Integrated genomic view of SARS-CoV-2 in India

  1. Pramod Kumar
  2. Rajesh Pandey
  3. Pooja Sharma
  4. Mahesh S Dhar
  5. A Vivekanand
  6. Bharathram Uppili
  7. Himanshu Vashisht
  8. Saruchi Wadhwa
  9. Nishu Tyagi
  10. Saman Fatihi
  11. Uma Sharma
  12. Priyanka Singh
  13. Hemlata Lall
  14. Meena Datta
  15. Poonam Gupta
  16. Nidhi Saini
  17. Aarti Tewari
  18. Bibhash Nandi
  19. Dhirendra Kumar
  20. Satyabrata Bag
  21. Deepanshi
  22. Surabhi Rathore
  23. Nidhi Jatana
  24. Varun Jaiswal
  25. Hema Gogia
  26. Preeti Madan
  27. Simrita Singh
  28. Prateek Singh
  29. Debasis Dash
  30. Manju Bala
  31. Sandhya Kabra
  32. Sujeet Singh
  33. Mitali Mukerji
  34. Lipi Thukral
  35. Mohammed Faruq
  36. Anurag Agrawal
  37. Partha Rakshit
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Abstract

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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