Phylogeographic analysis of SARS-CoV-2 variations from Indian isolates

Abstract

The aggressive multiplication of coronavirus in the Indian population is probably due to the faster mutation rate. At the time of commencement of this work, India was not present in the list of Top 10 worst-affected countries. However, upon completion of this manuscript, India is ranked No. 3 and during publication of this manuscript it may even elevate to the top two positions due to the pandemic. 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 majority of the sequence variations are associated with protein-coding regions, especially Orf1a and spike glycoproteins, while Orf7a had consistent variations, whereas 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 analysed dataset. The codon usage frequency indicated that UGU (code for cysteine) is the most frequent codon, while the least frequent was GCG (code for alanine). 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 were supplemented with few representative countries. 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.