Accepted for/Published in: JMIR Bioinformatics and Biotechnology
Date Submitted: May 27, 2020
Date Accepted: Aug 24, 2020
Date Submitted to PubMed: Dec 23, 2020
Warning: This is an author submission that is not peer-reviewed or edited. Preprints - unless they show as "accepted" - should not be relied on to guide clinical practice or health-related behavior and should not be reported in news media as established information.
The novel Coronavirus enigma: Phylogeny and analyses of co-evolving mutations among the SARS-CoV-2 viruses circulating in India during early 2020
ABSTRACT
Background:
The RNA genome of the emerging novel Coronavirus is rapidly mutating while human to human transmission, therefore temporal dissection of their evolutionary dynamics, nature of variations in different strains and understanding the single nucleotide polymorphisms in endemic settings is very crucial. Studying the heterogeneous genomic constellations of this rapidly mutating virus would help us to understand its complex epidemiology in that particular geographical region.
Objective:
This is a comprehensive analysis of 46 Indian SARS-CoV-2 genome sequences available from the NCBI and GISAID repository during early 2020. Evolutionary dynamics, gene-specific phylogeny and emergence of the novel co-evolving mutations in nine structural and non-structural genes among circulating SARS-CoV-2 strains in ten states of India have been assessed.
Methods:
46 SARS-CoV-2 nucleotide sequences submitted from India were downloaded from the GISAID (39/46) or from NCBI (7/46) database. Phylogenetic study and analyses of mutation were based on the nine structural and non-structural genes of SARS-CoV-2 strains. Secondary structure of RdRP/NSP12 protein was predicted with respect to the novel A97V mutation.
Results:
Phylogenetic analyses revealed the evolution of “genome-type clusters” and adaptive selection of “L” type SARS-CoV-2 strains with genetic closeness to the bat SARS-like coronaviruses than pangolin or MERS-CoVs. With regards to the novel co-evolving mutations, 2 groups are seen to circulate in India at present: the “major group” (52.2%) and the “minor group” (30.4%), harboring four and five co-existing mutations, respectively. The “major group” mutations fall in the A2a clade. All the minor group mutations, except 11083G>T (L37F, NSP6) were unique to the Indian isolates.
Conclusions:
The study highlights rapidly evolving SARS-CoV-2 virus and co-circulation of multiple clades and sub-clades, driving this pandemic worldwide. This comprehensive study is a potential resource for monitoring the novel mutations in the viral genome, changes in viral pathogenesis, for designing vaccines and other therapeutics.
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