31K, rIETR/HA:A172T, and rIETR/M2:R80Q) exhibited similar or increased replication properties, and of them, rIETR/PA:E31K resulted in the most enhanced replication titer. 2017 Scientific reports Discussion IV R136K;E31K;A172T;R80Q;E31K 63;79;94;114;197 68;83;99;118;201 HA;M2;PA;PA;PB2 91;111;76;194;59 93;113;78;196;62 28084423 Single PA mutation as a high yield determinant of avian influenza vaccines. Even though rIETR/4Mut, which harbored all the four mutations, showed the most increased replication property, we tried to find a single molecular determinant of high yield influenza CVVs and focused on the PA E31K mutation based on its beneficial effects on viral replication in the Vero cells. 2017 Scientific reports Discussion IV E31K 210 214 PA 207 209 28084423 Single PA mutation as a high yield determinant of avian influenza vaccines. Extension of the PA E31K mutation to human influenza CVVs should be further exploited for the development of diverse cell culture-based influenza CVVs in future studies. 2017 Scientific reports Discussion IV E31K 20 24 PA 17 19 Influenza 37 52 28084423 Single PA mutation as a high yield determinant of avian influenza vaccines. However, the beneficial effects of the PA E31K mutation on viral replication in the Vero cells could be more dependent of pH condition for HA fusion activity than defective type I interferon response because most human influenza viruses do not grow well in the Vero cells, compared with avian viruses. 2017 Scientific reports Discussion IV E31K 42 46 HA;PA 139;39 141;41 28084423 Single PA mutation as a high yield determinant of avian influenza vaccines. In conclusion, we demonstrated that the PA E31K mutation could increase viral yields and HA contents of different subtypes of avian influenza CVVs. 2017 Scientific reports Discussion IV E31K 43 47 HA;PA 89;40 91;42 28084423 Single PA mutation as a high yield determinant of avian influenza vaccines. Interestingly, PA E31K-mediated growth enhancement was bigger in the Vero cells than in the MDCK or in the chicken eggs, even though the PA E31K mutation was arisen during a viral adaptation process in the eggs. 2017 Scientific reports Discussion IV E31K;E31K 18;140 22;144 PA;PA 15;137 17;139 28084423 Single PA mutation as a high yield determinant of avian influenza vaccines. the PA E31K mutation surely increased luciferase expression in a dose-dependent manner, which was then confirmed by RNA and protein expression levels. 2017 Scientific reports Discussion IV E31K 7 11 PA 4 6 28084423 Single PA mutation as a high yield determinant of avian influenza vaccines. To narrow down what molecular changes brought in the increases of plaque size and viral replication, we compared the genomic sequences of the master seed rIETR and the passaged rIETR15 CVVs and identified the four amino acid mutations from rIETR15:PB2 R136K, PA E31K, HA A172T, and M2 R80Q (Table 1). 2017 Scientific reports Discussion IV R136K;E31K;A172T;R80Q 252;262;271;285 257;266;276;289 HA;M2;PA;PB2 268;282;259;248 270;284;261;251 28084423 Single PA mutation as a high yield determinant of avian influenza vaccines. We also evaluated the beneficial effects of the PA E31K mutation on viral replication of the other H5N1, H7N9, and H9N2 CVVs (Figs 5 and 6). 2017 Scientific reports Discussion IV E31K 51 55 PA 48 50 28084423 Single PA mutation as a high yield determinant of avian influenza vaccines. We also examined whether the PA E31K mutation would increase viral polymerase complex activity. 2017 Scientific reports Discussion IV E31K 32 36 PA 29 31 28087313 An M2-V27A channel blocker demonstrates potent in vitro and in vivo antiviral activities against amantadine-sensitive and -resistant influenza A viruses. Although the most frequent amantadine-resistant mutant M2-S31N remains partially sensitive to amantadine, the M2-V27A mutant was completely resistant to amantadine, which makes it a challenging drug target. 2017 Antiviral research Discussion IV S31N;V27A 58;113 62;117 M2;M2 55;110 57;112 28087313 An M2-V27A channel blocker demonstrates potent in vitro and in vivo antiviral activities against amantadine-sensitive and -resistant influenza A viruses. However, as has been demonstrated by compound 7 in inhibiting the M2-V27A channel, this assumption appears incorrect. 2017 Antiviral research Discussion IV V27A 69 73 M2 66 68 28087313 An M2-V27A channel blocker demonstrates potent in vitro and in vivo antiviral activities against amantadine-sensitive and -resistant influenza A viruses. In this report, we further evaluated the in vitro and in vivo antiviral activity of the M2-V27A inhibitors. 2017 Antiviral research Discussion IV V27A 91 95 M2 88 90 28087313 An M2-V27A channel blocker demonstrates potent in vitro and in vivo antiviral activities against amantadine-sensitive and -resistant influenza A viruses. M2-V27A is one of the most frequent amantadine-resistant mutations among influenza A viruses that are circulating among humans and avian species. 2017 Antiviral research Discussion IV V27A 3 7 M2 0 2 28087313 An M2-V27A channel blocker demonstrates potent in vitro and in vivo antiviral activities against amantadine-sensitive and -resistant influenza A viruses. More concerning is the fact that M2-V27A mutant is directly correlated with drug selection pressure. 2017 Antiviral research Discussion IV V27A 36 40 M2 33 35 28087313 An M2-V27A channel blocker demonstrates potent in vitro and in vivo antiviral activities against amantadine-sensitive and -resistant influenza A viruses. Nevertheless, propelled by an integrated approach involving molecular dynamics simulations, NMR, electrophysiology, and medicinal chemistry, we were able to design the first-in-class M2-V27A inhibitors. 2017 Antiviral research Discussion IV V27A 186 190 M2 183 185 28087313 An M2-V27A channel blocker demonstrates potent in vitro and in vivo antiviral activities against amantadine-sensitive and -resistant influenza A viruses. The representative compound, 3, not only had potent in vitro antiviral activity, but also potent in vivo antiviral activity against both M2-WT- and M2-V27A-containing influenza A viruses. 2017 Antiviral research Discussion IV V27A 151 155 M2;M2 137;148 139;150 28100622 Glycosylation of the Hemagglutinin Protein of H5N1 Influenza Virus Increases Its Virulence in Mice by Exacerbating the Host Immune Response. We further found that the substitution G158N introduced an N-linked glycosylation at positions 158 to 160 of the HA protein and that this N-linked glycosylation enhanced viral productivity in infected mammalian cells and exacerbated host immune and inflammatory responses to viral infection. 2017 Journal of virology Discussion IV G158N 39 44 HA 113 115 28102191 A broadly protective therapeutic antibody against influenza B virus with two mechanisms of action. Furthermore, 46B8 N297G, the Fc-defective mAb that was not able to induce ADCC in vitro, also lost efficacy against the mutant viruses in mouse, indicating the critical role of Fc functions in in vivo protection when an mAb loses its ability to neutralize virus via its Fab domain. 2017 Nature communications Discussion IV N297G 18 23 28102191 A broadly protective therapeutic antibody against influenza B virus with two mechanisms of action. We isolated three 46B8-resistant viruses that all harbour a S301F mutation. 2017 Nature communications Discussion IV S301F 60 65 28128091 Development of oseltamivir and zanamivir resistance in influenza A(H1N1)pdm09 virus, Denmark, 2014. 2012 shows that I223R alone confers reduced susceptibility to both oseltamivir and zanamivir and is primarily selected by oseltamivir. 2017 Euro surveillance Discussion IV I223R 16 21 28128091 Development of oseltamivir and zanamivir resistance in influenza A(H1N1)pdm09 virus, Denmark, 2014. By addition of antivirals it was possible to rescue viruses with the combination of both I223R and H275Y mutations but none of the viruses displayed adequate NA activity to perform NA inhibition test. 2017 Euro surveillance Discussion IV I223R;H275Y 89;99 94;104 NA;NA 158;181 160;183 28128091 Development of oseltamivir and zanamivir resistance in influenza A(H1N1)pdm09 virus, Denmark, 2014. G147R and S247N. 2017 Euro surveillance Discussion IV G147R;S247N 0;10 5;15 28128091 Development of oseltamivir and zanamivir resistance in influenza A(H1N1)pdm09 virus, Denmark, 2014. H1N1pdm09 viruses with both I223R and H275Y mutations are shown to have increased resistance against both oseltamivir and zanamivir. 2017 Euro surveillance Discussion IV I223R;H275Y 28;38 33;43 28128091 Development of oseltamivir and zanamivir resistance in influenza A(H1N1)pdm09 virus, Denmark, 2014. However, retrospective testing showed that the oseltamivir resistance mutation H275Y had been induced already after the first oseltamvir treatment, which means that the second course of oseltamivir treatment for 2 months had likely limited effect on the influenza virus infection. 2017 Euro surveillance Discussion IV H275Y 79 84 IV infections 254 279 28128091 Development of oseltamivir and zanamivir resistance in influenza A(H1N1)pdm09 virus, Denmark, 2014. In immunocompromised patients the frequency of developing antiviral resistance against oseltamivir due to the H275Y mutation in connection to treatment can reach 13% which is a substantially higher frequency compared with overall reporting of resistant H1N1pdm09 viruses which in the 2014/15 season was 0.4%. 2017 Euro surveillance Discussion IV H275Y 110 115 28128091 Development of oseltamivir and zanamivir resistance in influenza A(H1N1)pdm09 virus, Denmark, 2014. In this study we observed that the I223I/R mutation was selected after the introduction of zanamivir treatment, whereas the H275Y mutation was induced rapidly after initiation of oseltamivir treatment. 2017 Euro surveillance Discussion IV I223I;I223R;H275Y 35;35;124 42;42;129 28128091 Development of oseltamivir and zanamivir resistance in influenza A(H1N1)pdm09 virus, Denmark, 2014. It could perhaps be an evolvement toward better fitness in the presence of the H275Y and I223R mutations under the selection of the antiviral drugs. 2017 Euro surveillance Discussion IV H275Y;I223R 79;89 84;94 28128091 Development of oseltamivir and zanamivir resistance in influenza A(H1N1)pdm09 virus, Denmark, 2014. it was reported that H1N1pdm09 harbouring dual substitution at positions H275Y/G147R had a highly reduced inhibition by oseltamivir and peramivir, whereas, inhibition was within the normal range with zanamivir. 2017 Euro surveillance Discussion IV G147R;H275Y 79;73 84;78 28128091 Development of oseltamivir and zanamivir resistance in influenza A(H1N1)pdm09 virus, Denmark, 2014. The samples were obtained from a nasopharyngeal swab and a BAL, respectively, and the resistance mutation profiles differed, with the BAL sample having a higher frequency of the antiviral resistance mutations E119G, I223R and H275Y, whereas the nasopharyngeal sample, had a low frequency of additional mutations not found in the BAL sample. 2017 Euro surveillance Discussion IV E119G;I223R;H275Y 209;216;226 214;221;231 28128091 Development of oseltamivir and zanamivir resistance in influenza A(H1N1)pdm09 virus, Denmark, 2014. This coheres with the fact that only one mutation (H275Y) is needed to induce resistance against oseltamivir in H1N1pdm09 virus. 2017 Euro surveillance Discussion IV H275Y 51 56 28132927 Antigenic and genetic characterization of influenza viruses circulating in Bulgaria during the 2015/2016 season. D222G substitution was shown to cause a shift from alpha2,6-sialic acid receptor specificity to mixed alpha2,3/alpha2,6-sialic acid receptor specificity, adduced thereby to facilitate lung infection. 2017 Infection, genetics and evolution Discussion IV D222G 0 5 28132927 Antigenic and genetic characterization of influenza viruses circulating in Bulgaria during the 2015/2016 season. Four of these substitutions were present in all viruses analyzed, while A141T substitution was observed in 28% of the viruses. 2017 Infection, genetics and evolution Discussion IV A141T 72 77 28132927 Antigenic and genetic characterization of influenza viruses circulating in Bulgaria during the 2015/2016 season. Globally, oseltamivir resistance of A(H1N1)pdm09 viruses due to NA H275Y substitution has been low (~ 1% of viruses tested) and resistance of A(H3N2) and B viruses is extremely rare. 2017 Infection, genetics and evolution Discussion IV H275Y 67 72 64 66 28132927 Antigenic and genetic characterization of influenza viruses circulating in Bulgaria during the 2015/2016 season. However, substitutions in NP may affect a host's cytotoxic immune response because this protein contains many T-cell epitopes and it has been reported that the global frequency of substitutions D2E and E125D in NS1, M105 T in NP and Q208K in M1 observed in our study has increased drastically over the last two years. 2017 Infection, genetics and evolution Discussion IV D2E;E125D;Q208K;M105T 194;202;233;216 197;207;238;222 M1;NP;NP;NS1 242;26;226;211 244;28;228;214 28132927 Antigenic and genetic characterization of influenza viruses circulating in Bulgaria during the 2015/2016 season. In our previous study, we detected a single A(H1N1)pdm09 virus carrying NA H275Y substitution in a child treated with oseltamivir. 2017 Infection, genetics and evolution Discussion IV H275Y 75 80 72 74 28132927 Antigenic and genetic characterization of influenza viruses circulating in Bulgaria during the 2015/2016 season. Most HA substitutions were present in Bulgarian 3C.2a isolates from the previous season, with the exception of HA1 N171K and S312R, and HA2 I77V and G155E, substitutions found in viruses from the 2015/2016 season. 2017 Infection, genetics and evolution Discussion IV N171K;S312R;I77V;G155E 115;125;140;149 120;130;144;154 HA;HA;HA1 5;136;111 7;138;114 28132927 Antigenic and genetic characterization of influenza viruses circulating in Bulgaria during the 2015/2016 season. None of the studied viruses carried HA1 D222G/N/S or Q293H substitutions, reported to be found more frequently in patients with severe disease or fatal outcome earlier in the pandemic period. 2017 Infection, genetics and evolution Discussion IV D222G;D222N;D222S;Q293H 40;40;40;53 49;49;49;58 HA1 36 39 28132927 Antigenic and genetic characterization of influenza viruses circulating in Bulgaria during the 2015/2016 season. Substitution S185T was located in the RBS/190-helix (Sriwilaijaroen et al., 2012). 2017 Infection, genetics and evolution Discussion IV S185T 13 18 28166830 The T160A hemagglutinin substitution affects not only receptor binding property but also transmissibility of H5N1 clade 2.3.4 avian influenza virus in guinea pigs. Here, we verified that the T160A mutation enabled H5N1 clade 2.3.4 virus to not only acquire binding affinity for human-type glycans but also transmit among guinea pigs. 2017 Veterinary research Discussion IV T160A 27 32 28166830 The T160A hemagglutinin substitution affects not only receptor binding property but also transmissibility of H5N1 clade 2.3.4 avian influenza virus in guinea pigs. It was demonstrated that the additive glycosylation at 158N due to an A160T mutation on a clade 2.2 virus, abolished the viral ability to bind to the alpha-2,6 SA and transmission in guinea pigs. 2017 Veterinary research Discussion IV A160T 70 75 28166830 The T160A hemagglutinin substitution affects not only receptor binding property but also transmissibility of H5N1 clade 2.3.4 avian influenza virus in guinea pigs. Moreover, reassortant H5N1 viruses of clade 1 and 2.1.3 HA with N158D-induced deglycosylation were capable of airborne transmission in a ferret model. 2017 Veterinary research Discussion IV N158D 64 69 HA 56 58 28166830 The T160A hemagglutinin substitution affects not only receptor binding property but also transmissibility of H5N1 clade 2.3.4 avian influenza virus in guinea pigs. The results show that the single T160A substitution, which simultaneously led to the loss of glycosylation site at position 158N in HA dramatically enhanced the viral specificity for human-type receptors, and the HA mutant could spread efficiently in guinea pigs. 2017 Veterinary research Discussion IV T160A 33 38 HA;HA 132;213 134;215 28251891 Mid-season real-time estimates of seasonal influenza vaccine effectiveness in persons 65 years and older in register-based surveillance, Stockholm County, Sweden, and Finland, January 2017. Both the T131K and the R142K substitution are located in the antigenic epitope A and T131 is conserved in 45% of all human H1, H2 and H3 viruses. 2017 Euro surveillance Discussion IV T131K;R142K 9;23 14;28 28251891 Mid-season real-time estimates of seasonal influenza vaccine effectiveness in persons 65 years and older in register-based surveillance, Stockholm County, Sweden, and Finland, January 2017. In total 12/63 (19%) of the viruses in subclade 3C.2a were samples from vaccinated persons and nine of these had the additional amino acid substitutions T131K, R142K and R261Q. 2017 Euro surveillance Discussion IV T131K;R142K;R261Q 153;160;170 158;165;175 28251891 Mid-season real-time estimates of seasonal influenza vaccine effectiveness in persons 65 years and older in register-based surveillance, Stockholm County, Sweden, and Finland, January 2017. In total 29% of the characterised samples in Canada had T135K or T131K, while in our study, one of these two alterations was detected in 54% of all samples, and in 68% of the samples collected from vaccinated patients. 2017 Euro surveillance Discussion IV T135K;T131K 56;65 61;70 28251891 Mid-season real-time estimates of seasonal influenza vaccine effectiveness in persons 65 years and older in register-based surveillance, Stockholm County, Sweden, and Finland, January 2017. Only 19% of the 3C.2a1 samples had the T135K mutation and 74% of the 3C.2a samples had the T131K mutation. 2017 Euro surveillance Discussion IV T135K;T131K 39;91 44;96 28251891 Mid-season real-time estimates of seasonal influenza vaccine effectiveness in persons 65 years and older in register-based surveillance, Stockholm County, Sweden, and Finland, January 2017. The majority, 25/37 (68%), of the genetically characterised samples from vaccinated patients belonged to subclade 3C.2a1 and 16 of those had the additional amino acid substitution T135K. 2017 Euro surveillance Discussion IV T135K 180 185 28252002 NEDDylation of PB2 Reduces Its Stability and Blocks the Replication of Influenza A Virus. According to the structure of PB2 and other viral polymerase subunits, the PB2 K699R mutation would not affect the tertiary structure of PB2 or the trimeric viral polymerase. 2017 Scientific reports Discussion IV K699R 79 84 PB2;PB2;PB2 30;75;137 33;78;140 28252002 NEDDylation of PB2 Reduces Its Stability and Blocks the Replication of Influenza A Virus. In addition, the viral titers in the lungs of mice infected with WSN-PB2 K699R were higher than animals in the WSN group. 2017 Scientific reports Discussion IV K699R 73 78 PB2 69 72 28252002 NEDDylation of PB2 Reduces Its Stability and Blocks the Replication of Influenza A Virus. We compared WSN and WSN-PB2 K699R growth kinetics in cell culture, in addition to virulence in a mouse model. 2017 Scientific reports Discussion IV K699R 28 33 PB2 24 27 28252002 NEDDylation of PB2 Reduces Its Stability and Blocks the Replication of Influenza A Virus. We observed that WSN-PB2 K699R replicated better than WSN in MDCK cells, and consistently WSN-PB2 K699R causes more severe pulmonary damage and results in higher lethality rates. 2017 Scientific reports Discussion IV K699R;K699R 25;98 30;103 PB2;PB2 21;94 24;97 Lung lesions 123 139 28252002 NEDDylation of PB2 Reduces Its Stability and Blocks the Replication of Influenza A Virus. We postulate that the virus with PB2 K699R mutation may proliferate better in cultured cells due to avoiding been NEDDylated, but on the other hand it may not adapt to host as well as the strain with PB2 K699 which may limit it to spread out. 2017 Scientific reports Discussion IV K699R 37 42 PB2;PB2 33;200 36;203 28282440 H1N1 influenza viruses varying widely in hemagglutinin stability transmit efficiently from swine to swine and to ferrets. Cohousing of animals allows contact transmission, which was previously shown to be more permissive than airborne transmission between ferrets for the destabilized Y17H mutant. 2017 PLoS pathogens Discussion IV Y17H 163 167 28282440 H1N1 influenza viruses varying widely in hemagglutinin stability transmit efficiently from swine to swine and to ferrets. Comparing the two experiments, swine in the Y17H group were able to transmit with 100% efficiency to ferrets by the airborne route, whereas ferret donors promoted less efficient airborne transmission to ferrets (25%). 2017 PLoS pathogens Discussion IV Y17H 44 48 28323816 An NS-segment exonic splicing enhancer regulates influenza A virus replication in mammalian cells. Current NS-540A genotype H9N2 and H7N9 viruses replicate better in mammalian cells than mutant versions with a back mutation to A540G, but retain their ability to replicate in avian cells. 2017 Nature communications Discussion IV A540G 128 133 NS 8 10 28323816 An NS-segment exonic splicing enhancer regulates influenza A virus replication in mammalian cells. G540A enhances virus replication in mammalian cells, while retaining replication ability in avian cells. 2017 Nature communications Discussion IV G540A 0 5 28323816 An NS-segment exonic splicing enhancer regulates influenza A virus replication in mammalian cells. Human infections with H5N6 virus occurred in China since 2014, with 11/16 (69%) of isolates characterized from human cases contain NS-G540A. 2017 Nature communications Discussion IV G540A 134 139 NS 131 133 28323816 An NS-segment exonic splicing enhancer regulates influenza A virus replication in mammalian cells. It is notable that human infections with H10N8 confirmed in China were caused only by H10N8 viruses, which contain NS-G540A; no human cases involving H10N8 virus without this mutation were found. 2017 Nature communications Discussion IV G540A 118 123 NS 115 117 28323816 An NS-segment exonic splicing enhancer regulates influenza A virus replication in mammalian cells. It is possible that mutations in other gene segments may also have contributed to the emergence and predominance of the NS-G540A H9N2 virus, which provided the internal genes for the H7N9 virus, and it is suggested that antigenic variations may also have facilitated the emergence of an H9N2 variant in China. 2017 Nature communications Discussion IV G540A 123 128 NS 120 122 28323816 An NS-segment exonic splicing enhancer regulates influenza A virus replication in mammalian cells. Notably, a unique G540A substitution within this ESE was found in H7N9 and also in the H9N2 virus, which provided internal genes to the H7N9 virus. 2017 Nature communications Discussion IV G540A 18 23 28402848 The 150-Loop Restricts the Host Specificity of Human H10N8 Influenza Virus. Comparison of the structures of H10 wt and the H10LS-K158aA-D193T mutant with avian analogs indicates a change in the Sia-Gal bond rotation that creates a favorable interactions with Leu226 and eliminates steric clashes with the polar oxygen of the Sia-Gal bond, as in ferret-transmissible H5 HA and human H7N9 HA with Leu226 (Figure S2). 2017 Cell reports Discussion IV D193T 60 65 HA;HA 293;311 295;313 28402848 The 150-Loop Restricts the Host Specificity of Human H10N8 Influenza Virus. Similarly, mutating H7 Asp158a to Ala along with G228S enhanced binding of H7N9 HA to human receptors, but with no loss of binding to avian receptors. 2017 Cell reports Discussion IV G228S 49 54 HA 80 82 28402848 The 150-Loop Restricts the Host Specificity of Human H10N8 Influenza Virus. The acquisition of human-type receptor specificity by the H10LS-K158aA-D193T mutant is seen in all assays utilized including the glycan array, ELISA, and tissue binding. 2017 Cell reports Discussion IV D193T 71 76 28402848 The 150-Loop Restricts the Host Specificity of Human H10N8 Influenza Virus. with no receptor analogs bound) reveals no significant difference in this distance, but the upper part of the RBS becomes more accessible for binding of human receptors in the K158aA and D193T mutants (Figure S2A). 2017 Cell reports Discussion IV D193T 187 192 28410396 Evolution of the neuraminidase gene of seasonal influenza A and B viruses in Thailand between 2010 and 2015. As noted in a previous study, the H275Y seasonal A(H1N1) strains with reduced viral fitness had permissive substitutions at V234M (100%), R222Q (90%), K329E (100%), and D344N (100%), and compensatory mutation D354G (95%), which maintained the functionality of the NA protein. 2017 PloS one Discussion IV H275Y;V234M;R222Q;K329E;D344N;D354G 34;124;138;151;169;209 39;129;143;156;174;214 264 266 28410396 Evolution of the neuraminidase gene of seasonal influenza A and B viruses in Thailand between 2010 and 2015. Based on the DeltaDeltaCt method calculation using real-time RT-PCR, a mix of the wild-type susceptible strain (275H) and resistant strain (275Y) was detected in all the H275Y-positive samples and the relative quantities of RNA of the latter virus were higher than those of the former virus. 2017 PloS one Discussion IV H275Y 170 175 28410396 Evolution of the neuraminidase gene of seasonal influenza A and B viruses in Thailand between 2010 and 2015. Drug resistance characterized by E119V or R292K mutation (according to N2 numbering) was not observed in the present study. 2017 PloS one Discussion IV E119V;R292K 33;42 38;47 28410396 Evolution of the neuraminidase gene of seasonal influenza A and B viruses in Thailand between 2010 and 2015. Furthermore, the majority of individuals infected with the H275Y variants were in "at risk" groups. 2017 PloS one Discussion IV H275Y 59 64 28410396 Evolution of the neuraminidase gene of seasonal influenza A and B viruses in Thailand between 2010 and 2015. However, the catalytic site mutation (D151N/G) and framework mutation (I222T/V) of the NA protein were found. 2017 PloS one Discussion IV D151G;D151N;I222T;I222V 38;38;71;71 45;45;78;78 87 89 28410396 Evolution of the neuraminidase gene of seasonal influenza A and B viruses in Thailand between 2010 and 2015. In addition, we found V106I and N248D mutations in the NA protein, which are located at the subunit interfaces and the primary calcium ion binding site that is associated with the stability of A(H1N1)pdm09 virus at a low pH. 2017 PloS one Discussion IV V106I;N248D 22;32 27;37 55 57 28410396 Evolution of the neuraminidase gene of seasonal influenza A and B viruses in Thailand between 2010 and 2015. In influenza B virus, the A395E substitution located outside the active site of NA is associated with reduced susceptibility to oseltamivir and peramivir. 2017 PloS one Discussion IV A395E 26 31 80 82 28410396 Evolution of the neuraminidase gene of seasonal influenza A and B viruses in Thailand between 2010 and 2015. In present study, the antiviral susceptibility of the viruses with D151N/G, I222T/V, and A395E/V/T/D/S NA substitutions cannot be concluded by genotypic methods. 2017 PloS one Discussion IV A395V;A395T;A395D;A395S;D151N;D151G;I222T;I222V;A395E 89;89;89;89;67;67;76;76;89 102;102;102;102;74;74;83;83;102 103 105 28410396 Evolution of the neuraminidase gene of seasonal influenza A and B viruses in Thailand between 2010 and 2015. In Thailand, the prevalence of this S247N mutation in A(H1N1)pdm09 was lower (1.35%) than in Australia and Singapore, which might be due to sampling size bias. 2017 PloS one Discussion IV S247N 36 41 28410396 Evolution of the neuraminidase gene of seasonal influenza A and B viruses in Thailand between 2010 and 2015. In the NA gene of the A(H1N1)pdm09 circulated in Thailand, the H275Y strains had permissive mutations (define as mutations that allowed the virus to tolerate subsequent occurrences of H275Y) at residues V241I (63%) and N369K (68%). 2017 PloS one Discussion IV H275Y;H275Y;V241I;N369K 63;184;203;219 68;189;208;224 7 9 28410396 Evolution of the neuraminidase gene of seasonal influenza A and B viruses in Thailand between 2010 and 2015. In the present study, the proportion of H275Y strains during the period from 2007 to 2009 was 54.05% (20/37); which is consistent with findings from other studies. 2017 PloS one Discussion IV H275Y 40 45 28410396 Evolution of the neuraminidase gene of seasonal influenza A and B viruses in Thailand between 2010 and 2015. Interestingly, we found a high frequency of NA mutations A395V/T/D/S in the influenza B viruses circulating in Thailand. 2017 PloS one Discussion IV A395V;A395T;A395D;A395S 57;57;57;57 68;68;68;68 44 46 28410396 Evolution of the neuraminidase gene of seasonal influenza A and B viruses in Thailand between 2010 and 2015. Published surveillance data have demonstrated that the prevalence of oseltamivir resistance characterized by the mutation at residue H275Y in NA gene of A(H1N1)pdm09 viruses is still low (<3%). 2017 PloS one Discussion IV H275Y 133 138 142 144 28410396 Evolution of the neuraminidase gene of seasonal influenza A and B viruses in Thailand between 2010 and 2015. The H275Y mutation can confer cross-resistance to peramivir, but susceptibility to zanamivir and laninamivir is not significantly affected. 2017 PloS one Discussion IV H275Y 4 9 28410396 Evolution of the neuraminidase gene of seasonal influenza A and B viruses in Thailand between 2010 and 2015. The NA protein of influenza B virus in Thailand between 1990 and 2015 showed D197N mutation, which is associated with reduced susceptibility to oseltamivir and zanamivir. 2017 PloS one Discussion IV D197N 77 82 4 6 28421062 Identification of Rare PB2-D701N Mutation from a Patient with Severe Influenza: Contribution of the PB2-D701N Mutation to the Pathogenicity of Human Influenza. Although the importance of the HA-K403R change also present in this virus has not been previously characterized for pathogenesis of human influenza strains, this mutation was identified in a human influenza A H1N1 virus of swine origin (A/Saskatchewan/5351/2009), which produced mild symptoms in the infected patient. 2017 Frontiers in microbiology Discussion IV K403R 34 39 HA 31 33 28421062 Identification of Rare PB2-D701N Mutation from a Patient with Severe Influenza: Contribution of the PB2-D701N Mutation to the Pathogenicity of Human Influenza. As indicated above the PB2-D701N change produces increased polymerase activity in mini-replicon assays in the context of A(H1N1)pdm09 polymerase. 2017 Frontiers in microbiology Discussion IV D701N 27 32 PB2 23 26 28421062 Identification of Rare PB2-D701N Mutation from a Patient with Severe Influenza: Contribution of the PB2-D701N Mutation to the Pathogenicity of Human Influenza. However, PB2-D701N mutation is very scarcely found suggesting that it does not circulate in humans, but that it may be generated in some infected patients, probably as the result of particular virus-host interactions that allow the growth and establishment of the virus carrying this mutation. 2017 Frontiers in microbiology Discussion IV D701N 13 18 PB2 9 12 28421062 Identification of Rare PB2-D701N Mutation from a Patient with Severe Influenza: Contribution of the PB2-D701N Mutation to the Pathogenicity of Human Influenza. These data suggest that the previously described PB2-D701N change may be the main virulence determinant of this viral isolate. 2017 Frontiers in microbiology Discussion IV D701N 53 58 PB2 49 52 28465552 A reassortant H9N2 influenza virus containing 2009 pandemic H1N1 internal-protein genes acquired enhanced pig-to-pig transmission after serial passages in swine. Although specific receptor-binding tests would be necessary to elucidate the exact role of the HA-D225G mutation within the HA-RBS, our data suggest that it may be a marker for adaptation of H9N2 viruses to swine. 2017 Scientific reports Discussion IV D225G 98 103 HA;HA 95;124 97;126 28465552 A reassortant H9N2 influenza virus containing 2009 pandemic H1N1 internal-protein genes acquired enhanced pig-to-pig transmission after serial passages in swine. For example, the presence of the NP-N319K substitution was described as an important factor for the replication of H7N7 viruses in mice. 2017 Scientific reports Discussion IV N319K 36 41 NP 33 35 28465552 A reassortant H9N2 influenza virus containing 2009 pandemic H1N1 internal-protein genes acquired enhanced pig-to-pig transmission after serial passages in swine. Regarding the mutations detected during the analysis, only one of the mutations that appeared in the virus after seven passages and was maintained even after transmission, the HA-D225G substitution in the RBS. 2017 Scientific reports Discussion IV D225G 179 184 HA 176 178 28465552 A reassortant H9N2 influenza virus containing 2009 pandemic H1N1 internal-protein genes acquired enhanced pig-to-pig transmission after serial passages in swine. The presence of the HA-D225G mutation after seven passages may therefore explain the consistent replication in the lungs during passage eight. 2017 Scientific reports Discussion IV D225G 23 28 HA 20 22 28498306 A Conserved Residue, Tyrosine (Y) 84, in H5N1 Influenza A Virus NS1 Regulates IFN Signaling Responses to Enhance Viral Infection. Additionally, cells expressing the Y84F mutant NS1 revert to normal IFNAR1 cell surface expression. 2017 Viruses Discussion IV Y84F 35 39 NS1 47 50 28498306 A Conserved Residue, Tyrosine (Y) 84, in H5N1 Influenza A Virus NS1 Regulates IFN Signaling Responses to Enhance Viral Infection. In line with previous IAV replication studies performed in STAT1+/+ and STAT1-/- MEFs, both rWSN-GH-NS1-wt and rWSN-GH-NS1-Y84F replicated poorly in STAT1+/+ MEFs in comparison to STAT1-/- MEFs, thereby further highlighting a potential role for residue Y84 of NS1 in regulating the type I IFN response, and the importance of the host IFN response for limiting viral replication. 2017 Viruses Discussion IV Y84F 123 127 NS1;NS1;NS1 100;119;260 103;122;263 28498306 A Conserved Residue, Tyrosine (Y) 84, in H5N1 Influenza A Virus NS1 Regulates IFN Signaling Responses to Enhance Viral Infection. Specifically, we provide evidence that, in contrast to cells expressing the intact NS1, cells expressing NS1 with a single Y84F mutation in this conserved putative SH2-binding domain are able to respond fully to IFN treatment in terms of STAT phosphorylation. 2017 Viruses Discussion IV Y84F 123 127 NS1;NS1 83;105 86;108 28498306 A Conserved Residue, Tyrosine (Y) 84, in H5N1 Influenza A Virus NS1 Regulates IFN Signaling Responses to Enhance Viral Infection. These in vitro data provided the basis for generating recombinant H1N1 viruses (A/WSN/33 [H1N1]) encoding either the intact (rWSN-GH-NS1-wt) or Y84F mutant H5N1 NS1 (rWSN-GH-NS1-Y84F). 2017 Viruses Discussion IV Y84F;Y84F 144;178 148;182 NS1;NS1;NS1 133;161;174 136;164;177 28498306 A Conserved Residue, Tyrosine (Y) 84, in H5N1 Influenza A Virus NS1 Regulates IFN Signaling Responses to Enhance Viral Infection. This was reflected in the modest reduction in lung viral titers in IFN-beta-treated mice infected with virus encoding the Y84F mutant NS1, which was not observed in mice infected with virus expressing an intact NS1. 2017 Viruses Discussion IV Y84F 122 126 NS1;NS1 134;211 137;214 28659482 Complete Genome Sequencing of Influenza A Viruses within Swine Farrow-to-Wean Farms Reveals the Emergence, Persistence, and Subsidence of Diverse Viral Genotypes. Seventy-nine percent of the IAVs isolated in our study contained a signature mutation (S31N) in the matrix gene (segment 7) that might confer resistance to amantadine. 2017 Journal of virology Discussion IV S31N 87 91 M 100 106 28659482 Complete Genome Sequencing of Influenza A Viruses within Swine Farrow-to-Wean Farms Reveals the Emergence, Persistence, and Subsidence of Diverse Viral Genotypes. Whether the high frequency of S31N in the matrix gene among swine IAVs is due to random events, as indicated by Baranovich et al., or to reassortment events, as indicated by Krumbholz et al., is not clear and must be further investigated. 2017 Journal of virology Discussion IV S31N 30 34 M 42 48 28744280 Amino Acid Substitution K470R in the Nucleoprotein Increases the Virulence of H5N1 Influenza A Virus in Mammals. Importantly, the K470R mutant enhanced viral replication and pathogenicity in mammals. 2017 Frontiers in microbiology Discussion IV K470R 17 22 28744280 Amino Acid Substitution K470R in the Nucleoprotein Increases the Virulence of H5N1 Influenza A Virus in Mammals. In the current study, the RNP activity of K227R and K229R was higher compared with WT, but the mutants did not show increased the virus replication or virulence in mammals. 2017 Frontiers in microbiology Discussion IV K227R;K229R 42;52 47;57 RNP 26 29 28744280 Amino Acid Substitution K470R in the Nucleoprotein Increases the Virulence of H5N1 Influenza A Virus in Mammals. In this study, we revealed that K470R substitution in H5N1 facilitated viral replication and pathogenicity in vitro and in vivo. 2017 Frontiers in microbiology Discussion IV K470R 32 37 28744280 Amino Acid Substitution K470R in the Nucleoprotein Increases the Virulence of H5N1 Influenza A Virus in Mammals. Of these, K91R and K198R disrupted the NP cellular location and decreased the polymerase activity. 2017 Frontiers in microbiology Discussion IV K91R;K198R 10;19 14;24 NP 39 41 28744280 Amino Acid Substitution K470R in the Nucleoprotein Increases the Virulence of H5N1 Influenza A Virus in Mammals. The K198R mutation, located in the second NLS, affected the NP nuclear location; polymerase activity was lower, and the recombinant virus K198R was not viable. 2017 Frontiers in microbiology Discussion IV K198R;K198R 4;138 9;143 NP 60 62 28744280 Amino Acid Substitution K470R in the Nucleoprotein Increases the Virulence of H5N1 Influenza A Virus in Mammals. The roles of NP-K470R in influenza H1N1 2009 in viral life cycle, pathogenicity and mammal transmissibility will be examined in our further work. 2017 Frontiers in microbiology Discussion IV K470R 16 21 NP 13 15 28744280 Amino Acid Substitution K470R in the Nucleoprotein Increases the Virulence of H5N1 Influenza A Virus in Mammals. Therefore, K470R enhanced the polymerase activity in minireplicon assays, and the vRNA, cRNA, and mRNA levels were higher than those of WT. 2017 Frontiers in microbiology Discussion IV K470R 11 16 28744280 Amino Acid Substitution K470R in the Nucleoprotein Increases the Virulence of H5N1 Influenza A Virus in Mammals. Using Gal4-based yeast two-hybrid(Y2H) assay, phosphoribo-sylaminoimidazole succinocarboxamide synthetase (PAICS) was shown to interact with NP. 2017 Frontiers in microbiology Discussion IV Y2H 34 37 NP 141 143 28744280 Amino Acid Substitution K470R in the Nucleoprotein Increases the Virulence of H5N1 Influenza A Virus in Mammals. Viruses with single point mutations at K91R could not be rescued, indicating that the residue is essential for the survival of the virus, probably because of its important roles in PB2 binding. 2017 Frontiers in microbiology Discussion IV K91R 39 43 PB2 181 184 28754164 Data-driven interdisciplinary mathematical modelling quantitatively unveils competition dynamics of co-circulating influenza strains. Although there were compelling evidences that the clinical effects of A/H1N1 H275Y variants, which circulated globally during the 2007-2009 influenza seasons, were consistent with normal seasonal activity, the transmission efficiency of the variants, nevertheless, was not well studied but in one animal study. 2017 Journal of translational medicine Discussion IV H275Y 77 82 28754164 Data-driven interdisciplinary mathematical modelling quantitatively unveils competition dynamics of co-circulating influenza strains. However, given that oseltamivir was rarely prescribed before May 2009 in Taiwan, in the absence of selection pressure from the antiviral, the replacement of clade 2C-2 with clade 2B-2 could not be well explained by the combination effect of H275Y mutation with permissive mutation. 2017 Journal of translational medicine Discussion IV H275Y 241 246 28754164 Data-driven interdisciplinary mathematical modelling quantitatively unveils competition dynamics of co-circulating influenza strains. In our study, the model not only reported that clade 2B-2, carrying H275Y mutation in the neuraminidase, transmitted as efficiently as clade 2C-2 but also revealed that the transmission efficiency of clade 2B-2 could not sufficiently explain the vicissitudes of the two co-circulating clades. 2017 Journal of translational medicine Discussion IV H275Y 68 73 90 103 28754164 Data-driven interdisciplinary mathematical modelling quantitatively unveils competition dynamics of co-circulating influenza strains. Secondly, according to Hurt and Bloom et al., H275Y mutation was typically associated with poor replication and transmission, and permissive mutation could enable oseltamivir-resistant A/H1N1 variants to restore viral fitness. 2017 Journal of translational medicine Discussion IV H275Y 46 51 28790432 Conformational modulation of influenza virus hemagglutinin: characterization and in vivo efficacy of monomeric form. Among six mutants, R106E was designed to reduce intermonomer interactions by electrostatic repulsion, where negatively charged amino acids, Glu103, Glu105 and Asp109, are positioned very close at the stem region. 2017 Scientific reports Discussion IV R106E 19 24 28790432 Conformational modulation of influenza virus hemagglutinin: characterization and in vivo efficacy of monomeric form. In contrast, two mutants, F88E and V91W, were identified as a monomer in solution upon cleavage of the foldon, by disrupting intermonomer interactions of HA. 2017 Scientific reports Discussion IV F88E;V91W 26;35 30;39 HA 154 156 28790432 Conformational modulation of influenza virus hemagglutinin: characterization and in vivo efficacy of monomeric form. The double mutant also seems to have a lower stability in thermal denaturation experiments than the KR01 HA, possibly due to the introduction of two additional mutations (F88E and V91W) at the intermonomer interface. 2017 Scientific reports Discussion IV F88E;V91W 171;180 175;184 HA 105 107 28790432 Conformational modulation of influenza virus hemagglutinin: characterization and in vivo efficacy of monomeric form. The F88E/V91W double mutant also behaved as a monomer, which appeared to be more homogeneous than the single mutants. 2017 Scientific reports Discussion IV V91W;F88E 9;4 13;8 28790432 Conformational modulation of influenza virus hemagglutinin: characterization and in vivo efficacy of monomeric form. The S199F, G47E and R75L mutants also did not affect the monomer-trimer equilibrium. 2017 Scientific reports Discussion IV S199F;G47E;R75L 4;11;20 9;15;24 28814518 A Single-Amino-Acid Substitution at Position 225 in Hemagglutinin Alters the Transmissibility of Eurasian Avian-Like H1N1 Swine Influenza Virus in Guinea Pigs. HA-N224K/Q226L switched the receptor-binding specificity from avian to human type but simultaneously reduced HA heat stability, which was restored by the HA-T318I mutation. 2017 Journal of virology Discussion IV N224K;Q226L;T318I 3;9;157 8;14;162 HA;HA;HA 0;109;154 2;111;156 28814518 A Single-Amino-Acid Substitution at Position 225 in Hemagglutinin Alters the Transmissibility of Eurasian Avian-Like H1N1 Swine Influenza Virus in Guinea Pigs. Here, we found that the G225E mutation in HA increases the transmission of EAH1N1 viruses in guinea pigs by reducing virus affinity for the avian-type receptor and influencing the efficiency of virus assembly and budding. 2017 Journal of virology Discussion IV G225E 24 29 HA 42 44 28814518 A Single-Amino-Acid Substitution at Position 225 in Hemagglutinin Alters the Transmissibility of Eurasian Avian-Like H1N1 Swine Influenza Virus in Guinea Pigs. In the present study, we explored the genetic basis for the difference in transmissibility in guinea pigs of two EAH1N1 swine influenza viruses, GX/18 and HLJ/27, and found that the single-amino-acid mutation E225G in HA1 abolishes the transmissibility of GX/18 and that the mutation G225E in HA makes HLJ/27 highly transmissible in guinea pigs. 2017 Journal of virology Discussion IV E225G;G225E 209;284 214;289 HA;HA1 293;218 295;221 28814518 A Single-Amino-Acid Substitution at Position 225 in Hemagglutinin Alters the Transmissibility of Eurasian Avian-Like H1N1 Swine Influenza Virus in Guinea Pigs. It remains to be seen whether there are other viral factors in the GX/18 virus background that promote the acquisition of the D24N mutation in the HA1 of HLJ/27. 2017 Journal of virology Discussion IV D24N 126 130 HA1 147 150 28814518 A Single-Amino-Acid Substitution at Position 225 in Hemagglutinin Alters the Transmissibility of Eurasian Avian-Like H1N1 Swine Influenza Virus in Guinea Pigs. The rGX/18-HLJHA virus transmitted to one guinea pig, and the D24N mutation in HA1 occurred in the viruses that were recovered from the exposed animals in both experiments. 2017 Journal of virology Discussion IV D24N 62 66 HA1 79 82 28814518 A Single-Amino-Acid Substitution at Position 225 in Hemagglutinin Alters the Transmissibility of Eurasian Avian-Like H1N1 Swine Influenza Virus in Guinea Pigs. They found that a reassortant virus containing seven genes from pH1N1/09 and the HA gene from an H5N1 virus could transmit between ferrets by acquiring HA-N224K/Q226L/T318I mutations. 2017 Journal of virology Discussion IV N224K;Q226L;T318I 155;161;167 160;166;172 HA;HA 81;152 83;154 28814518 A Single-Amino-Acid Substitution at Position 225 in Hemagglutinin Alters the Transmissibility of Eurasian Avian-Like H1N1 Swine Influenza Virus in Guinea Pigs. Two amino acid mutations, D190E and D225G, abolished the ability of the 1918/H1N1 virus to transmit via respiratory droplet between ferrets. 2017 Journal of virology Discussion IV D190E;D225G 26;36 31;41 28814737 Susceptibility of influenza A(H1N1)/pdm2009, seasonal A(H3N2) and B viruses to Oseltamivir in Guangdong, China between 2009 and 2014. A novel A(H1N1)pdm09 variant containing NA-S247N mutation was found mainly in the Asia-Pacific area in recent years. 2017 Scientific reports Discussion IV S247N 43 48 40 42 28814737 Susceptibility of influenza A(H1N1)/pdm2009, seasonal A(H3N2) and B viruses to Oseltamivir in Guangdong, China between 2009 and 2014. Although A(H1N1)pdm09 viruses with the mutations NA-V241I, N369K, N386K and K432E are not clinically defined as oseltamivir-resistant strains according to the definition of the WHO, its greater reduction in susceptibility to oseltamivir (2.67-fold increase in IC50) suggested that these substitutions may have contributed for the significantly higher IC50 values obtained, compared to wild-type viruses. 2017 Scientific reports Discussion IV V241I;N369K;N386K;K432E 52;59;66;76 57;64;71;81 49 51 28814737 Susceptibility of influenza A(H1N1)/pdm2009, seasonal A(H3N2) and B viruses to Oseltamivir in Guangdong, China between 2009 and 2014. Anyway, it have been previously reported that A(H1N1)pdm09 mutation viruses possessed N44S, V106I, N200S, I223R/V, V241I, S247N, N369K and N386K substitutions in the NA gene. 2017 Scientific reports Discussion IV N44S;V106I;N200S;I223R;I223V;V241I;S247N;N369K;N386K 86;92;99;106;106;115;122;129;139 90;97;104;113;113;120;127;134;144 166 168 28814737 Susceptibility of influenza A(H1N1)/pdm2009, seasonal A(H3N2) and B viruses to Oseltamivir in Guangdong, China between 2009 and 2014. Apart that, the current study revealed that the NA-V241I/N369K/N386K/K432E mutation in conjunction with the H275Y substitution had emerged in the 2013/2014 resistant variants in Guangdong, China. 2017 Scientific reports Discussion IV V241I;N369K;N386K;K432E;H275Y 51;57;63;69;108 56;62;68;74;113 48 50 28814737 Susceptibility of influenza A(H1N1)/pdm2009, seasonal A(H3N2) and B viruses to Oseltamivir in Guangdong, China between 2009 and 2014. For example, NA-S247N and I223R/V mutations in A(H1N1)pdm09 influenza viruses can confer reduced susceptibility to oseltamivir. 2017 Scientific reports Discussion IV S247N;I223R;I223V 16;26;26 21;33;33 13 15 28814737 Susceptibility of influenza A(H1N1)/pdm2009, seasonal A(H3N2) and B viruses to Oseltamivir in Guangdong, China between 2009 and 2014. Further findings presented that all of eight oseltamivir-resistant strains occurred N44S, N200S, V241I, H275Y and N369K mutations in common, among these, there are three strains possessing NA-I321V, N386K and K432E mutations. 2017 Scientific reports Discussion IV N44S;N200S;V241I;H275Y;N369K;I321V;N386K;K432E 84;90;97;104;114;192;199;209 88;95;102;109;119;197;204;214 189 191 28814737 Susceptibility of influenza A(H1N1)/pdm2009, seasonal A(H3N2) and B viruses to Oseltamivir in Guangdong, China between 2009 and 2014. Furthermore, sensitive strain, like as A/Guangdong/452/2014 strain, also possessed NA-V241I/N369K/N386K/K432E quadruple mutation. 2017 Scientific reports Discussion IV V241I;N369K;N386K;K432E 86;92;98;104 91;97;103;109 83 85 28814737 Susceptibility of influenza A(H1N1)/pdm2009, seasonal A(H3N2) and B viruses to Oseltamivir in Guangdong, China between 2009 and 2014. However, the computational structural analysis showed that some amino acid residues, like as I34V, N44S, I106V, N200S and I321V, are not located in the oseltamivir-binding domain of NA. 2017 Scientific reports Discussion IV I34V;N44S;I106V;N200S;I321V 93;99;105;112;122 97;103;110;117;127 182 184 28814737 Susceptibility of influenza A(H1N1)/pdm2009, seasonal A(H3N2) and B viruses to Oseltamivir in Guangdong, China between 2009 and 2014. If NA-V241I mutation emerged in conjunction with H275Y, they will generate the synergy effect in the highly reduced sensitivity of viruses to oseltamivir. 2017 Scientific reports Discussion IV V241I;H275Y 6;49 11;54 3 5 28814737 Susceptibility of influenza A(H1N1)/pdm2009, seasonal A(H3N2) and B viruses to Oseltamivir in Guangdong, China between 2009 and 2014. In addition, the binding ability of oseltamivir to NA also decreased when mutations V241I and N386K were present. 2017 Scientific reports Discussion IV V241I;N386K 84;94 89;99 51 53 28814737 Susceptibility of influenza A(H1N1)/pdm2009, seasonal A(H3N2) and B viruses to Oseltamivir in Guangdong, China between 2009 and 2014. In addition, the other NA substitutions, like as V241I, N369K and N386K, which were presented in the oseltamivir-resistant strains studied here, may offset the destabilizing effect of the H275Y substitution. 2017 Scientific reports Discussion IV V241I;N369K;N386K;H275Y 49;56;66;188 54;61;71;193 23 25 28814737 Susceptibility of influenza A(H1N1)/pdm2009, seasonal A(H3N2) and B viruses to Oseltamivir in Guangdong, China between 2009 and 2014. In addition, when compared to two wild type strains, like as A/California/04/2009 and A/Mexico/4108/2009, a few 2012/2013/2014 sensitive strains have happened N44S, N200S, V241I, N369K and N386K mutations. 2017 Scientific reports Discussion IV N44S;N200S;V241I;N369K;N386K 159;165;172;179;189 163;170;177;184;194 28814737 Susceptibility of influenza A(H1N1)/pdm2009, seasonal A(H3N2) and B viruses to Oseltamivir in Guangdong, China between 2009 and 2014. In conclusion, the current studies suggest that V241I, N369K, N386K and K432E mutations, alone or in combination with H275Y, may change the binding affinity between oseltamivir and NA, and further have a impact on susceptibility of A(H1N1)pdm09 strains to oseltamivir. 2017 Scientific reports Discussion IV V241I;N369K;N386K;K432E;H275Y 48;55;62;72;118 53;60;67;77;123 181 183 28814737 Susceptibility of influenza A(H1N1)/pdm2009, seasonal A(H3N2) and B viruses to Oseltamivir in Guangdong, China between 2009 and 2014. In this work, we applied computational analysis methods to discuss whether the binding affinity between NA and oseltamivir will happen to change when NA occurred V241I, N369K, N386K and K432E mutations, alone or in combination with H275Y, and further have a impact on susceptibility of A(H1N1)pdm09 strains to oseltamivir. 2017 Scientific reports Discussion IV V241I;N369K;N386K;K432E;H275Y 162;169;176;186;232 167;174;181;191;237 NA;NA 104;150 106;152 28814737 Susceptibility of influenza A(H1N1)/pdm2009, seasonal A(H3N2) and B viruses to Oseltamivir in Guangdong, China between 2009 and 2014. It is well known that H275Y confers very strong resistance. 2017 Scientific reports Discussion IV H275Y 22 27 28814737 Susceptibility of influenza A(H1N1)/pdm2009, seasonal A(H3N2) and B viruses to Oseltamivir in Guangdong, China between 2009 and 2014. Likewise, when compared to the wild-type strains, clinical isolates with NA-I223R mutations had an approximately two-fold reduced affinity for the substrate; the isolates containing H275Y- and I223R- also showed decreased susceptibility to oseltamivir(246-fold). 2017 Scientific reports Discussion IV I223R;H275Y;I223R 76;182;193 81;187;198 73 75 28814737 Susceptibility of influenza A(H1N1)/pdm2009, seasonal A(H3N2) and B viruses to Oseltamivir in Guangdong, China between 2009 and 2014. On balance, the obtained results revealed that V241I, N369K, N386K and K432E mutations may alter the susceptibility of A(H1N1)pdm09 variants to oseltamivir. 2017 Scientific reports Discussion IV V241I;N369K;N386K;K432E 47;54;61;71 52;59;66;76 28814737 Susceptibility of influenza A(H1N1)/pdm2009, seasonal A(H3N2) and B viruses to Oseltamivir in Guangdong, China between 2009 and 2014. Once the H275Y mutation appears, the sensitivity of the A(H1N1)pdm2009 clinical isolates to oseltamivir can decrease by 1466-fold when compared to that of wild-type. 2017 Scientific reports Discussion IV H275Y 9 14 28814737 Susceptibility of influenza A(H1N1)/pdm2009, seasonal A(H3N2) and B viruses to Oseltamivir in Guangdong, China between 2009 and 2014. Particularly, the N369K mutation, which was computationally predicted to cause the largest change in NA protein stability, has previously been shown experimentally to increase NA surface expression and activity in combination with H275Y. 2017 Scientific reports Discussion IV N369K;H275Y 18;231 23;236 NA;NA 101;176 103;178 28814737 Susceptibility of influenza A(H1N1)/pdm2009, seasonal A(H3N2) and B viruses to Oseltamivir in Guangdong, China between 2009 and 2014. So in this work, the analysis primarily focused on mutations within the binding domains, including V241I, N369K, N386K and K432E. 2017 Scientific reports Discussion IV V241I;N369K;N386K;K432E 99;106;113;123 104;111;118;128 28814737 Susceptibility of influenza A(H1N1)/pdm2009, seasonal A(H3N2) and B viruses to Oseltamivir in Guangdong, China between 2009 and 2014. The H275Y mutation that confers resistance to oseltamivir has been detected in various human influenza N1 subtypes, including seasonal H1N1, highly pathogenic H5N1 and, more recently, A(H1N1)pdm2009 viruses. 2017 Scientific reports Discussion IV H275Y 4 9 28814737 Susceptibility of influenza A(H1N1)/pdm2009, seasonal A(H3N2) and B viruses to Oseltamivir in Guangdong, China between 2009 and 2014. The results showed that the binding pocket of NA became narrower upon mutation of N369 and K432 (N369K and K432E), so that the binding angles changed approximately 35.1 degrees, which led to decreased binding of oseltamivir to NA. 2017 Scientific reports Discussion IV N369K;K432E 97;107 102;112 NA;NA 46;227 48;229 28814737 Susceptibility of influenza A(H1N1)/pdm2009, seasonal A(H3N2) and B viruses to Oseltamivir in Guangdong, China between 2009 and 2014. The V241I mutation almost was presented in all resistant and sensitive strains circulating between the 2012-2014. 2017 Scientific reports Discussion IV V241I 4 9 28814737 Susceptibility of influenza A(H1N1)/pdm2009, seasonal A(H3N2) and B viruses to Oseltamivir in Guangdong, China between 2009 and 2014. There have been many studies on the resistance mechanism of NA-H275Y mutation A(H1N1)pdm2009 strains to oseltamivir. 2017 Scientific reports Discussion IV H275Y 63 68 60 62 28814737 Susceptibility of influenza A(H1N1)/pdm2009, seasonal A(H3N2) and B viruses to Oseltamivir in Guangdong, China between 2009 and 2014. This mutation reduces sensitivity and confers extremely high resistance to oseltamivir in combination with the H275Y mutation when compared to resistance conferred by the H275Y mutation alone. 2017 Scientific reports Discussion IV H275Y;H275Y 111;171 116;176 28815216 Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity. Additionally, we found that the mutagen resistance and fidelity phenotype of PB1 V43I is strain dependent. 2017 mSphere Discussion IV V43I 81 85 PB1 77 80 28815216 Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity. Both PB1 T123A and PB1 T123A; PA T97I are able to effectively maintain their titers in drug by limiting the impact of 5FU on genome production. 2017 mSphere Discussion IV T123A;T123A;T97I 9;23;33 14;28;37 PA;PB1;PB1 30;5;19 32;8;22 28815216 Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity. Drug resistance seems to be driven primarily by maintaining high genomic output during 5FU treatment, an effect that appears to be more pronounced than that of the PB1 T123A single mutant. 2017 mSphere Discussion IV T123A 168 173 PB1 164 167 28815216 Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity. Even though PB1 T123A and PA T97I evolved in different passage cultures, we combined them to make a double mutant. 2017 mSphere Discussion IV T123A;T97I 16;29 21;33 PA;PB1 26;12 28;15 28815216 Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity. Importantly, the mutant also maintained its genomic output in the presence of 5FU, a phenotype augmented by PA T97I. 2017 mSphere Discussion IV T97I 111 115 PA 108 110 28815216 Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity. It is currently unclear how PA T97I mediates its resistance to 5FU. 2017 mSphere Discussion IV T97I 31 35 PA 28 30 28815216 Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity. Previously, PB1 D27N was identified as a mutation that limited ribavirin inhibition of RNA synthesis in a replicon system. 2017 mSphere Discussion IV D27N 16 20 PB1 12 15 28815216 Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity. The fact that PB1 T123A did not counter the detrimental effects of ribavirin and 5-azacytidine suggests that the resistance phenotype mediated by PB1 T123A is not broadly applicable to other nucleoside analogs. 2017 mSphere Discussion IV T123A;T123A 18;150 23;155 PB1;PB1 14;146 17;149 28815216 Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity. The PB1 V43I mutant, which has been suggested to be a fidelity variant even in the PR8 background, shows no difference in the rate of transition mutations in PR8. 2017 mSphere Discussion IV V43I 8 12 PB1 4 7 28815216 Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity. The three mutagen-resistant viruses reported here are not high-fidelity variants, and the PB1 T123A variant paradoxically exhibits a higher baseline mutation rate for certain mutational classes. 2017 mSphere Discussion IV T123A 94 99 PB1 90 93 28815216 Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity. These two mutations led to a reduced fitness phenotype characteristic of reciprocal sign epistasis; the combination of a mutant with increased fitness (PB1 T123A) with a neutral mutant (PA T97I) led to a double mutant with very low fitness and significantly reduced genomic RNA output. 2017 mSphere Discussion IV T123A;T97I 156;189 161;193 PA;PB1 186;152 188;155 28815216 Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity. This mutant closely mirrored PB1 T123A in terms of its smaller decreases in infectious titer upon treatment with 5FU. 2017 mSphere Discussion IV T123A 33 38 PB1 29 32 28815216 Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity. This mutant, PA T97I, exhibited fitness and genome production phenotypes that were very similar to those of the wild type. 2017 mSphere Discussion IV T97I 16 20 PA 13 15 28815216 Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity. This phenotype is similar to that of the ribavirin-resistant FMDV mutant 3D M296I and may reflect increased selectivity against misincorporation of 5FU. 2017 mSphere Discussion IV M296I 76 81 28815216 Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity. Unlike PB1 T123A, the baseline and 5FU-induced mutation rates of PA T97I are similar to those of the wild-type virus for all transition mutation classes. 2017 mSphere Discussion IV T123A;T97I 11;68 16;72 PA;PB1 65;7 67;10 28815216 Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity. We also found evidence for epistasis in the previously identified ribavirin resistance mutants PB1 D27N and PB1 V43I, as they remain sensitive to the drug in the PR8 genetic background. 2017 mSphere Discussion IV D27N;V43I 99;112 103;116 PB1;PB1 95;108 98;111 28815216 Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity. We identified maintained genome output as the main mechanism of 5-fluroruracil resistance for PB1 T123A and resistance to drug-mediated RdRp inhibition as the mechanism for the PB1 T123A PA T97I double mutant. 2017 mSphere Discussion IV T123A;T123A;T97I 98;181;190 103;186;194 PA;PB1;PB1 187;94;177 189;97;180 28815216 Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity. We identified PB1 T123A and PA T97I as two 5-fluorouracil resistance mutations that interact epistatically. 2017 mSphere Discussion IV T123A;T97I 18;31 23;35 PA;PB1 28;14 30;17 28815216 Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity. We identified PB1 T123A as a mutation that mediates resistance to 5FU, but not ribavirin or 5-azacytidine. 2017 mSphere Discussion IV T123A 18 23 PB1 14 17 28815216 Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity. While mutagen selection has been used to identify high-fidelity variants in a number of viral systems, the PB1 T123A virus actually has a marginally elevated mutation rate. 2017 mSphere Discussion IV T123A 111 116 PB1 107 110 28837667 Influenza NS1 directly modulates Hedgehog signaling during infection. As IL6 was present at significantly higher levels in animals infected with PR8-A122V compared to PR8-WT, we speculate that the hastened lethality by the mutant virus may be caused, at least partially, by a direct induction of cytokine storms by NS1. 2017 PLoS pathogens Discussion IV A122V 79 84 NS1 245 248 28837667 Influenza NS1 directly modulates Hedgehog signaling during infection. However, activation in an uncontrolled manner, such as that induced by PR8-A122V, may result in more fibrotic tissue damage. 2017 PLoS pathogens Discussion IV A122V 75 80 28837667 Influenza NS1 directly modulates Hedgehog signaling during infection. However, this same mutation resulted in a more pronounced inflammatory response in vivo in mice where we observed higher expression of some Hh targets, and greater virulence when assayed in the context of viral infection (i.e., in PR8 infected mouse lungs) suggesting that other viral factors contribute to determining the net effect of the NS1-A122V mutation on the Hh response. 2017 PLoS pathogens Discussion IV A122V 345 350 NS1 341 344 28837667 Influenza NS1 directly modulates Hedgehog signaling during infection. Importantly, the single amino acid substitution, A122V, which was recovered by a forward genetic screen in Drosophila, dramatically altered most NS1 responses in flies, human lung epithelial cells, and airways of infected mice. 2017 PLoS pathogens Discussion IV A122V 49 54 NS1 145 148 28837667 Influenza NS1 directly modulates Hedgehog signaling during infection. Increased nuclear levels of NS1-A122V coupled with a reduced interaction with Ci/Gli1 (as was detected in flies) might favor alternative NS1-effector interactions that lead to a more pronounced inflammatory state. 2017 PLoS pathogens Discussion IV A122V 32 37 NS1;NS1 28;137 31;140 28837667 Influenza NS1 directly modulates Hedgehog signaling during infection. Interestingly, our initial screen in Drosophila revealed that NS1 from Swine flu (NS1(Sw)) behaved similarly to the A122V mutant of other strains despite the lack of such a mutation. 2017 PLoS pathogens Discussion IV A122V 116 121 NS1;NS1 62;82 65;85 28837667 Influenza NS1 directly modulates Hedgehog signaling during infection. Most notably, NS1-A122V, when expressed independently of other viral proteins (i.e., in flies and cultured human cells) had reduced activity compared to NS1-WT. 2017 PLoS pathogens Discussion IV A122V 18 23 NS1;NS1 14;153 17;156 28837667 Influenza NS1 directly modulates Hedgehog signaling during infection. Thus, during viral infection, the spectrum of interactions between NS1, viral factors, host defense components, and Hh targets, occurring specifically in the nucleus may be altered preferentially by the A122V mutation. 2017 PLoS pathogens Discussion IV A122V 203 208 NS1 67 70 28837667 Influenza NS1 directly modulates Hedgehog signaling during infection. We have shown that NS1-A122V localizes more to the nucleus than NS1-WT. 2017 PLoS pathogens Discussion IV A122V 23 28 NS1;NS1 19;64 22;67 28860593 Prerequisites for the acquisition of mammalian pathogenicity by influenza A virus with a prototypic avian PB2 gene. Acquisition of additional E627K, D701N, or Q591K/R mutations in 4 out of 5 mice during the first mammalian infection was unexpected, but it also supports the fact that the MVV mutations are the minimum essential predisposing mutations to acquire mutations for mammalian pathogenicity. 2017 Scientific reports Discussion IV Q591K;Q591R;E627K;D701N 43;43;26;33 50;50;31;38 28860593 Prerequisites for the acquisition of mammalian pathogenicity by influenza A virus with a prototypic avian PB2 gene. However, the combination of E627K with the MVV mutations was sufficient to cause severe body weight loss and mortality. 2017 Scientific reports Discussion IV E627K 28 33 28860593 Prerequisites for the acquisition of mammalian pathogenicity by influenza A virus with a prototypic avian PB2 gene. However, the K627E mutation eliminated the pathogenicity of the LOF mutants rPB2(PR8)-K627E and rPB2(PR8)-IIIE in mice. 2017 Scientific reports Discussion IV K627E;K627E 13;86 18;91 28860593 Prerequisites for the acquisition of mammalian pathogenicity by influenza A virus with a prototypic avian PB2 gene. In the present study, we identified the novel amino acid mutations I66M, I109V, and I133V, which increased polymerase activity and replication efficiency in mammalian and avian hosts as well as pathogenicity in mice both independently and in combination. 2017 Scientific reports Discussion IV I66M;I109V;I133V 67;73;84 71;78;89 28860593 Prerequisites for the acquisition of mammalian pathogenicity by influenza A virus with a prototypic avian PB2 gene. The conserved amino acids in PB1 and PA neighbouring the residues at positions 66, 109, and 133 of PB2 supports the importance of the I66M, I109V, and I133V mutations. 2017 Scientific reports Discussion IV I66M;I109V;I133V 134;140;151 138;145;156 PA;PB1;PB2 37;29;99 39;32;102 28860593 Prerequisites for the acquisition of mammalian pathogenicity by influenza A virus with a prototypic avian PB2 gene. The E627K mutation was previously reported to play a key role in the mammalian pathogenicity of avian IAVs. 2017 Scientific reports Discussion IV E627K 4 9 28860593 Prerequisites for the acquisition of mammalian pathogenicity by influenza A virus with a prototypic avian PB2 gene. The single E627K mutation in the prototypic 01310 PB2 increased polymerase activity and replication efficiency more effectively than the MVV mutations, but it did not cause apparent body weight loss or mortality in mice (Figs 1a,b and 2a,b). 2017 Scientific reports Discussion IV E627K 11 16 PB2 50 53 28860593 Prerequisites for the acquisition of mammalian pathogenicity by influenza A virus with a prototypic avian PB2 gene. Thus, the E627K mutation has more important implications than the MVV mutations, but the MVV mutations are present at a much higher frequency than E627K in avian, swine, and human IAVs and therefore may represent the first-step mutations acquired by the prototypic PB2. 2017 Scientific reports Discussion IV E627K;E627K 10;147 15;152 PB2 265 268 28860626 Topological N-glycosylation and site-specific N-glycan sulfation of influenza proteins in the highly expressed H1N1 candidate vaccines. In conclusion, we have provided a detailed structural study of N-glycans of the influenza proteins in two monovalent influenza vaccines derived from the highly expressed virus strains of NIBRG-121xp and NYMC-X181 A, and identified the novel N-glycan sulfation, fucosylation and bisecting GlcNAc at unique locations in these two proteins (HA and NA). 2017 Scientific reports Discussion IV X181A 208 214 HA;NA 338;345 340;347 28860626 Topological N-glycosylation and site-specific N-glycan sulfation of influenza proteins in the highly expressed H1N1 candidate vaccines. loss of the sulfated N-glycans, which is consistent with that of the high-yield candidate vaccine viruses (NIBRG-121xp and NYMC-X181 A) (data not shown). 2017 Scientific reports Discussion IV X181A 128 134 28940727 Whole-genome sequencing and antigenic analysis of the first equine influenza virus identified in Turkey. One unique substitution I214T was observed close to the HA antigenic site D. 2018 Influenza and other respiratory viruses Discussion IV I214T 24 29 HA 56 58 28951584 Identification of neuraminidase inhibitors against dual H274Y/I222R mutant strains. MD simulation revealed that the identified inhibitors was not greatly affected by the I222R/H274Y dual mutations. 2017 Scientific reports Discussion IV I222R;H274Y 86;92 91;97 28951584 Identification of neuraminidase inhibitors against dual H274Y/I222R mutant strains. Mutations of residues in various anchor regions of NA, including E199V, D151E, H274Y, R292K, and N294S strains, may alter their characteristics and interaction modes, disrupting drug binding. 2017 Scientific reports Discussion IV E199V;D151E;H274Y;R292K;N294S 65;72;79;86;97 70;77;84;91;102 51 53 28951584 Identification of neuraminidase inhibitors against dual H274Y/I222R mutant strains. Mutations with residues located in the sialic acid site, such as I222R and H274Y, have been shown to reduce the size of the hydrophobic pocket, thereby increasing its oseltamivir resistance. 2017 Scientific reports Discussion IV I222R;H274Y 65;75 70;80 28966609 Amino Acid Substitutions Associated with Avian H5N6 Influenza A Virus Adaptation to Mice. Among all six airborne-transmissible viruses, in addition to the three introduced mutations (Q222L and G224S in HA and E627K in PB2), two new amino acid substitutions were consistently detected: H103Y and T156A (both in HA). 2017 Frontiers in microbiology Discussion IV Q222L;G224S;E627K;H103Y;T156A 93;103;119;195;205 98;108;124;200;210 HA;HA;PB2 112;220;128 114;222;131 28966609 Amino Acid Substitutions Associated with Avian H5N6 Influenza A Virus Adaptation to Mice. Except for PB2 E627K, these amino acid changes were not found in our study. 2017 Frontiers in microbiology Discussion IV E627K 15 20 PB2 11 14 28966609 Amino Acid Substitutions Associated with Avian H5N6 Influenza A Virus Adaptation to Mice. In our work, four amino acid substitutions, PB2 E627K, PB2 T23I, PA T97I, and PA S388C, were found in the viral polymerase subunits PB2 and PA. 2017 Frontiers in microbiology Discussion IV E627K;T23I;T97I;S388C 48;59;68;81 53;63;72;86 PA;PA;PA;PB2;PB2;PB2 65;78;140;44;55;132 67;80;142;47;58;135 28966609 Amino Acid Substitutions Associated with Avian H5N6 Influenza A Virus Adaptation to Mice. The HA R239H mutation may be important for the attachment of adapted influenza viruses to their hosts airways; however, the specific effects of these amino acid substitutions on mammalian pathogenicity requires further study. 2017 Frontiers in microbiology Discussion IV R239H 7 12 HA 4 6 28966609 Amino Acid Substitutions Associated with Avian H5N6 Influenza A Virus Adaptation to Mice. The identified PB2 E627K and PA T97I amino acid substitutions were shown to play important roles in the adaptation of H5N6 to mammals. 2017 Frontiers in microbiology Discussion IV E627K;T97I 19;32 24;36 PA;PB2 29;15 31;18 28966609 Amino Acid Substitutions Associated with Avian H5N6 Influenza A Virus Adaptation to Mice. The Q222L and G224S amino acid mutations not only enhanced the binding of the H5N1 virus to alpha2,6 receptors, but also increased its affinity for alpha2,3 receptor, which probably conferred transmissibility to this H5N1 strain. 2017 Frontiers in microbiology Discussion IV Q222L;G224S 4;14 9;19 28966609 Amino Acid Substitutions Associated with Avian H5N6 Influenza A Virus Adaptation to Mice. While the PB2 E627K and PA T97I mutations contributed to the enhanced polymerase activity and higher pathogenicity of the P10 virus, and the functions of the other two mutations have yet to be determined. 2017 Frontiers in microbiology Discussion IV E627K;T97I 14;27 19;31 PA;PB2 24;10 26;13 29023600 Reduced accumulation of defective viral genomes contributes to severe outcome in influenza virus infected patients. Brownlee described some years ago that mutation A638R in the PA subunit was involved in the enormous accumulation of DGs in cell culture. 