TY  - JOUR
N1  - The copyright of this article belongs to Elsevier Science
ID  - open2983
UR  - https://www.sciencedirect.com/science/article/pii/S016817022100349X
A1  - Kumar , Sanjeet 
A1  - Bansal , Kanika 
Y1  - 2022/01/15/
N2  - 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.
PB  - Elsevier Science
JF  - Virus Research
VL  - 308
KW  - SARS-CoV-2;COVID-19;Genome-wide;Evolution; Deadly variants; VOC; VOI; SNP; Mutation;  Non-synonymous; Silent mutationSpikeRNA dependent RNA polymeraseNSPUTR
TI  - Cross-sectional genomic perspective of epidemic waves of SARS-CoV-2: A pan India study
ER  -