Abstract
Bovine coronavirus (BoCV) is an important pathogen of cattle, causing severe enteric disease and playing a role in the bovine respiratory disease complex. Similar to other coronaviruses, a remarkable variability characterizes both its genome and biology. Despite their potential relevance, different aspects of the evolution of BoCV remain elusive. The present study reconstructs the history and evolution of BoCV using a phylodynamic approach based on complete genome and spike protein sequences. The results demonstrate high mutation and recombination rates affecting different parts of the viral genome. In the spike gene, this variability undergoes significant selective pressures—particularly episodic pressure—located mainly on the protein surface, suggesting an immune-induced selective pressure. The occurrence of compensatory mutations was also identified. On the contrary, no strong evidence in favor of host and/or tissue tropism affecting viral evolution has been proven. The well-known plasticity is thus ascribable to the innate broad viral tropism rather than mid- or long-term adaptation. The evaluation of the geographic spreading pattern clearly evidenced two clusters: a European cluster and an American–Asian cluster. While a relatively dense and quick migration network was identified in the former, the latter was dominated by the primary role of the United States (US) as a viral exportation source. Since the viral spreading pattern strongly mirrored the cattle trade, the need for more intense monitoring and preventive measures cannot be underestimated as well as the need to enforce the vaccination of young animals before international trade, to reduce not only the clinical impact but also the transferal and mixing of BoCV strains.
Highlights
Bovine coronavirus (BoCV) belongs to the family Coronaviridae, genus Betacoronavirus
While no open reading frames (ORFs) or ORF region was preferentially affected by recombination events, some statistically significant recombination hot-spots were identified approximately in positions 4700, 21,600 and 23,900. These results were confirmed at the individual gene level and agree with the results reported by Salem et al (2020) [9], who identified a potential recombination event within the
The present study demonstrates that no long-term tissue adaptation has occurred, at least in the spike gene, without a clear association being demonstrated between tree topology and tropism
Summary
Bovine coronavirus (BoCV) belongs to the family Coronaviridae, genus Betacoronavirus (https://talk.ictvonline.org/). The genome is a single-stranded positive-sense RNA of about 31 Kb, which includes ten open reading frames (ORFs) flanked by 50 and 30 untranslated regions [1]. ORF1 codes for the polyproteins pp1a and—through a ribosomal frameshift—for pp1ab, which are proteolytically cleaved into multiple non-structural proteins (NSP) [2]. ORF3, 4, 8, 9, and 10 code for the structural proteins hemagglutinin–esterase protein (HE), spike glycoprotein (S), small membrane protein (SE), membrane protein (M), and nucleocapsid protein (N). Other ORFs encode additional NSPs, such as. As for other coronaviruses, the S protein is the most studied, constituting the typical protrusions on the viral surface.
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