Abstract
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.
Highlights
Bovine coronavirus (BCoV) is widespread in cattle and wild ruminant populations, resulting in neonatal calf diarrhea and winter dysentery in adult cattle, as well as upper and lower respiratory tract infection
While our starting point was French field BCoV, our study aims at a better understanding of BCoV genetic evolution at a global scale, looking both at the genetic characteristics of viruses and at the collection times in order to contribute to discussions on BCoV origin and global spread
Upper (NS) and lower (BAL) respiratory tract samples were collected from 16 calves exhibiting acute respiratory disease during 2014 in the south–west of France
Summary
Bovine coronavirus (BCoV) is widespread in cattle and wild ruminant populations, resulting in neonatal calf diarrhea and winter dysentery in adult cattle, as well as upper and lower respiratory tract infection. From upper and lower respiratory tract samples during BRD episodes worldwide [16,17,18,19]. While both forms of BCoV infection are widespread with high prevalence among cattle [12,13,15,20,21] and wild ruminants [22], the putative differences between strains isolated from enteric and respiratory tracts are still not clear, and it is unknown whether these differences are related to tissue tropism or to distinct times and locations of isolation. Using a short variable region of the BCoV genome and with sporadically collected samples from a few countries in Europe, Asia, and North America, it has been suggested that BCoV are segregated into European and American BCoV lineages [17,27,28,29], with periodic introductions of North American
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