literature

SARS_CoV_2 mutation literature information.

Efficacy of mRNA, adenoviral vector, and perfusion protein COVID-19 vaccines.

PMID: 34906769 2022 Biomedicine & pharmacotherapy

Introduction: In the spike protein of the B.1.1.28 strain, there are eleven mutations, including L18F, T20N, P26S, D138Y, R190S, H655Y, T1027I, D614G, K417T, E484K, and N501Y.

Table: D138Y

A screening strategy for identifying the dominant variant of SARS-COV-2 in the fifth peak of Kurdistan- Iran population using HRM and Probe-based RT-PCR assay.

PMID: 35271889 2022 Journal of virological methods

Table: D138Y

Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm.

PMID: 35266951 2022 Genetics and molecular biology

Introduction: Currently, the WHO has identified the Gamma lineage (B.1.1.28.1, P.1 or Gamma; Nextstrain clade 20J/V3) with the following key S mutations: L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, D614G, H655Y, T1027I, and V1176F.

Table: D138Y

SARS-CoV-2 Beta and Delta variants trigger Fc effector function with increased cross-reactivity.

PMID: 35233544 2022 Cell reports. Medicine

Method: The SARS-CoV-2 Wuhan-1 spike, cloned into pCDNA3.1 was mutated using the QuikChange Lightning Site-Directed Mutagenesis kit (Agilent Technologies) and NEBuilder HiFi DNA Assembly Master Mix (NEB) to include D614G (original) or lineage defining mutations for Alpha (DEL69-70, DEL144, N501Y, A570D, D614G, P681H, T716I, S982A, D1118H), Beta (L18F, D80A, D215G, 242-244del, K417N, E484K, N501Y, D614G and A701V<

Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil.

PMID: 35171035 2022 Microbiology spectrum

Table: D138Y

Pan-SARS neutralizing responses after third boost vaccination in non-human primate immunogenicity model.

PMID: 35101265 2022 Vaccine

Table: D138Y

A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients.

PMID: 34896524 2022 Gene

Discussion: The mutations Discussion: There was another sequence sampled from Shiraz in Oct 2020 that contained five specific mutations (D138Y, D614G, E484K, K417T, N501Y) as indicator of the Gamma variant (GR/501Y.V3 (P.1+P.1.x)) and was clustered along with the representative Gamma variant spike sequence in phylogenetic tree.

Discussion: We also observed triple co-occurring mutations, namely D138Y (in the NTD), S477N (in the RBD) with the well-established D614G mutation (near the furin cleavage site) in three spike sequences from Tehran and Shiraz sampled from Nov 2020 to Jan 2021.

Identification of genotypic variants and its proteomic mutations of Brazilian SARS-CoV-2 isolates.

PMID: 34740719 2022 Virus research

Table: D138Y

Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021.

PMID: 34848355 2022 Infection, genetics and evolution

Table: D138Y

In silico analysis of mutant epitopes in new SARS-CoV-2 lineages suggest global enhanced CD8+ T cell reactivity and also signs of immune response escape.

PMID: 35149224 2022 Infection, genetics and evolution

Abstract: Moreover, individual mutations such as Spike N501Y and Nucleocapsid D138Y were predicted to have an overall stronger affinity through HLA-I than the reference sequence while Spike E484K shows signs of evasion.

Result: In contrast, a significantly stronger binding (lower %Rank) was observed for peptides derived from the nsSNVs D138Y and N501Y.

Table: D138Y

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