Wellcome Open ResearchMicrobiologyPeer-reviewed journal article
Integrated genomic view of SARS-CoV-2 in India
P. Kumar, R. Pandey, P. Sharma, M. Dhar, A. Vivekanand, U. Bharathram, H. Vashistha, S. Wadhwa, N. Tyagi, S. Fatihi, U. Sharma, P. Singh, H. Lall, M. Datta, P. Gupta, N. Saini, A. Tiwari, B. Nandi, D. Kumar, S. Bag, D. Deepanshi, S. Rathore, N. Jatana, V. Jaiswal, H. Gogia, , P. Rakshit
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.
- organism: virus
- assay: whole-genome sequencing
- research focus: phylogenetics / evolution
- approach: experimental assay
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