literature

SARS_CoV_2 mutation literature information.

Spread of Mink SARS-CoV-2 Variants in Humans: A Model of Sarbecovirus Interspecies Evolution.

PMID: 34616371 2021 Frontiers in microbiology

Introduction: Based on the 3D modeling of the SARS-CoV-2 spike-human ACE2 interactions we visualized the location of amino acids described as major mutation sites in the SARS-CoV-2 variants infecting humans, i.e., the S477N, E484K, and N501Y/T mutations known to characterize the Marseille-4 variant (France), the 20I/501Y.V1 variant (United Kingdom), and the 20H/501Y.V2 variant (South Africa) (Figure 8A, left panel).

Emergence and Spread of a B.1.1.28-Derived P.6 Lineage with Q675H and Q677H Spike Mutations in Uruguay.

PMID: 34578382 2021 Viruses

Introduction: The lineages P.2, P.4, and P.5, carrying the concerning amino acid changes S:E484K, S:L452R, and S:E484Q/N501T, respectively, were also initially detected in samples from Brazil.

Emerging vaccine-breakthrough SARS-CoV-2 variants.

PMID: 34518803 2021 ArXiv

Result: Furthermore, the co-mutation set [K417N, T470N, E484K, N501T] that was first found in BR on April 06, 2020, has a BFE change of 0.625 kcal/mol and antibody disruption count 84, is an emerging vaccine breakthrough co-mutation in Brazil.

Result: Second, among the top 25 most observed RBD mutations, T478K, L452Q N440K, L452R, N501Y, N501T, F490S, A475V, and P384L are the 8 most infectious ones judged by their ability to strengthen the binding with ACE2, as shown in Figure 1c.

Evolutionary and codon usage preference insights into spike glycoprotein of SARS-CoV-2.

PMID: 33377145 2021 Briefings in bioinformatics

Abstract: The N501T mutation in SARS-CoV-2-CTD furnishes better support to hotspot 353 in comparison with SARS-CoV and shows higher affinity for receptor binding.

Method: Atomic details at the binding interface exhibit that key residue substitutions (N501T mutation) in the SARS-CoV-2 CTD, compared to the SARS-CoV RBD, reinforce this interaction and lead to receptor binding with higher affinity.

Computational Mutagenesis at the SARS-CoV-2 Spike Protein/Angiotensin-Converting Enzyme 2 Binding Interface: Comparison with Experimental Evidence.

PMID: 33733740 2021 ACS nano

Conclusion: As could be anticipated, most of the studied mutations act as protein-protein interface destabilizers; however, a non-negligible number of mis-sense variations are predicted to enhance ACE2/S-RBDCoV-2 binding; in particular, the variants Q24T, T27D/K/W, D30E, H34S/T/K, E35D, Q42K, L79I/W, R357K, and R393K on ACE2 and L455D/W, F456 K/W, Q493K, N501T, and Y505W on the S-protein receptor binding domain, respectively, are expected to increase the affinity of each mutant isoforms for the corresponding protein counterpart.

Figure: (D) Main interactions involving the S-RBDCoV-2 N501T mutant at the interface with ACE2 as obtained

SARS-CoV-2 infections in mRNA vaccinated individuals are biased for viruses encoding spike E484K and associated with reduced infectious virus loads that correlate with respiratory antiviral IgG levels.

PMID: 33977858 2021 Emerging microbes & infections

Introduction: While our screening efforts were continuing with newly collected March samples, we performed whole-genome sequencing (WGS) with a panel of 74 samples from earlier months representing different genotypes flagged by this screening tool, including 24 E484K, 25 N501Y, 5 N501T, and 20 WT at 484 and 501 loci.

A novel diagnostic test to screen SARS-CoV-2 variants containing E484K and N501Y mutations.

PMID: 33977858 2021 Emerging microbes & infections

Introduction: In addition, we discovered a new genotype at the 501-probe binding site from 12 samples (12/971, 1.2%), which thereafter was confirmed to be a N501T (AAT > ACT) mutation in subsequent sequencing.

Introduction: The melting profile of N501T is markedly different from that of WT and N501Y, with a signature Tm of 56.41 +- 0.15 C.

Introduction: This has been well exemplified by our discovery of the N501T and E484Q mutations from the clinical specimens.

Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries.

PMID: 34004284 2021 Genomics

Abstract: In particular, we discover new fast-growing RBD mutations N439K, S477N, S477R, and N501T that also enhance the RBD and ACE2 binding.

Introduction: We show that in addition to mutations N501Y, E484K, and K417N in the UK, South Africa, and Brazil(ian) variants, L452R, E484Q in the India variants, N439K, S477N, S477R, and N501T are also fast-growing mutations in 31 pandemic-devastated countries in the past few months.

Result: 13 , shows that, in ad

Novel SARS-CoV-2 variants: the pandemics within the pandemic.

PMID: 34015535 2021 Clinical microbiology and infection

4Method: In Brazil, a new lineage, provisionally named ""MG"" (with a suggested designation of P.4, but the designation is still pending) has been identified with N501T and E484Q mutations in Minas Gerais."

Machine Learning Reveals the Critical Interactions for SARS-CoV-2 Spike Protein Binding to ACE2.

PMID: 34086459 2021 The journal of physical chemistry letters

Introduction: As in previous computational and experimental studies, although most mutations from SARS-CoV to SARS-CoV-2 were favorable, there were several exceptions, notably N439R, Q498Y, and N501T.

Introduction: FEP indicates that the SARS-CoV residues are more favorable in both positions, by 4.0 kcal/mol (Q498Y) and 0.7 kcal/mol (N501T).

Table: N501T

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