Molecular epidemiology analysis of early variants of SARS-CoV-2 reveals the potential impact of mutations P504L and Y541C (NSP13) in the clinical COVID-19 outcomes.
PMID: 33798758
2021
Infection, genetics and evolution
Result: Clades are characterized as S (C8782T, T28144C, NS8-L84S), L (C241, C3037, A23403, C8782, G11083, G25563, G26144, T28144, G228882), V (NSP6-L37F, NS3-G251V), G (S-D614S), GH (S-D614S, NS3-Q57H), S (S-D614S, NG204R).
Result: Other key variants including ORF3a: Q57H, ORF1ab: T265I (NSP3: PMID: 33755704
2021
PloS one
Result: According to GISAID clade nomenclature (https://www.gisaid.org/references/statements-clarifications/clade-and-lineage-nomenclature-aids-in-genomic-epidemiology-of-active-hcov-19-viruses/), Pakistani strains NIH-44905 and NIH-HAS001 belong to S clade having characteristic genetic markers C8782T, T28144C, and NS8-L84S whereas strains NIH-45090, NIH-45143, and NIH-45579 belong to GH clade having marker variations C241T, C3037T, A23403G, G25563T, S-D614G, and NS3-Q57H.
Result: The two Pakistani strains of clade S contained five
SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan.
Result: L84S destabilizes the folding, which may cause upregulation of the host-immune activity (Figure 5).
Result: Among the three mutations (NS8_L84S, NS8_E92K, and NS8_W45L) in NS8 (ORF8) of SARS-CoV-2, the appearance of E92K has not been reported in earlier studies.
Result: Mutation L84S in ORF8 has been associated with decreased stability of ORF8.
Result: Mutation L84S in the current study has been detected in two isolates, which is a strain determining mutation of clade S (Table 3).
Mutations in spike protein and allele variations in ACE2 impact targeted therapy strategies against SARS-CoV-2.
Result: As shown in Figure 3F, we found that the SARS-CoV-2 mutant with L84S in ORF8 had a closer phylogenetic relationship to its ancestors compared to that of SARS-CoV-2-Wuhan01 (Figure 3F).
Result: Hence, the SARS-CoV-2 mutant L84S was more likely be an ancestral variant than a virus with increased infectivity.
Result: However, the 10 amino acid substitutions recurred in SARS-CoV-2, i.e., I789V of papain-like protease, H36Y and V354F of spike-S1, G251V of ORF3a, D209H of membrane glycoprotein, V62L, L84S, and PMID: 33725111
2021
Briefings in bioinformatics
Table: L84S
Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines.
Discussion: Clades were named based on variants L84S in ORF8 (S clade), D614G in S gene (G clade), and G251V in ORF3a (V clade).
Analysis of RNA sequences of 3636 SARS-CoV-2 collected from 55 countries reveals selective sweep of one virus type.
PMID: 32474553
2020
The Indian journal of medical research
Table: L84S
Mutations in SARS-CoV-2 viral RNA identified in Eastern India: Possible implications for the ongoing outbreak in India and impact on viral structure and host susceptibility.
SARS_CoV_2 mutation literature information.
PMID: 
2021
Infection, genetics and evolution
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