Emergence of Novel SARS-CoV-2 variants in India: second wave.

Introduction: Globally South-East Asia reported 40% of SARS-CoV-2 infected cases in the fourth week of April 2021. It continued to show an increase with India accounting for 50% of cases worldwide and 30% of global deaths. Genomic surveillance should continue at a rapid pace because of the continuously evolving nature of the virus. The time period of sample collection from the Global Initiative on Sharing All Influenza Data database was concurrent with the surge in new cases seen in the Indian subcontinent.

Methodology: 7,415 sequences were downloaded from Global Initiative on Sharing All Influenza Data between January and April 2021; out of which 4,411 were high coverage genome sequences and were considered for analysis. Phylogenetic analysis were carried out using Nextstrain.

Results: 21A or B.1.617 or delta was the most prevalent lineage in India accounting for 67.7% of the genomes. Next important clades were 20A, 20B and 20I accounting for 23.6%, 11.8% and 12.1% respectively collected between January 2021 and April 2021. The remaining sequences were assigned to clade 20H, 20J, 20D, 20C, 20G,20E,19A and 19B.The spike mutation frequencies of L452R, E484Q and P681R in Indian state of Maharashtra were 62.4%, 66.5% and 61.5% respectively. Two unique N-terminal domain deletion of spike protein were found at position 67 and 68.

Conclusions: The phylogenomics of the delta variant or 21A emerged in neighboring Asian countries of Thailand, Bangladesh, Indonesia and Japan. We analyzed the SARS-CoV-2 genomes from India for mutation characterization of the spike glycoprotein and the nucleocapsid protein.