Integrated genomic view of SARS-CoV-2 in India

Kumar, P.; Pandey, R.; Sharma, P.; Dhar, M.; Vivekanand, A.; Bharathram, U.; Vashistha, H.; Wadhwa, S.; Tyagi, N.; Fatihi, S.; Sharma, U.; Singh, P.; Lall, H.; Datta, M.; Gupta, P.; Saini, N.; Tiwari, A.; Nandi, B.; Kumar, D.; Bag, S.; Deepanshi, D.; Rathore, S.; Jatana, N.; Jaiswal, V.; Gogia, H.; Madan, P.; Singh, S.; Dash, D.; Bala, M.; Kabra, S.; Singh, S. K.; Mukerji, M.; Thukral, L.; Faruq, M.; Agarwal, A.; Rakshit, P.

doi:10.1101/2020.06.04.128751

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bioRxiv · 10.1101/2020.06.04.128751

Integrated genomic view of SARS-CoV-2 in India

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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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Kumar, P., Pandey, R., Sharma, P., Dhar, M., Vivekanand, A., Bharathram, U., Vashistha, H., Wadhwa, S., Tyagi, N., Fatihi, S., Sharma, U., Singh, P., Lall, H., Datta, M., Gupta, P., Saini, N., Tiwari, A., Nandi, B., Kumar, D., Bag, S., Deepanshi, D., Rathore, S., Jatana, N., Jaiswal, V., Gogia, H., Madan, P., Singh, S., Dash, D., Bala, M., Kabra, S., Singh, S. K., Mukerji, M., Thukral, L., Faruq, M., Agarwal, A., Rakshit, P.. 2020-06-04. Integrated genomic view of SARS-CoV-2 in India. https://doi.org/10.1101/2020.06.04.128751

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