Phyloepidemiology and adaptive evolution of SARS-CoV2 during the first
and second wave of COVID-19 in India
Abstract
This study was conducted to know the various circulating lineages of
SARS-CoV-2, prevalent mutations in lineages, and selective pressure
analysis on the genome of SARS-CoV-2 during the first and second wave of
the COVID-19 pandemic in India. For this purpose total of 1451 sequences
from June 2020-June 2021 spanning from various regions of India were
downloaded from NCBI and GISAID. The sequences were blasted using the
Pangolin COVID-19 lineage assigner. Total, forty-one lineages were found
to be circulating in India during this one year. Thirty-five lineages
were circulating during the first wave and twenty lineages were
circulating during the second wave out of which six were new lineages.
During the first wave, in 2020 only one Variant Of Concern (Alpha) was
found and during the second wave in 2021 three variants of concern
(Alpha, Beta, and Delta) were in circulation. One Variant Under
Monitoring was also prevalent during the second wave. The most frequent
mutations observed were S: D614G, NSP3: F106F, NSP 12b: P314L, ORF3a:
Q57H, M: Y71Y, NSP14:C279C, S: D294D, N: S194L. Interestingly, the ten
most mutated samples belonged to Delta variant of B.1.617.2 lineage and
all were found in the second wave which justifies the severity of the
second wave. Five mutations L452R, T478K, E484Q, N501Y, and D614G in the
spike protein responsible for increased transmissibility and reduction
in neutralization by convalescent sera were majorly prevalent during
second wave out of which D614G, L452R, and T478K were present at
prevalence rate of 88.25%, 21.04%, and 16.80%, respectively. The
major selection was purifying selection, however, few sites in the NSP2,
NSP3, NSP13, S protein, ORF3a, and ORF9 evolved under positive
selection. We hereby also report six novel mutations, three in NSP2
(P129A, V381A, V381F), one in NSP3 (P822S), and one in S protein (Q23R)
evolving under positive selection pressure.