Phylo-geo-network and haplogroup analysis of 611 novel Coronavirus (nCov-2019) genomes from India

Abstract

The novel Coronavirus from Wuhan China discovered in December 2019 (nCOV-2019) has since developed into a global epidemic with major concerns about the possibility of the virus evolving into something even more sinister. In the present study we constructed the phylo-geo-network of nCOV-2019 genomes from across India to understand the viral evolution in the country. A total of 611 full length genomes were extracted from different states of India from the EpiCov repository of GISAID initiative and NCBI. Their alignment uncovered 270 parsimony informative sites. Further, 339 genomes were divided into 51 haplogroups. The network revealed the core haplogroup as that of reference sequence NC_045512.2 (Haplogroup A1) with 157 identical sequences present across 16 states. The rest were having not more than ten identical sequences across not more than three locations. Interestingly, some locations with fewer samples have more haplogroups and most haplogroups (41) are localized exclusively to any one state only, suggesting the local evolution of viruses. The two most common lineages are B6 and B1 (Pangolin) whereas clade A2a (Covidex) appears to be the most predominant in India. However, since the pandemic is still emerging, the final outcome will be clear later only.