A distinct phylogenetic cluster of Indian SARS-CoV-2 isolates

Banu, Sofia; Jolly, Bani; Mukherjee, Payel; Singh, Priya; Khan, Shagufta; Zaveri, Lamuk; Shambhavi, Sakshi; Gaur, Namami; Reddy, Shashikala; Kaveri, K; Srinivasan, Sivasubramanian; Gopal, Dhinakar Raj; Siva, Archana Bharadwaj; Thangaraj, Kumarasamy; Tallapaka, Karthik Bharadwaj; Mishra, Rakesh K; Scaria, Vinod; Sowpati, Divya Tej

MOTIVATION: From an isolated epidemic, COVID-19 has now emerged as a global pandemic. The availability of genomes in the public domain following the epidemic provides a unique opportunity to understand the evolution and spread of the SARS-CoV-2 virus across the globe. RESULTS: We performed whole-genome sequencing of 303 Indian isolates, and analyzed them in the context of publicly available data from India. We describe a distinct phylogenetic cluster (Clade I/A3i) of SARS-CoV-2 genomes from India, which encompasses 22% of all genomes deposited in the public domain from India. Globally approximately 2% of genomes, which till date could not be mapped to any distinct known cluster fall in this clade. CONCLUSIONS: The cluster is characterized by a core set of 4 genetic variants and has a nucleotide substitution rate of 1.1 x 10 (-3) variants per site per year, lower than the prevalent A2a cluster. Epidemiological assessments suggest that the common ancestor emerged at the end of January 2020 and possibly resulted in an outbreak followed by countrywide spread. To the best of our knowledge, this is the first comprehensive study characterizing this cluster of SARS-CoV-2 in India.