@article{e5fa734ce2564884ae81ed55422dbbdf,
title = "Computational Analysis of SARS-CoV-2 and SARS-Like Coronavirus Diversity in Human, Bat and Pangolin Populations",
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.",
keywords = "codon usage, coronavirus, hackathon, host-associated divergences, variant discovery, Genome, Viral, SARS-CoV-2/genetics, Genomics, Humans, Molecular Sequence Annotation, Coronavirus/classification, Host Specificity, Phylogeny, Biodiversity, Chiroptera/virology, Gene Regulatory Networks, COVID-19/virology, Sequence Alignment, Animals, Pangolins/virology, Evolution, Molecular",
author = "Dimonaco, {Nicholas J.} and Mazdak Salavati and Shih, {Barbara B.}",
note = "Funding Information: Acknowledgments: This study was carried out with support from DataBiology, MindStreamAI, University of Edinburgh, The Roslin Institute Royal (Dick) School of Veterinary Studies, Institute of Genetics and Molecular Medicine and University of Aberystwyth. Authors of this manuscript were members of the team who one the 3rd joint position in https://medium.com/@pauldowling/ accelerating-scientific-collaboration-in-real-time-e1f682f54c87. The full team members were Mazdak Salavati, Barbara B. Shih, Nicholas J. Dimonaco and David A. Parry that contributed equally to the hackathon{\textquoteright}s outcome. The prize of the Hackathon sponsored by Slack, Fluidstack, Episode 1, Scan Computers, DataBiology, NVIDIA and MindStreamAI (£500) was used towards publication fees of this manuscript. NJD was awarded the Rhiannon Powell Science Bursary by the Old Students{\textquoteright} Association of Aberystwyth University in support of his contribution to the manuscript. Please refer to this link for the details of the event: https://www.coronahack.co.uk/. Thanks to Samantha Lycett, Roslin Institute for comments on the manuscript. BBS is supported by a BBSRC Core Capability Grant (BB/CCG1780/1) to the Roslin Institute. Funding Information: This study was carried out with support from DataBiology, MindStreamAI, University of Edinburgh, The Roslin Institute Royal (Dick) School of Veterinary Studies, Institute of Genetics and Molecular Medicine and University of Aberystwyth. Authors of this manuscript were members of the team who one the 3rd joint position in https://medium.com/@pauldowling/ accelerating-scientific-collaboration-in-real-time-e1f682f54c87. The full team members were Mazdak Salavati, Barbara B. Shih, Nicholas J. Dimonaco and David A. Parry that contributed equally to the hackathon?s outcome. The prize of the Hackathon sponsored by Slack, Fluidstack, Episode 1, Scan Computers, DataBiology, NVIDIA and MindStreamAI (?500) was used towards publication fees of this manuscript. NJD was awarded the Rhiannon Powell Science Bursary by the Old Students? Association of Aberystwyth University in support of his contribution to the manuscript. Please refer to this link for the details of the event: https://www.coronahack.co.uk/. Thanks to Samantha Lycett, Roslin Institute for comments on the manuscript. BBS is supported by a BBSRC Core Capability Grant (BB/CCG1780/1) to the Roslin Institute. Publisher Copyright: {\textcopyright} 2020 by the authors. Licensee MDPI, Basel, Switzerland.",
year = "2020",
month = dec,
day = "30",
doi = "10.3390/v13010049",
language = "English",
volume = "13",
journal = "Viruses",
issn = "1999-4915",
publisher = "Multidisciplinary Digital Publishing Institute",
number = "1",
}
