Integrated genomic view of SARS-CoV-2 in India

Kumar, Pramod; Pandey, Rajesh; Sharma, Pooja; Dhar, Mahesh S; Vivekanand, A; Uppili, Bharathram; Vashisht, Himanshu; Wadhwa, Saruchi; Tyagi, Nishu; Fatihi, Saman; Sharma, Uma; Singh, Priyanka; Lall, Hemlata; Datta, Meena; Gupta, Poonam; Saini, Nidhi; Tewari, Aarti; Nandi, Bibhash; Kumar, Dhirendra; Bag, Satyabrata; Deepanshi,; Rathore, Surabhi; Jatana, Nidhi; Jaiswal, Varun; Gogia, Hema; Madan, Preeti; Singh, Simrita; Singh, Prateek; Dash, Debasis; Bala, Manju; Kabra, Sandhya; Singh, Sujeet; Mukerji, Mitali; Thukral, Lipi; Faruq, Mohammed; Agrawal, Anurag; Rakshit, Partha

India first detected SARS-CoV-2, causal agent of COVID-19 in late January-2020, imported from Wuhan, China. March-2020 onwards; importation of cases from rest of the countries followed by seeding of local transmission triggered further outbreaks in India. We used ARTIC protocol based tiling amplicon sequencing of SARS-CoV-2 (n=104) from different states of India using a combination of MinION and MinIT from Oxford Nanopore Technology to understand introduction and local transmission. The analyses revealed multiple introductions of SARS-CoV-2 from Europe and Asia following local transmission. The most prevalent genomes with patterns of variance (confined in a cluster) remain unclassified, here, proposed as A4-clade based on its divergence within A-cluster. The viral haplotypes may link their persistence to geo-climatic conditions and host response. Despite the effectiveness of non-therapeutic interventions in India, multipronged strategies including molecular surveillance based on real-time viral genomic data is of paramount importance for a timely management of the pandemic.