2017 PLoS pathogens Discussion IV A638R 48 53 PA 61 63 29023600 Reduced accumulation of defective viral genomes contributes to severe outcome in influenza virus infected patients. It was there described that this high DGs generation was due to an elongation defect by destabilization of RNA-PA subunit interaction, and that this phenomenon could be reverted by another mutation in the same PA polymerase subunit (C453R). 2017 PLoS pathogens Discussion IV C453R 233 238 PA;PA 111;210 113;212 29023600 Reduced accumulation of defective viral genomes contributes to severe outcome in influenza virus infected patients. Moreover, recombinant viruses carrying PA D529N mutation displayed increased viral pathogenicity in the infected mice (PB2/PA mut and PA mut) (Fig 7). 2017 PLoS pathogens Discussion IV D529N 42 47 PA;PA;PA;PB2 39;123;134;119 41;125;136;122 29023600 Reduced accumulation of defective viral genomes contributes to severe outcome in influenza virus infected patients. None of the severe/fatal cohort viruses bore PA D529N change. 2017 PLoS pathogens Discussion IV D529N 48 53 PA 45 47 29023600 Reduced accumulation of defective viral genomes contributes to severe outcome in influenza virus infected patients. PA D529N mutation localizes on the interaction surface of this proposed dimerization model of the viral polymerase (S15 Fig). 2017 PLoS pathogens Discussion IV D529N 3 8 PA 0 2 29023600 Reduced accumulation of defective viral genomes contributes to severe outcome in influenza virus infected patients. This analysis showed that PA D529N change continues to be a rare mutation specific of F-IAV, but PB2 221 position admitted several changes including T. 2017 PLoS pathogens Discussion IV D529N 29 34 PA;PB2 26;97 28;100 29023600 Reduced accumulation of defective viral genomes contributes to severe outcome in influenza virus infected patients. This data correlates with our findings, which indicate that PB2 A221T change is not responsible for the increased pathogenicity of the F-IAV. 2017 PLoS pathogens Discussion IV A221T 64 69 PB2 60 63 29023600 Reduced accumulation of defective viral genomes contributes to severe outcome in influenza virus infected patients. This data suggests that PA D529N may be involved in the same elongation process, although this activity would need to be further explored. 2017 PLoS pathogens Discussion IV D529N 27 32 PA 24 26 29023600 Reduced accumulation of defective viral genomes contributes to severe outcome in influenza virus infected patients. This result suggest that low DVGs accumulation in severe/fatal-case viruses might be mediated by various changes other than D529N in PA polymerase subunit, or in distinct polymerase subunits (S3 Table), or in several viral proteins; this coincides with the complex, multigenic nature of the pathogenesis mechanisms. 2017 PLoS pathogens Discussion IV D529N 124 129 PA 133 135 29023600 Reduced accumulation of defective viral genomes contributes to severe outcome in influenza virus infected patients. We tested this hypothesis genetically by analyzing recombinant viruses bearing mutations identified in a fatal-outcome virus (F-IAV, mutations PB2 A221T and PA D529N) or described elsewhere (mutations M1 S30N + M2 V86S). 2017 PLoS pathogens Discussion IV A221T;D529N;S30N;V86S 147;160;204;214 152;165;208;218 M1;M2;PA;PB2 201;211;157;143 203;213;159;146 29023600 Reduced accumulation of defective viral genomes contributes to severe outcome in influenza virus infected patients. Whereas the non-pathogenic mutation PB2 A221T accumulates high levels of DVGs in cultured cells and is attenuated in mice (PB2 mut versus CAL), mutation PA D529N reduces DVGs accumulation alone or in combination with PB2 A221T change (Fig 5A) or with M1 S30N + M2 V86 S mutations (M-PA mut versus M mut) (Fig 5C). 2017 PLoS pathogens Discussion IV A221T;D529N;A221T;S30N;V86S 40;156;221;254;264 45;161;226;258;269 M;M;M1;M2;PA;PA;PB2;PB2;PB2 281;297;251;261;153;283;36;123;217 282;298;253;263;155;285;39;126;220 29097654 Role of influenza A virus NP acetylation on viral growth and replication. As shown by the cRNA stabilization assay, only reduced levels of cRNA are observed in cells infected with SC35M (in the presence of cycloheximide) and prior expression of the polymerase complex and NP-K77Q,K229Q. 2017 Nature communications Discussion IV K77Q;K229Q 201;206 205;211 NP 198 200 29097654 Role of influenza A virus NP acetylation on viral growth and replication. Despite the mutation K113R having no detectable effect on polymerase activity or viral growth, rescue of NP-K113Q virus was not possible. 2017 Nature communications Discussion IV K113R;K113Q 21;108 26;113 NP 105 107 29097654 Role of influenza A virus NP acetylation on viral growth and replication. In comparison to wt SC35M, the mutant virus encoding NP-K229R showed similar viral polymerase activity, time-dependent accumulation of vRNPs in the cytoplasm and co-segregation of distinct cytoplasmic vRNPs. 2017 Nature communications Discussion IV K229R 56 61 NP 53 55 29097654 Role of influenza A virus NP acetylation on viral growth and replication. Intriguingly, the NP mutation K113Q did not allow the generation of viable virus, despite unimpaired polymerase activity. 2017 Nature communications Discussion IV K113Q 30 35 NP 18 20 29097654 Role of influenza A virus NP acetylation on viral growth and replication. Mimicking a single constitutively acetylated lysine residue by substituting K229 with glutamine (K229Q) revealed a comparable defect in particle release, whereas the NP mutation K77Q displayed no effect. 2017 Nature communications Discussion IV K229Q;K77Q 97;178 102;182 NP 166 168 29097654 Role of influenza A virus NP acetylation on viral growth and replication. The block in viral growth mediated by NP-K77Q,K229Q appears to be at the stage of viral replication. 2017 Nature communications Discussion IV K77Q;K229Q 41;46 45;51 NP 38 40 29097654 Role of influenza A virus NP acetylation on viral growth and replication. This indicates that NP-K77Q,K229Q at least fails to properly encapsidate cRNA transcripts whereas PB2 binding seems not to be affected. 2017 Nature communications Discussion IV K77Q;K229Q 23;28 27;33 NP;PB2 20;98 22;101 29097654 Role of influenza A virus NP acetylation on viral growth and replication. Using a mutational approach in which we mimicked non-acetylated lysine residues by substitution with arginine (R), the mutation K229R in NP of SC35M was found to impair viral growth in multiple cell lines, whereas the replacement of the lysine residues at positions 77 and 113 with arginine had no detectable effect. 2017 Nature communications Discussion IV K229R 128 133 NP 137 139 29097654 Role of influenza A virus NP acetylation on viral growth and replication. Whereas the NP mutations K77Q and K229Q severely diminished viral replication, K77R and K229R had no effect in this regard, suggesting that simultaneous acetylation at these sites specifically interferes with a certain step in the viral life cycle. 2017 Nature communications Discussion IV K77Q;K229Q;K77R;K229R 25;34;79;88 29;39;83;93 NP 12 14 29100932 Evolution of equine influenza viruses (H3N8) during a Brazilian outbreak, 2015. As noticed by Legrand et al., the seven substitutions in residues G7D, R62K, V78A, D104N, A138S, N159S and V223I have apparently remained unchanged since 2008. 2018 Brazilian journal of microbiology Discussion IV G7D;R62K;V78A;D104N;A138S;N159S;V223I 66;71;77;83;90;97;107 69;75;81;88;95;102;112 29100932 Evolution of equine influenza viruses (H3N8) during a Brazilian outbreak, 2015. Epitopes at the NA head involving the residues 150, 199, 344-346, 367, 399 and 400 were conserved among the EIVs analyzed, with three exceptions: the changes Q199H on A/equine/Kentucky/2/12 and A/equine/Kentucky/3/12 and R150Q on A/equine/Spain/1/07. 2018 Brazilian journal of microbiology Discussion IV Q199H;R150Q 158;221 163;226 16 18 29100932 Evolution of equine influenza viruses (H3N8) during a Brazilian outbreak, 2015. The substitution G142R was unique to V1, V2 and V3 Brazilian-2015 strains and was not found in other EIVs from public databases, thus suggesting that this substitution might have happened before or during the outbreak. 2018 Brazilian journal of microbiology Discussion IV G142R 17 22 29100932 Evolution of equine influenza viruses (H3N8) during a Brazilian outbreak, 2015. The substitutions R62K (site E), D104N and A138S (site A) and V223I were previously described in FC1 strains. 2018 Brazilian journal of microbiology Discussion IV R62K;D104N;A138S;V223I 18;33;43;62 22;38;48;67 29100932 Evolution of equine influenza viruses (H3N8) during a Brazilian outbreak, 2015. The substitutions V78A and N159S that differentiate FC1 from FC2 remained. 2018 Brazilian journal of microbiology Discussion IV V78A;N159S 18;27 22;32 29100932 Evolution of equine influenza viruses (H3N8) during a Brazilian outbreak, 2015. The two substitutions at site A (aa 138 and 142), which were seen in all the Brazilian EIV strains from 2015, showed that the combination of these two resulted in greater change when compared to the single substitution (A138S) found in A/equine/Rio Grande do Sul/2012 and A/equine/Dubai/1/2012. 2018 Brazilian journal of microbiology Discussion IV A138S 220 225 29145498 Antigenicity of the 2015-2016 seasonal H1N1 human influenza virus HA and NA proteins. In addition, the mutations N44S and N386K respectively incorporate and abrogate N-linked glycosylation sites in the NA. 2017 PloS one Discussion IV N44S;N386K 27;36 31;41 116 118 29145498 Antigenicity of the 2015-2016 seasonal H1N1 human influenza virus HA and NA proteins. In fact, it was shown that a particular mutation (K180Q), present in the HA of isolates from the 2014-15 season as well as our 2015-16 isolates, facilitates virus escape from immune responses; however, it has no significant effect on the antigenicity of the protein measured using ferret sera. 2017 PloS one Discussion IV K180Q 50 55 HA 73 75 29145498 Antigenicity of the 2015-2016 seasonal H1N1 human influenza virus HA and NA proteins. Interestingly, mutation S179N, found in the HA protein of viruses circulating during the 2015-16 season, is located on top of the HA head in the Sa antigenic site and incorporates an additional N-linked glycosylation site. 2017 PloS one Discussion IV S179N 24 29 HA;HA 44;130 46;132 29145498 Antigenicity of the 2015-2016 seasonal H1N1 human influenza virus HA and NA proteins. Similarly, there was a V466I mutation in the in vitro derived antigenic mutants, which is proximal to the S468N and N472T mutations found in currently circulating strains. 2017 PloS one Discussion IV V466I;S468N;N472T 23;106;116 28;111;121 29145498 Antigenicity of the 2015-2016 seasonal H1N1 human influenza virus HA and NA proteins. These antigenic differences could be due to the mutations in defined Ab binding sites (N200S, N248D, N369K, and K432E). 2017 PloS one Discussion IV N200S;N248D;N369K;K432E 87;94;101;112 92;99;106;117 29145498 Antigenicity of the 2015-2016 seasonal H1N1 human influenza virus HA and NA proteins. While not at exactly the same position, the E391K mutation in the circulating viruses is close to the A388V mutation we and other described after growing the virus in the presence of 6F12 mAb, and may be part of the same epitope. 2017 PloS one Discussion IV E391K;A388V 44;102 49;107 29209052 Maintaining pH-dependent conformational flexibility of M1 is critical for efficient influenza A virus replication. A further look at M(NLS-88E)-neutral structure reveals that the G88E mutation results in three inter-subunit salt-bridge/hydrogen-bond interactions including Lys104-NZ to Glu88-OE1 (and its symmetry-related counterpart) and Arg134-NE to Glu88-OE2 (Figure 1F; see Supplementary Table S3) that may explain why M(NLS-88E)-neutral that is predicted to crystallize as monomers in a face-to-back arrangement is actually driven to dimerize in a face-to-face manner at neutral pH. 2017 Emerging microbes & infections Discussion IV G88E 64 68 M;M 18;308 19;309 29209052 Maintaining pH-dependent conformational flexibility of M1 is critical for efficient influenza A virus replication. Although differing by a single amino acid (G88R vs G88E), M(NLS-88R) M1 and M(NLS-88E) M1 respond to environmental pH differently as indicated by the crystal structures obtained in the current study. 2017 Emerging microbes & infections Discussion IV G88R;G88E 43;51 47;55 M;M;M1;M1 58;76;69;87 59;77;71;89 29209052 Maintaining pH-dependent conformational flexibility of M1 is critical for efficient influenza A virus replication. However, dimer 1 of M(NLS-88E)-acidic is more like M(NLS-88E)-neutral that owns a strong bifurcated hydrogen-bond interaction between Tyr100 and Glu88 because of the G88E mutation (see Supplementary Table S3) that makes it more difficult to dissemble M(NLS-88E) M1 in acidic conditions than M(NLS-88R) M1. 2017 Emerging microbes & infections Discussion IV G88E 166 170 M;M;M;M;M1;M1 20;51;251;291;262;302 21;52;252;292;264;304 29209052 Maintaining pH-dependent conformational flexibility of M1 is critical for efficient influenza A virus replication. In addition to these conserved inter-subunit hydrogen-bonds, the G88R mutation also results in an extra hydrogen-bond from Arg88-NE to Arg134-O in M(NLS-88)-acidic structure. 2017 Emerging microbes & infections Discussion IV G88R 65 69 M 147 148 29209052 Maintaining pH-dependent conformational flexibility of M1 is critical for efficient influenza A virus replication. Our results also indicate that the compensatory G88R mutation was not a random mutation but was chosen by the virus purposefully to retain pH-dependent conformational flexibility for efficient virus replication. 2017 Emerging microbes & infections Discussion IV G88R 48 52 29209052 Maintaining pH-dependent conformational flexibility of M1 is critical for efficient influenza A virus replication. The G88R mutation also results in two additional inter-subunit hydrogen-bonds (Lys104-NZ to Glu29-OE2 and Arg134-NE to Glu29-OE1) in M(NLS-88R)-neutral (see Supplementary Table S3) that make the subunit rotation slightly difficult than similarly face-to-back-oriented wt-M1 neutral structure 1EA3. 2017 Emerging microbes & infections Discussion IV G88R 4 8 M;M1 133;271 134;273 29209052 Maintaining pH-dependent conformational flexibility of M1 is critical for efficient influenza A virus replication. This is because the G88E mutation causes Tyr100-OH to interact with the side chain instead of the carbonyl oxygen of mutated Glu88-OE1 (OE2), and Asn85-ND2 to interact with Arg134-NE2 instead of Arg134-O in the dimeric structure of M(NLS-88E)-neutral (see Supplementary Table S3). 2017 Emerging microbes & infections Discussion IV G88E 20 24 M 232 233 29299528 Human Clade 2.3.4.4 A/H5N6 Influenza Virus Lacks Mammalian Adaptation Markers and Does Not Transmit via the Airborne Route between Ferrets. A/H5N6 GZ/14 and A/H5N8 ck/NL/14 do not possess known substitutions that have been reported to increase the acid stability and/or thermostability of A/H5 viruses from other clades of the GsGd lineage, such as H103Y, T315I, or K58I (HA2 numbering). 2018 mSphere Discussion IV H103Y;T315I;K58I 209;216;226 214;221;230 HA 232 234 29299528 Human Clade 2.3.4.4 A/H5N6 Influenza Virus Lacks Mammalian Adaptation Markers and Does Not Transmit via the Airborne Route between Ferrets. Acquisition of PB2-E627K might be the result of adaptation to the human host, although this substitution has also been detected in A/H5 avian virus isolates from other clades, as well as in other avian-origin influenza viruses such as A/H7N9. 2018 mSphere Discussion IV E627K 19 24 PB2 15 18 29299528 Human Clade 2.3.4.4 A/H5N6 Influenza Virus Lacks Mammalian Adaptation Markers and Does Not Transmit via the Airborne Route between Ferrets. Although most clade 2.3.4.4 viruses have retained alpha2,3-SA specificity, it was shown that the emergence of clade 2.3.4.4 viruses was accompanied with the capacity of these viruses to bind to fucosylated sialilosides, mediated by K218Q and S223R, substitutions that are conserved in clade 2.3.4.4 HAs. 2018 mSphere Discussion IV K218Q;S223R 232;242 237;247 29299528 Human Clade 2.3.4.4 A/H5N6 Influenza Virus Lacks Mammalian Adaptation Markers and Does Not Transmit via the Airborne Route between Ferrets. However, in contrast to these viruses that had acquired internal genes from LPAI viruses from wild birds, A/H5N6 GZ/14 possesses internal genes from the A/H5N1 GsGd lineage and also the adaptive substitution E627K in PB2 that might increase its pathogenicity in mammalian hosts. 2018 mSphere Discussion IV E627K 208 213 PB2 217 220 29299528 Human Clade 2.3.4.4 A/H5N6 Influenza Virus Lacks Mammalian Adaptation Markers and Does Not Transmit via the Airborne Route between Ferrets. Out of the 16 A/H5N6 human isolates, seven isolates carry the PB2-E627K, and one isolate, A/Sichuan/26221/2014, carries the PB2-D701N substitution, which has also been associated with increased replication and transmission in mammalian hosts. 2018 mSphere Discussion IV E627K;D701N 66;128 71;133 PB2;PB2 62;124 65;127 29299528 Human Clade 2.3.4.4 A/H5N6 Influenza Virus Lacks Mammalian Adaptation Markers and Does Not Transmit via the Airborne Route between Ferrets. Sequence analysis of A/H5N6 GZ/14 virus revealed a few amino acid substitutions that have previously been described as mammalian adaptation markers for other A/H5 viruses of the GsGd lineage: 94N, 133A, and 235P in HA, which have been associated with increased binding of A/H5N1 viruses to human-type receptors, and E627K in PB2, which has been associated with increased replication of influenza viruses in vitro and in vivo at temperatures equivalent to those of the mammalian upper respiratory tract (URT). 2018 mSphere Discussion IV E627K 316 321 HA;PB2 215;325 217;328 29299528 Human Clade 2.3.4.4 A/H5N6 Influenza Virus Lacks Mammalian Adaptation Markers and Does Not Transmit via the Airborne Route between Ferrets. Using a minireplicon assay, we demonstrated that A/H5N6 GZ/14 possessed a high polymerase activity, which was mediated by E627K in PB2. 2018 mSphere Discussion IV E627K 122 127 PB2 131 134 29299533 Cooperating H3N2 Influenza Virus Variants Are Not Detectable in Primary Clinical Samples. It is impossible to rule out the possibility that the D151G mutation reaches appreciable frequencies in some natural human infections, but strong and repeated selection for cooperation in cell culture seems to account for its prevalence among sequences in public databases. 2018 mSphere Discussion IV D151G 54 59 29299533 Cooperating H3N2 Influenza Virus Variants Are Not Detectable in Primary Clinical Samples. Mutations like D151G accumulate in cell culture within just a few passages and affect downstream analyses like inferences of positive selection. 2018 mSphere Discussion IV D151G 15 20 29299533 Cooperating H3N2 Influenza Virus Variants Are Not Detectable in Primary Clinical Samples. The results of our deep-sequencing study support prior studies that failed to detect the D151G mutation in unpassaged clinical samples by Sanger sequencing or pyrosequencing. 2018 mSphere Discussion IV D151G 89 94 29299533 Cooperating H3N2 Influenza Virus Variants Are Not Detectable in Primary Clinical Samples. These different growth conditions may also promote the emergence of D151G within cell culture, but natural infections may not. 2018 mSphere Discussion IV D151G 68 73 29308074 Neuraminidase Gene Variations in Influenza A(H1N1)pdm09 Virus among Patients Admitted to Refferal Pulmonary Hospital, Tehran, Iran in 2009-2013. Also, other known mutations, which cause resistance to NAIs (such as D199N, E119V/G, and I223V/R), were not observed in this study. 2017 Tanaffos Discussion IV D199N;E119V;E119G;I223V;I223R 69;76;76;89;89 74;83;83;96;96 NAI 55 59 29308074 Neuraminidase Gene Variations in Influenza A(H1N1)pdm09 Virus among Patients Admitted to Refferal Pulmonary Hospital, Tehran, Iran in 2009-2013. Also, V241I and N369K mutations were observed in all 2010-2011 and 2012-2013 strains and distinguished them from 2009-2010 strains. 2017 Tanaffos Discussion IV V241I;N369K 6;16 11;21 29308074 Neuraminidase Gene Variations in Influenza A(H1N1)pdm09 Virus among Patients Admitted to Refferal Pulmonary Hospital, Tehran, Iran in 2009-2013. Meanwhile, H275Y substitution, detected in this study, was of phylogenic importance and led to speciation of influenza strains in the phylogenetic tree (Figure 1). 2017 Tanaffos Discussion IV H275Y 11 16 29308074 Neuraminidase Gene Variations in Influenza A(H1N1)pdm09 Virus among Patients Admitted to Refferal Pulmonary Hospital, Tehran, Iran in 2009-2013. Meanwhile, N44S, V62I, and L40I mutations could internally distinguish 2010-2011 and 2012-2013 strains (Figure 1). 2017 Tanaffos Discussion IV N44S;V62I;L40I 11;17;27 15;21;31 29308074 Neuraminidase Gene Variations in Influenza A(H1N1)pdm09 Virus among Patients Admitted to Refferal Pulmonary Hospital, Tehran, Iran in 2009-2013. N200S substitution was observed in both 2012-2013 strains, whereas G201E was observed in only 1 strain from 2012-2013. 2017 Tanaffos Discussion IV N200S;G201E 0;67 5;72 29308074 Neuraminidase Gene Variations in Influenza A(H1N1)pdm09 Virus among Patients Admitted to Refferal Pulmonary Hospital, Tehran, Iran in 2009-2013. N200S was only detected among 2012-2013 strains and helped distinguish 2012-2013 influenza A isolates. 2017 Tanaffos Discussion IV N200S 0 5 29308074 Neuraminidase Gene Variations in Influenza A(H1N1)pdm09 Virus among Patients Admitted to Refferal Pulmonary Hospital, Tehran, Iran in 2009-2013. N248D substitution distinguished all Iranian A(H1N1)pdm09 strains from the vaccine strain, as seen in all the isolates. 2017 Tanaffos Discussion IV N248D 0 5 29308074 Neuraminidase Gene Variations in Influenza A(H1N1)pdm09 Virus among Patients Admitted to Refferal Pulmonary Hospital, Tehran, Iran in 2009-2013. Overall, N44S, V62I, V106I, N200S, V241I, N248D, and N369K substitutions were most commonly detected (Table 3). 2017 Tanaffos Discussion IV N44S;V62I;V106I;N200S;V241I;N248D;N369K 9;15;21;28;35;42;53 13;19;26;33;40;47;58 29308074 Neuraminidase Gene Variations in Influenza A(H1N1)pdm09 Virus among Patients Admitted to Refferal Pulmonary Hospital, Tehran, Iran in 2009-2013. The present study showed that 3 isolates (2 isolates from 2009-2010 and 1 isolate from 2013) included H275Y substitution in NA genes (Figure 1, Table 3). 2017 Tanaffos Discussion IV H275Y 102 107 124 126 29308074 Neuraminidase Gene Variations in Influenza A(H1N1)pdm09 Virus among Patients Admitted to Refferal Pulmonary Hospital, Tehran, Iran in 2009-2013. These changes included D103N and V106I substitutions in 100-118 amino acid residues, N200S and G201E substitutions in amino acid sequences at residues 195-211, R257K substitution at residues 250-258, and G414R substitution at residues 399-415. 2017 Tanaffos Discussion IV D103N;V106I;N200S;G201E;R257K;G414R 23;33;85;95;160;204 28;38;90;100;165;209 29312300 Histone Deacetylase 1 Plays an Acetylation-Independent Role in Influenza A Virus Replication. For another, both the WT and the K103A/R mutants containing IAV showed same replication inhibition in HDAC1-deficient cells, indicating a K103 deacetylation-independent regulation of HDAC1 in viral replication. 2017 Frontiers in immunology Discussion IV K103A;K103R 33;33 40;40 29312300 Histone Deacetylase 1 Plays an Acetylation-Independent Role in Influenza A Virus Replication. Moreover, the replication efficiencies of K229R mutant viruses were attenuated in vivo and in vitro. 2017 Frontiers in immunology Discussion IV K229R 42 47 29312300 Histone Deacetylase 1 Plays an Acetylation-Independent Role in Influenza A Virus Replication. Of these, the K91R and K198R showed decreased the polymerase activity, and K91R and K198R mutants cannot yield recombinant viruses, while K227R viruses showed a similar virulence as rWT. 2017 Frontiers in immunology Discussion IV K91R;K198R;K91R;K198R;K227R 14;23;75;84;138 18;28;79;89;143 29312300 Histone Deacetylase 1 Plays an Acetylation-Independent Role in Influenza A Virus Replication. Ubiqutination site NP-K184R mutant and sumolylation substitution NP-K7R had a lower level of acetylation compared with that of NP-WT (Figure S5 in Supplementary Material). 2017 Frontiers in immunology Discussion IV K7R;K184R 68;22 71;27 NP;NP;NP 19;65;127 21;67;129 29324781 Neuraminidase inhibitor susceptibility and neuraminidase enzyme kinetics of human influenza A and B viruses circulating in Thailand in 2010-2015. However, the I222V NA substitution has a compensatory effect on the influenza A(H3N2) virus carrying E119V, and the presence of these two substitutions resulted in partially improved viral fitness in cell culture and resistance to oseltamivir. 2018 PloS one Discussion IV I222V;E119V 13;101 18;106 19 21 29324781 Neuraminidase inhibitor susceptibility and neuraminidase enzyme kinetics of human influenza A and B viruses circulating in Thailand in 2010-2015. In our study, the A/PR8-I222V virus was susceptible to NAIs in a phenotypic NA inhibition assay and possessed slightly increased NA enzymatic activity. 2018 PloS one Discussion IV I222V 24 29 NA;NA;NAI 76;129;55 78;131;59 29324781 Neuraminidase inhibitor susceptibility and neuraminidase enzyme kinetics of human influenza A and B viruses circulating in Thailand in 2010-2015. It was previously reported that an influenza A(H3N2) virus with a single I222V NA amino acid substitution was susceptible to oseltamivir and possessed slightly higher NA enzymatic activity as compared to WT virus. 2018 PloS one Discussion IV I222V 73 78 NA;NA 79;167 81;169 29324781 Neuraminidase inhibitor susceptibility and neuraminidase enzyme kinetics of human influenza A and B viruses circulating in Thailand in 2010-2015. Moreover, B/YAM-D342S, B/YAM-A395T, and B/YAM-A395V viruses gave significantly higher viral yields at 48 hpi in MDCK cells, as compared to B/BR/60/08 virus. 2018 PloS one Discussion IV D342S;A395T;A395V 16;29;46 21;34;51 29324781 Neuraminidase inhibitor susceptibility and neuraminidase enzyme kinetics of human influenza A and B viruses circulating in Thailand in 2010-2015. NAs from influenza A(H3N2) PCR-positive samples with I222V, S331G, and S331R NA substitutions were generated in the A/PR8 (H1N1) backbone. 2018 PloS one Discussion IV I222V;S331G;S331R 53;60;71 58;65;76 NA;NA 77;0 79;3 29324781 Neuraminidase inhibitor susceptibility and neuraminidase enzyme kinetics of human influenza A and B viruses circulating in Thailand in 2010-2015. Our data revealed that recombinant A/PR8-I222V virus has only a minor effect on the NA enzymatic properties and virus replication efficiency in MDCK cells. 2018 PloS one Discussion IV I222V 41 46 84 86 29324781 Neuraminidase inhibitor susceptibility and neuraminidase enzyme kinetics of human influenza A and B viruses circulating in Thailand in 2010-2015. Regarding the S331G/R, D342S, and A395T/D/V NA amino acid substitutions, these are found outside the NA active site, and viruses with these substitutions showed normal inhibition by NAIs. 2018 PloS one Discussion IV S331G;S331R;D342S;A395T;A395D;A395V 14;14;23;34;34;34 21;21;28;43;43;43 NA;NA;NAI 44;101;182 46;103;186 29324781 Neuraminidase inhibitor susceptibility and neuraminidase enzyme kinetics of human influenza A and B viruses circulating in Thailand in 2010-2015. The A/PR8-S331G and A/PR8-S331R viruses were characterized by a loss of NA activity at higher temperature (55 C), whereas PR8-WT and A/PR8-I222V viruses did not lose their NA activity. 2018 PloS one Discussion IV S331G;S331R;I222V 10;26;139 15;31;144 NA;NA 72;172 74;174 29324781 Neuraminidase inhibitor susceptibility and neuraminidase enzyme kinetics of human influenza A and B viruses circulating in Thailand in 2010-2015. The A395V and D342S NA substitutions on the B/YAM background were unstable, and the NAs reverted to WT after three passages in vitro. 2018 PloS one Discussion IV A395V;D342S 4;14 9;19 NA;NA 20;84 22;87 29324781 Neuraminidase inhibitor susceptibility and neuraminidase enzyme kinetics of human influenza A and B viruses circulating in Thailand in 2010-2015. The B/YAM-D342S, B/YAM-A395T, and B/YAM-A395V viruses showed increased NA activity, whereas their Km and Vmax values decreased. 2018 PloS one Discussion IV D342S;A395T;A395V 10;23;40 15;28;45 71 73 29324781 Neuraminidase inhibitor susceptibility and neuraminidase enzyme kinetics of human influenza A and B viruses circulating in Thailand in 2010-2015. The NA activity of the A/PR8-S331G and A/PR8-S331R viruses was decreased, and their viral titers in MDCK cells were lower than those of the WT virus at 6 and 12 hpi. 2018 PloS one Discussion IV S331G;S331R 29;45 34;50 4 6 29324781 Neuraminidase inhibitor susceptibility and neuraminidase enzyme kinetics of human influenza A and B viruses circulating in Thailand in 2010-2015. The S331G and S331R substitutions affected the kinetic properties of the NA enzyme, changing its binding affinity (Km) for MUNANA substrate. 2018 PloS one Discussion IV S331G;S331R 4;14 9;19 73 75 29324781 Neuraminidase inhibitor susceptibility and neuraminidase enzyme kinetics of human influenza A and B viruses circulating in Thailand in 2010-2015. The significant decrease in NA activity and the increased Km value demonstrated that S331G and S331R NA substitutions are deleterious to NA functions. 2018 PloS one Discussion IV S331G;S331R 85;95 90;100 NA;NA;NA 28;101;137 30;103;139 29324781 Neuraminidase inhibitor susceptibility and neuraminidase enzyme kinetics of human influenza A and B viruses circulating in Thailand in 2010-2015. The Vmax of the A/PR8-S331G and A/PR8-S331R virus NAs was nearly double that of the A/PR8-WT NA, demonstrating the compensatory effect as reflected in the lower replication capacity of viruses carrying S331G and S331R substitutions when compared to viruses with WT or I222V NAs. 2018 PloS one Discussion IV S331G;S331R;S331G;S331R;I222V 22;38;202;212;268 27;43;207;217;273 NA;NA;NA 93;50;274 95;53;277 29409570 Early season co-circulation of influenza A(H3N2) and B(Yamagata): interim estimates of 2017/18 vaccine effectiveness, Canada, January 2018. Furthermore, a single subgroup of clade 3C.2a with T131K + R142K + R261Q substitutions. 2018 Euro surveillance Discussion IV T131K;R142K;R261Q 51;59;67 56;64;72 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. Among these two substitutions, V51I may enhance the fitness of M2 protein to increase the frequency of adamantine resistance associated with S31N mutation and the substitution of V51-affected viral replication.28 The I39 of M2 was located in the transmembrane region, and substitution of the transmembrane region could affect M2 function, aiding in resistance to M2 inhibitors and transport to the cell surface. 2018 Influenza and other respiratory viruses Discussion IV V51I;S31N 31;141 35;145 M2;M2;M2;M2 63;224;326;363 65;226;328;365 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. Further, sequences detected in the 2012-2013 season (HA clade 3C.2) showed I392T substitution in the NA gene. 2018 Influenza and other respiratory viruses Discussion IV I392T 75 80 HA;NA 53;101 55;103 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. However, other antidrug mutations, H274Y (N2 numbering) and I119V, were not confirmed. 2018 Influenza and other respiratory viruses Discussion IV H274Y;I119V 35;60 40;65 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. In addition, the NA genes were distinguished into two clusters: I392T in cluster 1 and T267K, I380V in the other cluster. 2018 Influenza and other respiratory viruses Discussion IV I392T;T267K;I380V 64;87;94 69;92;99 17 19 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. In the A/H3N2, the sequences in the 2013-2015 season carried substitutions: A138S, F159S, N225D, N241D, and K326R in HA1 or N144S, F159Y, N225D, and Q311H in HA1, and were categorized into clade 3C.3a and 3C.2a. 2018 Influenza and other respiratory viruses Discussion IV A138S;F159S;N225D;N241D;K326R;N144S;F159Y;N225D;Q311H 76;83;90;97;108;124;131;138;149 81;88;95;102;113;129;136;143;154 HA1;HA1 117;158 120;161 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. In the NP sequences, M374I and M481I were identified only in fatal case sequences. 2018 Influenza and other respiratory viruses Discussion IV M374I;M481I 21;31 26;36 NP 7 9 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. Interestingly, the I39M of M2 and M482I of NP were identified in the same isolates (A/Seoul/A1284/2015, A/Seoul/A1251/2015). 2018 Influenza and other respiratory viruses Discussion IV I39M;M482I 19;34 23;39 M2;NP 27;43 29;45 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. Previous studies have shown that the single I222V/M substitution in the NA protein is associated with marginal levels of resistance to oseltamivir, while synergistically increased drug resistance was associated with E119V and H274Y substitutions.15, 16, 19, 22, 23, 24, 25, 26 The S31N substitution in the M2 protein was frequently detected in the more recent viral sequences and reference sequences.27 In addition, V51I and I39M substitutions were identified in the 2011-2012 and 2014-2015 fatal case sequences. 2018 Influenza and other respiratory viruses Discussion IV I222M;I222V;E119V;H274Y;S31N;V51I;I39M 44;44;216;226;281;416;425 51;51;221;231;285;420;429 M2;NA 306;72 308;74 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. Previous studies recognized several antigenic sites (A-E) and receptor-binding sites (RBS) in the HA gene of A/H3N2.2, 17, 18, 19, 20 Several researchers reported that antigenic drift was caused by single amino acid substitutions near the RBS of the influenza A virus.2, 20, 21 The HA proteins of 3C.2a and 3C.3a viruses are substituted around the RBS, particularly D225N, 126NWT/AG, and 144NN/SSF in HA1, compared with A/Victoria/361/2011. 2018 Influenza and other respiratory viruses Discussion IV D225N 366 371 HA;HA;HA1 98;282;401 100;284;404 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. The A(H1N1)pdm09 in 2015-2016 was grouped into clade 6B and separated into two clusters by substitution V152T, V173I in group 1 and S84N, S162N, and I216T in group 2 over time. 2018 Influenza and other respiratory viruses Discussion IV V152T;V173I;S84N;S162N;I216T 104;111;132;138;149 109;116;136;143;154 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. The I222V substitution in the NA protein was found in only the two A/H3N2 viruses from the 2011-2012 season. 2018 Influenza and other respiratory viruses Discussion IV I222V 4 9 30 32 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. The I39M substitution of M2 and the M481I substitution of NP may be weakly correlated based on the P-value of .054. 2018 Influenza and other respiratory viruses Discussion IV I39M;M481I 4;36 8;41 M2;NP 25;58 27;60 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. The T48A in NS2 of A(H1N1)pdm09 contributed to the enhanced type I IFN antagonistic property of A/Vietnam/UT3062/04, leading to high virulence in ferrets. 2018 Influenza and other respiratory viruses Discussion IV T48A 4 8 NS2 12 15 29489060 Molecular genetic characteristics of influenza A virus clinically isolated during 2011-2016 influenza seasons in Korea. These substitutions have been reported to be involved a T-cell epitope presented by MHC molecules.29, 30 In addition, it was previously reported that other substitutions were identified in the A/Cheongju/G792/2013(H1N1) (T48A in NS2) and in the A/Seoul/A468/2013(H3N2) (K357R in NP). 2018 Influenza and other respiratory viruses Discussion IV T48A;K357R 221;270 225;275 NP;NS2 279;229 281;232 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. All the identified AM2 mutants were located at the drug-binding site of AM2-S31N and it is likely they have either a direct or indirect impact on the drug binding. 2018 Antiviral research Discussion IV S31N 76 80 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. AM2-S31N inhibitors are analogs of amantadine that are chemically substituted at the ammonium group. 2018 Antiviral research Discussion IV S31N 4 8 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. Analogs containing an isoxazole substitution were found to stabilize the AM2-S31N by forming optimal hydrogen bond networks with Asp31 and structural water molecules within the channel pore. 2018 Antiviral research Discussion IV S31N 77 81 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. As such, only a limited number of AM2 mutants were identified in transmissible viruses such as V27A, L26F, and S31N. 2018 Antiviral research Discussion IV V27A;L26F;S31N 95;101;111 99;105;115 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. Based on our findings, future efforts for AM2-S31N drug discovery should focus on compounds that not only inhibit the AM2-S31N channel, but also the AM2-S31N/V27I and AM2-S31N/L26I double mutants in order to further increase the genetic barrier to drug resistance. 2018 Antiviral research Discussion IV S31N;S31N;S31N;V27I;S31N;L26I 46;122;153;158;171;176 50;126;157;162;175;180 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. Based on the solution NMR structure of WJ332 in complex with AM2-S31N. 2018 Antiviral research Discussion IV S31N 65 69 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. Compounds 1 and 2 demonstrated partial activity against AM2-S31N/V27I and AM2-S31N/L26I both in antiviral and electrophysiological assays. 2018 Antiviral research Discussion IV S31N;V27I;L26I;S31N 60;65;83;78 64;69;87;82 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. In contrast, the non-conservative mutant channel AM2-S31N/L26I/A30T has attenuated channel function and could not support viral replication in vitro, and it shows higher level of resistance to both compounds 1 and 2. 2018 Antiviral research Discussion IV L26I;S31N;A30T 58;53;63 62;57;67 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. Overall, the electrophysiological assay results, together with the growth kinetics, and competition growth experiments, collectively suggest that the conservative mutants AM2-S31N/V27I and AM2-S31N/L26I are functionally equivalent to AM2-S31N in vitro while conferring partial resistance to compounds 1 and 2. 2018 Antiviral research Discussion IV S31N;V27I;L26I;S31N;S31N 175;180;198;193;238 179;184;202;197;242 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. Small populations of viruses containing the AM2-S31N/V27I and AM2-S31N/L26I double mutants were found in circulating human, avian, and swine strains, and our competition assays showed that these mutant viruses can sustain their population in the presence of AM2-S31N viruses in cell culture. 2018 Antiviral research Discussion IV S31N;V27I;L26I;S31N;S31N 48;53;71;66;262 52;57;75;70;266 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. Therefore, AM2-S31N inhibitors appear to be an ideal starting point for optimizing inhibitors against these double mutants. 2018 Antiviral research Discussion IV S31N 15 19 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. These results suggest AM2-S31N inhibitors have a higher genetic barrier to drug resistance than amantadine at least in cell culture. 2018 Antiviral research Discussion IV S31N 26 30 29518414 Profiling the in vitro drug-resistance mechanism of influenza A viruses towards the AM2-S31N proton channel blockers. Whereas amantadine orients its amine towards the C-terminal end facing histidine 37, AM2-S31N inhibitors bind S31N with the amine facing up (N-terminal lumen). 2018 Antiviral research Discussion IV S31N;S31N 89;110 93;114 29587786 Effects of the S42 residue of the H1N1 swine influenza virus NS1 protein on interferon responses and virus replication. According to John, the specific exchange of E for D at position 92 of A/HK/156/97 (H5N1) resulted in an order of magnitude higher quantum yield of IFN. 2018 Virology journal Discussion IV D92E 44 66 29587786 Effects of the S42 residue of the H1N1 swine influenza virus NS1 protein on interferon responses and virus replication. Another substitution at position 92 D-to-E had no effect on viral output or viral protein expression. 2018 Virology journal Discussion IV D92E 33 42 29587786 Effects of the S42 residue of the H1N1 swine influenza virus NS1 protein on interferon responses and virus replication. In contrast, Lipatov reported that a reassortant virus harboring a D92E mutation in its H5N1/NS1 gene provoked significantly higher levels of inflammatory cytokines than viruses whose NS1 protein contains D at position 92. 2018 Virology journal Discussion IV D92E 67 71 NS1;NS1 93;184 96;187 29587786 Effects of the S42 residue of the H1N1 swine influenza virus NS1 protein on interferon responses and virus replication. Previous studies found RBD with S42 residue bound double-stranded RNA (dsRNA), whereas that S42P mutation did not. 2018 Virology journal Discussion IV S42P 92 96 29587786 Effects of the S42 residue of the H1N1 swine influenza virus NS1 protein on interferon responses and virus replication. Since the NS1 S42P mutation showed lower virus titers and higher cellular IFN-beta production, we compared the NS1 and NS1 mutant 3D structures, hydrophilicity, antigenic index and instability index. 2018 Virology journal Discussion IV S42P 14 18 NS1;NS1;NS1 10;111;119 13;114;122 29587786 Effects of the S42 residue of the H1N1 swine influenza virus NS1 protein on interferon responses and virus replication. Some common variations of NS1 are amino-acid substitutions at particular sites (e.g., S42P, S42G, D92E, D92Y, I106M and A149V) that are responsible for virus growth, the ability to inhibit induction of IFN in vitro and in vivo, and viral pathogenesis in mice. 2018 Virology journal Discussion IV S42P;S42G;D92E;D92Y;I106M;A149V 86;92;98;104;110;120 90;96;102;108;115;125 NS1 26 29 29587786 Effects of the S42 residue of the H1N1 swine influenza virus NS1 protein on interferon responses and virus replication. The D92E substitution increased the instability index and had no effect on the hydrophilicity of the proteins, and D92E was still able to influence the antiviral response by inhibiting IFN-alpha/beta production. 2018 Virology journal Discussion IV D92E;D92E 4;115 8;119 29587786 Effects of the S42 residue of the H1N1 swine influenza virus NS1 protein on interferon responses and virus replication. The hydrophilicity of the NS1 S42P mutant was lower than NS1 [A/Swine/Shanghai/3/2014(H1N1)]. 2018 Virology journal Discussion IV S42P 30 34 NS1;NS1 26;57 29;60 29587786 Effects of the S42 residue of the H1N1 swine influenza virus NS1 protein on interferon responses and virus replication. The S42 residue was located within the RNA-binding domain (RBD) and the S42P site mutation decreased its protein hydrophobicity and thus might influence its interaction with RNAs or host proteins. 2018 Virology journal Discussion IV S42P 72 76 29587786 Effects of the S42 residue of the H1N1 swine influenza virus NS1 protein on interferon responses and virus replication. We found that substitution of proline for serine at position 42 led to elevated IFN-alpha and IFN-beta transcription levels. 2018 Virology journal Discussion IV S42P 30 63 29587792 Major contribution of the RNA-binding domain of NS1 in the pathogenicity and replication potential of an avian H7N1 influenza virus in chickens. As for the ED, our data show that it is involved in two activities that are both abolished by the A149V substitution. 2018 Virology journal Discussion IV A149V 98 103 29587792 Major contribution of the RNA-binding domain of NS1 in the pathogenicity and replication potential of an avian H7N1 influenza virus in chickens. First, it was recently shown that NS1, unlike its R38A-K41A mutant, binds both NXF1 and the late viral mRNAs (notably HA-mRNA and the unspliced viral M1 mRNA), thereby directing the latter to the nuclear export pathway. 2018 Virology journal Discussion IV K41A;R38A 55;50 59;54 HA;M1;NS1 118;150;34 120;152;37 29587792 Major contribution of the RNA-binding domain of NS1 in the pathogenicity and replication potential of an avian H7N1 influenza virus in chickens. Firstly, in agreement with previous reports, we observed that wt-NS1, unlike its A149V variant, decreased the IFN-response of L-poly(I:C)-stimulated avian cells, as measured by the activity of the chMx-promoter. 2018 Virology journal Discussion IV A149V 81 86 NS1 65 68 29587792 Major contribution of the RNA-binding domain of NS1 in the pathogenicity and replication potential of an avian H7N1 influenza virus in chickens. However, the R38A-K41A substitution did not abrogate this effect; on the contrary, it further reduced the activity of the IFN-responsive Mx promoter. 2018 Virology journal Discussion IV R38A;K41A 13;18 17;22 29587792 Major contribution of the RNA-binding domain of NS1 in the pathogenicity and replication potential of an avian H7N1 influenza virus in chickens. In a well-established chicken model of avian influenza virus infection, the wt-virus induced severe respiratory symptoms and deaths while the symptoms were much less severe in the A149V-inoculated birds and infection remained silent in the 3841AA-inoculated birds. 2018 Virology journal Discussion IV A149V 180 185 IV infections;Acute respiratory distress syndrome 45;100 70;120 29587792 Major contribution of the RNA-binding domain of NS1 in the pathogenicity and replication potential of an avian H7N1 influenza virus in chickens. in A149V-NS1), these two domains acted synergistically, resulting in a more than twofold increase in the polymerase activity. 2018 Virology journal Discussion IV A149V 3 8 NS1 9 12 29587792 Major contribution of the RNA-binding domain of NS1 in the pathogenicity and replication potential of an avian H7N1 influenza virus in chickens. In addition, we speculate that the R38A-K41A NS1 may still bind the synthetic dsRNA of L-poly(I:C) and thereby prevent the activation of the RIG-like receptor pathway. 2018 Virology journal Discussion IV R38A;K41A 35;40 39;44 NS1 45 48 29587792 Major contribution of the RNA-binding domain of NS1 in the pathogenicity and replication potential of an avian H7N1 influenza virus in chickens. Indeed, while NS1 reached a very high concentration in wt virus-infected cells, its concentration in 3841AA-infected cells was reduced by about 4 to 8-fold relative to that in wt-infected cells, and slightly reduced in A149V-infected cells. 2018 Virology journal Discussion IV A149V 219 224 NS1 14 17 29587792 Major contribution of the RNA-binding domain of NS1 in the pathogenicity and replication potential of an avian H7N1 influenza virus in chickens. More specifically, this interaction was shown to rely on the binding of NS1's RBD to the viral nucleoprotein NP, a binding that was abolished by the double substitution R38A-K41A. 2018 Virology journal Discussion IV R38A;K41A 169;174 173;178 NP;NS1;NP 109;72;95 111;75;108 29587792 Major contribution of the RNA-binding domain of NS1 in the pathogenicity and replication potential of an avian H7N1 influenza virus in chickens. On the one hand, we introduced in the RNA-binding domain the double substitution R38A-K41A, which is considered to abrogate its RNA-binding properties; on the other hand, the ED was modified by substitution A149V, which was previously shown to alter the IFN-antagonist activity of NS1 in avian cells. 2018 Virology journal Discussion IV R38A;K41A;A149V 81;86;207 85;90;212 NS1 281 284 29587792 Major contribution of the RNA-binding domain of NS1 in the pathogenicity and replication potential of an avian H7N1 influenza virus in chickens. On the other hand, we observed that the double substitution R38A-K41A did not substantially alter the binding of the recombinant RBD to a model dsRNA. 2018 Virology journal Discussion IV K41A;R38A 65;60 69;64 29587792 Major contribution of the RNA-binding domain of NS1 in the pathogenicity and replication potential of an avian H7N1 influenza virus in chickens. Specifically, transient expression of wt-NS1 from the WSN virus was shown to prevent the Sendai virus-induced IFN-beta response in 293 T cells, while WSN-NS1 harbouring the double substitution R38A-K41A was unable to reduce this IFN-beta response. 2018 Virology journal Discussion IV K41A;R38A 198;193 202;197 NS1;NS1 41;154 44;157 29587792 Major contribution of the RNA-binding domain of NS1 in the pathogenicity and replication potential of an avian H7N1 influenza virus in chickens. Substitution A149V consistently abolished this effect. 2018 Virology journal Discussion IV A149V 13 18 29587792 Major contribution of the RNA-binding domain of NS1 in the pathogenicity and replication potential of an avian H7N1 influenza virus in chickens. Substitution A149V in the ED abolished this effect, in agreement with the critical role of the effector domain in dampening the IFN response. 2018 Virology journal Discussion IV A149V 13 18 29587792 Major contribution of the RNA-binding domain of NS1 in the pathogenicity and replication potential of an avian H7N1 influenza virus in chickens. The different pathological outcomes were reflected both by the M-vRNA loads in tissues and in the histopathological findings, while the distinct replication efficiencies of the three viruses in vivo were correlated to similar phenotypes in vitro: replication of the A149V mutant was slightly reduced relative to that of the wt-virus in both embryonated eggs and in the chicken lung epithelial cell line CLEC213, while that of the 3841AA-virus was severely reduced in eggs and non-measurable in the avian cell line. 2018 Virology journal Discussion IV A149V 266 271 M 63 64 29587792 Major contribution of the RNA-binding domain of NS1 in the pathogenicity and replication potential of an avian H7N1 influenza virus in chickens. The polymerase enhancing property of NS1 was reduced by the double substitution R38A-K41A, and virtually unaltered by the A149V substitution. 2018 Virology journal Discussion IV R38A;K41A;A149V 80;85;122 84;89;127 NS1 37 40 29587792 Major contribution of the RNA-binding domain of NS1 in the pathogenicity and replication potential of an avian H7N1 influenza virus in chickens. The R38A-K41A NS1 mutant of the PR/8 virus was shown to exhibit a severe defect in the nuclear export of HA- and M1-mRNAs. 2018 Virology journal Discussion IV R38A;K41A 4;9 8;13 HA;M1;NS1 105;113;14 107;115;17 29587792 Major contribution of the RNA-binding domain of NS1 in the pathogenicity and replication potential of an avian H7N1 influenza virus in chickens. Therefore, if we disregard these potentially biased observations, our data indicated that (i) the individually-expressed wt-RBD, but not its 3841AA mutant, induced a ~ 38% increase in the polymerase activity; (ii) the individually-expressed A149V-ED induced a ~ 30% increase in the polymerase activity; (iii) when adjoined. 2018 Virology journal Discussion IV A149V 241 246 29593694 Amino Acid Substitutions HA A150V, PA A343T, and PB2 E627K Increase the Virulence of H5N6 Influenza Virus in Mice. All viruses containing single substitution has a lower mice survival rate than r6D2-WT, however, the results of cell infection and in vivo study seems that virus containing HA A150V and/or PA A343T attenuate PB2 mutation (Figure 2B). 2018 Frontiers in microbiology Discussion IV A150V;A343T 176;192 181;197 HA;PA;PB2 173;189;208 175;191;211 29593694 Amino Acid Substitutions HA A150V, PA A343T, and PB2 E627K Increase the Virulence of H5N6 Influenza Virus in Mice. Although we didn't observe any contribution by PA A343T to replication in A549 and MDCK (Figure 4), our results suggest that PA A343T mildly increases polymerase activity when compared to the wild-type influenza polymerase (Figure 6). 2018 Frontiers in microbiology Discussion IV A343T;A343T 50;128 55;133 PA;PA 47;125 49;127 29593694 Amino Acid Substitutions HA A150V, PA A343T, and PB2 E627K Increase the Virulence of H5N6 Influenza Virus in Mice. Another study indicated that PA A343T alone does not significantly enhance the replication capability. 2018 Frontiers in microbiology Discussion IV A343T 32 37 PA 29 31 29593694 Amino Acid Substitutions HA A150V, PA A343T, and PB2 E627K Increase the Virulence of H5N6 Influenza Virus in Mice. However, our receptor binding assay suggests the recombinant H5N6 virus bearing HA A150V not only abolished the SAalpha-2,3Gal affinity, but also greatly enhanced SAalpha-2,6Gal binding. 2018 Frontiers in microbiology Discussion IV A150V 83 88 HA 80 82 29593694 Amino Acid Substitutions HA A150V, PA A343T, and PB2 E627K Increase the Virulence of H5N6 Influenza Virus in Mice. However, they didn't generate the virus containing only HA A150V. 2018 Frontiers in microbiology Discussion IV A150V 59 64 HA 56 58 29593694 Amino Acid Substitutions HA A150V, PA A343T, and PB2 E627K Increase the Virulence of H5N6 Influenza Virus in Mice. However, with a single PB2 E627K, the avian influenza virus polymerase activity is still lower than the seasonal human influenza virus. 2018 Frontiers in microbiology Discussion IV E627K 27 32 PB2 23 26 29593694 Amino Acid Substitutions HA A150V, PA A343T, and PB2 E627K Increase the Virulence of H5N6 Influenza Virus in Mice. Our study revealed the role of HA A150V in the binding of human like receptor, as shown by virulence enhancement in mice and increase of virus titer in A549 cells. 2018 Frontiers in microbiology Discussion IV A150V 34 39 HA 31 33 29593694 Amino Acid Substitutions HA A150V, PA A343T, and PB2 E627K Increase the Virulence of H5N6 Influenza Virus in Mice. PA A343T and PB2 E627K improved the efficiency of viral polymerase. 2018 Frontiers in microbiology Discussion IV A343T;E627K 3;17 8;22 PA;PB2 0;13 2;16 29593694 Amino Acid Substitutions HA A150V, PA A343T, and PB2 E627K Increase the Virulence of H5N6 Influenza Virus in Mice. PA A343T may affect the binding between these two subunits and change the efficiency of viral polymerase. 2018 Frontiers in microbiology Discussion IV A343T 3 8 PA 0 2 29593694 Amino Acid Substitutions HA A150V, PA A343T, and PB2 E627K Increase the Virulence of H5N6 Influenza Virus in Mice. PB2 E627K is a well-characterized substitution in mammalian adaption of avian influenza viruses. 2018 Frontiers in microbiology Discussion IV E627K 4 9 PB2 0 3 29593694 Amino Acid Substitutions HA A150V, PA A343T, and PB2 E627K Increase the Virulence of H5N6 Influenza Virus in Mice. The finding that combined PA A343T and PB2 E627K act synergistically in minigenome assay provides a new avenue for influenza virus adaption research. 2018 Frontiers in microbiology Discussion IV A343T;E627K 29;43 34;48 PA;PB2 26;39 28;42 29593694 Amino Acid Substitutions HA A150V, PA A343T, and PB2 E627K Increase the Virulence of H5N6 Influenza Virus in Mice. used the HA from H5N1 and the other seven segments from PR8 and concluded that HA A150V reduced the affinity to avian like receptor with no human like receptor binding increase detected. 2018 Frontiers in microbiology Discussion IV A150V 82 87 HA;HA 9;79 11;81 29593694 Amino Acid Substitutions HA A150V, PA A343T, and PB2 E627K Increase the Virulence of H5N6 Influenza Virus in Mice. Using solid-phase direct binding assay, another study indicates that the HA A150V stabilized the interaction between SAalpha2,6Gal and the virus receptor binding site. 2018 Frontiers in microbiology Discussion IV A150V 76 81 HA 73 75 29593694 Amino Acid Substitutions HA A150V, PA A343T, and PB2 E627K Increase the Virulence of H5N6 Influenza Virus in Mice. We further explored the potential mechanism and concluded that HA A150V altered receptor binding preference, from avian to human type. 2018 Frontiers in microbiology Discussion IV A150V 66 71 HA 63 65 29630683 The use of plant lectins to regulate H1N1 influenza A virus receptor binding activity. According to previous studies, the S183P mutation enhances virulence by altering binding to SA receptors in a mouse animal model. 2018 PloS one Discussion IV S183P 35 40 29630683 The use of plant lectins to regulate H1N1 influenza A virus receptor binding activity. However, CA/04+Calu-3 carrying a single S183P mutation did not show higher replication titers in Calu-3 cells compared to the wild-type CA/04. 2018 PloS one Discussion IV S183P 40 45 29630683 The use of plant lectins to regulate H1N1 influenza A virus receptor binding activity. On the other hand, CA/04+MAA acquired the G201E NA mutation, which decreased NA activity in catalyzing 3'SLN and led to efficient virus attachment to this particular sialic receptor. 2018 PloS one Discussion IV G201E 42 47 NA;NA 48;77 50;79 29630683 The use of plant lectins to regulate H1N1 influenza A virus receptor binding activity. Our findings are consistent with the study by O'Donnell et al., and confirmed that the S183P was an absorptive mutation. 2018 PloS one Discussion IV S183P 87 92 29630683 The use of plant lectins to regulate H1N1 influenza A virus receptor binding activity. Our in vitro selection study led to the identification of three amino acid substitutions in the HA protein (N129D, G155E, and S183P) that affected the H1 HA receptor binding specificity. 2018 PloS one Discussion IV N129D;G155E;S183P 108;115;126 113;120;131 HA;HA 96;154 98;156 29630683 The use of plant lectins to regulate H1N1 influenza A virus receptor binding activity. Our studies identified N129D and G155E as antigenic mutations. 2018 PloS one Discussion IV N129D;G155E 23;33 28;38 29630683 The use of plant lectins to regulate H1N1 influenza A virus receptor binding activity. The G155E change completely abrogated binding by MAbs 28665 and 28668, and the N129D mutation diminished binding by MAb 28665, but increased affinity to MAb 28668 relative to G155E. 2018 PloS one Discussion IV G155E;N129D;G155E 4;79;175 9;84;180 29630683 The use of plant lectins to regulate H1N1 influenza A virus receptor binding activity. The N129D mutation is located outside the major antigenic site, Sa, where the amino acid 155 was previously mapped to. 2018 PloS one Discussion IV N129D 4 9 29630683 The use of plant lectins to regulate H1N1 influenza A virus receptor binding activity. The S183P mutation is located within the receptor-binding site, and overlaps with antigenic site, Sb. 2018 PloS one Discussion IV S183P 4 9 29630683 The use of plant lectins to regulate H1N1 influenza A virus receptor binding activity. The S183P mutation significantly increased binding to a number of alpha2,6 SA-linked receptors, including YDS, 6'SL(N), and 6-Su-6'SLN. 2018 PloS one Discussion IV S183P 4 9 29630683 The use of plant lectins to regulate H1N1 influenza A virus receptor binding activity. Thus, the G201E NA change compensated for the G155E HA1 mutation and provided an advantage for CA/04+MAA virus growth due to functional compatibility between HA and NA proteins. 2018 PloS one Discussion IV G201E;G155E 10;46 15;51 HA;HA1;NA;NA 158;52;16;165 160;55;18;167 29630683 The use of plant lectins to regulate H1N1 influenza A virus receptor binding activity. Thus, the N129D mutation present only in the CA/04+SNA virus may provide an advantage in overcoming the neutralizing effects of antibody by allowing and/or increasing recognition of host cell receptors even in the presence of such antibodies. 2018 PloS one Discussion IV N129D 10 15 29630683 The use of plant lectins to regulate H1N1 influenza A virus receptor binding activity. Two other changes, N129D and G155E, were sufficient to significantly increase binding to alpha2,6-linked glycans, 6'SLN and 6-Su-6'SLN, compared to S183P. 2018 PloS one Discussion IV N129D;G155E;S183P 19;29;148 24;34;153 29630683 The use of plant lectins to regulate H1N1 influenza A virus receptor binding activity. While it is unknown whether 183P has an effect on virulence in humans, the high frequency of the S183P mutation in contemporary H1N1 viruses in 2017 suggests that this mutation is being strongly selected for in humans. 2018 PloS one Discussion IV S183P 97 102 29643248 A Single Amino Acid in the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses. As rVc_BR60PA:K338R showed higher pathogenicity than rVc_BR60 in our mouse and ferret models. 2018 Journal of virology Discussion IV K338R 14 19 29643248 A Single Amino Acid in the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses. By showing that PA K338R could render both homologous and heterologous IBV pathogenicity, we demonstrated that specific amino acid signatures at PA residue 338 might determine IBV pathogenicity. 2018 Journal of virology Discussion IV K338R 19 24 PA;PA 16;145 18;147 29643248 A Single Amino Acid in the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses. Even though enhanced viral polymerase complex activities resulting from the PA K338R mutation were not sufficiently correlated with the pathogenicity of rVc_BR60/WI01PA:K338R and rYm_WI01/BR60PA:K338R. 2018 Journal of virology Discussion IV K338R;K338R;K338R 79;169;195 84;174;200 PA 76 78 29643248 A Single Amino Acid in the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses. Given all of these results, the PA K338R mutation can be suggested for its effects on IBV pathogenicity, which might result from the change of the functional activity of the viral polymerase complex. 2018 Journal of virology Discussion IV K338R 35 40 PA 32 34 29643248 A Single Amino Acid in the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses. Given that the PA K338R mutation can arise during the serial adaptation of IBVs in mice (our results) or in cell cultures, it should be noted that, as identified in some seasonal IBV strains (see Table S1 in the supplemental material), the PA K338R mutation that exhibited increased viral pathogenicity in mice and ferrets may also arise in circulating IBVs. 2018 Journal of virology Discussion IV K338R;K338R 18;243 23;248 PA;PA 15;240 17;242 29643248 A Single Amino Acid in the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses. Given the appearance of the K338R mutation in the PAs of both Victoria and Yamagata lineage viruses during adaptation in mice and the increased virulence in vitro and in vivo of the PA K338R mutants, we here suggest that the PA K338R mutation may be one of the molecular determinants of IBV pathogenicity and that its potential mechanism might be closely related to the change of the biological function of the viral polymerase complex of IBVs. 2018 Journal of virology Discussion IV K338R;K338R;K338R 28;185;228 33;190;233 PA;PA;PA 182;225;50 184;227;53 29643248 A Single Amino Acid in the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses. Given the reassortment incompatibility of the PA K338R mutation of Vc_BR60 with other viral polymerase complex protein genes. 2018 Journal of virology Discussion IV K338R 49 54 PA 46 48 29643248 A Single Amino Acid in the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses. Hence, due to the presence of various genetic clades within the PA of Yamagata lineage IBVs, not the genetic lineage of certain genetic segments but the overall gene constellation of IBVs should be considered for the effects of PA K338R on IBV pathogenicity. 2018 Journal of virology Discussion IV K338R 231 236 PA;PA 64;228 66;230 29643248 A Single Amino Acid in the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses. However, in contrast to our expectation, rYm_WI01/BR60PA and rYm_WI01/BR60PA:K338R appeared to be much less fit. 2018 Journal of virology Discussion IV K338R 77 82 29643248 A Single Amino Acid in the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses. However, there were no significant differences in viral replication kinetics between the parental and PA K338R mutant viruses under the tested temperature and infection conditions. 2018 Journal of virology Discussion IV K338R 105 110 PA 102 104 29643248 A Single Amino Acid in the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses. However, we paid attention to the PA K338R mutation because it was the only mutation identified from both maVc_BR60 and maYm_WI01, and this mutation alone appeared to transform IBV pathogenicity in mice. 2018 Journal of virology Discussion IV K338R 37 42 PA 34 36 29643248 A Single Amino Acid in the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses. In addition, PA residue 338 is found as one of the amino acid residues in alpha-helices of the PA protein structure, so the PA K338R mutation might eventually affect the polymerase complex activity and pathogenicity of IBVs. 2018 Journal of virology Discussion IV K338R 127 132 PA;PA;PA 13;95;124 15;97;126 29643248 A Single Amino Acid in the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses. In this regard, our finding, the PA K338R mutation, may have significance for assessments of health risks of IBVs. 2018 Journal of virology Discussion IV K338R 36 41 PA 33 35 29643248 A Single Amino Acid in the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses. Interestingly, in a recent study reported by Chai et al., the authors adapted the Vc_BR60 strain in MDCK cells under the pressure of an HA-specific human monoclonal antibody, and they observed the PA K338R mutation along with other mutations in the PB2-, PB1-, PA-, NA-, BM2-, and NS1-coding regions. 2018 Journal of virology Discussion IV K338R 200 205 BM2;HA;NA;NS1;PA;PA;PB1;PB2 271;136;266;281;197;261;255;249 274;138;268;284;199;263;258;252 29643248 A Single Amino Acid in the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses. pVc_BR60PA:K338R showed higher polymerase activity than pVc_BR60. 2018 Journal of virology Discussion IV K338R 11 16 29643248 A Single Amino Acid in the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses. S1B), it could be expected that viral pathogenicity and polymerase complex activity of rYm_WI01/BR60PA and rYm_WI01/BR60PA:K338R might be comparable to those of rYm_WI01 and rYm_WI01PA:K338R. 2018 Journal of virology Discussion IV K338R;K338R 123;185 128;190 29643248 A Single Amino Acid in the Polymerase Acidic Protein Determines the Pathogenicity of Influenza B Viruses. the PA K338R mutation affected the viral replication competence of rVc_BR60 and rYm_WI01 in the upper and lower respiratory tracts of ferrets. 2018 Journal of virology Discussion IV K338R 7 12 PA 4 6 29688498 Dynamic Variation and Reversion in the Signature Amino Acids of H7N9 Virus During Human Infection. A previous study indicated that the introduction of the R292K mutation into the NA segment leads to competitive fitness loss by avian H7N9 influenza virus. 2018 The Journal of infectious diseases Discussion IV R292K 56 61 80 82 29688498 Dynamic Variation and Reversion in the Signature Amino Acids of H7N9 Virus During Human Infection. A previous study showed that NA R292K emerged under antiviral pressure conferred by NAI treatment and was associated with adverse clinical outcomes. 2018 The Journal of infectious diseases Discussion IV R292K 32 37 NA;NAI 29;84 31;87 29688498 Dynamic Variation and Reversion in the Signature Amino Acids of H7N9 Virus During Human Infection. Although dual E627K and D701N mutations in the PB2 segment confer higher H7N9 viral polymerase activity and improve viral replication in mammalian cells over a single E627K or D701N mutation, this dual mutation did not achieve predominance in any sample during disease development, potentially hampering its capacity for human-to-human transmission. 2018 The Journal of infectious diseases Discussion IV E627K;D701N;E627K;D701N 14;24;167;176 19;29;172;181 PB2 47 50 29688498 Dynamic Variation and Reversion in the Signature Amino Acids of H7N9 Virus During Human Infection. Even under antiviral pressure conferred by NAI and the emergence of drug-resistant mutation NA R292K, the WT 292R virus persisted in viral populations, and selection for resistant genotypes was not obligatory. 2018 The Journal of infectious diseases Discussion IV R292K 95 100 NA;NAI 92;43 94;46 29688498 Dynamic Variation and Reversion in the Signature Amino Acids of H7N9 Virus During Human Infection. However, the E627K mutation is not always monodirectional, as the WT 627E genotype was maintained alongside the mammalian 627K genotype throughout 10 days of infection in cases 10 and 11, and the proportion of 627K was stable in case 10 (Figure 2B). 2018 The Journal of infectious diseases Discussion IV E627K 13 18 29688498 Dynamic Variation and Reversion in the Signature Amino Acids of H7N9 Virus During Human Infection. In case 8, the isoleucine detected at the first timepoint transformed to leucine after 4 days and persisted thereafter, indicating that isoleucine may be an intermediate amino acid during the transition from glutamine to leucine at the 226 position. 2018 The Journal of infectious diseases Discussion IV Q226L 208 248 29688498 Dynamic Variation and Reversion in the Signature Amino Acids of H7N9 Virus During Human Infection. Other molecular signatures, such as T160A and G186V/I mutations, were detected in some patients, but only a few samples contained mixed genotypes. 2018 The Journal of infectious diseases Discussion IV T160A;G186V;G186I 36;46;46 41;53;53 29688498 Dynamic Variation and Reversion in the Signature Amino Acids of H7N9 Virus During Human Infection. Our study also detected the PB2 K526R mutation (a "functionally equivalent" mutation) in cases 1 and 2, in whom the viruses lacked PB2 627K (Table 2). 2018 The Journal of infectious diseases Discussion IV K526R 32 37 PB2;PB2 28;131 31;134 29688498 Dynamic Variation and Reversion in the Signature Amino Acids of H7N9 Virus During Human Infection. Similarly, although the PB2 E627K and D701N mutations favor avian influenza virus infection in mammals, they undergo fluctuation and reversion during mammalian adaption. 2018 The Journal of infectious diseases Discussion IV E627K;D701N 28;38 33;43 PB2 24 27 IV infections 66 91 29688498 Dynamic Variation and Reversion in the Signature Amino Acids of H7N9 Virus During Human Infection. The D701N mutation was also present in the form of a mixed 701D/N population, and the ratio was constant throughout disease progression (Table 2). 2018 The Journal of infectious diseases Discussion IV D701N 4 9 29743603 Unexpected infection outcomes of China-origin H7N9 low pathogenicity avian influenza virus in turkeys. A dose effect is the likely cause of these differences, but it is speculated that a greater distribution of avian receptors in multiple turkey tissues may have assisted systemic dissemination of LPAIV infection (with consequences for virulence) following the L235Q switch. 2018 Scientific reports Discussion IV L235Q 259 264 IAV infections 195 210 29743603 Unexpected infection outcomes of China-origin H7N9 low pathogenicity avian influenza virus in turkeys. However, other than the L235Q switch, the HA protein sequences of the four H7N9 R2 turkey isolates and the chicken D0 isolate remained identical (Table 2), suggesting that HA acid-stability may be an unlikely factor in explaining differences in transmission, systemic dissemination and pathogenesis in both hosts. 2018 Scientific reports Discussion IV L235Q 24 29 HA;HA 42;172 44;174 29743603 Unexpected infection outcomes of China-origin H7N9 low pathogenicity avian influenza virus in turkeys. The fusion pH in H7N9 LPAIV decreased due to the L235Q polymorphism, but it is unclear whether this altered acid-stability may influence the enhanced dissemination and virulence in turkeys. 2018 Scientific reports Discussion IV L235Q 49 54 29743603 Unexpected infection outcomes of China-origin H7N9 low pathogenicity avian influenza virus in turkeys. The L235Q change in the HA was detected soon after infection of D0 birds (both species) and was maintained during efficient transmission to R2 turkeys. 2018 Scientific reports Discussion IV L235Q 4 9 HA 24 26 29743603 Unexpected infection outcomes of China-origin H7N9 low pathogenicity avian influenza virus in turkeys. The L235Q polymorphism appears to be a reversion away from human receptor binding, and was previously reported following chicken infection both in in vivo and in ovo. 2018 Scientific reports Discussion IV L235Q 4 9 29743603 Unexpected infection outcomes of China-origin H7N9 low pathogenicity avian influenza virus in turkeys. This polymorphism is long-known to affect avian to mammalian adaptation of IAVs, whereby Q235L influences a general change in host cell receptor preference from those which possess alpha-2,3 to alpha-2,6 sialic acid linkages, known as "avian" and "human" receptors respectively, although H7N9 wt (L235) binds to both alpha-2,3 and alpha-2,6 receptors with a slight preference for the former. 2018 Scientific reports Discussion IV Q235L 89 94 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. After several blind passages in A549, MDCK, or Vero cells, the NS1 R38A/K41A virus could hardly be detected. 2018 Frontiers in cellular and infection microbiology Discussion IV R38A;K41A 67;72 71;76 NS1 63 66 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. As previously reported, passaging the NS1 R38A/K41A virus in MDCK cells three times resulted in the selection of a mutant virus containing a third mutation at amino acid residue 42 of the NS1 protein (S42G) (Donelan et al.,). 