literature

SARS_CoV_2 mutation literature information.

SARS-CoV-2 variants of concern alpha, beta, gamma and delta have extended ACE2 receptor host ranges.

PMID: 35377298 2022 The Journal of general virology

Abstract: All four VOCs were able to overcome a previous restriction for mouse ACE2, with demonstrable differences also seen for individual VOCs with rat, ferret or civet ACE2 receptors, changes that we subsequently attributed to N501Y and E484K substitutions within the spike RBD.

SARS-CoV-2 BA.1 variant is neutralized by vaccine booster-elicited serum, but evades most convalescent serum and therapeutic antibodies.

PMID: 35380448 2022 Science translational medicine

Result: We compared the neutralization titers of these serum samples against pseudoviruses bearing spike proteins from the following variants: D614G, Omicron (A67V, del69-70, T95I, del142-144, Y145D, del211, L212I, ins214EPE, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R,

Emergence and phenotypic characterization of the global SARS-CoV-2 C.1.2 lineage.

PMID: 35396511 2022 Nature communications

Result: The spike protein substitutions observed in C.1.2 include five within the N-terminal domain (NTD: C136F, Y144del, R190S, D215G, and 242-243del or 2

Result: The majority of these substitutions (P9L, C136F, R190S, D215G, L242del, A243del, Y449H, E484K, N501Y, H655Y, and T716I), however, appeared simultaneously, further supporting a single, prolonged infection giving rise to this lineage.

The basis of mink susceptibility to SARS-CoV-2 infection.

PMID: 35396646 2022 Journal of applied genetics

Introduction: In the mouse model, the N501Y mutation has been associated with increased infectivity and virulence of SARS-CoV-2 (Gu et al.).

Introduction: Nowadays, the N501Y mutation characterizes the novel SARS-CoV-2 variant from the UK named VOC202012/01 (B.1.1.7) (European Centre for Disease Prevention and Control), which was recently detected in Poland (Hryhorowicz et al.).

Introduction: Some of these mutations, such as the 69-70 deletion in combination with the N501Y variant, increase the transmissibility of SARS-CoV-2.

Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry.

PMID: 35397208 2022 Cell reports

Result: This could be due to enhanced binding of RBD of B.1.1.7 with ACE2 due to N501Y mutation, which enhances receptor recognition and fusion, or simply due to enhanced triggering, consistent with previous data.

Inhibitor screening using microarray identifies the high capacity of neutralizing antibodies to Spike variants in SARS-CoV-2 infection and vaccination.

PMID: 35401825 2022 Theranostics

Result: An additional five mutations had <= 2-fold increased binding to human ACE2 (Figure 2C-D): L452R (in B.1.427/429 and B.1.617), Y453F (in B.1.1.298), E484Q (in B.1.617.1 and B.1.617.3) and N501Y (in B.1.1.529, B.1.1.7, B.1.351 and P.1).

Result: Notably, structural analyses show that 5 escape mutations (K417N/E484K/N501Y, G446V, F456E, N487R, F490L) are located within the interface of RBD-ACE2 interaction, indicating that this RBD subdomain is important in neutralizing SARS-CoV-2 infection.

Result: The most prevalen

Pathogenicity of SARS-CoV-2 Omicron (R346K) variant in Syrian hamsters and its cross-neutralization with different variants of concern.

PMID: 35405385 2022 EBioMedicine

Method: On deep sequencing following amino acid changes were found in the isolate.(NSP5_P132H,Spike_T95I,Spike_K417N,Spike_S373P,Spike_Q493R,Spike_N969K, Spike_H655Y,Spike_

Discussion: It harbours N501Y, K417N, T478K, E484A which are amino acid substitutions linked with immune escape.

Molecular Dynamics and MM-PBSA Analysis of the SARS-CoV-2 Gamma Variant in Complex with the hACE-2 Receptor.

PMID: 35408761 2022 Molecules (Basel, Switzerland)

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

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.

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,

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