Comparative genomics, evolutionary epidemiology, and RBD-hACE2 receptor binding pattern in B.1.1.7 (Alpha) and B.1.617.2 (Delta) related to their pandemic response in UK and India.
PMID: 35427787
2022
Infection, genetics and evolution
Discussion: N501Y, D614G L452R, and E484Q mutations are reported as significant mutations in different variants in SARS-CoV-2.
Discussion: Finally, we evaluated the comparative receptor binding (hACE2) pattern with the Wuhan strain, VOC B.1.1.7 variant (RBD N501Y mutation), and VOI B.1.617.2 variant of the spike protein (RBD double mutations L452R, E484Q).
Discussion: The variant was observed with some significant mutations in spike protein.Comparative genomics assessment of these two variants has revealed specific unique mutations, such as N501Y,
Increased Secondary Attack Rate among Unvaccinated Household Contacts of Coronavirus Disease 2019 Patients with Delta Variant in Japan.
PMID: 35409572
2022
International journal of environmental research and public health
Abstract: We studied household contacts of index cases of COVID-19 infected with Delta (L452R mutation), Alpha (N501Y mutation), and wild strain from December 2020 through November 2021 in Itako, Japan.
Method: Almost all cases with the N501Y mutation during the study period in Japan were confirmed to be the Alpha variant by RNA sequencing.
Method: Contact with the Alpha strain was defined as contact of the index patient with positive results for N501Y mutation until 20 June 2021 or negative results for L452R mutation after 21 June 2021 among the patient, or the patient's contacts.
Method: If the index case was reported after 22 March, and both N501Y and L452R mutation screening were not p
Molecular Dynamics and MM-PBSA Analysis of the SARS-CoV-2 Gamma Variant in Complex with the hACE-2 Receptor.
Introduction: Additionally, the mutation N501Y exhibits a compensatory effect since it favors pi-pi interaction with the residue Y41.
Introduction: The alpha variant has three mutations of interest in the spike protein: (i) the N501Y mutation that corresponds to the receptor-binding motif (RBM); (ii) a 69/70 deletion in the receptor binding domain (RBD) that triggers a notable change in the conformation of the RBM; and (iii) the P681H mutation found near the furin S1/S2 cleavage site.
Introduction: The beta variant, also known as 20H/501Y.V2, was identified in South Africa and is characterized by carrying the K417N, E484K and N501Y mutations in the RBM of the
E-Volve: understanding the impact of mutations in SARS-CoV-2 variants spike protein on antibodies and ACE2 affinity through patterns of chemical interactions at protein interfaces.
Introduction: As in cases of reinfection, by the non-synonymous convergent spike mutations N501Y, appearing in all of them, E484K occurring on the Gamma and in the Beta and K417T taking place in the Gamma variant.
Introduction: It presents the following mutations: L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, H655Y, and T1027I.
Introduction: One of those effects revealed by Nelson and collaborators is the increased affinity between the Receptor-Binding Domain ( PMID: 35367284
2022
Virus research
Table: N501Y
Evasion of vaccine-induced humoral immunity by emerging sub-variants of SARS-CoV-2.
Introduction: Beta+R346K and Mu+K417N share the same haplotype with R346K, K417N, E484K and N501Y mutations in the receptor-binding domain (RBD) in the spike protein, as shown in Figure 2.
Introduction: In late September, the Alpha variant (B.1.1.7) harboring the N501Y mutation that conferred higher infectivity emerged in the UK and spread rapidly all over the world before vaccines became widely available in December.
Discussion: reported that neutralization efficacy was reduced for the Mu variant harboring R346K, E484K and N501Y in the PMID: 35346184
2022
BMC medicine
Introduction: The beta variant bears genetic changes in the functional domain of the SARS-CoV-2 spike (S) protein including substitutions in the receptor-binding domain (RBD) (E484K, N501Y and K417N), four substitutions and a deletion in N-terminal domain (NTD) (L18F, D80A, D215G, L242H and R246I) and substitutions in S2 (D614G and A701V) regions.
SARS-CoV-2-specific antibody and T-cell responses 1 year after infection in people recovered from COVID-19: a longitudinal cohort study.
Discussion: The three mutations characterising the beta variant (K417N, E484K, and N501Y) are located at the receptor-binding domain, making the variant resistant to some potent neutralising antibodies.
Optimization and Application of a Multiplex Digital PCR Assay for the Detection of SARS-CoV-2 Variants of Concern in Belgian Influent Wastewater.
Abstract: Key mutations were targeted in the different VOC strains, including SDelta69/70 deletion, N501Y, SDelta241 and SDelta157.
Introduction: Multiple methods have been developed targeting single-nucleotide polymorphisms (e.g., N501Y and E484K) or characteristic deletions (e.g., spike SDelta69/70 deletion and ORF1a Delta3675-3677) in the genome (often the spike domain) of the SARS-CoV-2 virus.
Result: 1.1.7 and N501Y primer set, the assays for P1 and B.1.617.2 VOC were found specific with the RT-qPCR method.
Result: Additionally, the N501Y primer set did not target the B.1.617.2.
Result: As discussed earlier, the N501Y primer set should yield in
Protective Immunity of the Primary SARS-CoV-2 Infection Reduces Disease Severity Post Re-Infection with Delta Variants in Syrian Hamsters.
Discussion: The B.1.351 variant is known worldwide for its immune escape property due to the mutations K417N, E484K and N501Y in the RBD of the spike region.
SARS_CoV_2 mutation literature information.
PMID: 
2022
Infection, genetics and evolution
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