2018 Frontiers in cellular and infection microbiology Discussion IV K41A;R38A;S42G 47;42;201 51;46;205 NS1;NS1 38;188 41;191 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. However, we did not find the S42G mutation or any other mutation when the NS1 R38A/K41A virus was continuously passaged in NS1-expressing Vero cells for 20 passages. 2018 Frontiers in cellular and infection microbiology Discussion IV S42G;K41A;R38A 29;83;78 33;87;82 NS1;NS1 74;123 77;126 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. In our studies, the titers of the NS1 R38A/K41A virus reached 5-6 log10 PFU/mL in the NS1-expressing Vero cells after three passages. 2018 Frontiers in cellular and infection microbiology Discussion IV R38A;K41A 38;43 42;47 NS1;NS1 34;86 37;89 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. In summary, we observed that the IFN-sensitive NS1 R38A/K41A influenza virus exerted full infectivity but its replication was limited. 2018 Frontiers in cellular and infection microbiology Discussion IV K41A;R38A 56;51 60;55 NS1 47 50 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. In the present study, we selected the Vero cell line as the production cell line to propagate the NS1 R38A/K41A virus. 2018 Frontiers in cellular and infection microbiology Discussion IV R38A;K41A 102;107 106;111 NS1 98 101 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. In this study, we demonstrated that the NS1 R38A/K41A virus could not survive in cells and mice for a long time because of its functional defects and that its life cycle was limited. 2018 Frontiers in cellular and infection microbiology Discussion IV K41A;R38A 49;44 53;48 NS1 40 43 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. Our data showed that the NS1 R38A/K41A virus could not be detected in Vero cells after five passages, suggesting that the absence of IFN-alpha/beta was not sufficient for the replication of the NS1 R38A/K41A virus. 2018 Frontiers in cellular and infection microbiology Discussion IV R38A;K41A;R38A;K41A 29;34;198;203 33;38;202;207 NS1;NS1 25;194 28;197 29765910 A Promising IFN-Deficient System to Manufacture IFN-Sensitive Influenza Vaccine Virus. The NS1 R38A/K41A virus was able to steadily propagate in this NS1-expressing Vero cell line for at least 20 passages. 2018 Frontiers in cellular and infection microbiology Discussion IV R38A;K41A 8;13 12;17 NS1;NS1 4;63 7;66 29783694 Adaptive Mutations in Influenza A/California/07/2009 Enhance Polymerase Activity and Infectious Virion Production. A single amino acid substitution D222G was shown to increase binding of HA to alpha 2,3-sialic acid, and we identified this mutation in our CA/07-MA virus. 2018 Viruses Discussion IV D222G 33 38 HA 72 74 29783694 Adaptive Mutations in Influenza A/California/07/2009 Enhance Polymerase Activity and Infectious Virion Production. Another notable HA substitution that appeared at only a 44.5% frequency in CA/07-MA, S84N, was found in human isolates of pandemic H1N1 and was shown to increase in prevalence, yet has not been linked to mouse adaptation so far. 2018 Viruses Discussion IV S84N 85 89 HA 16 18 29783694 Adaptive Mutations in Influenza A/California/07/2009 Enhance Polymerase Activity and Infectious Virion Production. At the same time, we observed the emergence of an E349G substitution in PA that reached over 99% read frequency, and two substitutions in PB1: F740L at 49.8% and T156A at 36.3% (Figure 2). 2018 Viruses Discussion IV E349G;F740L;T156A 50;143;162 55;148;167 PA;PB1 72;138 74;141 29783694 Adaptive Mutations in Influenza A/California/07/2009 Enhance Polymerase Activity and Infectious Virion Production. Because the E349G substitution arose from several independent mouse adaptation studies, it may be important for RdRp function in mouse cells, potentially via interaction with a host factor, which in turn may influence DVG production. 2018 Viruses Discussion IV E349G 12 17 29783694 Adaptive Mutations in Influenza A/California/07/2009 Enhance Polymerase Activity and Infectious Virion Production. By contrast, three pre-existing non-synonymous sequence variations were negatively selected in mice and fell below a 1% frequency: HA D127E, NP D101G and NP G102R (Table S2). 2018 Viruses Discussion IV D127E;D101G;G102R 134;144;157 139;149;162 HA;NP;NP 131;141;154 133;143;156 29783694 Adaptive Mutations in Influenza A/California/07/2009 Enhance Polymerase Activity and Infectious Virion Production. Extrapolating from this model, we speculate that the E349G substitution may affect the formation of dimeric and/or tetrameric polymerase subcomplexes. 2018 Viruses Discussion IV E349G 53 58 29783694 Adaptive Mutations in Influenza A/California/07/2009 Enhance Polymerase Activity and Infectious Virion Production. In the reconstituted viral minireplicon assay, only the PA E349G substitution led to a significant increase in RNA polymerase activity compared to the wild-type (Figure 4). 2018 Viruses Discussion IV E349G 59 64 PA 56 58 29783694 Adaptive Mutations in Influenza A/California/07/2009 Enhance Polymerase Activity and Infectious Virion Production. Namely, the HA substitutions D222G (at 53.9% frequency, Table S2), S183P (22.8%) and D127E (5.2%) were described in, and NP D101G (3.1%) was described in. 2018 Viruses Discussion IV D222G;S183P;D127E;D101G 29;67;85;124 34;72;90;129 HA;NP 12;121 14;123 29783694 Adaptive Mutations in Influenza A/California/07/2009 Enhance Polymerase Activity and Infectious Virion Production. Of two additional HA mutations that reached >99% frequency in the CA/07-MA strain, S183P substitution was previously identified by Ilyushina et al., while N156D was found only in our study. 2018 Viruses Discussion IV S183P;N156D 83;155 88;160 HA 18 20 29783694 Adaptive Mutations in Influenza A/California/07/2009 Enhance Polymerase Activity and Infectious Virion Production. The HA D222G mutation was also found in the two similar CA/04 mouse adaptation studies, which distinguishes it from other adaptive mutations in HA that were less reproducible. 2018 Viruses Discussion IV D222G 7 12 HA;HA 4;144 6;146 29783694 Adaptive Mutations in Influenza A/California/07/2009 Enhance Polymerase Activity and Infectious Virion Production. The PA A638R mutation was previously linked to an increase in the production of DVGs, while the D529N mutation was shown to decrease DVG accumulation. 2018 Viruses Discussion IV A638R;D529N 7;96 12;101 PA 4 6 29783694 Adaptive Mutations in Influenza A/California/07/2009 Enhance Polymerase Activity and Infectious Virion Production. This mutation has been previously identified after sequential passaging of both A/Puerto Rico/8/34 (H1N1) and (A/chicken/Hubei/01/1999) (H9N2) viruses in mice, and Rolling et al., showed that PA E349G contributed to enhanced polymerase activity and increased titres in the mouse lung following the generation of a recombinant PR8 virus bearing this mutation. 2018 Viruses Discussion IV E349G 195 200 PA 192 194 29783694 Adaptive Mutations in Influenza A/California/07/2009 Enhance Polymerase Activity and Infectious Virion Production. This suggests that PA E349G is a marker of mouse adaptation because it dramatically increases minireplicon activity in mouse cells, while the increase in minireplicon activity in human cells is more modest (Figure 4). 2018 Viruses Discussion IV E349G 22 27 PA 19 21 29783694 Adaptive Mutations in Influenza A/California/07/2009 Enhance Polymerase Activity and Infectious Virion Production. Thus, despite its location away from the cluster of residues affecting DVG production, the E349G substitution could affect the efficiency of elongation. 2018 Viruses Discussion IV E349G 91 96 29783694 Adaptive Mutations in Influenza A/California/07/2009 Enhance Polymerase Activity and Infectious Virion Production. Two of these substitutions reached >99% frequency following serial lung-to-lung passaging in mice and plaque-purification in MDCK cells (D222G and S183P in HA). 2018 Viruses Discussion IV D222G;S183P 137;147 142;152 HA 156 158 29882021 Lethal Influenza in Two Related Adults with Inherited GATA2 Deficiency. Patients carried a novel, R396L, germline heterozygous mutation of the GATA2 gene. 2018 Journal of clinical immunology Discussion IV R396L 26 31 29927982 Influenza D virus M2 protein exhibits ion channel activity in Xenopus laevis oocytes. In both types of mutated DM2, the gating potential was decreased, although this decrease was greater in Y72A than in K76A (Table 1). 2018 PloS one Discussion IV Y72A;K76A 104;117 108;121 29927982 Influenza D virus M2 protein exhibits ion channel activity in Xenopus laevis oocytes. In DM2 Lys76Ala, the cation was removed and a hydrophobic side chain was introduced. 2018 PloS one Discussion IV K76A 7 15 29927982 Influenza D virus M2 protein exhibits ion channel activity in Xenopus laevis oocytes. The reversal potentials of the ion channels (Table 2) suggested that DM2, Y72A, and K76A conduct chloride ions as CM2 does, as their reversal potentials in ND96 solution (103.6 mM Cl-) do not differ significantly. 2018 PloS one Discussion IV Y72A;K76A 74;84 78;88 CM2 114 117 29927982 Influenza D virus M2 protein exhibits ion channel activity in Xenopus laevis oocytes. Trp41Ala substitution in AM2 was reported to result in the complete loss of ion channel activity. 2018 PloS one Discussion IV W41A 0 8 29927982 Influenza D virus M2 protein exhibits ion channel activity in Xenopus laevis oocytes. With DM2 Tyr72Ala, the pi provider was removed, so the amino acid remained hydrophobic. 2018 PloS one Discussion IV Y72A 9 17 29933553 Kinetic, Thermodynamic, and Structural Analysis of Drug Resistance Mutations in Neuraminidase from the 2009 Pandemic Influenza Virus. Compared to wt, the sensitivity of the H275Y single mutant to oseltamivir decreased considerably (more than 1000-fold increase in Ki). 2018 Viruses Discussion IV H275Y 39 44 29933553 Kinetic, Thermodynamic, and Structural Analysis of Drug Resistance Mutations in Neuraminidase from the 2009 Pandemic Influenza Virus. However, we did not confirm the loss of a hydrogen bond between R152 and the oseltamivir acetyl group, which was proposed by Le and co-workers based on molecular dynamics simulations as an additive molecular mechanism conferring drug resistance in H5N1 and H1N1 strains bearing H275Y mutations. 2018 Viruses Discussion IV H275Y 278 283 29933553 Kinetic, Thermodynamic, and Structural Analysis of Drug Resistance Mutations in Neuraminidase from the 2009 Pandemic Influenza Virus. In all crystal structures containing a H275Y mutation, the binding pose of oseltamivir was altered due to the bulkier, polar tyrosine side chain pushing E277 into the active site. 2018 Viruses Discussion IV H275Y 39 44 29933553 Kinetic, Thermodynamic, and Structural Analysis of Drug Resistance Mutations in Neuraminidase from the 2009 Pandemic Influenza Virus. Taken together, our kinetic, thermodynamic, and structural results show that while the I223V and S247N substitutions alone confer only mild oseltamivir resistance, combination with the major neuraminidase mutation H275Y leads to dramatic impairment of inhibition potency that can be attributed to the additive structural and hydration shell changes. 2018 Viruses Discussion IV I223V;S247N;H275Y 87;97;214 92;102;219 191 204 29933553 Kinetic, Thermodynamic, and Structural Analysis of Drug Resistance Mutations in Neuraminidase from the 2009 Pandemic Influenza Virus. The double mutations I223V/H275Y and S247N/H275Y led to dramatic increases in Ki values (3900- and 9000-fold higher than wt, respectively). 2018 Viruses Discussion IV I223V;H275Y;S247N;H275Y 21;27;37;43 26;32;42;48 29933553 Kinetic, Thermodynamic, and Structural Analysis of Drug Resistance Mutations in Neuraminidase from the 2009 Pandemic Influenza Virus. The effects of the I223V and S247N single mutations were more modest (approximately 30- and 20-fold increases in Ki, respectively). 2018 Viruses Discussion IV I223V;S247N 19;29 24;34 29933553 Kinetic, Thermodynamic, and Structural Analysis of Drug Resistance Mutations in Neuraminidase from the 2009 Pandemic Influenza Virus. The I223V and S247N substitutions did not have a dramatic effect on the oseltamivir binding pose. 2018 Viruses Discussion IV I223V;S247N 4;14 9;19 29933553 Kinetic, Thermodynamic, and Structural Analysis of Drug Resistance Mutations in Neuraminidase from the 2009 Pandemic Influenza Virus. The substantial decrease in strength of oseltamivir binding to the H275Y mutant is caused by a significant loss of binding enthalpy, which is partially compensated by a gain in binding entropy. 2018 Viruses Discussion IV H275Y 67 72 29933553 Kinetic, Thermodynamic, and Structural Analysis of Drug Resistance Mutations in Neuraminidase from the 2009 Pandemic Influenza Virus. These data are consistent with thermodynamic ITC data showing minor changes in the parameters of oseltamivir binding to the I223V and S247N single mutants compared to wt. 2018 Viruses Discussion IV I223V;S247N 124;134 129;139 29933553 Kinetic, Thermodynamic, and Structural Analysis of Drug Resistance Mutations in Neuraminidase from the 2009 Pandemic Influenza Virus. This observation explains the 1100-fold reduction in the binding affinity of the H275Y mutant to oseltamivir and is in agreement with previous structural analysis of the H275Y variant of avian influenza neuraminidase H5N1 by Collins and co-workers. 2018 Viruses Discussion IV H275Y;H275Y 81;170 86;175 203 216 29933553 Kinetic, Thermodynamic, and Structural Analysis of Drug Resistance Mutations in Neuraminidase from the 2009 Pandemic Influenza Virus. We observed only moderately decreased catalytic efficiency (kcat/Km) for the single mutants I223V and S247N, and much lower values for all variants containing the H275Y substitution (only 4-6% of the wt value for the H275Y, I223V/H275Y, and S247N/H275Y mutants). 2018 Viruses Discussion IV I223V;S247N;H275Y;H275Y;H275Y;I223V;H275Y;S247N 92;102;163;217;230;224;247;241 97;107;168;222;235;229;252;246 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. Although I38T mutation confers reduced sensitivity to BXA, we also show that recombinant influenza A viruses bearing this mutation have a significantly reduced fitness in canine and human cells, as measured by growth curves. 2018 Scientific reports Discussion IV I38T 9 13 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. However, compensatory substitutions have not yet been observed with variants such as A20S + I38F or I38T + E623K (Supp. 2018 Scientific reports Discussion IV A20S;I38F;I38T;E623K 85;92;100;107 89;96;104;112 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. Importantly, no correlation of the emergence of I38T or other substitutions with clinical influenza symptoms or relapse/persistence of fever has emerged so far. 2018 Scientific reports Discussion IV I38T 48 52 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. In contrast, for FluB, the I38F mutation does significantly impact viral fitness possibly because the larger phenylalanine side-chain more severely impacts productive substrate RNA binding. 2018 Scientific reports Discussion IV I38F 27 31 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. In future studies, exploration of compensatory substitutions that recover the replicative capacity of I38T viruses will be required. 2018 Scientific reports Discussion IV I38T 102 106 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. In particular, our structural studies comparing the wild-type and I38T mutant show that BXA binds in an almost identical manner with differences restricted locally to the I/T side-chain change only. 2018 Scientific reports Discussion IV I38T 66 70 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. In summary, this report shows that a minority of treated patients select for influenza variants that escape the high potency of BXA and we give a structure-based mechanistic explanation of how the most prominent of these, I38T, reduces susceptibility to the drug. 2018 Scientific reports Discussion IV I38T 222 226 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. Polymorphic I38V did not affect BXA sensitivity. 2018 Scientific reports Discussion IV I38V 12 16 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. Table 2) and is positioned to likely interact with the RNA substrate, perhaps by base stacking, we speculate that the substitution I38T to a less hydrophobic residue reduces the affinity to RNA as well as to BXA. 2018 Scientific reports Discussion IV I38T 131 135 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. That Met34 is also important for substrate RNA binding could explain why, in the case of FluB, the I38T mutation has little impact on viral fitness. 2018 Scientific reports Discussion IV I38T 99 103 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. The I38T had the largest effect in A/H1N1 and A/H3N2 viruses, which emerged in two (1.1%) of 182 in the phase 2 and in 15 (19.5%) of 77 of treated patients in the pediatric study, respectively, increasing the EC50 by approximately 30- to 50-fold, with lesser effects for I38F and I38M. 2018 Scientific reports Discussion IV I38T;I38F;I38M 4;271;280 8;275;284 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. The reduction of susceptibility to BXM for the I38T mutant is less for FluB compared to FluA. 2018 Scientific reports Discussion IV I38T 47 51 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. These two effects (less favourable van der Waals packing and induced fit change of threonine rotamer) plausibly account for the reduced affinity of the inhibitor for the I38T variant and hence the lower susceptibility of viruses bearing this mutation. 2018 Scientific reports Discussion IV I38T 170 174 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. This is consistent with our observation that the in vitro activity of the isolated endonuclease domain of both influenzas A and B is reduced for the I38T variant compared to wild-type. 2018 Scientific reports Discussion IV I38T 149 153 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. This reduced affinity is reflected in the ten degree lower melting temperature of the BXA-bound I38T endonuclease compared to the wild-type, indicative of a significantly less stable enzyme-inhibitor complex. 2018 Scientific reports Discussion IV I38T 96 100 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. We also found that E199G in FluA, located at the beginning of the linker between the PA N- (endonuclease) and C-terminal domains, slightly reduced BXA susceptibility by 4.46-fold. 2018 Scientific reports Discussion IV E199G 19 24 PA 85 87 29941893 Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. We also identified E23K, A37T and polymorphic A36V, as PA mutations that have a significant but lesser impact on compound susceptibility. 2018 Scientific reports Discussion IV E23K;A37T;A36V 19;25;46 23;29;50 PA 55 57 29999583 A 627K variant in the PB2 protein of H9 subtype influenza virus in wild birds. Here, we were interested in the two H9N2 virus strains (AH/DGG4 and AH/BLH12) isolated from fecal samples of pigeon and Anseriformes in Anhui in 2015, which had E627K mutations in their PB2 protein. 2018 Influenza and other respiratory viruses Discussion IV E627K 161 166 PB2 186 189 29999583 A 627K variant in the PB2 protein of H9 subtype influenza virus in wild birds. Thus, this gene cassette might be a genetic platform for new strains with zoonotic potential.33 More evidence has demonstrated that PB2 residue 627 is a key determinant of host range and virulence for influenza A viruses,34 and the PB2 E627K mutation directly increases the enzyme activity of the polymerase that facilitates virus growth in vitro.35 In the H5N1 virus, PB2 E627K mutation is associated with systemic infection and impaired T-cell activation in mice.36 Adaptation of H9N2 to mice is associated with multiple amino acid substitutions, including PB2 E627K.37 . 2018 Influenza and other respiratory viruses Discussion IV E627K;E627K;E627K 236;373;563 241;378;568 PB2;PB2;PB2;PB2 132;232;369;559 135;235;372;562 29999583 A 627K variant in the PB2 protein of H9 subtype influenza virus in wild birds. Thus, this gene cassette might be a genetic platform for new strains with zoonotic potential.33 More evidence has demonstrated that PB2 residue 627 is a key determinant of host range and virulence for influenza A viruses,34 and the PB2 E627K mutation directly increases the enzyme activity of the polymerase that facilitates virus growth in vitro.35 In the H5N1 virus, PB2 E627K mutation is associated with systemic infection and impaired T-cell activation in mice.36 Adaptation of H9N2 to mice is associated with multiple amino acid substitutions, including PB2 E627K.37. 2018 Influenza and other respiratory viruses Discussion IV E627K;E627K;E627K 236;373;563 241;378;568 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. None of the immunocompetent and immunocompromised ferrets had acquired the E119V, although this is also a common mutation associated with Oseltamivir treatment that is found in NA. 2018 PloS one Discussion IV E119V 75 80 177 179 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. Oseltamivir treatment led to the emergence the R292K substitution in immunocompromised and immunocompetent ferrets inoculated with A/H3N2 virus. 2018 PloS one Discussion IV R292K 47 52 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. Plasma levels of Oseltamivir have been shown to reach approximate concentrations between 2561 and 9603nM in ferrets, which is higher than the IC50 associated with the E119V mutation. 2018 PloS one Discussion IV E119V 167 172 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. The E119V mutation was found to cause a 20 to 1000-fold increase in the 50% inhibitory concentration (IC50) of Oseltamivir. 2018 PloS one Discussion IV E119V 4 9 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. The other substitutions in HA (T151A) and NA (I57T) have not been identified in previous studies and their functions remain unknown. 2018 PloS one Discussion IV T151A;I57T 31;46 36;50 HA;NA 27;42 29;44 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. The R292K substitution was found to cause a greater reduction in susceptibility to Oseltamivir compared to the E119V substitution, conferring a > 9000 increase of the Oseltamivir IC50. 2018 PloS one Discussion IV R292K;E119V 4;111 9;116 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. The resistant R292K genotype of the A/H3N2 virus was detected initially as a minor variant by msRT-PCR. 2018 PloS one Discussion IV R292K 14 19 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. The substitution T151A in HA is not common in circulating viruses in the human population, as it is not present in the HA sequences in the Global Initiative on Sharing All Influenza Data (GISAID) Epiflu database. 2018 PloS one Discussion IV T151A 17 22 HA;HA 26;119 28;121 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. The substitution was present together with the known E119V and I222V resistance substitutions. 2018 PloS one Discussion IV E119V;I222V 53;63 58;68 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. The T242I substitution in NA has previously only been detected in an immunocompromised child infected with multidrug resistant A/H3N2 virus. 2018 PloS one Discussion IV T242I 4 9 26 28 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. This could explain why the E119V mutation was not detected in the present study. 2018 PloS one Discussion IV E119V 27 32 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. Three immunocompromised ferrets in the present study acquired additional substitutions in the HA (T151A) and the NA (T242I) proteins besides the R292K resistance substitution, which could represent compensatory changes. 2018 PloS one Discussion IV T151A;T242I;R292K 98;117;145 103;122;150 HA;NA 94;113 96;115 30024940 Influenza A/H3N2 virus infection in immunocompromised ferrets and emergence of antiviral resistance. With Illumina NGS, resistance mutation R292K was already detected at 4 dpi in Oseltamivir treated ferrets. 2018 PloS one Discussion IV R292K 39 44 30141905 The Stabilities of the Soluble Ectodomain and Fusion Peptide Hairpins of the Influenza Virus Hemagglutinin Subunit II Protein Are Positively Correlated with Membrane Fusion. 4 and Table 1 support 65% average helicity for WT- and G1E- FHA2 and 58% average helicity for WT- and G1E- HA2. 2018 Biochemistry Discussion IV G1E;G1E 55;102 58;105 HA 107 109 30141905 The Stabilities of the Soluble Ectodomain and Fusion Peptide Hairpins of the Influenza Virus Hemagglutinin Subunit II Protein Are Positively Correlated with Membrane Fusion. 9 displays a structural model for the I173E SE in which there is dissociation of the strands from the bundle, with accompanying destabilization and loss of helicity near the bundle terminus. 2018 Biochemistry Discussion IV I173E 38 43 30141905 The Stabilities of the Soluble Ectodomain and Fusion Peptide Hairpins of the Influenza Virus Hemagglutinin Subunit II Protein Are Positively Correlated with Membrane Fusion. Although the SEC data for I173E-FHA2 in DM show predominant monomers, the cross-linking data are consistent with a significant fraction of trimers. 2018 Biochemistry Discussion IV I173E 26 31 30141905 The Stabilities of the Soluble Ectodomain and Fusion Peptide Hairpins of the Influenza Virus Hemagglutinin Subunit II Protein Are Positively Correlated with Membrane Fusion. Destabilization of the SE is surprising because the G1E mutation is more than 35-residues from the SE structure. 2018 Biochemistry Discussion IV G1E 52 55 30141905 The Stabilities of the Soluble Ectodomain and Fusion Peptide Hairpins of the Influenza Virus Hemagglutinin Subunit II Protein Are Positively Correlated with Membrane Fusion. G1E or I173E- HA-cells do not fuse with RBC's. 2018 Biochemistry Discussion IV I173E 7 12 HA 14 16 30141905 The Stabilities of the Soluble Ectodomain and Fusion Peptide Hairpins of the Influenza Virus Hemagglutinin Subunit II Protein Are Positively Correlated with Membrane Fusion. G1E- and I173E- FHA2 and WT- vs. 2018 Biochemistry Discussion IV I173E 9 14 30141905 The Stabilities of the Soluble Ectodomain and Fusion Peptide Hairpins of the Influenza Virus Hemagglutinin Subunit II Protein Are Positively Correlated with Membrane Fusion. G1E- and WT- FHA2 both exhibit 65% ambient-temperature helicity but the Tm for G1E-FHA2 is reduced by 32 C vs. 2018 Biochemistry Discussion IV G1E 79 82 30141905 The Stabilities of the Soluble Ectodomain and Fusion Peptide Hairpins of the Influenza Virus Hemagglutinin Subunit II Protein Are Positively Correlated with Membrane Fusion. G1E-FHA2, G1E-HA2, and I173E-FHA2 have respective DeltaHm values of 49, 44, and 30 kcal/mole that are determined from van't Hoff analyses over broad temperature ranges for which there are clear changes from mostly-folded to mostly-unfolded protein. 2018 Biochemistry Discussion IV G1E;I173E 10;23 13;28 HA 14 16 30141905 The Stabilities of the Soluble Ectodomain and Fusion Peptide Hairpins of the Influenza Virus Hemagglutinin Subunit II Protein Are Positively Correlated with Membrane Fusion. Gp160-cells also fuse with receptor-bearing cells, and the V2E mutation at the N-terminus of gp41 results in highly-impaired V2E- vs. 2018 Biochemistry Discussion IV V2E;V2E 59;125 62;128 30141905 The Stabilities of the Soluble Ectodomain and Fusion Peptide Hairpins of the Influenza Virus Hemagglutinin Subunit II Protein Are Positively Correlated with Membrane Fusion. However, the 65% helicity for WT- and G1E- FHA2 in the present study is higher than the respective ~25% and ~35% helicities of a 2011 study. 2018 Biochemistry Discussion IV G1E 38 41 30141905 The Stabilities of the Soluble Ectodomain and Fusion Peptide Hairpins of the Influenza Virus Hemagglutinin Subunit II Protein Are Positively Correlated with Membrane Fusion. less-direct G1E destabilization of the SE by weakening FP interhelical interactions, with consequent competition by the FP for binding to the strands. 2018 Biochemistry Discussion IV G1E 12 15 30141905 The Stabilities of the Soluble Ectodomain and Fusion Peptide Hairpins of the Influenza Virus Hemagglutinin Subunit II Protein Are Positively Correlated with Membrane Fusion. mixtures of trimer, monomer, and oligomers/aggregates in DM detergent; (2) similar helicities of WT- and G1E- proteins vs. 2018 Biochemistry Discussion IV G1E 105 108 30141905 The Stabilities of the Soluble Ectodomain and Fusion Peptide Hairpins of the Influenza Virus Hemagglutinin Subunit II Protein Are Positively Correlated with Membrane Fusion. Reduced cell/cell and vesicle fusion for I173E- and G1E- vs. 2018 Biochemistry Discussion IV G1E;I173E 52;41 55;46 30141905 The Stabilities of the Soluble Ectodomain and Fusion Peptide Hairpins of the Influenza Virus Hemagglutinin Subunit II Protein Are Positively Correlated with Membrane Fusion. Reduced fusion of the G1E FP of HA2 may also be correlated to shallower membrane insertion of the N-terminal FP. 2018 Biochemistry Discussion IV G1E 22 25 HA 32 34 30141905 The Stabilities of the Soluble Ectodomain and Fusion Peptide Hairpins of the Influenza Virus Hemagglutinin Subunit II Protein Are Positively Correlated with Membrane Fusion. reduced G1S- relative to WT- HA-cell/RBC fusion, and the ~50x higher density of HA-trimers/virion vs. 2018 Biochemistry Discussion IV G1S 8 11 HA;HA 29;80 31;82 30141905 The Stabilities of the Soluble Ectodomain and Fusion Peptide Hairpins of the Influenza Virus Hemagglutinin Subunit II Protein Are Positively Correlated with Membrane Fusion. reduced helicity of I173E- proteins; (3) hyper-thermostable WT- FHA2 and HA2 and less-stable FHA2 and HA2 mutants with respective reductions of ~40 and ~15 C in Tm; and (4) efficient HA2- induced vesicle fusion of neutral and anionic vesicles at pH 5.0 for WT-HA2 vs. 2018 Biochemistry Discussion IV I173E 20 25 HA;HA;HA;HA 73;102;184;261 75;104;186;263 30141905 The Stabilities of the Soluble Ectodomain and Fusion Peptide Hairpins of the Influenza Virus Hemagglutinin Subunit II Protein Are Positively Correlated with Membrane Fusion. Reduced I173E-HA2 fusion may also be associated with its larger monomer:trimer ratio. 2018 Biochemistry Discussion IV I173E 8 13 HA 14 16 30141905 The Stabilities of the Soluble Ectodomain and Fusion Peptide Hairpins of the Influenza Virus Hemagglutinin Subunit II Protein Are Positively Correlated with Membrane Fusion. Relative to WT-HA2, G1E- and I173E- HA2 exhibit similar reductions in fusion that correlate with their lower SE hairpin stabilities. 2018 Biochemistry Discussion IV G1E;I173E 20;29 23;34 HA;HA 15;36 17;38 30141905 The Stabilities of the Soluble Ectodomain and Fusion Peptide Hairpins of the Influenza Virus Hemagglutinin Subunit II Protein Are Positively Correlated with Membrane Fusion. SEC was done with [protein] 4 muM and with [NaCl] = 150 mM, and CD spectra of I173E-FHA2 evidence well-folded protein for these conditions and also for different protein concentrations and no NaCl. 2018 Biochemistry Discussion IV I173E 80 85 30141905 The Stabilities of the Soluble Ectodomain and Fusion Peptide Hairpins of the Influenza Virus Hemagglutinin Subunit II Protein Are Positively Correlated with Membrane Fusion. Such fusion is very similar to HA-cell/RBC fusion, with both fusion types requiring low-pH and exhibiting nearly-identical losses-of-function for the G1E mutant and for the I173E mutant. 2018 Biochemistry Discussion IV G1E;I173E 150;173 153;178 HA 31 33 30141905 The Stabilities of the Soluble Ectodomain and Fusion Peptide Hairpins of the Influenza Virus Hemagglutinin Subunit II Protein Are Positively Correlated with Membrane Fusion. The ~4-fold reduction in fusion extent for G1E- vs. 2018 Biochemistry Discussion IV G1E 43 46 30141905 The Stabilities of the Soluble Ectodomain and Fusion Peptide Hairpins of the Influenza Virus Hemagglutinin Subunit II Protein Are Positively Correlated with Membrane Fusion. The greater monomer fraction of I173E- vs. 2018 Biochemistry Discussion IV I173E 32 37 30141905 The Stabilities of the Soluble Ectodomain and Fusion Peptide Hairpins of the Influenza Virus Hemagglutinin Subunit II Protein Are Positively Correlated with Membrane Fusion. The HA238-89 peptide forms a trimer of parallel helices at lower temperatures and unfolded monomers at higher temperatures, and its Tm = 51 C is comparable to the Tm of I173E-FHA2. 2018 Biochemistry Discussion IV I173E 170 175 HA 4 6 30141905 The Stabilities of the Soluble Ectodomain and Fusion Peptide Hairpins of the Influenza Virus Hemagglutinin Subunit II Protein Are Positively Correlated with Membrane Fusion. The I173E mutation exerts significant destabilization of the SE of FHA2 as evidenced by loss of 30% of the overall helicity and reduction of Tm by 40 C (Table 1). 2018 Biochemistry Discussion IV I173E 4 9 30141905 The Stabilities of the Soluble Ectodomain and Fusion Peptide Hairpins of the Influenza Virus Hemagglutinin Subunit II Protein Are Positively Correlated with Membrane Fusion. The importance of HA density for fusion is supported by the correlation between comparable fusion of G1S- and WT- virions with vesicles vs. 2018 Biochemistry Discussion IV G1S 101 104 HA 18 20 30141905 The Stabilities of the Soluble Ectodomain and Fusion Peptide Hairpins of the Influenza Virus Hemagglutinin Subunit II Protein Are Positively Correlated with Membrane Fusion. The opposite trend is observed for PC:DOTAP at pH 5.0, with respective comparable and higher fusion extents of G1E- and I173E- vs. 2018 Biochemistry Discussion IV G1E;I173E 111;120 114;125 30141905 The Stabilities of the Soluble Ectodomain and Fusion Peptide Hairpins of the Influenza Virus Hemagglutinin Subunit II Protein Are Positively Correlated with Membrane Fusion. The present study also shows that the I173E mutants exhibit only 45% helicities and a model explaining this reduced helicity is presented below. 2018 Biochemistry Discussion IV I173E 38 43 30141905 The Stabilities of the Soluble Ectodomain and Fusion Peptide Hairpins of the Influenza Virus Hemagglutinin Subunit II Protein Are Positively Correlated with Membrane Fusion. The present study describes a structural and functional comparison between WT- full-length HA2 and the truncated construct lacking the TM, FHA2, and the G1E and I173E point mutants that are known to inhibit HA-mediated fusion. 2018 Biochemistry Discussion IV G1E;I173E 153;161 156;166 HA;HA 91;207 93;209 30141905 The Stabilities of the Soluble Ectodomain and Fusion Peptide Hairpins of the Influenza Virus Hemagglutinin Subunit II Protein Are Positively Correlated with Membrane Fusion. The relative populations of different species are more varied between the constructs in DM, and the monomer fractions are generally higher, particularly for I173E- FHA2 and HA2. 2018 Biochemistry Discussion IV I173E 157 162 HA 173 175 30141905 The Stabilities of the Soluble Ectodomain and Fusion Peptide Hairpins of the Influenza Virus Hemagglutinin Subunit II Protein Are Positively Correlated with Membrane Fusion. There are less accurate DeltaHm values for WT- FHA2 and HA2, and I173E-HA2, because these values are determined from van't Hoff analyses from limited temperature ranges, and unfolding is sometimes incomplete at the highest temperature. 2018 Biochemistry Discussion IV I173E 65 70 HA;HA 56;71 58;73 30141905 The Stabilities of the Soluble Ectodomain and Fusion Peptide Hairpins of the Influenza Virus Hemagglutinin Subunit II Protein Are Positively Correlated with Membrane Fusion. There are likely similar unfolded monomer states for all of the proteins, so the DeltaHm values likely reflect more favorable enthalpies for folded G1E- FHA2 and HA2 vs. 2018 Biochemistry Discussion IV G1E 148 151 HA 162 164 30141905 The Stabilities of the Soluble Ectodomain and Fusion Peptide Hairpins of the Influenza Virus Hemagglutinin Subunit II Protein Are Positively Correlated with Membrane Fusion. There is smaller but still significant destabilization of G1E- vs. 2018 Biochemistry Discussion IV G1E 58 61 30141905 The Stabilities of the Soluble Ectodomain and Fusion Peptide Hairpins of the Influenza Virus Hemagglutinin Subunit II Protein Are Positively Correlated with Membrane Fusion. There is smaller but still significant SE destabilization for I173E- vs. 2018 Biochemistry Discussion IV I173E 62 67 30141905 The Stabilities of the Soluble Ectodomain and Fusion Peptide Hairpins of the Influenza Virus Hemagglutinin Subunit II Protein Are Positively Correlated with Membrane Fusion. There may also be less membrane perturbation by the mutants because of FP binding with the C-terminal strand of the SE, and for G1E, because of shallower insertion of the FP in the target membrane. 2018 Biochemistry Discussion IV G1E 128 131 30141905 The Stabilities of the Soluble Ectodomain and Fusion Peptide Hairpins of the Influenza Virus Hemagglutinin Subunit II Protein Are Positively Correlated with Membrane Fusion. This I173E model is supported by data for shorter HA2 constructs with C-terminal truncation. 2018 Biochemistry Discussion IV I173E 5 10 HA 50 52 30141905 The Stabilities of the Soluble Ectodomain and Fusion Peptide Hairpins of the Influenza Virus Hemagglutinin Subunit II Protein Are Positively Correlated with Membrane Fusion. This interpretation is consistent with the previously-described direct I173E destabilization of binding between the C-terminal strands and the N-terminal helical bundle of the SE vs. 2018 Biochemistry Discussion IV I173E 71 76 30141905 The Stabilities of the Soluble Ectodomain and Fusion Peptide Hairpins of the Influenza Virus Hemagglutinin Subunit II Protein Are Positively Correlated with Membrane Fusion. This loss is due to competition with the G1E FP's for binding to the strands. 2018 Biochemistry Discussion IV G1E 41 44 30141905 The Stabilities of the Soluble Ectodomain and Fusion Peptide Hairpins of the Influenza Virus Hemagglutinin Subunit II Protein Are Positively Correlated with Membrane Fusion. This observation correlates with highly-impaired G1E- vs. 2018 Biochemistry Discussion IV G1E 49 52 30141905 The Stabilities of the Soluble Ectodomain and Fusion Peptide Hairpins of the Influenza Virus Hemagglutinin Subunit II Protein Are Positively Correlated with Membrane Fusion. We propose that the SE destabilization for G1E is similar to that for I173E, and is a result of loss of binding of C-terminal strands with the N-terminal helical bundle. 2018 Biochemistry Discussion IV G1E;I173E 43;70 46;75 30141905 The Stabilities of the Soluble Ectodomain and Fusion Peptide Hairpins of the Influenza Virus Hemagglutinin Subunit II Protein Are Positively Correlated with Membrane Fusion. WT- HA2 with PC vesicles matches well with the reduction previously observed for G1E- vs. 2018 Biochemistry Discussion IV G1E 81 84 HA 4 6 30141905 The Stabilities of the Soluble Ectodomain and Fusion Peptide Hairpins of the Influenza Virus Hemagglutinin Subunit II Protein Are Positively Correlated with Membrane Fusion. WT- proteins is correlated with the lower stability of the I173E trimer. 2018 Biochemistry Discussion IV I173E 59 64 30141905 The Stabilities of the Soluble Ectodomain and Fusion Peptide Hairpins of the Influenza Virus Hemagglutinin Subunit II Protein Are Positively Correlated with Membrane Fusion. WT-FHA2, which indicates significant destabilization of the SE by the G1E mutation. 2018 Biochemistry Discussion IV G1E 70 73 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. Although one of the human adaptation mutations identified in this study, PB2-Y658H, was located within the PB2-627 domain, it was at a substantial distance from PB2-627 and did not form a structural site with the PB2-627 residue. 2018 Scientific reports Discussion IV Y658H 77 82 PB2;PB2;PB2;PB2 73;107;161;213 76;110;164;216 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. Among these mutations, PB2-E627K and, to lesser extent, PB2-D701N have been described as being critical for avian H5N1 virus replication in mammalian hosts. 2018 Scientific reports Discussion IV E627K;D701N 27;60 32;65 PB2;PB2 23;56 26;59 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. In a high-throughput screening study of random mutagenesis libraries, the PB2-Y658S amino acid change was identified as a mutation that increased H5N1 replication in human cells. 2018 Scientific reports Discussion IV Y658S 78 83 PB2 74 77 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. In contrast, in this study we found synergistic effects with the PB2-T81A/V344M/D701N and PA-M86V/A343T multiple mutations, producing an additional increase in viral replication in human cells and mouse lungs. 2018 Scientific reports Discussion IV D701N;V344M;T81A;M86V;A343T 80;74;69;93;98 85;79;73;97;103 PA;PB2 90;65 92;68 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. In fact, the PB2-D701N and PB2-Q591R mutations alone, but not combined with the PB2-E627K mutation, produced a replication advantage for the avian H5N1 virus polymerase during human cell infection. 2018 Scientific reports Discussion IV D701N;Q591R;E627K 17;31;84 22;36;89 PB2;PB2;PB2 13;27;80 16;30;83 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. In particular, it should be noted that all Egyptian clade 2.2.1 viruses have the PB2-E627K mutation, whereas all avian viruses in the Asian H5N1 clades, including clade 2.3.4, clade 2.3.2 and clade 1.1 viruses, have the PB2-E627 residue. 2018 Scientific reports Discussion IV E627K 85 90 PB2;PB2 81;220 84;223 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. Likewise, the PA-M86V mutation alone had little effect on polymerase activity but had a synergistic effect with the PA-A343T mutation. 2018 Scientific reports Discussion IV M86V;A343T 17;119 21;124 PA;PA 14;116 16;118 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. Neither the PB2-T81A/V344M/D701N nor the PB2-Y658H mutation has been found in recent (i.e., during 2001-2017) isolates of human seasonal H1N1 and H3N2 viruses. 2018 Scientific reports Discussion IV D701N;V344M;T81A;Y658H 27;21;16;45 32;26;20;50 PB2;PB2 12;41 15;44 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. PB2-V344M has been reported to be one of the mutations in influenza virus A/Indonesia/UT3006/2005 (clade 2.1.3) that increased viral replication in human cells. 2018 Scientific reports Discussion IV V344M 4 9 PB2 0 3 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. Previous studies reported that PB2-E627K in the 627 domain and PB2-D701N in the NLS domain affected the interaction between the viral polymerase and host importin-alpha isoforms to adapt mammalian machinery. 2018 Scientific reports Discussion IV E627K;D701N 35;67 40;72 PB2;PB2 31;63 34;66 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. Some viruses isolated from these outbreaks had the PB2-Y658H polymerase human adaptation mutation that was identified in this study. 2018 Scientific reports Discussion IV Y658H 55 60 PB2 51 54 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. The PB2-T81A, PB2-V344M and PB2-T81A/V344M mutations alone had little effect but increased polymerase activity when the two mutations were combined with the PB2-D701N mutation (Figs 1 and S1), implying that both the PB2-T81A and PB2-V344M mutations probably need to cooperate with the PB2-D701N mutation to produce a synergistic effect. 2018 Scientific reports Discussion IV T81A;V344M;V344M;T81A;D701N;T81A;V344M;D701N 8;18;37;32;161;220;233;289 12;23;42;36;166;224;238;294 PB2;PB2;PB2;PB2;PB2;PB2;PB2 4;14;28;157;216;229;285 7;17;31;160;219;232;288 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. The PB2-T81A/V344M/D701N triple mutation has only been detected in influenza virus A/Hunan/1/2008 (clade 2.3.4). 2018 Scientific reports Discussion IV D701N;V344M;T81A 19;13;8 24;18;12 PB2 4 7 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. The PB2-Y658H mutation has also been detected in one avian H9N2 virus strain (A/chicken/Jiangsu/DT0112/2012), one avian H5N8 virus strain (A/quail/California/K1400794/2014) and seven avian H5N6 virus strains (A/mute swan/Kyoto/1T/2016, A/mute swan/Kyoto/2T/2016, A/mute swan/Kyoto/3T/2016, A/mute swan/Kyoto/4T/2016, A/mute swan/Kyoto/5T/2016, A/mute swan/Kyoto/6T/2016 and A/mute swan/Kyoto/8T/2016). 2018 Scientific reports Discussion IV Y658H 8 13 PB2 4 7 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. The PB2-Y658H mutation has been reported in three human clade 2.3.4.1 virus strains (A/Guizhou/1/2009, A/Hunan/1/2009 and A/Hunan/2/2009) and in four avian clade 2.3.4.1 virus strains (A/chicken/Lao/LH1/2010, A/duck/Lao/19/2010, A/duck/Lao/463/2010 and A/duck/Lao/567/2010). 2018 Scientific reports Discussion IV Y658H 8 13 PB2 4 7 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. These mutations increased the polymerase activity and replication of clade 2.3.4 viruses in both human cells and mouse lungs to levels similar to the PB2-D701N and PB2-E627K single mutations, which are known human adaptation polymerase mutations. 2018 Scientific reports Discussion IV D701N;E627K 154;168 159;173 PB2;PB2 150;164 153;167 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. This is in agreement with recent studies showing that several polymerase mutations act cooperatively with PB2-E627K to increase viral growth in mammals. 2018 Scientific reports Discussion IV E627K 110 115 PB2 106 109 30166556 Multiple polymerase gene mutations for human adaptation occurring in Asian H5N1 influenza virus clinical isolates. This targeted bioinformatics approach enabled us to identify a number of polymerase gene mutations in H5N1 viruses that had not been previously reported to be human adaptation mutations, in addition to the previously reported PB2-D701N human adaptation mutation. 2018 Scientific reports Discussion IV D701N 230 235 PB2 226 229 30186261 Acquisition of Innate Inhibitor Resistance and Mammalian Pathogenicity During Egg Adaptation by the H9N2 Avian Influenza Virus. Although we do not have data on which mutations in HA and NA occurred first, the T133N mutations located in the vicinity of RBS in HA1 and the 18 amino acid deletion of the NA stalk of 01310-CE20 may be the best combination for viral fitness, balancing optimal affinities to receptors on host cells and innate inhibitors. 2018 Frontiers in microbiology Discussion IV T133N 81 86 HA;HA1;NA;NA 51;131;58;173 53;134;60;175 30186261 Acquisition of Innate Inhibitor Resistance and Mammalian Pathogenicity During Egg Adaptation by the H9N2 Avian Influenza Virus. However, considering the higher affinity of rH20N20-N133T to avian-like receptors than rH20N20, the resistance to innate inhibitor may also play an important role in the viral pathogenicity in mice. 2018 Frontiers in microbiology Discussion IV N133T 52 57 30186261 Acquisition of Innate Inhibitor Resistance and Mammalian Pathogenicity During Egg Adaptation by the H9N2 Avian Influenza Virus. However, considering the higher virus titer of rH20N20-N133T (with V216G and E439D mutations) than rH2N20 (without V216G and E439D mutations) in the lungs of infected mice, these mutations may influence their replication in mice (Figure 3C). 2018 Frontiers in microbiology Discussion IV N133T;V216G;E439D;V216G;E439D 55;67;77;115;125 60;72;82;120;130 30186261 Acquisition of Innate Inhibitor Resistance and Mammalian Pathogenicity During Egg Adaptation by the H9N2 Avian Influenza Virus. In addition, rH20N20-N133T showed lower replication efficiency in the mouse lung than rH20N20, but higher than rH2N2 and rH2N20. 2018 Frontiers in microbiology Discussion IV N133T 21 26 30186261 Acquisition of Innate Inhibitor Resistance and Mammalian Pathogenicity During Egg Adaptation by the H9N2 Avian Influenza Virus. The LOF mutant rH20N20-N133T showed higher affinities to avian-like and mammalian-like receptors but significantly lower replication efficiency in MDCK cells than rH20N20 in the period 24-48 h post-inoculation. 2018 Frontiers in microbiology Discussion IV N133T 23 28 30186261 Acquisition of Innate Inhibitor Resistance and Mammalian Pathogenicity During Egg Adaptation by the H9N2 Avian Influenza Virus. Therefore, the decreased replication efficiency of rH20N20-N133T may be associated with its increased affinity to mammalian-like receptor on apically secreted glycoproteins from MDCK cells. 2018 Frontiers in microbiology Discussion IV N133T 59 64 30186261 Acquisition of Innate Inhibitor Resistance and Mammalian Pathogenicity During Egg Adaptation by the H9N2 Avian Influenza Virus. V216G and E439D mutations in HA may not be present in the vicinity of the receptor binding site (Figure 5). 2018 Frontiers in microbiology Discussion IV V216G;E439D 0;10 5;15 HA 29 31 30201817 Characterization of Influenza B Virus Variants with Reduced Neuraminidase Inhibitor Susceptibility. A previous study using an influenza B virus (B/Rochester/02/2001) with the D197N NA substitution also showed that when ferrets were infected with a mixture of wild-type and variant viruses, a mixture was still maintained at 5 days postinfection. 2018 Antimicrobial agents and chemotherapy Discussion IV D197N 75 80 81 83 30201817 Characterization of Influenza B Virus Variants with Reduced Neuraminidase Inhibitor Susceptibility. Although the frequency of influenza B viruses with the D197N NA substitution circulating in the community is still less than 1%, it has remained the most commonly reported NAI-resistant strain in recent years. 2018 Antimicrobial agents and chemotherapy Discussion IV D197N 55 60 NA;NAI 61;172 63;175 30201817 Characterization of Influenza B Virus Variants with Reduced Neuraminidase Inhibitor Susceptibility. Genetic analysis showed that the MUT-Y273 virus which transmitted to one of the recipient ferrets contained an M403V NA change, while all of the WT-H273 viruses that infected recipient ferrets contained the L274I PA substitution. 2018 Antimicrobial agents and chemotherapy Discussion IV M403V;L274I 111;207 116;212 NA;PA 117;213 119;215 30201817 Characterization of Influenza B Virus Variants with Reduced Neuraminidase Inhibitor Susceptibility. In the future, it is possible that the NA variants examined in our study may gain additional "permissive" mutations that improve their fitness, as was observed with the H275Y NA substitution in seasonal H1N1 viruses. 2018 Antimicrobial agents and chemotherapy Discussion IV H275Y 169 174 NA;NA 39;175 41;177 30201817 Characterization of Influenza B Virus Variants with Reduced Neuraminidase Inhibitor Susceptibility. Previous experiments using an rg-H273Y virus showed that relative to the rg-WT, the rg-H273Y virus had significantly higher NA activity and surface expression and superior replication kinetics in a competitive-mixtures experiment in normal human bronchial epithelial cells. 2018 Antimicrobial agents and chemotherapy Discussion IV H273Y;H273Y 33;87 38;92 124 126 30201817 Characterization of Influenza B Virus Variants with Reduced Neuraminidase Inhibitor Susceptibility. The discrepancy in these fitness outcomes between our 2015 H273Y virus and a 1998 rg-H273Y virus may be due to differences in viral background (16 amino acid differences). 2018 Antimicrobial agents and chemotherapy Discussion IV H273Y;H273Y 59;85 64;90 30201817 Characterization of Influenza B Virus Variants with Reduced Neuraminidase Inhibitor Susceptibility. The results from our experiments suggest that of two influenza B viruses with reduced NAI susceptibility, the viral fitness of a recent influenza B virus with the H273Y NA substitution was reduced compared to that of an equivalent wild-type virus, but an influenza B virus with a D197N NA substitution showed little reduction in reproduction or transmission in the ferret model. 2018 Antimicrobial agents and chemotherapy Discussion IV H273Y;D197N 163;280 168;285 NA;NA;NAI 169;286;86 171;288;89 30201817 Characterization of Influenza B Virus Variants with Reduced Neuraminidase Inhibitor Susceptibility. This may be more likely for viruses with the D197N NA substitution, which appear to have a smaller fitness deficit than do viruses with the H273Y NA substitution. 2018 Antimicrobial agents and chemotherapy Discussion IV D197N;H273Y 45;140 50;145 NA;NA 51;146 53;148 30201817 Characterization of Influenza B Virus Variants with Reduced Neuraminidase Inhibitor Susceptibility. This study aimed to characterize two contemporary influenza B variants with either the D197N or H273Y NA substitution. 2018 Antimicrobial agents and chemotherapy Discussion IV D197N;H273Y 87;96 92;101 102 104 30202644 Molecular identification of avian influenza virus subtypes H5N1 and H9N2 in birds from farms and live bird markets and in respiratory patients. All the isolates showed the R325K substitution at the cleavage site, which has been characteristic of 2.2.1.2 clade viruses since 2011 and is consistent with. 2018 PeerJ Discussion IV R325K 28 33 30202644 Molecular identification of avian influenza virus subtypes H5N1 and H9N2 in birds from farms and live bird markets and in respiratory patients. Interestingly, Q322K substitution was obvious in four of our isolates compared to the reference and vaccine strains. 2018 PeerJ Discussion IV Q322K 15 20 30227889 Effects of mutations in the effector domain of influenza A virus NS1 protein. Our finding that the E96A/E97A mutation also induces binding of hsp70 further suggests effects on protein folding and that interpreting results obtained with this mutation may be complicated. 2018 BMC research notes Discussion IV E96A;E97A 21;26 25;30 30227889 Effects of mutations in the effector domain of influenza A virus NS1 protein. Potential pleiotropic effects of the E96A/E97A mutation have been noted previously, including poor expression of the polypeptide as seen here and an intriguing effect on PI3K activation. 2018 BMC research notes Discussion IV E96A;E97A 37;42 41;46 30227889 Effects of mutations in the effector domain of influenza A virus NS1 protein. The effect of NS1 mutations L95A/S99A on mRNA export should also be tested. 2018 BMC research notes Discussion IV L95A;S99A 28;33 32;37 NS1 14 17 30227889 Effects of mutations in the effector domain of influenza A virus NS1 protein. Thirdly, identification of an NS1 mutant (E96A/E97A) that still binds NXF1 and enhances its interaction with segment 7 mRNA without upregulating mRNA nuclear export suggests that at least one other factor is needed for export. 2018 BMC research notes Discussion IV E96A;E97A 42;47 46;51 NS1 30 33 30245911 The 2015 Outbreak of Severe Influenza in Kashmir, North India: Emergence of a New Clade of A/H1n1 Influenza Virus. Another important observation in our study was the absence of the H275Y mutation on neuraminidase in our isolates which suggested that the isolates were susceptible to oseltamivir. 2018 PLoS currents Discussion IV H275Y 66 71 84 97 30245911 The 2015 Outbreak of Severe Influenza in Kashmir, North India: Emergence of a New Clade of A/H1n1 Influenza Virus. Our data along with the analysis of the 285 Indian HA sequences showed that the K166Q mutation was established in Indian strains since 2013. 2018 PLoS currents Discussion IV K166Q 80 85 HA 51 53 30245911 The 2015 Outbreak of Severe Influenza in Kashmir, North India: Emergence of a New Clade of A/H1n1 Influenza Virus. The D225N mutation has also been reported to affect receptor binding of the HA whereas it also results in reduced susceptibility to neuraminidase (NA), and has previously also been reported to be associated with serious influenza illness requiring hospitalisation or death. 2018 PLoS currents Discussion IV D225N 4 9 HA;NA;NA 76;147;132 78;149;145 30245911 The 2015 Outbreak of Severe Influenza in Kashmir, North India: Emergence of a New Clade of A/H1n1 Influenza Virus. The D225N mutation has not been observed in our isolates (including the fatal cases) or other Indian strains with the exception of 3 of 289 Indian strains isolated form severe as well as non severe cases of the year 2013 from Pune. 2018 PLoS currents Discussion IV D225N 4 9 30245911 The 2015 Outbreak of Severe Influenza in Kashmir, North India: Emergence of a New Clade of A/H1n1 Influenza Virus. The D225N mutation reported by MIT investigators was not demonstrated but T200A was found to be conserved. 2018 PLoS currents Discussion IV D225N;T200A 4;74 9;79 30245911 The 2015 Outbreak of Severe Influenza in Kashmir, North India: Emergence of a New Clade of A/H1n1 Influenza Virus. The first report of genotype 6B strains circulating in India reported by Parida et al who demonstrated genotype 6B forming two sub-lineages circulated during the outbreak in Madhya Pradesh in central India harbouring the signature amino acid substitutions of genogroup 6B (D97N, K163Q, S185T, S203T, A256T and K283E). 2018 PLoS currents Discussion IV D97N;K163Q;S185T;S203T;A256T;K283E 273;279;286;293;300;310 277;284;291;298;305;315 30245911 The 2015 Outbreak of Severe Influenza in Kashmir, North India: Emergence of a New Clade of A/H1n1 Influenza Virus. The investigators from the Massachusetts Institute of Technology, on the basis of an in-silico analysis of the Genbank submitted Indian-origin strain A/India/6427/2014 reported amino acid T200A and D225N changes that were different from the original A/H1N1pdm09 strain. 2018 PLoS currents Discussion IV T200A;D225N 188;198 193;203 30245911 The 2015 Outbreak of Severe Influenza in Kashmir, North India: Emergence of a New Clade of A/H1n1 Influenza Virus. The set of mutations that they reported to characterise the strain were K166Q, T200A, and D225N. 2018 PLoS currents Discussion IV K166Q;T200A;D225N 72;79;90 77;84;95 30245911 The 2015 Outbreak of Severe Influenza in Kashmir, North India: Emergence of a New Clade of A/H1n1 Influenza Virus. The T200A aminoacid substitution ensures an enhanced human glycan receptor binding of the HA antigen of the influenza virus and the D225N substitution leads to increased virulence and disease severity. 2018 PLoS currents Discussion IV T200A;D225N 4;132 9;137 HA 90 92 30245911 The 2015 Outbreak of Severe Influenza in Kashmir, North India: Emergence of a New Clade of A/H1n1 Influenza Virus. They also noted a new mutation E164G in HA2 sequences. 2018 PLoS currents Discussion IV E164G 31 36 HA 40 42 30282714 Amino Acid Residue 217 in the Hemagglutinin Glycoprotein Is a Key Mediator of Avian Influenza H7N9 Virus Antigenicity. Although A125T and A151T substitutions were identified as egg adaptation mutations, the A125T+A151T double mutation was not found in the egg-amplified wild-type H7N9 viruses. 2019 Journal of virology Discussion IV A125T;A151T;A125T;A151T 9;19;88;94 14;24;93;99 30282714 Amino Acid Residue 217 in the Hemagglutinin Glycoprotein Is a Key Mediator of Avian Influenza H7N9 Virus Antigenicity. As a result, it will be interesting to examine the differences in receptor binding when the L217Q substitution is introduced into the current prevailing virus strains. 2019 Journal of virology Discussion IV L217Q 92 97 30282714 Amino Acid Residue 217 in the Hemagglutinin Glycoprotein Is a Key Mediator of Avian Influenza H7N9 Virus Antigenicity. Compared with the 2013 CVV strain Anhui/13, HK125/17 has A112T, S118N, and A125V substitutions in the HA, while SF003 has 7 substitutions in the HA: I38T, A112P, S118N, A125V, K164E, L217Q, and G261R. 2019 Journal of virology Discussion IV A112T;S118N;A125V;I38T;A112P;S118N;A125V;K164E;L217Q;G261R 57;64;75;149;155;162;169;176;183;194 62;69;80;153;160;167;174;181;188;199 HA;HA 102;145 104;147 30282714 Amino Acid Residue 217 in the Hemagglutinin Glycoprotein Is a Key Mediator of Avian Influenza H7N9 Virus Antigenicity. Here, we showed that A125T and A151T were found more often in human than in poultry isolates, although the sample size is small. 2019 Journal of virology Discussion IV A125T;A151T 21;31 26;36 30282714 Amino Acid Residue 217 in the Hemagglutinin Glycoprotein Is a Key Mediator of Avian Influenza H7N9 Virus Antigenicity. Here, we showed that the L217Q substitution drove a major antigenic change in H7N9 viruses under immune pressure. 2019 Journal of virology Discussion IV L217Q 25 30 30282714 Amino Acid Residue 217 in the Hemagglutinin Glycoprotein Is a Key Mediator of Avian Influenza H7N9 Virus Antigenicity. Here, we showed that the L217Q substitution in the HA of HK125/17, a virus isolate from epidemic wave 5, resulted in large reductions in HI titers to ferret and chicken antisera in comparison to those with Anhui/13. 2019 Journal of virology Discussion IV L217Q 25 30 HA 51 53 30282714 Amino Acid Residue 217 in the Hemagglutinin Glycoprotein Is a Key Mediator of Avian Influenza H7N9 Virus Antigenicity. However, validation of the potential glycosylation in the mutant A151T in H7N9 viruses still needs to be performed. 2019 Journal of virology Discussion IV A151T 65 70 30282714 Amino Acid Residue 217 in the Hemagglutinin Glycoprotein Is a Key Mediator of Avian Influenza H7N9 Virus Antigenicity. In addition to the L217Q substitution, A125T and A151T double mutations resulted in modest reductions in HI titers to ferret and chicken antisera. 2019 Journal of virology Discussion IV L217Q;A125T;A151T 19;39;49 24;44;54 30282714 Amino Acid Residue 217 in the Hemagglutinin Glycoprotein Is a Key Mediator of Avian Influenza H7N9 Virus Antigenicity. In addition to the receptor binding switch, L217Q together with an N149D or G209E substitution was also found in the H7N9 virus egg adaptation mutant. 2019 Journal of virology Discussion IV L217Q;N149D;G209E 44;67;76 49;72;81 30282714 Amino Acid Residue 217 in the Hemagglutinin Glycoprotein Is a Key Mediator of Avian Influenza H7N9 Virus Antigenicity. In summary, A125T, A151T, and L217Q mutations were identified in H7N9 HA using in vitro polyclonal antiserum escape mutant selection. 2019 Journal of virology Discussion IV A125T;A151T;L217Q 12;19;30 17;24;35 HA 70 72 30282714 Amino Acid Residue 217 in the Hemagglutinin Glycoprotein Is a Key Mediator of Avian Influenza H7N9 Virus Antigenicity. It is noteworthy that the A125T substitution has been found to emerge in the HA of an H7N9 virus isolated from a contact ferret during a transmission experiment. 2019 Journal of virology Discussion IV A125T 26 31 HA 77 79 30282714 Amino Acid Residue 217 in the Hemagglutinin Glycoprotein Is a Key Mediator of Avian Influenza H7N9 Virus Antigenicity. Likewise, the glycosylation of H7N9 HA by the A125T substitution has been shown to favor production of HA pseudoviruses. 2019 Journal of virology Discussion IV A125T 46 51 HA;HA 36;103 38;105 30282714 Amino Acid Residue 217 in the Hemagglutinin Glycoprotein Is a Key Mediator of Avian Influenza H7N9 Virus Antigenicity. LPAI H7N9 virus (Anhui/13) maintains its dual receptor binding capacity for both avian and human hosts despite the L217Q substitution. 2019 Journal of virology Discussion IV L217Q 115 120 30282714 Amino Acid Residue 217 in the Hemagglutinin Glycoprotein Is a Key Mediator of Avian Influenza H7N9 Virus Antigenicity. Moreover, the A125T and A151T double mutations resulted in an 8-fold reduction in HI titer to ferret antiserum. 2019 Journal of virology Discussion IV A125T;A151T 14;24 19;29 30282714 Amino Acid Residue 217 in the Hemagglutinin Glycoprotein Is a Key Mediator of Avian Influenza H7N9 Virus Antigenicity. Of note, all three mutations (A125T, A151T, and L217Q) identified in the HA of H7N9 immune escape mutants have appeared in nature, indicating that in vitro antiserum escape mutant selection is a feasible and powerful tool to predict the antigenic change of influenza viruses. 2019 Journal of virology Discussion IV A125T;A151T;L217Q 30;37;48 35;42;53 HA 73 75 30282714 Amino Acid Residue 217 in the Hemagglutinin Glycoprotein Is a Key Mediator of Avian Influenza H7N9 Virus Antigenicity. Of these three mutations, L217Q was found to be a key mediator of LPAI H7N9 antigenic variation. 2019 Journal of virology Discussion IV L217Q 26 31 30282714 Amino Acid Residue 217 in the Hemagglutinin Glycoprotein Is a Key Mediator of Avian Influenza H7N9 Virus Antigenicity. The A151T substitution has also previously introduced glycosylation in H5N1, resulting in reduced virus binding toward human-like receptors. 2019 Journal of virology Discussion IV A151T 4 9 30282714 Amino Acid Residue 217 in the Hemagglutinin Glycoprotein Is a Key Mediator of Avian Influenza H7N9 Virus Antigenicity. We demonstrated that residue 217 is a major antigenic epitope for H7N9 avian influenza viruses and that the L217Q substitution resulted in large reductions in both ferret and chicken antiserum binding. 2019 Journal of virology Discussion IV L217Q 108 113 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. Beside the S212P substitution that decreased the ability of H7N9-NS1 to inhibit the host innate immunity, we also identified another NS1 amino acid substitution I178V, which can significantly decrease the steady state of NS1 protein. 2018 Veterinary research Discussion IV S212P;I178V 11;161 16;166 NS1;NS1;NS1 65;133;221 68;136;224 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. By blocking gene expression in infected cells, the H7N9 NS1 protein suppresses the expression of IFN-alpha, IFN-beta, IL-28 and several ISGs, whereas this ability was destroyed due to S212P substitution. 2018 Veterinary research Discussion IV S212P 184 189 NS1 56 59 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. Consistent with the data, S212P mutation could no longer promote virus growth, and the viral titer was slightly lower in NS1-S212P transfected cells than that in NS1-WT transfected cells. 2018 Veterinary research Discussion IV S212P;S212P 26;125 31;130 NS1;NS1 121;162 124;165 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. For example, G219S and K58I combined mutations or three-amino-acid mutations (V186G/K-K193T-G228S or V186N-N224K-G228S) in H7N9 HA protein resulted in high affinity to alpha-2,6-linked sialic acid (SA) and increased HA stability, and a R292K mutation in H7N9 NA protein facilitated drug resistance through decreasing the binding interaction with oseltamivir, the most commonly used anti-influenza drug. 2018 Veterinary research Discussion IV G219S;K58I;V186G;V186K;K193T;G228S;G228S;V186N;N224K;R292K 13;23;78;78;86;92;113;101;107;236 18;27;85;85;91;97;118;106;112;241 HA;HA;NA 128;216;259 130;218;261 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. Given the previous reports and the fact that influenza virus NS1 protein can inhibit host gene expression by binding and inhibiting the cellular factor CPSF30, the verification whether the NS1 mutation S212P affects its binding to CPSF30 should be further studied. 2018 Veterinary research Discussion IV S212P 202 207 NS1;NS1 61;189 64;192 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. Here, to identify new residues in H7N9 NS1 that are associated with virus virulence, we screened eight substitutions including R55E, H63Q, E70K, P87S, S114P, A143T, I178V and S212P that distinguish the NS1s of avian-origin influenza viruses from those of human strains. 2018 Veterinary research Discussion IV R55E;H63Q;E70K;P87S;S114P;A143T;I178V;S212P 127;133;139;145;151;158;165;175 131;137;143;149;156;163;170;180 NS1;NS1 39;202 42;206 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. However, S212P mutation decreased the ability of NS1 to suppress RIG-I expression. 2018 Veterinary research Discussion IV S212P 9 14 NS1 49 52 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. In addition, either E627K or V598T/I substitution in PB2 contributes to the higher virulence of H7N9 influenza virus than the 2009 pandemic H1N1 influenza virus and the seasonal H3N2 influenza virus through enhancing replication and pathogenicity of H7N9 influenza virus in mammals. 2018 Veterinary research Discussion IV E627K;V598T;V598I 20;29;29 25;36;36 PB2 53 56 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. In addition, we also identified that I178V mutation led to NS1 degradation through proteasome pathway. 2018 Veterinary research Discussion IV I178V 37 42 NS1 59 62 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. Interestingly, we observed that the mice infected with PR8-S212 or PR8-I178 exhibited faster weight loss, shorter survival time, increased viral load, and more severe organ damage as compared with those infected with PR8-WT, suggesting that P212S or V178I mutation in PR8 NS1 protein increased virulence, which probably correlates with increased antagonism to innate immunity and steady state of NS1 protein respectively. 2018 Veterinary research Discussion IV P212S;V178I 241;250 246;255 NS1;NS1 272;396 275;399 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. Previous study has shown that influenza virus NS1 could enhance its stability by sumoylation, and NS1 K221 is the major SUMO1 acceptor site, since NS1 K221R mutation displayed a significant decrease of sumoylation. 2018 Veterinary research Discussion IV K221R 151 156 NS1;NS1;NS1 46;98;147 49;101;150 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. The subsequent function analysis showed that S212P mutation seriously impaired NS1 ability of inhibiting host interferon response, indicating that S212 residue in H7N9 NS1 protein may contribute to the higher virulence of H7N9 influenza virus. 2018 Veterinary research Discussion IV S212P 45 50 NS1;NS1 79;168 82;171 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. To analyze the importance of the residues 212 and 178 in NS1 protein on virus growth and virulence, two recombinant PR8 viruses incorporating the mutation P212S (PR8-S212) or V178I (PR8-I178) were generated by reverse genetics. 2018 Veterinary research Discussion IV P212S;V178I 155;175 160;180 NS1 57 60 30285871 Identification of two residues within the NS1 of H7N9 influenza A virus that critically affect the protein stability and function. We postulated that I178V mutation might have altered the structure of the NS1 protein and caused its degradation. 2018 Veterinary research Discussion IV I178V 19 24 NS1 74 77 30301950 Tree shrew as a new animal model to study the pathogenesis of avian influenza (H9N2) virus infection. In our experiments, the wild-type H9N2/Y280 virus replicated efficiently in ferrets even without the PB2-E627K mutation, while the difference between the wild type and the PB2 mutant was more significant in tree shrews, supporting the previous finding that tree shrews are susceptible to avian H9N2 virus infection. 2018 Emerging microbes & infections Discussion IV E627K 105 110 PB2;PB2 101;172 104;175 Influenza A virus H9N2 infection 288 314 30301950 Tree shrew as a new animal model to study the pathogenesis of avian influenza (H9N2) virus infection. In our study, both ferrets and tree shrews supported the replication of the H9N2 virus, and this replication was further enhanced by the PB2-E627K mutation. 2018 Emerging microbes & infections Discussion IV E627K 141 146 PB2 137 140 30301950 Tree shrew as a new animal model to study the pathogenesis of avian influenza (H9N2) virus infection. Interestingly, the PB2-E627K mutant clearly replicated more efficiently than the wild-type virus in the ex vivo study, while virus replication was observed only in the lungs of two tree shrews that were infected with the mutant. 2018 Emerging microbes & infections Discussion IV E627K 23 28 PB2 19 22 30301950 Tree shrew as a new animal model to study the pathogenesis of avian influenza (H9N2) virus infection. Moreover, our newly established tree shrew ex vivo cultures demonstrated that the PB2-E627K mutation enhanced the early cycles of H9N2 virus replication in the nasal turbinate and trachea, in which the kinetics were consistent with our findings from in vivo infection. 2018 Emerging microbes & infections Discussion IV E627K 86 91 PB2 82 85 30301950 Tree shrew as a new animal model to study the pathogenesis of avian influenza (H9N2) virus infection. Specifically, the PB2-E627K mutation is associated with an increase in the virulence and replication of the avian influenza virus in both in vitro and in vivo models. 2018 Emerging microbes & infections Discussion IV E627K 22 27 PB2 18 21 30301950 Tree shrew as a new animal model to study the pathogenesis of avian influenza (H9N2) virus infection. This result suggests that the PB2-E627K mutant has adapted by gaining the ability to replicate in the lower lung, but replication in this site may not occur in every infected individual and may be caused by other factors, which is similar to the situation in humans. 2018 Emerging microbes & infections Discussion IV E627K 34 39 PB2 30 33 30301950 Tree shrew as a new animal model to study the pathogenesis of avian influenza (H9N2) virus infection. We also found that H9N2 virus with the E627K mutation (Y280-PB2-E627K) was shed by tree shrews in higher quantities and for a longer period than its wild-type control. 2018 Emerging microbes & infections Discussion IV E627K;E627K 39;64 44;69 PB2 60 63 30301950 Tree shrew as a new animal model to study the pathogenesis of avian influenza (H9N2) virus infection. We and others have previously studied the pathogenesis of H9N2 virus infection and the contribution of the PB2-E627K mutation in mice. 2018 Emerging microbes & infections Discussion IV E627K 111 116 PB2 107 110 Influenza A virus H9N2 infection 58 78 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. Acquisition of each of these alleles either further reduced (P70S) or abolished (TT) IFNlambda4 activity. 