Phylogeographic Analysis of SARS-CoV-2 Variations from India

The aggressive spread of coronavirus in general is probably due to its faster mutation rate. At the time of the viral strains reviewed in this study, India was not among the worst affected countries. In this study, SARS-CoV-2 isolates of Indian origin were compared with the Wuhan reference sequence. Phylogenomic, proteomic and phylogeographic analyses were performed. The genome comparisons indicated that most of the sequence variations were associated with protein-coding regions, especially Orf1a and spike glycoproteins, while Orf7a had consistent variations, and Orfs 6a, 8 and 10 had negligible variations. The terminals of the genomes compared had high sequence entropy. However, the polyadenylation signal was invariant in the analyzed dataset. The codon usage frequency indicated that UGU (cysteine codon) was the most frequent codon, while the least frequent was GCG (alanine codon). The amino acid frequency showed that the most abundant was leucine (12.5%), and the least was histidine (2.45%). The phylogeographical patterns were mapped for all the representative states of India, and an attempt has been made to predict and classify mutations of Indian origin. The unique differences in the sequence of the Kerala isolate (EPI_ISL_413522) were resolved to be sequence errors rather than mutations. Based on the phylogeographic analysis, the high probability of mutations likely to be of Indian origin is attributed to the Gujarat cluster. A new SARS-CoV-2 UK strain, VUI202012/01, was also included for comparison.