title: Cross-sectional genomic perspective of epidemic waves of SARS-CoV-2: A pan India study
creator: Kumar , Sanjeet 
creator: Bansal , Kanika 
subject: QR Microbiology
description: 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.
publisher: Elsevier Science
date: 2022-01-15
type: Article
type: PeerReviewed
relation: https://www.sciencedirect.com/science/article/pii/S016817022100349X
identifier:   Kumar , Sanjeet  and Bansal , Kanika   (2022) Cross-sectional genomic perspective of epidemic waves of SARS-CoV-2: A pan India study.  Virus Research, 308.       
relation: http://crdd.osdd.net/open/2983/