literature

Crucial Mutations of Spike Protein on SARS-CoV-2 Evolved to Variant Strains Escaping Neutralization of Convalescent Plasmas and RBD-Specific Monoclonal Antibodies.

PMID: 34484190 2021 Frontiers in immunology

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: 34512928 2021 Computational and structural biotechnology journal

Result: Among the 17 sites, 11 caused amino acid changes, of which 5 mutation sites were located on the S protein (including N501Y, P681H, T716I, S982A, and D1118H) (Table 3).

In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2.

PMID: 34534263 2021 PLoS pathogens

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: Examining each variant and their single mutations more closely, though full B.1.1.7 Spike did not significantly reduce plasma binding in previously-infected vaccinated individuals, three of its single mutations, DeltaY144, P681H, and S982A significantly affected plasma recognition.

Result: Substitution S982A in the S2 showed the most important reduction, by ~2 folds compared to D614G.

Case Report: Paucisymptomatic College-Age Population as a Reservoir for Potentially Neutralization-Resistant Severe Acute Respiratory Syndrome Coronavirus 2 Variants.

PMID: 34544043 2021 The American journal of tropical medicine and hygiene

Conclusion: Of these, 56 (60%) sequences were of B.1.1.7/20I/501Y.V1 lineage; four isolated from early February through mid-March were of a B.1.1.519/20B lineage including three sequences with the T478K mutation that has been reported from the designated BV-2 (hCoV-19/USA/GHRC-BV2-EQ04518823/2021, hCOV-19/USA/GHRC-BV2-EQ04526485/2021 and hCoV-19/USA/GHRC-BV2-EQ04531246/2021), a lineage was first detected in the United States, but subsequently became common in Canada and Mexico with a peak near the end of March 2021; 22 were B.1.2/20G including BV-3, a genome very similar to other local 20G lineage sequences, except for the addition of a cluster of four spike mutations (P681H, T716I, S982A, and D1118H) that were not present in any local 20G lineage genomes, but were all present on all local 20

Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants.

PMID: 34549975 2021 Journal of virology

Table: S982A

SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation.

PMID: 34601723 2021 The EMBO journal

Result: Alpha S contains the 69/70 and Y144 deletions in the N-terminal domain (NTD), P681H and T716I mutations in the S1/S2 cleavage site, the S982A mutation in the heptad repeat 1 (HR1) site and the D1118H mutation in between HR1 and HR2.

Rapid and High-Throughput Reverse Transcriptase Quantitative PCR (RT-qPCR) Assay for Identification and Differentiation between SARS-CoV-2 Variants B.1.1.7 and B.1.351.

PMID: 34612692 2021 Microbiology spectrum

Method: This enabled the first identification of the B.1.1.7-related mutations 69-70Del, 144Del, N501Y, S982A, and D1118H and B.1.351-related mutations D215G, 242Del K417N, N501Y, and E484K.

Result: Sanger sequencing of the spike gene region from sample 7075 contained the following mutations, all of which are characteristic of the B.1.1.7 variant: 69 to 70 deletion, 144 deletion, N501Y, S982A, and D1118H.

Evaluation of the clinical and analytical performance of the Seegene allplex SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI).

PMID: 34628158 2021 Journal of clinical virology

Introduction: In September 2020, the B.1.1.7 lineage emerged as a variant of concern in the United Kingdom (UK), subsequently termed the alpha variant, with 9 spike protein mutations (del69/70HV, del144Y, N501Y, A570D, D614G, P681H, T761I, S982A, and D1118H).

Table: S982A

The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients.

PMID: 34676574 2021 Journal of medical virology

Result: List of variations displayed in structure (nearest residue if in loop/termini region): H69del V70del(69) Y144del(143) N501Y A570D D614G P681H(674) T716I S982A D1118H as seen in Table 3.

Table: S982A