Integrated genomic view of SARS-CoV-2 in India
Pramod Kumar; Rajesh Pandey; Pooja Sharma; Mahesh Dhar; A Vivekanand; Upilli Bharathram; Himanshu Vashistha; Saruchi Wadhwa; Nishu Tyagi; Saman Fatihi; Uma Sharma; Priyanka Singh; Hemlata Lall; Meena Datta; Poonam Gupta; Nidhi Saini; Aarti Tiwari; Bibhash Nandi; Dhirendra Kumar; Satyabrata Bag; Deepanshi Deepanshi; Surabhi Rathore; Nidhi Jatana; Varun Jaiswal; Hema Gogia; Preeti Madan; Simrita Singh; Prateek Singh; Debasis Dash; Manju Bala; Sandhya Kabra; Sujeet K Singh; Mitali Mukerji; Lipi Thukral; Mohammed Faruq; Anurag Agarwal; Partha Rakshit.
Preprint
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| PREPRINT-BIORXIV | ID: ppbiorxiv-128751
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.
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