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. 2015 Dec 2;7(12):6279-90.
doi: 10.3390/v7122937.

Alphacoronaviruses Detected in French Bats Are Phylogeographically Linked to Coronaviruses of European Bats

Anne Goffard  1 , Christine Demanche  2 , Laurent Arthur  3 , Claire Pinçon  4 , Johan Michaux  5   6 , Jean Dubuisson  7
Affiliations

Alphacoronaviruses Detected in French Bats Are Phylogeographically Linked to Coronaviruses of European Bats

Anne Goffard et al. Viruses. .

Abstract

Bats are a reservoir for a diverse range of viruses, including coronaviruses (CoVs). To determine the presence of CoVs in French bats, fecal samples were collected between July and August of 2014 from four bat species in seven different locations around the city of Bourges in France. We present for the first time the presence of alpha-CoVs in French Pipistrellus pipistrellus bat species with an estimated prevalence of 4.2%. Based on the analysis of a fragment of the RNA-dependent RNA polymerase (RdRp) gene, phylogenetic analyses show that alpha-CoVs sequences detected in French bats are closely related to other European bat alpha-CoVs. Phylogeographic analyses of RdRp sequences show that several CoVs strains circulate in European bats: (i) old strains detected that have probably diverged a long time ago and are detected in different bat subspecies; (ii) strains detected in Myotis and Pipistrellus bat species that have more recently diverged. Our findings support previous observations describing the complexity of the detected CoVs in bats worldwide.

Keywords: Europe; alphacoronavirus; bats; coronavirus; molecular characterization; phylogenetic analysis; phylogeographic analysis.

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Figures

Figure 1
Figure 1
Geographical locations of bat colonies where guano samples were taken during the summer of 2014. The colonies are numbered 1 to 7 and georeferenced as: 1 (02°34′54″ E; 47°00′39″ N), 2 (02°31′02″ E; 47°04′59″ N), 3 (02°32′19″ E; 46°56′23″ N), 4 (02°33′38″ E; 47°02′39″ N), 5 (02°31′22″ E; 47°04′24″ N), 6 (02°18′59″ E; 46°51′27″ N), and 7 (02°23′21″ E, 46°49′28″ N). They are scattered around the city of Bourges, in the central region of France.
Figure 2
Figure 2
Phylogenetic tree of the partial RNA-dependent RNA polymerase (RdRp) gene (277 bp) of coronavirus strains found in bats. The phylogram results from bootstrapped data sets obtained using PhyML 3.0 program [26]. The tree was visualized using the FigTree program, version 1.4.2. The percentages above the branches are the frequencies with which a given branch appeared in 1000 bootstrap replications. Bootstrap values below 60% are not displayed. Taxa are named according to the following pattern: bat species/country of origin/year of detection. Sequences belonging to lineage 1 are presented in the green box, those belonging to lineage 2 in the red box. French bat sequences are presented in grey.
Figure 3
Figure 3
Minimum spanning network constructed using RdRp gene sequences of bat alpha-CoV. Bat species and subspecies, geographic origins and year of detection are indicated. Numbers correspond to the mutational steps observed between sequences. Sequences belonging to lineage 1 are presented in the green box, those belonging to lineage 2 in the red box. Among lineage 2, groups I–III are presented in white boxes. French bat sequences are presented in dotted bold circles.
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