2018 PLoS pathogens Discussion IV P70S 61 65 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. Based on the above speculation, we would predict that the response to HCV infection in chimpanzees may be similar in Pygmies with the K154E variant. 2018 PLoS pathogens Discussion IV K154E 134 139 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. By comparing IFNlambda4 from different species we demonstrate that the genus Homo evolved an IFNlambda4 gene with attenuated activity (prior to the TT allele), and that the vast majority of extant humans carry an IFNlambda4 variant with lower antiviral potential due to a mutation of a single highly-conserved amino acid residue (E154K). 2018 PLoS pathogens Discussion IV E154K 330 335 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. Further biophysical studies using highly-purified recombinant protein measuring affinity and avidity of HsIFNlambda4 wt and K154E for each receptor molecule [as in ] combined with studies on the mechanism of IFNlambda4 release will help address these hypotheses. 2018 PLoS pathogens Discussion IV K154E 124 129 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. How might IFNlambda4 E154K reduce antiviral activity? 2018 PLoS pathogens Discussion IV E154K 21 26 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. How might IFNlambda4 E154K reduce antiviral activity. 2018 PLoS pathogens Discussion IV E154K 21 26 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. Implications of the E154K substitution for IFNlambda4 evolution. 2018 PLoS pathogens Discussion IV E154K 20 25 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. One explanation for this difference could be higher IFNlambda4 activity in populations with the K154E variant, which may enhance HCV clearance. 2018 PLoS pathogens Discussion IV K154E 96 101 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. Other rare variants have arisen in humans with little impact on HsIFNlambda4 antiviral potential based on our in vitro assays, except for variants L79F and K154E, which lower and increase activity respectively. 2018 PLoS pathogens Discussion IV L79F;K154E 147;156 151;161 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. Our analysis suggests that the Homo IFNlambda4 orthologue acquired the E154K substitution, yielding a less active protein, after the genetic divergence of the hominid Homo and Pan ancestral lineages (estimated to be at most 6 million years ago in Africa) but before human/Neanderthal divergence (~370,000 years ago,). 2018 PLoS pathogens Discussion IV E154K 71 76 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. Since this variant was not present in the genetic data for San and Archaic Neanderthal and Denisovan human lineages, we speculate that these populations likely reacquired K154E following divergence of chimpanzees and humans. 2018 PLoS pathogens Discussion IV K154E 171 176 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. Subsequently, the IFNL4 gene acquired two further variants, the P70S and TT alleles that are now common in the human population. 2018 PLoS pathogens Discussion IV P70S 64 68 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. To conclude, our study further supports a significant and non-redundant role for IFNlambda4 in controlling the host response to viral infections yet one whose activity has been repeatedly attenuated during human evolution, commencing with E154K. 2018 PLoS pathogens Discussion IV E154K 239 244 30308076 A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. To us, the most intriguing of these variants is K154E, which was found in a high proportion of rainforest 'Pygmy' hunter-gatherers from west central Africa but was rarely present in the African population. 2018 PLoS pathogens Discussion IV K154E 48 53 30349332 Antiviral resistance markers in influenza virus sequences in Mexico, 2000-2017. In the present analysis, the sequences of the H1N1 pdm09 during the period 2009-2012 present a higher frequency of H275Y, which could suggest that this mutation is being adapted, maintained, and disseminated in this subtype in Mexico. 2018 Infection and drug resistance Discussion IV H275Y 115 120 30349332 Antiviral resistance markers in influenza virus sequences in Mexico, 2000-2017. In the sequences analyzed in this work, the predominant mutation was H275Y in both the H1N1 pdm09 and seasonal H1N1 subtypes, while the H3N2 subtype did not present this mutation (H274Y), and its overall resistance proportion was lower than that of the other two influenza A viruses. 2018 Infection and drug resistance Discussion IV H275Y;H274Y 69;180 74;185 30349332 Antiviral resistance markers in influenza virus sequences in Mexico, 2000-2017. The predominant resistance-associated change is H275Y (N1 numbering). 2018 Infection and drug resistance Discussion IV H275Y 48 53 30352857 The mechanism of resistance to favipiravir in influenza. Additional research would be needed to determine whether the nonmutagenic mechanisms of favipiravir play a significant role in inhibiting influenza and whether the K229R mutation could also provide resistance to these alternative mechanisms. 2018 Proc Natl Acad Sci U S A Discussion IV K229R 164 169 30352857 The mechanism of resistance to favipiravir in influenza. As the P653L mutant is not critical for favipiravir resistance per se, we will address the contribution of P653 to polymerase activity in more detail elsewhere. 2018 Proc Natl Acad Sci U S A Discussion IV P653L 7 12 30352857 The mechanism of resistance to favipiravir in influenza. imply that the K229R mutation prevents F-RTP incorporation into nascent RNA during both viral transcription and replication. 2018 Proc Natl Acad Sci U S A Discussion IV K229R 15 20 30352857 The mechanism of resistance to favipiravir in influenza. In the context of infectious virus, PB1 K229R reduced the mutagenic effect of favipiravir at a cost to growth and this effect could be alleviated by PA P653L. 2018 Proc Natl Acad Sci U S A Discussion IV K229R;P653L 40;152 45;157 PA;PB1 149;36 151;39 30352857 The mechanism of resistance to favipiravir in influenza. is likely different from our findings as the location of the mutations is distant from K229R and the site of nucleotide incorporation. 2018 Proc Natl Acad Sci U S A Discussion IV K229R 87 92 30352857 The mechanism of resistance to favipiravir in influenza. It is tempting to speculate that the proline-to-leucine mutation makes the connection between the fingers and thumb subdomains more flexible, which could alleviate the decrease in nucleotide binding space that results from the K229R mutation. 2018 Proc Natl Acad Sci U S A Discussion IV K229R 227 232 30352857 The mechanism of resistance to favipiravir in influenza. showed that the key mutation that led to favipiravir resistance of chikungunya virus was also a K-to-R mutation in motif F of the viral polymerase and this mutation is equivalent to the PB1 K229R mutation we report here. 2018 Proc Natl Acad Sci U S A Discussion IV K229R 190 195 PB1 186 189 30352857 The mechanism of resistance to favipiravir in influenza. The double mutant polymerase containing both P653L and K229R has wild-type polymerase activity while still preventing the incorporation of favipiravir, and it will be important to assess the transmissibility and pathogenicity of this virus in future studies. 2018 Proc Natl Acad Sci U S A Discussion IV P653L;K229R 45;55 50;60 30352857 The mechanism of resistance to favipiravir in influenza. The fitness cost imparted by the K229R mutation in PB1 and the requirement for a second compensatory mutation to restore viral fitness may explain why resistance has not been observed in other studies. 2018 Proc Natl Acad Sci U S A Discussion IV K229R 33 38 PB1 51 54 30352857 The mechanism of resistance to favipiravir in influenza. The increase in mutation frequency that we observe for P653L in the presence of favipiravir. 2018 Proc Natl Acad Sci U S A Discussion IV P653L 55 60 30352857 The mechanism of resistance to favipiravir in influenza. The key mutation was K229R in the PB1 subunit, which prevented the incorporation of favipiravir into nascent viral RNA by polymerases from H1N1, H3N2, and H7N9 influenza A viruses albeit at a cost to the RNA polymerase activity in cell culture assays. 2018 Proc Natl Acad Sci U S A Discussion IV K229R 21 26 PB1 34 37 30352857 The mechanism of resistance to favipiravir in influenza. This cost was compensated for by a P653L mutation in the PA subunit. 2018 Proc Natl Acad Sci U S A Discussion IV P653L 35 40 PA 57 59 30352857 The mechanism of resistance to favipiravir in influenza. This occlusion of the NTP binding pocket likely reduces the efficiency of normal NTP incorporation in cell culture as well and may account for reduction in both polymerase activity and viral growth of the single K229R mutant. 2018 Proc Natl Acad Sci U S A Discussion IV K229R 212 217 30352857 The mechanism of resistance to favipiravir in influenza. We observed that the K229R mutation did not confer any resistance to ribavirin or increase polymerase fidelity in general. 2018 Proc Natl Acad Sci U S A Discussion IV K229R 21 26 30353004 Genome-wide characterization of the seasonal H3N2 virus in Shanghai reveals natural temperature-sensitive strains conferred by the I668V mutation in the PA subunit. In the PA protein, the 2017sum strains exhibited a V668I substitution located in the PB1 interaction domain. 2018 Emerging microbes & infections Discussion IV V668I 51 56 PA;PB1 7;85 9;88 30353004 Genome-wide characterization of the seasonal H3N2 virus in Shanghai reveals natural temperature-sensitive strains conferred by the I668V mutation in the PA subunit. The 2017sum viral strains differed from the 2016-2017win viral strains in regard to the K299R and K340R mutations in the PB2 protein. 2018 Emerging microbes & infections Discussion IV K299R;K340R 88;98 93;103 PB2 121 124 30353004 Genome-wide characterization of the seasonal H3N2 virus in Shanghai reveals natural temperature-sensitive strains conferred by the I668V mutation in the PA subunit. The I668V mutation may regulate the PA-PB1 interaction or inhibit polymerase function. 2018 Emerging microbes & infections Discussion IV I668V 4 9 PA;PB1 36;39 38;42 30353004 Genome-wide characterization of the seasonal H3N2 virus in Shanghai reveals natural temperature-sensitive strains conferred by the I668V mutation in the PA subunit. The mechanism by which the PA I668V mutation suppressed polymerase activity at high temperatures was not elucidated. 2018 Emerging microbes & infections Discussion IV I668V 30 35 PA 27 29 30353004 Genome-wide characterization of the seasonal H3N2 virus in Shanghai reveals natural temperature-sensitive strains conferred by the I668V mutation in the PA subunit. The N127S mutation identified in NS1 has not been reported previously; however, this position had been confirmed to be part of the PKR-binding site of the NS1 protein (position 123-127). 2018 Emerging microbes & infections Discussion IV N127S 4 9 NS1;NS1 33;155 36;158 30353004 Genome-wide characterization of the seasonal H3N2 virus in Shanghai reveals natural temperature-sensitive strains conferred by the I668V mutation in the PA subunit. This finding is consistent with our results showing that polymerases of both the H1N1 and H3N2 viruses with the PA I668V residue exhibit reduced activity at high temperatures. 2018 Emerging microbes & infections Discussion IV I668V 115 120 PA 112 114 30353004 Genome-wide characterization of the seasonal H3N2 virus in Shanghai reveals natural temperature-sensitive strains conferred by the I668V mutation in the PA subunit. Viruses with the N127S mutation may lose the ability to interact with the viral polymerase and exhibit low synthesis of vRNA at the early infection stage. 2018 Emerging microbes & infections Discussion IV N127S 17 22 30353004 Genome-wide characterization of the seasonal H3N2 virus in Shanghai reveals natural temperature-sensitive strains conferred by the I668V mutation in the PA subunit. We hypothesize that the decrease in the RNA accumulation and TCID50 value in cells infected with the 2016-2017win viruses may result from the N127S mutation in the NS1 protein. 2018 Emerging microbes & infections Discussion IV N127S 142 147 NS1 164 167 30405591 Identification of Amino Acid Residues Responsible for Inhibition of Host Gene Expression by Influenza A H9N2 NS1 Targeting of CPSF30. Residue changes L103F, I106M, P114S, G125D, and N139D in HK/97 NS1 protein (HK 13 mutant) completely restored the ability of NS1 to bind to CPSF30 (Figure 9). 2018 Frontiers in microbiology Discussion IV L103F;I106M;P114S;G125D;N139D 16;23;30;37;48 21;28;35;42;53 NS1;NS1 63;125 66;128 30428893 Analysis of influenza B virus lineages and the HA1 domain of its hemagglutinin gene in Guangzhou, southern China, during 2016. Among these variations, C196S and E198D were only in a single isolate, but all isolates had the I132V andN144D variations (120-loop and 150-loop). 2018 Virology journal Discussion IV C196S;E198D;I132V 24;34;96 29;39;101 30428893 Analysis of influenza B virus lineages and the HA1 domain of its hemagglutinin gene in Guangzhou, southern China, during 2016. In this study, we found some antigenicity-related variations in the HA1 domain of influenza B viruses in the Victoria lineage, including I132V, N144D, C196S, and E198D. 2018 Virology journal Discussion IV N144D;I132V;C196S;E198D 144;137;151;162 149;142;156;167 HA1 68 71 30439983 Influenza B viruses circulated during last 5 years in Mongolia. According to NA sequences, G140R, I114T and E105K mutations were found in Mongolian resistant isolates. 2018 PloS one Discussion IV G140R;I114T;E105K 27;34;44 32;39;49 13 15 30439983 Influenza B viruses circulated during last 5 years in Mongolia. Among the mutations, G104R has been occurred during the propagation in MDCK cell culture. 2018 PloS one Discussion IV G104R 21 26 30439983 Influenza B viruses circulated during last 5 years in Mongolia. Isolate which have G104R mutation showed strong resistant to NAIs as compared to isolates having E105K mutation, suggesting that G104R mutation might play a key role in development of the drug resistance of influenza B virus. 2018 PloS one Discussion IV G104R;E105K;G104R 19;97;129 24;102;134 NAI 61 65 30463209 A PB1-K577E Mutation in H9N2 Influenza Virus Increases Polymerase Activity and Pathogenicity in Mice. A PA-T97I mutation detected in a HK-MA2 virus was previously shown to increase the polymerase activity and mouse pathogenicity of H5N1 avian influenza viruses. 2018 Viruses Discussion IV T97I 5 9 PA 2 4 30463209 A PB1-K577E Mutation in H9N2 Influenza Virus Increases Polymerase Activity and Pathogenicity in Mice. Although PB1 residue 577 is not directly involved in these polar contacts, a conformational change in the PB1 alpha-helix due to the K577E mutation might occur, which could affect the binding affinity for the PB2 alpha-helix. 2018 Viruses Discussion IV K577E 133 138 PB1;PB1;PB2 9;106;209 12;109;212 30463209 A PB1-K577E Mutation in H9N2 Influenza Virus Increases Polymerase Activity and Pathogenicity in Mice. Although there is no previous report of an HA-N132D mutation, the lack of N-glycosylation at residue 132 may alter its receptor-binding property because it is located at a similar distance as the N198 residue to the receptor binding site in the top region of the globular head of HA (Figure 6A,B). 2018 Viruses Discussion IV N132D 46 51 HA;HA 43;280 45;282 30463209 A PB1-K577E Mutation in H9N2 Influenza Virus Increases Polymerase Activity and Pathogenicity in Mice. Another possible mechanism of PB1-K577E-mediated enhancement of polymerase activity is the involvement of a host factor that interacts with the viral polymerase and supports its activity. 2018 Viruses Discussion IV K577E 34 39 PB1 30 33 30463209 A PB1-K577E Mutation in H9N2 Influenza Virus Increases Polymerase Activity and Pathogenicity in Mice. Here, we identified a novel PB1 mutation, K577E, in H9N2 viruses serially passaged in mice that could increase pathogenicity in mice, suggesting that the PB1-K577E mutation could be considered to be one of the signatures for mammalian adaptation of avian influenza viruses. 2018 Viruses Discussion IV K577E;K577E 42;158 47;163 PB1;PB1 28;154 31;157 30463209 A PB1-K577E Mutation in H9N2 Influenza Virus Increases Polymerase Activity and Pathogenicity in Mice. Here, we selected H9N2 MA viruses (HK-MA1 and -MA2) harboring the PB2-E627K mutation. 2018 Viruses Discussion IV E627K 70 75 PB2 66 69 30463209 A PB1-K577E Mutation in H9N2 Influenza Virus Increases Polymerase Activity and Pathogenicity in Mice. However, its receptor binding property may change to a lesser extent compared to the HA-N198S/T mutation, supported by a slight increase in the pathogenicity of rHA-N132D (Figure 2A,B). 2018 Viruses Discussion IV N198T;N198S;N132D 88;88;165 95;95;170 HA 85 87 30463209 A PB1-K577E Mutation in H9N2 Influenza Virus Increases Polymerase Activity and Pathogenicity in Mice. However, our finding that the pathogenicity of the H9N2 virus was drastically increased by the PB1-K577E mutation alone provides new insight into the role of the polymerase complex in mammalian adaption of avian influenza viruses. 2018 Viruses Discussion IV K577E 99 104 PB1 95 98 30463209 A PB1-K577E Mutation in H9N2 Influenza Virus Increases Polymerase Activity and Pathogenicity in Mice. However, the detailed mechanisms including identification of host factors that interact with the PB1 region and structural dynamics of the PB1-K577E mutation need to be analyzed. 2018 Viruses Discussion IV K577E 143 148 PB1;PB1 97;139 100;142 30463209 A PB1-K577E Mutation in H9N2 Influenza Virus Increases Polymerase Activity and Pathogenicity in Mice. However, there is no report of the PB1-K577E mutation in regards to mammalian adaptation of avian viruses, such as H9N2 viruses. 2018 Viruses Discussion IV K577E 39 44 PB1 35 38 30463209 A PB1-K577E Mutation in H9N2 Influenza Virus Increases Polymerase Activity and Pathogenicity in Mice. In addition, this PA mutation enhanced H6N1 avian virus pathogenicity and expanded tissue tropism in mice when combined with PB2-E627K. 2018 Viruses Discussion IV E627K 129 134 PA;PB2 18;125 20;128 30463209 A PB1-K577E Mutation in H9N2 Influenza Virus Increases Polymerase Activity and Pathogenicity in Mice. In conclusion, a novel PB1-K577E mutation emerges during mouse adaptation of an H9N2 virus, thus we propose PB1-K577E as an additional signature of mammalian adaptation of avian influenza viruses. 2018 Viruses Discussion IV K577E;K577E 27;112 32;117 PB1;PB1 23;108 26;111 30463209 A PB1-K577E Mutation in H9N2 Influenza Virus Increases Polymerase Activity and Pathogenicity in Mice. In fact, the PB1-K577E mutation enhanced viral polymerase activity in human cells, even at a lower temperature (Figure 3), suggesting the likely acquisition of efficient growth in the upper respiratory tract of humans, an obligatory phenotype of human-adapted viruses. 2018 Viruses Discussion IV K577E 17 22 PB1 13 16 30463209 A PB1-K577E Mutation in H9N2 Influenza Virus Increases Polymerase Activity and Pathogenicity in Mice. It is well known that the PB2-E627K and PB2-D701N mutations are determinants for mammalian adaptation of avian influenza viruses through their interaction with host species-specific factors, such as importin-alpha isoforms. 2018 Viruses Discussion IV E627K;D701N 30;44 35;49 PB2;PB2 26;40 29;43 30463209 A PB1-K577E Mutation in H9N2 Influenza Virus Increases Polymerase Activity and Pathogenicity in Mice. Many studies have demonstrated that avian influenza viruses bearing the PB2-E627K mutant show increased replication ability in mammalian hosts and higher virulence in mammals. 2018 Viruses Discussion IV E627K 76 81 PB2 72 75 30463209 A PB1-K577E Mutation in H9N2 Influenza Virus Increases Polymerase Activity and Pathogenicity in Mice. Our rHA-N198S virus showed increased virulence (Figure 1A,B), possibly due to the same reason. 2018 Viruses Discussion IV N198S 8 13 30463209 A PB1-K577E Mutation in H9N2 Influenza Virus Increases Polymerase Activity and Pathogenicity in Mice. PB2-E627K is a well-known mutation that increases viral polymerase activity in mammalian cells, and is a critical factor for human adaptation of avian influenza viruses. 2018 Viruses Discussion IV E627K 4 9 PB2 0 3 30463209 A PB1-K577E Mutation in H9N2 Influenza Virus Increases Polymerase Activity and Pathogenicity in Mice. Previous reports have shown that H9N2 mutant viruses possessing the HA-N198T mutation, including our HK-MA1 and -MA2 viruses, lack N-glycosylation at residue 198 and exhibit higher affinity for the human-type receptor and higher pathogenicity in mice than the parent virus with 198N. 2018 Viruses Discussion IV N198T 71 76 HA 68 70 30463209 A PB1-K577E Mutation in H9N2 Influenza Virus Increases Polymerase Activity and Pathogenicity in Mice. Separate from this PB2 mutation, we demonstrated that a PB1-K577E mutation increased both the pathogenicity of H9N2 virus in mice (Figure 1 and Figure 2) and polymerase activity in human cells (Figure 3), suggesting that the PB1-K577E mutation, like the PB2-E627K, could contribute to human adaption of avian viruses. 2018 Viruses Discussion IV K577E;K577E;E627K 60;229;258 65;234;263 PB1;PB1;PB2;PB2 56;225;19;254 59;228;22;257 30463209 A PB1-K577E Mutation in H9N2 Influenza Virus Increases Polymerase Activity and Pathogenicity in Mice. Since the PB1 subunit of the PB1-PA complex interacts with PB2 in the nucleus, the PB1-K577E mutation could alter polymerase activity, likely leading to cold-adaptation of the virus, similar to the PB2-E627K mutation. 2018 Viruses Discussion IV K577E;E627K 87;202 92;207 PA;PB1;PB1;PB1;PB2;PB2 33;10;29;83;59;198 35;13;32;86;62;201 30463209 A PB1-K577E Mutation in H9N2 Influenza Virus Increases Polymerase Activity and Pathogenicity in Mice. The charge environment in this region may be altered by the K577E mutation due to the change from a negatively-charged K to a positively-charged E, possibly resulting in different binding properties for a host-specific factor. 2018 Viruses Discussion IV K577E 60 65 30463209 A PB1-K577E Mutation in H9N2 Influenza Virus Increases Polymerase Activity and Pathogenicity in Mice. The HA-N132D or HA-N198S mutations detected in the HK-MA viruses abolished N-linked glycosylation (Figure 4). 2018 Viruses Discussion IV N132D;N198S 7;19 12;24 HA;HA 4;16 6;18 30463209 A PB1-K577E Mutation in H9N2 Influenza Virus Increases Polymerase Activity and Pathogenicity in Mice. The molecular mechanism of the enhanced polymerase activity in mammalian cells due to the PB1-K577E mutation is unknown. 2018 Viruses Discussion IV K577E 94 99 PB1 90 93 30463209 A PB1-K577E Mutation in H9N2 Influenza Virus Increases Polymerase Activity and Pathogenicity in Mice. There was a recent report on the PB1-K577E mutation, showing that this mutation was observed during serial passage of a human H3N2 laboratory strain (A/Hong Kong/1/68) in mice. 2018 Viruses Discussion IV K577E 37 42 PB1 33 36 30463209 A PB1-K577E Mutation in H9N2 Influenza Virus Increases Polymerase Activity and Pathogenicity in Mice. Therefore, PA-T97I is likely important for mammalian adaptation of H9N2 viruses as well. 2018 Viruses Discussion IV T97I 14 18 PA 11 13 30463209 A PB1-K577E Mutation in H9N2 Influenza Virus Increases Polymerase Activity and Pathogenicity in Mice. To investigate the distribution of PB1-K577E mutation in nature, we analyzed the genome sequences of influenza viruses in the NCBI database and found out that not only are there no naturally occurring H9N2 isolates possessing a Glu (E) at position 577 of PB1 but also that viruses possessing an E at this position are very rare, even among other subtype mammalian viruses (Table 2). 2018 Viruses Discussion IV K577E;E577E 39;228 44;253 PB1;PB1 35;256 38;259 30509291 Conserved methionine 165 of matrix protein contributes to the nuclear import and is essential for influenza A virus replication. Although M165A protein accumulates around the nucleus where is co-localized with CLUH and CRM1 proteins, the transport into the nucleus is restricted. 2018 Virology journal Discussion IV M165A 9 14 30509291 Conserved methionine 165 of matrix protein contributes to the nuclear import and is essential for influenza A virus replication. However, we have observed the same distribution of M1 and M165A proteins in the cells transiently co-transfected with plasmid encoding only M1 protein with or without plasmid encoding NP protein, as well as in the cells transfected with five plasmids: pHW182-PB1, pHW181-PB2, pHW183-PA, pHW185-NP, and pHW127M. 2018 Virology journal Discussion IV M165A 58 63 M1;M1;NP;NP;PA;PB1;PB2 51;140;184;294;283;259;271 53;142;186;296;285;262;274 30509291 Conserved methionine 165 of matrix protein contributes to the nuclear import and is essential for influenza A virus replication. In M165A transfected cells, M165A-CLUH complexes were detected mostly in the cytoplasm and around the nucleus. 2018 Virology journal Discussion IV M165A;M165A 3;28 8;33 30509291 Conserved methionine 165 of matrix protein contributes to the nuclear import and is essential for influenza A virus replication. In the cells transfected with M1, NP protein was localized mainly in the nucleus unlike the NP in the cells transfected with M165A mutant where it was localized mainly in the cytoplasm and around the nuclear membrane. 2018 Virology journal Discussion IV M165A 125 130 M1;NP;NP 30;34;92 32;36;94 30509291 Conserved methionine 165 of matrix protein contributes to the nuclear import and is essential for influenza A virus replication. M165A which is not transported into the nucleus and stays near the nucleus where associates with CRM1 present in this region. 2018 Virology journal Discussion IV M165A 0 5 30509291 Conserved methionine 165 of matrix protein contributes to the nuclear import and is essential for influenza A virus replication. Mutation M165A in M1 protein had a striking effect on the distribution of NP protein. 2018 Virology journal Discussion IV M165A 9 14 M1;NP 18;74 20;76 30509291 Conserved methionine 165 of matrix protein contributes to the nuclear import and is essential for influenza A virus replication. Mutation V166A is presented in some avian viruses and thereby it is not surprising that this mutation is well tolerated in our system. 2018 Virology journal Discussion IV V166A 9 14 30509291 Conserved methionine 165 of matrix protein contributes to the nuclear import and is essential for influenza A virus replication. Since co-localization of M165A protein with the plasma membrane is not impaired, we assume that neither is affected the transport and interaction of M165A with HA, NA, and M2 proteins. 2018 Virology journal Discussion IV M165A;M165A 25;149 30;154 HA;M2;NA 160;172;164 162;174;166 30509291 Conserved methionine 165 of matrix protein contributes to the nuclear import and is essential for influenza A virus replication. Transport of NP protein can be restricted by accumulated CLUH-M165A and CRM1-M165A complexes on the nuclear membrane and/or some cellular proteins involved in the transport could be dysregulated. 2018 Virology journal Discussion IV M165A;M165A 62;77 67;82 NP 13 15 30509291 Conserved methionine 165 of matrix protein contributes to the nuclear import and is essential for influenza A virus replication. We have also prolonged the incubation time after re-infection in MDCK cells but M165A mutant virus was never rescued. 2018 Virology journal Discussion IV M165A 80 85 30509291 Conserved methionine 165 of matrix protein contributes to the nuclear import and is essential for influenza A virus replication. We have also tried to make a virus with M165 V mutation and this mutation was also lethal. 2018 Virology journal Discussion IV M165V 40 46 30509291 Conserved methionine 165 of matrix protein contributes to the nuclear import and is essential for influenza A virus replication. We have found that mutation M165A does not change the distribution and co-localization pattern with importin-alpha (data not shown). 2018 Virology journal Discussion IV M165A 28 33 30509291 Conserved methionine 165 of matrix protein contributes to the nuclear import and is essential for influenza A virus replication. We suggest that M165A mutation disturbed the transport of CLUH-M165A complex into the nucleus and blocked the CRM1 translocation into the nucleus. 2018 Virology journal Discussion IV M165A;M165A 16;63 21;68 30509291 Conserved methionine 165 of matrix protein contributes to the nuclear import and is essential for influenza A virus replication. We were not able to study co-localization of other virus proteins with CLUH, CRM-1 or importin-alpha in the cell transfected with revers genetic plasmids including M165A mutant since we did not possess suitable antibodies for multiple labelling and transfection with eight different plasmids did not ensure expression of all proteins in one cell. 2018 Virology journal Discussion IV M165A 164 169 30533399 Potential Pandemic of H7N9 Avian Influenza A Virus in Human. Amino acid change PB2-A588V which showed much higher proportion in human-isolated than avian-isolated H7N9 in the 5th wave, was proved to promote the adaptation of H7N9 to mammals (Xiao et al.,). 2018 Frontiers in cellular and infection microbiology Discussion IV A588V 22 27 PB2 18 21 30533399 Potential Pandemic of H7N9 Avian Influenza A Virus in Human. Amino acid changes E/D627K/N and D701N in PB2 were shown to be critical adaptations for infecting mammals (Subbarao et al.,; Hatta et al.,; Gabriel et al.,; Li et al.,). 2018 Frontiers in cellular and infection microbiology Discussion IV E627K;E627N;D627K;D627N;D701N 19;19;19;19;33 28;28;28;28;38 PB2 42 45 30533399 Potential Pandemic of H7N9 Avian Influenza A Virus in Human. Amino acid changes S155N, T156A, G182V, S205Y, and Q222L (H5 numbering) in HA increase virus-binding to human alpha-2,6 sialo-saccharides (Suzuki et al.,; Yamada et al.,; Wang et al.,; Herfst et al.,; Imai et al.,). 2018 Frontiers in cellular and infection microbiology Discussion IV S155N;T156A;G182V;S205Y;Q222L 19;26;33;40;51 24;31;38;45;56 HA 75 77 30533399 Potential Pandemic of H7N9 Avian Influenza A Virus in Human. E627K in PB2, which is the best characterized mammalian adaptive mutation (de Wit et al.,), has very high proportions only in human-isolated H7N9 viruses. 2018 Frontiers in cellular and infection microbiology Discussion IV E627K 0 5 PB2 9 12 30533399 Potential Pandemic of H7N9 Avian Influenza A Virus in Human. For these sites, except for V100A in PA, and K526R, D627K, and D701N in PB2, H9N2, and H7N9 do not differ significantly at other amino acid changes. 2018 Frontiers in cellular and infection microbiology Discussion IV V100A;K526R;D627K;D701N 28;45;52;63 33;50;57;68 PA;PB2 37;72 39;75 30533399 Potential Pandemic of H7N9 Avian Influenza A Virus in Human. Mutations Q222L in HA and K526R in PB2 show very low proportions (0 and 9.52%, respectively) in HP avian-isolated H7N9 viruses, yet 100% in LP viruses. 2018 Frontiers in cellular and infection microbiology Discussion IV Q222L;K526R 10;26 15;31 HA;PB2 19;35 21;38 30533399 Potential Pandemic of H7N9 Avian Influenza A Virus in Human. The D701N substitution in PB2 was found to increase virulence, and to expand the host range of avian H5N1 to mammals in the absence of E627K (Steel et al.,). 2018 Frontiers in cellular and infection microbiology Discussion IV D701N;E627K 4;135 9;140 PB2 26 29 30548432 Consecutive influenza surveillance of neuraminidase mutations and neuraminidase inhibitor resistance in Japan. Consequently, NA AA mutations associated with NAI resistance were only H275Y of H1N1pdm09. 2019 Influenza and other respiratory viruses Discussion IV H275Y 71 76 NA;NAI 14;46 16;49 30548432 Consecutive influenza surveillance of neuraminidase mutations and neuraminidase inhibitor resistance in Japan. Even in Japan, the largest consumer of NAIs, no spread of NAI-resistant viruses with mutations related to clinical ineffectiveness, such as a prolonged duration of fever, has been observed, and the emergence of A/H1N1pdm09 viruses carrying H275Y remains limited. 2019 Influenza and other respiratory viruses Discussion IV H275Y 240 245 NAI;NAI 58;39 61;43 30548432 Consecutive influenza surveillance of neuraminidase mutations and neuraminidase inhibitor resistance in Japan. However, it is highly possible that T148I and D151G/N are AA mutations induced by an MDCK passage, based on their previous reports,22, 23 although these mutations did not cause a substantial increase in their IC50 values (Table 3). 2019 Influenza and other respiratory viruses Discussion IV T148I;D151G;D151N 36;46;46 41;53;53 30548432 Consecutive influenza surveillance of neuraminidase mutations and neuraminidase inhibitor resistance in Japan. The dissemination of the H275Y-resistant viruses may remain restricted, due to impaired viral fitness mechanism that is caused by additional mutations. 2019 Influenza and other respiratory viruses Discussion IV H275Y 25 30 30548432 Consecutive influenza surveillance of neuraminidase mutations and neuraminidase inhibitor resistance in Japan. The frequency of H275Y detected in Japan was approximately 1%, which was similar to that reported by a global surveillance.6 For A/H3N2 and B, no virus exhibiting reduced inhibition by NAIs was detected in Japan. 2019 Influenza and other respiratory viruses Discussion IV H275Y 17 22 NAI 185 189 30548432 Consecutive influenza surveillance of neuraminidase mutations and neuraminidase inhibitor resistance in Japan. The sporadic community spread of the H275Y-resistant viruses was reported in Newcastle, Australia, in 2011 and in Sapporo, Japan, in 2013.27, 28 These viruses discovered in the two cities carried additional AA mutations, V241I and N369K, which were presumed to confer a positive effect on viral fitness.29 These viruses were also shown to have carried the third additional AA mutation, N386S/K, which was in contrast suggested to cause a negative effect on viral fitness in the presence of the V241I and N369K mutations.29, 30 In our data (Table S15), both N386 and K386 in addition to I241 and K369 were detected in the 2013-2014 season; in contrast, only K386 together with I241 and K369 was detected in the subsequent seasons. 2019 Influenza and other respiratory viruses Discussion IV H275Y;V241I;N369K;N386S;N386K;V241I;N369K 37;221;231;386;386;494;504 42;226;236;393;393;499;509 30548432 Consecutive influenza surveillance of neuraminidase mutations and neuraminidase inhibitor resistance in Japan. The two oseltamivir-resistant H275Y viruses isolated in the 2015-2016 season contained V241I, N369K, and N386K. 2019 Influenza and other respiratory viruses Discussion IV H275Y;V241I;N369K;N386K 30;87;94;105 35;92;99;110 30548432 Consecutive influenza surveillance of neuraminidase mutations and neuraminidase inhibitor resistance in Japan. These results were also similar to those reported by a global surveillance, which indicated that NAI-resistant A/H3N2 and B viruses were detected at a lower frequency (<1.0%) compared with NAI-resistant A/H1N1pdm09 viruses.6 This study showed that few AA mutations in the catalytic sites of A/H3N2 viruses were found without their D151G/N mutations. 2019 Influenza and other respiratory viruses Discussion IV D151G;D151N 331;331 338;338 NAI;NAI 97;189 100;192 30548432 Consecutive influenza surveillance of neuraminidase mutations and neuraminidase inhibitor resistance in Japan. This study showed that oseltamivir-resistant A/H1N1pdm09 viruses carrying H275Y did not spread throughout Japan. 2019 Influenza and other respiratory viruses Discussion IV H275Y 74 79 30574137 Susceptibility of Influenza Viruses to the Novel Cap-Dependent Endonuclease Inhibitor Baloxavir Marboxil. Furthermore, A37T, E199G, N412D, V517A, and P632S substitutions were each detected in an A(H3N2) virus. 2018 Frontiers in microbiology Discussion IV A37T;E199G;N412D;V517A;P632S 13;19;26;33;44 17;24;31;38;49 30574137 Susceptibility of Influenza Viruses to the Novel Cap-Dependent Endonuclease Inhibitor Baloxavir Marboxil. In contrast, influenza B viruses with the PA I38T and I38M substitutions replicated comparable to the wild-type virus, although the PA I38F substitution in influenza B virus conferred impaired replication capability. 2018 Frontiers in microbiology Discussion IV I38T;I38M;I38F 45;54;135 49;58;139 PA;PA 42;132 44;134 30574137 Susceptibility of Influenza Viruses to the Novel Cap-Dependent Endonuclease Inhibitor Baloxavir Marboxil. In our study, none of the currently circulating viruses tested possessed the PA I38T substitution. 2018 Frontiers in microbiology Discussion IV I38T 80 84 PA 77 79 30574137 Susceptibility of Influenza Viruses to the Novel Cap-Dependent Endonuclease Inhibitor Baloxavir Marboxil. In the case of oseltamivir- and peramivir-resistant A(H1N1) and A(H1N1)pdm09 viruses with an NA H275Y substitution, some amino acid substitutions in the NA protein were able to compensate for the detrimental effect of the H275Y substitution on viral fitness. 2018 Frontiers in microbiology Discussion IV H275Y;H275Y 96;222 101;227 NA;NA 93;153 95;155 30574137 Susceptibility of Influenza Viruses to the Novel Cap-Dependent Endonuclease Inhibitor Baloxavir Marboxil. In the clinical trial of baloxavir efficacy in children aged 6 months to <12 years, the PA I38T and I38M substitutions were detected in 18 (23.4%) of 77 A(H3N2) viruses. 2018 Frontiers in microbiology Discussion IV I38T;I38M 91;100 95;104 PA 88 90 30574137 Susceptibility of Influenza Viruses to the Novel Cap-Dependent Endonuclease Inhibitor Baloxavir Marboxil. In the Phase II clinical trial of baloxavir efficacy in adults aged 20-64 years, PA I38T, I38F, and E23K substitutions were detected in A(H1N1)pdm09 viruses and a PA G548R substitution was detected in a B virus. 2018 Frontiers in microbiology Discussion IV I38T;I38F;E23K;G548R 84;90;100;166 88;94;104;171 PA;PA 81;163 83;165 30574137 Susceptibility of Influenza Viruses to the Novel Cap-Dependent Endonuclease Inhibitor Baloxavir Marboxil. In the Phase III clinical trial in patients aged 12-64 years, PA I38T and I38M substitutions were detected in A(H3N2) viruses. 2018 Frontiers in microbiology Discussion IV I38T;I38M 65;74 69;78 PA 62 64 30574137 Susceptibility of Influenza Viruses to the Novel Cap-Dependent Endonuclease Inhibitor Baloxavir Marboxil. In vitro studies have revealed that influenza A(H1N1) viruses with the PA I38T, I38F, or E23K substitutions show 27.2, 10.6, and 4.7-fold higher EC50 values, respectively, whereas the PA G548R substitution in influenza B virus does not affect baloxavir susceptibility. 2018 Frontiers in microbiology Discussion IV I38T;I38F;E23K;G548R 74;80;89;187 78;84;93;192 PA;PA 71;184 73;186 30574137 Susceptibility of Influenza Viruses to the Novel Cap-Dependent Endonuclease Inhibitor Baloxavir Marboxil. In vitro studies of another new PA endonuclease inhibitor, RO-7, revealed that the PA I38T substitution was detected after serial passages of influenza A(H1N1) viruses in MDCK cells in the presence of RO-7. 2018 Frontiers in microbiology Discussion IV I38T 86 90 PA;PA 32;83 34;85 30574137 Susceptibility of Influenza Viruses to the Novel Cap-Dependent Endonuclease Inhibitor Baloxavir Marboxil. Influenza A(H3N2) viruses with the PA I38T, I38M, A37T, or E199G substitutions showed 56.6, 13.8, 8.1, and 4.5-fold higher EC50 values, respectively, whereas the baloxavir susceptibility was not affected by the PA N412D, V517A, or P632S substitution. 2018 Frontiers in microbiology Discussion IV I38T;I38M;A37T;E199G;N412D;V517A;P632S 38;44;50;59;214;221;231 42;48;54;64;219;226;236 PA;PA 35;211 37;213 30574137 Susceptibility of Influenza Viruses to the Novel Cap-Dependent Endonuclease Inhibitor Baloxavir Marboxil. Our data demonstrated that the reference virus possessing the PA I38T substitution showed 54- and 44-fold higher IC50 values to baloxavir in the plaque reduction and the focus reduction assay, respectively, indicating the validity of both systems for monitoring baloxavir susceptibility. 2018 Frontiers in microbiology Discussion IV I38T 65 69 PA 62 64 30574137 Susceptibility of Influenza Viruses to the Novel Cap-Dependent Endonuclease Inhibitor Baloxavir Marboxil. reported that A(H1N1) and A(H3N2) viruses with the PA I38T, I38F, and I38M substitutions had impaired replication capability compared with the wild-type virus in vitro. 2018 Frontiers in microbiology Discussion IV I38T;I38F;I38M 54;60;70 58;64;74 PA 51 53 30574137 Susceptibility of Influenza Viruses to the Novel Cap-Dependent Endonuclease Inhibitor Baloxavir Marboxil. These viruses possessed the I38T substitution in their PA protein. 2018 Frontiers in microbiology Discussion IV I38T 28 32 PA 55 57 30621708 Multiple amino acid substitutions involved in the adaption of three avian-origin H7N9 influenza viruses in mice. All these findings demonstrated that though E627K substitution is the common mutation of the three mouse-adapted viruses and it has been proved to increase virulence in mice, it is not the only virulence-determination mutation, there must be other substitutions correlate with E627K to influence virulence of mouse-adapted H7N9 virus. 2019 Virology journal Discussion IV E627K;E627K 44;277 49;282 30621708 Multiple amino acid substitutions involved in the adaption of three avian-origin H7N9 influenza viruses in mice. Another substitution worth noting is T97I at PA protein. 2019 Virology journal Discussion IV T97I 37 41 PA 45 47 30621708 Multiple amino acid substitutions involved in the adaption of three avian-origin H7N9 influenza viruses in mice. Further comparation of the amino acids substitutions discovered that only E627K at PB2 protein shared by the three mouse-adapted H7N9 viruses. 2019 Virology journal Discussion IV E627K 74 79 PB2 83 86 30621708 Multiple amino acid substitutions involved in the adaption of three avian-origin H7N9 influenza viruses in mice. In addition to the most often-observed substitution of E627K, there are several other important mutations in the PB2 protein, such as E158G, D253N, T271A, K526R, Q591K, A588V, D701N and so on, and these mutations had been proved to enhance polymerase activity. 2019 Virology journal Discussion IV E627K;E158G;D253N;T271A;K526R;Q591K;A588V;D701N 55;134;141;148;155;162;169;176 60;139;146;153;160;167;174;181 PB2 113 116 30621708 Multiple amino acid substitutions involved in the adaption of three avian-origin H7N9 influenza viruses in mice. Many subtypes of influenza virus, including H3N2, H5N1, H5N5, H5N6, H6N1, H6N6, H7N1, H7N7, H7N9 and H9N2 have been reported increasing virulence by substitution of E627K at PB2 protein. 2019 Virology journal Discussion IV E627K 165 170 PB2 174 177 30621708 Multiple amino acid substitutions involved in the adaption of three avian-origin H7N9 influenza viruses in mice. PA T97I substitution was reported in mouse adaption of H5N2, H6N1, H7N1, H10N7 and H7N9 subtypes of influenza viruses. 2019 Virology journal Discussion IV T97I 3 7 PA 0 2 30640922 Molecular characterization of influenza A(H1N1)pdm09 in Cameroon during the 2014-2016 influenza seasons. However, some substitutions in the NA gene (I117M, N248D, and N369K) as recorded with the FluSurver (http://flusurver.bii.a-star.edu.sg) might be involved in drug susceptibility. 2019 PloS one Discussion IV I117M;N248D;N369K 44;51;62 49;56;67 35 37 30640922 Molecular characterization of influenza A(H1N1)pdm09 in Cameroon during the 2014-2016 influenza seasons. Meanwhile, the amino acid substitution S31N in the M2 protein was found to be present in all but the 2014 strains. 2019 PloS one Discussion IV S31N 39 43 M2 51 53 30640922 Molecular characterization of influenza A(H1N1)pdm09 in Cameroon during the 2014-2016 influenza seasons. Some Cameroon strains had two additional glycosylation sites, 10(NNS) and 162(NQS), not found in the vaccine strain: The glycosylation site 162(NQS) is the consequence of the amino acid substitution S162N found in viruses of sub-clade 6B.1 represented mainly by the 2016 viruses. 2019 PloS one Discussion IV S162N 199 204 30640922 Molecular characterization of influenza A(H1N1)pdm09 in Cameroon during the 2014-2016 influenza seasons. The 2014 virus strains differed from the vaccine strain by acquiring an amino acid substitution on antigenic site Ca (K142R). 2019 PloS one Discussion IV K142R 118 123 30640922 Molecular characterization of influenza A(H1N1)pdm09 in Cameroon during the 2014-2016 influenza seasons. These results are however different from that noted on H1N1 strains collected between 2007 and 2008 from Cameroon in which the H275Y mutation peculiar of resistance to NAIs was observed despite the non-exposition to this antiviral. 2019 PloS one Discussion IV H275Y 127 132 NAI 168 172 30640922 Molecular characterization of influenza A(H1N1)pdm09 in Cameroon during the 2014-2016 influenza seasons. Whereas, 2015 and 2016 Cameroon strains possessed mutations on antigenic sites Sa (S162N, K163Q) and Sb (S185T). 2019 PloS one Discussion IV S162N;K163Q;S185T 83;90;105 88;95;110 30670142 Detection of influenza A(H3N2) viruses exhibiting reduced susceptibility to the novel cap-dependent endonuclease inhibitor baloxavir in Japan, December 2018. During the Phase II trial, the PA I38T and I38F substitutions emerged after baloxavir treatment in four (3.6%) of 112 A(H1N1)pdm09 viruses isolated from adults aged 20-64 years. 2019 Euro surveillance Discussion IV I38T;I38F 34;43 38;47 PA 31 33 30670142 Detection of influenza A(H3N2) viruses exhibiting reduced susceptibility to the novel cap-dependent endonuclease inhibitor baloxavir in Japan, December 2018. Furthermore, influenza A/Victoria/3/75(H3N2) viruses with the PA I38T or I38M substitutions showed 56.6- and 13.8-fold higher EC50 values, respectively. 2019 Euro surveillance Discussion IV I38T;I38M 65;73 69;77 PA 62 64 30670142 Detection of influenza A(H3N2) viruses exhibiting reduced susceptibility to the novel cap-dependent endonuclease inhibitor baloxavir in Japan, December 2018. Furthermore, our sequencing analysis revealed that these two PA I38T mutant viruses possessed different PA sequences and thus originated from different viruses, suggesting no human-to-human transmission. 2019 Euro surveillance Discussion IV I38T 64 68 PA;PA 61;104 63;106 30670142 Detection of influenza A(H3N2) viruses exhibiting reduced susceptibility to the novel cap-dependent endonuclease inhibitor baloxavir in Japan, December 2018. In the Phase III trials, the PA I38T and I38M substitutions emerged in 36 (9.7%) of 370 A(H3N2) viruses obtained from patients aged 12-64 years and in 18 (23.4%) of 77 A(H3N2) viruses obtained from children aged 6 months to < 12 years. 2019 Euro surveillance Discussion IV I38T;I38M 32;41 36;45 PA 29 31 30670142 Detection of influenza A(H3N2) viruses exhibiting reduced susceptibility to the novel cap-dependent endonuclease inhibitor baloxavir in Japan, December 2018. In the present study, we obtained two influenza A(H3N2) clinical isolates possessing the PA I38T substitution. 2019 Euro surveillance Discussion IV I38T 92 96 PA 89 91 30670142 Detection of influenza A(H3N2) viruses exhibiting reduced susceptibility to the novel cap-dependent endonuclease inhibitor baloxavir in Japan, December 2018. In vitro studies using the plaque reduction assay revealed that influenza A/WSN/33(H1N1) viruses with the PA I38T or I38F substitutions show 27.2- and 10.6-fold higher EC50 values (the 50% effective concentration) to baloxavir compared with the wild-type virus. 2019 Euro surveillance Discussion IV I38T;I38F 109;117 113;121 PA 106 108 30670142 Detection of influenza A(H3N2) viruses exhibiting reduced susceptibility to the novel cap-dependent endonuclease inhibitor baloxavir in Japan, December 2018. Our data thus demonstrate that the PA I38T substitution is associated with reduced susceptibility to baloxavir in currently circulating influenza A(H3N2) viruses. 2019 Euro surveillance Discussion IV I38T 38 42 PA 35 37 30670142 Detection of influenza A(H3N2) viruses exhibiting reduced susceptibility to the novel cap-dependent endonuclease inhibitor baloxavir in Japan, December 2018. PA I38 is highly conserved in influenza A and B viruses, and the I38T substitution was not detected among 17,227 PA sequences from A(H3N2) viruses in the National Institute of Allergy and Infectious Diseases (NIAID) Influenza Research Database (IRD). 2019 Euro surveillance Discussion IV I38T 65 69 PA;PA 0;113 2;115 30670142 Detection of influenza A(H3N2) viruses exhibiting reduced susceptibility to the novel cap-dependent endonuclease inhibitor baloxavir in Japan, December 2018. These observations suggest that the emergence of PA I38T mutant viruses may increase as the use of baloxavir marboxil increases in the 2018/19 influenza season. 2019 Euro surveillance Discussion IV I38T 52 56 PA 49 51 30670142 Detection of influenza A(H3N2) viruses exhibiting reduced susceptibility to the novel cap-dependent endonuclease inhibitor baloxavir in Japan, December 2018. These results suggest that the PA I38T substitution has a marked impact on baloxavir susceptibility. 2019 Euro surveillance Discussion IV I38T 34 38 PA 31 33 30670142 Detection of influenza A(H3N2) viruses exhibiting reduced susceptibility to the novel cap-dependent endonuclease inhibitor baloxavir in Japan, December 2018. We isolated two PA I38T mutant influenza A(H3N2) viruses from baloxavir-treated children in December 2018. 2019 Euro surveillance Discussion IV I38T 19 23 PA 16 18 30733797 In silico thermodynamic stability of mammalian adaptation and virulence determinants in polymerase complex proteins of H9N2 virus. Identification of virulence markers of (PB2, PB1, and PA) genes of Egyptian LPAI-LPAI-H9N2 viruses under study revealed Seven Virulence markers, The substitutions (PB2-D391E and I504V), (PB1-M/V317I and N66S of PB1-F2), and (PA -127V, 550 L, and 672 L) which tend to increase virus virulence. 2018 Journal, genetic engineering & biotechnology Discussion IV M317I;D391E;I504V;V317I;N66S 191;168;178;191;203 198;173;183;198;207 PA;PA;PB1;PB1;PB1F2;PB2;PB2 54;225;45;187;211;40;164 56;227;48;190;217;43;167 30733797 In silico thermodynamic stability of mammalian adaptation and virulence determinants in polymerase complex proteins of H9N2 virus. it is recorded that the PB1-V14A substitution reduced polymerase activity, viral shedding, and transmissibility of H5N1 but does not always correlate with pathogenicity in chickens. 2018 Journal, genetic engineering & biotechnology Discussion IV V14A 28 32 PB1 24 27 30733797 In silico thermodynamic stability of mammalian adaptation and virulence determinants in polymerase complex proteins of H9N2 virus. Substitution M/V317I, similar to the precursor strain Q/Hk/G1/97 and to the human virus A/Hong Kong/1073/99, furthermore it showed to be characteristic for LPAI-H9N2 and H5N1 of human origin. 2018 Journal, genetic engineering & biotechnology Discussion IV M317I;V317I 13;13 20;20 30733797 In silico thermodynamic stability of mammalian adaptation and virulence determinants in polymerase complex proteins of H9N2 virus. The deduced PA amino acid sequence shows mammalian-host associated substitution at residues K328R it was recorded that K328R PA enhances the ability of a human H7N9 virus to replicate and cause severe disease in mice. 2018 Journal, genetic engineering & biotechnology Discussion IV K328R;K328R 92;119 97;124 PA;PA 12;125 14;127 30733797 In silico thermodynamic stability of mammalian adaptation and virulence determinants in polymerase complex proteins of H9N2 virus. The Free-energy analysis showed that (PB1-F2-L82, PB2-D391E, and A661 and PA-S225, I400S, S409N) have a structural stabilizing effect on polymerase complex protein, the free-energy change upon mutation (DeltaDeltaG) showing Positive values indicate a stabilizing effect, while the others selected substitutions showing negative values to indicate a destabilizing effect on polymerase subunits, according to the result the residue A is consistently more stabilizing than T at site PB2-661, and S is consistently more stabilizing than G at site 225-PA; This "stability-function" predicts that it usually possible to replace residues known to be important for function, reducing protein activity but concomitantly increasing its stability. 2018 Journal, genetic engineering & biotechnology Discussion IV D391E;I400S;S409N 54;83;90 59;88;95 PA;PA;PB1F2;PB2;PB2 74;547;38;50;480 76;549;44;53;483 30733797 In silico thermodynamic stability of mammalian adaptation and virulence determinants in polymerase complex proteins of H9N2 virus. The mammalian-host-associated substitution PB1-F2 L82S was also identified in all of the viruses under study; whereas T68I was not detected in any of Egyptian viruses under study. 2018 Journal, genetic engineering & biotechnology Discussion IV L82S;T68I 50;118 54;122 PB1F2 43 49 30733797 In silico thermodynamic stability of mammalian adaptation and virulence determinants in polymerase complex proteins of H9N2 virus. The mutation G186S was found recently in PA of Egyptian viruses for the first time by, and also found in all viruses under this study. 2018 Journal, genetic engineering & biotechnology Discussion IV G186S 13 18 PA 41 43 30733797 In silico thermodynamic stability of mammalian adaptation and virulence determinants in polymerase complex proteins of H9N2 virus. The naturally occurring substitutions (L89V, G309A, R477G and A676T) were detected in Egyptian LPAI-H9N2 viruses. 2018 Journal, genetic engineering & biotechnology Discussion IV L89V;G309A;R477G;A676T 39;45;52;62 43;50;57;67 30733797 In silico thermodynamic stability of mammalian adaptation and virulence determinants in polymerase complex proteins of H9N2 virus. The PB2 protein displayed valine at position 627 (E627V) is typical of G1 viruses lineage, group A. 2018 Journal, genetic engineering & biotechnology Discussion IV E627V 50 55 PB2 4 7 30733797 In silico thermodynamic stability of mammalian adaptation and virulence determinants in polymerase complex proteins of H9N2 virus. The substitution N383D in PA found in all viruses under study and may play an important role in the activity of the polymerase and in the accumulation of the PA and PB1 subunits in the nucleus of infected cells. 2018 Journal, genetic engineering & biotechnology Discussion IV N383D 17 22 PA;PA;PB1 26;158;165 28;160;168 30733797 In silico thermodynamic stability of mammalian adaptation and virulence determinants in polymerase complex proteins of H9N2 virus. The substitution S409N determined in our study is known to be important for changing host range from avian to human. 2018 Journal, genetic engineering & biotechnology Discussion IV S409N 17 22 30733797 In silico thermodynamic stability of mammalian adaptation and virulence determinants in polymerase complex proteins of H9N2 virus. The substitution S516P cited in The catalytic domain for endonuclease (508 to 522). 2018 Journal, genetic engineering & biotechnology Discussion IV S516P 17 22 30733797 In silico thermodynamic stability of mammalian adaptation and virulence determinants in polymerase complex proteins of H9N2 virus. The substitutions (K318R, I504V, 647I, E627V, and A661 T) Also, were detected suggesting increased polymerase activity and virus replication concluding that the PB2 subunit of the LPAI-H9N2 viruses. 2018 Journal, genetic engineering & biotechnology Discussion IV K318R;I504V;E627V;A661T 19;26;39;50 24;31;44;56 PB2 161 164 30733797 In silico thermodynamic stability of mammalian adaptation and virulence determinants in polymerase complex proteins of H9N2 virus. The substitutions K355M and P453T in PB2 became dominant in Egyptian viruses; also the substitutions 355I-PB2 and S516P-PB1 which was not previously described. 2018 Journal, genetic engineering & biotechnology Discussion IV K355M;P453T;S516P 18;28;114 23;33;119 PB1;PB2;PB2 120;37;106 123;40;109 30733797 In silico thermodynamic stability of mammalian adaptation and virulence determinants in polymerase complex proteins of H9N2 virus. The substitutions L13P, 317I, and 473V suggested to enhancing polymerase activity of LPAI-H9N2 in mammalian hosts and in mice . 2018 Journal, genetic engineering & biotechnology Discussion IV L13P 18 22 30733797 In silico thermodynamic stability of mammalian adaptation and virulence determinants in polymerase complex proteins of H9N2 virus. This mutation (E627V) suggested increasing H5N1 virus replication in mammalian cells and virulence in mice compared with PB2-627E.the three mutations (L13P, V14A, 317I, and 473V) in PB1 protein affect the virus replication in mammalian hosts. 2018 Journal, genetic engineering & biotechnology Discussion IV E627V;L13P;V14A 15;151;157 20;155;161 PB1;PB2 182;121 185;124 30792414 Molecular evolution of influenza B virus during 2011-2017 in Chaoyang, Beijing, suggesting the free influenza vaccine policy. As expected, substitution N116K was key mutation in 2013-2015 seasons and caused Yamagata-lineage to be absolute prevalence. 2019 Scientific reports Discussion IV N116K 26 31 30899824 Evolved avian influenza virus (H7N9) isolated from human cases in a middle Yangtze River city in China, from February to April 2017. However, a minority of successfully infections are presented with deficiency of PB2 E627K mutant. 2019 Heliyon Discussion IV E627K 84 89 PB2 80 83 30899824 Evolved avian influenza virus (H7N9) isolated from human cases in a middle Yangtze River city in China, from February to April 2017. Moreover, PB2 Ala588Val showed more efficiently enhanced virulence than the PB2 Glu627Lys in mice, but similar growth dynamics in cell lines. 2019 Heliyon Discussion IV A588V;E627K 14;80 23;89 PB2;PB2 10;76 13;79 30899824 Evolved avian influenza virus (H7N9) isolated from human cases in a middle Yangtze River city in China, from February to April 2017. Our results showed that the ratio of Ala588Val mutant in PB2 gene was increasing continuously, which may causing more capable of infection in mammals. 2019 Heliyon Discussion IV A588V 37 46 PB2 57 60 30899824 Evolved avian influenza virus (H7N9) isolated from human cases in a middle Yangtze River city in China, from February to April 2017. PB2 E627K mutation can be detected in most of human infection cases, and this result in significantly higher polymerase activity and virulence in H5N1 or H7N9 virus infections. 2019 Heliyon Discussion IV E627K 4 9 PB2 0 3 Influenza A virus H7N9 infection 154 175 30899824 Evolved avian influenza virus (H7N9) isolated from human cases in a middle Yangtze River city in China, from February to April 2017. Previous studies demonstrated that one or more of the Ile292Val, Ala588Val, Glu627Lys, and Asp701Asn substitutions are important for avian influenza viruses to break the host species barrier to infect mammals. 2019 Heliyon Discussion IV I292V;A588V;E627K;D701N 54;65;76;91 63;74;85;100 30899824 Evolved avian influenza virus (H7N9) isolated from human cases in a middle Yangtze River city in China, from February to April 2017. The mutation in other sites, including Ile292Val, Ala588Val and D701N in PB2, could be found effective to compensate for the absence of E627K. 2019 Heliyon Discussion IV I292V;A588V;D701N;E627K 39;50;64;136 48;59;69;141 PB2 73 76 30909490 The PB2 Polymerase Host Adaptation Substitutions Prime Avian Indonesia Sub Clade 2.1 H5N1 Viruses for Infecting Humans. E627K is the most well recognized adaptation marker for human infections caused by avian H5N1, H7N7 and H7N9 viruses. 2019 Viruses Discussion IV E627K 0 5 30909490 The PB2 Polymerase Host Adaptation Substitutions Prime Avian Indonesia Sub Clade 2.1 H5N1 Viruses for Infecting Humans. Here, we propose that K526R is a pre-existing mammalian adaptive marker of avian H5N1 viruses in the Indonesia lineage and provide the following supporting evidence: (1) K526R is rarely found in avian influenza viruses but was identified in H5N1 viruses 2-3 years after the virus emerged in Indonesia, coincident with the emergence of H5N1 human infections in Indonesia; (2) K526R is required for efficient replication of Indonesia H5N1 virus in mammalian cells in vitro and in vivo and reverse substitution to 526K in human isolates abolishes this ability; (3) Indonesian H5N1 virus, which contains K526R-PB2, is stable and does not further acquire E627K following replication in infected mice; and (4) virus containing K526R PB2 shows no fitness deficit in avian species. 2019 Viruses Discussion IV K526R;K526R;K526R;K526R;E627K;K526R 22;170;375;600;650;721 27;175;380;605;655;726 PB2;PB2 606;727 609;730 Influenza A virus H5N1 infection 335 356 30909490 The PB2 Polymerase Host Adaptation Substitutions Prime Avian Indonesia Sub Clade 2.1 H5N1 Viruses for Infecting Humans. However, avian influenza viruses containing pre-existing genetic markers of mammalian adaptation for viral replication function, such as K526R and E627K in the PB2 polymerase, are equally as likely to become prevalent, as evidenced by the subclade 2.2 (Egyptian) and 2.1 (Indonesian) H5N1 viruses. 2019 Viruses Discussion IV K526R;E627K 137;147 142;152 PB2 160 163 30909490 The PB2 Polymerase Host Adaptation Substitutions Prime Avian Indonesia Sub Clade 2.1 H5N1 Viruses for Infecting Humans. However, most human H5N1 isolates from Indonesia do not harbor the E627K or D701N substitutions frequently observed in other human isolates from avian H5N1 or H7N9 virus infections. 2019 Viruses Discussion IV E627K;D701N 67;76 72;81 30909490 The PB2 Polymerase Host Adaptation Substitutions Prime Avian Indonesia Sub Clade 2.1 H5N1 Viruses for Infecting Humans. Similarly, a D701N adaptation in a duck H5N1 virus which predisposed towards transmission to a mammalian host has also been reported. 2019 Viruses Discussion IV D701N 13 18 30909490 The PB2 Polymerase Host Adaptation Substitutions Prime Avian Indonesia Sub Clade 2.1 H5N1 Viruses for Infecting Humans. The contention that the gene constellation of K526R harboring virus is stable in the mammalian host, without needing to acquire other known adaptations, was also observed in a previous study where A/Indonesia/5/2005, which contains only K526R but no other known adaptive markers, did not acquire E627K or other known adaptations in PB2 even after being passaged 10 times in ferrets. 2019 Viruses Discussion IV K526R;K526R;E627K 46;237;296 51;242;301 PB2 332 335 30909490 The PB2 Polymerase Host Adaptation Substitutions Prime Avian Indonesia Sub Clade 2.1 H5N1 Viruses for Infecting Humans. The functions of K526R-PB2 in H5N1 virus from Indonesia and E627K in H5N1 virus from Egypt to predispose towards the ability to replicate in humans suggests that mammalian host adaptive mutations can be stably acquired by avian influenza viruses and maintained in poultry. 2019 Viruses Discussion IV K526R;E627K 17;60 22;65 PB2 23 26 30909490 The PB2 Polymerase Host Adaptation Substitutions Prime Avian Indonesia Sub Clade 2.1 H5N1 Viruses for Infecting Humans. We previously reported that the K526R substitution enhances the effect of E627K in promoting replication of H3N2 and H7N9 viruses, and that K526R is present in 80% of H5N1 human isolates from Indonesia. 2019 Viruses Discussion IV K526R;E627K;K526R 32;74;140 37;79;145 30909490 The PB2 Polymerase Host Adaptation Substitutions Prime Avian Indonesia Sub Clade 2.1 H5N1 Viruses for Infecting Humans. We propose that the PB2 K526R substitution primes avian H5N1 viruses from Indonesia for infecting humans. 2019 Viruses Discussion IV K526R 24 29 PB2 20 23 30914078 Influenza A(H3N2) virus exhibiting reduced susceptibility to baloxavir due to a polymerase acidic subunit I38T substitution detected from a hospitalised child without prior baloxavir treatment, Japan, January 2019. A previous study reported that influenza A/Victoria/3/75(H3N2) viruses with the PA I38T, I38M, or I38F substitutions showed less growth capability than the wild-type virus in cell culture. 2019 Euro surveillance Discussion IV I38T;I38M;I38F 83;89;98 87;93;102 PA 80 82 30914078 Influenza A(H3N2) virus exhibiting reduced susceptibility to baloxavir due to a polymerase acidic subunit I38T substitution detected from a hospitalised child without prior baloxavir treatment, Japan, January 2019. Although we could not obtain specimens from family members of either children, these observations could point to a possible transmission of the PA I38T mutant A(H3N2) viruses among humans. 2019 Euro surveillance Discussion IV I38T 147 151 PA 144 146 30914078 Influenza A(H3N2) virus exhibiting reduced susceptibility to baloxavir due to a polymerase acidic subunit I38T substitution detected from a hospitalised child without prior baloxavir treatment, Japan, January 2019. Among the 11 persons infected with PA I38T or I38M mutant A(H3N2) viruses in the 2018/19 season in Japan, all but one were children younger than 12 years. 2019 Euro surveillance Discussion IV I38T;I38M 38;46 42;50 PA 35 37 30914078 Influenza A(H3N2) virus exhibiting reduced susceptibility to baloxavir due to a polymerase acidic subunit I38T substitution detected from a hospitalised child without prior baloxavir treatment, Japan, January 2019. Deep sequencing analysis revealed that eight of these viruses possessed mixed PA I38T/I or I38T/M/I substitutions in the clinical specimens and six of these eight possessed increased proportion of the PA I38T or I38M substitution after virus isolation. 2019 Euro surveillance Discussion IV I38I;I38M;I38I;I38T;I38T;I38T;I38M 81;91;91;81;91;204;212 87;99;99;87;99;208;216 PA;PA 78;201 80;203 30914078 Influenza A(H3N2) virus exhibiting reduced susceptibility to baloxavir due to a polymerase acidic subunit I38T substitution detected from a hospitalised child without prior baloxavir treatment, Japan, January 2019. In addition, during our nationwide monitoring, we detected nine PA I38T or I38M mutant A(H3N2) viruses from baloxavir-treated patients (Table 3). 2019 Euro surveillance Discussion IV I38T;I38M 67;75 71;79 PA 64 66 30914078 Influenza A(H3N2) virus exhibiting reduced susceptibility to baloxavir due to a polymerase acidic subunit I38T substitution detected from a hospitalised child without prior baloxavir treatment, Japan, January 2019. In contrast, our results indicate that recently circulating A(H3N2) viruses with the PA I38T or I38M substitution grow well, at least in cell culture. 2019 Euro surveillance Discussion IV I38T;I38M 88;96 92;100 PA 85 87 30914078 Influenza A(H3N2) virus exhibiting reduced susceptibility to baloxavir due to a polymerase acidic subunit I38T substitution detected from a hospitalised child without prior baloxavir treatment, Japan, January 2019. In Phase III clinical trials of baloxavir marboxil, the PA I38T and I38M substitutions emerged in 36 (9.7%) of 370 A(H3N2) viruses obtained from patients aged 12-64 years and in 18 (23.4%) of 77 A(H3N2) viruses obtained from children aged 6 months to < 12 years. 2019 Euro surveillance Discussion IV I38T;I38M 59;68 63;72 PA 56 58 30914078 Influenza A(H3N2) virus exhibiting reduced susceptibility to baloxavir due to a polymerase acidic subunit I38T substitution detected from a hospitalised child without prior baloxavir treatment, Japan, January 2019. In the United States, the frequency of reduced susceptibility to baloxavir ( threefold change) due to a PA I38M substitution was 0.032% for A(H3N2) viruses during the 2016/17 and 2017/18 seasons. 2019 Euro surveillance Discussion IV I38M 108 112 PA 105 107 30914078 Influenza A(H3N2) virus exhibiting reduced susceptibility to baloxavir due to a polymerase acidic subunit I38T substitution detected from a hospitalised child without prior baloxavir treatment, Japan, January 2019. In this study, we detected two PA I38T mutant A(H3N2) viruses respectively from two hospitalised children. 2019 Euro surveillance Discussion IV I38T 34 38 PA 31 33 30914078 Influenza A(H3N2) virus exhibiting reduced susceptibility to baloxavir due to a polymerase acidic subunit I38T substitution detected from a hospitalised child without prior baloxavir treatment, Japan, January 2019. Of the two children described as infected with a PA I38T mutant virus in this report, one (infected with A/YOKOHAMA/88/2019) had not received baloxavir treatment. 2019 Euro surveillance Discussion IV I38T 52 56 PA 49 51 30914078 Influenza A(H3N2) virus exhibiting reduced susceptibility to baloxavir due to a polymerase acidic subunit I38T substitution detected from a hospitalised child without prior baloxavir treatment, Japan, January 2019. This might indicate that the recently circulating A(H3N2) viruses with the PA I38T substitution have, to some extent, retained replication and possible transmission capability in humans. 2019 Euro surveillance Discussion IV I38T 78 82 PA 75 77 30996301 Bacterial glycosyltransferase-mediated cell-surface chemoenzymatic glycan modification. Although Pm2,3ST-M144D can only label the terminal Gal, Pd2,6ST is capable of labeling galactoses of internal LacNAc units. 2019 Nature communications Discussion IV M144D 17 22 30996301 Bacterial glycosyltransferase-mediated cell-surface chemoenzymatic glycan modification. Among these three enzymes, Pm2,3ST-M144D and Pd2,6ST were found to tolerate a CMP-Sia donor functionalized with biotin or Cy3, enabling cell-surface acceptor glycans to be tagged with these probes for enrichment or visualization. 2019 Nature communications Discussion IV M144D 35 40 30996301 Bacterial glycosyltransferase-mediated cell-surface chemoenzymatic glycan modification. Applying Pm2,3ST-M144D and Pd2,6ST-mediated chemoenzymatic glycan modification to label whole embryo frozen sections from C57BL/6 mice (E16), we found that the salivary gland expressed high levels of acceptor glycans of both enzymes. 2019 Nature communications Discussion IV M144D 17 22 30996301 Bacterial glycosyltransferase-mediated cell-surface chemoenzymatic glycan modification. In this study, we discovered that bacteria-derived Pm2,3ST-M144D, Pd2,6ST, and Hm1,2FT can be exploited for cell-surface glycan labeling and modification. 2019 Nature communications Discussion IV M144D 59 64 30996301 Bacterial glycosyltransferase-mediated cell-surface chemoenzymatic glycan modification. Interestingly, in the developing bones Pd2,6ST-labeling yielded much higher signals than Pm2,3ST-M144D-labeling. 2019 Nature communications Discussion IV M144D 97 102 30996301 Bacterial glycosyltransferase-mediated cell-surface chemoenzymatic glycan modification. pylori 1,3FT, Pm2,3ST-M144D and Pd2,6ST were used to create a diverse array of sialylated and fucosylated glycan epitopes on the cell surface. 2019 Nature communications Discussion IV M144D 22 27 31150476 Pathogenicity of the H1N1 influenza virus enhanced by functional synergy between the NPV100I and NAD248N pair. We observed that a transfected NA (D248N) protein or recombinant virus with an NA (D248N) substitution was recruited to the lipid raft compartment more frequently than was the control protein or virus, respectively. 2019 PloS one Discussion IV D248N;D248N 35;83 40;88 NA;NA 31;79 33;81 31151913 Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. Mutational incompatibility between G186V and L194P is an extreme form of epistasis and can be attributed to their opposing structural effects. 2019 Cell host & microbe Discussion IV G186V;L194P 35;45 40;50 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. Acquiring the potent polymerase substitution PB2 E627K is an effective way to overcome the species barrier. 2019 mBio Discussion IV E627K 49 54 PB2 45 48 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. Furthermore, ANP32A depletion diverts the H7N9 polymerase adaptation from acquiring the PB2 E627K mutation, instead forcing the polymerase adaptation into an alternative pathway of acquiring PB2 D701N. 2019 mBio Discussion IV E627K;D701N 92;195 97;200 PB2;PB2 88;191 91;194 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. However, these studies did not explore the role of huANP32A in the emergence of the PB2 E627K mutation during the replication of AIVs under unfavorable conditions in human cells. 2019 mBio Discussion IV E627K 88 93 PB2 84 87 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. However, whether importin alpha is involved in the emergence of the PB2 D701N mutation in the background of H7N9 viruses remains to be further investigated. 2019 mBio Discussion IV D701N 72 77 PB2 68 71 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. Importantly, we found that the low polymerase activity attributed to the PA protein of H7N9 AIVs in human cells is the intrinsic driving force to acquire the PB2 E627K mutation during replication in wild-type mice. 2019 mBio Discussion IV E627K 162 167 PA;PB2 73;158 75;161 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. In summary, our study provides new insights into the biological mechanism employed by H7N9 AIVs to acquire the PB2 E627K substitution in order to adapt and become pathogenic in humans. 2019 mBio Discussion IV E627K 115 120 PB2 111 114 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. In this study, we used the H7N9 virus model, which easily acquires the PB2 E627K mutation when it infects humans, to investigate the molecular basis for the emergence of PB2 E627K during human adaptation. 