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

Nicholas J Dimonaco,Mazdak Salavati,Barbara B Shih

doi:10.3390/v13010049

Abstract

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.

Highlights

The continued and increasing occurrence of pandemics that threaten worldwide public health due to human activity is often considered to be inevitable [1,2]
The COVID-19 (2019–current) pandemic caused by the emergence in Hubei, China, of what has been identified as Severe Acute Respiratory Syndrome Coronavirus 2/Novel Coronavirus 2019 (SARS-CoV-2/2019-nCoV) by The Coronaviridae Study Group [3], has brought a number of questions regarding its transmission, containment and treatment to the urgent attention of researchers and clinicians
We examined the complete set of 269 genomes

Summary

Introduction

The continued and increasing occurrence of pandemics that threaten worldwide public health due to human activity is often considered to be inevitable [1,2]. (SARS-CoV-2/2019-nCoV) by The Coronaviridae Study Group [3], has brought a number of questions regarding its transmission, containment and treatment to the urgent attention of researchers and clinicians. The urgency of such questions has spurred a number of atypical approaches and collaborations between experts of different fields and as such, this study was carried out as part of a “CoronaHack” hackathon event in April 2020 where the authors gained access to genomes and related metadata available at the time Viruses of the Coronaviridae family have long been studied and while there have been great advances in our understanding, each new emergence has brought about its own questions.

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