Kumar , Sanjeet and Bansal , Kanika (2022) Cross-sectional genomic perspective of epidemic waves of SARS-CoV-2: A pan India study. Virus Research, 308.
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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. Objective Here, we aim for pan Indian cross-sectional evolutionary analysis since inception of SARS-CoV-2. 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_045512.2) as reference. 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). 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.
| Item Type: | Article |
|---|---|
| Additional Information: | The copyright of this article belongs to Elsevier Science |
| Uncontrolled Keywords: | SARS-CoV-2;COVID-19;Genome-wide;Evolution; Deadly variants; VOC; VOI; SNP; Mutation; Non-synonymous; Silent mutationSpikeRNA dependent RNA polymeraseNSPUTR |
| Subjects: | Q Science > QR Microbiology |
| Depositing User: | Dr. K.P.S.Sengar |
| Date Deposited: | 22 Jul 2022 05:36 |
| Last Modified: | 22 Jul 2022 05:36 |
| URI: | http://crdd.osdd.net/open/id/eprint/2983 |
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