2019 mBio Discussion IV E627K;E627K 75;174 80;179 PB2;PB2 71;170 74;173 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. Moreover, the depletion of ANP32A abolished the acquisition of the adaptive PB2 E627K mutation, forcing the virus to use an alternative adaptive pathway to acquire the PB2 D701N mutation. 2019 mBio Discussion IV E627K;D701N 80;172 85;177 PB2;PB2 76;168 79;171 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. Our data thus reveal that the prominent ability of H7N9 AIVs to acquire the mammalian-adaptive PB2 E627K mutation is driven by the intrinsic low polymerase activity attributed to the viral PA protein, which also involves interplay with mammalian ANP32A. 2019 mBio Discussion IV E627K 99 104 PA;PB2 189;95 191;98 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. Previous studies have shown that the PB2 D701N mutation is responsible for enhanced binding with importin alpha, leading to increased virus replication in mammalian cells. 2019 mBio Discussion IV D701N 41 46 PB2 37 40 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. The introduction of CK/5(H9N2) PB1 into the PG/S1421(H7N9) backbone led to the appearance of the adaptive mutation PB2 D701N, during the replication of PG/S1421-CK/5PB1(H7N9) in mice. 2019 mBio Discussion IV D701N 119 124 PB1;PB2 31;115 34;118 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. The role of the PB2 E627K mutation in mammalian adaptation has been well established for a wide range of AIVs, such as the H5N1, H7N7, H7N9, and H10N8 subtypes. 2019 mBio Discussion IV E627K 20 25 PB2 16 19 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. This finding suggests that the acquisition of the PB2 D701N mutation may correlate with the origin of the viral PB1 gene. 2019 mBio Discussion IV D701N 54 59 PB1;PB2 112;50 115;53 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. Under such conditions, ANP32A depletion abolishes the acquisition of the PB2 E627K mutation, thereby forcing the virus to acquire the alternative adaptive PB2 D701N mutation. 2019 mBio Discussion IV E627K;D701N 77;159 82;164 PB2;PB2 73;155 76;158 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. We discovered that the low polymerase activity of H7N9 AIVs in human cells, an attribute conferred by the viral PA protein, is the intrinsic driving force in the emergence of the adaptive PB2 E627K mutation, which also involves mammalian ANP32A. 2019 mBio Discussion IV E627K 192 197 PA;PB2 112;188 114;191 31213560 Low Polymerase Activity Attributed to PA Drives the Acquisition of the PB2 E627K Mutation of H7N9 Avian Influenza Virus in Mammals. When PG/S1421(H7N9) PA was replaced with CK/5(H9N2) PA, PG/S1421-CK/5PA1-191, or PG/S1421-PA142R-147V-171V-182L, the polymerase activity increased, abrogating the need to acquire the PB2 E627K mutation during virus replication in mice. 2019 mBio Discussion IV E627K 187 192 PA;PA;PA;PB2 20;52;90;183 22;54;92;186 31223581 Genetic and Phylogenetic Characterization of the M Gene of Influenza A Virus Isolated from Iranian Patients. However, some limited studies carried on Iranian isolates got from 2005 to 2008 have demonstrated the prevalence of amantadine-resistance A (H3N2) mutants, all resulted in the amino acid substitution S31N in the M2 protein. 2019 Iranian journal of public health Discussion IV S31N 200 204 M2 212 214 31223581 Genetic and Phylogenetic Characterization of the M Gene of Influenza A Virus Isolated from Iranian Patients. The present study showed that all strains of H1N1 and H3N2 subtypes contained the amino acid substitutions S31N, as expected. 2019 Iranian journal of public health Discussion IV S31N 107 111 31223581 Genetic and Phylogenetic Characterization of the M Gene of Influenza A Virus Isolated from Iranian Patients. The single point mutation at position 31 (S31N) is common and has been identified as the most frequent adamantine-resistant A (H3N2 and H1N1) viruses distributed across the world. 2019 Iranian journal of public health Discussion IV S31N 42 46 31266524 Highly pathogenic avian influenza H7N9 viruses with reduced susceptibility to neuraminidase inhibitors showed comparable replication capacity to their sensitive counterparts. a crystal structure model of the NA monomer of the A/Anhui/1/2013 H7N9 virus (PDB ID: 4MWJ) was used to display and label the four drug resistance mutations (292 K, E119V, A246T or H274Y) in the HPAI H7N9 virus. 2019 Virology journal Discussion IV A246T;E119V;H274Y 172;165;181 177;170;186 33 35 Influenza A virus H7N9 infection 195 204 31266524 Highly pathogenic avian influenza H7N9 viruses with reduced susceptibility to neuraminidase inhibitors showed comparable replication capacity to their sensitive counterparts. Additionally, A246T conferred reduced inhibition by zanamivir. 2019 Virology journal Discussion IV A246T 14 19 31266524 Highly pathogenic avian influenza H7N9 viruses with reduced susceptibility to neuraminidase inhibitors showed comparable replication capacity to their sensitive counterparts. Four NA mutations showed reduced susceptibility to NAIs, and R292 K, E119V, A246T and H274Y were identified in highly pathogenic H7N9 viruses from infected cases. 2019 Virology journal Discussion IV R292K;E119V;A246T;H274Y 61;69;76;86 67;74;81;91 NA;NAI 5;51 7;55 31266524 Highly pathogenic avian influenza H7N9 viruses with reduced susceptibility to neuraminidase inhibitors showed comparable replication capacity to their sensitive counterparts. It has been reported that the NA R292K substitution also decreased the sensitivity of HPAI H7N9 to peramivir. 2019 Virology journal Discussion IV R292K 33 38 30 32 Influenza A virus H7N9 infection 86 95 31266524 Highly pathogenic avian influenza H7N9 viruses with reduced susceptibility to neuraminidase inhibitors showed comparable replication capacity to their sensitive counterparts. Regarding LPAI H7N9, the increase in the IC50 of oseltamivir conferred by E119V and H274Y were 169-fold and 812-fold, respectively. 2019 Virology journal Discussion IV E119V;H274Y 74;84 79;89 31266524 Highly pathogenic avian influenza H7N9 viruses with reduced susceptibility to neuraminidase inhibitors showed comparable replication capacity to their sensitive counterparts. Single drug resistance to oseltamivir or zanamivir to varying degrees was observed in NA E119V, H274Y or A246T of HPAI H7N9 virus. 2019 Virology journal Discussion IV E119V;H274Y;A246T 89;96;105 94;101;110 86 88 31266524 Highly pathogenic avian influenza H7N9 viruses with reduced susceptibility to neuraminidase inhibitors showed comparable replication capacity to their sensitive counterparts. The increases in the IC50 of oseltamivir conferred by E119V and H274Y were 90.77-fold and 23.40-fold, respectively. 2019 Virology journal Discussion IV E119V;H274Y 54;64 59;69 31267843 Mammalian-adaptive mutation NP-Q357K in Eurasian H1N1 Swine Influenza viruses determines the virulence phenotype in mice. A previous study found that the substitution of N319K in NP protein was located on the surface at the right-hand side of the nucleoprotein body domain and resulted in an increase of polymerase activity. 2019 Emerging microbes & infections Discussion IV N319K 48 53 NP;NP 57;125 59;138 31267843 Mammalian-adaptive mutation NP-Q357K in Eurasian H1N1 Swine Influenza viruses determines the virulence phenotype in mice. Dual mutations K305R + V313F increased the fatality of the viruses. 2019 Emerging microbes & infections Discussion IV K305R;V313F 15;23 20;28 31267843 Mammalian-adaptive mutation NP-Q357K in Eurasian H1N1 Swine Influenza viruses determines the virulence phenotype in mice. Furthermore, when compared to that of rgHuN-WT, the occurrence of a single substitution V313F or K305R increased viral pathogenicity in mice, while K357Q obviously reduced the viral pathogenicity. 2019 Emerging microbes & infections Discussion IV V313F;K305R;K357Q 88;97;148 93;102;153 31267843 Mammalian-adaptive mutation NP-Q357K in Eurasian H1N1 Swine Influenza viruses determines the virulence phenotype in mice. However, the introduction of the K305R into dual mutation K305R + V313F led to a similar degree of viral pathogenicity as rgHuN-WT (Figure 4). 2019 Emerging microbes & infections Discussion IV K305R;K305R;V313F 33;58;66 38;63;71 31267843 Mammalian-adaptive mutation NP-Q357K in Eurasian H1N1 Swine Influenza viruses determines the virulence phenotype in mice. In addition, the human-like amino acid mutants NP-Q357K was reported to be likely required for transmission of the 1918 precursor virus to humans. 2019 Emerging microbes & infections Discussion IV Q357K 50 55 NP 47 49 31267843 Mammalian-adaptive mutation NP-Q357K in Eurasian H1N1 Swine Influenza viruses determines the virulence phenotype in mice. Q357K in the NP protein is also a typical mammalian-adaptive molecular marker in the influenza A viruses (Figure 3 and Supplementary Table 3). 2019 Emerging microbes & infections Discussion IV Q357K 0 5 NP 13 15 31267843 Mammalian-adaptive mutation NP-Q357K in Eurasian H1N1 Swine Influenza viruses determines the virulence phenotype in mice. Taken together, our findings suggest that the mutation Q357K in NP is an adaptive signature of the influenza A viruses, allowing them to cross species barriers and altering the viral virulence phenotype in mice (Figure 6). 2019 Emerging microbes & infections Discussion IV Q357K 55 60 NP 64 66 31267843 Mammalian-adaptive mutation NP-Q357K in Eurasian H1N1 Swine Influenza viruses determines the virulence phenotype in mice. The substitution of NP-Q357K could also enhance pathogenicity of avian H5N1 virus in mice. 2019 Emerging microbes & infections Discussion IV Q357K 23 28 NP 20 22 31267843 Mammalian-adaptive mutation NP-Q357K in Eurasian H1N1 Swine Influenza viruses determines the virulence phenotype in mice. Therefore, because EA H1N1 SIVs have acquired the trait necessary to cause a human influenza pandemic, EA SIVs with NP-Q357K pose a greater risk than those without NP-Q357K, and is a matter of great concern. 2019 Emerging microbes & infections Discussion IV Q357K;Q357K 119;167 124;172 NP;NP 116;164 118;166 Influenza 77 92 31267843 Mammalian-adaptive mutation NP-Q357K in Eurasian H1N1 Swine Influenza viruses determines the virulence phenotype in mice. Therefore, the NP-Q357K substitution was already present when the avian influenza viruses circulated in pigs, allowing the viruses to infect humans. 2019 Emerging microbes & infections Discussion IV Q357K 18 23 NP 15 17 31267843 Mammalian-adaptive mutation NP-Q357K in Eurasian H1N1 Swine Influenza viruses determines the virulence phenotype in mice. Thus, the NP-Q357K mutation in the EA SIVs is fully responsible for the enhanced pathogenicity phenotype, and enhanced the polymerase activity, replication, and infectivity of the viruses in mice. 2019 Emerging microbes & infections Discussion IV Q357K 13 18 NP 10 12 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. As desirable as the phenotypic trait of improved replication in both MDCK cells and eggs, the antigenicity of both rgSH2-G218E and rgGD-G218E was comparable to that of the counterparts bearing G218, which was confirmed by two-way HI assay and MN assay, and highlighted by the effective protection of ferrets from challenge with the parental HPAI virus. 2019 Journal of virology Discussion IV G218E;G218E 121;136 126;141 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. Because no genotypic alteration was found in the NA of rgSH2-G218E and, moreover, neither the NA amount nor the enzymatic activity toward the soluble substrate MU-NANA was significantly different between rgSH2WT and rgSH2-G218E, the feasible rationale could be that G218E in HA increased SA accessibility for NA. 2019 Journal of virology Discussion IV G218E;G218E;G218E 61;222;266 66;227;271 HA;NA;NA;NA 275;49;94;309 277;51;96;311 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. Ferrets immunized with rgGD-G218E or rgGD17 were protected from HPAI GD17WT challenge, suggesting that the G218E substitution does not alter the HA antigenicity of the GD17 virus. 2019 Journal of virology Discussion IV G218E;G218E 28;107 33;112 HA 145 147 Influenza 64 68 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. G218E resulted in significant decrease in human- and avian-type receptor binding avidity and facilitated N9 NA activity, which apparently balanced H7 HA binding and N9 NA cleavage capacity, thus enabling the progeny to disseminate more efficiently. 2019 Journal of virology Discussion IV G218E 0 5 HA;N9;N9;NA;NA 150;105;165;108;168 152;107;167;110;170 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. In addition, the T401A mutation could also contribute to the reduced NA function. 2019 Journal of virology Discussion IV T401A 17 22 69 71 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. In summary, we have generated high-growth H7N9 CVVs by introduction of a single amino acid substitution (G218E) in HA, which increased virus replication by balancing HA-NA functions. 2019 Journal of virology Discussion IV G218E 105 110 HA;HA;NA 115;166;169 117;168;171 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. Interestingly, our data demonstrated that G218E significantly reduced H7 receptor binding and apparently facilitated N9 function. 2019 Journal of virology Discussion IV G218E 42 47 N9 117 119 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. Interestingly, the G218E substitution in HA was correlated with increased NA-mediated dissociation of the HA from the receptor analogs. 2019 Journal of virology Discussion IV G218E 19 24 HA;HA;NA 41;106;74 43;108;76 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. Moreover, both rgGD17 and rgGD-G218E were tested nonpathogenic in egg embryos, chickens, or ferrets, and the modified sequence of the HA gene coding for the HA1/HA2 cleavage site remained unchanged after 10 passages in eggs (data not shown). 2019 Journal of virology Discussion IV G218E 31 36 HA;HA;HA1 134;161;157 136;163;160 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. The G218E substitution in HA possibly reduced the binding stability of the HA-receptor complexes, which made the SA more accessible for cleavage by viral NA. 2019 Journal of virology Discussion IV G218E 4 9 HA;HA;NA 26;75;154 28;77;156 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. The residue at position 218 of HA is at the interfaces of monomers, whereas G218E was previously reported to increase H3 HA membrane fusion pH that decreases HA acid stability. 2019 Journal of virology Discussion IV G218E 76 81 HA;HA;HA 31;121;158 33;123;160 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. The single amino acid substitution Q226L in HA is known to change the HA receptor binding specificity from avian-type to human-type. 2019 Journal of virology Discussion IV Q226L 35 40 HA;HA 44;70 46;72 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. This limited role of NA receptor binding could result from the T401A substitution of the second SA binding site in the NA from SH2 virus, which causes decreased N9 NA receptor binding, as well as reduced specific enzymatic activity. 2019 Journal of virology Discussion IV T401A 63 68 N9;NA;NA;NA 161;21;119;164 163;23;121;166 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. To address the role of the second SA binding site in the N9 NA of rgSH2 and rgSH2-G218E, we replaced the N9 NA with the N1 NA from PR8 to generate H7N1 reassortants. 2019 Journal of virology Discussion IV G218E 82 87 N9;N9;NA;NA;NA 57;105;60;108;123 59;107;62;110;125 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. To elucidate the mechanisms underlying the G218E phenotype, we further investigated the functional alteration related to the G218E substitution. 2019 Journal of virology Discussion IV G218E;G218E 43;125 48;130 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. To optimize the growth of H7N9 CVV in MDCK cells and eggs, we introduced G218E, a previously selected H7 virus adaptation mutation, into the HAs of both SH2 and GD17 strains. 2019 Journal of virology Discussion IV G218E 73 78 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. We therefore assessed the possible impact of G218E on HA stability in H7 viruses by a syncytium assay and found no significant difference in HA fusion pH between NL12WT and NL12ad or between rgSH2 and rgSH2-G218E (data not shown), which indicated that G218E does not result in a significant change in H7 HA acid stability. 2019 Journal of virology Discussion IV G218E;G218E;G218E 45;207;252 50;212;257 HA;HA;HA 54;141;304 56;143;306 31270231 A Single Amino Acid Substitution at Residue 218 of Hemagglutinin Improves the Growth of Influenza A(H7N9) Candidate Vaccine Viruses. With the high yield in cells and eggs, the expected antigenic properties, as well as the low-pathogenic characteristics in eggs and animals, H7N9 CVV with G218E mutation, recently designated CBER-RG7D (https://www.who.int/influenza/vaccines/virus/en/), is anticipated to facilitate the pandemic preparedness against the A(H7N9) influenza threat. 2019 Journal of virology Discussion IV G218E 155 160 31292247 Serial Section Array Scanning Electron Microscopy Analysis of Cells from Lung Autopsy Specimens following Fatal A/H1N1 2009 Pandemic Influenza Virus Infection. A/H1N1/pdm09-D222G proliferated in the lung, and many viral antigens and much viral RNA were detected in AEC-IIs. 2019 Journal of virology Discussion IV D222G 13 18 31305236 Prevailing I292V PB2 mutation in avian influenza H9N2 virus increases viral polymerase function and attenuates IFN-beta induction in human cells. A similar situation is seen with the predominant PA-K356R and HA-Q226L mutations in H9N2 virus; they each specifically promote mammalian adaptation. 2019 The Journal of general virology Discussion IV K356R;Q226L 52;65 57;70 HA;PA 62;49 64;51 31305236 Prevailing I292V PB2 mutation in avian influenza H9N2 virus increases viral polymerase function and attenuates IFN-beta induction in human cells. In this study, we identified a new mammalian adaptive mutation, PB2-I292V, which is highly prevalent in circulating H9N2, its reassortants and pdm H1N1 virus. 2019 The Journal of general virology Discussion IV I292V 68 73 PB2 64 67 31305236 Prevailing I292V PB2 mutation in avian influenza H9N2 virus increases viral polymerase function and attenuates IFN-beta induction in human cells. Increased polymerase activity conferred by other mutations on PB2, such as PB2-E627K, has been shown to be crucial for AIVs to adapt to mammalian hosts. 2019 The Journal of general virology Discussion IV E627K 79 84 PB2;PB2 62;75 65;78 31305236 Prevailing I292V PB2 mutation in avian influenza H9N2 virus increases viral polymerase function and attenuates IFN-beta induction in human cells. Interestingly, PB2-292I and PB2-292V mutations in H9N2 virus show no difference in viral polymerase activity in avian cells, suggesting that PB2-I292V mutation specifically promotes infectivity in mammalian cells. 2019 The Journal of general virology Discussion IV I292V 145 150 PB2;PB2;PB2 15;28;141 18;31;144 31305236 Prevailing I292V PB2 mutation in avian influenza H9N2 virus increases viral polymerase function and attenuates IFN-beta induction in human cells. Other mutations, such as HA-A316S, however, were found to function efficiently in both avian and mammalian hosts. 2019 The Journal of general virology Discussion IV A316S 28 33 HA 25 27 31305236 Prevailing I292V PB2 mutation in avian influenza H9N2 virus increases viral polymerase function and attenuates IFN-beta induction in human cells. PB2-E627K mutation alters polymerase activity by affecting the interaction of PB2 with NP and exhibits higher binding affinity for RNA, in particular the 5' vRNA promoter. 2019 The Journal of general virology Discussion IV E627K 4 9 NP;PB2;PB2 87;0;78 89;3;81 31305236 Prevailing I292V PB2 mutation in avian influenza H9N2 virus increases viral polymerase function and attenuates IFN-beta induction in human cells. PB2-I292V mutation could conceivably improve cap recognition and promote viral replication in human cells. 2019 The Journal of general virology Discussion IV I292V 4 9 PB2 0 3 31305236 Prevailing I292V PB2 mutation in avian influenza H9N2 virus increases viral polymerase function and attenuates IFN-beta induction in human cells. Unlike the PB2-I292V mutation reported in the current study, the well-known human adaptive mutations of PB2-E627K and -D701N are rarely found in prevailing avian H9N2 viruses. 2019 The Journal of general virology Discussion IV I292V;E627K;D701N 15;108;119 20;113;124 PB2;PB2 11;104 14;107 31329089 Biological properties of influenza A virus mutants with amino acid substitutions in the HA2 glycoprotein of the HA1/HA2 interaction region. In vivo, the T64H substitution in mutant 64 caused greater lung damage in infected mice (70-90 %), which was comparable to the wt virus, while the V66H substitution confer to virus 66 a milder pathogenicity, resulting in 10-20 % lung damage. 2019 The Journal of general virology Discussion IV T64H;V66H;T64H;V66H 14;148;13;147 18;152;17;151 31329089 Biological properties of influenza A virus mutants with amino acid substitutions in the HA2 glycoprotein of the HA1/HA2 interaction region. Moreover, a double HA2 mutant comprising both substitutions, T642H and V662H, was prepared. 2019 The Journal of general virology Discussion IV T642H;V662H 61;71 66;76 HA 19 21 31329089 Biological properties of influenza A virus mutants with amino acid substitutions in the HA2 glycoprotein of the HA1/HA2 interaction region. Such a difference in expression level of wt and 64 vRNA in mouse brains probably results from different tissue tropism of wt and 64 viruses caused by mutation in HA (T64H) in relation to neuronal cells. 2019 The Journal of general virology Discussion IV T64H 166 170 HA 162 164 31329089 Biological properties of influenza A virus mutants with amino acid substitutions in the HA2 glycoprotein of the HA1/HA2 interaction region. The increased manifestation of lung damage in D mutant-infected mice compared to 66 virus could be attributed to the second, T64H substitution introduced into the D mutant. 2019 The Journal of general virology Discussion IV T64H 125 129 31356626 Severe cases of seasonal influenza in Russia in 2017-2018. Among the 87 analyzed isolates of influenza A and B viruses, only one A(H1N1)pdm09 strain isolated from a lethal case of influenza was resistant to oseltamivir while remaining susceptible to zanamivir; it contained the H275Y amino acid substitution in the NA protein. 2019 PloS one Discussion IV H275Y 219 224 256 258 31356626 Severe cases of seasonal influenza in Russia in 2017-2018. Analysis of the presence of minor variants of the mutations revealed simultaneous presence of the virus variants with D222G and D222N mutations in three of the six cases examined (Table 2). 2019 PloS one Discussion IV D222G;D222N 118;128 123;133 31356626 Severe cases of seasonal influenza in Russia in 2017-2018. Considering demonstrated genetic stability of the viral isolates after the first passage on MDCK cells, the presence of D222G/N mutations in major proportion in viral isolates obtained after one passage on MDCK cells, as was observed in our study, is indicative of the presence of the mutations in the original specimens, possibly in smaller proportions. 2019 PloS one Discussion IV D222G;D222N 120;120 127;127 31356626 Severe cases of seasonal influenza in Russia in 2017-2018. Detecting D222G/N polymorphism, monitoring the increase in circulation of variants with D222G/N mutations and studying the evolution of A(H1N1)pdm09 viruses with D222G/N mutations, especially studying transmissibility, reassortment and the effect of genetic and virological properties of the virus on the pandemic potential, are necessary for timely identification of the emergence of potential pandemic threats in the circulating population of A(H1N1)pdm2009 viruses and are of particular importance for epidemiological analysis and prognosis. 2019 PloS one Discussion IV D222G;D222N;D222G;D222N;D222G;D222N 10;10;88;88;162;162 17;17;95;95;169;169 31356626 Severe cases of seasonal influenza in Russia in 2017-2018. For epidemiological analysis, it is important to determine the factors influencing transmissibility and selection of A(H1N1)pdm09 viruses with D222G/N mutations in humans. 2019 PloS one Discussion IV D222G;D222N 143;143 150;150 31356626 Severe cases of seasonal influenza in Russia in 2017-2018. For more precise data interpretation it is important to note that in our study, we observed 2-3 fold increase in quasispecies with D222G/N mutations in HA of two viral isolates obtained after one passage on MDCK cells compared to the original material, where these mutations were already present in significant quantities (Table 2). 2019 PloS one Discussion IV D222G;D222N 131;131 138;138 HA 152 154 31356626 Severe cases of seasonal influenza in Russia in 2017-2018. In this study, analysis of the presence of polymorphism in the 222 position of the HA protein using NGS data revealed a minor presence of D222G/N mutations in the viruses from the primary material of two lethal cases of A(H1N1)pdm09 infection (Table 2). 2019 PloS one Discussion IV D222G;D222N 138;138 145;145 HA 83 85 31356626 Severe cases of seasonal influenza in Russia in 2017-2018. It is known that the presence of D222G and D222N mutations in the HA gene often correlates with increased disease severity and mortality. 2019 PloS one Discussion IV D222G;D222N 33;43 38;48 HA 66 68 31356626 Severe cases of seasonal influenza in Russia in 2017-2018. It is suggested that these mutations accumulate as a result of selection from a mixture of influenza virus variants (quasi-species) in the lower parts of the respiratory tract where avian-like alpha-2,3 receptors with higher affinity for viruses with D222G/N mutations in the HA are more common compared to the upper respiratory tract. 2019 PloS one Discussion IV D222G;D222N 251;251 258;258 HA 276 278 31356626 Severe cases of seasonal influenza in Russia in 2017-2018. Molecular genetic analysis revealed the presence of D222G and D222N amino acid substitutions (H1 numbering) in the receptor-binding site of HA in the most predominant variant of the virus in four virus isolates from the 19 studied lethal cases of A(H1N1)pdm09 influenza (Table 2, S1 and S2 Tables). 2019 PloS one Discussion IV D222G;D222N 52;62 57;67 HA 140 142 31356626 Severe cases of seasonal influenza in Russia in 2017-2018. Probability of the origin and speed of selection of D222G/N mutations in MDCK viral isolates needs to be further investigated in order to more precisely evaluate the significance of the observed genetic changes of seasonal influenza viruses in studies that employ virus isolation using MDCK cells. 2019 PloS one Discussion IV D222G;D222N 52;52 59;59 31356626 Severe cases of seasonal influenza in Russia in 2017-2018. Receptor specificity mutations such as D222G/N in the HA gene, which increase tropism to 2,3-linked sialic acid receptors, are known to be selected during virus cultivation in embryonated chicken eggs which have avian-like 2,3-linked sialic acid receptors in allantoic cells. 2019 PloS one Discussion IV D222G;D222N 39;39 46;46 HA 54 56 31356626 Severe cases of seasonal influenza in Russia in 2017-2018. Selection of D222G/N mutations inside an infected organism occurs due to the acquired increased ability of the virus to bind to alpha-2,3-type sialic acid receptors, which are present in the lower respiratory tract. 2019 PloS one Discussion IV D222G;D222N 13;13 20;20 31356626 Severe cases of seasonal influenza in Russia in 2017-2018. Some researchers suggest that increased virulence and lethality of A(H1N1)pdm09 influenza virus may be caused by the presence of D222G/N mutations in HA. 2019 PloS one Discussion IV D222N;D222G 129;129 136;136 HA 150 152 31356626 Severe cases of seasonal influenza in Russia in 2017-2018. The reduced ability of the virus to spread through an infection of the upper respiratory tract may explain the low circulation of viruses with major variants of D222G/N mutations. 2019 PloS one Discussion IV D222G;D222N 161;161 168;168 31356626 Severe cases of seasonal influenza in Russia in 2017-2018. This feature of D222G/N mutations highlights the critical importance of detecting the presence of minor quasi-species of the viruses with these mutations in clinical samples, since their presence can lead to selection of more pathogenic virus variants inside the body under favorable conditions. 2019 PloS one Discussion IV D222G;D222N 16;16 23;23 31356626 Severe cases of seasonal influenza in Russia in 2017-2018. This selection occurs inside the infected organism, and at the stage of infection, D222G/N mutations are either absent or not dominant. 2019 PloS one Discussion IV D222G;D222N 83;83 90;90 31477028 A study of the relationship between human infection with avian influenza a (H5N6) and environmental avian influenza viruses in Fujian, China. The Q226L and G228S mutations in HA were reported to bind with the alpha-2,6 sialyl glycan receptors. 2019 BMC infectious diseases Discussion IV Q226L;G228S 4;14 9;19 HA 33 35 31538644 Baloxavir Marboxil in Japanese Pediatric Patients With Influenza: Safety and Clinical and Virologic Outcomes. An important finding in this study was the detection of treatment-emergent PA/I38T/M-substituted viruses in 23.4% of patients with paired-sequence data, a frequency over 2-fold higher than in baloxavir-treated adults with A(H3N2) infections. 2020 Clinical infectious diseases Discussion IV I38M;I38T 78;78 84;84 PA 75 77 Influenza A virus H3N2 infection 222 240 31538644 Baloxavir Marboxil in Japanese Pediatric Patients With Influenza: Safety and Clinical and Virologic Outcomes. Consequently, a follow-up pediatric study was conducted during the 2018-2019 season to assess whether a higher dose (2 mg/kg) might reduce PA/I38X-substituted virus emergence (JapicCTI-194577). 2020 Clinical infectious diseases Discussion IV I38X 142 146 PA 139 141 31538644 Baloxavir Marboxil in Japanese Pediatric Patients With Influenza: Safety and Clinical and Virologic Outcomes. Depending on the assay method, clinical isolates of A(H3N2) virus harboring I38T showed 65- to 155-fold reduced susceptibility in vitro. 2020 Clinical infectious diseases Discussion IV I38T 76 80 31538644 Baloxavir Marboxil in Japanese Pediatric Patients With Influenza: Safety and Clinical and Virologic Outcomes. Further study is required to assess whether alternative dose regimens of baloxavir might reduce the frequency of PA/I38X variant virus emergence. 2020 Clinical infectious diseases Discussion IV I38X 116 120 PA 113 115 31538644 Baloxavir Marboxil in Japanese Pediatric Patients With Influenza: Safety and Clinical and Virologic Outcomes. Next-generation sequencing revealed that PA/I38T-substituted viruses emerged after 48 hours (day 3) post-treatment of baloxavir in association with decreasing plasma BXA concentrations, consistent with the previous report in adult and adolescent patients with influenza. 2020 Clinical infectious diseases Discussion IV I38T 44 48 PA 41 43 31538644 Baloxavir Marboxil in Japanese Pediatric Patients With Influenza: Safety and Clinical and Virologic Outcomes. Of note, a clear prolongation of TTIA was only seen in patients with PA/I38T/M-substituted viruses with low baseline antibody titer. 2020 Clinical infectious diseases Discussion IV I38M;I38T 72;72 78;78 PA 69 71 31538644 Baloxavir Marboxil in Japanese Pediatric Patients With Influenza: Safety and Clinical and Virologic Outcomes. One published case and 2 additional cases of detecting PA/I38T-substituted viruses in non-baloxavir-treated patients have been reported recently in Japan. 2020 Clinical infectious diseases Discussion IV I38T 58 62 PA 55 57 31538644 Baloxavir Marboxil in Japanese Pediatric Patients With Influenza: Safety and Clinical and Virologic Outcomes. PA/I38T-substituted viruses emerged when plasma BXA concentrations declined to levels that inhibit viral replication of wild-type virus but not I38T-substituted viruses in vitro. 2020 Clinical infectious diseases Discussion IV I38T;I38T 3;144 7;148 PA 0 2 31538644 Baloxavir Marboxil in Japanese Pediatric Patients With Influenza: Safety and Clinical and Virologic Outcomes. The possibility that the association between the emergence of PA/I38X variants and prolongation of symptom alleviation requires additional investigation, including data on innate and acquired cellular immune responses before and at the time of variant emergence. 2020 Clinical infectious diseases Discussion IV I38X 65 69 PA 62 64 31538644 Baloxavir Marboxil in Japanese Pediatric Patients With Influenza: Safety and Clinical and Virologic Outcomes. We speculate that despite subinhibitory baloxavir concentration for PA/I38X-substituted viruses, patients with higher baseline antibody titers were better able to control replication and reduce the risk of variant emergence. 2020 Clinical infectious diseases Discussion IV I38X 71 75 PA 68 70 31575766 Influenza Virus Polymerase Mutation Stabilizes a Foreign Gene Inserted into the Virus Genome by Enhancing the Transcription/Replication Efficiency of the Modified Segment. Although we do not conclusively know how the PB2-E712D mutation overcomes the impairment of transcription/replication, one possible explanation is that the binding affinity between the polymerase complex and the RNA templates is increased. 2019 mBio Discussion IV E712D 49 54 PB2 45 48 31575766 Influenza Virus Polymerase Mutation Stabilizes a Foreign Gene Inserted into the Virus Genome by Enhancing the Transcription/Replication Efficiency of the Modified Segment. How is the transcription/replication efficiency reduced on modified RNA segments specifically, and how is it enhanced by the PB2-E712D mutation? The RNA secondary structure and the binding affinity between the polymerase complex and the RNA templates likely hold the answer to these questions. 2019 mBio Discussion IV E712D 129 134 PB2 125 128 31575766 Influenza Virus Polymerase Mutation Stabilizes a Foreign Gene Inserted into the Virus Genome by Enhancing the Transcription/Replication Efficiency of the Modified Segment. However, these amino acids may not necessarily cause the stabilization of a foreign gene in all influenza virus strains, since PB2-V25A, which stabilizes the Venus gene in Venus-H5N1, had a negative effect on virus replication in Venus-PR8 and did not cause Venus stabilization (our unpublished data). 2019 mBio Discussion IV V25A 131 135 PB2 127 130 31575766 Influenza Virus Polymerase Mutation Stabilizes a Foreign Gene Inserted into the Virus Genome by Enhancing the Transcription/Replication Efficiency of the Modified Segment. In contrast, the transcription/replication efficiency of segments that do not contain additional sequences is not changed in the presence or absence of the PB2-E712D mutation. 2019 mBio Discussion IV E712D 160 165 PB2 156 159 31575766 Influenza Virus Polymerase Mutation Stabilizes a Foreign Gene Inserted into the Virus Genome by Enhancing the Transcription/Replication Efficiency of the Modified Segment. In the present study, we explored the mechanism of PB2-E712D-induced stabilization of the Venus gene inserted into the NS segment of an H1N1 virus. 2019 mBio Discussion IV E712D 55 60 NS;PB2 119;51 121;54 31575766 Influenza Virus Polymerase Mutation Stabilizes a Foreign Gene Inserted into the Virus Genome by Enhancing the Transcription/Replication Efficiency of the Modified Segment. Moreover, we previously showed that polymerase activity is reduced, not enhanced, by the PB2-E712D mutation in a minireplicon assay. 2019 mBio Discussion IV E712D 93 98 PB2 89 92 31575766 Influenza Virus Polymerase Mutation Stabilizes a Foreign Gene Inserted into the Virus Genome by Enhancing the Transcription/Replication Efficiency of the Modified Segment. PB2-E712D may also be involved in the occurrence of internal deletions. 2019 mBio Discussion IV E712D 4 9 PB2 0 3 31575766 Influenza Virus Polymerase Mutation Stabilizes a Foreign Gene Inserted into the Virus Genome by Enhancing the Transcription/Replication Efficiency of the Modified Segment. The insertion of foreign genes appears to impair the transcription/replication of the modified segments, and the polymerase overcomes this impairment in the presence of the PB2-E712D mutation. 2019 mBio Discussion IV E712D 177 182 PB2 173 176 31575766 Influenza Virus Polymerase Mutation Stabilizes a Foreign Gene Inserted into the Virus Genome by Enhancing the Transcription/Replication Efficiency of the Modified Segment. Therefore, the stabilization of the Venus gene in Venus-PR8-PB2-E712D may be caused not only by the enhancement of the transcription/replication on the modified segment but also by the reduced frequency of internal deletions. 2019 mBio Discussion IV E712D 64 69 PB2 60 63 31575766 Influenza Virus Polymerase Mutation Stabilizes a Foreign Gene Inserted into the Virus Genome by Enhancing the Transcription/Replication Efficiency of the Modified Segment. Therefore, viruses expressing Venus are not purged by selective pressure in the presence of the PB2-E712D mutation, which enables Venus-PR8-PB2-E712D to stably maintain the inserted Venus gene. 2019 mBio Discussion IV E712D;E712D 100;144 105;149 PB2;PB2 96;140 99;143 31575766 Influenza Virus Polymerase Mutation Stabilizes a Foreign Gene Inserted into the Virus Genome by Enhancing the Transcription/Replication Efficiency of the Modified Segment. These results indicate that the alteration of the transcription/replication efficiency caused by PB2-E712D is specific to modified RNA segments. 2019 mBio Discussion IV E712D 101 106 PB2 97 100 31575766 Influenza Virus Polymerase Mutation Stabilizes a Foreign Gene Inserted into the Virus Genome by Enhancing the Transcription/Replication Efficiency of the Modified Segment. This finding suggests that the PB2-E712D mutation stabilizes the inserted foreign gene due to the enhanced transcription/replication efficiency of the modified RNA segment. 2019 mBio Discussion IV E712D 35 40 PB2 31 34 31575766 Influenza Virus Polymerase Mutation Stabilizes a Foreign Gene Inserted into the Virus Genome by Enhancing the Transcription/Replication Efficiency of the Modified Segment. Venus-PR8-PB2-E712D restores the transcription/replication efficiency of the NS segment, leading to efficient virus replication. 2019 mBio Discussion IV E712D 14 19 NS;PB2 77;10 79;13 31575766 Influenza Virus Polymerase Mutation Stabilizes a Foreign Gene Inserted into the Virus Genome by Enhancing the Transcription/Replication Efficiency of the Modified Segment. We found that the transcription/replication efficiency of the modified segment was significantly reduced in WT-Venus-PR8 compared to Venus-PR8-PB2-E712D. 2019 mBio Discussion IV E712D 147 152 PB2 143 146 31575766 Influenza Virus Polymerase Mutation Stabilizes a Foreign Gene Inserted into the Virus Genome by Enhancing the Transcription/Replication Efficiency of the Modified Segment. We previously found that amino acids in the influenza virus polymerase complex play crucial roles in the stabilization of foreign gene insertions; the Venus gene inserted into the NS segment was stabilized by PB2-E712D in an H1N1 virus and by PB2-V25A and PA-R443K in an H5N1 virus. 2019 mBio Discussion IV E712D;V25A;R443K 213;247;259 218;251;264 NS;PA;PB2;PB2 180;256;209;243 182;258;212;246 31581279 Influenza virus polymerase subunits co-evolve to ensure proper levels of dimerization of the heterotrimer. Intriguingly, the PA-E349G and PB1-K577E mutations were found to contribute to enhanced polymerase activity and increased virulence of IAV in mice, suggesting that the optimal FluPol conformational balance is not only determined by the FluPol gene constellation but also by the host-cell environment. 2019 PLoS pathogens Discussion IV E349G;K577E 21;35 26;40 PA;PB1 18;31 20;34 31581279 Influenza virus polymerase subunits co-evolve to ensure proper levels of dimerization of the heterotrimer. Remarkably however, in the PR8xWSN-PB2 genetic background, each of the PA-E349K, PB2-G74R and PB1-K577G mutations affects FluPol dimerization and restore wild-type-like FluPol activity in a minigenome assay. 2019 PLoS pathogens Discussion IV E349K;G74R;K577G 74;85;98 79;89;103 PA;PB1;PB2;PB2 71;94;35;81 73;97;38;84 31581279 Influenza virus polymerase subunits co-evolve to ensure proper levels of dimerization of the heterotrimer. They lie very close to each other, and the PA-E31G and PA-L28R mutations alter the surface charge distribution in the same direction, from negative/neutral to neutral/positive. 2019 PLoS pathogens Discussion IV E31G;L28R 46;58 50;62 PA;PA 43;55 45;57 31590265 Insights into the Acquisition of Virulence of Avian Influenza Viruses during a Single Passage in Ferrets. Although various combinations of mutations have been described in the literature for promoting mammalian adaptation, the PB2 S489P and NP V408I combination appears to be novel. 2019 Viruses Discussion IV S489P;V408I 125;138 130;143 NP;PB2 135;121 137;124 31590265 Insights into the Acquisition of Virulence of Avian Influenza Viruses during a Single Passage in Ferrets. During the course of our study we also identified other polymerase changes that occurred in the liver of ferret F8, namely PB2 I385V, PB2 N456D and PA E623G. 2019 Viruses Discussion IV I385V;N456D;E623G 127;138;151 132;143;156 PA;PB2;PB2 148;123;134 150;126;137 31590265 Insights into the Acquisition of Virulence of Avian Influenza Viruses during a Single Passage in Ferrets. In fact, the amplified virus was shown to contain two mutations, PB2 S489P and NP V408I, which were, like the PB2 E627K mutation, able to enhance polymerase activity in mammalian cells when present in combination. 2019 Viruses Discussion IV S489P;V408I;E627K 69;82;114 74;87;119 NP;PB2;PB2 79;65;110 81;68;113 31590265 Insights into the Acquisition of Virulence of Avian Influenza Viruses during a Single Passage in Ferrets. It has also been detected in combination with the PB2 E627K mutation during experimental infection of mice with an H7N1 highly pathogenic avian influenza virus that developed enhanced pathogenicity during murine infection. 2019 Viruses Discussion IV E627K 54 59 PB2 50 53 31590265 Insights into the Acquisition of Virulence of Avian Influenza Viruses during a Single Passage in Ferrets. The most widely studied of these polymerase mutations is PB2 E627K, which is commonly identified in H5N1 and H7N9 viruses isolated from humans. 2019 Viruses Discussion IV E627K 61 66 PB2 57 60 31590265 Insights into the Acquisition of Virulence of Avian Influenza Viruses during a Single Passage in Ferrets. The PB2 E627K mutation was initially described as being associated with overcoming cold-sensitivity, improving replication in the nasal turbinates and in tissue culture at 33 C. 2019 Viruses Discussion IV E627K 8 13 PB2 4 7 31590265 Insights into the Acquisition of Virulence of Avian Influenza Viruses during a Single Passage in Ferrets. The PB2 S489P single mutation has previously been described for its ability to enhance avian H5N1 polymerase activity in cultured human cells. 2019 Viruses Discussion IV S489P 8 13 PB2 4 7 31590265 Insights into the Acquisition of Virulence of Avian Influenza Viruses during a Single Passage in Ferrets. The results of this study support the findings that the acquisition of the PB2 E627K mutation is the most common route to efficient replication in the mammalian host, though not the only one, and underscore the fact that such mutations can occur readily within a single passage in ferrets. 2019 Viruses Discussion IV E627K 79 84 PB2 75 78 31590265 Insights into the Acquisition of Virulence of Avian Influenza Viruses during a Single Passage in Ferrets. The work presented in this study, using the ferret model, demonstrates that H5N1 viruses are capable of mutating to achieve high levels of replication in mammals by acquiring polymerase changes such as PB2 E627K or the PB2 S489P, NP V408I combination, rapidly and at high frequency. 2019 Viruses Discussion IV E627K;S489P;V408I 206;223;233 211;228;238 NP;PB2;PB2 230;202;219 232;205;222 31597771 Identification of Key Amino Acids in the PB2 and M1 Proteins of H7N9 Influenza Virus That Affect Its Transmission in Guinea Pigs. Although the PB2 E627K mutation has been reported to affect the transmission of different influenza viruses in ferrets and guinea pigs, this is the first report that the amino acids 292V of PB2 and 156D of M1 are important for influenza virus transmission. 2019 Journal of virology Discussion IV E627K 17 22 M1;PB2;PB2 206;13;190 208;16;193 31597771 Identification of Key Amino Acids in the PB2 and M1 Proteins of H7N9 Influenza Virus That Affect Its Transmission in Guinea Pigs. In other words, the I292V mutation in PB2 increases the polymerase activity of H7N9 viruses in both avian and mammalian cells. 2019 Journal of virology Discussion IV I292V 20 25 PB2 38 41 31597771 Identification of Key Amino Acids in the PB2 and M1 Proteins of H7N9 Influenza Virus That Affect Its Transmission in Guinea Pigs. In this study, we found that the amino acid 156D of M1 is critical for H7N9 virus transmission, since the single amino acid mutation of D156E in M1 abolished the transmission of the AH/1 virus in guinea pigs. 2019 Journal of virology Discussion IV D156E 136 141 M1;M1 52;145 54;147 31597771 Identification of Key Amino Acids in the PB2 and M1 Proteins of H7N9 Influenza Virus That Affect Its Transmission in Guinea Pigs. reported that none of the H7N9 avian isolates bear the 627K or 701N mutation in the PB2 gene, but over 83% of H7N9 human isolates have these mutations, indicating that the E627K and D701N mutations in the PB2 protein of H7N9 human virus isolates are mammal-adapted mutations, although they have occasionally been detected in H5 influenza viruses isolated from avian species. 2019 Journal of virology Discussion IV E627K;D701N 172;182 177;187 PB2;PB2 84;205 87;208 31597771 Identification of Key Amino Acids in the PB2 and M1 Proteins of H7N9 Influenza Virus That Affect Its Transmission in Guinea Pigs. reported that the emergence of the PB2 E627K mutation in H7N9 human influenza virus is driven by the intrinsic low polymerase activity conferred by the viral acid polymerase (PA) protein, which is also involved in the engagement of the mammalian ANP32A protein. 2019 Journal of virology Discussion IV E627K 39 44 PA;PB2 175;35 177;38 31597771 Identification of Key Amino Acids in the PB2 and M1 Proteins of H7N9 Influenza Virus That Affect Its Transmission in Guinea Pigs. The D156E mutation in M1 reduced the replication of the AH/1 virus in A549 cells and therefore reduced the transmissibility of the AH/1 virus in guinea pigs. 2019 Journal of virology Discussion IV D156E 4 9 M1 22 24 31597771 Identification of Key Amino Acids in the PB2 and M1 Proteins of H7N9 Influenza Virus That Affect Its Transmission in Guinea Pigs. The V292I mutation in PB2 abolished the transmission of the rAH/1 virus, even though this virus bears PB2 627K. 2019 Journal of virology Discussion IV V292I 4 9 PB2;PB2 22;102 25;105 31597771 Identification of Key Amino Acids in the PB2 and M1 Proteins of H7N9 Influenza Virus That Affect Its Transmission in Guinea Pigs. These findings indicate that I292V in PB2 is a host-independent mutation that promotes the transmission of H7N9 virus in mammals and facilitates the replication and spread of influenza viruses in avian species. 2019 Journal of virology Discussion IV I292V 29 34 PB2 38 41 31597771 Identification of Key Amino Acids in the PB2 and M1 Proteins of H7N9 Influenza Virus That Affect Its Transmission in Guinea Pigs. Two amino acid mutations in PB2, E627K and D701N, have been previously reported to be important for the replication and transmission of different avian influenza viruses in mammals. 2019 Journal of virology Discussion IV E627K;D701N 33;43 38;48 PB2 28 31 31597771 Identification of Key Amino Acids in the PB2 and M1 Proteins of H7N9 Influenza Virus That Affect Its Transmission in Guinea Pigs. Unlike the K627E mutation in PB2, which decreased the polymerase activity of the RNP complex of H7N9 virus in only mammalian cells and not avian cells, the V292I mutation decreased the polymerase activity of the RNP complex in both mammalian and avian cells. 2019 Journal of virology Discussion IV K627E;V292I 11;156 16;161 PB2;RNP;RNP 29;81;212 32;84;215 31597771 Identification of Key Amino Acids in the PB2 and M1 Proteins of H7N9 Influenza Virus That Affect Its Transmission in Guinea Pigs. Using a loss-of-function strategy, we found that low NA enzymatic activity impaired the transmission of H7N9 virus and that three amino acid mutations:V292I and K627E in PB2 and D156E in M1:independently abolished the transmission of the AH/1 virus. 2019 Journal of virology Discussion IV V292I;K627E;D156E 151;161;178 156;166;183 M1;NA;PB2 187;53;170 189;55;173 31600274 Adaptation of H3N2 canine influenza virus to feline cell culture. Although a previous study showed that K299G or K299E mutations in HA1 of X-31 strain (H3 subtype) increased the optimal pH for conformational change into membrane fusion, CIV HA1-K299R mutation observed in our study did not affect the optimal pH of the membrane fusion (Fig 3). 2019 PloS one Discussion IV K299G;K299E;K299R 38;47;179 43;52;184 HA1;HA1 66;175 69;178 31600274 Adaptation of H3N2 canine influenza virus to feline cell culture. Among them, two HA mutations, HA1-S107P and -S116G (H3 numbering), were found in cat isolates, implicating that these mutations might be responsible for CIV adaptation to cats. 2019 PloS one Discussion IV S107P;S116G 34;45 39;50 HA;HA1 16;30 18;33 31600274 Adaptation of H3N2 canine influenza virus to feline cell culture. Here, we generated feline cell-adapted CIVs and revealed that both HA1-K299R and HA2-T107I mutations enhanced virus growth in feline cell lines, by altering the optimal pH for viral membrane fusion and/or promoting thermostability of the virus. 2019 PloS one Discussion IV K299R;T107I 71;85 76;90 HA;HA1 81;67 83;70 31600274 Adaptation of H3N2 canine influenza virus to feline cell culture. In addition, we found that NA-L35R and M-W41C mutations could improve CIV growth in feline cell lines, albeit less efficiently, compared to HA mutations. 2019 PloS one Discussion IV L35R;W41C 30;41 34;45 HA;M;NA 140;39;27 142;40;29 31600274 Adaptation of H3N2 canine influenza virus to feline cell culture. In our study, HA2-T107I mutation may have lost a polar contact with HA2-51K (Fig 7C), thereby increasing the optimal pH for membrane fusion. 2019 PloS one Discussion IV T107I 18 23 HA;HA 14;68 16;70 31600274 Adaptation of H3N2 canine influenza virus to feline cell culture. Interestingly, these locations are near the position 299 in HA1-K299R mutation found in our study (Fig 7A). 2019 PloS one Discussion IV K299R 64 69 HA1 60 63 31600274 Adaptation of H3N2 canine influenza virus to feline cell culture. M2-W41C mutation caused high membrane conductance under high pH condition of an external virion, suggesting that the M2-W41C mutant could allow protons to flow into the virion even at a higher pH of the endosomes. 2019 PloS one Discussion IV W41C;W41C 3;120 7;124 M2;M2 0;117 2;119 31600274 Adaptation of H3N2 canine influenza virus to feline cell culture. On the contrary, HA2-T107I mutation increased both the optimal pH of membrane fusion as well as thermal resistance of virus. 2019 PloS one Discussion IV T107I 21 26 HA 17 19 31600274 Adaptation of H3N2 canine influenza virus to feline cell culture. Therefore, NA-L35R mutation found in the mutants may affect the raft association of NA, resulting in a change in the amount of this protein in the virions. 2019 PloS one Discussion IV L35R 14 18 NA;NA 11;84 13;86 31600274 Adaptation of H3N2 canine influenza virus to feline cell culture. These findings suggest that HA1-K299R, HA2-T107I, NA-L35R, and M-W41C mutations might be responsible for CIV adaptation to cats, although studies need to be conducted by experimentally infecting the feline cell-adapted CIVs into cats. 2019 PloS one Discussion IV K299R;T107I;L35R;W41C 32;43;53;65 37;48;57;69 HA;HA1;M;NA 39;28;63;50 41;31;64;52 31600274 Adaptation of H3N2 canine influenza virus to feline cell culture. Together with HA2-T107I mutation that raises the pH condition for membrane fusion, CIVs may have been adapted to endosomal pH environment in the feline cells by HA as well as M2 mutations. 2019 PloS one Discussion IV T107I 18 23 HA;HA;M2 14;161;175 16;163;177 31608791 Insights into species-specific regulation of ANP32A on the mammalian-restricted influenza virus polymerase activity. Furthermore, we did not detect the chANP32A-X1 and huANP32A in the RNPs or cRNPs of PB2 K627E or 627K polymerase (Figure 8), suggesting that ANP32A transiently interacted with the trimeric polymerase before the generation of RNPs. 2019 Emerging microbes & infections Discussion IV K627E 88 93 PB2;RNP;RNP 84;67;225 87;71;229 31608791 Insights into species-specific regulation of ANP32A on the mammalian-restricted influenza virus polymerase activity. The 3' promoter mutations (A3G + U8C) or 5' promoter mutations (C3U + G8A) of cRNA perhaps changing the RNA template structure may lead to uneffective binding to the polymerase active site for decreasing polymerase activity. 2019 Emerging microbes & infections Discussion IV A3G;G8A 27;70 30;73 31608791 Insights into species-specific regulation of ANP32A on the mammalian-restricted influenza virus polymerase activity. The C3U and G8A mutation at the 5'promoter and the A3G and U8C mutation at the 3' promoter of cRNA were performed for stabilizing the panhandle structure. 2019 Emerging microbes & infections Discussion IV A3G;G8A 51;12 54;15 31608791 Insights into species-specific regulation of ANP32A on the mammalian-restricted influenza virus polymerase activity. The PB2 E627K mutation or expression of ANP32A29 (chANP32A-X2) increased the RNPs (PB2 627E) formation using vRNA template in mammalian cells. 2019 Emerging microbes & infections Discussion IV E627K 8 13 PB2;PB2;RNP 4;83;77 7;86;81 31608791 Insights into species-specific regulation of ANP32A on the mammalian-restricted influenza virus polymerase activity. The vRNA 3' promoter mutations (G3A + C8U) increased vRNA replication of PB2 627E polymerase activity in mammalian cells. 2019 Emerging microbes & infections Discussion IV G3A 32 35 PB2 73 76 31635227 Antigenic Site Variation in the Hemagglutinin of Pandemic Influenza A(H1N1)pdm09 Viruses between 2009-2017 in Ukraine. A hypothesis has been suggested that middle-age people previously infected by seasonal influenza A(H1N1) viruses may be immune to new pandemic A(H1N1)pdm09 viruses that have acquired K163Q substitution. 2019 Pathogens (Basel, Switzerland) Discussion IV K163Q 183 188 31635227 Antigenic Site Variation in the Hemagglutinin of Pandemic Influenza A(H1N1)pdm09 Viruses between 2009-2017 in Ukraine. Importantly, substitution D222G is located in the receptor-binding pocket in the antigenic site Ca HA and may alter the properties of the RBS. 2019 Pathogens (Basel, Switzerland) Discussion IV D222G 26 31 HA 99 101 31635227 Antigenic Site Variation in the Hemagglutinin of Pandemic Influenza A(H1N1)pdm09 Viruses between 2009-2017 in Ukraine. In 2013-2014, the genetic clade 6B emerged with the K163Q (H1 numbering) in HA, in antigenic site Sa. 2019 Pathogens (Basel, Switzerland) Discussion IV K163Q 52 57 HA 76 78 31635227 Antigenic Site Variation in the Hemagglutinin of Pandemic Influenza A(H1N1)pdm09 Viruses between 2009-2017 in Ukraine. In addition, the K163I substitution observed in A/Zaporizza/417/2013 may impart altered antibody-binding properties. 2019 Pathogens (Basel, Switzerland) Discussion IV K163I 17 22 31635227 Antigenic Site Variation in the Hemagglutinin of Pandemic Influenza A(H1N1)pdm09 Viruses between 2009-2017 in Ukraine. Since then, the 6B clade viruses have diverged further into 6B.1 and 6B.2 subclades, still bearing K163Q. 2019 Pathogens (Basel, Switzerland) Discussion IV K163Q 99 104 31635227 Antigenic Site Variation in the Hemagglutinin of Pandemic Influenza A(H1N1)pdm09 Viruses between 2009-2017 in Ukraine. The emergence of S162T and D127E substitutions has led to the acquisition of a potential site for glycosylation, which may increase the virulence of influenza viruses. 2019 Pathogens (Basel, Switzerland) Discussion IV S162T;D127E 17;27 22;32 31635227 Antigenic Site Variation in the Hemagglutinin of Pandemic Influenza A(H1N1)pdm09 Viruses between 2009-2017 in Ukraine. The S185T substitution in antigenic site Sb falls within a domain defining the receptor-binding site (RBS). 2019 Pathogens (Basel, Switzerland) Discussion IV S185T 4 9 31635227 Antigenic Site Variation in the Hemagglutinin of Pandemic Influenza A(H1N1)pdm09 Viruses between 2009-2017 in Ukraine. The substitution in antigenic site Sb A186T was also in the RBS. 2019 Pathogens (Basel, Switzerland) Discussion IV A186T 38 43 31703251 Evolution of H5-Type Avian Influenza A Virus Towards Mammalian Tropism in Egypt, 2014 to 2015. According to the binding affinity and replication kinetics of the viruses investigated in this study, we chose a representative for each of the following AIV H5N1 clades: LP-2006 clade 2.2.1, LP-Q1995D clade 2.2.1.1, LP-S10739C clade 2.2.1.2, and human LP-7271 clade 2.2.1.2. 2019 Pathogens (Basel, Switzerland) Discussion IV Q1995D;S10739C 195;220 201;227 31703251 Evolution of H5-Type Avian Influenza A Virus Towards Mammalian Tropism in Egypt, 2014 to 2015. All of the viruses tested displayed four characteristic mutations (D43N, S120D, S129Delta, and I151T) (Table 2), three of which were previously reported to increase binding to the human receptor. 2019 Pathogens (Basel, Switzerland) Discussion IV D43N;S120D;I151T 67;73;95 71;78;100 31703251 Evolution of H5-Type Avian Influenza A Virus Towards Mammalian Tropism in Egypt, 2014 to 2015. Concerning the other two mutations, G269E did not change the amplitude ratio, AF (0.236)/AF (0.076), and K309R is present in many viruses. 2019 Pathogens (Basel, Switzerland) Discussion IV G269E;K309R 36;105 41;110 31703251 Evolution of H5-Type Avian Influenza A Virus Towards Mammalian Tropism in Egypt, 2014 to 2015. Conclusively, mutations C4G and L296F, single or in combination, might be considered as potential pandemic markers of H5N1 viruses. 2019 Pathogens (Basel, Switzerland) Discussion IV C4G;L296F 24;32 27;37 31703251 Evolution of H5-Type Avian Influenza A Virus Towards Mammalian Tropism in Egypt, 2014 to 2015. Even though receptor-binding affinities of human LP-7271 and avian LP-S10739C to both human- and avian-type receptors were comparable, the improved replication ability of avian LP-S10739C in mammalian cell lines could augment its pathogenicity in mice and, consequently, provide the possibility for faster adaptation, which might ultimately lead to stronger pathogenicity. 2019 Pathogens (Basel, Switzerland) Discussion IV S10739C;S10739C 70;180 77;187 31703251 Evolution of H5-Type Avian Influenza A Virus Towards Mammalian Tropism in Egypt, 2014 to 2015. Following the ISM sequence analysis of LP-S10739C and human LP-7271, it shows that the key mutations which significantly increase the amplitude ratio, AF (0.236)/AF (0.076), in the HA of H5N1 viruses from 2015 are C4G and L296F. 2019 Pathogens (Basel, Switzerland) Discussion IV C4G;S10739C;L296F 214;42;222 217;49;227 HA 181 183 31703251 Evolution of H5-Type Avian Influenza A Virus Towards Mammalian Tropism in Egypt, 2014 to 2015. However, the H5-HA proteins, derived from several tested strains including LP-D10551C, LP-Q10920C, LP-A/Du/Eg/4/2015, and LP-D10552B, have higher affinity to alpha2,3-SA. 2019 Pathogens (Basel, Switzerland) Discussion IV D10551C;Q10920C 78;90 85;97 HA 16 18 31703251 Evolution of H5-Type Avian Influenza A Virus Towards Mammalian Tropism in Egypt, 2014 to 2015. In A549 cells, the majority of viruses expressing H5 HA from clade 2.2.1.2 (LP-Q10920C, LP-S10738B, LP-S10739C, and LP-A10540A) demonstrated a higher replication rates than the human LP-7271 isolate. 2019 Pathogens (Basel, Switzerland) Discussion IV Q10920C;S10739C;A10540A 79;103;119 86;110;126 HA 53 55 31703251 Evolution of H5-Type Avian Influenza A Virus Towards Mammalian Tropism in Egypt, 2014 to 2015. In addition, the aa substitutions D154N and D43N, which were fixed in strains from 2014 to 2015 increase the affinity to human receptors and possibly enhance airborne transmissibility in mammals. 2019 Pathogens (Basel, Switzerland) Discussion IV D154N;D43N 34;44 39;48 31703251 Evolution of H5-Type Avian Influenza A Virus Towards Mammalian Tropism in Egypt, 2014 to 2015. In comparison to human LP-7271, the examination revealed aa substitutions in various positions (C4G, L297F, R373K, and S537F) of the LP-S10739C H5-HA protein (Table 2). 2019 Pathogens (Basel, Switzerland) Discussion IV C4G;L297F;R373K;S537F;S10739C 96;101;108;119;136 99;106;113;124;143 HA 147 149 31703251 Evolution of H5-Type Avian Influenza A Virus Towards Mammalian Tropism in Egypt, 2014 to 2015. Interestingly, compared to LP-7271, LP-S10739C seemed to have slightly lower affinity for alpha2,6-SA, but comparable affinity for binding to alpha2,3-SA. 2019 Pathogens (Basel, Switzerland) Discussion IV S10739C 39 46 31703251 Evolution of H5-Type Avian Influenza A Virus Towards Mammalian Tropism in Egypt, 2014 to 2015. LP-Q1995D, was highly similar in alpha2,3-SA and alpha2,6-SA binding to the human isolate LP-7271 as well. 2019 Pathogens (Basel, Switzerland) Discussion IV Q1995D 3 9 31703251 Evolution of H5-Type Avian Influenza A Virus Towards Mammalian Tropism in Egypt, 2014 to 2015. LP-S10739C replicated to higher titers at 12, 24, and 36 h p.i. 2019 Pathogens (Basel, Switzerland) Discussion IV S10739C 3 10 31703251 Evolution of H5-Type Avian Influenza A Virus Towards Mammalian Tropism in Egypt, 2014 to 2015. Mutation L296F is present in 12, and C4G in six, of the 7568 H5N1 virus aa sequences in the GISAID depository, respectively. 2019 Pathogens (Basel, Switzerland) Discussion IV C4G;L296F 37;9 40;14 31703251 Evolution of H5-Type Avian Influenza A Virus Towards Mammalian Tropism in Egypt, 2014 to 2015. Mutation L296F is present in only one of 1156 viruses from Egypt (data not shown). 2019 Pathogens (Basel, Switzerland) Discussion IV L296F 9 14 31703251 Evolution of H5-Type Avian Influenza A Virus Towards Mammalian Tropism in Egypt, 2014 to 2015. Of note is that five of six C4G mutations were isolated in Egypt. 2019 Pathogens (Basel, Switzerland) Discussion IV C4G 28 31 31703251 Evolution of H5-Type Avian Influenza A Virus Towards Mammalian Tropism in Egypt, 2014 to 2015. Other viruses from different clades (LP-2006, LP-Q1995D, LP-M2583A, and LP-M7217B) showed higher replication rates than the human LP-7271 at early time points and comparable rates at later time points. 2019 Pathogens (Basel, Switzerland) Discussion IV Q1995D;M2583A 49;60 55;66 31703251 Evolution of H5-Type Avian Influenza A Virus Towards Mammalian Tropism in Egypt, 2014 to 2015. Our results showed that the LP-S10739C causes the highest morbidity and mortality rates as compared with human LP-7271, followed by the LP-2006 clade 2.2.1. 2019 Pathogens (Basel, Switzerland) Discussion IV S10739C 31 38 31703251 Evolution of H5-Type Avian Influenza A Virus Towards Mammalian Tropism in Egypt, 2014 to 2015. The amplitude ratio for frequencies F (0.236) and F (0.076), which is a marker for the human propensity is 1.34 for S10739C and 1.22 for MOH-7271. 2019 Pathogens (Basel, Switzerland) Discussion IV S10739C 116 123 31703251 Evolution of H5-Type Avian Influenza A Virus Towards Mammalian Tropism in Egypt, 2014 to 2015. The replication efficiency results showed that LP-S10739C, LP-A10540A, LP-D10552B, and LP-A/Du/Eg/4/2015 have a higher replication rate in MDCK-SIAT1 cells at 24 h p.i. 2019 Pathogens (Basel, Switzerland) Discussion IV S10739C;A10540A 50;62 57;69 31719554 Synergistic PA and HA mutations confer mouse adaptation of a contemporary A/H3N2 influenza virus. Genomic analysis indicated that the MA-H3N2 variant acquired seven amino acid substitutions among four gene segments, PA(K615E), NP(G384R), HA(N144E, N144D, N246K, and A304T), and NA(G320E). 2019 Scientific reports Discussion IV K615E;G384R;N144E;N144D;N246K;A304T;G320E 121;132;143;150;157;168;183 126;137;148;155;162;173;188 HA;NA;NP;PA 140;180;129;118 142;182;131;120 31719554 Synergistic PA and HA mutations confer mouse adaptation of a contemporary A/H3N2 influenza virus. In recent years, studies have shown that multiple amino acid substitutions in the PA gene such as PA-T20A, K22R, T97I, M155T, D216N, P277S, L315F, P355S, and K615N/R, have been associated with adaptation in mice. 2019 Scientific reports Discussion IV T20A;K22R;T97I;M155T;D216N;P277S;L315F;P355S;K615N;K615R 101;107;113;119;126;133;140;147;158;158 105;111;117;124;131;138;145;152;165;165 PA;PA 82;98 84;100 31719554 Synergistic PA and HA mutations confer mouse adaptation of a contemporary A/H3N2 influenza virus. In summary, we generated a lethal mouse model of seasonal A/H3N2 virus following serial lung-to-lung passages of a wild-type virus in mice and found that both HA (N144E, N246K, and A304T) and PA (K615E) genes co-contribute to enhance viral pathogenicity and virulence in mice. 2019 Scientific reports Discussion IV N144E;N246K;A304T;K615E 163;170;181;196 168;175;186;201 HA;PA 159;192 161;194 31719554 Synergistic PA and HA mutations confer mouse adaptation of a contemporary A/H3N2 influenza virus. In vitro, the HA (N122D, N144D, N246K, and A304T) mutants displayed the highest replication kinetics in ST6-GalI-MDCK cells, but these mutations alone did not correlate with increased pathogenicity in mice. 2019 Scientific reports Discussion IV N122D;N144D;N246K;A304T 18;25;32;43 23;30;37;48 HA 14 16 31719554 Synergistic PA and HA mutations confer mouse adaptation of a contemporary A/H3N2 influenza virus. The HA (A304T) mutation was not reported in previous studies and its functional role in the enhanced virulence of rec MA-H3N2 is unknown, but our study showed that this mutation is necessary to increase the virulence in mice. 2019 Scientific reports Discussion IV A304T 8 13 HA 4 6 31719554 Synergistic PA and HA mutations confer mouse adaptation of a contemporary A/H3N2 influenza virus. The HA (N144E and N246K) substitutions found in the MA-H3N2 virus potentially abolished N-linked glycosylation sites. 2019 Scientific reports Discussion IV N144E;N246K 8;18 13;23 HA 4 6 31719554 Synergistic PA and HA mutations confer mouse adaptation of a contemporary A/H3N2 influenza virus. The RNP complexes containing the PA(K615E) presented significant higher transcription activity in 293 T cells compared to the parental virus while this single mutant did not influence replication kinetics in ST6-GalI-MDCK cells and pathogenicity in mice, indicating that adaptation requires additional mutations. 2019 Scientific reports Discussion IV K615E 36 41 PA;RNP 33;4 35;7 31719554 Synergistic PA and HA mutations confer mouse adaptation of a contemporary A/H3N2 influenza virus. Therefore, the PA (K615E) and HA (N144E, N246K, and A304T) are necessary for adaptation and acquisition of the virulence in mice. 2019 Scientific reports Discussion IV K615E;N144E;N246K;A304T 19;34;41;52 24;39;46;57 HA;PA 30;15 32;17 31719554 Synergistic PA and HA mutations confer mouse adaptation of a contemporary A/H3N2 influenza virus. These results suggest that the PA(K615E) substitution in MA-H3N2 may play a similar role to that of previously identified mutations at position 615 in the PA protein. 2019 Scientific reports Discussion IV K615E 34 39 PA;PA 31;155 33;157 31719554 Synergistic PA and HA mutations confer mouse adaptation of a contemporary A/H3N2 influenza virus. Thus, our findings suggest that the substitutions in the PA (K615E) and HA (N144E, N246K, and A304T) proteins are all required for a virulent phenotype of the MA-H3N2 in mice. 2019 Scientific reports Discussion IV K615E;N144E;N246K;A304T 61;76;83;94 66;81;88;99 HA;PA 72;57 74;59 31783761 Influenza A virus hemagglutinin mutations associated with use of neuraminidase inhibitors correlate with decreased inhibition by anti-influenza antibodies. According to the previous studies, the S183P mutation enhanced virulence by altering binding to sialyl receptors in a mouse animal model. 2019 Virology journal Discussion IV S183P 39 44 31783761 Influenza A virus hemagglutinin mutations associated with use of neuraminidase inhibitors correlate with decreased inhibition by anti-influenza antibodies. Consistent with the previous reports, our data showed that recombinant virus containing D222G resulted in ~ 2 log10PFU/mL higher titers over 72 h of replication in cell culture. 2019 Virology journal Discussion IV D222G 88 93 31783761 Influenza A virus hemagglutinin mutations associated with use of neuraminidase inhibitors correlate with decreased inhibition by anti-influenza antibodies. For example, the HA1 S162 N mutation was selected during intravenous zanamivir treatment. 2019 Virology journal Discussion IV S162N 21 27 HA1 17 20 31783761 Influenza A virus hemagglutinin mutations associated with use of neuraminidase inhibitors correlate with decreased inhibition by anti-influenza antibodies. In addition, S183P and D222G altered receptor binding avidity of the A/Puerto Rico/8/34 (H1N1) strain; however, whether a specific mutation results in increased or decreased receptor binding avidity depends on its genetic context. 2019 Virology journal Discussion IV S183P;D222G 13;23 18;28 31783761 Influenza A virus hemagglutinin mutations associated with use of neuraminidase inhibitors correlate with decreased inhibition by anti-influenza antibodies. Moreover, the high frequency of the S183P mutation in contemporary H1N1 viruses in 2017-2018 (~ 28%) indicates that this mutation is being strongly selected for in humans. 2019 Virology journal Discussion IV S183P 36 41 31783761 Influenza A virus hemagglutinin mutations associated with use of neuraminidase inhibitors correlate with decreased inhibition by anti-influenza antibodies. Subjects with the HA1 D222G mutation had significantly longer ICU stays: 22.8 days vs 14.0 days for those without this substitution. 2019 Virology journal Discussion IV D222G 22 27 HA1 18 21 31783761 Influenza A virus hemagglutinin mutations associated with use of neuraminidase inhibitors correlate with decreased inhibition by anti-influenza antibodies. The D222G mutation, which maps to the antigenic site Ca, was shown to be closely associated with the enhanced virulence of A(H1N1)pdm09 virus through the increased binding affinity to alpha2,3-linked sialyl receptors, while maintaining alpha2,6 specificity. 2019 Virology journal Discussion IV D222G 4 9 31783761 Influenza A virus hemagglutinin mutations associated with use of neuraminidase inhibitors correlate with decreased inhibition by anti-influenza antibodies. The D222G substitution was also found with considerable frequency in fatal and severe cases but was virtually absent among clinically mild cases. 2019 Virology journal Discussion IV D222G 4 9 31783761 Influenza A virus hemagglutinin mutations associated with use of neuraminidase inhibitors correlate with decreased inhibition by anti-influenza antibodies. The G155E mutation, which maps to the antigenic site Sa, and the S183P mutation, which is located within the RBS and overlaps with antigenic site Sb, have been shown to significantly increase HA receptor binding to alpha2,6-linked sialyl receptors. 2019 Virology journal Discussion IV G155E;S183P 4;65 9;70 HA 192 194 31783761 Influenza A virus hemagglutinin mutations associated with use of neuraminidase inhibitors correlate with decreased inhibition by anti-influenza antibodies. Viruses containing two specific HA mutations (G155E and D222G) also demonstrated significantly decreased inhibition by anti-CA/04 mAbs and human sera collected from three different donors in MN assay. 2019 Virology journal Discussion IV G155E;D222G 46;56 51;61 HA 32 34 31805964 The tyrosine 73 and serine 83 dephosphorylation of H1N1 swine influenza virus NS1 protein attenuates virus replication and induces high levels of beta interferon. In this study, we found that knockdown of RIG-I dramatically impaired the induction of IFN-beta and ISG56 in NS1 Y73F or S83A mutant-infected cells, indicating that RIG-I plays a role in the IFN-beta response upon rSIV NS1 Y73F and rSIV NS1 S83A infection. 2019 Virology journal Discussion IV Y73F;S83A;Y73F;S83A 113;121;223;241 117;125;227;245 NS1;NS1;NS1 109;219;237 112;222;240 31805964 The tyrosine 73 and serine 83 dephosphorylation of H1N1 swine influenza virus NS1 protein attenuates virus replication and induces high levels of beta interferon. We found that Y-to-F substitution at position 73 or S-to-A substitution at position 83 increased the levels of unphosphorylated NS1 protein, suggesting that Y73 and S83 are phosphorylated in wt NS1 proteins. 