Population genetic analysis of Indian SARS-CoV-2 isolates reveals a unique phylogenetic cluster

The SARS-CoV-2 pandemic originated from Wuhan, China in December 2019 raised an alarming situation all over the globe. Sequencing of this novel virus provides an opportunity to evaluate the genetic polymorphism present in the viral population. Herein, we analysed 173 sequences isolated from Indian patients and performed SNP linkage, clustering and phylogenetic analysis to understand the local genetic diversity. We found that the SNP linkages that lead to the identification of some global clades, do not hold true for the local clade classification. In addition to the unique cluster, established by another Indian study, we identified a new cluster (I-20D) that encompasses 28% of the analysed sequences. This cluster is defined by two linked variations – C22444T and C28854T. A detailed study of such polymorphisms can be useful for drug and vaccine development.