SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation.
PMID: 33905892
2021
Infection, genetics and evolution
Result: In addition, no structural variants in the receptor-binding domain (RBD) of the Spike protein (N439K, T481I, V483A, E484E, N501Y nor G476S) were identified.
Discussion: Recently, a variant N501Y in the Spike has been reported in the United Kingdom, which is located in the RBD and the impact on the transmission or severity is not known.
The Genetic Variant of SARS-CoV-2: would It Matter for Controlling the Devastating Pandemic?
PMID: 33907511
2021
International journal of biological sciences
Introduction: N501Y is also presented in the VOC 202012/01 varia
Introduction: Different from N501Y and E484K, the mutation of K417 locates outside the RBM.
Introduction: However, the neutralization by sera from participants vaccinated with BNT162b2 against N501Y, Delta69/Delta70+ N501Y + D614G and E484K+ N501Y+D614G pseudoviruses only demonstrated small effects of these mutations on neutralization.
Introduction: Indeed, N501Y has been shown to increase the affinity to hACE2 receptor.
Introduction: Mutant N501Y has demonstrated significant increase in the binding affinity to ACE2.
Post-vaccination SARS-CoV-2 infections and incidence of the B.1.427/B.1.429 variant among healthcare personnel at a northern California academic medical center.
Abstract: Chart extraction of demographic and clinical information was performed, and available specimens meeting cycle threshold value criteria were tested for L452R, N501Y and E484K mutations by RT-PCR.
Abstract: Of 115 samples available for mutation testing, 42 were positive for L452R alone, presumptive of B.1.427/B.1.429; three had N501Y mutation alone and none were found with E484K mutation.
Method: Between December 1,2020 and March 1,2021 all available specimens testing positive fo
Result: Three PVSCs were found to have N501Y mutation; all were symptomatic, two tested positive while partially vaccinated (>14 days after first vaccine dose but prior to the second dose) and one was fully vaccinated (>14 days after second dose).
Impact of meteorological parameters and population density on variants of SARS-CoV-2 and outcome of COVID-19 pandemic in Japan.
Result: However, during the second wave starting from October 2020 substitution point mutations E780Q, K417N, T478I, N501Y, E484K, N439K, V1176F, S477N and A222V became common at spike protein in the isolates in Japan.
Result: Point mutation at
Discussion: Variants with substitutions namely, K417N, T478I, N501Y, E484K, N439K and S477N at RBDs have been detected recently in Japan.
Emergence in southern France of a new SARS-CoV-2 variant harbouring both N501Y and E484K substitutions in the spike protein.
Abstract: Here, we assessed the neutralizing activity and binding affinity of a panel of 12 monoclonal antibodies against the wild type and N501Y mutant SARS-CoV-2 pseudovirus and
Conclusion: This work suggested that most of published nAbs with diverse recognizing epitopes still neutralized the SARS-CoV-2_N501Y as similar potencies as that of the wild type virus, except a few of nAbs which targeted the N501 residual directly.
Table: N501Y
Figure: (a) Examples of binding affinities of CB6 to spike RBD of Wuhan strain (WT) or the N501Y mutant.
Figure: (a) Examples of neutralization of indicated mAbs against pseudovirus bearing the spike of Wuhan strain (WT) or the N501Y mutant.
Emergence in southern France of a new SARS-CoV-2 variant harbouring both N501Y and E484K substitutions in the spike protein.
Method: For cryo-EM, both N501Y and unmutated SARS-CoV-2 spike ectodomain preparations were deposited on grids at a concentration of 2.25 mg/ml.
Method: One hundred microliters of wild-type or N501Y SARS-CoV-2 S protein preparation was coated onto 96-well MaxiSorp plates at 2 mug/ml in PBS overnight at 4 C.
Method: SARS-CoV-2 S and SARS-CoV-2 S N501Y pseudotyped retroviral particles were produced in HEK293T cells as described previously.
Method: SARS-CoV-2 S N501Y plasmid was obtained from SARS-CoV-2 S plasmid (HDM-IDTSpike-fixK) by site-directed mutagenesis (Q5 Site-Directed Mutagenesis Kit, New England Biolabs).
The Impact on Infectivity and Neutralization Efficiency of SARS-CoV-2 Lineage B.1.351 Pseudovirus.
Result: However, the spike variants (N501Y, K417N, E484K) harboring SARS-CoV-2 B.1.351 lineage was partially resistant against Casirivimab.
Result: However, the molecular mechanism by which spike mutant harboring either K417N/N501Y/D614G or E484K/N501Y/ D614G mutation promotes the cleavage efficacy of S1/S2 to facilitate membrane fusion activity needs to be further studied.
Result: Importantly, even with this reduced activity, Imdevimab that was tested was still capable to fully neutralize the pseudoviruses harboring K417N/
Emergence in southern France of a new SARS-CoV-2 variant harbouring both N501Y and E484K substitutions in the spike protein.
Introduction: A recent study adopted individual patients' data from more than 2 million SARS-CoV-2 infections in the UK, and found significant positive association of B.1.1.7 lineage (which is dominant by N501Y substitution) and the fatality risk in terms of the hazard and absolute risks.
Introduction: Around September 2020, genetic variants carrying the N501Y substitution on the spike (S) protein of SARS-CoV-2 were first detected in the United Kingdom (UK), then spread to elsewhere globally, and trended to reach fixation rapidly in many places, for example, South Africa, Brazil, and the U.S.
Introduction: By contrast, whether the N501Y substitution leads to a difference in disease severity among SARS-CoV-2 infections remains lar
Emergence in southern France of a new SARS-CoV-2 variant harbouring both N501Y and E484K substitutions in the spike protein.
Abstract: One sequence in lineage B.1.1.70 had an N501Y substitution while lacking the Delta69/70 in S.
Abstract: RESULTS AND CONCLUSION: We found 28 different lineages of SARS-CoV-2 circulating during the study period, including the variant of concern B.1.1.7 (Delta69/70, N501Y).
Introducti
Introduction: A number of substitutions in S have been associated with immune escape (e.g., E484K, K417N), or increased binding to the ACE-2 receptor (e.g., N501Y).
Introduction: Lineage B.1.1.7 has seventeen lineage-defining mutations including a deletion at positions 69/70 (Delta69/70) and 144, and substitutions N501Y and P681H in S.
A Potential SARS-CoV-2 Variant of Interest (VOI) Harboring Mutation E484K in the Spike Protein Was Identified within Lineage B.1.1.33 Circulating in Brazil.
Abstract: Lineage P.1 is considered a Variant of Concern (VOC) because of the presence of multiple mutations in the S protein (including K417T, E484K,
Introduction: The VOC P.1, first described in January 2021, displayed an unusual number of lineage-defining mutations in the S protein (L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, H655Y, T1027I) and its emergence was associated with a second COVID-19 epidemic wave in the Amazonas state.
SARS_CoV_2 mutation literature information.
PMID: 
2021
Infection, genetics and evolution
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