Abstract
The emergence of novel variants of SARS-CoV-2 in several countries has been associated with increased transmissibility or reduced neutralization potential of antibodies against the Wuhan virus (wild type). From August 2021 onwards, India experienced a progressive decline in the number of active SARS-CoV-2 infections, indicative of a downward trend in the explosive second wave. This prospective study was conducted quarterly for one year (May 2020 to June 2021) at a tertiary care hospital in the city of Pune in 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 the first and second waves were used for analysis. No Brazilian, South African, or California variants were detected in this study. Until December 2020, only the wild-type strain was prevalent. Concurrent with the upsurge of the second wave in March 2021, 73% (33/45) of RBD sequences harboured L452R/E484Q mutations characteristic of the Kappa variant. In April 2021, co-circulation of Kappa (37%) and Delta (L452R/T478K, 59%) variants was recorded. During May and June 2021, the Delta variant became the predominant circulating variant, and this 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 the Kappa and Delta variant. With several states witnessing a reduction in the number of COVID-19 cases, continuous monitoring of newer mutations and assessment of their effect on virus transmissibility and their impact on vaccinated or previously exposed individuals is necessary.Supplementary InformationThe online version contains supplementary material available at 10.1007/s00705-021-05320-7.
Highlights
Coronavirus disease 2019 (COVID-19), caused by SARSCoV-2, was declared a pandemic on March 11, 2020, and continued to be a global public health concern in 2021
In March 2021, there was a rapid increase in the number of COVID-19 cases, which reached a peak of 150,175 cases in April 2021
We report the association of the emergence of two SARS-CoV-2 variants with the progression of the second wave of COVID-19, as evidenced by the data from a large tertiary care hospital in Pune, India
Summary
Coronavirus disease 2019 (COVID-19), caused by SARSCoV-2, was declared a pandemic on March 11, 2020, and continued to be a global public health concern in 2021. Several countries have experienced a resurgence leading to Handling Editor: Tim Skern. The original SARS-CoV-2 strain from Wuhan (wildtype) was rapidly transmitted in a large number of countries through infected travellers, followed by establishment of community transmission and further rapid spread. In India, the first COVID-19 case was reported on January 29, 2020, in a student returning from China [3]. At the peak in September 2020, 97,860 cases were recorded [4]. The second wave started from the middle of March 2021, with the highest number of cases (414,188) recorded on May 6, 2021. India is experiencing a significant drop in the number of active infections, with 41,831 as of July 31, 2021 [4]. The state of Maharashtra was the first to report an
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