Transmission of SARS-CoV-2 in South Asian countries: molecular evolutionary model based phylogenetic and mutation analys
- PDF / 1,712,176 Bytes
- 9 Pages / 595.276 x 790.866 pts Page_size
- 24 Downloads / 141 Views
ORIGINAL ARTICLE
Transmission of SARS‑CoV‑2 in South Asian countries: molecular evolutionary model based phylogenetic and mutation analysis Anand Prakash Maurya1 · Rupesh V. Chikhale2 · Piyush Pandey1 Received: 13 July 2020 / Revised: 29 August 2020 / Accepted: 31 August 2020 © Society for Environmental Sustainability 2020
Abstract The on-going coronavirus disease 19 (COVID-19) pandemic has caused a very high number of infections and deaths around the globe. The absence of vaccine/drugs to counter COVID-19 has scrambled scientific communities to repurpose available medicines/vaccines. As the virus is known to mutate, using the whole genome sequences, the transmission dynamics and molecular evolutionary models were evaluated for South Asian countries to determine the evolutionary rate of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Phylogenetic analyses were done using the data available on National Center for Biotechnology Information (NCBI). Different nucleotide substitution models and molecular evolutionary models were analyzed to see how SARS-CoV-2 was transmitted in the populations. Models for the viral ‘S’ and ‘N’ protein from selected strains were constructed, validated, and analyzed to determine the mutations and discover the potential therapeutics against this deadly viral disease. We found that the Hasegawa-Kishino-Yano (HKY) nucleotide substitution model was the best model with the lowest Bayesian information criterion (BIC) scores. Molecular clock RelTime analysis showed the evolutionary rate of SARS-CoV-2 substitutions in the genome was at 95% confidence interval, and heterogeneity was observed. Several mutations in the viral S-protein were found with one in the receptor-binding domain concerning SARS-CoV-2/ Wuhan-1/S-Protein. Nucleocapsid protein also showed mutations in the strains from India and Sri Lanka. Our analysis suggests that SARS-CoV-2 is evolving at a diverse rate. The mutation leading to substitution in the nucleotide sequence occurred in the genome during the transmission of COVID-19 among individuals in the South Asian countries. Keywords COVID-19 · Pandemic · Coronavirus · Genetic variability · Receptor binding domain (RBD) · Human mobility
Introduction In the past two decades, outbreaks of Severe Acute Respiratory Syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV) had caused deadly human diseases (Cheng et al. 2007; Chan Anand Prakash Maurya and Rupesh V. Chikhale contributed equally. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s42398-020-00123-z) contains supplementary material, which is available to authorized users. * Piyush Pandey [email protected]; [email protected] 1
Department of Microbiology, Assam University, Silchar 788011, Assam, India
School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
2
et al. 2015). The current pandemic of pandemic coronavirus disease 19 (COVID-19) is caused by severe acute respiratory synd
Data Loading...
