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Viruses 2019, 11(2), 125; https://doi.org/10.3390/v11020125

Shared Common Ancestry of Rodent Alphacoronaviruses Sampled Globally

1
School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK
2
School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
3
Wildlife Zoonoses and Vector-borne Diseases Research Group, Animal and Plant Health Agency (APHA), Weybridge-London KT15 3NB, UK
4
Anses, Laboratoire de la rage et de la faune sauvage, 54220 Malzéville, France
5
Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, 10117 Berlin, Germany
6
Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia
*
Author to whom correspondence should be addressed.
Received: 14 January 2019 / Revised: 25 January 2019 / Accepted: 28 January 2019 / Published: 30 January 2019
(This article belongs to the Section Animal Viruses)
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Abstract

The recent discovery of novel alphacoronaviruses (alpha-CoVs) in European and Asian rodents revealed that rodent coronaviruses (CoVs) sampled worldwide formed a discrete phylogenetic group within this genus. To determine the evolutionary history of rodent CoVs in more detail, particularly the relative frequencies of virus-host co-divergence and cross-species transmission, we recovered longer fragments of CoV genomes from previously discovered European rodent alpha-CoVs using a combination of PCR and high-throughput sequencing. Accordingly, the full genome sequence was retrieved from the UK rat coronavirus, along with partial genome sequences from the UK field vole and Poland-resident bank vole CoVs, and a short conserved ORF1b fragment from the French rabbit CoV. Genome and phylogenetic analysis showed that despite their diverse geographic origins, all rodent alpha-CoVs formed a single monophyletic group and shared similar features, such as the same gene constellations, a recombinant beta-CoV spike gene, and similar core transcriptional regulatory sequences (TRS). These data suggest that all rodent alpha CoVs sampled so far originate from a single common ancestor, and that there has likely been a long-term association between alpha CoVs and rodents. Despite this likely antiquity, the phylogenetic pattern of the alpha-CoVs was also suggestive of relatively frequent host-jumping among the different rodent species. View Full-Text
Keywords: coronavirus; alphacoronavirus; rodents; ancestry; recombination; evolution coronavirus; alphacoronavirus; rodents; ancestry; recombination; evolution
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Tsoleridis, T.; Chappell, J.G.; Onianwa, O.; Marston, D.A.; Fooks, A.R.; Monchatre-Leroy, E.; Umhang, G.; Müller, M.A.; Drexler, J.F.; Drosten, C.; Tarlinton, R.E.; McClure, C.P.; Holmes, E.C.; Ball, J.K. Shared Common Ancestry of Rodent Alphacoronaviruses Sampled Globally. Viruses 2019, 11, 125.

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