literature

Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus).

PMID: 33568759 2021 Scientific reports

Conclusion: Notable mutation in this gene is L84S, which occurs in 1000 sequences with the first case collected at the beginning of the pandemic in China: Wuhan on 2019-12-30 and the latest case in Australia: Victoria on 2020-05-27.

Table: L84S

Figure: Protein ORF3a: two spikes at Q57H (2795) and G251V (206); protein ORF8: two spikes at S24L (320) and L84S (1000); protein N: R203K (876) and G204R (433); Other proteins E, M, ORF6,

PMID: 33588026 2021 Microbial pathogenesis

Table: L84S

Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants.

PMID: 33589648 2021 Communications biology

Introduction: Additionally, three concurrent missense mutations 17747C>T-(P504L), 17858A>G-(Y541C), and 28144T>C-(L84S) tend to fade out, while the other eight concurrent mutations may enhance the infectivity of SARS-CoV-2.

Introduction: Furthermore, the US SARS-CoV-2 strains that have 1059C>T-(T85I), 14408C>T-(P323L), 23403A>G-(D614G), 25563G>T-(Q57H), 28144T>C-(L84S

Table: L84S

Comparative Genomics and Integrated Network Approach Unveiled Undirected Phylogeny Patterns, Co-mutational Hot Spots, Functional Cross Talk, and Regulatory Interactions in SARS-CoV-2.

PMID: 33622851 2021 mSystems

Result: Mutation in ORF8 sequence (L84S) was found conserved; therefore, to predict its effect, it was critical to examine its biological function in SARS-CoV-2 interaction with human proteins.

Result: Out of 14 high-frequency SNPs, only 9 mutations (Nsp2 [T85I], Nsp3 [S1103P], Nsp6 [L37F], Nsp12 [P324L], Nsp13 [P409L and Y446C], S [D614G], Orf3a [Q577H], and

Genomic characterization and evolution of SARS-CoV-2 of a Canadian population.

PMID: 33662015 2021 PloS one

Discussion: In addition, replacement of Leucine with Serine at 84 position of ORF8 was found to have significant effect on the structure of the protein C-terminal which was possibly a phosphorylation target for the human Serine/Threonine kinases.

A hijack mechanism of Indian SARS-CoV-2 isolates for relapsing contemporary antiviral therapeutics.

PMID: 33705994 2021 Computers in biology and medicine

Table: L84S

Discussion: Spike-D614G, Nsp3-G251V, Nsp3: F106F, Nsp12b: P314L, ORF3a: Q57H, ORF8-L84S, N: RG203KR, and 5'UTR:241 were the most frequent mutations in global SARS-CoV-2 isolates similar to earlier analyses.

Global dynamics of SARS-CoV-2 clades and their relation to COVID-19 epidemiology.

PMID: 33875719 2021 Scientific reports

Introduction: Such changes include: L84S in NS8 for clade S; coexisting L37F and G251V mutations in NSP6 and NS3, respectively for clade V; D614G mutation in the spike protein (S) for clade G.

Association of SARS-CoV-2 clades with clinical, inflammatory and virologic outcomes: An observational study.

PMID: 33840632 2021 EBioMedicine

Introduction: The global initiative on sharing all influenza data (GISAID) nomenclature describes four major SARS-CoV-2 clades in the early outbreak: clade L, clade V (variant of the ORF3a coding protein NS3-G251), clade G (variant of the spike protein S-D614G with further subclades GR, GH and GV collectively called clade G here), and clade S (variant ORF8-L84S).

Introduction: The global initiative on sharing all influenza data (GISAID) nomenclature describes the emergence of four major SARS-CoV-2 clades: clade L, clade V (variant of the ORF3a coding protein NS3-G251), clade G (variant of the spike pro

The extent of molecular variation in novel SARS-CoV-2 after the six-month global spread.

PMID: 33677109 2021 Infection, genetics and evolution

Abstract: Phylogenetic tree analysis with Neighbor-Joining and Maximum-Parsimony methods indicated that the haplotypes of SARS-CoV-2 genome sequences were classified into four clades with the unique nucleotide and amino acid changes: T27879C (ORF8 L84S) in clade 1 (25.34%), A23138G (spike D614G) in clade 2 (63.54%), G10818T (nsp6 L37F), Discussion: Notably, Subclade 1C variants with the mutations ORF8 L84S and Helicase P504L was over 79% (842 out of 1072) within Clade 1.

Structure-Function Analyses of New SARS-CoV-2 Variants B.1.1.7, B.1.351 and B.1.1.28.1: Clinical, Diagnostic, Therapeutic and Public Health Implications.

PMID: 33803400 2021 Viruses

Introduction: The recent temporal analyses of SARS-CoV-2 epidemics highlighted selective global sweep of the D614G variant S protein (Clade G) over G251V in ORF3a (Clade V) and L84S in ORF 8 (Clade S) variants.

Result: The P.1 specific E92K in ORF8 showed >90% co-occurrence with its L84S mutation and S202N, M86I in N and nsp6 (ORF1ab) proteins, respectively.