2019 Virology journal Discussion IV S83A 52 86 NS1;NS1 128;194 131;197 31810278 Equine Mx1 Restricts Influenza A Virus Replication by Targeting at Distinct Site of its Nucleoprotein. A similar substitution in H3N8JL89 NP (H3N8JL89-H52Y) produced a reverse effect and eqMx1 inhibited the polymerase activity, confirming the importance of this site. 2019 Viruses Discussion IV H52Y 48 52 NP 35 37 31810278 Equine Mx1 Restricts Influenza A Virus Replication by Targeting at Distinct Site of its Nucleoprotein. A single amino acid mutation H52N of NP alters this resistance and interaction to eqMx1 and changed the viral replication ability when eqMx1 was present. 2019 Viruses Discussion IV H52N 29 33 NP 37 39 31810278 Equine Mx1 Restricts Influenza A Virus Replication by Targeting at Distinct Site of its Nucleoprotein. In our study, we showed that in the H7N9ZJ13 NP the mutation N52H enabled it to escape the eqMx1 restriction. 2019 Viruses Discussion IV N52H 61 65 NP 45 47 31810278 Equine Mx1 Restricts Influenza A Virus Replication by Targeting at Distinct Site of its Nucleoprotein. Interestingly, the S34G substitution in the H7N9ZJ13 did not reverse the activity against eqMx1. 2019 Viruses Discussion IV S34G 19 23 31810278 Equine Mx1 Restricts Influenza A Virus Replication by Targeting at Distinct Site of its Nucleoprotein. Substituting tyrosine (Y) at position 52 with histidine (H) in H5N1 altered the polymerase activity of H5N1 drastically and eqMx1 almost lost its restriction affect towards H5N1-Y52H. 2019 Viruses Discussion IV Y52H;Y52Y 178;12 182;41 31839904 Complete genome sequencing of H1N1pdm09 swine influenza isolates from Nigeria reveals likely reverse zoonotic transmission at the human-animal interface in intensive piggery. Though the observation of host-induced selection of variants was reported for Q226R or D225G of earlier human H1N1pdm09 viruses, this study observed Q240R substitution. 2019 Infection ecology & epidemiology Discussion IV Q226R;D225G;Q240R 78;87;149 83;92;154 31839904 Complete genome sequencing of H1N1pdm09 swine influenza isolates from Nigeria reveals likely reverse zoonotic transmission at the human-animal interface in intensive piggery. Whether the Q240R substitution is a natural substitution or avian host induced can be further investigated by culture in mammalian cells or animal experimental studies. 2019 Infection ecology & epidemiology Discussion IV Q240R 12 17 31842256 Antiviral Activity of Benzoic Acid Derivative NC-5 Against Influenza A Virus and Its Neuraminidase Inhibition. However, OS failed to protect mice infected with H1N1-H275Y virus, and all of the mice died on day nine post-infection. 2019 International journal of molecular sciences Discussion IV H275Y 54 59 31842256 Antiviral Activity of Benzoic Acid Derivative NC-5 Against Influenza A Virus and Its Neuraminidase Inhibition. NC-5 effectively alleviated the CPE and inhibited the replication of H1N1 and H1N1-H275Y viruses with 50% effective concentration (EC50) values of 33.6 muM and 32.8 muMu. 2019 International journal of molecular sciences Discussion IV H275Y 83 88 31852473 Continuing evolution of H6N2 influenza a virus in South African chickens and the implications for diagnosis and control. Isolate 432/19 had an additional single codon deletion at position 46 in the NA stalk and an additional compensatory predicted N-glycosylation site in the HA compared to all the other sub-lineage I viruses. 2019 BMC veterinary research Discussion IV del 46X 33 69 HA;NA 155;77 157;79 31852473 Continuing evolution of H6N2 influenza a virus in South African chickens and the implications for diagnosis and control. Most sub-lineage I viruses isolated since 2015 also acquired the K702R mutation in PB2 associated with the ability to infect humans, whereas prior to 2015 most viruses in sub-lineages I and II contained the typical avian lysine marker. 2019 BMC veterinary research Discussion IV K702R 65 70 PB2 83 86 31852473 Continuing evolution of H6N2 influenza a virus in South African chickens and the implications for diagnosis and control. Sub-lineage I H6N2 viruses acquired three of the nine HA mutations associated with human receptor-binding preference (A13S, V187D and A193N) since 2002. 2019 BMC veterinary research Discussion IV A13S;V187D;A193N 118;124;134 122;129;139 HA 54 56 31852473 Continuing evolution of H6N2 influenza a virus in South African chickens and the implications for diagnosis and control. The unusual HA0 motif of PQVETRGIF (the typical H6 LPAI HA0 sequence is PQRETRGLF) in sub-lineage I viruses was evident from 2012 onwards (Additional file 4: Figure S1) but H44954/2016 acquired an additional E343G mutation that produced the unique motif of PQVGTRGIF. 2019 BMC veterinary research Discussion IV E343G 208 213 31906790 Contribution of Fc-dependent cell-mediated activity of a vestigial esterase-targeting antibody against H5N6 virus infection. In this study, we show that 9F4-WT, 9F4-LALA and 9F4-K322A bind and neutralize the reassortant HPAI H5N6 strain both in vitro and in vivo. 2020 Emerging microbes & infections Discussion IV K322A 53 58 Influenza A virus H5N6 infection 95 104 31906790 Contribution of Fc-dependent cell-mediated activity of a vestigial esterase-targeting antibody against H5N6 virus infection. On the contrary, the observation that 9F4-K322A had similar antiviral efficacy compared to 9F4-WT indicates that CDC does not play a major role in 9F4's antiviral function (Figure 5). 2020 Emerging microbes & infections Discussion IV K322A 42 47 31906790 Contribution of Fc-dependent cell-mediated activity of a vestigial esterase-targeting antibody against H5N6 virus infection. Our results suggest that the ADCC and/or ADCP pathways are partially responsible for 9F4's antiviral potency and concurs with another study demonstrating that a D265A ADCC deficient mutant of the VE-targeting antibody 1H5 was able to protect mice from H7 infections but is less potent compared to wild type 1H5. 2020 Emerging microbes & infections Discussion IV D265A 161 166 31917822 The effect of mutations derived from mouse-adapted H3N2 seasonal influenza A virus to pathogenicity and host adaptation. Analysis of the effects of the NP mutation on viral polymerase activity is required to determine how the NP D34N mutation contributes to enhanced replication competence in mice. 2020 PloS one Discussion IV D34N 108 112 NP;NP 31;105 33;107 31917822 The effect of mutations derived from mouse-adapted H3N2 seasonal influenza A virus to pathogenicity and host adaptation. In previous studies, virulence of the reassortant virus containing NP D34N was enhanced by increasing the dose inoculated into mice. 2020 PloS one Discussion IV D34N 70 74 NP 67 69 31917822 The effect of mutations derived from mouse-adapted H3N2 seasonal influenza A virus to pathogenicity and host adaptation. In the present study, the NP mutant containing the D34N mutation efficiently replicated in MDCK cells (Fig 4) and mouse organs (Fig 3E) without enhancing morbidity and mortality (Figs 1D and 2D). 2020 PloS one Discussion IV D34N 51 55 NP 26 28 31917822 The effect of mutations derived from mouse-adapted H3N2 seasonal influenza A virus to pathogenicity and host adaptation. Moreover, the F323L mutation in PB2 may be associated with the high-yield properties of IAVs in MDCK cells. 2020 PloS one Discussion IV F323L 14 19 PB2 32 35 31917822 The effect of mutations derived from mouse-adapted H3N2 seasonal influenza A virus to pathogenicity and host adaptation. Notably, three substitutions (N160D, T183A, and N262T) might lead to loss of N-linked glycosylation of HA (Asn-X-Ser/Thr, where X is any amino acid, other than proline). 2020 PloS one Discussion IV N160D;T183A;N262T 30;37;48 35;42;53 HA 103 105 31917822 The effect of mutations derived from mouse-adapted H3N2 seasonal influenza A virus to pathogenicity and host adaptation. Six of the 13 mutations in MA_SW are harbored by the HA gene (Table 5), with four of these resulting amino acid substitutions (K18Q, N160D, T183A, and N262T) rarely detected in circulating seasonal H3N2 viruses (<0.05%) (Table 6). 2020 PloS one Discussion IV K18Q;N160D;T183A;N262T 127;133;140;151 131;138;145;156 HA 53 55 31917822 The effect of mutations derived from mouse-adapted H3N2 seasonal influenza A virus to pathogenicity and host adaptation. Taken together, NP D34N may be considered as a determinant of IAV pathogenicity. 2020 PloS one Discussion IV D34N 19 23 NP 16 18 31917822 The effect of mutations derived from mouse-adapted H3N2 seasonal influenza A virus to pathogenicity and host adaptation. The D34N substitution in NP is rarely identified in circulating H3N2 viruses (0.07%) (Table 6); however, this mutation has been frequently detected in mouse-adapted H3N2 viruses according to previous studies. 2020 PloS one Discussion IV D34N 4 8 NP 25 27 31917822 The effect of mutations derived from mouse-adapted H3N2 seasonal influenza A virus to pathogenicity and host adaptation. The exact role of the NP D34N mutation is not yet known but expected to be related to interactions with the RNP complex and viral polymerase activity. 2020 PloS one Discussion IV D34N 25 29 NP;RNP 22;108 24;111 31917822 The effect of mutations derived from mouse-adapted H3N2 seasonal influenza A virus to pathogenicity and host adaptation. These results suggest that NP D34N is an important factor in mouse-adapted IAV. 2020 PloS one Discussion IV D34N 30 34 NP 27 29 31932446 A molecularly engineered antiviral banana lectin inhibits fusion and is efficacious against influenza virus infection in vivo. Carbohydrate binding is essential for both binding and fusion inhibition, as the carbohydrate binding site mutant D133G does not bind as efficiently and is not inhibitory to fusion. 2020 Proc Natl Acad Sci U S A Discussion IV D133G 114 119 31932446 A molecularly engineered antiviral banana lectin inhibits fusion and is efficacious against influenza virus infection in vivo. H84T, and to a much lesser extent D133G, localize to the late endosome/lysosome. 2020 Proc Natl Acad Sci U S A Discussion IV D133G 34 39 31948040 H7N9 Influenza Virus Containing a Polybasic HA Cleavage Site Requires Minimal Host Adaptation to Obtain a Highly Pathogenic Disease Phenotype in Mice. A previous study identified a D347N mutation in the PA of H9N2 avian influenza viruses to be important for mouse adaptation. 2020 Viruses Discussion IV D347N 30 35 PA 52 54 31948040 H7N9 Influenza Virus Containing a Polybasic HA Cleavage Site Requires Minimal Host Adaptation to Obtain a Highly Pathogenic Disease Phenotype in Mice. For example, the PB2 E627K mutation is known to increase virus replication at lower temperatures that are typically found in the upper respiratory tract of humans, and consequently can increase virulence and possibly the transmissibility of the virus as well. 2020 Viruses Discussion IV E627K 21 26 PB2 17 20 31948040 H7N9 Influenza Virus Containing a Polybasic HA Cleavage Site Requires Minimal Host Adaptation to Obtain a Highly Pathogenic Disease Phenotype in Mice. Here we also identified the amino acid residue at 347 of PA to be important for virulence, specifically a PA-D347G mutation was found in the mouse-passaged H7N9-PBC virus. 2020 Viruses Discussion IV D347G 109 114 PA;PA 57;106 59;108 31948040 H7N9 Influenza Virus Containing a Polybasic HA Cleavage Site Requires Minimal Host Adaptation to Obtain a Highly Pathogenic Disease Phenotype in Mice. Here we have also identified a novel HA mutation (A452T) that plays a critical role in virulence of HPAI H7N9 viruses in mice. 2020 Viruses Discussion IV A452T 50 55 HA 37 39 Influenza A virus H7N9 infection 100 109 31948040 H7N9 Influenza Virus Containing a Polybasic HA Cleavage Site Requires Minimal Host Adaptation to Obtain a Highly Pathogenic Disease Phenotype in Mice. In a subsequent study, both PA-A343S and PA-D347E mutations were identified in an avian H5N1 virus and shown to increase replication and virulence in mice. 2020 Viruses Discussion IV A343S;D347E 31;44 36;49 PA;PA 28;41 30;43 31948040 H7N9 Influenza Virus Containing a Polybasic HA Cleavage Site Requires Minimal Host Adaptation to Obtain a Highly Pathogenic Disease Phenotype in Mice. In addition to the PBC site in HA, we also found three additional mutations in PA (D347G), PB2 (M483K), and HA (A452T) that all contributed to increased pathogenesis in mice. 2020 Viruses Discussion IV D347G;M483K;A452T 83;96;112 88;101;117 HA;HA;PA;PB2 31;108;79;91 33;110;81;94 31948040 H7N9 Influenza Virus Containing a Polybasic HA Cleavage Site Requires Minimal Host Adaptation to Obtain a Highly Pathogenic Disease Phenotype in Mice. Interestingly, mouse passaged H7N9-PBC mP2 and the single mutant H7N9-PBC HA viruses retained their preference towards alpha-2,3-linked SA, and suggests that the A452T mutation in HA did not change receptor specificity. 2020 Viruses Discussion IV A452T 162 167 HA;HA 74;180 76;182 31948040 H7N9 Influenza Virus Containing a Polybasic HA Cleavage Site Requires Minimal Host Adaptation to Obtain a Highly Pathogenic Disease Phenotype in Mice. Interestingly, sequencing of the mouse-passaged H7N9-2017PBC virus revealed a different set of mutations in addition to the PBC in HA, such as PB2-Q73R/D256G and HA-I399M. 2020 Viruses Discussion IV Q73R;D256G;I399M 147;152;165 151;157;170 HA;HA;PB2 131;162;143 133;164;146 31948040 H7N9 Influenza Virus Containing a Polybasic HA Cleavage Site Requires Minimal Host Adaptation to Obtain a Highly Pathogenic Disease Phenotype in Mice. Of the three mutations, the mutation in HA (A452T) played the strongest role in increasing the virulence of H7N9-PBC virus in mice. 2020 Viruses Discussion IV A452T 44 49 HA 40 42 31948040 H7N9 Influenza Virus Containing a Polybasic HA Cleavage Site Requires Minimal Host Adaptation to Obtain a Highly Pathogenic Disease Phenotype in Mice. Recent studies have identified mutations in the receptor binding domain of H7N9 HA including G186V, K193T, Q226L and G228S, that are able to switch receptor binding from its original preference for avian-virus to human-virus receptors. 2020 Viruses Discussion IV G186V;K193T;Q226L;G228S 93;100;107;117 98;105;112;122 HA 80 82 31948040 H7N9 Influenza Virus Containing a Polybasic HA Cleavage Site Requires Minimal Host Adaptation to Obtain a Highly Pathogenic Disease Phenotype in Mice. The two mutations PB2-Q73R and HA-I399M have not been described previously; however, the D256G mutation has been described to enhance viral polymerase activity in vitro and was important for replication of an avian H5N1 virus in pigs. 2020 Viruses Discussion IV Q73R;I399M;D256G 22;34;89 26;39;94 HA;PB2 31;18 33;21 31948040 H7N9 Influenza Virus Containing a Polybasic HA Cleavage Site Requires Minimal Host Adaptation to Obtain a Highly Pathogenic Disease Phenotype in Mice. While it remains unknown what effect the PB2 M483K mutation has on polymerase function, it is clear from these results that it is contributing to increased viral replication at earlier time points in human and mouse cells, thus contributing to the overall virulence of the virus that contains this mutation. 2020 Viruses Discussion IV M483K 45 50 PB2 41 44 31951605 Reassortment and adaptive mutations of an emerging avian influenza virus H7N4 subtype in China. Last, C19Y mutation in M2, with tyrosine in place of cysteine, could limit disulfide linkage to the neighbor cysteine 17 and prevent the formation of M2 dimerization. 2020 PloS one Discussion IV C19Y 6 10 M2;M2 23;150 25;152 31951605 Reassortment and adaptive mutations of an emerging avian influenza virus H7N4 subtype in China. Second, E627K in PB2 of the human H7N4 virus may have been a determinant of host range. 2020 PloS one Discussion IV E627K 8 13 PB2 17 20 31951605 Reassortment and adaptive mutations of an emerging avian influenza virus H7N4 subtype in China. The K683T mutant conferred enhanced polymerase activity at low temperatures and promoted efficient replication in the upper respiratory tract. 2020 PloS one Discussion IV K683T 4 9 31951605 Reassortment and adaptive mutations of an emerging avian influenza virus H7N4 subtype in China. The new K683T mutation in PB2 may also be crucial for increased polymerase activity in mammalian cells. 2020 PloS one Discussion IV K683T 8 13 PB2 26 29 31951605 Reassortment and adaptive mutations of an emerging avian influenza virus H7N4 subtype in China. We identified an N47S mutation in PB1-F2 that might behave similarly to the N66S mutation which inhibited an early interferon response due to spatial proximity. 2020 PloS one Discussion IV N47S;N66S 17;76 21;80 PB1F2 34 40 31955521 Antigenic variants of influenza B viruses isolated in Japan during the 2017-2018 and 2018-2019 influenza seasons. Further investigations are required to determine whether this NA-G407S mutation affects the transmissibility of influenza B viruses. 2020 Influenza and other respiratory viruses Discussion IV G407S 65 70 62 64 31955521 Antigenic variants of influenza B viruses isolated in Japan during the 2017-2018 and 2018-2019 influenza seasons. Influenza B viruses carrying the G407S mutation in their NA, which confers reduced susceptibility to NA inhibitors, were sporadically detected in Japan during the 2004-2005 season15 and in Australia and the United States during the 2015-2016 season.23 In this study, we also detected an influenza B virus with the NA-G407S mutation during the 2017-2018 season in Japan (Table 4). 2020 Influenza and other respiratory viruses Discussion IV G407S;G407S 33;317 38;322 NA;NA;NA 57;101;314 59;103;316 32064779 Rapid detection of an I38T amino acid substitution in influenza polymerase acidic subunit associated with reduced susceptibility to baloxavir marboxil. A/H3 PA_I38T rhPCR was designed to discriminate between PA I38 (T at nucleotide 113) and T38 (C at nucleotide 113), not to identify M38, which is also encoded by a T at nucleotide 113; thus, rhPCR reported the amino acid as PA I38. 2020 Influenza and other respiratory viruses Discussion IV I38T 8 12 PA;PA;PA 5;56;224 7;58;226 32064779 Rapid detection of an I38T amino acid substitution in influenza polymerase acidic subunit associated with reduced susceptibility to baloxavir marboxil. According to A/H3 PA_I38T rhPCR, A/KANAGAWA/IC1807/2018 was determined to carry PA I38, whereas a mixture of PA I38 and T38 was detected by NGS. 2020 Influenza and other respiratory viruses Discussion IV I38T 21 25 PA;PA;PA 18;80;109 20;82;111 32064779 Rapid detection of an I38T amino acid substitution in influenza polymerase acidic subunit associated with reduced susceptibility to baloxavir marboxil. Based on these results, rhPCR assays should be considered a useful tool for the screening of the PA I38T substitution and monitoring of the emergence of baloxavir-resistant influenza viruses. 2020 Influenza and other respiratory viruses Discussion IV I38T 100 104 PA 97 99 32064779 Rapid detection of an I38T amino acid substitution in influenza polymerase acidic subunit associated with reduced susceptibility to baloxavir marboxil. By using in vitro-transcribed RNA controls, A/H3 PA_I38T rhPCR was able to detect at least 5% of T38 in the mixture, whereas it failed to detect 10% of PA T38 in A/KANAGAWA/IC1807/2018. 2020 Influenza and other respiratory viruses Discussion IV I38T 52 56 PA;PA 49;152 51;154 32064779 Rapid detection of an I38T amino acid substitution in influenza polymerase acidic subunit associated with reduced susceptibility to baloxavir marboxil. Five and 18 influenza A(H1N1)pdm09 and A(H3N2) clinical strains or viruses contained in clinical specimens isolated or collected in the 2018/2019 influenza season were tested by A/H1pdm PA_I38T rhPCR and A/H3 PA_I38T rhPCR, respectively. 2020 Influenza and other respiratory viruses Discussion IV I38T;I38T 189;212 193;216 PA;PA 186;209 188;211 32064779 Rapid detection of an I38T amino acid substitution in influenza polymerase acidic subunit associated with reduced susceptibility to baloxavir marboxil. In previous analyses involving the focus reduction assay, comparison of median IC50 values indicated that influenza A(H3N2) clinical strains carrying PA T38 in Japan exhibited >100-fold reduced susceptibilities to baloxavir compared to those of influenza A(H3N2) clinical strains carrying PA I38.5, 6, 7 In contrast, influenza viruses carrying the PA I38M or PA I38F substitutions exhibited only moderate reductions in susceptibility to baloxavir.3, 4, 20 As of July 2019, five A(H1N1)pdm09 and 30 A(H3N2) viruses in Japan had been found to carry a mutation at PA amino acid residue 38 by NGS.18 Of these, two A(H1N1)pdm09 viruses carried PA I38F or I38S substitutions, and two A(H3N2) viruses carried PA I38M substitution. 2020 Influenza and other respiratory viruses Discussion IV I38M;I38F;I38F;I38S;I38M 351;362;642;650;705 355;366;646;654;709 PA;PA;PA;PA;PA;PA;PA 150;289;348;359;561;639;702 152;291;350;361;563;641;704 32064779 Rapid detection of an I38T amino acid substitution in influenza polymerase acidic subunit associated with reduced susceptibility to baloxavir marboxil. Regardless of the type and subtype of influenza virus, all clinical strains isolated in the 2017/2018 influenza season were determined to carry PA I38 by A/H1pdm PA_I38T rhPCR, A/H3 PA_I38T rhPCR, and B PA_I38T rhPCR. 2020 Influenza and other respiratory viruses Discussion IV I38T;I38T 185;206 189;210 PA;PA;PA;PA 144;162;182;203 146;164;184;205 32064779 Rapid detection of an I38T amino acid substitution in influenza polymerase acidic subunit associated with reduced susceptibility to baloxavir marboxil. The rhPCR assays developed in this study can rapidly detect already typed and/or subtyped influenza viruses carrying the I38T substitution in PA with high sensitivity and specificity within 3-4 hours, and can be performed on many samples at a time. 2020 Influenza and other respiratory viruses Discussion IV I38T 121 125 PA 142 144 32064779 Rapid detection of an I38T amino acid substitution in influenza polymerase acidic subunit associated with reduced susceptibility to baloxavir marboxil. These results are in agreement with previous reports that PA I38 is highly conserved among influenza A and B viruses,3 that the I38T substitution in PA was not detected in seasonal influenza strains isolated in the 2017/2018 influenza season in Japan,18 and that influenza viruses circulating in the Asia-Pacific region between 2012 and 2018 were susceptible to baloxavir.19 . 2020 Influenza and other respiratory viruses Discussion IV I38T 128 132 PA;PA 58;149 60;151 32064779 Rapid detection of an I38T amino acid substitution in influenza polymerase acidic subunit associated with reduced susceptibility to baloxavir marboxil. These results are in agreement with previous reports that PA I38 is highly conserved among influenza A and B viruses,3 that the I38T substitution in PA was not detected in seasonal influenza strains isolated in the 2017/2018 influenza season in Japan,18 and that influenza viruses circulating in the Asia-Pacific region between 2012 and 2018 were susceptible to baloxavir.19. 2020 Influenza and other respiratory viruses Discussion IV I38T 128 132 32093780 Acetylation at K108 of the NS1 protein is important for the replication and virulence of influenza virus. In the present study, we identified and characterized the acetylation of K108 in the NS1 protein, and the deacetylation of K108Q affected viral replication in cells at 36 and 48 hpi. 2020 Veterinary research Discussion IV K108Q 123 128 NS1 85 88 32093780 Acetylation at K108 of the NS1 protein is important for the replication and virulence of influenza virus. Interestingly, the deacetylation-mimic K108R substitution retained NS1 protein in the cytoplasm of infected cells, resulting in a possible impaired interaction between CPSF30 and the NS1 protein, subsequently leading to attenuated IFN antagonism. 2020 Veterinary research Discussion IV K108R 39 44 NS1;NS1 67;183 70;186 32093780 Acetylation at K108 of the NS1 protein is important for the replication and virulence of influenza virus. Notably, in this study, acetylation of K108 located outside of the NLS affected the cellular localization of NS1 protein, and the deacetylation-mimic K108R substitution blocked the nuclear localization of the NS1 protein in infected cells; however, the underlying mechanism remains unknown. 2020 Veterinary research Discussion IV K108R 150 155 NS1;NS1 109;209 112;212 32093780 Acetylation at K108 of the NS1 protein is important for the replication and virulence of influenza virus. Single point mutations, either R35A, R38A, or K41A, completely eliminated importin protein binding, which transports target proteins to the nucleus. 2020 Veterinary research Discussion IV R35A;R38A;K41A 31;37;46 35;41;50 32093780 Acetylation at K108 of the NS1 protein is important for the replication and virulence of influenza virus. The 2009 pandemic H1N1 has 108R in NS1, which causes inefficient general host gene expression shutoff, while R108K restores its ability to block general host genes and bind CPSF30. 2020 Veterinary research Discussion IV R108K 109 114 NS1 35 38 32093780 Acetylation at K108 of the NS1 protein is important for the replication and virulence of influenza virus. The expression levels of NS1-K108Q and NS1-K108R in transfected 293T cells were similar (Figure 4E), while the NS1 levels in infected MDCK and A549 cells were different (Figures 2C and D). 2020 Veterinary research Discussion IV K108Q;K108R 29;43 34;48 NS1;NS1;NS1 25;39;111 28;42;114 32093780 Acetylation at K108 of the NS1 protein is important for the replication and virulence of influenza virus. The mRNA levels of IFN-beta, IL-1beta, and TNF-alpha in mouse lungs of the WSN-NS1-K108R-infected group were significantly higher than those in the other two groups at 3 dpi, which indicated that NS1-108R was less efficient at inhibiting the production of innate antiviral cytokines at 3 dpi in mice. 2020 Veterinary research Discussion IV K108R 83 88 NS1;NS1 79;196 82;199 32093780 Acetylation at K108 of the NS1 protein is important for the replication and virulence of influenza virus. The NS1-K108R substitution impaired the suppression of IFN promoter activation by poly(I:C), RIG-1 CARD, TBK-1, and IRF3, which suggested that the NS1-K108R substitution affected the IFN antagonism of NS1 either through targeting downstream of IRF3 or a general mechanism that NS1 uses to inhibit IFN, such as interaction with CPSF30, resulting in inhibition of the processing of mRNA, including IFN mRNA. 2020 Veterinary research Discussion IV K108R;K108R 8;151 13;156 NS1;NS1;NS1;NS1 4;147;201;277 7;150;204;280 32093780 Acetylation at K108 of the NS1 protein is important for the replication and virulence of influenza virus. This could explain why attenuation of the IFN antagonistic ability of NS1-K108R is independent of RIG-I CARD, TBK-1, and IRF3 activation. 2020 Veterinary research Discussion IV K108R 74 79 NS1 70 73 32095441 Comparison of antigenic mutation during egg and cell passage cultivation of H3N2 influenza virus. According to the structural analysis of the hemagglutinin, the structure before and after mutation was quite different at position 156 where histidine was changed to arginine and 219 where serine was changed to phenylalanine. 2020 Clinical and experimental vaccine research Discussion IV H156R;S219F 131;179 174;224 HA 44 57 32095441 Comparison of antigenic mutation during egg and cell passage cultivation of H3N2 influenza virus. G186S and H156R are mutations that normally occur characteristically in egg adaptation, and show the effect of improving replication by increasing the binding avidity of alpha2,3-linked receptors rather than alpha2,6-linked receptors. 2020 Clinical and experimental vaccine research Discussion IV G186S;H156R 0;10 5;15 32095441 Comparison of antigenic mutation during egg and cell passage cultivation of H3N2 influenza virus. However, G186S is known to show an insignificant effect in terms of antigenicity. 2020 Clinical and experimental vaccine research Discussion IV G186S 9 14 32095441 Comparison of antigenic mutation during egg and cell passage cultivation of H3N2 influenza virus. In addition, the C704T mutation was further identified in the 9th to 15th passaged viruses, and the corresponding amino acid sequence mutation was identified as S219F. 2020 Clinical and experimental vaccine research Discussion IV C704T;S219F 17;161 22;166 32095441 Comparison of antigenic mutation during egg and cell passage cultivation of H3N2 influenza virus. In the case of egg cultured viruses, no mutation was observed in the sequence of the hemagglutinin gene up to the 2nd passage, but there were three changes identified for A516G, G604A, and C942T in the 3rd to 8th passaged viruses, and the corresponding amino acid sequence mutations were H156R, G186S, and silent mutation, respectively. 2020 Clinical and experimental vaccine research Discussion IV A516G;G604A;C942T;H156R;G186S 171;178;189;288;295 176;183;194;293;300 HA 85 98 32095441 Comparison of antigenic mutation during egg and cell passage cultivation of H3N2 influenza virus. In this study, three amino acid mutations were identified in the influenza virus cultured in egg, including H156R, G186S, and S219F. 2020 Clinical and experimental vaccine research Discussion IV H156R;G186S;S219F 108;115;126 113;120;131 32095441 Comparison of antigenic mutation during egg and cell passage cultivation of H3N2 influenza virus. On the other hand, the change of glutamic acid to serine at amino acid position 186 was not significant in the structural difference. 2020 Clinical and experimental vaccine research Discussion IV E186S 33 83 32095441 Comparison of antigenic mutation during egg and cell passage cultivation of H3N2 influenza virus. S219F mutation also affects binding avidity, especially in the case of phenylalanine, which is an amino acid containing a bulky aromatic ring, which may affect 220-loop conformation and physically alter the receptor binding site. 2020 Clinical and experimental vaccine research Discussion IV S219F 0 5 32130243 Epidemic of influenza A(H1N1)pdm09 analyzed by full genome sequences and the first case of oseltamivir-resistant strain in Myanmar 2017. Another known important amino acid change, D222N/G in HA, was not detected in viruses from Myanmar in-patients. 2020 PloS one Discussion IV D222N;D222G 43;43 50;50 HA 54 56 32130243 Epidemic of influenza A(H1N1)pdm09 analyzed by full genome sequences and the first case of oseltamivir-resistant strain in Myanmar 2017. Global analysis on the susceptibility of human influenza viruses to the NAI reported that the most common NA amino acid substitution was H275Y in A(H1N1)pdm09 viruses, which confers HRI by oseltamivir and peramivir without affecting the susceptibility to zanamivir and laninamivir. 2020 PloS one Discussion IV H275Y 137 142 NA;NAI 106;72 108;75 32130243 Epidemic of influenza A(H1N1)pdm09 analyzed by full genome sequences and the first case of oseltamivir-resistant strain in Myanmar 2017. Here, we report the identification and detection of a H275Y mutation in NA that confer resistant to oseltamivir from an influenza A(H1N1)pdm09 isolate in community samples of Myanmar, which was detected for the first time in Myanmar; however, its detection rate was low at only 0.5%. 2020 PloS one Discussion IV H275Y 54 59 72 74 32130243 Epidemic of influenza A(H1N1)pdm09 analyzed by full genome sequences and the first case of oseltamivir-resistant strain in Myanmar 2017. In contrast to Myanmar strains, amino acid substitutions A73V, V321I, T508A, and I510T, were reported from Central India sequences in 2017 with low global occurrence. 2020 PloS one Discussion IV A73V;V321I;T508A;I510T 57;63;70;81 61;68;75;86 32130243 Epidemic of influenza A(H1N1)pdm09 analyzed by full genome sequences and the first case of oseltamivir-resistant strain in Myanmar 2017. In Myanmar, influenza A(H1N1)pdm09 was first detected in 2009 and the oseltamivir-resistant H275Y variant has not been detected in specimens, either from the community or hospitalized patients since then, although all isolates tested showed the S31N mutation in M2 that conferred resistance to amantadine. 2020 PloS one Discussion IV H275Y;S31N 92;245 97;249 M2 262 264 32130243 Epidemic of influenza A(H1N1)pdm09 analyzed by full genome sequences and the first case of oseltamivir-resistant strain in Myanmar 2017. In NA phylogeny, amino acid substitutions V13I, I34V, and I314M were found in all Myanmar strains. 2020 PloS one Discussion IV V13I;I34V;I314M 42;48;58 46;52;63 3 5 32130243 Epidemic of influenza A(H1N1)pdm09 analyzed by full genome sequences and the first case of oseltamivir-resistant strain in Myanmar 2017. Indeed, all of Myanmar and Indian strains in this study also possessed S31N mutation. 2020 PloS one Discussion IV S31N 71 75 32130243 Epidemic of influenza A(H1N1)pdm09 analyzed by full genome sequences and the first case of oseltamivir-resistant strain in Myanmar 2017. It was known that S74R, I295V mutations in HA protein were recently acquired by the virus; this mutation has high frequency of detection (66%) globally. 2020 PloS one Discussion IV S74R;I295V 18;24 22;29 HA 43 45 32130243 Epidemic of influenza A(H1N1)pdm09 analyzed by full genome sequences and the first case of oseltamivir-resistant strain in Myanmar 2017. M2 gene mutations associated with resistance to amantadine were found in only about 1% of V27A mutations compared to 95% of S31N mutation. 2020 PloS one Discussion IV V27A;S31N 90;124 94;128 M2 0 2 32130243 Epidemic of influenza A(H1N1)pdm09 analyzed by full genome sequences and the first case of oseltamivir-resistant strain in Myanmar 2017. Moreover, about 32% of global strains had the S164T mutation, and it is reported as the most recent mutation observed among 2017 strains. 2020 PloS one Discussion IV S164T 46 51 32159230 Antigenic drift of hemagglutinin and neuraminidase in seasonal H1N1 influenza viruses from Saudi Arabia in 2014 to 2015. Amino acid changes at key antigenic sites in our study, such as position N179S, Q180T (antigenic site-Sa), S200P, T202N (antigenic site-Sb) along with N101S, N114S, and T233I in the head domain might have resulted in antigenic drift and emergence of variant viruses. 2020 Journal of medical virology Discussion IV N179S;Q180T;S200P;T202N;N101S;N114S;T233I 73;80;107;114;151;158;169 78;85;112;119;156;163;174 32159230 Antigenic drift of hemagglutinin and neuraminidase in seasonal H1N1 influenza viruses from Saudi Arabia in 2014 to 2015. H1 gene sequences in comparison to 2010-2016 vaccine strain recently in India have shown mutations K166Q and S188T resulting in the emergence of variants. 2020 Journal of medical virology Discussion IV K166Q;S188T 99;109 104;114 32159230 Antigenic drift of hemagglutinin and neuraminidase in seasonal H1N1 influenza viruses from Saudi Arabia in 2014 to 2015. These antigenic differences could be due to the amino acid changes in defined Ab binding sites (N200S, N248D, N369K, and K432E). 2020 Journal of medical virology Discussion IV N200S;N248D;N369K;K432E 96;103;110;121 101;108;115;126 32211197 Detection of H3N8 influenza A virus with multiple mammalian-adaptive mutations in a rescued Grey seal (Halichoerus grypus) pup. D701N is common in canine and horse H3N8 IAV (see Supplementary Table S4), but does not occur in birds, and was found associated with highly-pathogenic H5N1 viruses which infected humans. 2020 Virus evolution Discussion IV D701N 0 5 32211197 Detection of H3N8 influenza A virus with multiple mammalian-adaptive mutations in a rescued Grey seal (Halichoerus grypus) pup. D701N mutation was also found in the A/harbor_seal/Massachusetts/1/2011, but not in the H10N7 outbreak, despite sustained transmission in seals for several months, nor in any other previously sequenced seal PB2 genes. 2020 Virus evolution Discussion IV D701N 0 5 PB2 207 210 32211197 Detection of H3N8 influenza A virus with multiple mammalian-adaptive mutations in a rescued Grey seal (Halichoerus grypus) pup. This likely indicates adaptation to the seal environment, a hypothesis supported by the occurrence of the D701N mutation, a known rare marker of mammalian adaptation. 2020 Virus evolution Discussion IV D701N 106 111 32231159 Insertion of Basic Amino Acids in the Hemagglutinin Cleavage Site of H4N2 Avian Influenza Virus (AIV)-Reduced Virus Fitness in Chickens is Restored by Reassortment with Highly Pathogenic H5N1 AIV. Another finding was that T327K was advantageous over T327R; it increased plaque size, virulence in chickens after IV injection, tropism and excretion from inoculated birds, particularly when combined with H5N1 gene segments. 2020 International journal of molecular sciences Discussion IV T327K;T327R 25;53 30;58 32231159 Insertion of Basic Amino Acids in the Hemagglutinin Cleavage Site of H4N2 Avian Influenza Virus (AIV)-Reduced Virus Fitness in Chickens is Restored by Reassortment with Highly Pathogenic H5N1 AIV. Furthermore, compared to the H4N2 virus, HPAIV H5N1 used in this study possessed residues in the NP (S377N), NS1 (deletion of AAs 80-84) and PB1 (V14A). 2020 International journal of molecular sciences Discussion IV S377N;V14A 101;146 106;150 NP;NS1;PB1 97;109;141 99;112;144 32231159 Insertion of Basic Amino Acids in the Hemagglutinin Cleavage Site of H4N2 Avian Influenza Virus (AIV)-Reduced Virus Fitness in Chickens is Restored by Reassortment with Highly Pathogenic H5N1 AIV. Intriguingly, the majority of HPAIV H5/H7 possessed lysine at position P2, resembling the T327K in this study, which may support our assumption. 2020 International journal of molecular sciences Discussion IV T327K 90 95 32231159 Insertion of Basic Amino Acids in the Hemagglutinin Cleavage Site of H4N2 Avian Influenza Virus (AIV)-Reduced Virus Fitness in Chickens is Restored by Reassortment with Highly Pathogenic H5N1 AIV. Moreover, we showed that furin-like protease(s) can also cleave the HA of H4N2_T327K in transfected HEK293T independent of the presence of HAT and TMPRSS2 that activate some viruses with monobasic CS and some H9N2 viruses with monobasic VSSR/G, dibasic RSSR/G or tribasic RSRR/G cleavage site motifs. 2020 International journal of molecular sciences Discussion IV T327K 79 84 HA 68 70 32231159 Insertion of Basic Amino Acids in the Hemagglutinin Cleavage Site of H4N2 Avian Influenza Virus (AIV)-Reduced Virus Fitness in Chickens is Restored by Reassortment with Highly Pathogenic H5N1 AIV. Remarkably, the pathology of H5N1_HA4_T327R was more severe in the bursa, thymus, pancreas and brain compared to H5N1_HA4_T327K and H5N1_HA4. 2020 International journal of molecular sciences Discussion IV T327R;T327K 38;122 43;127 32272772 Influenza PB1-F2 Inhibits Avian MAVS Signaling. Previously, we showed that tandem mutation of the residues T175K/T176E in d2CARD allowed it to engage the appropriate residues on the CARD of human MAVS and restore filament formation and immunostimulatory activity. 2020 Viruses Discussion IV T175K;T176E 59;65 64;70 32326238 Experimental Infection Using Mouse-Adapted Influenza B Virus in a Mouse Model. One of the amino acid substitutions identified (T214I in HA) is localized in the antigenically active subunit HA-HA1, thereby affecting the biological properties of the virus. 2020 Viruses Discussion IV T214I 48 53 HA;HA;HA1 57;110;113 59;112;116 32415096 mRNA display with library of even-distribution reveals cellular interactors of influenza virus NS1. Functionally, the D92Y mutant fails to recruit the CPSF complex and therefore fails to block host mRNA synthesis and induction of the IFN responsive genes. 2020 Nature communications Discussion IV D92Y 18 22 32415096 mRNA display with library of even-distribution reveals cellular interactors of influenza virus NS1. Using md-LED, we found that the IFN-inducing D92Y mutation results in a loss of NS1 interaction with CPSF1. 2020 Nature communications Discussion IV D92Y 45 49 NS1 80 83 32433222 Baloxavir Marboxil 2% Granules in Japanese Children With Influenza: An Open-label Phase 3 Study. Age-based analyses showed that young children with PA/I38X-substituted virus had longer TTIA and some also had co-infections with other viruses (Figure, Supplemental Digital Content 8, http://links.lww.com/INF/D975), which were also observed in the miniSTONE-2 study. 2020 The Pediatric infectious disease journal Discussion IV I38X 54 58 PA 51 53 32433222 Baloxavir Marboxil 2% Granules in Japanese Children With Influenza: An Open-label Phase 3 Study. In children with fever resolution before day 4, fever recurrence was observed in approximately 60% of children with PA/I38X-substituted virus or influenza B after day 4, although fever resolved again during the 14-day observation period (Figure, Supplemental Digital Content 7B, http://links.lww.com/INF/D974). 2020 The Pediatric infectious disease journal Discussion IV I38X 119 123 PA 116 118 32433222 Baloxavir Marboxil 2% Granules in Japanese Children With Influenza: An Open-label Phase 3 Study. In the current study, 5 children (19.2% of 26 children with paired sequence data available) were identified as having PA/I38X-substituted virus. 2020 The Pediatric infectious disease journal Discussion IV I38X 121 125 PA 118 120 32433222 Baloxavir Marboxil 2% Granules in Japanese Children With Influenza: An Open-label Phase 3 Study. Increases in infectious virus were observed in most children with A(H3N2), particularly those with PA/I38X-substituted virus, and B infections. 2020 The Pediatric infectious disease journal Discussion IV I38X 102 106 PA 99 101 32433222 Baloxavir Marboxil 2% Granules in Japanese Children With Influenza: An Open-label Phase 3 Study. No influenza-related complication was observed in those children with PA/I38X-substituted virus, all of whom recovered without any additional influenza medication. 2020 The Pediatric infectious disease journal Discussion IV I38X 73 77 PA 70 72 32433222 Baloxavir Marboxil 2% Granules in Japanese Children With Influenza: An Open-label Phase 3 Study. Our analyses suggest a potential association between the immature immune status of children and co-infection, fever recurrence, symptoms, or PA/I38X-substituted virus emergence. 2020 The Pediatric infectious disease journal Discussion IV I38X 144 148 PA 141 143 32433222 Baloxavir Marboxil 2% Granules in Japanese Children With Influenza: An Open-label Phase 3 Study. The higher rate of PA/I38X-substituted virus emergence in this study appears to be associated, in part, with low hemagglutination inhibition antibody titer in children (Table, Supplemental Digital Content 5, http://links.lww.com/INF/D972). 2020 The Pediatric infectious disease journal Discussion IV I38X 22 26 PA 19 21 32433222 Baloxavir Marboxil 2% Granules in Japanese Children With Influenza: An Open-label Phase 3 Study. The PA/I38X-substituted A(H3N2) was 4 of 9 children with paired sequence data available, which was more frequent than that in the previous pediatric study (age <12 years). 2020 The Pediatric infectious disease journal Discussion IV I38X 7 11 PA 4 6 32433222 Baloxavir Marboxil 2% Granules in Japanese Children With Influenza: An Open-label Phase 3 Study. The previous pediatric study reported that children with PA/I38X-substituted viruses showed transient increases and prolongation of infectious virus detection. 2020 The Pediatric infectious disease journal Discussion IV I38X 60 64 PA 57 59 32433222 Baloxavir Marboxil 2% Granules in Japanese Children With Influenza: An Open-label Phase 3 Study. Treatment-emergent PA/I38X-substituted viruses with reduced susceptibility to baloxavir were detected in the previous adult and pediatric phase 3 studies. 2020 The Pediatric infectious disease journal Discussion IV I38X 22 26 PA 19 21 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. A(H1N1)pdm09 HA1 D222G/N/S or Q293H substitutions have been associated with cases of severe disease and fatalities earlier in the pandemic period. 2020 Journal of medical microbiology Discussion IV D222G;D222N;D222S;Q293H 17;17;17;30 26;26;26;35 HA1 13 16 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. D222G/N polymorphism has been reported in recently circulating viruses and two of the recent Bulgarian viruses (A/Bulgaria/013/2019 and A/Bulgaria/043/2019) carried D222N substitution. 2020 Journal of medical microbiology Discussion IV D222G;D222N;D222N 0;0;165 7;7;170 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. However, recent subclade 6B.1A A(H1N1)pdm09 viruses with HA S183P substitution [58 % of the sequenced Bulgarian A(H1N1)pdm09 viruses] were antigenically distinguishable from the vaccine virus by panels of post-vaccination human sera, and this resulted in the choice of A/Brisbane/02/2018 as a vaccine component for the Northern Hemisphere 2019/2020 influenza season. 2020 Journal of medical microbiology Discussion IV S183P 60 65 HA 57 59 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. Of the A(H3N2) HA amino acid substitutions seven at positions in HA1 were located within antigenic sites A, B (T160K substitution associated with egg-adaptation), C and E, and these changes could potentially alter the antigenicity of the HA. 2020 Journal of medical microbiology Discussion IV T160K 111 116 HA;HA;HA1 15;238;65 17;240;68 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. showed that N449D is one of three NA substitutions resulting in loss of reactivity with some human monoclonal antibodies. 2020 Journal of medical microbiology Discussion IV N449D 12 17 34 36 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. The D222G substitution was shown to cause a shift from alpha2,6-sialic acid receptor specificity to mixed alpha2,3/alpha2,6-sialic acid receptor specificity, adduced thereby to facilitate lung infection. 2020 Journal of medical microbiology Discussion IV D222G 4 9 32459617 Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. V263I in NA and K196E in NS1, associated with increased clinical severity in some reports, were not identified in Bulgarian isolates. 2020 Journal of medical microbiology Discussion IV V263I;K196E 0;16 5;21 NA;NS1 9;25 11;28 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. After annotating the H9 molecular crystal, we determined that K131R, A168T, A198V, N201D, and Q234L are located near the head area of HA. 2020 AMB Express Discussion IV K131R;A168T;A198V;N201D;Q234L 62;69;76;83;94 67;74;81;88;99 HA 134 136 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. In viruses passaged 5 times, although the A198V mutation could be stably passed down to subsequent generations, such cases still appeared; for example, in 1VL, 2VL, 4VL and 5VL, the A198V mutation was obvious, but amino acid 198 in 3VL virus was not mutated. 2020 AMB Express Discussion IV A198V;A198V 42;182 47;187 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. It should be mentioned that after serial passaging in the host chicken, the Q234L mutation of the HA gene (H3 No. 2020 AMB Express Discussion IV Q234L 76 81 HA 98 100 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. Mutation on the RNP complex will increase the infectivity and host range of influenza viruses, such as 588V, E627K, G685R and D701N on PB2 (Song et al.; Wei and Liu; Xiao et al.; Zhang et al.). 2020 AMB Express Discussion IV E627K;G685R;D701N 109;116;126 114;121;131 PB2;RNP 135;16 138;19 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. On PB2 of the viruses obtained without selection pressure of vaccine antibodies, there was only one amino acid mutation (R318K), and it existed on most quasispecies viruses. 2020 AMB Express Discussion IV R318K 121 126 PB2 3 6 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. PB2 can generate the specific and stable mutations R355K with R355K. 2020 AMB Express Discussion IV R355K;R355K 51;62 56;67 PB2 0 3 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. Regarding mutation of the antigen, we discovered after sequencing that there were K131R, A168T, A198V, N201D and Q234L mutation hotspots in the HA genes of progeny viruses with selection pressure of vaccine antibodies and there were E114K, M224K, A198V, Q234L, L281F and N285D mutation hotspots in the HA genes of progeny viruses without selection pressure of vaccine antibodies. 2020 AMB Express Discussion IV K131R;A168T;A198V;N201D;Q234L;E114K;M224K;A198V;Q234L;L281F;N285D 82;89;96;103;113;233;240;247;254;261;271 87;94;101;108;118;238;245;252;259;266;276 HA;HA 144;302 146;304 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. There was no mutation on NP with selection pressure of vaccine antibodies, while there were two high-frequency mutations on NP without selection pressure of vaccine antibodies, namely, V186I (19/19) and L466I (9/19). 2020 AMB Express Discussion IV V186I;L466I 185;203 190;208 NP;NP 25;124 27;126 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. There were 4 mutations on NS for progeny viruses isolated after serial passaging without selection pressure of vaccine antibodies, and L77I existed on all the progeny viruses. 2020 AMB Express Discussion IV L77I 135 139 NS 26 28 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. There were two mutation hotspots, R318K and R355K, in the PB2 gene of quasispecies viruses obtained with selection pressure of vaccine antibodies. 2020 AMB Express Discussion IV R318K;R355K 34;44 39;49 PB2 58 61 32462233 Effect of the selection pressure of vaccine antibodies on evolution of H9N2 avian influenza virus in chickens. This result indicates that the selection pressure of vaccine antibodies makes the F/98 strain generate specific HA gene mutations, namely, K131, A168T and N201D. 2020 AMB Express Discussion IV A168T;N201D 145;155 150;160 HA 112 114 32483655 Genetic and antigenic characterization of influenza A/H5N1 viruses isolated from patients in Indonesia, 2008-2015. Although some genetic diversity was observed in the polymerase genes, well-known substitutions such as PB2-E627K and PB2-D701N, which are often selected upon infection of humans and affects the virulence of avian influenza viruses such as H5N1, were not commonly found in the new samples. 2020 Virus genes Discussion IV E627K;D701N 107;121 112;126 PB2;PB2 103;117 106;120 32599753 Virtual Screening Identifies Chebulagic Acid as an Inhibitor of the M2(S31N) Viral Ion Channel and Influenza A Virus. Although it is formally possible that this observation is due to the ability of chebulagic acid to restore yeast growth by a mechanism other than M2, this appears unlikely as growth restoration was observed by 25 microg/mL chebulagic acid only in the presence of M2(S31N) and not M2(S31). 2020 Molecules (Basel, Switzerland) Discussion IV S31N 266 270 M2;M2;M2 146;263;280 148;265;282 32599753 Virtual Screening Identifies Chebulagic Acid as an Inhibitor of the M2(S31N) Viral Ion Channel and Influenza A Virus. Here we describe a VS-based approach to identify natural product-derived pure compounds which structurally resemble known M2(S31N) inhibitors. 2020 Molecules (Basel, Switzerland) Discussion IV S31N 125 129 M2 122 124 32599753 Virtual Screening Identifies Chebulagic Acid as an Inhibitor of the M2(S31N) Viral Ion Channel and Influenza A Virus. However, using an established yeast growth restoration assay and molecular modelling, we show that chebulagic acid, or at least its hydrolysis fragments, also interfere with M2(S31N). 2020 Molecules (Basel, Switzerland) Discussion IV S31N 177 181 M2 174 176 32599753 Virtual Screening Identifies Chebulagic Acid as an Inhibitor of the M2(S31N) Viral Ion Channel and Influenza A Virus. In cell culture, chebulagic acid also restores the growth of M2(S31N)-expressing yeast cells and inhibits virus replication. 2020 Molecules (Basel, Switzerland) Discussion IV S31N 64 68 M2 61 63 32599753 Virtual Screening Identifies Chebulagic Acid as an Inhibitor of the M2(S31N) Viral Ion Channel and Influenza A Virus. Taken together, chebulagic acid is likely to inhibit influenza A virus by targeting multiple mechanisms including M2(S31N) and also serves as a chemical starting point for the development of potential M2(S31N) inhibitors, which are structurally distinct from existing agents. 2020 Molecules (Basel, Switzerland) Discussion IV S31N;S31N 117;204 121;208 M2;M2 114;201 116;203 32599753 Virtual Screening Identifies Chebulagic Acid as an Inhibitor of the M2(S31N) Viral Ion Channel and Influenza A Virus. We also observed similar inhibition of virus strains containing either M2(S31N) or M2(S31), which further supports that chebulagic acid is likely to act on one or more additional viral or host targets independent of M2. 2020 Molecules (Basel, Switzerland) Discussion IV S31N 74 78 M2;M2;M2 71;83;216 73;85;218 32601336 Pre-existing immunity to influenza virus hemagglutinin stalk might drive selection for antibody-escape mutant viruses in a human challenge model. Although our study suggests that V388 mutation would be substantially more resistant to multiple potent bNAbs, or to currently existing human serum antibodies in general, the neutralization efficacy of FI6V3 antibody was not affected by the A388V mutation. 2020 Nature medicine Discussion IV A388V 241 246 32601336 Pre-existing immunity to influenza virus hemagglutinin stalk might drive selection for antibody-escape mutant viruses in a human challenge model. For example, only five of approximately 25,000 human H1N1pdm HA sequences reported in the Influenza Research Database (https://www.fludb.org) carry the A388V mutation. 2020 Nature medicine Discussion IV A388V 152 157 HA 61 63 32601336 Pre-existing immunity to influenza virus hemagglutinin stalk might drive selection for antibody-escape mutant viruses in a human challenge model. further investigated the escape potential of the A388V mutation. 2020 Nature medicine Discussion IV A388V 49 54 32601336 Pre-existing immunity to influenza virus hemagglutinin stalk might drive selection for antibody-escape mutant viruses in a human challenge model. However, these surveillance data suggest that stalk escape mutations such as A388V do arise spontaneously in nature. 2020 Nature medicine Discussion IV A388V 77 82 32601336 Pre-existing immunity to influenza virus hemagglutinin stalk might drive selection for antibody-escape mutant viruses in a human challenge model. In the same study, an escape V41I mutant was generated under immune pressure by human serum without losing viral fitness, suggesting that influenza viruses are capable of escaping polyclonal immune pressure targeting the conserved HA stalk region. 2020 Nature medicine Discussion IV V41I 29 33 HA 231 233 32601336 Pre-existing immunity to influenza virus hemagglutinin stalk might drive selection for antibody-escape mutant viruses in a human challenge model. Interestingly, both A388V and V41I mutations are also consistent with this hypothesis as they did not reduce, or only minimally reduced, viral fitness and had a less than ten-fold effect on neutralization. 2020 Nature medicine Discussion IV A388V;V41I 20;30 25;34 32601336 Pre-existing immunity to influenza virus hemagglutinin stalk might drive selection for antibody-escape mutant viruses in a human challenge model. Moreover, human serum placed 'biased, rather than broad, immune pressures that rapidly expanded the A388V mutant in vitro. 2020 Nature medicine Discussion IV A388V 100 105 32601336 Pre-existing immunity to influenza virus hemagglutinin stalk might drive selection for antibody-escape mutant viruses in a human challenge model. Our study, however, demonstrated minimal to no loss of replicative fitness associated with the A388V escape mutation in vitro, in vivo and in humans. 2020 Nature medicine Discussion IV A388V 95 100 32601336 Pre-existing immunity to influenza virus hemagglutinin stalk might drive selection for antibody-escape mutant viruses in a human challenge model. The A388V mutation might cause subtle loss in viral fitness in humans that is below the threshold of detection in our small study and/or cause reduced transmissibility. 2020 Nature medicine Discussion IV A388V 4 9 32601336 Pre-existing immunity to influenza virus hemagglutinin stalk might drive selection for antibody-escape mutant viruses in a human challenge model. The A388V stalk mutation of the 2009 H1N1pdm virus was first reported by Tan et al. 2020 Nature medicine Discussion IV A388V 4 9 32629810 Replication of a Dog-Origin H6N1 Influenza Virus in Cell Culture and Mice. Both E01EE and E01GK in this study harbored the HA G228S substitution and NS1 PL with EPEV residues, which might account for their infectivity in mice. 2020 Viruses Discussion IV G228S 51 56 HA;NS1 48;74 50;77 32629810 Replication of a Dog-Origin H6N1 Influenza Virus in Cell Culture and Mice. Both the human and dog H6N1 viruses were of avian origin and had HA G228S substitution, which might be a factor enabling the viral infection in mammals. 2020 Viruses Discussion IV G228S 68 73 HA 65 67 32629810 Replication of a Dog-Origin H6N1 Influenza Virus in Cell Culture and Mice. H6N1 viruses with HA G228S substitution have become predominant in poultry after 2005. 2020 Viruses Discussion IV G228S 21 26 HA 18 20 32629810 Replication of a Dog-Origin H6N1 Influenza Virus in Cell Culture and Mice. However, based on the molecular biology evidence, we conclude that the adaptation might have occurred since the virus possessed PB2 E627K mutation besides HA G228S substitution. 2020 Viruses Discussion IV E627K;G228S 132;158 137;163 HA;PB2 155;128 157;131 32629810 Replication of a Dog-Origin H6N1 Influenza Virus in Cell Culture and Mice. It suggests that PB2 K627E mutation resulted from an adaptation of the virus to the avian host. 2020 Viruses Discussion IV K627E 21 26 PB2 17 20 32629810 Replication of a Dog-Origin H6N1 Influenza Virus in Cell Culture and Mice. Moreover, the PB2 E627K mutation was a key residue of the viral pathogenicity. 2020 Viruses Discussion IV E627K 18 23 PB2 14 17 32629810 Replication of a Dog-Origin H6N1 Influenza Virus in Cell Culture and Mice. Some chicken H6N1 viruses in Taiwan have acquired a G228S substitution in viral HA protein since 2000. 2020 Viruses Discussion IV G228S 52 57 HA 80 82 32629810 Replication of a Dog-Origin H6N1 Influenza Virus in Cell Culture and Mice. The HA G228S substitution was considered to contribute to HA protein specificity for the human SAalpha2-6Gal receptors. 2020 Viruses Discussion IV G228S 7 12 HA;HA 4;58 6;60 32629810 Replication of a Dog-Origin H6N1 Influenza Virus in Cell Culture and Mice. The PB2 E627K substitution could contribute viral replication ability in hosts and was regarded the best characterized mammalian adaptation. 2020 Viruses Discussion IV E627K 8 13 PB2 4 7 32629810 Replication of a Dog-Origin H6N1 Influenza Virus in Cell Culture and Mice. Whether the PB1 E739G mutation also arose from the virus adaptation to the mammalian host needs more studies to clarify. 2020 Viruses Discussion IV E739G 16 21 PB1 12 15 32631240 Successful treatment with baloxavir marboxil of a patient with peramivir-resistant influenza A/H3N2 with a dual E119D/R292K substitution after allogeneic hematopoietic cell transplantation: a case report. Each one oseltamivir and peramivir cross-resistant A/H3N2 virus with the R292K mutation was detected in the 2010-11, 2011-12, and 2014-2015 seasons, respectively. 2020 BMC infectious diseases Discussion IV R292K 73 78 32631240 Successful treatment with baloxavir marboxil of a patient with peramivir-resistant influenza A/H3N2 with a dual E119D/R292K substitution after allogeneic hematopoietic cell transplantation: a case report. Here, we demonstrated the first case of successful treatment using baloxavir for the dual E119D/R292K NA-mutated peramivir-resistant influenza A/H3N2 in a highly immunocompromised patient. 2020 BMC infectious diseases Discussion IV E119D;R292K 90;96 95;101 102 104 32631240 Successful treatment with baloxavir marboxil of a patient with peramivir-resistant influenza A/H3N2 with a dual E119D/R292K substitution after allogeneic hematopoietic cell transplantation: a case report. In the global surveillance, the frequency of viruses with reduced susceptibility to one or more NA inhibitors has remained low (2012-13: 0.6%; 2013-14: 1.9%; 2014-15: 0.5%; 2015-16: 0.8%; 2016-17: 0.2%), while oseltamivir and peramivir cross-resistant A/H1N1pdm09 viruses with an NA H275Y substitution were the most frequently observed. 2020 BMC infectious diseases Discussion IV H275Y 283 288 NA;NA 96;280 98;282 32631240 Successful treatment with baloxavir marboxil of a patient with peramivir-resistant influenza A/H3N2 with a dual E119D/R292K substitution after allogeneic hematopoietic cell transplantation: a case report. In the present case, a dual E119D/R292K mutant influenza A/H3N2 was found. 2020 BMC infectious diseases Discussion IV E119D;R292K 28;34 33;39 32631240 Successful treatment with baloxavir marboxil of a patient with peramivir-resistant influenza A/H3N2 with a dual E119D/R292K substitution after allogeneic hematopoietic cell transplantation: a case report. On the basis of these observations, the dual E119D/R292K mutation in A/H3N2 could have contributed to reduced susceptibility to oseltamivir, peramivir, and zanamivir. 2020 BMC infectious diseases Discussion IV E119D;R292K 45;51 50;56 32631240 Successful treatment with baloxavir marboxil of a patient with peramivir-resistant influenza A/H3N2 with a dual E119D/R292K substitution after allogeneic hematopoietic cell transplantation: a case report. reported that the E119D mutation in A/H3N2 showed reduced susceptibility to zanamivir, although it has not been detected after zanamivir treatment in vivo. 2020 BMC infectious diseases Discussion IV E119D 18 23 32631240 Successful treatment with baloxavir marboxil of a patient with peramivir-resistant influenza A/H3N2 with a dual E119D/R292K substitution after allogeneic hematopoietic cell transplantation: a case report. The patient developed seasonal influenza A/H3N2 infection while in a highly immunocompromised state post-transplant-relapsed leukemia; treatment with 1-day oseltamivir and switched to 15-day peramivir were unable to improve the respiratory symptoms and influenza viral shedding possibly due to peramivir resistance caused by the dual E119D/R292K NA mutation. 2020 BMC infectious diseases Discussion IV E119D;R292K 334;340 339;345 346 348 Leukemia;Influenza A virus H3N2 infection 125;31 133;57 32631240 Successful treatment with baloxavir marboxil of a patient with peramivir-resistant influenza A/H3N2 with a dual E119D/R292K substitution after allogeneic hematopoietic cell transplantation: a case report. The R292K mutation in A/H3N2 was detected in immunocompromised patients after oseltamivir and/or peramivir treatment. 2020 BMC infectious diseases Discussion IV R292K 4 9 32631240 Successful treatment with baloxavir marboxil of a patient with peramivir-resistant influenza A/H3N2 with a dual E119D/R292K substitution after allogeneic hematopoietic cell transplantation: a case report. These R292K mutant viruses showed highly reduced inhibition by oseltamivir and peramivir and reduced inhibition by zanamivir, but susceptible to laninamivir. 2020 BMC infectious diseases Discussion IV R292K 6 11 32631440 Characterization of neuraminidase inhibitor-resistant influenza virus isolates from immunocompromised patients in the Republic of Korea. Although NAI-resistant virus has been rarely observed since 2000, the KCDC, through the KINRESS, identified oseltamivir and peramivir-resistant A(H1N1)pdm09 viruses harboring the H275Y NA variation in patients with acute lymphoblastic leukemia and relapsed lymphoma hospitalized in the same general hospital, with both exhibiting prolonged virus excretion. 2020 Virology journal Discussion IV H275Y 179 184 NA;NAI 185;9 187;12 Acute lymphoblastic leukemia;Relapsed lymphoma 215;248 243;265 32631440 Characterization of neuraminidase inhibitor-resistant influenza virus isolates from immunocompromised patients in the Republic of Korea. Although the HA N158D substitution increases the binding affinity of H5N1 avian influenza virus and human receptor (alpha2-6-linked sialoside), the function of the A/Korea/S0002/2019 HA A158E substitution functionality remains unknown (but it was not involved in antigenicity in this study). 2020 Virology journal Discussion IV N158D;A158E 16;186 21;191 HA;HA 13;183 15;185 32631440 Characterization of neuraminidase inhibitor-resistant influenza virus isolates from immunocompromised patients in the Republic of Korea. demonstrated that A(H1N1)pdm09 virus-infected immunocompromised ferrets exhibited prolonged virus replication despite antiviral therapy, along with the H275Y substitution observed in the virus population from day 8 onwards only in ferrets that received oseltamivir. 2020 Virology journal Discussion IV H275Y 152 157 32631440 Characterization of neuraminidase inhibitor-resistant influenza virus isolates from immunocompromised patients in the Republic of Korea. The NAI-resistant A(H1N1) virus harboring the NA gene H275Y variation was first identified in 2007, and was frequently identified worldwide in 2008-2009. 2020 Virology journal Discussion IV H275Y 54 59 NA;NAI 46;4 48;7 32631440 Characterization of neuraminidase inhibitor-resistant influenza virus isolates from immunocompromised patients in the Republic of Korea. These results suggest that the H275Y substitution emerges rapidly in immunocompromised hosts under continuous antiviral selective pressure. 2020 Virology journal Discussion IV H275Y 31 36 32636820 Enhanced Potency of a Broad H7N9-Neutralizing Antibody HNIgGA6 Through Structure-Based Design. Although, the differences in survival rate were slightly between S28H- and HNIgGA6-treated mice, these results together demonstrated enhanced in vivo potency of the optimized S28H mutant. 2020 Frontiers in microbiology Discussion IV S28H;S28H 65;175 69;179 32636820 Enhanced Potency of a Broad H7N9-Neutralizing Antibody HNIgGA6 Through Structure-Based Design. As seen in Figure 4, with the S28H mutation on the light chain, the variant showed enhanced potency in inhibiting pulmonary virus proliferation and lung lesions compared to the parent HNIgGA6. 2020 Frontiers in microbiology Discussion IV S28H 30 34 Lung lesions 148 160 32636820 Enhanced Potency of a Broad H7N9-Neutralizing Antibody HNIgGA6 Through Structure-Based Design. HNIgGA6 and its derivative S28H mutant were originally isolated from H7N9-infected patients and broadly neutralized divergent H7N9 strains from 2013 to 2017. 2020 Frontiers in microbiology Discussion IV S28H 27 31 32636820 Enhanced Potency of a Broad H7N9-Neutralizing Antibody HNIgGA6 Through Structure-Based Design. In HCDR3, both D100E and Y103R mutants retained the capacity to bind to mAb HNIgGA6, suggesting that it might be difficult to alter the amino acid identity in HCDR3 to achieve greater affinity (Figure 2B). 2020 Frontiers in microbiology Discussion IV D100E;Y103R 15;25 20;30 32636820 Enhanced Potency of a Broad H7N9-Neutralizing Antibody HNIgGA6 Through Structure-Based Design. More importantly, the amino acid substitution at S28H improved potency without disturbing the neutralization breath of HNIgGA6. 2020 Frontiers in microbiology Discussion IV S28H 49 53 32636820 Enhanced Potency of a Broad H7N9-Neutralizing Antibody HNIgGA6 Through Structure-Based Design. Strikingly, when serine was mutated to histidine at position 28 on LCDR1, the antibody exhibited an ~three-fold higher HA-binding affinity and a 10-fold increase in virus neutralizing activity compared to the wild-type (Figures 2B, 3A). 2020 Frontiers in microbiology Discussion IV S28H 17 63 HA 119 121 32636820 Enhanced Potency of a Broad H7N9-Neutralizing Antibody HNIgGA6 Through Structure-Based Design. The S28H mutation created a hydrophobic environment for residues G144 and S145 of HA and stabilized the 130-loop conformation, which might affect its subsequent affinity to HNIgGA6. 2020 Frontiers in microbiology Discussion IV S28H 4 8 HA 82 84 32636820 Enhanced Potency of a Broad H7N9-Neutralizing Antibody HNIgGA6 Through Structure-Based Design. The S28H variant was generated, and successfully increased the in vitro HA-binding affinity and correlated with substantially increased neutralization potency in vivo. 2020 Frontiers in microbiology Discussion IV S28H 4 8 HA 72 74 32636820 Enhanced Potency of a Broad H7N9-Neutralizing Antibody HNIgGA6 Through Structure-Based Design. To investigate in vivo neutralization efficacy, the S28H variant was further tested by using BALB/c mice models. 2020 Frontiers in microbiology Discussion IV S28H 52 56 32636820 Enhanced Potency of a Broad H7N9-Neutralizing Antibody HNIgGA6 Through Structure-Based Design. When tyrosine was mutated to arginine at position 51 in HCDR2, it bound viral HA with an affinity of 2.25e-11 M, similar to that of the wild-type HNIgGA6. 2020 Frontiers in microbiology Discussion IV Y51R 5 52 HA 78 80 32677963 Influenza A virus NS1 optimises virus infectivity by enhancing genome packaging in a dsRNA-binding dependent manner. Moreover, NS1 R38A mutant impairs VLP genome packaging. 2020 Virology journal Discussion IV R38A 14 18 NS1 10 13 32677963 Influenza A virus NS1 optimises virus infectivity by enhancing genome packaging in a dsRNA-binding dependent manner. R38A mutation impaired the incorporation of NS1 into the virion and VLP. 2020 Virology journal Discussion IV R38A 0 4 NS1 44 47 32677963 Influenza A virus NS1 optimises virus infectivity by enhancing genome packaging in a dsRNA-binding dependent manner. This NS1 R38A was also unable to increase M1 and HA2 expression in infected cells. 2020 Virology journal Discussion IV R38A 9 13 HA;M1;NS1 49;42;5 51;44;8 32709116 Genetic Characterization of a Novel North American-Origin Avian Influenza A (H6N5) Virus Isolated from Bean Goose of South Korea in 2018. According to the molecular analysis of gene segments between K6 and A/aquatic bird/Korea/CN5/2009 (H6N5), the D701N mutation in PB2 may contribute to the increased virulence observed for H6N5 in the mammalian host (Table 2). 2020 Viruses Discussion IV D701N 110 115 PB2 128 131 32709116 Genetic Characterization of a Novel North American-Origin Avian Influenza A (H6N5) Virus Isolated from Bean Goose of South Korea in 2018. Additionally, K6 may increase the possibility of host jumping by providing the PB2 with A274T mutation or/and the PA gene with E382D alteration to CN5-2009 or other Korea strains reassortment (Table 2). 2020 Viruses Discussion IV A274T;E382D 88;127 93;132 PA;PB2 114;79 116;82 32709116 Genetic Characterization of a Novel North American-Origin Avian Influenza A (H6N5) Virus Isolated from Bean Goose of South Korea in 2018. However, an important G228S (H3 numbering) substitution at the receptor-binding site of HA, as well as a 14-amino acid deletion in the stalk region of NA noted in a human-infecting H6N1 strain, were not identified in the K6 or K17 isolates (Table 2). 2020 Viruses Discussion IV G228S 22 27 HA;NA 88;151 90;153 32709116 Genetic Characterization of a Novel North American-Origin Avian Influenza A (H6N5) Virus Isolated from Bean Goose of South Korea in 2018. Particularly, the PB2 and/or PA gene of the CN5-2009 strain harboring D701N and L653P substitutions, respectively, can become reassorted with other K6 genes, resulting in potentially increased virulence in mammals. 2020 Viruses Discussion IV D701N;L653P 70;80 75;85 PA;PB2 29;18 31;21 32721992 Differential Viral-Host Immune Interactions Associated with Oseltamivir-Resistant H275Y and Wild-Type H1N1 A(pdm09) Influenza Virus Pathogenicity. Despite some studies reporting a statistically significant impairment in viral growth in vitro, other groups' analysis have not identified significant differences regarding the replicative capacity between the pdm09 Wt virus and its H275Y variant. 2020 Viruses Discussion IV H275Y 233 238 32721992 Differential Viral-Host Immune Interactions Associated with Oseltamivir-Resistant H275Y and Wild-Type H1N1 A(pdm09) Influenza Virus Pathogenicity. In addition, in vitro assessment of the oseltamivir H275Y NA mutation seems to reduce viral fitness by means of viral replication when compared with the Wt F virus at the initial stages of infection, as previously described. 2020 Viruses Discussion IV H275Y 52 57 58 60 32721992 Differential Viral-Host Immune Interactions Associated with Oseltamivir-Resistant H275Y and Wild-Type H1N1 A(pdm09) Influenza Virus Pathogenicity. In general, OR pdm09 viral strains with the H275Y NA mutation are less virulent than Wt viruses. 2020 Viruses Discussion IV H275Y 44 49 50 52 32721992 Differential Viral-Host Immune Interactions Associated with Oseltamivir-Resistant H275Y and Wild-Type H1N1 A(pdm09) Influenza Virus Pathogenicity. Interestingly, it has been shown that viruses from both the Newcastle and Sapporo clusters contained permissive NA mutations V241I and N369K that enhance the replication and transmission fitness of viruses containing the H275Y mutation. 2020 Viruses Discussion IV V241I;N369K;H275Y 125;135;221 130;140;226 112 114 32721992 Differential Viral-Host Immune Interactions Associated with Oseltamivir-Resistant H275Y and Wild-Type H1N1 A(pdm09) Influenza Virus Pathogenicity. Previous studies have highlighted that a particular combination of residues in seasonal and pdm09 viruses, such as V234M or R222Q, which were not observed in earlier H1N1 viruses, resulted in an increased affinity of the NA cleavage balance. 