Emergence of Two Distinct Variants of SARS-CoV-2 and Explosive Second Wave of COVID-19: An Experience From A Tertiary Care Hospital, Pune, India
Abstract The emergence of novel variants of SARS-CoV-2 in several countries has been associated with the increased transmission/ reduced neutralization potential of antibodies against the Wuhan virus (wild type). Currently, India is recovering from an explosive second wave of COVID-19. This prospective study was conducted quarterly for one year (May 2020 to June 2021) at a tertiary care hospital, Pune city, western India. Receptor binding domain (RBD, n = 319) and full genome (n = 20) sequences from viral RNA positive nasopharyngeal swabs of COVID-19 patients representing first and second waves were used for analysis. We did not detect Brazil, South Africa and California variants. Till December, only wild type strain was prevalent. Concurrent with the upsurge of second wave in March-2021, 73% (33/45) of RBD sequences harboured L452R/E484Q mutations characteristic of Kappa variant. In April, co-circulation of Kappa (37%) and Delta (L452R/T478K, 59%) variants was recorded. During May and June, delta variant became the predominant circulating variant and coincided with a significant decline in the number of COVID-19 cases. Of the 20 full genome sequences, six isolates each exhibited signature mutations of Kappa and Delta variants respectively. With several states witnessing reduction in the number of COVID-19 cases, continuous monitoring of newer mutations and assessment of these mutations in influencing virus transmissibility and impact on vaccinated / previously exposed individuals would be necessary.