Résumé
The emergence of SARS-CoV and MERS-CoV, triggered the discovery of a high diversity of coronaviruses in bats. Studies from Europe have shown that coronaviruses circulate in bats in France but this reflects only a fraction of the whole diversity. In the current study the diversity of coronaviruses circulating in western Europe was extensively explored. Ten alphacoronaviruses in eleven bat species belonging to the Miniopteridae, Vespertilionidae and Rhinolophidae families and, a SARS-CoV-related Betacoronavirus in Rhinolophus ferrumequinum were identified. The diversity and prevalence of bat coronaviruses presently reported from western Europe is much higher than previously described and includes a SARS-CoV sister group. This diversity demonstrates the dynamic evolution and circulation of coronaviruses in this species. That said, the identified coronaviruses were consistently associated with a particular bat species or genus, and these relationships were maintained no matter the geographic location. The observed phylogenetic grouping of coronaviruses from the same species in Europe and Asia, emphasizes the role of host/pathogen coevolution in this group.
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•A SARS-CoV sister clade member, Betacoronavirus EPI1, found in Western Europe.•Betacoronavirus EPI1 circulates in Rhinolophus ferrumequinum bat in Western Europe.•9 alphacoronaviruses species found in Vespertillionidae and Miniopteridae bats.•Rhinolophus ferrumequinum hosts Betacov EPI1 and Alphacov EPI4, EPI6 and EPI7.•Alphacoronavirus EPI6 is strictly associated with Rhinolophus ferrumequinum.