Polymorphic landscape of SARS-CoV-2 genomes isolated from Indian population in 2020 demonstrates rapid evolution in ORF3a, ORF8, nucleocapsid phosphoprotein and spike glycoprotein.
CDS
Codon
Evolution
Genetic distance
Genome
India
SARS-CoV-2
SNP
Selection
Journal
Computational biology and chemistry
ISSN: 1476-928X
Titre abrégé: Comput Biol Chem
Pays: England
ID NLM: 101157394
Informations de publication
Date de publication:
Dec 2021
Dec 2021
Historique:
received:
04
08
2021
revised:
30
09
2021
accepted:
21
10
2021
pubmed:
5
11
2021
medline:
15
12
2021
entrez:
4
11
2021
Statut:
ppublish
Résumé
India, with around 15 million COVID-19 cases, recently became the second worst-hit nation by the SARS-CoV-2 pandemic. In this study, we analyzed the mutation and selection landscape of 516 unique and complete genomes of SARS-CoV-2 isolates from India in a 12-month span (from Jan to Dec 2020) to understand how the virus is evolving in this geographical region. We identified 953 genome-wide loci displaying single nucleotide polymorphism (SNP) and the Principal Component Analysis and mutation plots of the datasets indicate an increase in genetic variance with time. The 42% of the polymorphic sites display substitutions in the third nucleotide position of codons indicating that non-synonymous substitutions are more prevalent. These isolates displayed strong evidence of purifying selection in ORF1ab, spike, nucleocapsid, and membrane glycoprotein. We also find some evidence of localized positive selections ORF1ab, spike glycoprotein, and nucleocapsid. The CDSs for ORF3a, ORF8, nucleocapsid phosphoprotein, and spike glycoprotein were found to evolve at rapid rate. This study will be helpful in understanding the dynamics of rapidly evolving SARS-CoV-2.
Identifiants
pubmed: 34736125
pii: S1476-9271(21)00164-X
doi: 10.1016/j.compbiolchem.2021.107594
pmc: PMC8547785
pii:
doi:
Substances chimiques
Codon
0
Coronavirus Nucleocapsid Proteins
0
Phosphoproteins
0
Spike Glycoprotein, Coronavirus
0
nucleocapsid phosphoprotein, SARS-CoV-2
0
spike protein, SARS-CoV-2
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
107594Informations de copyright
Copyright © 2021 Elsevier Ltd. All rights reserved.
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