title: Alphacoronaviruses Detected in French Bats Are Phylogeographically Linked to Coronaviruses of European Bats.
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.
authors.affiliation: Molecular &amp; Cellular Virology, University Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 8204-CIIL-Centre d'Infection et d'Immunité de Lille, Bâtiment IBL. 1 rue du Pr. Calmette CS 50447, 59021 Lille Cedex, France. anne.goffard@univ-lille2.fr.
authors.forename: Anne
authors.initials: A
authors.lastname: Goffard
authors.affiliation: Bacterial Respiratory Infections: Pertussis and Tuberculosis, University Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 8204-CIIL-Centre d'Infection et d'Immunité de Lille, F-59000 Lille, France. christine.demanche@univ-lille2.fr.
authors.forename: Christine
authors.initials: C
authors.lastname: Demanche
authors.affiliation: Museum d'Histoire Naturelle de Bourges, Les Rives d'Auron, allée René Ménard, 18000 Bourges, France. laurent.arthur@ville-bourges.fr.
authors.forename: Laurent
authors.initials: L
authors.lastname: Arthur
authors.affiliation: University Lille, CHU Lille, EA 2694-Santé publique: épidémiologie et qualité des soins, F-59000 Lille, France. claire.pincon@univ-lille2.fr.
authors.forename: Claire
authors.initials: C
authors.lastname: Pinçon
authors.affiliation: Conservation Genetics Unit, Institute of Botany (B. 22), University Liège, 4000 Liège, Belgium. johan.michaux@ulg.ac.be.|CIRAD TA C-22/E-Campus international de Baillarguet, 34398 Montpellier Cedex 5, France. johan.michaux@ulg.ac.be.
authors.forename: Johan
authors.initials: J
authors.lastname: Michaux
authors.affiliation: Molecular &amp; Cellular Virology, University Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 8204-CIIL-Centre d'Infection et d'Immunité de Lille, Bâtiment IBL. 1 rue du Pr. Calmette CS 50447, 59021 Lille Cedex, France. jean.dubuisson@ibl.cnrs.fr.
authors.forename: Jean
authors.initials: J
authors.lastname: Dubuisson
mesh_terms: D000818:Animals; D002685:Chiroptera / Q000821:virology*; D016000:Cluster Analysis; D017934:Coronavirus / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D018352:Coronavirus Infections / Q000453:epidemiology / Q000662:veterinary* / Q000821:virology; D005243:Feces / Q000821:virology; D005602:France / Q000453:epidemiology; D058974:Phylogeography; D015995:Prevalence; D012367:RNA, Viral / Q000235:genetics; D012324:RNA-Dependent RNA Polymerase / Q000235:genetics; D017422:Sequence Analysis, DNA; D017385:Sequence Homology
chemical_list: D012367:RNA, Viral; D012324:RNA-Dependent RNA Polymerase
keywords: Europe; alphacoronavirus; bats; coronavirus; molecular characterization; phylogenetic analysis; phylogeographic analysis