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Article

Computational Analysis of SARS-CoV-2 and SARS-Like Coronavirus Diversity in Human, Bat and Pangolin Populations

1
Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Wales SY3 3FL, UK
2
The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
*
Authors to whom correspondence should be addressed.
Academic Editor: Luis Martinez-Sobrido
Received: 3 December 2020 / Revised: 21 December 2020 / Accepted: 22 December 2020 / Published: 30 December 2020
(This article belongs to the Collection Coronaviruses)
In 2019, a novel coronavirus, SARS-CoV-2/nCoV-19, emerged in Wuhan, China, and has been responsible for the current COVID-19 pandemic. The evolutionary origins of the virus remain elusive and understanding its complex mutational signatures could guide vaccine design and development. As part of the international “CoronaHack” in April 2020, we employed a collection of contemporary methodologies to compare the genomic sequences of coronaviruses isolated from human (SARS-CoV-2; n = 163), bat (bat-CoV; n = 215) and pangolin (pangolin-CoV; n = 7) available in public repositories. We have also noted the pangolin-CoV isolate MP789 to bare stronger resemblance to SARS-CoV-2 than other pangolin-CoV. Following de novo gene annotation prediction, analyses of gene–gene similarity network, codon usage bias and variant discovery were undertaken. Strong host-associated divergences were noted in ORF3a, ORF6, ORF7a, ORF8 and S, and in codon usage bias profiles. Last, we have characterised several high impact variants (in-frame insertion/deletion or stop gain) in bat-CoV and pangolin-CoV populations, some of which are found in the same amino acid position and may be highlighting loci of potential functional relevance. View Full-Text
Keywords: coronavirus; hackathon; host-associated divergences; codon usage; variant discovery coronavirus; hackathon; host-associated divergences; codon usage; variant discovery
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MDPI and ACS Style

Dimonaco, N.J.; Salavati, M.; Shih, B.B. Computational Analysis of SARS-CoV-2 and SARS-Like Coronavirus Diversity in Human, Bat and Pangolin Populations. Viruses 2021, 13, 49. https://0-doi-org.brum.beds.ac.uk/10.3390/v13010049

AMA Style

Dimonaco NJ, Salavati M, Shih BB. Computational Analysis of SARS-CoV-2 and SARS-Like Coronavirus Diversity in Human, Bat and Pangolin Populations. Viruses. 2021; 13(1):49. https://0-doi-org.brum.beds.ac.uk/10.3390/v13010049

Chicago/Turabian Style

Dimonaco, Nicholas J.; Salavati, Mazdak; Shih, Barbara B. 2021. "Computational Analysis of SARS-CoV-2 and SARS-Like Coronavirus Diversity in Human, Bat and Pangolin Populations" Viruses 13, no. 1: 49. https://0-doi-org.brum.beds.ac.uk/10.3390/v13010049

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