literature

Genome-wide identification and prediction of SARS-CoV-2 mutations show an abundance of variants: Integrated study of bioinformatics and deep neural learning.

PMID: 34812411 2021 Informatics in medicine unlocked

Result: Mutations [L5F, and R80I], S97I, and [L46C, V48G, G49I, Q57H, W131R, G172V, Q185H, and Y206S] were identified to have a deleterious effect on ORF7a, ORF8, and ORF3a proteins, respectively.

Result: Out of 46, 25 missense mutations (D1118H, S194L, R262H, M809L, P314L, A8D,

PMID: 34834948 2021 Viruses

Result: We found amino acid substitutions in Spike (D614G), N (D377Y, P67S, P199L), NS3 (G172V, Q57H), NS8 (S24L) NSP2 (T85I), NSP4 (M458I), NSP5 (L89F), NSP12 (P323L), NSP14 (N129D), and NSP16 (R216C) proteins.

A next generation sequencing (NGS) analysis to reveal genomic and proteomic mutation landscapes of SARS-CoV-2 in South Asia.

PMID: 34841355 2021 Current research in microbial sciences

Result: According to the H-clades (Q57H), 71 South Asian samples (13.71%) were clustered where the samples of India (44) were found as the most dominant one.

Table: Q57H

Genome-wide characterization of SARS-CoV-2 cytopathogenic proteins in the search of antiviral targets.

PMID: 34845452 2021 bioRxiv

Abstract: To further characterize the mechanism, we tested a natural ORF3a Beta variant, Q57H, and a mutant with deletion of the highly conserved residue, DeltaG188.

Method: The ORF3a mutant variants (Q57H and DeltaG188) were generated by overlapping PCR with mutant-specific primers (Table S1) and cloned onto the same pLVX-EF1alpha-IRES-Puro plasmid via Gibson assembly method.

Discussion: For example, the Q57H mutant was predicted to bind S protein, whereas the wildtype does not.

SARS-CoV-2 genetic variations associated with COVID-19 pathogenicity.

PMID: 34870573 2021 Microbial genomics

Table: Q57H

Mutational landscape of SARS-CoV-2 genome in Turkey and impact of mutations on spike protein structure.

PMID: 34871297 2021 PloS one

Table: Gln57His

Hotspot Mutations in SARS-CoV-2.

PMID: 34912372 2021 Frontiers in genetics

Table: Q57H

SARS-CoV-2 genetic diversity and variants of concern in Saudi Arabia.

PMID: 35044933 2021 Journal of infection in developing countries

Abstract: Risk of death was highest with the NSP12_P323L mutation (OR = 1.84; 95% CI = 0.37-9.30) and lowest with the NS3_Q57H mutation (OR = 0.43; 95% CI = 0.25-0.727).

Abstract: The NS3_Q57H mutation was the only variant associated with better patient outcome than the wild type.

Abstract: The most common variants detected were the NSP12_P323L mutation 94.9%, followed by the D614G mutation (76%) and the NS3_Q57H mutation (71.4%).

Genome Sequencing Reveals a Mixed Picture of SARS-CoV-2 Variant of Concern Circulation in Eastern Uttar Pradesh, India.

PMID: 35071267 2021 Frontiers in medicine

Result: It is noteworthy that substitution D614G in spike (S) protein was found in all G and its variant clade GH and GR, while Q57H substitution located in ORF3a protein was only found in 15 cases distributed among GH (n = 9), GR (n = 5), and O (n = 1) clade from the first wave (Supplementary Table 3).

Importation, circulation, and emergence of variants of SARS-CoV-2 in the South Indian state of Karnataka.

PMID: 35243004 2021 Wellcome open research

Discussion: The lineage is characterized by the following amino acid replacements- nsp12-P323L(95.38%), S-D614G (93.85%), S-N440K (56.92%), ORF 3a-Q57H (90.77%), ORF 3a-E261*(81.54%), nsp3-T183I (81.54%), nsp16-L126F(80%), N-S2P (72.31%), ORF 8-S97I (72.31%) (extended data, Supplementary Table 7 ).