1. Characterizing genomic variants and mutations in SARS-CoV-2 proteins from Indian isolates
- Author
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Jayanta Kumar Das, Swarup Roy, Antara Sengupta, and Pabitra Pal Choudhury
- Subjects
0301 basic medicine ,2019-20 coronavirus outbreak ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,Non-synonymous mutations ,Deleterious substitutions ,Disease pathogenesis ,Biology ,medicine.disease_cause ,Genome ,Functional domain ,Article ,03 medical and health sciences ,Codon position ,0302 clinical medicine ,Protein stability ,NS, non-synonymous ,TM, transmembrane domain ,Genetics ,medicine ,Coding region ,SARS, severe acute respiratory syndrome ,NTD, N-terminal domain ,AA, amino acid ,Mut, mutation ,chemistry.chemical_classification ,Mutation ,COVID-19 ,CTD, C-terminal domain ,Amino acid ,030104 developmental biology ,chemistry ,CP, codon position ,030220 oncology & carcinogenesis ,Syn, synonymous ,HR, heptapeptide repeat ,CoV, coronaviruses - Abstract
SARS-CoV-2 is mutating and creating divergent variants by altering the composition of essential constituent proteins. Pharmacologically, it is crucial to understand the diverse mechanism of mutations for stable vaccine or anti-viral drug design. Our current study concentrates on all the constituent proteins of 469 SARS-CoV-2 genome samples, derived from Indian patients. However, the study may easily be extended to the samples across the globe. We perform clustering analysis towards identifying unique variants in each of the SARS-CoV-2 proteins. A total of 536 mutated positions within the coding regions of SARS-CoV-2 proteins are detected among the identified variants from Indian isolates. We quantify mutations by focusing on the unique variants of each SARS-CoV-2 protein. We report the average number of mutation per variant, percentage of mutated positions, synonymous and non-synonymous mutations, mutations occurring in three codon positions and so on. Our study reveals the most susceptible six (06) proteins, which are ORF1ab, Spike (S), Nucleocapsid (N), ORF3a, ORF7a, and ORF8. Several non-synonymous substitutions are observed to be unique in different SARS-CoV-2 proteins. A total of 57 possible deleterious amino acid substitutions are predicted, which may impact on the protein functions. Several mutations show a large decrease in protein stability and are observed in putative functional domains of the proteins that might have some role in disease pathogenesis. We observe a good number of physicochemical property change during above deleterious substitutions.
- Published
- 2021