Cross-sectional genomic perspective of epidemic waves of SARS-CoV-2: A pan India study.
Virus Res
; 308: 198642, 2022 01 15.
Article
in English
| MEDLINE | ID: covidwho-1525982
Preprint
This scientific journal article is probably based on a previously available preprint. It has been identified through a machine matching algorithm, human confirmation is still pending.
See preprint
This scientific journal article is probably based on a previously available preprint. It has been identified through a machine matching algorithm, human confirmation is still pending.
See preprint
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.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 (â¼34). In accordance with mutation rate, VOCs and VOIs started appearing in the first wave (1.5%), which dominated the second (â¼96%) 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.Keywords
Full text:
Available
Collection:
International databases
Database:
MEDLINE
Main subject:
Phylogeny
/
Genome, Viral
/
SARS-CoV-2
/
COVID-19
Type of study:
Observational study
/
Randomized controlled trials
Topics:
Variants
Limits:
Humans
Country/Region as subject:
Asia
Language:
English
Journal:
Virus Res
Journal subject:
Virology
Year:
2022
Document Type:
Article
Affiliation country:
J.virusres.2021.198642
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