SARS-CoV related Betacoronavirus and diverse Alphacoronavirus members found in western old-world

Abstract

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.

Keywords: Bats; Chiroptera; Coronavirus; Diversity; Emergence; Europe; Evolution; MERS-CoV; Phylogenetics; SARS-CoV.

Graphical abstract

Fig. 1

Bayesian phylogeny of 127 genetic sequences representative of coronavirus strains detected in the study with sequences representing the world diversity of Coronavirinae. A) Nsp12 sequences were aligned using Mafft 7 (http://mafft.cbrc.jp). Statistical support (posterior probability) of nodes are depicted using a gradual color code of the tree, red indicating significant posterior probability values (>0.95). Strain names and main information is written in taxa labels. Viruses detected in this study are highlighted in purple.

Fig. 2

Phylogenetic analysis and geo-localisation of coronaviruses detected in the Western Palearctic region. A) Bayesian phylogeny depicted in Fig. 1 (selected nodes collapsed for clarity reasons) showing clusters including a number of sequences ranging from 3 to 63 with a mean of 14 per clade. Statistical support (posterior probability) of nodes are depicted using a gradual color code of the tree, red indicating significant posterior probability values (>0.95). Labels of viruses detected in this study are bolded and coloured in blue. Corresponding host names are indicated in the right panel, in front of each taxa reported in the study. When significant mixing of species at the roost was observed, the name of the co-roosting coronavirus-negative species is added in brackets. Country of origin and identity score (ID) to the closest reference found in GenBank were also added for each coronavirus clade detected in this study. B) Map of the study region depicting the 39 investigated sites and highlighting in red those where bat samples were found positive for coronaviruses.

Fig. S2

Detail of the alignment of several coronavirus phylogroups belonging to Betacoronavirus and Alphacoronavirus genera. Details of the alignment generated by MAFFT and used for phylogenetic reconstruction exhibiting regions with genetic differences between sequences (i.e. SNPs). GenBank identification numbers, strain partial names and partial sequences extracted from the alignment which shows variable positions affecting phylogroups Betacoronavirus EPI1 and Alphacoronavirus EPI4.