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Open AccessArticle

Global Transmission, Spatial Segregation, and Recombination Determine the Long-Term Evolution and Epidemiology of Bovine Coronaviruses

1
IHAP, Université de Toulouse, INRAE, ENVT, 31076 Toulouse, France
2
Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, VIC 3800, Australia
3
Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
4
Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan Kansas, KS 66506-5802, USA
5
SIGENAE, GenPhySE, Université de Toulouse, INRAE, INPT, ENVT, 31326 Castanet Tolosan, France
*
Author to whom correspondence should be addressed.
Viruses 2020, 12(5), 534; https://doi.org/10.3390/v12050534
Received: 20 April 2020 / Revised: 10 May 2020 / Accepted: 11 May 2020 / Published: 13 May 2020
(This article belongs to the Section Animal Viruses)
Bovine coronavirus (BCoV) is widespread in cattle and wild ruminant populations throughout the world. The virus causes neonatal calf diarrhea and winter dysentery in adult cattle, as well as upper and lower respiratory tract infection in young cattle. We isolated and deep sequenced whole genomes of BCoV from calves with respiratory distress in the south–west of France and conducted a comparative genome analysis using globally collected BCoV sequences to provide insights into the genomic characteristics, evolutionary origins, and global diversity of BCoV. Molecular clock analyses allowed us to estimate that the BCoV ancestor emerged in the 1940s, and that two geographically distinct lineages diverged from the 1960s–1970s. A recombination event in the spike gene (breakpoint at nt 1100) may be at the origin of the genetic divergence sixty years ago. Little evidence of genetic mixing between the spatially segregated lineages was found, suggesting that BCoV genetic diversity is a result of a global transmission pathway that occurred during the last century. However, we found variation in evolution rates between the European and non-European lineages indicating differences in virus ecology. View Full-Text
Keywords: bovine coronavirus; France; recombination; geographic clustering; molecular clock bovine coronavirus; France; recombination; geographic clustering; molecular clock
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Salem, E.; Dhanasekaran, V.; Cassard, H.; Hause, B.; Maman, S.; Meyer, G.; Ducatez, M.F. Global Transmission, Spatial Segregation, and Recombination Determine the Long-Term Evolution and Epidemiology of Bovine Coronaviruses. Viruses 2020, 12, 534.

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