2020 Viruses Discussion IV V234M;R222Q 115;124 120;129 221 223 32721992 Differential Viral-Host Immune Interactions Associated with Oseltamivir-Resistant H275Y and Wild-Type H1N1 A(pdm09) Influenza Virus Pathogenicity. Previously, it was reported that the Wt pdm09 virus and H275Y mutant variant induced comparable mortality rates, weight loss, and lung titers in mice. 2020 Viruses Discussion IV H275Y 56 61 32721992 Differential Viral-Host Immune Interactions Associated with Oseltamivir-Resistant H275Y and Wild-Type H1N1 A(pdm09) Influenza Virus Pathogenicity. This study investigated the viral pathogenicity of two OR pdm09 viral isolates containing the H275Y NA mutation in relation to a Wt pdm09 viral isolate and assessed the presence of distinctive viral-host immune interactions associated with viral pathogenicity in each case. 2020 Viruses Discussion IV H275Y 94 99 100 102 32746754 A single N342D substitution in Influenza B Virus NA protein determines viral pathogenicity in mice. An A390E substitution located on the HA stalk region, might play a limited role in the viral replication and pathogenicity of IAV. 2020 Emerging microbes & infections Discussion IV A390E 3 8 HA 37 39 32746754 A single N342D substitution in Influenza B Virus NA protein determines viral pathogenicity in mice. An N342D substitution in the NA protein significantly enhanced the pathogenicity of IBVs in mice. 2020 Emerging microbes & infections Discussion IV N342D 3 8 29 31 32746754 A single N342D substitution in Influenza B Virus NA protein determines viral pathogenicity in mice. For IBV, a previous study found that a single substitution from D to N at position 457 of NA destroyed the salt bridge acting as a contact surface between the monomers. 2020 Emerging microbes & infections Discussion IV D457N 64 86 90 92 32746754 A single N342D substitution in Influenza B Virus NA protein determines viral pathogenicity in mice. K110E mutation in NA significantly promoted NA enzyme activity and enhanced mice pathogenicity combined with PB2 mutations in H10N7. 2020 Emerging microbes & infections Discussion IV K110E 0 5 NA;NA;PB2 18;44;109 20;46;112 32746754 A single N342D substitution in Influenza B Virus NA protein determines viral pathogenicity in mice. Moreover, the enhanced pathogenicity contributed by the substitution N342D substitution in the NA protein may be due to the increased neuraminidase activity caused by this substitution (Figure 7(B)). 2020 Emerging microbes & infections Discussion IV N342D 69 74 NA;NA 95;134 97;147 32750468 Functional neuraminidase inhibitor resistance motifs in avian influenza A(H5Nx) viruses. In the H5N2 background the R292K mutation reduced sensitivity to all three drugs tested as determined by MUNANA assay. 2020 Antiviral research Discussion IV R292K 27 32 32750468 Functional neuraminidase inhibitor resistance motifs in avian influenza A(H5Nx) viruses. In this study we investigated whether known resistance mutations that occur in human isolated IAV strains (E119V, H274Y, R292K and N294S) function to reduce the susceptibility to NAI drugs in the highly pathogenic H5Nx viruses (H5N2, H5N6 and H5N8) that have been responsible for large scale poultry outbreaks in recent years. 2020 Antiviral research Discussion IV E119V;H274Y;R292K;N294S 107;114;121;131 112;119;126;136 NAI 179 182 32750468 Functional neuraminidase inhibitor resistance motifs in avian influenza A(H5Nx) viruses. Investigation of the two viruses carrying these mutations, Y98F (R292K NA mutant) and A189T (N294S NA mutant), showed a reduced binding to sialic acid as was reported in the literature for these mutations in H3N2 and H1N1, respectively. 2020 Antiviral research Discussion IV Y98F;R292K;A189T;N294S 59;65;86;93 63;70;91;98 NA;NA 71;99 73;101 32750468 Functional neuraminidase inhibitor resistance motifs in avian influenza A(H5Nx) viruses. Moreover, E119V and H274Y mutations in N8 displayed similar NAI susceptibility profile to the one reported in respective pH1N1 mutants - with E119V showing RI to all three NAIs, and H274Y to OSE and PER. 2020 Antiviral research Discussion IV E119V;H274Y;E119V;H274Y 10;20;142;182 15;25;147;187 NAI;NAI 60;172 63;176 32750468 Functional neuraminidase inhibitor resistance motifs in avian influenza A(H5Nx) viruses. Prior to the 2009 pandemic the seasonal H1N1 human virus that was circulating contained a H274Y mutation in the NA gene that conferred reduced susceptibility to OSE. 2020 Antiviral research Discussion IV H274Y 90 95 112 114 32750468 Functional neuraminidase inhibitor resistance motifs in avian influenza A(H5Nx) viruses. Some mutations such as E119D/Q, H274Y/R or N294S, albeit rare in avian isolated H5Nx viruses, were found to have naturally arisen (Table 1) and we would predict that the strains we identified in the database of the H5N6 and H5N8 subtype with an alternative E119 residue in the NA coding region and the H5N6 H274Y mutation would result in these viruses having functionally reduced susceptibility to OSE. 2020 Antiviral research Discussion IV E119D;E119Q;H274Y;H274R;N294S;H274Y 23;23;32;32;43;307 30;30;39;39;48;312 277 279 32750468 Functional neuraminidase inhibitor resistance motifs in avian influenza A(H5Nx) viruses. The caveat with this being that the R292K mutation reduced the NA activity to such low levels that for the H5N6 and H5N8 viruses we were unable to read reliable fluorescence signals and thus determine the sensitivity level to tested compounds. 2020 Antiviral research Discussion IV R292K 36 41 63 65 32750468 Functional neuraminidase inhibitor resistance motifs in avian influenza A(H5Nx) viruses. The four mutations: E119V, H274Y, R292K and N294S did therefore confer variable reduced drug susceptibility to the NA proteins of highly pathogenic H5N2, H5N6 and H5N8. 2020 Antiviral research Discussion IV E119V;H274Y;R292K;N294S 20;27;34;44 25;32;39;49 115 117 32750468 Functional neuraminidase inhibitor resistance motifs in avian influenza A(H5Nx) viruses. The H274Y mutation alone resulted in reduced viral fitness but additional NA mutations that occurred concurrently enabled this mutation to be supported as they increased the NA activity of the viruses. 2020 Antiviral research Discussion IV H274Y 4 9 NA;NA 74;174 76;176 32750468 Functional neuraminidase inhibitor resistance motifs in avian influenza A(H5Nx) viruses. The H274Y mutation in all three H5Nx virus backgrounds did not demonstrate any reduction in inhibition for ZAN. 2020 Antiviral research Discussion IV H274Y 4 9 32750468 Functional neuraminidase inhibitor resistance motifs in avian influenza A(H5Nx) viruses. The largest effect of the H274Y mutation on susceptibility to OSE and PER was observed with the N8 NA, the only group 1 NA in our panel which agrees with the published literature that the H274Y mutation causes reduced inhibition against OSE and PER for group 1 NAs. 2020 Antiviral research Discussion IV H274Y;H274Y 26;188 31;193 NA;NA;NA 99;120;261 101;122;264 32750468 Functional neuraminidase inhibitor resistance motifs in avian influenza A(H5Nx) viruses. The R292K mutation alters one of the three residues in the active site of the NA enzyme responsible for direct binding to the sialic acid substrate and sialic acid analogue compounds. 2020 Antiviral research Discussion IV R292K 4 9 78 80 32750468 Functional neuraminidase inhibitor resistance motifs in avian influenza A(H5Nx) viruses. Today a high proportion of the circulating avian influenza viruses possess mutations such as L26I or S31N, which confer resistance to amantadine. 2020 Antiviral research Discussion IV L26I;S31N 93;101 97;105 32750468 Functional neuraminidase inhibitor resistance motifs in avian influenza A(H5Nx) viruses. We observed that the E119V mutation reduced the inhibition to OSE for all three H5Nx virus strains. 2020 Antiviral research Discussion IV E119V 21 26 32873642 Dynamic PB2-E627K substitution of influenza H7N9 virus indicates the in vivo genetic tuning and rapid host adaptation. Amino acid changes revealed amino acid substitutions also located in HA (H3 numbering: R220G, L226S, and G279R) in addition to PB2-E627K. 2020 Proc Natl Acad Sci U S A Discussion IV R220G;L226S;G279R;E627K 87;94;105;131 92;99;110;136 HA;PB2 69;127 71;130 32873642 Dynamic PB2-E627K substitution of influenza H7N9 virus indicates the in vivo genetic tuning and rapid host adaptation. An increase in charged surface residues, such as E627K, during host adaptation may increase the rate of association of PB2 to importins. 2020 Proc Natl Acad Sci U S A Discussion IV E627K 49 54 PB2 119 122 32873642 Dynamic PB2-E627K substitution of influenza H7N9 virus indicates the in vivo genetic tuning and rapid host adaptation. D701N appears to enhance the binding of PB2 to importin and to correspondingly increase PB2 levels in the nucleus in mammalian cells, but not avian cells. 2020 Proc Natl Acad Sci U S A Discussion IV D701N 0 5 PB2;PB2 40;88 43;91 32873642 Dynamic PB2-E627K substitution of influenza H7N9 virus indicates the in vivo genetic tuning and rapid host adaptation. E627V is reportedly associated with H5N1 adaptation in MDCK cells and can also enhance H9N2 polymerase activity in human cells and mouse virulence. 2020 Proc Natl Acad Sci U S A Discussion IV E627V 0 5 32873642 Dynamic PB2-E627K substitution of influenza H7N9 virus indicates the in vivo genetic tuning and rapid host adaptation. Furthermore, PB2-K526R is found in human isolates of H7N9 (84%), H5N1 (74%), and H3N2 (99.7%). 2020 Proc Natl Acad Sci U S A Discussion IV K526R 17 22 PB2 13 16 32873642 Dynamic PB2-E627K substitution of influenza H7N9 virus indicates the in vivo genetic tuning and rapid host adaptation. In addition to E627K and D701N, previous studies also identified a series of other mammalian adaptation substitutions (e.g., Q591K on the basic surface PB2 of influenza virus) that may have compensatory functions in the activity of polymerase complexes of influenza viruses. 2020 Proc Natl Acad Sci U S A Discussion IV E627K;D701N;Q591K 15;25;125 20;30;130 PB2 152 155 32873642 Dynamic PB2-E627K substitution of influenza H7N9 virus indicates the in vivo genetic tuning and rapid host adaptation. In contrast, K526R/E627K multiple mutations occurred in the field and had strong orchestral effects on mammalian adaptation of H7N9 and H9N2 viruses. 2020 Proc Natl Acad Sci U S A Discussion IV K526R;E627K 13;19 18;24 32873642 Dynamic PB2-E627K substitution of influenza H7N9 virus indicates the in vivo genetic tuning and rapid host adaptation. PB2-K526R has been shown to interact with nuclear export protein, which enhances virus replication, particularly in combination with 627K. 2020 Proc Natl Acad Sci U S A Discussion IV K526R 4 9 NEP;PB2 42;0 64;3 32873642 Dynamic PB2-E627K substitution of influenza H7N9 virus indicates the in vivo genetic tuning and rapid host adaptation. Previous studies have implied distinct roles of D701N and K526R when combined with E627K. 2020 Proc Natl Acad Sci U S A Discussion IV D701N;K526R;E627K 48;58;83 53;63;88 32873642 Dynamic PB2-E627K substitution of influenza H7N9 virus indicates the in vivo genetic tuning and rapid host adaptation. reported multiple mutations of E627K/D701N in ferrets infected with H7N9 viruses, D701N has not been detected together with PB2-E627K among field AIV strains with a few exceptions, implying little synergistic effect with PB2-E627K. 2020 Proc Natl Acad Sci U S A Discussion IV D701N;E627K;D701N;E627K;E627K 37;31;82;128;225 42;36;87;133;230 PB2;PB2 124;221 127;224 32873642 Dynamic PB2-E627K substitution of influenza H7N9 virus indicates the in vivo genetic tuning and rapid host adaptation. showed that PB2-E627V/E543D/A655V/K526R mutations act cooperatively to produce the high polymerase activity of PB2 and efficient replication of the H9N2 virus in human cells and to increase replication and pathogenicity in mice in vivo. 2020 Proc Natl Acad Sci U S A Discussion IV E627V;E543D;A655V;K526R 16;22;28;34 21;27;33;39 PB2;PB2 12;111 15;114 32873642 Dynamic PB2-E627K substitution of influenza H7N9 virus indicates the in vivo genetic tuning and rapid host adaptation. The adaptation of D701N during the natural infection of H7N9 in humans may be less essential for virus replication. 2020 Proc Natl Acad Sci U S A Discussion IV D701N 18 23 32873642 Dynamic PB2-E627K substitution of influenza H7N9 virus indicates the in vivo genetic tuning and rapid host adaptation. The adaptation patterns of E627K coupled with substitutions in these positions and their association with the outcome of the patients require further exploration. 2020 Proc Natl Acad Sci U S A Discussion IV E627K 27 32 32873642 Dynamic PB2-E627K substitution of influenza H7N9 virus indicates the in vivo genetic tuning and rapid host adaptation. The D701N adaptation could readily occur during transmission of the virus among ferrets. 2020 Proc Natl Acad Sci U S A Discussion IV D701N 4 9 32873642 Dynamic PB2-E627K substitution of influenza H7N9 virus indicates the in vivo genetic tuning and rapid host adaptation. We found a linked and simultaneous adaptation of 701E with 627V in the PB2 of H7N9 viruses from seven patients in Shenzhen, possibly indicating that D701E coemerges on the same alleles carrying E627V in the virus quasi-species. 2020 Proc Natl Acad Sci U S A Discussion IV D701E;E627V 149;194 154;199 PB2 71 74 32929001 RNA-seq accuracy and reproducibility for the mapping and quantification of influenza defective viral genomes. We confirmed and extended the initial observations by on the PA-R638A mutant, as we found an increased diversity and frequency of DVGs produced by the PA-R638A and also to a larger extent by the PA-K635A mutant virus compared to the wild-type. 2020 RNA (New York, N.Y.) Discussion IV R638A;R638A;K635A 64;154;198 69;159;203 PA;PA;PA 61;151;195 63;153;197 32962203 PA from a Recent H9N2 (G1-Like) Avian Influenza a Virus (AIV) Strain Carrying Lysine 367 Confers Altered Replication Efficiency and Pathogenicity to Contemporaneous H5N1 in Mammalian Systems. Except for NP segment from H5N1/Q4596D, all internal protein-encoding segments were compatible with the complementary seven segments from H9N2/S4456B and viruses could be rescued. 2020 Viruses Discussion IV Q4596D 32 38 NP 11 13 32962203 PA from a Recent H9N2 (G1-Like) Avian Influenza a Virus (AIV) Strain Carrying Lysine 367 Confers Altered Replication Efficiency and Pathogenicity to Contemporaneous H5N1 in Mammalian Systems. In complement to this study, we previously tested the genetic compatibility of viral segments derived from HPAI A/duck/Egypt/Q4596D/2012 (H5N1) (H5N1/Q4596D) in the genetic backbone of LPAI A/chicken/Egypt/S4456B/2011 (H9N2) (H9N2/S4456B) using Rg approach of influenza viruses. 2020 Viruses Discussion IV Q4596D;Q4596D 150;125 156;131 Influenza A virus H5N1 infection;Influenza A virus H5N1 infection;Influenza A virus H9N2 infection;Influenza A virus H9N2 infection 138;145;226;219 142;149;230;223 32962203 PA from a Recent H9N2 (G1-Like) Avian Influenza a Virus (AIV) Strain Carrying Lysine 367 Confers Altered Replication Efficiency and Pathogenicity to Contemporaneous H5N1 in Mammalian Systems. The NS1 proteins of our H9N2EGY and CL42 strains belong to allele "A" and share the same pattern of mammalian-like markers including P42S and mammalian like PDZ motifs "ESKV for H5N1EGY and KSEV for CL42". 2020 Viruses Discussion IV P42S 133 137 NS1 4 7 33024040 Structure-Based Modification of an Anti-neuraminidase Human Antibody Restores Protection Efficacy against the Drifted Influenza Virus. As Z2B3 might have been useful as a therapeutic agent, we tried restoring its activity by placing a positively charged amino acid (R) to replace the glutamic acid (E) at position 102 in VH. 2020 mBio Discussion IV E102E 148 183 33024040 Structure-Based Modification of an Anti-neuraminidase Human Antibody Restores Protection Efficacy against the Drifted Influenza Virus. For Z2B3, this led to a loss of activity on H1N1 viruses isolated after 2013 associated with the substitution K432E. 2020 mBio Discussion IV K432E 110 115 33028722 PA Mutations Inherited during Viral Evolution Act Cooperatively To Increase Replication of Contemporary H5N1 Influenza Virus with an Expanded Host Range. A comprehensive evolutionary analysis reported S388N to be one of the evolution-associated mutations in H7N9 virus, which was presumably associated with its host range and infection of humans, although its biological significance has not been tested. 2020 Journal of virology Discussion IV S388N 47 52 33028722 PA Mutations Inherited during Viral Evolution Act Cooperatively To Increase Replication of Contemporary H5N1 Influenza Virus with an Expanded Host Range. A recent study showed that low polymerase activity due to PA in the trimeric polymerase complex can drive the PB2-E627K substitution in human cells, implying a functional association of PB2 and PA during AI virus adaptation in mammals. 2020 Journal of virology Discussion IV E627K 114 119 PA;PA;PB2;PB2 58;194;110;186 60;196;113;189 33028722 PA Mutations Inherited during Viral Evolution Act Cooperatively To Increase Replication of Contemporary H5N1 Influenza Virus with an Expanded Host Range. Almost all the contemporary clade 2.2.1 viruses in this study have retained A448E and S388R. 2020 Journal of virology Discussion IV A448E;S388R 76;86 81;91 33028722 PA Mutations Inherited during Viral Evolution Act Cooperatively To Increase Replication of Contemporary H5N1 Influenza Virus with an Expanded Host Range. In addition, the A448E, S388R, and E18G mutations had a replication-enhancing effect in viruses in the clade 2.2.1 background carrying PB2-627K, implying cooperative polymerase activity with PB2-E627K. 2020 Journal of virology Discussion IV A448E;S388R;E18G;E627K 17;24;35;195 22;29;39;200 PB2;PB2 135;191 138;194 33028722 PA Mutations Inherited during Viral Evolution Act Cooperatively To Increase Replication of Contemporary H5N1 Influenza Virus with an Expanded Host Range. In our apo-form model, A448E created a new hydrogen bond to N444, probably stabilizing the helix alpha16 structure. 2020 Journal of virology Discussion IV A448E 23 28 33028722 PA Mutations Inherited during Viral Evolution Act Cooperatively To Increase Replication of Contemporary H5N1 Influenza Virus with an Expanded Host Range. Indeed, the A448E/S388R signature mutation had more prominent effects on improving polymerase and replication activity in human cells than in avian cells, especially in human cells at the lower temperature of 33 C. 2020 Journal of virology Discussion IV A448E;S388R 12;18 17;23 33028722 PA Mutations Inherited during Viral Evolution Act Cooperatively To Increase Replication of Contemporary H5N1 Influenza Virus with an Expanded Host Range. PA-E18G is in PA-N and was characterized here as an auxiliary mutation for increasing polymerase activity and unique to an EG13 virus strain. 2020 Journal of virology Discussion IV E18G 3 7 PA;PA 0;14 2;16 33028722 PA Mutations Inherited during Viral Evolution Act Cooperatively To Increase Replication of Contemporary H5N1 Influenza Virus with an Expanded Host Range. PA-E18G was found in H1N1 pdm09 virus during a marmoset infection (nonhuman primate model) and during serial passages in mice. 2020 Journal of virology Discussion IV E18G 3 7 PA 0 2 33028722 PA Mutations Inherited during Viral Evolution Act Cooperatively To Increase Replication of Contemporary H5N1 Influenza Virus with an Expanded Host Range. PB2-E627K is the most characterized human adaptation mutation. 2020 Journal of virology Discussion IV E627K 4 9 PB2 0 3 33028722 PA Mutations Inherited during Viral Evolution Act Cooperatively To Increase Replication of Contemporary H5N1 Influenza Virus with an Expanded Host Range. Recently, it has become apparent that PA plays a role in the host adaptation of AI viruses, with mutations identified throughout the PA gene sequence (i.e., A36T, S37A, T85I, G186S, L336M, A343S/T, K356R, N383D, and N409S). 2020 Journal of virology Discussion IV A36T;S37A;T85I;G186S;L336M;A343S;A343T;K356R;N383D;N409S 157;163;169;175;182;189;189;198;205;216 161;167;173;180;187;196;196;203;210;221 PA;PA 38;133 40;135 33028722 PA Mutations Inherited during Viral Evolution Act Cooperatively To Increase Replication of Contemporary H5N1 Influenza Virus with an Expanded Host Range. Several of these PA mutations (i.e., A448E, S388R, and E18G) acted cooperatively to increase polymerase activity and viral replication in both avian and human cells. 2020 Journal of virology Discussion IV A448E;S388R;E18G 37;44;55 42;49;59 PA 17 19 33028722 PA Mutations Inherited during Viral Evolution Act Cooperatively To Increase Replication of Contemporary H5N1 Influenza Virus with an Expanded Host Range. The effect of PA-E18G was different from those of the above-described two mutations. 2020 Journal of virology Discussion IV E18G 17 21 PA 14 16 33028722 PA Mutations Inherited during Viral Evolution Act Cooperatively To Increase Replication of Contemporary H5N1 Influenza Virus with an Expanded Host Range. The H5N1 clade 2.2.1 viruses that are unique to Egypt generally carry the human adaptation PB2-E627K mutation in the field and have no history of reassortment during long-term dissemination. 2020 Journal of virology Discussion IV E627K 95 100 PB2 91 94 33028722 PA Mutations Inherited during Viral Evolution Act Cooperatively To Increase Replication of Contemporary H5N1 Influenza Virus with an Expanded Host Range. The PA-S388R and -A448E mutations, which were identified in this study as main contributors to the higher polymerase activity of contemporary clade 2.2.1.2 viruses, were both localized in PA-C. 2020 Journal of virology Discussion IV S388R;A448E 7;18 12;23 PA;PA 4;188 6;190 33028722 PA Mutations Inherited during Viral Evolution Act Cooperatively To Increase Replication of Contemporary H5N1 Influenza Virus with an Expanded Host Range. The PB2 genes from clade 2.2.1.2 and H9N2 G1-A/B subclade viruses in Egypt have commonly acquired PB2-E627K and PB2-E627V, respectively, both of which have been reported to confer improved replication and an expanded host range. 2020 Journal of virology Discussion IV E627K;E627V 102;116 107;121 PB2;PB2;PB2 4;98;112 7;101;115 33028722 PA Mutations Inherited during Viral Evolution Act Cooperatively To Increase Replication of Contemporary H5N1 Influenza Virus with an Expanded Host Range. Therefore, E18G may also affect the function of PA-X. 2020 Journal of virology Discussion IV E18G 11 15 PA-X 48 52 33028722 PA Mutations Inherited during Viral Evolution Act Cooperatively To Increase Replication of Contemporary H5N1 Influenza Virus with an Expanded Host Range. Therefore, the A448E substitution may affect polymerase activity by changing the core structure of the polymerase complex or its interaction with cellular Pol II. 2020 Journal of virology Discussion IV A448E 15 20 33028722 PA Mutations Inherited during Viral Evolution Act Cooperatively To Increase Replication of Contemporary H5N1 Influenza Virus with an Expanded Host Range. Therefore, the E18G substitution may produce more fit polymerase activity in specific host species, but this mutation may not be associated with H5N1 evolutionary dynamics since it has not been found in any other clade 2.2.1 virus. 2020 Journal of virology Discussion IV E18G 15 19 33028722 PA Mutations Inherited during Viral Evolution Act Cooperatively To Increase Replication of Contemporary H5N1 Influenza Virus with an Expanded Host Range. Therefore, the signature PA-S388R/A448E mutation, in particular paired with PB2-627K/V, may be a viral marker for severe risk to human health in the Middle East, centered in Egypt. 2020 Journal of virology Discussion IV S388R;A448E 28;34 33;39 PA;PB2 25;76 27;79 33028722 PA Mutations Inherited during Viral Evolution Act Cooperatively To Increase Replication of Contemporary H5N1 Influenza Virus with an Expanded Host Range. These results suggested that the continuing dissemination of clade 2.2.1 viruses in the field has allowed these viruses to accumulate multiple PA mutations that enabled higher polymerase activity by themselves and in concert with PB2-E627K to fine-tune the viral polymerase function for host range expansion. 2020 Journal of virology Discussion IV E627K 234 239 PA;PB2 143;230 145;233 33028722 PA Mutations Inherited during Viral Evolution Act Cooperatively To Increase Replication of Contemporary H5N1 Influenza Virus with an Expanded Host Range. This gave us the opportunity to identify novel human adaptation mutations in the polymerase complex, other than PB2-E627K, that have accumulated during viral evolution in nature, especially in PA and PB1. 2020 Journal of virology Discussion IV E627K 116 121 PA;PB1;PB2 193;200;112 195;203;115 33028722 PA Mutations Inherited during Viral Evolution Act Cooperatively To Increase Replication of Contemporary H5N1 Influenza Virus with an Expanded Host Range. This indicated that the S388R substitution created flexibility at this position, implying the possible association of the basic amino acid with the vRNA promoter. 2020 Journal of virology Discussion IV S388R 24 29 33028722 PA Mutations Inherited during Viral Evolution Act Cooperatively To Increase Replication of Contemporary H5N1 Influenza Virus with an Expanded Host Range. Thus, S388R may affect viral polymerase activity by altering the interaction between the polymerase complex and the viral RNA promoter. 2020 Journal of virology Discussion IV S388R 6 11 33063654 Detection and discrimination of influenza B Victoria lineage deletion variant viruses by real-time RT-PCR. One limitation of our assay is that it cannot distinguish between the two antigenically distinct groups within the V1A-3DEL viruses (V1A.2 and V1A.3), but it does detect V1A-3DEL viruses, regardless of antigenicity. 2020 Euro surveillance Discussion IV V1A;V1A;V1A;V1A 115;133;143;170 118;136;146;173 33063654 Detection and discrimination of influenza B Victoria lineage deletion variant viruses by real-time RT-PCR. The key genetic distinction between V1A, V1A-2DEL, and V1A-3DEL viruses is within the same nucleic acid region, presenting a challenge for rRT-PCR probe design. 2020 Euro surveillance Discussion IV V1A;V1A;V1A 36;41;55 39;44;58 33063654 Detection and discrimination of influenza B Victoria lineage deletion variant viruses by real-time RT-PCR. The number and percentage of circulating V1A-2DEL and V1A-3DEL viruses has increased significantly since initial identification, making it critical to have a simplified and sensitive assay capable of detecting these genetic variants during influenza surveillance. 2020 Euro surveillance Discussion IV V1A;V1A 41;54 44;57 33063654 Detection and discrimination of influenza B Victoria lineage deletion variant viruses by real-time RT-PCR. The probes for V1A and V1A-2DEL were designed using BHQplus chemistry, allowing for stabilisation and enhanced mismatch detection with an overall shorter probe length. 2020 Euro surveillance Discussion IV V1A;V1A 15;23 18;26 33063654 Detection and discrimination of influenza B Victoria lineage deletion variant viruses by real-time RT-PCR. We have further shown that the primers and probes of the VIC deletion assay are specific to V1A, V1A-2DEL and V1A-3DEL viruses and do not cross-react with B/YAM viruses, seasonal influenza A, or avian influenza A viruses including HPAI A(H5N1) and Asian lineage A(H7N9) influenza viruses. 2020 Euro surveillance Discussion IV V1A;V1A;V1A 92;97;110 95;100;113 33099886 Comprehensive assessment of amino acid substitutions in the trimeric RNA polymerase complex of influenza A virus detected in clinical trials of baloxavir marboxil. However, these substitutions were unable to restore the growth impairment of the I38T-substituted viruses. 2021 Influenza and other respiratory viruses Discussion IV I38T 81 85 33099886 Comprehensive assessment of amino acid substitutions in the trimeric RNA polymerase complex of influenza A virus detected in clinical trials of baloxavir marboxil. In addition, the replicative capacity of I38N viruses was reduced to a comparable level to I38T viruses. 2021 Influenza and other respiratory viruses Discussion IV I38N;I38T 41;91 45;95 33099886 Comprehensive assessment of amino acid substitutions in the trimeric RNA polymerase complex of influenza A virus detected in clinical trials of baloxavir marboxil. In this study, we characterized PA/I38 substitutions detected in clinical studies (I38T/F/M/N/R/S) and as naturally occurring polymorphisms (I38V/L). 2021 Influenza and other respiratory viruses Discussion IV I38F;I38M;I38N;I38R;I38S;I38L;I38T;I38V 83;83;83;83;83;141;83;141 97;97;97;97;97;147;97;147 PA 32 34 33099886 Comprehensive assessment of amino acid substitutions in the trimeric RNA polymerase complex of influenza A virus detected in clinical trials of baloxavir marboxil. PA/I38N was newly identified in the clinical setting, and we demonstrated that BXA susceptibility of I38N viruses was reduced compared with wild-type virus (24-fold for A(H1N1) and 10-fold for A(H3N2)). 2021 Influenza and other respiratory viruses Discussion IV I38N;I38N 3;101 7;105 PA 0 2 33099886 Comprehensive assessment of amino acid substitutions in the trimeric RNA polymerase complex of influenza A virus detected in clinical trials of baloxavir marboxil. The replicative capacity was previously evaluated for substitutions A20S + I38F and I38T + E623K, 11 and I38T + S60P and I38T + I201T were tested in this study (Figure S2). 2021 Influenza and other respiratory viruses Discussion IV I38F;A20S;I38T;E623K;I38T;S60P;I38T;I201T 75;68;84;91;106;113;122;129 79;72;88;96;110;117;126;134 33099886 Comprehensive assessment of amino acid substitutions in the trimeric RNA polymerase complex of influenza A virus detected in clinical trials of baloxavir marboxil. While in vitro results of the replicative capacity of I38X mutant viruses from different studies vary, further investigation of potential compensatory mutations that could recover the fitness cost of I38T substitution will be needed. 2021 Influenza and other respiratory viruses Discussion IV I38X;I38T 54;200 58;204 33179567 Adsorptive mutation and N-linked glycosylation modulate influenza virus antigenicity and fitness. First, growing wild type SKP-827/16 virus that naturally contains T180 led to the addition of HA D189N which glycosylated residue 189, indicating proven biological relevance to studying N-linked glycans. 2020 Emerging microbes & infections Discussion IV D189N 97 102 HA 94 96 33179567 Adsorptive mutation and N-linked glycosylation modulate influenza virus antigenicity and fitness. In fact, the addition of N148 to virus with any avidity background led to reduced binding avidity to all tested receptor analogues and a significant impact on virus replication apart from T180A viruses in MDCK cells. 2020 Emerging microbes & infections Discussion IV T180A 188 193 33179567 Adsorptive mutation and N-linked glycosylation modulate influenza virus antigenicity and fitness. In the data presented here, it is plausible that an H9N2 virus could escape immunity through addition of an N-linked glycan at residues 134, 148 or 189 and subsequently achieve viral fitness with a mutation that modulated avidity such as with substitutions A180 T/V, or vice versa. 2020 Emerging microbes & infections Discussion IV A180T;A180V 257;257 265;265 33179567 Adsorptive mutation and N-linked glycosylation modulate influenza virus antigenicity and fitness. Indeed, N148 facilitated a receptor binding profile that resembled low avidity non-glycosylated T180A virus suggesting that the significant reduction in HI titre was because of the antigenic mechanism whereby an N-linked glycan occludes the receptor binding site. 2020 Emerging microbes & infections Discussion IV T180A 96 101 33179567 Adsorptive mutation and N-linked glycosylation modulate influenza virus antigenicity and fitness. We confirm that in the background of the SKP-827/16 HA, replication of high avidity non-glycosylated viruses, including viruses carrying T180 and T180 V, there was attenuated replication kinetics in MDCK and CK cells, as shown before. 2020 Emerging microbes & infections Discussion IV T180V 146 152 HA 52 54 33281788 Altering Intracellular Localization of the RNA Interference Factors by Influenza A Virus Non-structural Protein 1. A single Glu-to-Lys substitution at position 627 of PB2 protein allows the influenza virus to infect mammalian cells more effectively and Asn at position 701 of PB2 protein is involved in the pathogenicity of the influenza virus in mice. 2020 Frontiers in microbiology Discussion IV E627K 9 48 PB2;PB2 52;161 55;164 33281788 Altering Intracellular Localization of the RNA Interference Factors by Influenza A Virus Non-structural Protein 1. However, IAV-PR8 and IAV-PR8/NS1 (D101H) replicated to similar levels in lung tissues, indicating that such an effect on antiviral RNAi, if any, is undetectable in the mouse model. 2020 Frontiers in microbiology Discussion IV D101H 34 39 NS1 29 32 33281788 Altering Intracellular Localization of the RNA Interference Factors by Influenza A Virus Non-structural Protein 1. S200P and D144E mutations of HA reported in the 1918 H1N1 viruses can increase the virulence of pHIN1 virus in mice. 2020 Frontiers in microbiology Discussion IV S200P;D144E 0;10 5;15 HA 29 31 33408229 Next-Generation Sequencing Analysis of the Within-Host Genetic Diversity of Influenza A(H1N1)pdm09 Viruses in the Upper and Lower Respiratory Tracts of Patients with Severe Influenza. Conversely, previous studies have identified that the HA-D222G/N and other substitutions in the antigenic sites were under positive selection through alignment of HA genes in A(H1N1)pdm from clinical specimens, including lower respiratory samples. 2021 mSphere Discussion IV D222G;D222N 57;57 64;64 HA;HA 54;163 56;165 33408229 Next-Generation Sequencing Analysis of the Within-Host Genetic Diversity of Influenza A(H1N1)pdm09 Viruses in the Upper and Lower Respiratory Tracts of Patients with Severe Influenza. However, we could not find a clear association between the HA-D222G/N substitution and increased disease severity because it is difficult to collect TLA from patients with mild infection; thus, we could not compare prior results with those from patients with mild disease in this study. 2021 mSphere Discussion IV D222G;D222N 62;62 69;69 HA 59 61 33408229 Next-Generation Sequencing Analysis of the Within-Host Genetic Diversity of Influenza A(H1N1)pdm09 Viruses in the Upper and Lower Respiratory Tracts of Patients with Severe Influenza. In contrast, numerous other studies have associated HA-D222G with disease severity as this substitution has been described in Europe, the United States, and other countries with a significant frequency in fatal and severe cases. 2021 mSphere Discussion IV D222G 55 60 HA 52 54 33408229 Next-Generation Sequencing Analysis of the Within-Host Genetic Diversity of Influenza A(H1N1)pdm09 Viruses in the Upper and Lower Respiratory Tracts of Patients with Severe Influenza. In previous reports, the HA-D222G substitution resulted in a higher binding intensity to alpha2,3-SA and a lower binding intensity to alpha2,6-SA in isolated viruses. 2021 mSphere Discussion IV D222G 28 33 HA 25 27 33408229 Next-Generation Sequencing Analysis of the Within-Host Genetic Diversity of Influenza A(H1N1)pdm09 Viruses in the Upper and Lower Respiratory Tracts of Patients with Severe Influenza. In recent studies, the HA-D222G/N substitution has been detected in 30% (4/13) of ICU-admitted patients in Italy and the HA-D222G substitution has been detected in 44% (4/9) of severe cases in Norway. 2021 mSphere Discussion IV D222G;D222N;D222G 26;26;124 33;33;129 HA;HA 23;121 25;123 33408229 Next-Generation Sequencing Analysis of the Within-Host Genetic Diversity of Influenza A(H1N1)pdm09 Viruses in the Upper and Lower Respiratory Tracts of Patients with Severe Influenza. In the present study, other than the HA-D222G/N substitution, no amino acid substitution previously associated with severity or other viral phenotypic characteristics was identified in the samples. 2021 mSphere Discussion IV D222G;D222N 40;40 47;47 HA 37 39 33408229 Next-Generation Sequencing Analysis of the Within-Host Genetic Diversity of Influenza A(H1N1)pdm09 Viruses in the Upper and Lower Respiratory Tracts of Patients with Severe Influenza. It thus seems these 46 substitutions appeared randomly, whereas the HA-D222G/N substitution may have occurred owing to tissue-specific virus diversity. 2021 mSphere Discussion IV D222G;D222N 71;71 78;78 HA 68 70 33408229 Next-Generation Sequencing Analysis of the Within-Host Genetic Diversity of Influenza A(H1N1)pdm09 Viruses in the Upper and Lower Respiratory Tracts of Patients with Severe Influenza. Some studies do not support the association of D222G/N substitution with severe disease, because this substitution is detected even in mild outpatient cases. 2021 mSphere Discussion IV D222G;D222N 47;47 54;54 33408229 Next-Generation Sequencing Analysis of the Within-Host Genetic Diversity of Influenza A(H1N1)pdm09 Viruses in the Upper and Lower Respiratory Tracts of Patients with Severe Influenza. The HA-D222G/N substitution exists as a minor population, whereas HA-D222G appears in <1.8% of A(H1N1)pdm worldwide. 2021 mSphere Discussion IV D222G;D222N;D222G 7;7;69 14;14;74 HA;HA 4;66 6;68 33408229 Next-Generation Sequencing Analysis of the Within-Host Genetic Diversity of Influenza A(H1N1)pdm09 Viruses in the Upper and Lower Respiratory Tracts of Patients with Severe Influenza. The HA-D222G/N substitution has been mapped to the receptor-binding site of HA protein. 2021 mSphere Discussion IV D222G;D222N 7;7 14;14 HA;HA 4;76 6;78 33408229 Next-Generation Sequencing Analysis of the Within-Host Genetic Diversity of Influenza A(H1N1)pdm09 Viruses in the Upper and Lower Respiratory Tracts of Patients with Severe Influenza. The HA-D222G/N substitution has been reported in several previous studies. 2021 mSphere Discussion IV D222G;D222N 7;7 14;14 HA 4 6 33408229 Next-Generation Sequencing Analysis of the Within-Host Genetic Diversity of Influenza A(H1N1)pdm09 Viruses in the Upper and Lower Respiratory Tracts of Patients with Severe Influenza. The results showed the HA-D222G/N, as well as the other 46 substitutions, were not under positive selection. 2021 mSphere Discussion IV D222G;D222N 26;26 33;33 HA 23 25 33424035 The Effect of I155T, K156Q, K156E and N186K Mutations in Hemagglutinin on the Virulence and Reproduction of Influenza A/H5N1 Viruses. According to Naughtin et al., influenza viruses with the A138V mutation in HA reproduce well in chicken embryos and in the MDCK mammalian cell culture. 2020 Molecular biology Discussion IV A138V 57 62 HA 75 77 33424035 The Effect of I155T, K156Q, K156E and N186K Mutations in Hemagglutinin on the Virulence and Reproduction of Influenza A/H5N1 Viruses. All these characteristics suggest that the N186K substitution can promote the transfer of H5N1 influenza viruses to a new host (mammals). 2020 Molecular biology Discussion IV N186K 43 48 33424035 The Effect of I155T, K156Q, K156E and N186K Mutations in Hemagglutinin on the Virulence and Reproduction of Influenza A/H5N1 Viruses. Among them, 11 viruses were isolated from people during the period from 2004 to 2010, which confirms that the A138V mutation is associated with adaptation. 2020 Molecular biology Discussion IV A138V 110 115 33424035 The Effect of I155T, K156Q, K156E and N186K Mutations in Hemagglutinin on the Virulence and Reproduction of Influenza A/H5N1 Viruses. failed to reconstruct the influenza virus with a single A138V mutation in HA from A/Thailand/676/2005 (H5N1) and other genes from PR8 (H1N1) by reverse genetics, which they believed was due to incompatibility between this mutation and other genes. 2020 Molecular biology Discussion IV A138V 56 61 HA 74 76 33424035 The Effect of I155T, K156Q, K156E and N186K Mutations in Hemagglutinin on the Virulence and Reproduction of Influenza A/H5N1 Viruses. In all likelihood, the initial RGVN virus containing an adaptation-associated mutation A138V has a well-balanced structure, which allows it to successfully reproduce in chicken embryos. 2020 Molecular biology Discussion IV A138V 87 92 33424035 The Effect of I155T, K156Q, K156E and N186K Mutations in Hemagglutinin on the Virulence and Reproduction of Influenza A/H5N1 Viruses. In all likelihood, this was not accidental and explains all our unsuccessful attempts to obtain a RG mutant with a single K156E substitution. 2020 Molecular biology Discussion IV K156E 122 127 33424035 The Effect of I155T, K156Q, K156E and N186K Mutations in Hemagglutinin on the Virulence and Reproduction of Influenza A/H5N1 Viruses. In the mutants obtained, the A138V substitution was always accompanied by an additional mutation in HA. 2020 Molecular biology Discussion IV A138V 29 34 HA 100 102 33424035 The Effect of I155T, K156Q, K156E and N186K Mutations in Hemagglutinin on the Virulence and Reproduction of Influenza A/H5N1 Viruses. In the study of HA quasispecies diversity in different organs of patients who fell victims to the H5N1 avian flu in Thailand in 2004-2005, the I155T mutation was observed only once in viral material from a patient's lungs on day 17 of the disease. 2020 Molecular biology Discussion IV I155T 143 148 HA 16 18 33424035 The Effect of I155T, K156Q, K156E and N186K Mutations in Hemagglutinin on the Virulence and Reproduction of Influenza A/H5N1 Viruses. In this context, it is significant that there is a considerable delay of growth of the RGN186K mutant carrying, in addition to 138V, the N186K substitution that switches the receptor specificity of HA from "avian" to "human". 2020 Molecular biology Discussion IV N186K 137 142 HA 198 200 33424035 The Effect of I155T, K156Q, K156E and N186K Mutations in Hemagglutinin on the Virulence and Reproduction of Influenza A/H5N1 Viruses. In this work we used site-specific mutagenesis to obtain viral variants with the I155T, K156Q, K156E+V138A and N186K substitutions in H5 HA, with the same structure of other genes, and have shown that phenotypic changes in these variants are due to single mutations in HA. 2020 Molecular biology Discussion IV I155T;K156Q;K156E;V138A;N186K 81;88;95;101;111 86;93;100;106;116 HA;HA 137;269 139;271 33424035 The Effect of I155T, K156Q, K156E and N186K Mutations in Hemagglutinin on the Virulence and Reproduction of Influenza A/H5N1 Viruses. It should be noted that the overwhelming majority of H5 influenza viruses (8514 HA sequences) have an alanine residue in position 138, and only 12 natural isolates of the highly pathogenic H5N1 line contain the A138V substitution. 2020 Molecular biology Discussion IV A138V 211 216 HA 80 82 33424035 The Effect of I155T, K156Q, K156E and N186K Mutations in Hemagglutinin on the Virulence and Reproduction of Influenza A/H5N1 Viruses. Later on (2004-2012), the K156Q mutation was observed in the isolates from chickens in Thailand, Indonesia and India and from crows (India, 2012), as well as in two isolates from humans in Egypt (2008 and 2009) and from pigs in China (2014). 2020 Molecular biology Discussion IV K156Q 26 31 33424035 The Effect of I155T, K156Q, K156E and N186K Mutations in Hemagglutinin on the Virulence and Reproduction of Influenza A/H5N1 Viruses. Over the past 10 years (2010-2020), the frequency of occurrence of the I155T substitution in HA of influenza viruses isolated from humans is 48.5%. 2020 Molecular biology Discussion IV I155T 71 76 HA 93 95 33424035 The Effect of I155T, K156Q, K156E and N186K Mutations in Hemagglutinin on the Virulence and Reproduction of Influenza A/H5N1 Viruses. Previously we revealed a single K156E mutation only in escape mutants of the VNH5N1-PR8/CDC-RG virus with HA containing an alanine residue (A138) in position 138. 2020 Molecular biology Discussion IV K156E 32 37 HA 106 108 33424035 The Effect of I155T, K156Q, K156E and N186K Mutations in Hemagglutinin on the Virulence and Reproduction of Influenza A/H5N1 Viruses. The 156E+138A combination, like in the RG(K156E+V138A) mutant, has been found in 18 natural isolates from birds, with 12 viruses belonging to the GsGD-lineage and the rest of them being nonpathogenic influenza viruses from the American continent and South Africa. 2020 Molecular biology Discussion IV K156E;V138A 42;48 47;53 33424035 The Effect of I155T, K156Q, K156E and N186K Mutations in Hemagglutinin on the Virulence and Reproduction of Influenza A/H5N1 Viruses. The A138V and N186K mutations are associated with adaptation in mammalian influenza viruses. 2020 Molecular biology Discussion IV A138V;N186K 4;14 9;19 33424035 The Effect of I155T, K156Q, K156E and N186K Mutations in Hemagglutinin on the Virulence and Reproduction of Influenza A/H5N1 Viruses. The A138V mutation provides the high virulence, thermostability and enhanced reproduction of the virus in the temperature range from 33 to 40 S. 2020 Molecular biology Discussion IV A138V 4 9 33424035 The Effect of I155T, K156Q, K156E and N186K Mutations in Hemagglutinin on the Virulence and Reproduction of Influenza A/H5N1 Viruses. The analysis of the frequency of occurrence of these mutations in natural isolates indicates that the K156E/Q and N186K mutations have little chance of being preserved during evolution, in contrast to the I155T mutation, which is maximally responsible for the antigenic drift of HA. 2020 Molecular biology Discussion IV K156E;K156Q;N186K;I155T 102;102;114;205 109;109;119;210 HA 279 281 33424035 The Effect of I155T, K156Q, K156E and N186K Mutations in Hemagglutinin on the Virulence and Reproduction of Influenza A/H5N1 Viruses. The I155T and K156E+V138A mutations contribute to viral reproduction at the lower temperature (33 C) with the maintenance of high virulence. 2020 Molecular biology Discussion IV I155T;K156E;V138A 4;14;20 9;19;25 33424035 The Effect of I155T, K156Q, K156E and N186K Mutations in Hemagglutinin on the Virulence and Reproduction of Influenza A/H5N1 Viruses. The I155T mutation leads to a decrease in HA thermostability and attenuation of virulence of the virus for mice but has no significant effect on viral reproduction in the temperature range under study compared to the initial virus. 2020 Molecular biology Discussion IV I155T 4 9 HA 42 44 33424035 The Effect of I155T, K156Q, K156E and N186K Mutations in Hemagglutinin on the Virulence and Reproduction of Influenza A/H5N1 Viruses. The I155T substitution is widespread in nature among the viruses of domestic and wild birds, as well as humans. 2020 Molecular biology Discussion IV I155T 4 9 33424035 The Effect of I155T, K156Q, K156E and N186K Mutations in Hemagglutinin on the Virulence and Reproduction of Influenza A/H5N1 Viruses. The introduced K156Q, K156E+V138A and N186K mutations disturb this balance as is evidenced by the decrease in the virus titer in the first 24 h after the infection of chicken embryos. 2020 Molecular biology Discussion IV N186K;K156Q;K156E;V138A 38;15;22;28 43;20;27;33 33424035 The Effect of I155T, K156Q, K156E and N186K Mutations in Hemagglutinin on the Virulence and Reproduction of Influenza A/H5N1 Viruses. The K156E substitution leads to a change in the amino acid charge from positive to negative, thereby weakening the electrostatic interaction between the virus and the cell surface and contributing to more effective distribution of progeny viruses. 2020 Molecular biology Discussion IV K156E 4 9 33424035 The Effect of I155T, K156Q, K156E and N186K Mutations in Hemagglutinin on the Virulence and Reproduction of Influenza A/H5N1 Viruses. The K156Q amino acid substitution, similar to the N186K mutation, resulted in lower HA thermostability and reproduction at an elevated temperature (40 S). 2020 Molecular biology Discussion IV K156Q;N186K 4;50 9;55 HA 84 86 33424035 The Effect of I155T, K156Q, K156E and N186K Mutations in Hemagglutinin on the Virulence and Reproduction of Influenza A/H5N1 Viruses. The K156Q and N186K mutations lead to attenuation of virulence and a decrease in the reproductive ability of the influenza virus at 40 S. 2020 Molecular biology Discussion IV K156Q;N186K 4;14 9;19 33424035 The Effect of I155T, K156Q, K156E and N186K Mutations in Hemagglutinin on the Virulence and Reproduction of Influenza A/H5N1 Viruses. The K156Q mutation was found in 24 natural H5N1 influenza viruses isolated mainly from birds. 2020 Molecular biology Discussion IV K156Q 4 9 33424035 The Effect of I155T, K156Q, K156E and N186K Mutations in Hemagglutinin on the Virulence and Reproduction of Influenza A/H5N1 Viruses. The pathological material from patients infected with the H5N1 influenza virus was shown to contain mutant HA variants (quasispecies) with the following as the most frequently occurring mutations: A138V, N186D, S227N, I155T, K156Q, and N186K. 2020 Molecular biology Discussion IV A138V;N186D;S227N;I155T;K156Q;N186K 197;204;211;218;225;236 202;209;216;223;230;241 HA 107 109 33424035 The Effect of I155T, K156Q, K156E and N186K Mutations in Hemagglutinin on the Virulence and Reproduction of Influenza A/H5N1 Viruses. The revealed decrease in virus reproduction at a higher (40 S) temperature and the thermostability of HA of the RGN186K mutant is in agreement with the data of other authors showing, in addition to these properties, that a single N186K mutation results in a higher affinity to "human"-type receptors, enhanced replication in the culture of epithelial cells of the human respiratory tract, and increased pH (from 5.6 to 5.9) of activation of conformational changes in HA (the parameter essential for penetration of the virus into the cell). 2020 Molecular biology Discussion IV N186K 230 235 HA;HA 102;467 104;469 33424035 The Effect of I155T, K156Q, K156E and N186K Mutations in Hemagglutinin on the Virulence and Reproduction of Influenza A/H5N1 Viruses. The RG(K156E+V138A) mutant successfully reproduced in chicken embryos within the entire range of temperatures under study, though its thermostability was lower compared to the initial RGVN virus (Table 1); at the same time, virulence was lower compared to RGVN but remained at a rather high level for mice. 2020 Molecular biology Discussion IV K156E;V138A 7;13 12;18 33424035 The Effect of I155T, K156Q, K156E and N186K Mutations in Hemagglutinin on the Virulence and Reproduction of Influenza A/H5N1 Viruses. The same A138V mutation is present in all the RG mutants that we studied, except for RG(K156E+V138A), where the concomitant V138A mutation emerged as a return to the wild type. 2020 Molecular biology Discussion IV A138V;V138A;K156E;V138A 9;94;88;124 14;99;93;129 33436086 N-linked glycosylation at site 158 of the HA protein of H5N6 highly pathogenic avian influenza virus is important for viral biological properties and host immune responses. reported that addition of an N158D mutation to an HA protein containing N224K/Q226L increases virus stability. 2021 Veterinary research Discussion IV N158D;N224K;Q226L 29;72;78 34;77;83 HA 50 52 33451024 Identification of Important N-Linked Glycosylation Sites in the Hemagglutinin Protein and Their Functional Impact on DC-SIGN Mediated Avian Influenza H5N1 Infection. Further, we used monocyte derived iDCs and mDCs to confirm these findings and found that only N27Q and N39Q mutations significantly reduced DC-SIGN mediated H5N1 virus infection. 2021 International journal of molecular sciences Discussion IV N27Q;N39Q 94;103 98;107 Influenza A virus H5N1 infection 157 177 33451024 Identification of Important N-Linked Glycosylation Sites in the Hemagglutinin Protein and Their Functional Impact on DC-SIGN Mediated Avian Influenza H5N1 Infection. However, this amelioration effect was not observed in H5N1 virus carrying N181Q mutation. 2021 International journal of molecular sciences Discussion IV N181Q 74 79 33451024 Identification of Important N-Linked Glycosylation Sites in the Hemagglutinin Protein and Their Functional Impact on DC-SIGN Mediated Avian Influenza H5N1 Infection. Our results demonstrated that most single mutations on N-linked glycosylation sites on HA5 did not influence the binding between DC-SIGN and HA (H5), whereas only three mutations (N27Q, N39Q, and N181Q) reduced this interaction; suggesting that the DC-SIGN CRD may interact minimally with a N-glycosylation with high-mannose oligosaccharides expression on HA protein. 2021 International journal of molecular sciences Discussion IV N27Q;N39Q;N181Q 180;186;196 184;190;201 HA;HA;HA 87;141;356 89;143;358 33518109 Characterization of the low-pathogenic H7N7 avian influenza virus in Shanghai, China. In this study, no key amino acid mutations were found in PB2, especially the E627 K and D701 N mutations, which have been shown to increase adaptation of other AIVs to mammals. 2021 Poultry science Discussion IV E627K;D701N 77;88 83;94 PB2 57 60 33518109 Characterization of the low-pathogenic H7N7 avian influenza virus in Shanghai, China. Other mutations including A135 T, T136S, and T160 A in HA; N30D and T215 A in M1; P42S and D97 E in NS1; R389 K in PB2; and N383D in PA were found in CM1216. 2021 Poultry science Discussion IV A135T;T136S;T160A;N30D;T215A;P42S;D97E;R389K;N383D 26;34;45;59;68;82;91;105;124 32;39;51;63;74;86;96;111;129 HA;M1;NS1;PA;PB2 55;78;100;133;115 57;80;103;135;118 33518109 Characterization of the low-pathogenic H7N7 avian influenza virus in Shanghai, China. The HA protein of an H7N9 AIV isolated from humans in China has both T160 A and Q226 L (H3 numbering) substitutions, which may enhance binding of the virus to SA alpha-2, 6 Gal receptors, enabling transmission from birds. 2021 Poultry science Discussion IV T160A;Q226L 69;80 75;86 HA 4 6 33518109 Characterization of the low-pathogenic H7N7 avian influenza virus in Shanghai, China. The T160 A substitution in HA has been shown to affect not only receptor-binding property but also transmissibility of H5N1 AIV clade 2.3.4 in guinea pigs. 2021 Poultry science Discussion IV T160A 4 10 HA 27 29 33568453 Identification and Characterization of Novel Antibody Epitopes on the N2 Neuraminidase. as a variable residue, our S331N EMV did not behave as a proper escape mutant. 2021 mSphere Discussion IV S331N 27 32 33568453 Identification and Characterization of Novel Antibody Epitopes on the N2 Neuraminidase. For example, the A272D EMV escaped neutralization by the MAb 229-1F06; however, there was only a 4-fold increase in the NAI IC50. 2021 mSphere Discussion IV A272D 17 22 NAI 120 123 33568453 Identification and Characterization of Novel Antibody Epitopes on the N2 Neuraminidase. In addition, E258K was present in A/New York/PV190/2017 and allowed the virus to completely escape the MAb 229-2C06 (which selected the E258K EMV). 2021 mSphere Discussion IV E258K;E258K 13;136 18;141 33568453 Identification and Characterization of Novel Antibody Epitopes on the N2 Neuraminidase. In addition, the S331N EMV did not become resistant to any MAbs in the panel. 2021 mSphere Discussion IV S331N 17 22 33568453 Identification and Characterization of Novel Antibody Epitopes on the N2 Neuraminidase. Mutations A272D and S331N have not been identified in other studies. 2021 mSphere Discussion IV A272D;S331N 10;20 15;25 33568453 Identification and Characterization of Novel Antibody Epitopes on the N2 Neuraminidase. Our A272D EMV showed resistance toward the MAb 229-1F06 in neutralization assays; however, it retained NAI activity. 2021 mSphere Discussion IV A272D 4 9 NAI 103 106 33568453 Identification and Characterization of Novel Antibody Epitopes on the N2 Neuraminidase. These data suggest that mutations such as A272D and S331N may not be sufficient for complete escape from MAb NAI activity. 2021 mSphere Discussion IV A272D;S331N 42;52 47;57 NAI 109 112 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. Because the SUMO acceptor site K612 is located in the vRNA binding domain of the PB1 protein, we tested whether the K612R mutation affects the binding of PB1 to vRNA. 2021 PLoS pathogens Discussion IV K612R 116 121 PB1;PB1 81;154 84;157 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. Consistent with the in vitro growth properties, the PB1/K612R mutant viruses replicated to much lower titers in mouse organs compared with the corresponding wild-type viruses; of note, the replication of the VN/1180-PB1K612R (H5N1) mutant virus was restricted to respiratory organs, whereas the wild-type VN/1180 (H5N1) virus caused systemic infection. 2021 PLoS pathogens Discussion IV K612R;K612R 56;219 61;224 PB1;PB1 52;216 55;219 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. Functionally, we found that the vRNP complex activity decreased significantly when the PB1 protein could not undergo SUMO modification at the mutated K612R residue. 2021 PLoS pathogens Discussion IV K612R 150 155 PB1 87 90 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. In characterizing the effect of SUMOylation at K612 of PB1 on the replication of IAVs, we found that SUMOylation-defective PB1 K612R mutant viruses formed much smaller plaques in MDCK cells than the wild-type viruses, and that their growth kinetics were also severely compromised in MDCK cells. 2021 PLoS pathogens Discussion IV K612R 127 132 PB1;PB1 55;123 58;126 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. In the mouse model, we found that the virulence of the SUMOylation-defective PB1 K612R mutant viruses was significantly attenuated compared with that of the wild-type WSN (H1N1), VN/1180 (H5N1) or AH/1 (H7N9) virus, indicating that SUMOylation at K612 of PB1 is necessary for IAVs to be virulent in mice. 2021 PLoS pathogens Discussion IV K612R 81 86 PB1;PB1 77;255 80;258 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. In the WSN (H1N1) and VN/1180 (H5N1) virus backgrounds, the vRNP complex activity was reduced by about 50% due to the PB1/K612R mutation, and in the AH/1 (H7N9) virus background, this mutation led to an approximately 95% reduction in vRNP complex activity. 2021 PLoS pathogens Discussion IV K612R 122 127 PB1 118 121 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. Notably, the R612K reversion mutation was identified on day 2 p.i., and accounted for 100% of the residues at position 612 of PB1 on day 4 p.i., in all three inoculated ferrets; virus shedding in one of the two positive exposed ferrets was detected until day 7 p.e., and almost all shed viruses carried the R612K reversion mutation. 2021 PLoS pathogens Discussion IV R612K;R612K 13;307 18;312 PB1 126 129 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. The wild-type 2009 pandemic H1N1 virus, A/Fuzhou/1/2009, transmitted to all three exposed ferrets via respiratory droplets, whereas the PB1-K612R mutant virus transmitted to two of the three exposed ferrets. 2021 PLoS pathogens Discussion IV K612R 140 145 PB1 136 139 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. These findings indicate that the stress condition, caused by the SUMOylation-defective PB1/K612R mutation, drives the reversion of the mutant virus to the wild-type phenotype. 2021 PLoS pathogens Discussion IV K612R 91 96 PB1 87 90 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. vRNP complex activity and viral replication were severely attenuated in the presence of the SUMOylation-defective PB1/K612R mutation, which were attributed to the impaired binding affinity to vRNA caused by this mutation. 2021 PLoS pathogens Discussion IV K612R 118 123 PB1 114 117 33571308 Viral RNA-binding ability conferred by SUMOylation at PB1 K612 of influenza A virus is essential for viral pathogenesis and transmission. We found that lack of SUMOylation of PB1 at the mutated K612R residue significantly impaired the ability of the PB1 protein to bind to vRNA, thereby severely limiting the replication and transcription of IAVs. 2021 PLoS pathogens Discussion IV K612R 56 61 PB1;PB1 37;112 40;115 33581212 Susceptibility of widely diverse influenza a viruses to PB2 polymerase inhibitor pimodivir. A potential role of H357N in pimodivir resistance was previously suggested, but no supporting phenotypic data was presented. 2021 Antiviral research Discussion IV H357N 20 25 33581212 Susceptibility of widely diverse influenza a viruses to PB2 polymerase inhibitor pimodivir. Additionally, H357N enhanced polymerase activity in a mini-genome replication assay. 2021 Antiviral research Discussion IV H357N 14 19 33581212 Susceptibility of widely diverse influenza a viruses to PB2 polymerase inhibitor pimodivir. Engineered virus with H357N demonstrated replicative fitness comparable to a wild-type virus in human A549 cells, while its growth was elevated in porcine PK15 and murine LA-4 cells. 2021 Antiviral research Discussion IV H357N 22 27 33581212 Susceptibility of widely diverse influenza a viruses to PB2 polymerase inhibitor pimodivir. In the phase 2a clinical trial of pimodivir, variant virus containing M431I was reported to display 12.5-fold reduced in vitro replication capacity compared to wild-type virus. 2021 Antiviral research Discussion IV M431I 70 75 33581212 Susceptibility of widely diverse influenza a viruses to PB2 polymerase inhibitor pimodivir. Information on how H357N may affect viral fitness and pathogenicity is limited. 2021 Antiviral research Discussion IV H357N 19 24 33581212 Susceptibility of widely diverse influenza a viruses to PB2 polymerase inhibitor pimodivir. Our study showed that H357N, found in PB2 of ty/MN/80 viruses, indeed conferred a high level of pimodivir-resistance. 2021 Antiviral research Discussion IV H357N 22 27 PB2 38 41 33581212 Susceptibility of widely diverse influenza a viruses to PB2 polymerase inhibitor pimodivir. Zhu and colleagues demonstrated the role of H357N, which was originally found in a mouse adapted A(H1N1)pdm09 virus, on in vitro replicative fitness and pathogenicity in mice. 2021 Antiviral research Discussion IV H357N 44 49 33604005 In silico analysis and molecular characterization of Influenza A (H1N1) pdm09 virus circulating and causing major outbreaks in central India, 2009-2019. According to him, S202T and D239G are responsible for increased mortality and morbidity. 2020 Iranian journal of microbiology Discussion IV S202T;D239G 18;28 23;33 33604005 In silico analysis and molecular characterization of Influenza A (H1N1) pdm09 virus circulating and causing major outbreaks in central India, 2009-2019. D114N, S202 T, S220 T and K300E amino acid substitutions in HA protein are characteristics of genogroup 6. 2020 Iranian journal of microbiology Discussion IV D114N;S202T;S220T;K300E 0;7;15;26 5;13;21;31 HA 60 62 33604005 In silico analysis and molecular characterization of Influenza A (H1N1) pdm09 virus circulating and causing major outbreaks in central India, 2009-2019. Frequency distribution of amino acid substitution from 2009 to 2019 at different key positions of HA protein among 59 studied H1N1 viruses isolated in Central India resulted that S220T (100%) amino acid substitution was highly frequent similar to study conducted in MEENA followed by S202T (84.7%), K300E (76.27%), A273T (74.57%), K180Q (69.4%), A214T (6.77%), S179N (3.38%), I233T (3.38%), V251I (3.38%), G279E (3.38%), S181T (3.38%), V216 (3.38%), A151T (1.69%), H155R (1.69%), I166M (1.69%), G172E (1.69%), Y175S (1.69%), K177R (1.69%), S200P (1.69%), S221P (1.69%), D239G (1.69%), D239Y (1.69%), N245I (1.69%), Y246N (1.69%), T262P (1.69%), T266M (1.69%). 2020 Iranian journal of microbiology Discussion IV S220T;S202T;K300E;A273T;K180Q;A214T;S179N;I233T;V251I;G279E;S181T;A151T;H155R;I166M;G172E;Y175S;K177R;S200P;S221P;D239G;D239Y;N245I;Y246N;T262P;T266M 179;284;299;315;331;346;361;376;391;406;421;450;465;480;495;510;525;540;555;570;585;600;615;630;645 184;289;304;320;336;351;366;381;396;411;426;455;470;485;500;515;530;545;560;575;590;605;620;635;650 HA 98 100 33604005 In silico analysis and molecular characterization of Influenza A (H1N1) pdm09 virus circulating and causing major outbreaks in central India, 2009-2019. I223T amino acid substitution linked to increased binding affinity to human alpha2-6-linked sialic acids receptors. 2020 Iranian journal of microbiology Discussion IV I223T 0 5 33604005 In silico analysis and molecular characterization of Influenza A (H1N1) pdm09 virus circulating and causing major outbreaks in central India, 2009-2019. K180Q substitution triggers conformational variation to ligand binding which might important for virulence. 2020 Iranian journal of microbiology Discussion IV K180Q 0 5 33604005 In silico analysis and molecular characterization of Influenza A (H1N1) pdm09 virus circulating and causing major outbreaks in central India, 2009-2019. S179 N associated with glycosylation is responsible for enhanced pathogenicity of virus by prevention of antigenic sites for immune recognition. 2020 Iranian journal of microbiology Discussion IV S179N 0 6 33604005 In silico analysis and molecular characterization of Influenza A (H1N1) pdm09 virus circulating and causing major outbreaks in central India, 2009-2019. S200P alter receptor binding affinity. 2020 Iranian journal of microbiology Discussion IV S200P 0 5 33604005 In silico analysis and molecular characterization of Influenza A (H1N1) pdm09 virus circulating and causing major outbreaks in central India, 2009-2019. S200P and S202 T substitutions are responsible for enhancement of receptor-binding avidity whereas A214T substitution linked to decrease binding avidity. 2020 Iranian journal of microbiology Discussion IV S200P;S202T;A214T 0;10;99 5;16;104 33604005 In silico analysis and molecular characterization of Influenza A (H1N1) pdm09 virus circulating and causing major outbreaks in central India, 2009-2019. The amino acid substitutions such as P100S, S101N, D114N, K180Q, S181T, S202T, S220T, I233T, A273T, K300E present in the isolates from Central India in the HA gene are also reflected in the recent studies from other parts of India and world. 2020 Iranian journal of microbiology Discussion IV P100S;S101N;D114N;K180Q;S181T;S202T;S220T;I233T;A273T;K300E 37;44;51;58;65;72;79;86;93;100 42;49;56;63;70;77;84;91;98;105 HA 156 158 33647314 The active form of the influenza cap-snatching endonuclease inhibitor baloxavir marboxil is a tight binding inhibitor. Here we employed a biochemical approach to study mechanisms associated with the high potency of the drug and its reduction in the presence of I38T. 2021 The Journal of biological chemistry Discussion IV I38T 142 146 33647314 The active form of the influenza cap-snatching endonuclease inhibitor baloxavir marboxil is a tight binding inhibitor. It will be interesting to see how the I38T mutation affects these parameters. 2021 The Journal of biological chemistry Discussion IV I38T 38 42 33647314 The active form of the influenza cap-snatching endonuclease inhibitor baloxavir marboxil is a tight binding inhibitor. Mutations at position I38, predominantly I38T, were shown to confer resistance to BXM in vitro and in vivo. 2021 The Journal of biological chemistry Discussion IV I38T 41 45 33647314 The active form of the influenza cap-snatching endonuclease inhibitor baloxavir marboxil is a tight binding inhibitor. The endonuclease reaction was monitored with purified FluB-ht WT and FluB-ht PA I38T in the presence of Mg2+ and a 20mer, capped model RNA. 2021 The Journal of biological chemistry Discussion IV I38T 80 84 PA 77 79 33647314 The active form of the influenza cap-snatching endonuclease inhibitor baloxavir marboxil is a tight binding inhibitor. The FluB-ht PA I38T mutant shows the same pattern, albeit with reduced intensity when compared with WT. 2021 The Journal of biological chemistry Discussion IV I38T 15 19 PA 12 14 33647314 The active form of the influenza cap-snatching endonuclease inhibitor baloxavir marboxil is a tight binding inhibitor. We observed an 18-fold difference in Kiapp between WT and I38T FluB-ht, while plots of IC50 as a function of enzyme concentration yielded in both cases linear plots with slopes of ~0.5. 2021 The Journal of biological chemistry Discussion IV I38T 58 62 33679636 Improved in vitro Efficacy of Baloxavir Marboxil Against Influenza A Virus Infection by Combination Treatment With the MEK Inhibitor ATR-002. Here we demonstrate that, despite the potent effect of BXA against both WT strains, its antiviral effect was significantly reduced by ~40% against the mutant strains, while ATR-002 still impaired the PA-I38T mutants to a similar extent as the respective wild type strains (Figure 3). 2021 Frontiers in microbiology Discussion IV I38T 203 207 PA 200 202 33679636 Improved in vitro Efficacy of Baloxavir Marboxil Against Influenza A Virus Infection by Combination Treatment With the MEK Inhibitor ATR-002. In regard to comparability and to exclude unwanted additional mutations/differences, we generated these viruses as recombinant wild type and mutant variants (rgH1N1-WT/- PA-I38T, rgH3N2-WT/- PA-I38T) allowing us to perform unbiased comparison of the activities exerted by BXA or ATR-002. 2021 Frontiers in microbiology Discussion IV I38T;I38T 173;194 177;198 PA;PA 170;191 172;193 33679636 Improved in vitro Efficacy of Baloxavir Marboxil Against Influenza A Virus Infection by Combination Treatment With the MEK Inhibitor ATR-002. Moreover, another study reported that even though the IC50 of BXA against a wide type pandemic H1N1-type IAV (WT/H1N1 pdm09) was 0.42 +- 0.37 nM, its IC50 against the I38T variant was 41.96 +- 9.42 nM; and the IC50 value for WT H3N2 virus was 0.66 +- 0.17 nM, but 139.73 +- 24.97 nM for the I38t mutant. 2021 Frontiers in microbiology Discussion IV I38T 167 171 33679636 Improved in vitro Efficacy of Baloxavir Marboxil Against Influenza A Virus Infection by Combination Treatment With the MEK Inhibitor ATR-002. On the contrary, in a growth-competition experiment, the growth-kinetics analysis revealed that the I38T substitution impairs the replication fitness of A/H1N1pdm viruses, while this mutation does not alter the fitness of A/H3N2 viruses in vitro. 2021 Frontiers in microbiology Discussion IV I38T 100 104 33679636 Improved in vitro Efficacy of Baloxavir Marboxil Against Influenza A Virus Infection by Combination Treatment With the MEK Inhibitor ATR-002. The PA-I38T mutation was described to be associated with reduced IAV susceptibility to BXA and IAV variants harboring an I38T, I38F, or I38M substitution showed reduced BXA susceptibility during phase 2 and phase 3 trials, respectively. 2021 Frontiers in microbiology Discussion IV I38T;I38T;I38F;I38M 7;121;127;136 11;125;131;140 PA 4 6 33679636 Improved in vitro Efficacy of Baloxavir Marboxil Against Influenza A Virus Infection by Combination Treatment With the MEK Inhibitor ATR-002. To evaluate whether the indirectly antiviral acting host-targeting MEK inhibitor could overcome viral resistance of IAV carrying substitutions mounted against the directly acting antiviral BXA, the inhibitory activity of ATR-002 was validated against two recombinant IAVs, a H1N1- and a H3N2-strain, both either wild type or carrying the BXA resistance-associated PA-I38T mutation. 2021 Frontiers in microbiology Discussion IV I38T 367 371 PA 364 366 33782012 Discovery of a Novel Respiratory Syncytial Virus Replication Inhibitor. In our study, we employed a novel counterscreen assay in which inhibition of the F_K394R mutant virus replication by compounds was tested to filter out a part of the fusion inhibitors. 2021 Antimicrobial agents and chemotherapy Discussion IV K394R 83 88 33782012 Discovery of a Novel Respiratory Syncytial Virus Replication Inhibitor. More importantly, L(T1684A) variants were not found in the RSV sequences currently deposited in GenBank, suggesting that the likelihood of naturally occurring resistance against triazole-1 is low. 2021 Antimicrobial agents and chemotherapy Discussion IV T1684A 20 26 33782012 Discovery of a Novel Respiratory Syncytial Virus Replication Inhibitor. Moreover, in our study, the minigenome assay was successfully used to verify if the T1684A mutation alone is sufficient to cause resistance to triazole-1, demonstrating that the minigenome assay is a very useful and convenient reverse genetics tool. 2021 Antimicrobial agents and chemotherapy Discussion IV T1684A 84 90 33782012 Discovery of a Novel Respiratory Syncytial Virus Replication Inhibitor. Of course, concerns over the potential of rapid generation of resistance mutants in clinical applications due to the rapid appearance of resistant L(T1684A) variants in the in vitro experiment are reasonable. 2021 Antimicrobial agents and chemotherapy Discussion IV T1684A 149 155 33782012 Discovery of a Novel Respiratory Syncytial Virus Replication Inhibitor. One important question to be answered in the future is that of the fitness of the L(T1684A) mutant compared with the wild-type virus. 2021 Antimicrobial agents and chemotherapy Discussion IV T1684A 84 90 33782012 Discovery of a Novel Respiratory Syncytial Virus Replication Inhibitor. The rationale for using the F_K394R mutant virus is that the mutation was reported to confer resistance to different chemical types of fusion inhibitors. 