Molecular characterization, phylogenetic and variation analyses of
SARS-CoV-2 strains in India
Abstract
In the wake of the havoc caused by the Covid-19 pandemic, it is
imperative to use the available genomic sequence data to gain insight
into the mutational and genomic diversity of SARS-CoV-2. Here we have
performed comparative phylogenetic, mutational and genetic diversity
analysis on 1962 SARS-CoV-2 genome sequences from seven worst hit Indian
states during the third Covid-19 wave, to determine the Covid-19 strains
and mutations in circulation during the third wave and the transmission
pattern and disease epidemiology across the states and gain valuable
insight into the viral evolution. 6083 Single nucleotide polymorphisms
(SNPs) were discovered in the analysis with 93 SNPs common to all
states. The genetic relatedness among the statewise multilocus genotypes
was visualized by plotting a minimum spanning tree based on Bruvo’s
distance framework. The phylogenetic tree based on Nei’s genetic
distance showed distinct clades. The AMOVA results indicated that large
proportion of the total genetic variation is distributed within the
samples, rather than between the samples within each population and
between the populations. Our findings provide insight into the
SARS-CoV-2 variants and mutations which dominated the third Covid-19
wave in India and thus provide a basis to monitor and further assess
these variants and their sub lineages and mutations for their clinical
impact and reaction to existing and newly designed drugs and vaccines.
The genetic diversity analysis helps in comprehending the viral
transmission scenarios across the Indian states so as to enable the
State government and researchers in developing state specific prevention
measures for future.