title: Genetic diversity of coronaviruses in bats in Lao PDR and Cambodia.
abstract: South-East Asia is a hot spot for emerging zoonotic diseases, and bats have been recognized as hosts for a large number of zoonotic viruses such as Severe Acute Respiratory Syndrome (SARS), responsible for acute respiratory syndrome outbreaks. Thus, it is important to expand our knowledge of the presence of viruses in bats which could represent a risk to humans. Coronaviruses (CoVs) have been reported in bat species from Thailand, China, Indonesia, Taiwan and the Philippines. However no such work was conducted in Cambodia or Lao PDR. Between 2010 and 2013, 1965 bats were therefore sampled at interfaces with human populations in these two countries. They were tested for the presence of coronavirus by consensus reverse transcription-PCR assay. A total of 93 samples (4.7%) from 17 genera of bats tested positive. Sequence analysis revealed the presence of potentially 37 and 56 coronavirus belonging to alpha-coronavirus (αCoV) and beta-CoV (βCoV), respectively. The βCoVs group is known to include some coronaviruses highly pathogenic to human, such as SARS-CoV and MERS-CoV. All coronavirus sequences generated from frugivorous bats (family Pteropodidae) (n=55) clustered with other bat βCoVs of lineage D, whereas one coronavirus from Pipistrellus coromandra fell in the lineage C of βCoVs which also includes the MERS-CoV. αCoVs were all detected in various genera of insectivorous bats and clustered with diverse bat αCoV sequences previously published. A closely related strain of PEDV, responsible for severe diarrhea in pigs (PEDV-CoV), was detected in 2 Myotis bats. We highlighted the presence and the high diversity of coronaviruses circulating in bats from Cambodia and Lao PDR. Three new bat genera and species were newly identified as host of coronaviruses, namely Macroglossus sp., Megaerops niphanae and Myotis horsfieldii.
authors.affiliation: Institut Pasteur du Cambodge, Virology Unit, Phnom Penh, Cambodia.
authors.forename: Audrey
authors.initials: A
authors.lastname: Lacroix
authors.affiliation: Institut Pasteur du Cambodge, Virology Unit, Phnom Penh, Cambodia.
authors.forename: Veasna
authors.initials: V
authors.lastname: Duong
authors.affiliation: Institut Pasteur du Cambodge, Virology Unit, Phnom Penh, Cambodia.
authors.forename: Vibol
authors.initials: V
authors.lastname: Hul
authors.affiliation: National Veterinary Research Institute, Ministry of Agriculture Forestry and Fisheries, Cambodia.
authors.forename: Sorn
authors.initials: S
authors.lastname: San
authors.affiliation: National Veterinary Research Institute, Ministry of Agriculture Forestry and Fisheries, Cambodia.
authors.forename: Hull
authors.initials: H
authors.lastname: Davun
authors.affiliation: Forest Administration, Ministry of Agriculture Forestry and Fisheries, Cambodia.
authors.forename: Keo
authors.initials: K
authors.lastname: Omaliss
authors.affiliation: Wildlife Conservation Society, Cambodia.
authors.forename: Sokha
authors.initials: S
authors.lastname: Chea
authors.affiliation: Muséum national d'Histoire naturelle, Institut de Systématique, Evolution, Biodiversité (ISYEB), UMR 7205 MNHN CNRS UPMC, France.
authors.forename: Alexandre
authors.initials: A
authors.lastname: Hassanin
authors.affiliation: National Animal Health Laboratory, Ministry of Agriculture Forestry and Fisheries, Lao Democratic People's Republic.
authors.forename: Watthana
authors.initials: W
authors.lastname: Theppangna
authors.affiliation: Wildlife Conservation Society, Lao Democratic People's Republic; Metabiota Inc., Vientiane, Lao Democratic People's Republic.
authors.forename: Soubanh
authors.initials: S
authors.lastname: Silithammavong
authors.affiliation: Wildlife Conservation Society, Lao Democratic People's Republic.
authors.forename: Kongsy
authors.initials: K
authors.lastname: Khammavong
authors.affiliation: Wildlife Conservation Society, Lao Democratic People's Republic.
authors.forename: Sinpakone
authors.initials: S
authors.lastname: Singhalath
authors.affiliation: Wildlife Conservation Society, Lao Democratic People's Republic.
authors.forename: Zoe
authors.initials: Z
authors.lastname: Greatorex
authors.affiliation: Wildlife Conservation Society, Vietnam Program, Hanoi, Vietnam.
authors.forename: Amanda E
authors.initials: AE
authors.lastname: Fine
authors.affiliation: One Health Institute, School of Veterinary Medicine, University of California, Davis, USA.
authors.forename: Tracey
authors.initials: T
authors.lastname: Goldstein
authors.affiliation: Wildlife Conservation Society, Wildlife Health Program, Bronx, New York, USA.
authors.forename: Sarah
authors.initials: S
authors.lastname: Olson
authors.affiliation: Wildlife Conservation Society, Wildlife Health Program, Bronx, New York, USA; Metabiota Inc., Nanaimo, British Columbia, Canada.
authors.forename: Damien O
authors.initials: DO
authors.lastname: Joly
authors.affiliation: Wildlife Conservation Society, Cambodia.
authors.forename: Lucy
authors.initials: L
authors.lastname: Keatts
authors.affiliation: Institut Pasteur du Cambodge, Virology Unit, Phnom Penh, Cambodia.
authors.forename: Philippe
authors.initials: P
authors.lastname: Dussart
authors.affiliation: Institute of Physical Geography, Faculty of Geography and Regional Studies, University of Warsaw, Warsaw, Poland.
authors.forename: Aneta
authors.initials: A
authors.lastname: Afelt
authors.affiliation: Cirad, UMR 17, Cirad-Ird, TA-A17/G, Montpellier, France; Université de Montpellier, IES, UMR 5214, CNRS-UM, Montpellier, France. Electronic address: roger.frutos@ies.univ-montp2.fr.
authors.forename: Roger
authors.initials: R
authors.lastname: Frutos
authors.affiliation: Institut Pasteur du Cambodge, Virology Unit, Phnom Penh, Cambodia; GSK Vaccines R&D, 150 Beach road, # 22-00, 189720, Singapore. Electronic address: buchyphilippe@hotmail.com.
authors.forename: Philippe
authors.initials: P
authors.lastname: Buchy
mesh_terms: D000818:Animals; D001483:Base Sequence; D002160:Cambodia; D002685:Chiroptera / Q000821:virology*; D017934:Coronavirus / Q000235:genetics*; D004197:Disease Reservoirs; D019143:Evolution, Molecular; D005814:Genes, Viral; D014644:Genetic Variation; D007812:Laos; D010802:Phylogeny; D058974:Phylogeography; D012324:RNA-Dependent RNA Polymerase / Q000235:genetics; D017422:Sequence Analysis, DNA; D014764:Viral Proteins / Q000235:genetics
chemical_list: D014764:Viral Proteins; D012324:RNA-Dependent RNA Polymerase
keywords: Bats; Cambodia; Coronaviruses; Genetic diversity; Lao PDR