Integrated genomic view of SARS-CoV-2 in India

India first detected SARS-CoV-2, causal agent of COVID-19 in late January 2020, imported from Wuhan, China. From March 2020 onwards, the importation of cases from countries in the rest of the world followed by seeding of local transmission triggered further outbreaks in India. We used ARTIC protocol...

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Bibliographic Details
Published in:Wellcome open research 2020, Vol.5, p.184-184
Main Authors: Kumar, Pramod, Pandey, Rajesh, Sharma, Pooja, Dhar, Mahesh S, A, Vivekanand, 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, Gahlot, 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
Format: Article
Language:English
Subjects:
Coronaviruses
COVID-19
Disease transmission
Epidemics
Epidemiology
Genomes
Pandemics
Peer review
Proteins
Severe acute respiratory syndrome coronavirus 2
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Summary:India first detected SARS-CoV-2, causal agent of COVID-19 in late January 2020, imported from Wuhan, China. From March 2020 onwards, the importation of cases from countries in the rest of the world 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 sequencing from Oxford Nanopore Technology to understand how introduction and local transmission occurred. The analyses revealed multiple introductions of SARS-CoV-2 genomes, including the A2a cluster from Europe and the USA, A3 cluster from Middle East and A4 cluster (haplotype redefined) from Southeast Asia (Indonesia, Thailand and Malaysia) and Central Asia (Kyrgyzstan). The local transmission and persistence of genomes A4, A2a and A3 was also observed in the studied locations. The most prevalent genomes with patterns of variance (confined in a cluster) remain unclassified, and are here proposed as A4-clade based on its divergence within the A cluster. The viral haplotypes may link their persistence to geo-climatic conditions and host response. Multipronged strategies including molecular surveillance based on real-time viral genomic data is of paramount importance for a timely management of the pandemic.
ISSN:2398-502X
2398-502X
DOI:10.12688/wellcomeopenres.16119.1