Phylodynamics and Phylogenetic Analysis of Recent SARS CoV 2 Viral Strains from Pune, Maharashtra

Abstract

In December 2019, medical practitioners from China identified a novel strain of severe acute respiratory syndrome-CoV (SARS-CoV). The disease was allotted a zoonotic origin and the spillover event is associated with Huanan Wholesale Seafood Market in Wuhan City, Hubei Province, China. On 30 January 2020, the World Health Organization (WHO) declared COVID- 19 as an international public-health emergency concern. In India, the index case was reported on 30th January in the district of Thrissur, state of Kerala and by 25th March 2020, the country was lockdown.  This research aims to analyze the viral phylogenetic and phylodynamics of strains from Pune, Maharashtra, followed by a comparison against real time data and an analysis of the potency of government prevention strategies. Publicly available SARS-CoV-2 sequences, specific to Pune, Maharashtra, were downloaded from GISAID during the time frame of the epidemics. Phylogenetic analysis of the sequences, including Maximum Likelihood trees and the nucleotide substitution model, were done using IQ-TREE software. Phylodynamic tools available as part of the BEAST2 software was used to estimate the evolution of R number through time. GTR+F+I was found to be the best-fit nucleotide substitution model for the data acquired. ML trees constructed reported a log likelihood of 44842.9931. Analysis of trace estimates reported R number with an average of 1, indicating transmission of virus. The data contains controversial elements which can only be clarified upon further sequencing of the SARS- CoV-2 strains, however, the results obtained are parallel to real time statistics.