Phylogenetic analysis of 17271 Indian SARS-CoV-2 genomes to identify temporal and spatial hotspot mutations

The second wave of SARS-CoV-2 has hit India hard and though the vaccination drive has started, moderate number of COVID affected patients is still present in the country, thereby leading to the analysis of the evolving virus strains. In this regard, multiple sequence alignment of 17271 Indian SARS-CoV-2 sequences is performed using MAFFT followed by their phylogenetic analysis using Nextstrain. Subsequently, mutation points as SNPs are identified by Nextstrain. Thereafter, from the aligned sequences temporal and spatial analysis are carried out to identify top 10 hotspot mutations in the coding regions based on entropy. Finally, to judge the functional characteristics of all the non-synonymous hotspot mutations, their changes in proteins are evaluated as biological functions considering the sequences by using PolyPhen-2 while I-Mutant 2.0 evaluates their structural stability. For both temporal and spatial analysis, there are 21 non-synonymous hotspot mutations which are unstable and damaging.