Genomics of Indian SARS-CoV-2: Implications in genetic diversity, possible origin and spread of virus

World Health Organization (WHO) declared COVID-19 as a pandemic disease on 11 March 2020 Comparison of genome sequences from diverse locations allows us to identify the genetic diversity among viruses which would help in ascertaining viral virulence, disease pathogenicity, origin and spread of the SARS-CoV-2 between countries The aim of this study is to determine the genetic diversity among Indian SARS-CoV-2 isolates Initial examination of the phylogenetic data of SARS-CoV-2 genomes (n = 3123) from different continents deposited at GISAID (Global Initiative on Sharing All Influenza Data) revealed multiple origin for Indian isolates An in-depth analysis of 558 viral genomes derived from samples representing countries from USA, Europe, China, East Asia, South Asia, Oceania, Middle East regions and India revealed that most Indian samples are divided into two clusters A1 sub-cluster showed more similarity to Oceania and Kuwait samples, while A2 sub-cluster grouped with South Asian samples In contrast, cluster B grouped with countries from Europe, Middle East and South Asia Viral clade analysis of Indian samples revealed a high occurrence of G clade (D614G in spike protein;37%), which is a European clade, followed by I clade (V378I in ORF1ab;12%), which is an Oceania clade with samples having Iran connections While A1 cluster is enriched with I clade, the cluster B is enriched with G clade type Thus our study identifies that the Indian SARS-CoV-2 viruses are enriched with G and I clades in addition to 50% samples with unknown genetic variations The potential origin to be countries mainly from Europe, Middle East Oceania and South Asia regions, which strongly imply the spread of virus through most travelled countries The study also emphasizes the importance of pathogen genomics through phylogenetic analysis to discover viral genetic diversity and understand the viral transmission dynamics with eventual grasp on viral virulence and disease pathogenesis