PT  - JOURNAL ARTICLE
AU  - Pramod Kumar
AU  - Rajesh Pandey
AU  - Pooja Sharma
AU  - Mahesh S Dhar
AU  - A Vivekanand
AU  - Bharathram Uppili
AU  - Himanshu Vashisht
AU  - Saruchi Wadhwa
AU  - Nishu Tyagi
AU  - Saman Fatihi
AU  - Uma Sharma
AU  - Priyanka Singh
AU  - Hemlata Lall
AU  - Meena Datta
AU  - Poonam Gupta
AU  - Nidhi Saini
AU  - Aarti Tewari
AU  - Bibhash Nandi
AU  - Dhirendra Kumar
AU  - Satyabrata Bag
AU  - Deepanshi
AU  - Surabhi Rathore
AU  - Nidhi Jatana
AU  - Varun Jaiswal
AU  - Hema Gogia
AU  - Preeti Madan
AU  - Simrita Singh
AU  - Prateek Singh
AU  - Debasis Dash
AU  - Manju Bala
AU  - Sandhya Kabra
AU  - Sujeet Singh
AU  - Mitali Mukerji
AU  - Lipi Thukral
AU  - Mohammed Faruq
AU  - Anurag Agrawal
AU  - Partha Rakshit
TI  - Integrated genomic view of SARS-CoV-2 in India
AID  - 10.1101/2020.06.04.128751
DP  - 2020 Jan 01
TA  - bioRxiv
PG  - 2020.06.04.128751
4099  - http://biorxiv.org/content/early/2020/06/04/2020.06.04.128751.short
4100  - http://biorxiv.org/content/early/2020/06/04/2020.06.04.128751.full
AB  - 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.Competing Interest StatementThe authors have declared no competing interest.