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Cross-sectional genomic perspective of epidemic waves of SARS-CoV-2: A pan India study.
- Source :
-
Virus research [Virus Res] 2022 Jan 15; Vol. 308, pp. 198642. Date of Electronic Publication: 2021 Nov 22. - Publication Year :
- 2022
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Abstract
- Background: COVID-19 has posed unforeseen circumstances and throttled major economies worldwide. India has witnessed two waves affecting around 31 million people representing 16% of the cases globally. To date, the epidemic waves have not been comprehensively investigated to understand pandemic progress in India.<br />Objective: Here, we aim for pan Indian cross-sectional evolutionary analysis since inception of SARS-CoV-2.<br />Methods: High quality genomes, along with their collection date till 26th July 2021, were downloaded. Whole genome-based phylogeny was obtained. Further, the mutational analysis was performed using SARS-CoV-2 first reported from Wuhan (NC&#95;045512.2) as reference.<br />Results: Based on reported cases and mutation rates, we could divide the Indian epidemic into seven phases. The average mutation rate for the pre-first wave was <11, which elevated to 17 in the first wave and doubled in the second wave (∼34). In accordance with mutation rate, VOCs and VOIs started appearing in the first wave (1.5%), which dominated the second (∼96%) and post-second wave (100%). Nation-wide mutational analysis depicted >0.5 million mutation events with four major mutations in >19,300 genomes, including two mutations in coding (spike (D614G), and NSP 12b (P314L) of rdrp), one silent mutation (NSP3 F106F) and one extragenic mutation (5' UTR 241).<br />Conclusion: Whole genome-based phylogeny could demarcate post-first wave isolates from previous ones by point of diversification leading to incidences of VOCs and VOIs in India. Such analysis is crucial in the timely management of pandemic.<br /> (Copyright © 2021. Published by Elsevier B.V.)
Details
- Language :
- English
- ISSN :
- 1872-7492
- Volume :
- 308
- Database :
- MEDLINE
- Journal :
- Virus research
- Publication Type :
- Academic Journal
- Accession number :
- 34822953
- Full Text :
- https://doi.org/10.1016/j.virusres.2021.198642