Crucial Mutations of Spike Protein on SARS-CoV-2 Evolved to Variant Strains Escaping Neutralization of Convalescent Plasmas and RBD-Specific Monoclonal Antibodies.
Introduction: In addition, several recent studies have focused on the neutralizing activity of vaccine-elicited humoral immunity against new circulating mutant lineages, including B.1.1.7 (United Kingdom, bearing mutations 69-70 del, 144 del, N501Y, A570D, D614G, P681H, T716I, S982A, and D1118H in the spike protein), B.1.429 (United States, bearing mutations S13I, W152C, L452R, and D614G in the spike protein), B.1.351(South Africa, bearing mutations D80A, D215G, PMID: 34508827
2021
Biochimie
Method: The chosen sequences of single mutations included the following amino acid substitutions: L5F, L18F, D80A, S98F, A222V, A262S, P272L, K417 N, N439K, L452R, Y453F, S477 N, E484K, E484Q, N501T, N501Y, E583D, D614G, Q675H, Q675P, Q677H, PMID: 34526698
2021
Nature medicine
Method: SARS-CoV-2 neutralizing antibodies were quantified using lentivirus particles that incorporate SARS-CoV-2 S protein (Wuhan-Hu-1 isolate mutated to contain D614G) or the B.1.351 variant S protein (L18F-D80A-D215G- L242- A243- L244-K417N-E484K-N501Y-D614G-A701V) on their surface and express firefly luciferase reporter gene for quantitative measurements of infection by relative luminescence units (RLUs) as described.
In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2.
Method: We used the following amino acids replacements and deletions in Spike for each lineage-based COG-UK defined changes for each lineage; Beta (B1.351; L18F, D80A, D215G, R246L, K417N, E484K, N501Y, A701V), Gamma (P.1; L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y H655Y, T1027I), Alpha (B.1.1.7; Delta69-70, D144, PMID: 34536797
2021
Virology
Result: Only the A701V substitution present in the B.1.526 reduced plasma binding.
Result: The B.1.351 Spike was efficiently recognized by plasma from previously-infected vaccinated individuals with a single mutation presenting lower detection (A701V).
Emergence in southern France of a new SARS-CoV-2 variant harbouring both N501Y and E484K substitutions in the spike protein.
Result: Additionally, whereas a convergent A701V mutation is also found in the B.1.526 and S/E484K carrying lineage that was first identified in New York, P681H is found in the S/E484K and S/N501Y carrying P.3 lineage first identified in the Philippines, and both S/H655Y and S/P681H are found in the highly mutated S/E484K carrying A.VOI.V2 lineage first identified in Tanzanian travelers.
The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages.
Result: Whereas sites S/655 and S/681 are also detectably evolving under positive selection in at least one of the lineage specific datasets, S/655, S/681, A/701, and S/716 are all detectably evolving under positive selection in the March and April 2021 global SARS-CoV-2 datasets; important additional indicators that are consistent with the H655Y, P681H, A701V, and T716I mutations being adaptive.
Result: Whereas some V2 and V3 sequences had, by March 2021, independently acquired the signature V1 mutations, P681H and T716I, some V1 and V2 sequences had independently acquired the V3 signature mutation, H655Y, and some V1 sequences had independently acquired the V2 signature mutation, A701V.
Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants.
Discussion: Moreover, mutations close to or at the polybasic cleavage site at the S1/S2 boundary have been reported in several VOCs and VOIs, including: Alpha (S:P681H), Beta (A701V), Delta (P681R), Eta (Q677H), Iota (A701V), Kappa (P681R), and Theta (P.3, P681H).
Result: The Beta S is comprised of the L18F, D80A, D215G, and 242-244 mutations in the NTD, K417N and E484K mutations in the receptor-binding domain (RBD), and A701V in the S1/S2 cleavage site.
SARS_CoV_2 mutation literature information.
PMID: 
2021
Frontiers in immunology
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