Comparative insight into the genomic landscape of SARS‐CoV‐2 and identification of mutations associated with the origin of infection and diversity

Abstract

The analyses of 2325 severe acute respiratory syndrome coronavirus‐2 (SARS‐CoV‐2) genomes revealed 107, 162, and 65 nucleotide substitutions in the coding region of SARS‐CoV‐2 from the three continents America, Europe, and Asia, respectively. Of these nucleotide substitutions 58, 94, and 37 were nonsynonymous types mostly present in the Nsp2, Nsp3, Spike, and ORF9. A continent‐specific phylogram analyses clustered the SARS‐CoV‐2 in the different group based on the frequency of nucleotide substitutions. Detailed analyses about the continent‐specific amino acid changes and their effectiveness by SNAP2 software was investigated. We found 11 common nonsynonymous mutations; among them, two novel effective mutations were identified in ORF9 (S194L and S202N). Intriguingly, ORF9 encodes nucleocapsid phosphoprotein possessing many effective mutations across continents and could be a potential candidate after the spike protein for studying the role of mutation in viral assembly and pathogenesis. Among the two forms of certain frequent mutation, one form is more prevalent in Europe continents (Nsp12:L314, Nsp13:P504, Nsp13:Y541, Spike:G614, and ORF8:L84) while other forms are more prevalent in American (Nsp12:P314, Nsp13:L504, Nsp13:C541, Spike:D614, and ORF8:L84) and Asian continents (Spike:D614), indicating the spatial and temporal dynamics of SARS‐CoV‐2. We identified highly conserved 38 regions and among these regions, 11 siRNAs were predicted on stringent criteria that can be used to suppress the expression of viral genes and the corresponding reduction of human viral infections. The present investigation provides information on different mutations and will pave the way for differentiating strains based on virulence and their use in the development of better antiviral therapy.

The SARS-CoV-2 Y453F mink variant displays a striking increase in ACE-2 affinity but does not challenge antibody neutralization

“…The emergence of nonsynonymous mutations in the SARS-CoV-2 spike gene has been reported since the beginning of 2020. The main part of these mutations have been identified within the European continent (>20), with fewer identifications on the Asian and American continents (21). The vast majority of these residue substitutions are located in the spike regions outside of the receptor-binding domain (RBD) with the D614G mutation being a common variant reported on all continents and which seems to be taking over likely due to selective advantages (22)(23)(24)(25)(26).…”

Analysis of the mutation dynamics of SARS-CoV-2 genome in the samples from Georgia State of the United States

“…Three other mutations, viz., C241T (5’ UTR region), C3037T (F106F, synonymous mutation), and C14408T, were almost always accompanied by D614G (A2303G) ( Korber et al, 2020 ) ( Figure 4 ). The C14408T mutation in the ORF 1b ( Figure 5 B ) resulted an amino acid change, P314L, near the potential docking sites of viral RNA-dependent RNA polymerase (RdRp) ( Mishra et al, 2021 ). The strains with D614G and P314L mutations were dominant variant in Europe and to some extent in the U.S. during the early COVID-19 pandemic ( Eskier et al, 2020 ).…”

Improved understanding of biorisk for research involving microbial modification using annotated sequences of concern

“…Manipulate host membrane dynamics (Díaz, 2020;Mishra et al, 2021); Suppress host immune signaling (Xia et al, 2020;Shemesh et al, 2021); PATHGO:0000382 (suppresses interferon signaling in another organism) (Xia et al, 2020); PATHGO: 0000236 (modulates cell endomembrane dynamics in another organism) (Díaz, 2020);…”