title: Detection of new genetic variants of Betacoronaviruses in Endemic Frugivorous Bats of Madagascar.
abstract: BACKGROUND
  Bats are amongst the natural reservoirs of many coronaviruses (CoVs) of which some can lead to severe infection in human. African bats are known to harbor a range of pathogens (e.g., Ebola and Marburg viruses) that can infect humans and cause disease outbreaks. A recent study in South Africa isolated a genetic variant closely related to MERS-CoV from an insectivorous bat. Though Madagascar is home to 44 bat species (41 insectivorous and 3 frugivorous) of which 34 are endemic, no data exists concerning the circulation of CoVs in the island's chiropteran fauna. Certain Malagasy bats can be frequently found in close contact with humans and frugivorous bats feed in the same trees where people collect and consume fruits and are hunted and consumed as bush meat. The purpose of our study is to detect and identify CoVs from frugivorous bats in Madagascar to evaluate the risk of human infection from infected bats.
  
  
  METHODS
  Frugivorous bats belonging to three species were captured in four different regions of Madagascar. We analyzed fecal and throat swabs to detect the presence of virus through amplification of the RNA-dependent RNA polymerase (RdRp) gene, which is highly conserved in all known coronaviruses. Phylogenetic analyses were performed from positive specimens.
  
  
  RESULTS
  From 351 frugivorous bats, we detected 14 coronaviruses from two endemic bats species, of which 13 viruses were identified from Pteropus rufus and one from Eidolon dupreanum, giving an overall prevalence of 4.5%. Phylogenetic analysis revealed that the Malagasy strains belong to the genus Betacoronavirus but form three distinct clusters, which seem to represent previously undescribed genetic lineages.
  
  
  CONCLUSIONS
  Our findings suggest that CoVs circulate in frugivorous bats of Madagascar, demonstrating the needs to evaluate spillover risk to human populations especially for individuals that hunt and consume infected bats. Possible dispersal mechanisms as to how coronaviruses arrived on Madagascar are discussed.
authors.affiliation: Virology Unit, Institut Pasteur of Madagascar, Ambatofotsikely, BP 1274, Antananarivo, Madagascar, Dummy_Only. norosoa@pasteur.mg.
authors.forename: Norosoa H
authors.initials: NH
authors.lastname: Razanajatovo
authors.affiliation: Virology Unit, Institut Pasteur of Madagascar, Ambatofotsikely, BP 1274, Antananarivo, Madagascar, Dummy_Only. lalaina@pasteur.mg.
authors.forename: Lalaina A
authors.initials: LA
authors.lastname: Nomenjanahary
authors.affiliation: Centre de Recherche et de Veille sur les Maladies Emergentes dans l'Ocean Indien (CRVOI), Plateforme de Recherche CYROI, 2 rue Maxime Riviere, 97490, Sainte Clotilde, La Reunion, France. dwilkin799@gmail.com.
authors.forename: David A
authors.initials: DA
authors.lastname: Wilkinson
authors.affiliation: Madagasikara Voakajy, BP 5181, Antananarivo, Madagascar. hantajulie@gmail.com.|Department of Animal Biology, Faculty of Sciences, University of Antananarivo, BP 906, Antananarivo, Madagascar. hantajulie@gmail.com.
authors.forename: Julie H
authors.initials: JH
authors.lastname: Razafimanahaka
authors.affiliation: Association Vahatra, BP 3972, Antananarivo, Madagascar. sgoodman@fieldmuseum.org.
authors.forename: Steven M
authors.initials: SM
authors.lastname: Goodman
authors.affiliation: School of Environment, Natural Resources and Geography, Bangor University, Bangor, Gwynedd, United Kingdom. rkbjenkins@gmail.com.
authors.forename: Richard K
authors.initials: RK
authors.lastname: Jenkins
authors.affiliation: School of Environment, Natural Resources and Geography, Bangor University, Bangor, Gwynedd, United Kingdom. julia.jones@bangor.ac.uk.
authors.forename: Julia P G
authors.initials: JP
authors.lastname: Jones
authors.affiliation: Virology Unit, Institut Pasteur of Madagascar, Ambatofotsikely, BP 1274, Antananarivo, Madagascar, Dummy_Only. jmheraud@pasteur.mg.
authors.forename: Jean-Michel
authors.initials: JM
authors.lastname: Heraud
mesh_terms: D000818:Animals; D002685:Chiroptera / Q000821:virology*; D003332:Coronaviridae / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D003333:Coronaviridae Infections / Q000662:veterinary*; D005814:Genes, Viral; D014644:Genetic Variation; D005843:Geography; D008270:Madagascar; D010802:Phylogeny