literature

SARS_CoV_2 mutation literature information.

Evaluation of a Rapid and Accessible Reverse Transcription-Quantitative PCR Approach for SARS-CoV-2 Variant of Concern Identification.

PMID: 35465708 2022 Journal of clinical microbiology

Abstract: We designed and analytically validated a two-reaction multiplex reverse transcription-quantitative PCR (RT-qPCR) assay targeting spike protein mutations L452R, E484K, and N501Y in reaction 1 and del69-70, K417N, and T478K in reaction 2.

Evidence for an ACE2-Independent Entry Pathway That Can Protect from Neutralization by an Antibody Used for COVID-19 Therapy.

PMID: 35467423 2022 mBio

Abstract: SARS-CoV-2 variants of concern (VOC) acquired mutations in the spike (S) protein, including E484K, that confer resistance to neutralizing antibodies.

SARS-CoV-2 mutations acquired during serial passage in human cell lines are consistent with several of those found in recent natural SARS-CoV-2 variants.

PMID: 35474907 2022 Computational and structural biotechnology journal

Introduction: Notably, some mutations, such as N439K and E484K, are thought to be related to protective immune responses.

Discussion: Although this site was ultimately selected as aspartate (D) after 12 passages in all cell types, it may be crucial for viral adaptation in host cells; importantly, E484K and E484D have been associated with a protective immune response and viral permissiveness in several host cells.

RBD-mRNA vaccine induces broadly neutralizing antibodies against Omicron and multiple other variants and protects mice from SARS-CoV-2 challenge.

PMID: 35489692 2022 Translational research

Abstract: The RBD-mRNA-induced antibodies exerted moderate neutralization against authentic B.1.617.2 and B.1.1.529 variants, and pseudotyped B.1.351 and P.1 lineage variants containing K417N/T, E484K, and N501Y mutations, the B.1.617.2 lineage variant harboring L452R, T478K, and P681R mutations, and the B.1.1.529 lineage variant containing 38 mutations in the S protein.

COVID-19 patient serum less potently inhibits ACE2-RBD binding for various SARS-CoV-2 RBD mutants.

PMID: 35505068 2022 Scientific reports

Abstract: ACE2 binding inhibition was reduced for ten out of eleven variants examined compared to wild-type, especially for those displaying the E484K mutation such as VOCs beta and gamma.

Pseudotyped Bat Coronavirus RaTG13 is efficiently neutralised by convalescent sera from SARS-CoV-2 infected patients.

PMID: 35505237 2022 Communications biology

Abstract: Moreover, introducing the 484 K mutation into RaTG13 resulted in increased neutralisation, in contrast to the same mutation in SARS-CoV-2 (E484K).

Abstract: This is despite E484K having a well-documented role in immune evasion in variants of concern (VOC) such as B.1.351 (Beta).

Convergent Evolution of Multiple Mutations Improves the Viral Fitness of SARS-CoV-2 Variants by Balancing Positive and Negative Selection.

PMID: 35511584 2022 Biochemistry

Abstract: E484K escapes Class 2 antibodies; however, it has decreased receptor binding, stability, and expression.

Abstract: Triple mutant K417T/E484K/N501Y has increased receptor binding, escapes both Class 1 and Class 2 antibodies, and has similar stability and expression as that of the wild-type.

Abstract: We examined the physical mechanisms underlying the convergent evolution of three mutations K417T/E484K/N501Y by delineating the individual and collective effects of mutations on binding to angiotensin converting enzyme 2 receptor, immune escape from neutralizing antibodies, protein stability, and expression.

Targeted Sanger sequencing to recover key mutations in SARS-CoV-2 variant genome assemblies produced by next-generation sequencing.

PMID: 35294336 2022 Microbial genomics

Abstract: We applied the primer set and wet-laboratory protocol to sequence 222 samples that were missing positions with key mutations K417N, E484K, and N501Y due to poor coverage after NGS sequencing.

Abstract: We successfully sequenced 153 samples of 222 (69 %) using Sanger sequencing and confirmed the occurrence of key beta variant mutations (K417N, E484K, N501Y) in the S genes of 142 of 153 (93 %) samples.

Identifying SARS-CoV-2 Variants of Concern through saliva-based RT-qPCR by targeting recurrent mutation sites.

PMID: 35262087 2022 medRxiv

Method: SARS-CoV-2 TaqMan Assays for S substitutions K417T, E484K, E484Q, and L452R were performed per manufacturer's instructions (Thermo Fisher) with 4 muL of template.

Result: Amplification failure was expected and occurred for strains lacking both reference and mutation sequences at the locus (e.g., B.1.351 lacks both alleles at K417T, B.1.351 and P.1 lack both alleles at E484Q, and B.1.617.1 lacks both alleles at E484K) which indicates high specificity of all assays performed on synthetic RNA.

Result: Furthermore, of the 96 replicates that produced an inconclusive result, 74 were due to the presence of an alternate allele: 70 replicates containing E484K (B.1.351 an

Vaccine-Induced Antibody Responses against SARS-CoV-2 Variants-Of-Concern Six Months after the BNT162b2 COVID-19 mRNA Vaccination.

PMID: 35262410 2022 Microbiology spectrum

Discussion: Amino acid changes in spike proteins of variants contribute to immune evasion, and it has been suggested that N501Y is associated with increased infectivity, whereas L452R, T478K, and E484K with K417N reduce the interaction of neutralizing antibodies with RBD.

Discussion: However, Eta with slightly reduced neutralization results has solely an E484K substitution, indicating that the E484K substitution alone is not able to substantially decrease the neutralization efficacy of vaccine-induced antibodies.

Discussion: Similar findings have been observed by others, and especially amino acid change E484K in Beta has been linked

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