literature

SARS_CoV_2 mutation literature information.

SARS-CoV-2 B.1.617 Indian variants: Are electrostatic potential changes responsible for a higher transmission rate?

PMID: 34260088 2021 Journal of medical virology

Result: However, in this case, our results predict that both mutants (K417N and K417T) could destabilize the protein and increase local flexibility.

Table: K417T

SARS-CoV-2 testing and sequencing for international arrivals reveals significant cross border transmission of high risk variants into the United Kingdom.

PMID: 34278277 2021 EClinicalMedicine

Introduction: The combination of nearby RBD mutations K417N/T, E484K and N501Y found in B.1.351 (South Africa) and P.1 (Brazil) make these particularly concerning variants.

Neutralization of SARS-CoV-2 by highly potent, hyperthermostable, and mutation-tolerant nanobodies.

PMID: 34302370 2021 The EMBO journal

Abstract: We constructed nanobody tandems and identified nanobody monomers that tolerate the K417N/T, E484K, N501Y, and L452R immune-escape mutations found in the Alpha, Beta, Gamma, Epsilon, Iota, and Delta/Kappa lineages.

Neutralizing activity of Sputnik V vaccine sera against SARS-CoV-2 variants.

PMID: 34312390 2021 Nature communications

Introduction: The S genes of B.1.351 and P.1 viruses each carry a number of mutations, but include three in the receptor binding domain (RBD) that are particularly notable, the S: N501Y substitution, found in B.1.1.7, alongside polymorphisms at positions 417 and 484, K417N/T and E484K.

Discussion: B.1.351 and P.1 have in common three RBD substitutions (K417N/T, E484K and N501Y) whereas B.1.351, P.1 and B.1.1.7 contain the N501Y substitution.

The challenge of screening SARS-CoV-2 variants of concern with RT-qPCR: One variant can hide another.

PMID: 34332998 2021 Journal of virological methods

Abstract: From week 18 we used in addition the new NovaplexSARS-CoV-2 Variants II Assay for samples with no targets found with the Variants I assay or with the mutation E484K alone, in order to screen the mutations L452R, K417N/T

Discussion: It distinguishes the VOC B.1.351 from the VOC P.1 by amplification of the K417N and K417T mutations respectively when both the N501Y and E484K mutations were found positive with the Variant I Assay.

Discussion: Since early May 2021, a new NovaplexSARS-CoV-2 Variants II Assay has been available on the market to detect L452R, K417N, K417T and W152C mutations.

Conformational Variability Correlation Prediction of Transmissibility and Neutralization Escape Ability for Multiple Mutation SARS-CoV-2 Strains using SSSCPreds.

PMID: 34337269 2021 ACS omega

Conclusion: Introduction: On the other hand, P.1 that emerged in Brazil has K417T, E484K, N501Y, and D614G mutations (Figure 1B).

Result: K417N with the more flexible SSSC sequence can escape neutralization more effectively than K417T with the less flexible one.

Differential Interactions Between Human ACE2 and Spike RBD of SARS-CoV-2 Variants of Concern.

PMID: 34341794 2021 bioRxiv

Introduction: To gain molecular insight into the difference of all variants that are classified as the variants of concern (Alpha (first identified in United Kingdom, B.1.1.7: N501Y), Beta (first identified in South Africa, B.1.351: K417N, E484K, N501Y), Gamma (first identified in Japan/Brazil, P.1: K417T, E484K, N501Y), and Delta (first identified in India, B.1.617.2: L452R, T478K)) and two additional variants of interest (Epsilon (first identified in US-California, B.1.427: L452R) and Kappa (first identified in India, B.1.617.1: L452R, E484Q)), pulling force analysis was perform

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

PMID: 34351895 2021 PLoS computational biology

Result: However, mutations like K417N and K417T were not observed to cause favourable changes on expression (a proxy measurement for stability) or binding as well as immune recognition, but in our high throughput evaluation they were, as well as several substitutions in this position, predicted to increase the occupancy of the open state.

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

SARS-CoV-2 Spike Mutations, L452R, T478K, E484Q and P681R, in the Second Wave of COVID-19 in Maharashtra, India.

PMID: 34361977 2021 Microorganisms

Introduction: These variants are known to possess multiple mutations across the genome, including several in the S protein and its RBD, such as N501Y, E484K and K417N/T.

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

PMID: 34363852 2021 Virus research

Introduction: It has the same three mutations (except for K417T instead of K417N) in RBD as B.1.351, but it arose independently.

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.

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