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bioRxiv · 10.1101/2020.11.24.391763

Hacking the diversity of SARS-CoV-2 and SARS-like coronaviruses in human, bat and pangolin populations

Dimonaco, N. J.·Salavati, M.·Shih, B.
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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 (https://www.coronahack.co.uk/), 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. 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. Lastly, we have characterised several high impact variants (inframe 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.

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Dimonaco, N. J., Salavati, M., Shih, B.. 2020-11-24. Hacking the diversity of SARS-CoV-2 and SARS-like coronaviruses in human, bat and pangolin populations. https://doi.org/10.1101/2020.11.24.391763

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