literature

SARS_CoV_2 mutation literature information.

Tracking cryptic SARS-CoV-2 lineages detected in NYC wastewater.

PMID: 35115523 2022 Nature communications

Figure: WNY1 = E484A/F486P/S494P/Q498Y/H519N/F572N, WNY2 = Q493K/S494P/Q498Y/H519N/T572N, WNY3 = K417T/K444T/E484A/F590Y/Q498H, WNY4 = K417T/N439K/K444N/Y449R/L452R/N460K/S477N/Delta484/

A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2.

PMID: 34990583 2022 Cell reports

Introduction: Given that the B.1.351 and P.1 strains harbor K417N/T, E484K, and N501Y mutations in the RBD domain, B.1.526 harbors E484K, and B.1.617.1 harbors L452R and E484Q (Figure S4C), we wanted to develop a D614G- and E484K/Q-specific bivalent vaccine.

Emergence of two distinct variants of SARS-CoV-2 and an explosive second wave of COVID-19: the experience of a tertiary care hospital in Pune, India.

PMID: 35000004 2022 Archives of virology

Result: Until December 2020, none of the samples exhibited the characteristic mutations (K417N/T, E484K, N501Y, T478K) found in the variants of concern that have been identified so far.

Modeling SARS-CoV-2 spike/ACE2 protein-protein interactions for predicting the binding affinity of new spike variants for ACE2, and novel ACE2 structurally related human protein targets, for COVID-19 handling in the 3PM context.

PMID: 35013687 2022 The EPMA journal

Result: From an energetical point of view, the P.1 Japan/Brazil VoC, showing the three mutations N501Y_E484K_K417T at the RBD, has the highest binding affinity (- 21.37 kcal/mol or - 89.41 kJ/mol; Table 1) for ACE2 (increased of 4% with respect to the Wuhan spike RBD, - 20.51 kcal/mol or - 85.81 kJ/mol, Table 1), followed by the B.1.141-VoC showing the single N439K amino acid replacement at the RBD and the single mutant E484K firstly detected in the spike RBD of the P.1 Japan/Brazil VoC (Table 1).

Result: Indeed, it is possible to count a slight increase in the hydrophobic interactions within a

SARS-CoV-2 multiplex RT-PCR to detect variants of concern (VOCs) in Malaysia, between January to May 2021.

PMID: 35026305 2022 Journal of virological methods

Introduction: Notable spike (S) amino acid mutations are: HV69/70 deletion and P681H in B.1.1.7, K417N in B.1.351, and K417T in P.1.

Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift.

PMID: 35032057 2022 Journal of medical virology

Introduction: Mutations such as N501Y, S477N, N439K, L452R, E484K, K417N, T478K, and K417T were observed in VOCs and VOIs, and these sites were listed as RBD high-frequency mutation sites, suggesting that these sites are mutation-prone.

Result: The neutralization results for the possible VOC single variants showed that the N501Y mutation escape the mAbs CB6 and 03-10D12-1C3, while the N501T substitution in the Alpha+N501T variant does not escape mAb 03-10D12-1C3 (Figure 5A); the mAbs BGB-DXP593, 05-9G11, MW07-LALA, AM128, AM180, and AbG3 were escaped by the

PMID: 35093235 2022 Cell reports

Result: It appears L452R, E484K, and N501Y may promote use of ferret ACE2, while K417N/T may result in a greater reduction in ferret ACE2 usage relative to human ACE2.

Pan-SARS neutralizing responses after third boost vaccination in non-human primate immunogenicity model.

PMID: 35101265 2022 Vaccine

Table: K417T

Discussion: The Beta and Gamma variants are the most resistant to monoclonal antibodies (mAbs) and convalescent plasma from SARS CoV-2-infected individuals, and the resistance profiles correspond to several deletions in the N-terminal domain and the K417N/T, E484K/Q, and N501Y mutations in the RBD of SARS-CoV-2 Spike protein.

Mutations in the receptor-binding domain of human SARS CoV-2 spike protein increases its affinity to bind human ACE-2 receptor.

PMID: 35109768 2022 Journal of biomolecular structure & dynamics

Abstract: Here, we use the crystal structure of the RBD in complex with ACE-2 available in the public domain and analyse the 250 ns molecular dynamics (MD) simulations of wild-type and mutants; K417N, K417T, N440K, N501Y, L452R, T478K, E484K and S494P.

Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil.

PMID: 35171035 2022 Microbiology spectrum

Introduction: The P.1 lineage-defining mutations in the Spike protein, especially in the receptor-binding domains (RBD) such as K417T, E484K and N501Y, are of concern because they may enhance ACE2 affinity and contribute to antibody evasion.

Table: K417T

Discussion: According to our results, most of the P.1 sequences carried the 22 lineage-defining mutations, including the three mutations in the Spike protein, RBD domain (K417T, E484K and N501Y) associated with evasion of the immune system and greater transmissibility.

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