2021 Antimicrobial agents and chemotherapy Discussion IV K394R 30 35 33782012 Discovery of a Novel Respiratory Syncytial Virus Replication Inhibitor. This result is consistent with the identification of L(T1684A) as the resistant mutation for triazole-1, as T1684A and its neighboring sequences are highly conserved in subtype A and subtype B viruses. 2021 Antimicrobial agents and chemotherapy Discussion IV T1684A;T1684A 55;108 61;114 33782012 Discovery of a Novel Respiratory Syncytial Virus Replication Inhibitor. Triazole-1 most likely has a different mechanism of action from that of BI compound D, which targets cotranscriptional mRNA guanylylation, as T1684 is distant from the L protein mutations in compound D-resistant viruses (I1381S, E1269D, and L1421F). 2021 Antimicrobial agents and chemotherapy Discussion IV I1381S;E1269D;L1421F 221;229;241 227;235;247 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. A meta-analysis of published data from 2009 to 2012 showed that there is a statistically significant association between the mutation D222G and severe disease and fatality. 2021 PloS one Discussion IV D222G 134 139 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. A(H1N1)pdm09 viruses with the D222G mutation in HA have a preferential affinity for SA-alpha-2,3 receptors. 2021 PloS one Discussion IV D222G 30 35 HA 48 50 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. Also, the D222G mutation was more common than D222N in samples from fatal cases in other studies. 2021 PloS one Discussion IV D222G;D222N 10;46 15;51 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. An increase in the frequency of D222G/N mutations was found in the lungs compared to the upper parts of the respiratory system (Table 5). 2021 PloS one Discussion IV D222G;D222N 32;32 39;39 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. Analysis of the presence of major and minor virus variants with the mutations also revealed the coexistence of two mutations D222G and D222N in 41% of the studied fatal cases (mutation frequency from 1-93.9%). 2021 PloS one Discussion IV D222G;D222N 125;135 130;140 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. Analysis of the presence of polymorphism at the 222 position in the HA protein using NGS data revealed D222G/N mutations in minor virus variants (proportion of virus variants with the mutations ranged from 1% to 47%) in samples from 9 fatal cases of influenza A(H1N1)pdm09 (Table 2). 2021 PloS one Discussion IV D222G;D222N 103;103 110;110 HA 68 70 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. At the stage of infection, D222G/N mutations may be absent or not dominant. 2021 PloS one Discussion IV D222G;D222N 27;27 34;34 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. D222G/N mutations were detected in major virus variants in 38% of fatal cases (Table 1). 2021 PloS one Discussion IV D222G;D222N 0;0 7;7 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. Despite the low prevalence of viruses with D222G/N mutations in the general circulation, it is important to monitor the circulation of viruses with these mutations for epidemiological prognosis. 2021 PloS one Discussion IV D222G;D222N 43;43 50;50 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. Due to the increased mortality associated with A(H1N1)pdm09 observed in some reports it is important to study pathogenicity markers such as HA D222G/N and other virulence and pathogenicity markers. 2021 PloS one Discussion IV D222G;D222N 143;143 150;150 HA 140 142 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. Epidemiological significance of D222G/N mutations. 2021 PloS one Discussion IV D222G;D222N 32;32 39;39 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. For this purpose, the NGS sequencing method was optimized in order to increase the coverage (number of reads) of the HA region containing the D222G/N mutation position (an amplicon containing the amino acid 222 codon was used for targeted NGS sequencing). 2021 PloS one Discussion IV D222G;D222N 142;142 149;149 HA 117 119 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. If influenza viruses with D222G/N mutations are already present during an infection, then the accumulation of viruses with the mutations can occur more rapidly, contributing to disease severity and the development of clinical sequelae. 2021 PloS one Discussion IV D222G;D222N 26;26 33;33 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. In a previous study the presence of minor virus variants with the D222G mutation (less than 1%) was also observed in all analyzed influenza virus samples from mild cases. 2021 PloS one Discussion IV D222G 66 71 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. In addition, the observed accumulation of viruses with D222G/N mutations in the lungs of patients with severe influenza can lead to the release of the mutated virus from the lungs into the upper respiratory tract and this may possibly lead to greater danger in persons in contact with those with the disease, especially those in the influenza risk group. 2021 PloS one Discussion IV D222G;D222N 55;55 62;62 Influenza 103 119 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. In addition, the use of targeted NGS revealed the low frequency of D222G/N mutations (from 0.2 to 0.6%) in samples from 14 fatal cases of influenza A(H1N1)pdm09 (Table 3). 2021 PloS one Discussion IV D222G;D222N 67;67 74;74 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. In animal studies, viruses with the D222G mutation have also been shown to be more virulent than the wild type. 2021 PloS one Discussion IV D222G 36 41 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. In the analysis of the samples from the 2018-2019 epidemic season, a major virus variant with mutation D222G (87%) was detected in one swab from a fatal case taken prior to fatal outcome (Table 5); in addition, minor virus variants with mutations D222G (11.5%) and D222N (11.6%) were detected in one swab from a fatal case taken prior to fatal outcome (Table 5). 2021 PloS one Discussion IV D222G;D222G;D222N 103;247;265 108;252;270 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. In the studied samples, mutation D222G was observed more often than D222N in samples from fatal cases (14 D222G and 4 D222N in major virus variant) (Table 1). 2021 PloS one Discussion IV D222G;D222N;D222G;D222N 33;68;106;118 38;73;111;123 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. It should be noted that the risk group for severe disease caused by influenza A(H1N1)pdm09 viruses with 222D/G/N polymorphism should include people with underlying lung conditions associated with an increased number of regenerating type 2 pneumocytes, which provide preferential receptor binding for viruses with D222G/N mutations (e.g. 2021 PloS one Discussion IV D222G;D222N 313;313 320;320 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. Molecular genetic analysis revealed the significant presence of D222G/N mutations in the hemagglutinin receptor-binding site. 2021 PloS one Discussion IV D222G;D222N 64;64 71;71 HA 89 102 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. Monitoring of A(H1N1)pdm09 viruses in Russia in the 2017-2018 epidemic season revealed the significant presence of D222G/N mutations in major and minor viral variants in samples from fatal influenza cases. 2021 PloS one Discussion IV D222G;D222N 115;115 122;122 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. More research is needed to understand the role of D222G/N mutations in A(H1N1)pdm09 pathogenicity. 2021 PloS one Discussion IV D222G;D222N 50;50 57;57 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. Moreover, the D222N mutation was often present in the minor variant. 2021 PloS one Discussion IV D222N 14 19 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. Mutation D222N was also associated with severe disease and fatality, but this association was not statistically significant and the study did not show any association of D222E with severe disease. 2021 PloS one Discussion IV D222N;D222E 9;170 14;175 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. Optimization of the sequencing method led to an increase in coverage by 10-50 times (up to 100,000 reads per codon) and made it possible to detect the presence of the D222G/N mutation with a detection limit of 0.2%. 2021 PloS one Discussion IV D222G;D222N 167;167 174;174 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. Some researchers have suggested that the increased virulence and pathogenicity of influenza A(H1N1)pdm09 virus may be due to the presence of D222G/N mutations in HA. 2021 PloS one Discussion IV D222G;D222N 141;141 148;148 HA 162 164 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. Such high levels of the D222G/N mutation in A(H1N1)pdm09 viruses from severe and fatal cases have been shown in a number of previous studies. 2021 PloS one Discussion IV D222G;D222N 24;24 31;31 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. The absence of a significant effect of D222G/N mutations on the antigenic properties of the virus was shown in our previous studies and another study. 2021 PloS one Discussion IV D222G;D222N 39;39 46;46 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. The affinity of A(H1N1)pdm09 viruses with mutation HA D222N for both SA-alpha-2,3 and SA-alpha-2,6 receptors was shown to be increased compared to the wild type, with stronger affinity for SA-alpha-2,3 receptors. 2021 PloS one Discussion IV D222N 54 59 HA 51 53 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. The D222G mutation is caused by an A to G transition at the second codon position (GAT to GGT), and the mutation D222N results from a reverse G to A transition at the first codon position (GAT to AAT). 2021 PloS one Discussion IV D222G;D222N 4;113 9;118 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. The D222G mutation occurs in the hemagglutinin (HA) gene in the HA1 region. 2021 PloS one Discussion IV D222G 4 9 HA;HA1;HA 48;64;33 50;67;46 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. The D222G/N mutations were not detected in non-lethal cases in major or minor virus variants at frequencies of more than 1% in a sample in influenza cases in Russia during the 2017-2019 epidemiological seasons. 2021 PloS one Discussion IV D222G;D222N 4;4 11;11 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. The importance of epidemiological monitoring of D222G/N mutations was recognised by the WHO in 2009. 2021 PloS one Discussion IV D222G;D222N 48;48 55;55 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. The presence of a significant proportion of viruses with D222G/N mutations in the URT may lead to the adaptation and evolution of the viruses to the URT receptors while preserving affinity to the LRT receptors. 2021 PloS one Discussion IV D222N;D222G 57;57 64;64 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. The presence of D222G/N was discovered in a significant proportion of A(H1N1)pdm09 fatal cases. 2021 PloS one Discussion IV D222G;D222N 16;16 23;23 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. The presence of the D222G/N mutations was also demonstrated in cases with recovery but only at a very low frequency (from 0.2 to 0.4%) (Table 7) in all samples with sufficient NGS coverage (20,000 reads per codon and more). 2021 PloS one Discussion IV D222G;D222N 20;20 27;27 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. The results of the NGS analysis indicate the importance of testing for the possible presence of D222G/N mutations in minor variants in most circulating viruses. 2021 PloS one Discussion IV D222G;D222N 96;96 103;103 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. The simultaneous presence of wild-type virus and viruses with D222G/N mutations could lead to higher transmissibility of the mixture compared to a viral sample with 100% of the virus variant with D222G/N mutations, since viruses from the mixture have an affinity for both types of receptor and may enter and reproduce in both the URT and LRT. 2021 PloS one Discussion IV D222G;D222N;D222G;D222N 62;62;196;196 69;69;203;203 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. The study of D222G/N mutations is important for assessing their effect on the virological properties of the A(H1N1)pdm09 virus. 2021 PloS one Discussion IV D222G;D222N 13;13 20;20 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. This indicates that the vaccine remains effective in protecting against variants of viruses with D222G/N mutations. 2021 PloS one Discussion IV D222G;D222N 97;97 104;104 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. This may contribute to the higher occurrence of the D222G mutation compared to D222N and other variants. 2021 PloS one Discussion IV D222G;D222N 52;79 57;84 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. Thus, D222G/N mutations (>1% in sequenced sample) were detected in 57% of the samples from all studied fatal cases. 2021 PloS one Discussion IV D222G;D222N 6;6 13;13 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. Thus, D222G/N mutations increase virus tropism to the cells in the human lower respiratory tract, which favors the development of viral pneumonia. 2021 PloS one Discussion IV D222G;D222N 6;6 13;13 Pneumonia 130 145 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. Thus, monitoring influenza viruses A(H1N1)pdm09 for the presence of D222G/N mutations in circulation, including assessing the proportion of minor virus variants, would be of epidemiological significance. 2021 PloS one Discussion IV D222G;D222N 68;68 75;75 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. We thus found D222G/N mutations (with a frequency of 0.2-98%) in samples from all studied fatal cases with sufficient NGS coverage (20,000 reads per codon and more) (Tables 1-3). 2021 PloS one Discussion IV D222G;D222N 14;14 21;21 33914831 Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. While D222G/N mutations are often associated with severe disease and mortality, the association of D222Y/A/V/E mutations with the severity of the disease has not been established. 2021 PloS one Discussion IV D222G;D222N;D222Y;D222A;D222V;D222E 6;6;99;99;99;99 13;13;110;110;110;110 33941189 Cell culture-based production and in vivo characterization of purely clonal defective interfering influenza virus particles. The protective activity of MX1 against IAV was originally discovered in A2G mice that carry a wild-type Mx1 allele. 2021 BMC biology Discussion IV A2G 72 75 33941189 Cell culture-based production and in vivo characterization of purely clonal defective interfering influenza virus particles. The wild type functional Mx1 allele has been transferred from A2G to C57BL/6 mice to generate strain B6.A2G-Mx1r/r (B6-Mx1r/r). 2021 BMC biology Discussion IV A2G 62 65 33975931 Analysis of the Evolution of Pandemic Influenza A(H1N1) Virus Neuraminidase Reveals Entanglement of Different Phenotypic Characteristics. Analysis of NA antigenicity using a recombinant protein approach in combination with polyclonal ferret sera revealed a relatively large effect of substitutions in the 2SBS (N369K and K432E). 2021 mBio Discussion IV N369K;K432E 173;183 178;188 12 14 33975931 Analysis of the Evolution of Pandemic Influenza A(H1N1) Virus Neuraminidase Reveals Entanglement of Different Phenotypic Characteristics. as exemplified by K432E affecting both NA activity and antigenicity, may be an important determining factor in NA evolution. 2021 mBio Discussion IV K432E 18 23 NA;NA 39;111 41;113 33975931 Analysis of the Evolution of Pandemic Influenza A(H1N1) Virus Neuraminidase Reveals Entanglement of Different Phenotypic Characteristics. Because of the multiple effects of K432E on NA activity, it may require a receptive background for its selection. 2021 mBio Discussion IV K432E 35 40 44 46 33975931 Analysis of the Evolution of Pandemic Influenza A(H1N1) Virus Neuraminidase Reveals Entanglement of Different Phenotypic Characteristics. N369K increased while K432E decreased cleavage of fetuin-containing alpha2,3-linked SIAs but not that of monovalent substrates or of transferrin containing only alpha2,6-linked SIAs. 2021 mBio Discussion IV N369K;K432E 0;22 5;27 33975931 Analysis of the Evolution of Pandemic Influenza A(H1N1) Virus Neuraminidase Reveals Entanglement of Different Phenotypic Characteristics. N369K was previously reported to abolish binding of monoclonal antibody HF5 to CA/09 NA, suggesting that it is part of an epitope that may also be targeted by human NA-specific antibodies. 2021 mBio Discussion IV N369K 0 5 NA;NA 85;165 87;167 33975931 Analysis of the Evolution of Pandemic Influenza A(H1N1) Virus Neuraminidase Reveals Entanglement of Different Phenotypic Characteristics. Of note, the negative effect of K432E on cleavage of multivalent substrates was partly compensated for by N386K, which resulted in the loss of an N-glycosylation consensus sequence. 2021 mBio Discussion IV K432E;N386K 32;106 37;111 33975931 Analysis of the Evolution of Pandemic Influenza A(H1N1) Virus Neuraminidase Reveals Entanglement of Different Phenotypic Characteristics. Of the several substitutions that are located relatively close to the active site (N200S, N248D, V241I, and K432E), K432E had the largest effect on NA catalytic activity. 2021 mBio Discussion IV N200S;N248D;V241I;K432E;K432E 83;90;97;108;116 88;95;102;113;121 148 150 33975931 Analysis of the Evolution of Pandemic Influenza A(H1N1) Virus Neuraminidase Reveals Entanglement of Different Phenotypic Characteristics. Particularly low NA activity, at least for multivalent substrates, was observed after the substitution K432E in the 2SBS (in NC/13 NA), indicating that low-affinity binding via this site may also enhance NA catalytic activity for a human virus. 2021 mBio Discussion IV K432E 103 108 NA;NA;NA 17;131;204 19;133;206 33975931 Analysis of the Evolution of Pandemic Influenza A(H1N1) Virus Neuraminidase Reveals Entanglement of Different Phenotypic Characteristics. Substitution K432E, which resulted in the formation of two additional hydrogen bonds with water molecules, may therefore indirectly affect the catalytic site. 2021 mBio Discussion IV K432E 13 18 33975931 Analysis of the Evolution of Pandemic Influenza A(H1N1) Virus Neuraminidase Reveals Entanglement of Different Phenotypic Characteristics. The K432E substitution also altered antigenicity of NA, which may explain its selection. 2021 mBio Discussion IV K432E 4 9 52 54 33975931 Analysis of the Evolution of Pandemic Influenza A(H1N1) Virus Neuraminidase Reveals Entanglement of Different Phenotypic Characteristics. The positive effect of N386K may therefore rather be explained by its localization in a Ca2+-binding site. 2021 mBio Discussion IV N386K 23 28 33975931 Analysis of the Evolution of Pandemic Influenza A(H1N1) Virus Neuraminidase Reveals Entanglement of Different Phenotypic Characteristics. Thus, changes in NA activity and antigenicity, e.g., resulting from K432E, may subsequently drive compensatory substitutions in NA (such as N386K) but also in HA. 2021 mBio Discussion IV K432E;N386K 68;140 73;145 HA;NA;NA 159;17;128 161;19;130 33975931 Analysis of the Evolution of Pandemic Influenza A(H1N1) Virus Neuraminidase Reveals Entanglement of Different Phenotypic Characteristics. While the K432E substitution was maintained, enzymatic activity of subsequent NAs increased again by additional substitutions. 2021 mBio Discussion IV K432E 10 15 78 81 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. 750-PFU infection with Y17H stimulated local lymphocyte infiltration and was previously shown to enhance type I interferon responses in dendritic cells. 2021 PloS one Discussion IV Y17H 23 27 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. At these times, stimulation of innate immune responses to infection by Y17H may help control viral replication, especially during the early stages of infection, while subsequent CD4 and CD8 activation help promote viral clearance and recovery. 2021 PloS one Discussion IV Y17H 71 75 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. In agreement with these findings, we found that infection with both WT and Y17H IAVs changed the extracellular and intracellular pH during infection. 2021 PloS one Discussion IV Y17H 75 79 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. In the background of A/England/195/2009 (H1N1), air-emitted Y17H virus produced significantly fewer plaques than those produced by E31K, which has an activation pH of 5.3. 2021 PloS one Discussion IV Y17H;E31K 60;131 64;135 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. Inoculation of Y17H at a 500-fold higher dose (i.e., 375,000 PFU) increased weight loss, mortality, viral loads, and lymphocyte infiltration to levels comparable to infection with 750 PFU WT. 2021 PloS one Discussion IV Y17H 15 19 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. Moreover, 375K infection with Y17H caused airway acidification as seen with WT with the following maximal reductions in extracellular pH: naris 6.5, nasal sinus 6.5, soft palate 6.4, and trachea 6.4. 2021 PloS one Discussion IV Y17H 30 34 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. Mutant virus HA1-Y17H had a destabilized HA protein that is activated at pH 6.0, and this virus has been shown to susceptible to inactivation in pH 6.4 media. 2021 PloS one Discussion IV Y17H 17 21 HA;HA1 41;13 43;16 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. Replication and host responses in mice infected with 750 PFU Y17H were highly attenuated. 2021 PloS one Discussion IV Y17H 61 65 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. Such effects are displayed, in part, in mice infected with Y17H or WT at 7 and 10 DPI. 2021 PloS one Discussion IV Y17H 59 63 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. The activation of DCs and alveolar macrophages in the Y17H group may also play important roles in clearing virus-infected cells by recruiting phagocytes, macrophages, and natural killer cells. 2021 PloS one Discussion IV Y17H 54 58 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. Under these mildly acidic conditions, Y17H is increasingly susceptible to inactivation; therefore, an increase in Y17H dose to overcome attenuation triggered a negative feedback loop that would be expected to attenuate replication further than type I interferon responses described previously. 2021 PloS one Discussion IV Y17H;Y17H 38;114 42;118 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. When inoculated intranasally in ferrets, Y17H-infected animals had reduced and delayed nasal titers and were incapable of transmitting by the airborne route; however, selection of a stabilized HA variant (H17H/R106K) that had an activation pH of 5.3 enabled airborne transmission. 2021 PloS one Discussion IV Y17H;H17H;R106K 41;205;210 45;209;215 HA 193 195 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. Y17H caused no weight loss or mortality, and viral titers were reduced compared to WT approximately 100-fold in nasal, soft palate, and tracheal tissues. 2021 PloS one Discussion IV Y17H 0 4 33979408 Interplay between H1N1 influenza a virus infection, extracellular and intracellular respiratory tract pH, and host responses in a mouse model. Y17H was previously shown to be susceptible to inactivation by pH 6.4 but not pH 7.0 media, thus its attenuation and resultant dampened acidification would be only expected to lead to feedback inactivation in the soft palate but not the naris, nasal sinus, or trachea. 2021 PloS one Discussion IV Y17H 0 4 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. A lower cost to polymerase activity of K229R might decrease the barrier to developing resistance in other influenza strains because the higher fitness of a K229R mutant might give more opportunities for a compensatory mutation to evolve. 2021 PLoS pathogens Discussion IV K229R;K229R 39;156 44;161 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. As the compensatory mutation, P653L, was present in our experiment, the favipiravir resistant virus transmitted successfully without a clear fitness cost unlike virus resistant to baloxavir. 2021 PLoS pathogens Discussion IV P653L 30 35 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. Despite the fitness advantage of the P653L single mutant, there was a slight increase in frequency of P653 within some ferrets. 2021 PLoS pathogens Discussion IV P653L 37 42 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. Given that the compensatory mutation, P653L, is not currently found in sequenced isolates, it suggests that favipiravir resistance without a fitness cost requires multiple mutations. 2021 PLoS pathogens Discussion IV P653L 38 43 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. Here a single mutation PA I38T gave resistance to baloxavir. 2021 PLoS pathogens Discussion IV I38T 26 30 PA 23 25 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. Here we showed that Eng195 polymerases reconstituted with PA harbouring N321K derive no additional benefit to polymerase activity from L653. 2021 PLoS pathogens Discussion IV N321K 72 77 PA 58 60 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. However, in a polymerase constellation based on the third wave virus Eng687 harbouring K229R in PB1, the P653L mutation was still required to fully compensate and to attain comparative activity to the wild-type polymerase. 2021 PLoS pathogens Discussion IV K229R;P653L 87;105 92;110 PB1 96 99 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. However, in all influenza A viruses tested so far, P653L is still required for full compensation of polymerase activity. 2021 PLoS pathogens Discussion IV P653L 51 56 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. However, we also found that the K229R mutation was lost over time within a single ferret which implies that if the virus can be outcompeted, resistance is less likely to spread in the absence of drug. 2021 PLoS pathogens Discussion IV K229R 32 37 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. In our model, reassortment, coupled with the fitness cost of the K229R single mutant, led to the rapid loss of the P653 allele. 2021 PLoS pathogens Discussion IV K229R 65 70 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. In our previous work, we have shown that PB1 K229R causes a reduction in polymerase activity compensated by PA P653L in H1N1, H3N2 and H7N9 viruses. 2021 PLoS pathogens Discussion IV K229R;P653L 45;111 50;116 PA;PB1 108;41 110;44 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. Interestingly, Eng195 seems to suffer a greater cost to polymerase activity of K229R than more recent H1N1 viruses containing N321K, H3N2 or H7N9. 2021 PLoS pathogens Discussion IV K229R;N321K 79;126 84;131 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. It is notable that in 4/5 ferrets where only R229 transmitted, K229 was not generated by reversion of the K229R mutation demonstrating that reassortment was necessary for the initial production of the K229 + L653 virus and that the R229 + L653 virus was fit and capable of a productive infection. 2021 PLoS pathogens Discussion IV K229R 106 111 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. No ferret had a frequency of P653 higher than K229 confirming that the main driver of frequency changes was the fitness advantage of the P653L single mutant. 2021 PLoS pathogens Discussion IV P653L 137 142 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. Our modelling showed that this was not due to the fitness cost of the R229 mutation as that was adequately compensated by L653, but rather due to a fitness advantage for the P653L single mutant. 2021 PLoS pathogens Discussion IV P653L 174 179 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. Surprisingly, PA N321K could partially compensate for the low polymerase activity of PB1 K229R despite not being structurally close to the active site (S4 Fig). 2021 PLoS pathogens Discussion IV N321K;K229R 17;89 22;94 PA;PB1 14;85 16;88 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. The authors found that there was a fitness cost to the PA I38T mutation which reduced transmission in competition with WT in H1N1 and H3N2 viruses although in ferrets infected with 100% resistant virus, the PA I38T mutation could still transmit. 2021 PLoS pathogens Discussion IV I38T;I38T 58;210 62;214 PA;PA 55;207 57;209 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. The P653 allele was only maintained when there was either no reassortment or no fitness cost to the K229R single mutant (see S1 Appendix). 2021 PLoS pathogens Discussion IV K229R 100 105 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. This might imply that favipiravir-resistance could evolve more easily in more recent pH1N1 viruses containing PA K321 as the cost to polymerase activity of the PB1 K229R mutation is lessened by PA N321K. 2021 PLoS pathogens Discussion IV K229R;N321K 164;197 169;202 PA;PA;PB1 110;194;160 112;196;163 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. We have previously shown that later isolates from the third wave could outcompete first wave isolates in vitro due to the N321K mutation in PA. 2021 PLoS pathogens Discussion IV N321K 122 127 PA 140 142 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. Whilst our simple model was capable of showing the rise in the P653L single mutant, it could not reproduce the stochastic changes in the frequency of P653. 2021 PLoS pathogens Discussion IV P653L 63 68 34061908 Favipiravir-resistant influenza A virus shows potential for transmission. Within the ferrets, there were likely areas within the nose infected by solely one type of virus meaning there would be reduced reassortment between the wildtype and K229R + P653L virus. 2021 PLoS pathogens Discussion IV K229R;P653L 166;174 171;179 34065033 Novel Clade 2.3.4.4b Highly Pathogenic Avian Influenza A H5N8 and H5N5 Viruses in Denmark, 2020. The genetic characterization revealed that one of the Danish H5N8 viruses contained a PB2-M64T substitution. 2021 Viruses Discussion IV M64T 90 94 PB2 86 89 34068322 Dual R108K and G189D Mutations in the NS1 Protein of A/H1N1 Influenza Virus Counteract Host Innate Immune Responses. A previous study showed that reinstating R108K, E125D, and G189D rescued the ability to inhibit CPSF30. 2021 Viruses Discussion IV R108K;E125D;G189D 41;48;59 46;53;64 34068322 Dual R108K and G189D Mutations in the NS1 Protein of A/H1N1 Influenza Virus Counteract Host Innate Immune Responses. Compared with the pandemic CA07 virus, the seasonal XJ49 virus contained N204S, R221Q, L229S mutations in PA-X, which may be the reason for the different morbidity, even though it contained the same triple R108K, E125D, and G189D mutations. 2021 Viruses Discussion IV N204S;R221Q;L229S;R108K;E125D;G189D 73;80;87;206;213;224 78;85;92;211;218;229 PA-X 106 110 34068322 Dual R108K and G189D Mutations in the NS1 Protein of A/H1N1 Influenza Virus Counteract Host Innate Immune Responses. Here, we compared the sequences of 2155 strains of H1N1 virus identified since 2009 and found that, although some had R108K and G189D mutations in the NS1 protein, most retained R108 and G189. 2021 Viruses Discussion IV R108K;G189D 118;128 123;133 NS1 151 154 34068322 Dual R108K and G189D Mutations in the NS1 Protein of A/H1N1 Influenza Virus Counteract Host Innate Immune Responses. Here, we used a double luciferase assay to examine the regulatory effect of the NS1 protein on the IFN promoter; we found that WT NS1 did not affect IFN expression, whereas NS1 harboring R108K/G189D suppressed it. 2021 Viruses Discussion IV R108K;G189D 187;193 192;198 NS1;NS1;NS1 80;130;173 83;133;176 34068322 Dual R108K and G189D Mutations in the NS1 Protein of A/H1N1 Influenza Virus Counteract Host Innate Immune Responses. In addition, the levels of IL-28 and IL-29 in cells infected with rXJ49-NS1mut decreased significantly, indicating that the R108K/G189D mutation in the NS1 protein could indeed inhibit host immunity during the early stage of virus infection by suppressing activation of the JAK-Stat pathway. 2021 Viruses Discussion IV R108K;G189D 124;130 129;135 NS1 152 155 34068322 Dual R108K and G189D Mutations in the NS1 Protein of A/H1N1 Influenza Virus Counteract Host Innate Immune Responses. It can be speculated that the R108K and G189D mutations in the NS1 protein enhance the innate immune response of the influenza virus against the host, resulting in the weakening of the host antiviral response, thus achieving the purpose of immune escape. 2021 Viruses Discussion IV R108K;G189D 30;40 35;45 NS1 63 66 34068322 Dual R108K and G189D Mutations in the NS1 Protein of A/H1N1 Influenza Virus Counteract Host Innate Immune Responses. We sequenced it and found that the NS1 protein contained the E125D mutation but retained R108 and G189. 2021 Viruses Discussion IV E125D 61 66 NS1 35 38 34070388 Molecular Characterization of Seasonal Influenza A and B from Hospitalized Patients in Thailand in 2018-2019. Among these additional substitutions, the V303I amino acid substitution has been reported in the A/H3N2 viruses with a low resistance to neuraminidase inhibitors. 2021 Viruses Discussion IV V303I 42 47 137 150 34070388 Molecular Characterization of Seasonal Influenza A and B from Hospitalized Patients in Thailand in 2018-2019. For H3N2 viruses, we did not detect the mutations conferring resistance to neuraminidase inhibitors such as E119V, D151E, I222V, R224K, E276D, N249S, R292K, and R371K in the NA gene segment of our H3N2 isolates. 2021 Viruses Discussion IV E119V;D151E;I222V;R224K;E276D;N249S;R292K;R371K 108;115;122;129;136;143;150;161 113;120;127;134;141;148;155;166 NA;NA 174;75 176;88 34070388 Molecular Characterization of Seasonal Influenza A and B from Hospitalized Patients in Thailand in 2018-2019. However, an additional mutation (S200P) was detected in the Thai A/H1N1 isolates. 2021 Viruses Discussion IV S200P 33 38 34070388 Molecular Characterization of Seasonal Influenza A and B from Hospitalized Patients in Thailand in 2018-2019. Our Flu B isolates contain amino acid substitutions at R152K, D198N, and R371K, which have been reported to associate with the neuraminidase inhibitor resistance phenotype of influenza B. 2021 Viruses Discussion IV R152K;D198N;R371K 55;62;73 60;67;78 127 140 34070388 Molecular Characterization of Seasonal Influenza A and B from Hospitalized Patients in Thailand in 2018-2019. The other six amino acid differences (Q51K, F74S, G77R, V81T, and T462I) for segment NA relative to A/Brisbane/02/2018 (H1N1) were found in our A/H1N1 isolates. 2021 Viruses Discussion IV Q51K;F74S;G77R;V81T;T462I 38;44;50;56;66 42;48;54;60;71 85 87 34070388 Molecular Characterization of Seasonal Influenza A and B from Hospitalized Patients in Thailand in 2018-2019. The sequence analysis of the NA gene reveals one potential NA drug-resistance substitution (V116A) but not other amino acid substitutions such as I117V, Q136K, D151A, Y155H, R156K, D198V, I222R, R224K, Q226H, E227D, E227Q, H274Y, R293K, N294S, E425G, and I436N. 2021 Viruses Discussion IV V116A;I117V;Q136K;D151A;Y155H;R156K;D198V;I222R;R224K;Q226H;E227D;E227Q;H274Y;R293K;N294S;E425G;I436N 92;146;153;160;167;174;181;188;195;202;209;216;223;230;237;244;255 97;151;158;165;172;179;186;193;200;207;214;221;228;235;242;249;260 NA;NA 29;59 31;61 34070388 Molecular Characterization of Seasonal Influenza A and B from Hospitalized Patients in Thailand in 2018-2019. These two mutations (Q51K and F74S) were similar to the recent isolated A/H1N1 viruses from Korea, but the substitution functionality remains unknown. 2021 Viruses Discussion IV Q51K;F74S 21;30 25;34 34070388 Molecular Characterization of Seasonal Influenza A and B from Hospitalized Patients in Thailand in 2018-2019. We also found a mutation at the receptor binding site (S220T) as previously reported in the Indian isolates which suspected that this mutation would increase the receptor-binding avidity. 2021 Viruses Discussion IV S220T 55 60 34070388 Molecular Characterization of Seasonal Influenza A and B from Hospitalized Patients in Thailand in 2018-2019. We also found additional mutations such as P99S, C123S, and S139 at NA segments. 2021 Viruses Discussion IV P99S;C123S 43;49 47;54 68 70 34070388 Molecular Characterization of Seasonal Influenza A and B from Hospitalized Patients in Thailand in 2018-2019. We found three additional amino acid differences (P126L, K220N, and V303I) in the NA gene of our A/H3N2 isolates relative to A/Kansas/14/2017 (H3N2). 2021 Viruses Discussion IV P126L;K220N;V303I 50;57;68 55;62;73 82 84 34131512 Identification of H3N2 NA and PB1-F2 genetic variants and their association with disease symptoms during the 2014-15 influenza season. An H3N2 influenza A virus genotype, NAg+F2P, within HA clade 3C.2a with a glycosylation site on the rim of the NA sialidase pocket and the mutation H75P in its PB1-F2 protein was identified. 2021 Virus evolution Discussion IV F2P;H75P 40;148 43;152 HA;NA;PB1F2 52;111;160 54;113;166 34131512 Identification of H3N2 NA and PB1-F2 genetic variants and their association with disease symptoms during the 2014-15 influenza season. Experiments with engineered viruses that differ only by the PB1-F2 mutation H75P should be performed to determine its role in increasing transmission. 2021 Virus evolution Discussion IV H75P 76 80 PB1F2 60 66 34131512 Identification of H3N2 NA and PB1-F2 genetic variants and their association with disease symptoms during the 2014-15 influenza season. In 1987, the PB1-F2 mutation R75H became fixed in human circulating H3N2 influenza viruses. 2021 Virus evolution Discussion IV R75H 29 33 PB1F2 13 19 34131512 Identification of H3N2 NA and PB1-F2 genetic variants and their association with disease symptoms during the 2014-15 influenza season. In the influenza virus strain A/Wuhan/359/1995, the PB1-F2 mutation H75R increased pathogenicity in mice. 2021 Virus evolution Discussion IV H75R 68 72 PB1F2 52 58 34131512 Identification of H3N2 NA and PB1-F2 genetic variants and their association with disease symptoms during the 2014-15 influenza season. It follows that the AA mutations S245N and S245T, which encode a glycosylation site near the sialidase rim of the 3C.2a NA, were selected to evade human immunity despite a detrimental effect on virus replication in hNEC cultures. 2021 Virus evolution Discussion IV S245N;S245T 33;43 38;48 120 122 34131512 Identification of H3N2 NA and PB1-F2 genetic variants and their association with disease symptoms during the 2014-15 influenza season. The D225G and NAg+F2P associations with increased pathogenicity or symptoms appeared after a pandemic and after an antigenic drift event that each led to viral population dominance by a single genotype and its descendants. 2021 Virus evolution Discussion IV F2P;D225G 18;4 21;9 34131512 Identification of H3N2 NA and PB1-F2 genetic variants and their association with disease symptoms during the 2014-15 influenza season. The NAg-F2H and NAg+F2P genotypes both had the HA mutations associated with antigenic drift, but the eventual dominance of the NAg+F2P genotype suggests a selective advantage over the NAg-F2H genotype. 2021 Virus evolution Discussion IV F2H;F2P;F2P;F2H 8;20;131;188 11;23;134;191 HA 47 49 34131512 Identification of H3N2 NA and PB1-F2 genetic variants and their association with disease symptoms during the 2014-15 influenza season. The seventy-fifth AA remained H until the 2014-15 season after which, as described here, the H75P mutation became dominant. 2021 Virus evolution Discussion IV H75P 93 97 34131512 Identification of H3N2 NA and PB1-F2 genetic variants and their association with disease symptoms during the 2014-15 influenza season. This selection occurred despite NAg+F2P viruses showing reduced infectious virus production in hNEC cultures. 2021 Virus evolution Discussion IV F2P 36 39 34131512 Identification of H3N2 NA and PB1-F2 genetic variants and their association with disease symptoms during the 2014-15 influenza season. Viruses with the NAg+F2P genotype were first detected in the 2014-15 influenza virus season and they outcompeted the NAg-F2H genotype in the 2015-16 season. 2021 Virus evolution Discussion IV F2P;F2H 21;121 24;124 34131512 Identification of H3N2 NA and PB1-F2 genetic variants and their association with disease symptoms during the 2014-15 influenza season. We also compared the growth in hNEC cultures of two virus isolates of the NAg-F2H and NAg+F2P genotypes. 2021 Virus evolution Discussion IV F2H;F2P 78;90 81;93 34131512 Identification of H3N2 NA and PB1-F2 genetic variants and their association with disease symptoms during the 2014-15 influenza season. While the NAg+F2P might have reduced in vitro fitness, in the presence of antibodies that inhibit NA activity, this virus could have an advantage over the NAg-F2H virus. 2021 Virus evolution Discussion IV F2P;F2H 14;159 17;162 98 100 34131512 Identification of H3N2 NA and PB1-F2 genetic variants and their association with disease symptoms during the 2014-15 influenza season. Within human H1N1 viruses, recent pandemic strains with the HA mutation D225G associated with infection of the lower airways, likely due to the increased binding of alpha2,3-linked sialic acid, and increased disease. 2021 Virus evolution Discussion IV D225G 72 77 HA 60 62 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. 6 and 7 show that in the WT NA, the 150-loop region undergoes conformational changes with large fluctuations between the open and closed states, whereas in the H274Y mutant NA, the 150-loop remains open. 2021 PeerJ Discussion IV H274Y 160 165 NA;NA 28;173 30;175 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. After the H274Y mutation, however, the structural fluctuation of the 150-loop became much smaller. 2021 PeerJ Discussion IV H274Y 10 15 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. As already mentioned, the 150 loop of NA is reported to open after the H274Y mutation (). 2021 PeerJ Discussion IV H274Y 71 76 38 40 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. Figure 6 shows the conformational changes of the 150-loop region (residues 147-152) in the WT and H274Y mutant NA by superimposing 100 snapshot images obtained from the MD simulations. 2021 PeerJ Discussion IV H274Y 98 103 111 113 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. Figure 7 shows the structural fluctuations of each residue as B-factor values for the WT and H274Y mutant NA. 2021 PeerJ Discussion IV H274Y 93 98 106 108 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. Hence, the NA-H274Y mutant becomes highly resistant to OTV. 2021 PeerJ Discussion IV H274Y 14 19 11 13 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. However, these interface residues remain in close contact with OTV even after H274Y mutation. 2021 PeerJ Discussion IV H274Y 78 83 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. In the case of the H274Y mutant NA, however, the 150-loop region is open, so D151 and R152 cannot form hydrogen bonds with OTV. 2021 PeerJ Discussion IV H274Y 19 24 32 34 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. In this study, we studied the drug resistance mechanism of the H5N1-H274Y mutant NA, and similar to their study, no water-mediated binding of OTV was observed. 2021 PeerJ Discussion IV H274Y 68 73 81 83 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. It has been indicated that the H274Y mutation in NA causes a large shift in the position of E276 compared to WT NA, facilitating a large shift in the orientation of OTV (). 2021 PeerJ Discussion IV H274Y 31 36 NA;NA 49;112 51;114 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. The above discussion based on the dRIN analysis supports these previous studies and provides a new perspective for comprehensively understanding the OTV drug resistance acquisition in influenza viruses associated with the H274Y mutation in NA. 2021 PeerJ Discussion IV H274Y 222 227 240 242 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. The detailed molecular mechanism of OTV drug resistance associated with the H274Y mutation in NA can be explained as follows based on the dRINs shown in. 2021 PeerJ Discussion IV H274Y 76 81 94 96 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. The occupancies of the interactions between Y274 and its surrounding residues, including these aromatic residues, remained almost unchanged after the H274Y mutation, except for S246, E276, R292, and H296. 2021 PeerJ Discussion IV H274Y 150 155 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. The results obtained from the dRIN analysis of the WT and H274Y mutant NA clearly showed that the residue interactions at both the OTV binding site and the H274Y mutation site were partially altered after the mutation. 2021 PeerJ Discussion IV H274Y;H274Y 58;156 63;161 71 73 34141489 Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus. Thus, it leads to a decrease in the binding free energy of the H274Y mutant NA-OTV complex. 2021 PeerJ Discussion IV H274Y 63 68 76 78 34164347 Risk of Environmental Exposure to H7N9 Influenza Virus via Airborne and Surface Routes in a Live Poultry Market in Hebei, China. Based on our data, we found that H115Q in PB1 and E627K in PB2 might play an important role in the pathogenesis of the MA-P5 virus in mice. 2021 Frontiers in cellular and infection microbiology Discussion IV H115Q;E627K 33;50 38;55 PB1;PB2 42;59 45;62 34164347 Risk of Environmental Exposure to H7N9 Influenza Virus via Airborne and Surface Routes in a Live Poultry Market in Hebei, China. In addition, the N66S mutation of the PB1-F2 protein of influenza A virus increased the virulence of the virus by inhibiting the interferon response in the host at an early stage. 2021 Frontiers in cellular and infection microbiology Discussion IV N66S 17 21 PB1F2 38 44 34164347 Risk of Environmental Exposure to H7N9 Influenza Virus via Airborne and Surface Routes in a Live Poultry Market in Hebei, China. Previous studies have shown that E627K of the PB2 gene has a limited effect on the transmission of influenza virus. 2021 Frontiers in cellular and infection microbiology Discussion IV E627K 33 38 PB2 46 49 34164347 Risk of Environmental Exposure to H7N9 Influenza Virus via Airborne and Surface Routes in a Live Poultry Market in Hebei, China. Some studies have shown that an H9N2 strain with the E627K and Q591K mutations in PB2 was more pathogenic in mice than the unmutated H9N2 strain. 2021 Frontiers in cellular and infection microbiology Discussion IV E627K;Q591K 53;63 58;68 PB2 82 85 34164347 Risk of Environmental Exposure to H7N9 Influenza Virus via Airborne and Surface Routes in a Live Poultry Market in Hebei, China. Studies have confirmed that the enhancement of the polymerase activity of the E627K mutation in the H7N9 PB2 protein was mainly because the PB2 627K residue forms a continuous fundamental plane in the PB2 627K domain, which is very important for RNA binding and polymerase function in mammalian cells. 2021 Frontiers in cellular and infection microbiology Discussion IV E627K 78 83 PB2;PB2;PB2 105;140;201 108;143;204 34164347 Risk of Environmental Exposure to H7N9 Influenza Virus via Airborne and Surface Routes in a Live Poultry Market in Hebei, China. Studies have found that the K480R mutation of the PB1 protein can cause H5N1 and H1N1 influenza viruses to polymerize in mice, and the increase in enzyme activity is believed to be due to changes in conserved amino acids. 2021 Frontiers in cellular and infection microbiology Discussion IV K480R 28 33 PB1 50 53 34164347 Risk of Environmental Exposure to H7N9 Influenza Virus via Airborne and Surface Routes in a Live Poultry Market in Hebei, China. The G622D mutation of the PB1 protein of H5N1 AIV weakened the binding of PB1 to vRNA, which significantly reduced the polymerase activity in mice, thereby weakening the virulence of the H5N1 virus. 2021 Frontiers in cellular and infection microbiology Discussion IV G622D 4 9 PB1;PB1 26;74 29;77 34164347 Risk of Environmental Exposure to H7N9 Influenza Virus via Airborne and Surface Routes in a Live Poultry Market in Hebei, China. The K480R mutation of the PB1 protein may originate from swine flu, and it is found at a higher frequency in swine flu viruses than in human and avian viruses. 2021 Frontiers in cellular and infection microbiology Discussion IV K480R 4 9 PB1 26 29 34164347 Risk of Environmental Exposure to H7N9 Influenza Virus via Airborne and Surface Routes in a Live Poultry Market in Hebei, China. We identified the E627K mutation in the PB2 gene and the H115Q mutation in the PB1 gene. 2021 Frontiers in cellular and infection microbiology Discussion IV E627K;H115Q 18;57 23;62 PB1;PB2 79;40 82;43 34207098 Virus Adaptation Following Experimental Infection of Chickens with a Domestic Duck Low Pathogenic Avian Influenza Isolate from the 2017 USA H7N9 Outbreak Identifies Polymorphic Mutations in Multiple Gene Segments. A 105I substitution was carried by 39% of turkeys, 10.4% mallards, 6% chicken, and less than 1% human H5Nx AIVs. 2021 Viruses Discussion IV A105I 0 6 34207098 Virus Adaptation Following Experimental Infection of Chickens with a Domestic Duck Low Pathogenic Avian Influenza Isolate from the 2017 USA H7N9 Outbreak Identifies Polymorphic Mutations in Multiple Gene Segments. A similar search of NP sequences demonstrated that 66% of mallard isolates carried 105M, whereas AIV isolated from chicken, turkey, or human species carried the substitution M105V in NP (93%, 89%, and 85%, respectively). 2021 Viruses Discussion IV M105V 174 179 NP;NP 20;183 22;185 34207098 Virus Adaptation Following Experimental Infection of Chickens with a Domestic Duck Low Pathogenic Avian Influenza Isolate from the 2017 USA H7N9 Outbreak Identifies Polymorphic Mutations in Multiple Gene Segments. Furthermore, position 143 is located in an HA antigenic site, and amino acid changes in natural isolates are principally chosen for changeable substitutions in this site such as P143S in H3HA protein during evolution. 2021 Viruses Discussion IV P143S 178 183 HA 43 45 34207098 Virus Adaptation Following Experimental Infection of Chickens with a Domestic Duck Low Pathogenic Avian Influenza Isolate from the 2017 USA H7N9 Outbreak Identifies Polymorphic Mutations in Multiple Gene Segments. have found PB2 change V649I in the genome of H5N2 HPAIV that contribute to increased virus fitness in chickens. 2021 Viruses Discussion IV V649I 22 27 PB2 11 14 34207098 Virus Adaptation Following Experimental Infection of Chickens with a Domestic Duck Low Pathogenic Avian Influenza Isolate from the 2017 USA H7N9 Outbreak Identifies Polymorphic Mutations in Multiple Gene Segments. have shown that T160A HA substitution in a H5N1 clade 2.3.4 virus resulted in the loss of a glycosylation site at 158N and led to enhanced binding specificity for human-type receptors and transmissibility among guinea pigs. 2021 Viruses Discussion IV T160A 16 21 HA 22 24 34207098 Virus Adaptation Following Experimental Infection of Chickens with a Domestic Duck Low Pathogenic Avian Influenza Isolate from the 2017 USA H7N9 Outbreak Identifies Polymorphic Mutations in Multiple Gene Segments. In addition, M105V and M105I were also found as the H5N2 HPAIV Clade 2.3.4.4 adapted to poultry in the USA. 2021 Viruses Discussion IV M105V;M105I 13;23 18;28 34207098 Virus Adaptation Following Experimental Infection of Chickens with a Domestic Duck Low Pathogenic Avian Influenza Isolate from the 2017 USA H7N9 Outbreak Identifies Polymorphic Mutations in Multiple Gene Segments. Interestingly, the H7N9 LPAIV duck isolate along with the H7N9 HPAIV chicken isolates carried M105I mutation in nucleoprotein genes. 2021 Viruses Discussion IV M105I 94 99 NP 112 125 34207098 Virus Adaptation Following Experimental Infection of Chickens with a Domestic Duck Low Pathogenic Avian Influenza Isolate from the 2017 USA H7N9 Outbreak Identifies Polymorphic Mutations in Multiple Gene Segments. It was previously demonstrated that amino acid substitutions in NS1 protein, including N139D of A/quail/Hong Kong/G1/97 (HK/97) H9N2, resulted in binding to the 30 kDa subunit of the cleavage and polyadenylation specificity factor (CPSF30), and, in consequence, inhibition of host immune response. 2021 Viruses Discussion IV N139D 87 92 NS1 64 67 34207098 Virus Adaptation Following Experimental Infection of Chickens with a Domestic Duck Low Pathogenic Avian Influenza Isolate from the 2017 USA H7N9 Outbreak Identifies Polymorphic Mutations in Multiple Gene Segments. Sequence analysis of RNA extracts obtained at day 3 post challenge from that bird showing the more severe clinical signs found a minor population of viruses shed thorough cloaca carrying the substitution K337N (K328N H3 numbering) (almost 40% of viruses) in the HA cleavage site, and A169V (A160V H3 numbering) (13% of viruses) in the HA receptor binding site. 2021 Viruses Discussion IV K337N;K328N;A169V;A160V 204;211;284;291 209;216;289;296 HA;HA 262;335 264;337 34207098 Virus Adaptation Following Experimental Infection of Chickens with a Domestic Duck Low Pathogenic Avian Influenza Isolate from the 2017 USA H7N9 Outbreak Identifies Polymorphic Mutations in Multiple Gene Segments. Some of the changes observed in the viral genomes of Mexican H7N3 between 2012 and 2016 were associated with a point mutation at A125T in HA, NP M105V, and NP S377N. 2021 Viruses Discussion IV A125T;M105V;S377N 129;145;159 134;150;164 HA;NP;NP 138;142;156 140;144;158 34240696 Nanopore metagenomic sequencing of influenza virus directly from respiratory samples: diagnosis, drug resistance and nosocomial transmission, United Kingdom, 2018/19 influenza season. A previous study reported a similar observation that the emergence and rapid global spread of adamantane resistant H3N2 IAVs (conferred by a S31N mutation in the Matrix protein 2) was associated with a single genotype generated through intra-subtype reassortment. 2021 Euro surveillance Discussion IV S31N 141 145 M2 162 178 34240696 Nanopore metagenomic sequencing of influenza virus directly from respiratory samples: diagnosis, drug resistance and nosocomial transmission, United Kingdom, 2018/19 influenza season. S31N now occurs in almost all circulating IAV globally, causing the cessation of use of adamantane to treat influenza. 2021 Euro surveillance Discussion IV S31N 0 4 34240696 Nanopore metagenomic sequencing of influenza virus directly from respiratory samples: diagnosis, drug resistance and nosocomial transmission, United Kingdom, 2018/19 influenza season. The genesis, prevalence, distribution and clinical impact of the S331R mutation merits additional study to evaluate potential implications for the clinical usefulness of oseltamivir, which is widely used as a first-line agent when treatment is indicated. 2021 Euro surveillance Discussion IV S331R 65 70 34240696 Nanopore metagenomic sequencing of influenza virus directly from respiratory samples: diagnosis, drug resistance and nosocomial transmission, United Kingdom, 2018/19 influenza season. The S331R NA mutation in H3N2 IAV has been associated with reduced susceptibility to oseltamivir. 2021 Euro surveillance Discussion IV S331R 4 9 10 12 34253060 In Vivo Therapy with M2e-Specific IgG Selects for an Influenza A Virus Mutant with Delayed Matrix Protein 2 Expression. A D238G (D225G in H3 numbering) mutation was detected in several samples at a high frequency. 2021 mBio Discussion IV D238G;D225G 2;9 7;14 34253060 In Vivo Therapy with M2e-Specific IgG Selects for an Influenza A Virus Mutant with Delayed Matrix Protein 2 Expression. For example, the I504V mutation in PB2, which we identified in several of the challenged SCID mice, is associated with an increased replication efficiency and increased virus yield. 2021 mBio Discussion IV I504V 17 22 PB2 35 38 34253060 In Vivo Therapy with M2e-Specific IgG Selects for an Influenza A Virus Mutant with Delayed Matrix Protein 2 Expression. From this, we can conclude that it may be unlikely that P10H/L or I11T escape mutants in M2e will emerge in a host that has been immunized with a M2e-based vaccine. 2021 mBio Discussion IV P10L;P10H;I11T 56;56;66 62;62;70 34253060 In Vivo Therapy with M2e-Specific IgG Selects for an Influenza A Virus Mutant with Delayed Matrix Protein 2 Expression. However, the PA I550T mutation, which emerged in some of the MAb 37- and MAb148-treated SCID mice, does not result in enhanced polymerase activity and even reduces the otherwise enhanced polymerase activity associated with PB2 K443R and PB2 I504V in the minireplicon system. 2021 mBio Discussion IV I550T;K443R;I504V 16;227;241 21;232;246 PA;PB2;PB2 13;223;237 15;226;240 34253060 In Vivo Therapy with M2e-Specific IgG Selects for an Influenza A Virus Mutant with Delayed Matrix Protein 2 Expression. hvPR8, which contains, among others, the PB2 I504V and PA I550L mutations, is a PR8 variant that is virulent in Mx1-congenic mice, although it exhibits normal sensitivity to growth restriction by this protein. 2021 mBio Discussion IV I504V;I550L 45;58 50;63 PA;PB2 55;41 57;44 34253060 In Vivo Therapy with M2e-Specific IgG Selects for an Influenza A Virus Mutant with Delayed Matrix Protein 2 Expression. In addition, MAb 148 could still bind to cells that had been infected with the P10H/L and I11T M2e escape variant viruses. 2021 mBio Discussion IV P10L;P10H;I11T 79;79;90 85;85;94 34253060 In Vivo Therapy with M2e-Specific IgG Selects for an Influenza A Virus Mutant with Delayed Matrix Protein 2 Expression. In addition, the E169K (E156K in H3 numbering) mutation that emerged in several of our samples, is known to increase the receptor binding avidity of PR8 HA. 2021 mBio Discussion IV E169K;E156K 17;24 22;29 HA 153 155 34253060 In Vivo Therapy with M2e-Specific IgG Selects for an Influenza A Virus Mutant with Delayed Matrix Protein 2 Expression. In addition, we also demonstrated that polymerase activity is enhanced when PB2 K443R or I504V are present. 2021 mBio Discussion IV K443R;I504V 80;89 85;94 PB2 76 79 34253060 In Vivo Therapy with M2e-Specific IgG Selects for an Influenza A Virus Mutant with Delayed Matrix Protein 2 Expression. In addition, we found several other mutations that have been linked to increased virulence in the polymerases at frequencies greater than 10%, e.g., D309N, R318K, and R355K in PB2 and V127I in PA. 2021 mBio Discussion IV D309N;R318K;R355K;V127I 149;156;167;184 154;161;172;189 PA;PB2 193;176 195;179 34253060 In Vivo Therapy with M2e-Specific IgG Selects for an Influenza A Virus Mutant with Delayed Matrix Protein 2 Expression. In MAb 37- and MAb 65-treated mice, M2e diversity was only observed at positions 10 and 11 and was limited to P10L/H and I11T, which appeared either alone or in combination. 2021 mBio Discussion IV P10L;P10H;I11T 110;110;121 116;116;125 34253060 In Vivo Therapy with M2e-Specific IgG Selects for an Influenza A Virus Mutant with Delayed Matrix Protein 2 Expression. It has been reported that the I504V mutation in PB2 and I550L in PA increase the in vitro polymerase activity and that a virus that carries these mutations displays higher pathogenicity in immunocompetent mice. 2021 mBio Discussion IV I504V;I550L 30;56 35;61 PA;PB2 65;48 67;51 34253060 In Vivo Therapy with M2e-Specific IgG Selects for an Influenza A Virus Mutant with Delayed Matrix Protein 2 Expression. Moreover, it has been stated that, when PR8-infected SCID mice were treated with a combination of MAbs that can bind to wild-type M2e, as well as P10H and P10L M2e variants, no viruses with an altered M2e sequence emerged. 2021 mBio Discussion IV P10H;P10L 146;155 150;159 34253060 In Vivo Therapy with M2e-Specific IgG Selects for an Influenza A Virus Mutant with Delayed Matrix Protein 2 Expression. reported that mice that had been immunized with M2e-MAP, which carries four identical human consensus M2e peptides, were fully protected against challenge with PR8-M2 P10L or PR8-M2 P10H virus. 2021 mBio Discussion IV P10L;P10H 167;182 171;186 M2;M2 164;179 166;181 34253060 In Vivo Therapy with M2e-Specific IgG Selects for an Influenza A Virus Mutant with Delayed Matrix Protein 2 Expression. Several of the mutations that were found in the current study (see Tables S2 to S7 in the supplemental material) have also been reported to be associated with influenza A virus mouse adaptation, e.g., D740N in PB2, M205I in PB1, and P199S in HA. 2021 mBio Discussion IV D740N;M205I;P199S 201;215;233 206;220;238 HA;PB1;PB2 242;224;210 244;227;213 34253060 In Vivo Therapy with M2e-Specific IgG Selects for an Influenza A Virus Mutant with Delayed Matrix Protein 2 Expression. The I504V mutation in PB2 was present at a frequency above 10% in virus isolated from half of the anti-M2e MAb-treated mice, and virus isolated from 20% of the mice carried a mutation at position 550 in PA. 2021 mBio Discussion IV I504V 4 9 PA;PB2 203;22 205;25 34253060 In Vivo Therapy with M2e-Specific IgG Selects for an Influenza A Virus Mutant with Delayed Matrix Protein 2 Expression. The reconstituted PR8-HPP virus (with PB2-K443R, PA-I550T, HA-A231S, HA-I361M, and HA-V458M mutations), however, displayed a general delay of viral protein expression in vitro. 2021 mBio Discussion IV K443R;I550T;A231S;I361M;V458M 42;52;62;72;86 47;57;67;77;91 HA;HA;HA;PA;PB2 59;69;83;49;38 61;71;85;51;41 34253060 In Vivo Therapy with M2e-Specific IgG Selects for an Influenza A Virus Mutant with Delayed Matrix Protein 2 Expression. We confirmed that the I504V mutation in PB2 enhances polymerase activity. 2021 mBio Discussion IV I504V 22 27 PB2 40 43 34337007 Full Genomic Sequences of H5N1 Highly Pathogenic Avian Influenza Virus in Human Autopsy Specimens Reveal Genetic Variability and Adaptive Changes for Growth in MDCK Cell Cultures. Furthermore, the amino acid substitution S31N in the M2 protein of our viruses suggested that the virus was resistant to amantadine and rimantidine, and the 274H residue in the NA protein suggested that the viruses were susceptible to oseltamivir. 2021 BioMed research international Discussion IV S31N 41 45 M2;NA 53;177 55;179 34337007 Full Genomic Sequences of H5N1 Highly Pathogenic Avian Influenza Virus in Human Autopsy Specimens Reveal Genetic Variability and Adaptive Changes for Growth in MDCK Cell Cultures. Moreover, we showed that the M315I amino acid change may be essential for the trachea virus to adapt for growth in MDCK cells since the 315I was found in virus isolates from all types of clinical specimens. 2021 BioMed research international Discussion IV M315I 29 34 34358217 Mutation E48K in PB1 Polymerase Subunit Improves Stability of a Candidate Live Attenuated Influenza B Virus Vaccine. Another unexpected finding was the E48K mutation emerging and stabilizing the K391E mutation during serial passages in SPF eggs. 2021 Vaccines Discussion IV E48K;K391E 35;78 39;83 34358217 Mutation E48K in PB1 Polymerase Subunit Improves Stability of a Candidate Live Attenuated Influenza B Virus Vaccine. Female and male mice were equally protected against a lethal dose of the antigenically homologous B/Bris/PB2 F406Y strain, exhibiting no weight loss and no mortality. 2021 Vaccines Discussion IV F406Y 109 114 PB2 105 108 34358217 Mutation E48K in PB1 Polymerase Subunit Improves Stability of a Candidate Live Attenuated Influenza B Virus Vaccine. Genomic analysis of the B/Bris PB1att 4M strain after four passages in eggs revealed the stability of the E48K, K391E, E580G, and S660A mutations. 2021 Vaccines Discussion IV E48K;K391E;E580G;S660A 106;112;119;130 110;117;124;135 34358217 Mutation E48K in PB1 Polymerase Subunit Improves Stability of a Candidate Live Attenuated Influenza B Virus Vaccine. In a previous study using an IBV LAIV candidate with the PB1 gene segment carrying three ts mutations:K391E, E580G, and S660A:and a C-terminus HA tag, the K391E mutation reverted to its wild type form (E391K) during the initial passages in SPF eggs. 2021 Vaccines Discussion IV K391E;E580G;S660A;K391E;E391K 102;109;120;155;202 107;114;125;160;207 HA;PB1 143;57 145;60 34358217 Mutation E48K in PB1 Polymerase Subunit Improves Stability of a Candidate Live Attenuated Influenza B Virus Vaccine. In contrast, passage in MDCK cells led to the quick emergence of the E48K mutation and retention of the K391E. 2021 Vaccines Discussion IV E48K;K391E 69;104 73;109 34358217 Mutation E48K in PB1 Polymerase Subunit Improves Stability of a Candidate Live Attenuated Influenza B Virus Vaccine. In contrast, the B/Bris PB1 3M strain passaged four times in eggs showed the presence of not only the intended mutations (K391E, E580G, and S660A) but also the acquisition of the potentially compensatory mutation E48K and the additional G161C mutation whose role remains unknown. 2021 Vaccines Discussion IV K391E;E580G;S660A;E48K;G161C 122;129;140;213;237 127;134;145;217;242 PB1 24 27 34358217 Mutation E48K in PB1 Polymerase Subunit Improves Stability of a Candidate Live Attenuated Influenza B Virus Vaccine. In contrast, the non-vaccinated B/Bris/PB2 F406Y-challenged mice showed significant signs of disease, weight loss, and mortality, and only one non-vaccinated mice survived the virus challenge. 2021 Vaccines Discussion IV F406Y 43 48 PB2 39 42 34358217 Mutation E48K in PB1 Polymerase Subunit Improves Stability of a Candidate Live Attenuated Influenza B Virus Vaccine. In this report, we found that the K391E mutation was indeed maintained in the presence of the E48K mutation, and the resulting B/Bris PB1att 4M strain was attenuated and safe, resulting in efficacious protection against homologous challenge. 2021 Vaccines Discussion IV K391E;E48K 34;94 39;98 34358217 Mutation E48K in PB1 Polymerase Subunit Improves Stability of a Candidate Live Attenuated Influenza B Virus Vaccine. In vitro kinetics studies confirmed that the B/Bris PB1att 4M strain retained its ts phenotype despite the E48K mutation. 2021 Vaccines Discussion IV E48K 107 111 34358217 Mutation E48K in PB1 Polymerase Subunit Improves Stability of a Candidate Live Attenuated Influenza B Virus Vaccine. Interestingly, a similar number of passages in MDCK cells did not affect the stability of the PB1 gene segment in the B/Bris PB1 3M strain, and the E48K mutation was not observed. 2021 Vaccines Discussion IV E48K 148 152 PB1;PB1 94;125 97;128 34358217 Mutation E48K in PB1 Polymerase Subunit Improves Stability of a Candidate Live Attenuated Influenza B Virus Vaccine. It is important to note that in our previous work, a virus rescued without the HA tag also showed the PB1 E48K mutation that seemed to stabilize the K391E mutation after nine serial passages in eggs. 2021 Vaccines Discussion IV E48K;K391E 106;149 110;154 HA;PB1 79;102 81;105 34358217 Mutation E48K in PB1 Polymerase Subunit Improves Stability of a Candidate Live Attenuated Influenza B Virus Vaccine. It is tempting to speculate that the C-terminal HA tag further impairs the polymerase function of the PB1 subunit protein forcing the K391E mutation to quickly revert to wild type when passaged in eggs. 2021 Vaccines Discussion IV K391E 134 139 HA;PB1 48;102 50;105 34358217 Mutation E48K in PB1 Polymerase Subunit Improves Stability of a Candidate Live Attenuated Influenza B Virus Vaccine. Our initial observations suggested that the E48K mutation could stabilize the ts K391E mutation in the vaccine candidate strain and, therefore, could contribute to a more stable and safe attenuated vaccine candidate. 2021 Vaccines Discussion IV E48K;K391E 44;81 48;86 34358217 Mutation E48K in PB1 Polymerase Subunit Improves Stability of a Candidate Live Attenuated Influenza B Virus Vaccine. Regardless of the potential bottleneck effect of the HA tag for PB1 activity and the effect of initial virus stock amplification in eggs, our results strongly suggest a functional link between amino acids 48 and 391 and significant stability of the other two ts mutations (E580G, S660A) in the PB1 protein of IBV. 2021 Vaccines Discussion IV E580G;S660A 273;280 278;285 HA;PB1;PB1 53;64;294 55;67;297 34358217 Mutation E48K in PB1 Polymerase Subunit Improves Stability of a Candidate Live Attenuated Influenza B Virus Vaccine. The E48K mutation was only found in 3 natural isolates as revealed by the analysis of 1699 unique complete IBV PB1 protein sequences deposited in the Influenza Research Database (IRD;(accessed on 2 July 2021)). 2021 Vaccines Discussion IV E48K 4 8 PB1 111 114 34358217 Mutation E48K in PB1 Polymerase Subunit Improves Stability of a Candidate Live Attenuated Influenza B Virus Vaccine. The stability of the B/Bris PB1att 4M strain in either eggs or MDCK cells and the acquisition of the E48K mutation in the egg-passaged B/Bris PB1 3M is consistent with the notion of a stabilizing role of the E48K that maintained the K391E mutation. 2021 Vaccines Discussion IV E48K;E48K;K391E 101;208;233 105;212;238 PB1 142 145 34358217 Mutation E48K in PB1 Polymerase Subunit Improves Stability of a Candidate Live Attenuated Influenza B Virus Vaccine. This finding was unexpected considering prior observations with our original IBV LAIV candidate in which the E48K mutation was initially identified after the first serial passage in MDCK cells. 2021 Vaccines Discussion IV E48K 109 113 34358217 Mutation E48K in PB1 Polymerase Subunit Improves Stability of a Candidate Live Attenuated Influenza B Virus Vaccine. This reveals that the viral genome of the B/Bris PB1 4M strain is stable even after several passages in MDCKs and SPF eggs, indicating the introduction of the compensatory mutation E48K does not significantly alter the overall genome structure. 2021 Vaccines Discussion IV E48K 181 185 PB1 49 52 34702977 Ancestral sequence reconstruction pinpoints adaptations that enable avian influenza virus transmission in pigs. Further studies are needed to delineate the functional role conferred by the NP-R351K mutation. 2021 Nature microbiology Discussion IV R351K 80 85 NP 77 79 34702977 Ancestral sequence reconstruction pinpoints adaptations that enable avian influenza virus transmission in pigs. Interestingly, further analyses using RG-EA2 and RG-EA3 viruses that differed in the receptor binding specificity and transmission potential in pigs, identified that the NP-R351K mutation was the minimal molecular change required to significantly enhance transmissibility in pigs. 2021 Nature microbiology Discussion IV R351K 173 178 NP 170 172 34702977 Ancestral sequence reconstruction pinpoints adaptations that enable avian influenza virus transmission in pigs. Since the NP-R351K mutation was also fixed in 97.08% (1,993/2,053) of the classical swine influenza viruses, the A(H1N1)pdm09 virus continues to harbour the NP-R351K mutation at a high frequency (99.97%, 17,621/17,626) from 2009 to 2019. 2021 Nature microbiology Discussion IV R351K;R351K 13;160 18;165 NP;NP 10;157 12;159 34702977 Ancestral sequence reconstruction pinpoints adaptations that enable avian influenza virus transmission in pigs. The fact that introducing the NP-R351K mutation was able to facilitate efficient transmission of RG-EA2, an early EA swine virus that possessed dual binding specificity, indicates that an exclusive alpha-2,6 binding specificity may not be essential for efficient influenza transmission in pigs. 2021 Nature microbiology Discussion IV R351K 33 38 NP 30 32 34702977 Ancestral sequence reconstruction pinpoints adaptations that enable avian influenza virus transmission in pigs. The NP-R351K amino acid change has been fixed not only in the EA swine viruses but also in other human and swine influenza viruses. 2021 Nature microbiology Discussion IV R351K 7 12 NP 4 6 34702977 Ancestral sequence reconstruction pinpoints adaptations that enable avian influenza virus transmission in pigs. The NP-R351K mutation has been quickly fixed among the human seasonal A(H1N1) viruses from 1918 to 1957, with 39 out of 42 (92.86%) available sequences containing K351. 2021 Nature microbiology Discussion IV R351K 7 12 NP 4 6 34702977 Ancestral sequence reconstruction pinpoints adaptations that enable avian influenza virus transmission in pigs. The potential interaction of the NP-R351K mutation with Mx1 and MxA has been studied in the context of A(H1N1)pdm09 and EA swine influenza viruses, highlighting that the NP-R351K mutation alone did not confer resistance to Mx1 or MxA. 2021 Nature microbiology Discussion IV R351K;R351K 36;173 41;178 NP;NP 33;170 35;172 35044215 N-Glycolylneuraminic Acid Binding of Avian and Equine H7 Influenza A Viruses. Here, we demonstrate that avian H7 and H15 HAs can bind both NeuAc and NeuGc by the introduction of A135E. 2022 Journal of virology Discussion IV A135E 100 105 35044215 N-Glycolylneuraminic Acid Binding of Avian and Equine H7 Influenza A Viruses. Nevertheless, here we demonstrated that avian H7 and H15 HAs, although genetically distinct from equine H7 viruses, are able to bind NeuGc after the introduction of mutation A135E. 2022 Journal of virology Discussion IV A135E 174 179 35044215 N-Glycolylneuraminic Acid Binding of Avian and Equine H7 Influenza A Viruses. We previously studied the NeuAc-specific HA of A/Vietnam/1203/2004 H5N1 (H5VN) and its Y161A mutant that is specific for NeuGc, which showed complete specificity on the glycan microarray, in the hemagglutination assay, and on tracheal epithelium tissue. 2022 Journal of virology Discussion IV Y161A 87 92 HA 41 43