literature

SARS_CoV_2 mutation literature information.

E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil.

PMID: 34044192 2021 Infection, genetics and evolution

Result: For these residues under adaptive pressure, six are included in known mutation sites of spike protein, including E484K (L5F, S12F, P26S, D138Y, A688V).

Result: Regarding the lineage-defining mutations from P.1 lineages, 14 of a total of 19 genomes from the Amazonas monophyletic group present the spike mutations L18F, T20N, P26S, D138Y, and R190S.

Table: D138Y

SARS-CoV-2 Brazil variants in Latin America: More serious research urgently needed on public health and vaccine protection.

PMID: 34109031 2021 Annals of medicine and surgery (2012)

Introduction: These mutations are L18F, T20N, P26S, D138Y, R190S, D614G H655Y, T1027I, and V1176F.

Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species.

PMID: 34166623 2021 Immunity

Method: The variant P.1 (GISAID: EPI_ISL_792681) was constructed with 12 mutations including L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, D614G, H655Y, T1027I and V1176F.

Immune Evasion of SARS-CoV-2 Emerging Variants: What Have We Learnt So Far?

PMID: 34206453 2021 Viruses

Introduction: Five mutations are located within NTD (L18F, T20N, P26S, D138Y, R190S), three in RBD (K417T, E484K, N501Y), two in the C-terminal domain of S1 and near the furin cleavage site (D614G, H655Y), and one in S2 (T1027I) (Figure 3).

Genomic monitoring unveil the early detection of the SARS-CoV-2 B.1.351 (beta) variant (20H/501Y.V2) in Brazil.

PMID: 34241897 2021 Journal of medical virology

Result: P.1 defining mutations related to each genomic region were the following: ORF1ab: S1188L, K1795Q, E5665D; spike: L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, H655Y, T1027I; Orf8: E92K; and nucleocapsid: P80.

Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach.

PMID: 34346317 2021 Computers in biology and medicine

Result: As a meta result, i-stable predicted, out of 62 nonsynonymous mutations, 40 nonsynonymous mutations (L5F, L8V, L8W, L18F, L54F, T76I, V120I, D138Y, Y145H, M153T, F157S, L176F, G181V, D215H, A262T, V367F, G476S, V483A, L611F, Q675H, Table: D138Y

Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants.

PMID: 34351895 2021 PLoS computational biology

Result: P.1 variant includes the mutations L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, D614G, H655Y, T1027I.

Neutralizing Activity of Sera from Sputnik V-Vaccinated People against Variants of Concern (VOC: B.1.1.7, B.1.351, P.1, B.1.617.2, B.1.617.3) and Moscow Endemic SARS-CoV-2 Variants.

PMID: 34358195 2021 Vaccines

Method: Determination of NtAb titers was evaluated using the following SARS-CoV-2 variants: B.1.1.1 (PMVL-1, S: D614G; hCoV-19/Russia/Moscow_PMVL-1/2020), B.1.1.7 (hCoV-19/Netherlands/NoordHolland_20432/2020, VOC 202012/01), B.1.351 (hCoV-19/Russia/SPE-RII-27029S/2021), B.1.1.141 (PMVL-31, S: M153T, T385I, D614G; hCoV-19/Russia/MOW-PMVL-31/2020), B.1.1.317 (PMVL-43, S: D138Y, S477N, A522S, D614G, Q675R, A845S; hCoV-19/Russia/MOW-PMVL-43/2021), B.1.1.28/P.1 (hCoV-19/Netherlands/NoordHolland_10915/2021), B.1.617.2 (T19R

Mutation hotspots and spatiotemporal distribution of SARS-CoV-2 lineages in Brazil, February 2020-2021.

PMID: 34363852 2021 Virus research

Table: D138Y

Discussion: Of the 10 new amino acid mutations in the spike protein (L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, H655Y, T1027I) compared to its immediate ancestor (B.1.1.28), molecular selection analyses found evidence that 8 of these 10 mutations are under diversifying positive selection.

Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies.

PMID: 33664494 2021 Nature medicine

Method: Amino acid substitutions for B.1.1.7, P.1 (Brazilian lineage: L18F, T20N,

Result: Given these results with viruses encoding E484K mutations, we performed separate studies with human convalescent serum (n =10) and a chimeric SARS-CoV-2 WA1/2020 strain encoding a Brazilian variant spike gene (Wash BR-B.1.1.248; L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, D614G, H655Y, T1027I, and V1176F [Extended Data Fig 5a]).

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