Sofia Banu, Bani Jolly, Payel Mukherjee, Priya Singh, Shagufta Khan, Lamuk Zaveri, Sakshi Shambhavi, Namami Gaur, Shashikala Reddy, K Kaveri, Sivasubramanian Srinivasan, Dhinakar Raj Gopal, Archana Bharadwaj Siva, Kumarasamy Thangaraj, Karthik Bharadwaj Tallapaka, Rakesh K Mishra, Vinod Scaria, Divya Tej SowpatiAuthor NotesOpen Forum Infectious Diseases, Volume 7, Issue 11, November 2020, ofaa434, https://doi.org/10.1093/ofid/ofaa434
Published: 18 September 2020
Abstract
Background
From an isolated epidemic, coronavirus disease 2019 has now emerged as a global pandemic. The availability of genomes in the public domain after the epidemic provides a unique opportunity to understand the evolution and spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus across the globe.Methods
We performed whole-genome sequencing of 303 Indian isolates, and we analyzed them in the context of publicly available data from India.Results
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 to date could not be mapped to any distinct known cluster, fall within this clade.Conclusions
The cluster is characterized by a core set of 4 genetic variants and has a nucleotide substitution rate of 1.1 × 10–3 variants per site per year, which is 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.