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Viruses 2019, 11(2), 125;

Shared Common Ancestry of Rodent Alphacoronaviruses Sampled Globally

School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK
School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
Wildlife Zoonoses and Vector-borne Diseases Research Group, Animal and Plant Health Agency (APHA), Weybridge-London KT15 3NB, UK
Anses, Laboratoire de la rage et de la faune sauvage, 54220 Malzéville, France
Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, 10117 Berlin, Germany
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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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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