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

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.Viruses 2020, 12, 534 2 of 16 epithelium damage, [7] and altering commensal microbiota and local biofilm [8][9][10], thus leading to complex secondary bacterial infections [8,10,11].BCoV is a pneumoenteric virus frequently isolated from the fecal samples of diarrheic calves [12-15] and 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 simply to distinct times and locations of isolation. Some reports indeed suggest that all the BCoV are similar at genomic and antigenic levels [18,23], while others suggest that enteric and respiratory strains are genetically and antigenically different [24,25]. Zhang et al. highlighted molecular differences within a single host, with intra-host quasispecies and enteric strains more prone to genetic changes than their respiratory counterparts [26]. The global genetic and antigenic diversity of BCoV is also poorly understood. 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 BCoV observed in Asian countries (for example in Japan during the 1990s [30]) highlighting global movement of BCoV likely through cattle trade. Coronaviruses are enveloped particles with a large non-segmented, linear, polyadenylated, single-stranded positive sense RNA genome [31]. They belong to the family Coronaviridae in the order Nidoviral...

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