literature

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: Mutations apparently contributing to the reduction of plasma recognition of the B.1.1.7 Spike are the DeltaY144 deletion in the NTD, P681H and T716I near the S1/S2 cleavage site.

The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages.

PMID: 34537136 2021 Cell

Result: Any of H655Y, P681H, A701V, or T716I might directly impact the efficiency of viral entry into host cells.

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

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: T716I

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.

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

Table: T716I

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: T716I

Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach.

PMID: 34700382 2021 mBio

Result: At least 3,776 S protein variants belonging to alpha (B.1.1.7) variant lineage were identified, in which all contain 2 deletion events (amino acids 69 to 70 and 144) and 7 mutations (N501Y, A570D, D614G, P681H, T716I, S982A, and D1118H).

Result: Dual mutants containing D614G and other amino acid changes, including those under positive selection or observed in VOCs (L5F, L18F, S98F, W152L/C, E154K, L222V, and A262S in S1-

Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity.

PMID: 34722330 2021 Frontiers in cellular and infection microbiology

Result: In contrast, T716I, A570D, D118H and A701V mutations caused a modest reduction in viral infectivity.

Result: The results indicated that pseudovirions bearing HV69-70 deletion, 144 deletion, E484K, D614G, P681H, S982A or D1118H single-site mutations were more stable than SARS-CoV-2 WT, whereas A570D and T716I mutations decrease the stability of SARS-CoV-2 pseudovirion.

Discussion: Pseudovirion with HV69-70 deletion could enhance the infectivity of the virus, while single-site mutation T716I, A570D,