GISAID-Clade and Pangolin Lineage Wise Distribution Patterns of COVID-19 Virus, in India

Abstract

Transmissible coronavirus (SARS-CoV-2), created a universal pandemic situation since the last of 2019 and has outspread widely until now. Where India was the second most affected country and 3^rd in mortality rate around the world. At present, we analyzed the diversity of SARS-CoV-2 viral genomes in India to know the evolutionary patterns of viruses in the country through their pangolin lineage and GISAID-Clade. We extracted a total of 2189 full-length SARS-CoV-2 viral genomes from various states of India from the EpiCov repository of the GISAID initiative on 12 June 2020. We observed that a total of 66 pangolin lineage and 9 GISAID-Clade were placed in Indian territory. The most dominant lineages and clades in India as predicted by Pangolin lineage and GISAID-Clade genome sequences were B1, B6, B1.1.7, B.1.617.2, B1.36 and B1.1.306, G and GR, respectively. Out of fifteen states of India, maximum lineage diversity i.e., 63.64% of lineage was found in Maharashtra; also, all types of GISAID-Clades found in India were also present in Maharashtra. Whereas, the lowest lineage and GISAID-Clade diversity were observed in West Bengal. Because the pandemic is still emerging, the observation needs to be monitored.