A Distinct Phylogenetic Cluster of Indian Severe Acute Respiratory Syndrome Coronavirus 2 Isolates.

Open Forum Infectious Diseases
Sofia BanuDivya Tej Sowpati

Abstract

From an isolated epidemic, coronavirus disease 2019 has now emerged as a global pandemic. The availability of genomes in the public domain after the epidemic provides a unique opportunity to understand the evolution and spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus across the globe. We performed whole-genome sequencing of 303 Indian isolates, and we analyzed them in the context of publicly available data from India. We describe a distinct phylogenetic cluster (Clade I/A3i) of SARS-CoV-2 genomes from India, which encompasses 22% of all genomes deposited in the public domain from India. Globally, approximately 2% of genomes, which to date could not be mapped to any distinct known cluster, fall within this clade. The cluster is characterized by a core set of 4 genetic variants and has a nucleotide substitution rate of 1.1 × 10-3 variants per site per year, which is lower than the prevalent A2a cluster. Epidemiological assessments suggest that the common ancestor emerged at the end of January 2020 and possibly resulted in an outbreak followed by countrywide spread. To the best of our knowledge, this is the first comprehensive study characterizing this cluster of SARS-CoV-2 in India.

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Citations

Oct 24, 2020·Transboundary and Emerging Diseases·Denis C BauerSeshadri S Vasan
Feb 16, 2021·Influenza and Other Respiratory Viruses·Rindra Vatosoa RandremananaJean-Michel Heraud
Feb 16, 2021·The Journal of General Virology·Asmita GuptaMurali Dharan Bashyam
Feb 17, 2021·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·Onkar KulkarniDivya Tej Sowpati
Jun 11, 2021·Virusdisease·Swaraj MohantyYasmin Ahmad
Jul 6, 2021·Indian Journal of Clinical Biochemistry : IJCB·Sagar DholariyaDigishaben Patel
Oct 3, 2021·Critical Reviews in Clinical Laboratory Sciences·Marco CiottiSergio Bernardini
Sep 22, 2021·Methods : a Companion to Methods in Enzymology·Nimisha GhoshNikhil Sharma

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Methods Mentioned

BETA
GISAID

Software Mentioned

Samtools
BEAST
PROVEAN
UCSC Genome Browser
bcftools
seqtk
Trimmomatic
hisat2
SIFT
GISAID

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