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Computational Analysis of SARS-CoV-2 and SARS-Like Coronavirus Diversity in Human, Bat and Pangolin Populations.
Viruses. 2020 12 30; 13(1)V

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.

Authors+Show Affiliations

Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, WalesWales SY3 3FL, UK.The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK.The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

33396801

Citation

Dimonaco, Nicholas J., et al. "Computational Analysis of SARS-CoV-2 and SARS-Like Coronavirus Diversity in Human, Bat and Pangolin Populations." Viruses, vol. 13, no. 1, 2020.
Dimonaco NJ, Salavati M, Shih BB. Computational Analysis of SARS-CoV-2 and SARS-Like Coronavirus Diversity in Human, Bat and Pangolin Populations. Viruses. 2020;13(1).
Dimonaco, N. J., Salavati, M., & Shih, B. B. (2020). Computational Analysis of SARS-CoV-2 and SARS-Like Coronavirus Diversity in Human, Bat and Pangolin Populations. Viruses, 13(1). https://doi.org/10.3390/v13010049
Dimonaco NJ, Salavati M, Shih BB. Computational Analysis of SARS-CoV-2 and SARS-Like Coronavirus Diversity in Human, Bat and Pangolin Populations. Viruses. 2020 12 30;13(1) PubMed PMID: 33396801.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Computational Analysis of SARS-CoV-2 and SARS-Like Coronavirus Diversity in Human, Bat and Pangolin Populations. AU - Dimonaco,Nicholas J, AU - Salavati,Mazdak, AU - Shih,Barbara B, Y1 - 2020/12/30/ PY - 2020/12/03/received PY - 2020/12/21/revised PY - 2020/12/22/accepted PY - 2021/1/5/entrez PY - 2021/1/6/pubmed PY - 2021/1/20/medline KW - codon usage KW - coronavirus KW - hackathon KW - host-associated divergences KW - variant discovery JF - Viruses JO - Viruses VL - 13 IS - 1 N2 - 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. SN - 1999-4915 UR - https://www.unboundmedicine.com/medline/citation/33396801/Computational_Analysis_of_SARS_CoV_2_and_SARS_Like_Coronavirus_Diversity_in_Human_Bat_and_Pangolin_Populations_ DB - PRIME DP - Unbound Medicine ER -