Analysis of RNA sequences of 3636 SARS-CoV-2 collected from 55 countries reveals selective sweep of one virus type.
PMID: 32474553
2020
The Indian journal of medical research
Abstract: INTERPRETATION & CONCLUSIONS: SARS-CoV-2 belonging to the A2a type possesses a non-synomymous variant (D614G) that possibly eases the entry of the virus into the lung cells of the host.
Introduction: Although the effect of the D614G mutation is unclear, this mutation is located in the S1-S2 junction near the furin recognition site (R667) for the cleavage of S protein that is required for the entry of the virion into the host cell.
Introduction: Another mutation, A23403G, located in the gene encoding the spike glycoprotein results in an amino acid change (
Result: The non-synonymous D614G mutation in the spike protein occurred at a high frequency.
Table: D614G
The origin of SARS-CoV-2 in Istanbul: Sequencing findings from the epicenter of the pandemic in Turkey.
Result: Since all three isolates have a D614G variant in spike glycoprotein
Discussion: All three viral isolates carried the D614G marker variant indicating the isolates belong to clade G, which encompasses mostly European countries according to GISAID classification.
Discussion: Clades were named based on variants L84S in ORF8 (S clade), D614G in S gene (G clade), and G251V in ORF3a (V clade).
Discussion: Three isolates in this analysis carried the D614G variant in the S gene, indicating they are all in G clade, which was mostly detected in European countries.
An insertion unique to SARS-CoV-2 exhibits superantigenic character strengthened by recent mutations.
Method: Two mutants associated with European Covid-19 patients were constructed using CHARMM-GUI: one is the main strain mutant D614G and the other contains four mutations including Q239K, A831V, D614G and D839Y.
Result: Interestingly, the SARS-CoV-2 spike binding region harbors three residues that have been recently reported to have mutated in new strains from Europe and USA: D614G, A831V and D839Y/N/E).
Mutations in SARS-CoV-2 viral RNA identified in Eastern India: Possible implications for the ongoing outbreak in India and impact on viral structure and host susceptibility.
Abstract: More importantly, the possible implications of mutation D614G (in SD domain) and G1124V (in S2 subunit) on the structural stability of S protein have also been discussed.
Abstract: Specific mutations, characteristic of the A2a clade, were also detected, which included the P323L in RNA-dependent RNA polymerase and D614G in the Spike glycoprotein.
Discussion: Interestingly, the mutations D614G (in SD domain) is supposed to confer flexibility in the SD domain and the mutation G1124V might impart partial rigidity in the conformation of S2 domain.
Discussion: Notably, the D614G mutation is close to the Furin recogniti
SARS-CoV-2 genomic surveillance in Taiwan revealed novel ORF8-deletion mutant and clade possibly associated with infections in Middle East.
Result: In addition to the signature mutation S-D614G annotated by GISAID in clade III, all the Taiwanese genomes shared two ORF1ab mutations C2772T and C14144T (P4715L) (Figure 3E).
Result: To better illustrate phylogenetic clades, we designated and numbered yellow clade as IV harbouring ORF1ab-V378I mutation in this study and three others (blue clade I of ORF8-L84S, gray clade II of ORF3a-G251V, and pink clade III of S-D614G) identified based on previous GISAID annotations of clades S,
SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes.
Abstract: Several Spike-protein mutations, including D614G, which has been associated with increased transmission, disrupt otherwise-perfectly-conserved amino acids, and could be novel adaptations to human hosts.
Result: First, we investigated Sarbecovirus conservation of 14 amino acids in the spike protein in which mutations appear to be accumulating in the SARS-CoV-2 population, namely D614G, L5F, L8V/W, H49Y, Y145H, Q239K, V367F, G476S, V483A, V615I/F, A831V, PMID: 32587973
2020
bioRxiv
Abstract: SARS coronavirus 2 (SARS-CoV-2) isolates encoding a D614G mutation in the viral spike (S) protein predominate over time in locales where it is found, implying that this change enhances viral transmission.
Introduction: Instead, these data show there is more S1 domain in the SG614-expressing cells, a result again consistent with the observation that the D614G mutation reduces S1 shedding.
Introduction: It has also been speculated that the D614G mutation woul
Method: Logo plots of D614G variation were generated by WebLogo after sequence alignment.
Method: To track D614G variation among SARS-CoV-2 isolates, S protein sequences were downloaded from GenBank and separated by the month.
An updated analysis of variations in SARS-CoV-2 genome.
Result: A23403G variation is one of the most important variations that have been reported previously (Phan et al., 2020) caused D614G substitution on S protein.
Table: D614G
Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey.
Discussion: A23403G substitution was found to be present in isolates from Europe and leads to an amino acid change from aspartate to glycine at position 614 (D614G) within the spike glycoprotein, where these amino acids differ by means of their isoelectric points (Pachetti et al., 2020).
Discussion: In a recent study which performed multivariate generalized linear model (GLM) analysis with outpatient and hospitalized patients in the Sheffield Teaching Hospitals NHS Foundation Trust as the outcome revealed that patients carrying G614 mutation had higher viral loads compared to D614, although D614G status did not significantly affect the hospitalization status (Korber et al., 2020).
Discussion: It also seems that the viral isolates which carry PMID: 32637944
2020
bioRxiv
Result: Additionally, when HEK-293 cells or SupT1 cells had been rendered infectable by stable expression of exogenous ACE2 and TMPRSS2, D614G was 9-fold more infectious than D614 (Figure 2).
Result: Although recent data for South America are sparse, available sequences suggest D614G is approaching fixation in this continent as well.
Result: Although these sequences suggest that the D614G variant first emerged in China or Germany, given how few virus genomes have been sequenced from early in the outbreak, its geographic origin cannot be determined.
Result: Analysis of D614G variant frequency is expected to gain resolution as sequences are released for samples banked across the duration of the pandemic.
Result: As a first step to examine whether the increased infectivity of D614G is species-sp
SARS_CoV_2 mutation literature information.
PMID: 
2020
The Indian journal of medical research
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