Mutational analysis and assessment of its impact on proteins of SARS-CoV-2 genomes from India

Mutational status of SARS-CoV-2 genomes from India along with their impact on proteins was ascertained through multiple tools including MEGA, Genome Detective, SIFT, PROVEAN and ws-SNPs&GO. Excluding gaps and ambiguous sequences, 493 variable sites (152 parsimony informative and 341 singleton) were observed. NSP3 had the highest incidence of 101 sites followed by S protein (74), NSP12b (43) and ORF3a (31). Average mutations per sample for males and females was 2.56 and 2.88 respectively. Non-uniform geographical distribution of mutations suggests that sequences in some regions are mutating faster than others. There were 281 mutations (198 Neutral and 83 Disease) affecting amino acid sequence. NSP13 has a maximum of 14 Disease variants followed by S protein and ORF3a with 13 each. Disease mutations in genomes from asymptomatic people was mere 11% but those from deceased patients was at 38% indicating contribution of these mutations to the pathophysiology of the SARS-CoV-2.