Unique mutational changes in SARS-CoV2 genome of different state of India

COVID-19 leads to a global emergency that causes more than 7 million causalities until mid-August throughout the world. In India alone, 2 million confirmed cases were reported that increased abruptly day by day with the lowest fatality rate. The availability of a large number of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV2) genome in the public domain provides a great opportunity to study mutational changes in COVID-19 genomes in Indian populations.

In this study, we sequenced the genomes of SARS-CoV2 viruses isolated from 47 individuals from 13 districts of Uttar Pradesh (UP), the largest state of India using Third Generation Sequencing Technology. We further did the phylogenetic clustering of UP state of Indian SARS-CoV2 genomes revealed a perceivable point that no UP samples were aligned on the USA defined clade where the fatality rate is high. We also identified 56 distinctive Single Nucleotide Polymorphism variations in UP state that majorly clustered into two groups which shows the deleterious effects on the genome.

Additionally, we conducted the mutation analysis of the 2323 SARS-CoV2 genome of different states of India from the Global Initiative on Sharing All Influenza Data (GISAID) where we find ~80% unique mutations rate in each sample of the Indian population. Thus, this is the first extensive mutational study of the largest state of Indian populations in which we report the novel deleterious SNPs in virus genome along with the other states which access the less infectious form of SARS-CoV2 genome through synonymous to nonsynonymous mutation variation.