literature

SARS_CoV_2 mutation literature information.

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

Discussion: Indeed, while it is expected that mutations at the RBD need to be monitored because those mutations can be responsible for an increase in the binding affinity for the ACE2 receptor, it is matter of debate the increased efficiency in entering host-cells proposed for variants showing supplementary mutations far from the RBD, i.e., D614G or P681H shown by several VoC and other variants of interest or under monitoring (https://www.ecdc.europa.eu/en/covid-19/variants-concern).

Discussion: It is retained that mutations like D614G and P681H, being located in the N-terminal portion of the spike pre-fusion conformation, despite of their relatively great distance from t

A novel antibody against the furin cleavage site of SARS-CoV-2 spike protein: Effects on proteolytic cleavage and ACE2 binding.

PMID: 35007661 2022 Immunology letters

Discussion: In contrast, the mutation of P681H (Alpha variant) and P681R (Delta variant) significantly increased viral replication and transmission, largely due to increased cleavage of S1/S2 site by furin enzyme.

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: Importantly, P681H was present in the UK variant B.1.1.7 (Table 2).

Discussion: It is pertinent to note here that a recent increase in COVID-19 cases in New York, USA, was observed to be due to the introduction of B.1.243 lineage strain with P681H and T478K mutations.

Discussion: The rapid global spread of the UK variant with P681H and P681R mutations is well known.

Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations.

PMID: 34801754 2022 Infection, genetics and evolution

Figure: 1 associated with the Alpha variant of concern first detected in the United Kingdom are H69_V70del, Y144del (identified as Y145del by alignment software), N501Y, A570D, D614G, P681H, T716I, S982A, and D1118H.

Figure: Mutations associated with the Alpha variant of concern (H69_V70del, Y145del, N501Y, A570D, D614G, P681H, T716I, S982A, and D1118H) have rapidly increased in prevalen

A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients.

PMID: 34896524 2022 Gene

Table: P681H

Discussion: Also, there were two other sequences sampled from Shiraz in January 2021, which had five specific mutations as indicator of the Alpha variant (D614G, H69del, N501Y, V70del, Y144del) and were clustered along with the Alpha variants in phylogenetic tree; however, these sequences did not contain the other specific mutations of Alpha variant including A570D, D1118H, L699I, P681H, S982A and T716I.

The significant immune escape of pseudotyped SARS-CoV-2 variant Omicron.

PMID: 34890524 2022 Emerging microbes & infections

Result: There are 32 mutations on the Spike of Omicron, including the following sites: A67V, H69del-V70del, T95I, G142D-V143del-Y144del-Y145del, N211del-L212I, ins214EPE, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H,

PMID: 34856891 2022 Emerging microbes & infections

Discussion: Both Alpha and Delta variants have mutations near the classical furin cleavage site (P681H/R).

Discussion: Previous studies suggested that the P681H mutation enhanced the cleavage of S protein by furin, while P681R promoted cell-cell fusion.

Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021.

PMID: 34848355 2022 Infection, genetics and evolution

Abstract: In addition, the profiling of sub-haplotypes indicated that sub-haplotype 2A_1 with the mutations at N501Y, A570D, D614G, P681H, T716I, S982A, and D118H in Spike was over 58% in May 2021 in the high partly vaccinated rate group (US, Canada, and Germany).

Discussion: Our complete genome sequence dataset of SARS-CoV-2 variants in 2021, sub-haplotype 2A_1 variant had two deleted-amino acids (H69del, V143del) and six amino acid changes in spike protein (N501Y, A570D, P681H,

A year living with SARS-CoV-2: an epidemiological overview of viral lineage circulation by whole-genome sequencing in Barcelona city (Catalonia, Spain).

PMID: 34842496 2022 Emerging microbes & infections

Result: The D614G (96.4%) substitution was observed in most viral genomes, in addition to multiple mutations defining lineages, such as the mutation set Delta69-70, Delta144, N501Y, A570D, P681H, T716I, S982A, and D1118H for B.1.1.7 viruses.

Monitoring the SARS-CoV-2 pandemic: screening algorithm with single nucleotide polymorphism detection for the rapid identification of established and emerging variants.

PMID: 34537361 2022 Clinical microbiology and infection

Discussion: The proposed algorithm uses SGTF as first discriminator, which could be considered a limitation but alternative strategies including the E484K/Q, L452R, P681R/H and H655Y or K417N/T mutations could be used to discriminate between variants without the requirement of the SGTF.

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