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Cross-sectional genomic perspective of epidemic waves of SARS-CoV-2: A pan India study

DIR@IMTECH: CSIR-Institute of Microbial Technology

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Field Value
 
Title Cross-sectional genomic perspective of epidemic waves of SARS-CoV-2: A pan India study
 
Creator Kumar , Sanjeet
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 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
PeerReviewed
 
Relation https://www.sciencedirect.com/science/article/pii/S016817022100349X
http://crdd.osdd.net/open/2983/
 
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.