Integrated genomic view of SARS-CoV-2 in India

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 geoclimatic 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. India, 2020). However, while the global focus was on China and other eastern countries like South Korea and Japan; European countries, middle-east and the USA reported a surge in cases of COVID-19, pressing the WHO to declare it as a pandemic. March 2020 onwards, India also witnessed a surge of imported cases from countries other than China which has been further assisted with local transmission. In March, imposition of nationwide lockdown checked the epidemic curve. Despite these measurements, India is at the verge of a large outbreak as the transmission is rapidly increasing with more than 100,000 cases of COVID-19 having been reported in the third week of May, 2020.We carried out WGS of SARS-CoV-2 (n=104) from Pan-India through the network of Integrated Disease Surveillance Program (IDSP) of National Centre of Disease Control (NCDC), Delhi. We report here a comprehensive and integrative genomic view of SARS-CoV-2 in the Indian subcontinent. In this study, we combine genetic and epidemiological data to understand the genetic diversity, evolution, and epidemiology of SARS-CoV-2 across India. The spectrum of variations would be an important tool towards contact tracing, effective diagnostics and backbone for drug and vaccine development. METHODS Subject recruitmentThe study was conducted jointly by the NCDC and CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB). Institutional ethical clearance was obtained at both the places prior to initiation of research. A total of 127 laboratory confirmed cases of COVID-19 from a targeted testing representing different locations (as described in Table- 1 and supplementary figure-1) were included in the study for genomic analyses. Targeted testing involved suspected cases;having symptoms (fever, cough and breathlessness) with recent travel history to high-risk countries or positive contacts of COVID-19 cases. Sample collection and Viral RNA isolationThe nasopharyngeal and oropharyngeal swabs (in ...

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