Whole-genome sequencing of SARS-CoV-2 virus in clinical isolates at a tertiary care centre: A retrospective cross-sectional study.
Abstract
Background
Surveillance of SARS-CoV-2 variants, including rapidly spreading mutants, through rapid, real-time genome sequencing has been widely reported as an important tool for informed health policy decision-making during the COVID-19 pandemic. This study aimed to perform whole-genome sequencing of SARS-CoV-2 RT-PCR-positive samples to identify circulating variants of SARS-CoV-2 in central India, with an emphasis on new variants of interest (VOIs) and variants of concern (VOCs).
Methods
We established a nanopore sequencing platform for genetic surveillance of SARS-CoV-2 and focused on identifying the variants circulating in Central India. This retrospective, cross-sectional study involves genomic sequencing and data analysis of samples from laboratory-confirmed RT-PCR positive COVID-19 patients between May 2022 and December 2023. The study included samples with CT value of ≤ 25 to achieve more than 70% genome coverage upon sequencing
Results
Our analysis identified the Omicron variant and its sublineages in circulation, which were classified into five clades: 23B, 22D, 21L, 22F, and 24A. Clade 23B was the most prevalent, accounting for 42.8% of samples, followed by Clades 22D and 21L, which collectively accounted for 52.3% of samples. The predominant variant within clade 23B is XBB.1, whereas BA.2.75.1 predominated within clade 22D.
Conclusion
These findings clarify the evolutionary pattern of SARS-CoV-2 and, in turn, support policy decisions for the prevention and control of COVID-19. This study asserts that early detection of variants of concern (VOCs) and variants of interest (VOIs) is essential to tackle the upsurge.