OmniVira

Detection of new genetic variants of Betacoronaviruses in Endemic Frugivorous Bats of Madagascar.

Norosoa H Razanajatovo1 Lalaina A Nomenjanahary2 David A Wilkinson3 Julie H Razafimanahaka4,5 Steven M Goodman6 Richard K Jenkins7 Julia P G Jones8 Jean-Michel Heraud9
Affiliations 9 institutions
  1. Virology Unit, Institut Pasteur of Madagascar, Ambatofotsikely, BP 1274, Antananarivo, Madagascar, Dummy_Only. [email protected].
  2. Virology Unit, Institut Pasteur of Madagascar, Ambatofotsikely, BP 1274, Antananarivo, Madagascar, Dummy_Only. [email protected].
  3. 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. [email protected].
  4. Madagasikara Voakajy, BP 5181, Antananarivo, Madagascar. [email protected].
  5. Department of Animal Biology, Faculty of Sciences, University of Antananarivo, BP 906, Antananarivo, Madagascar. [email protected].
  6. Association Vahatra, BP 3972, Antananarivo, Madagascar. [email protected].
  7. School of Environment, Natural Resources and Geography, Bangor University, Bangor, Gwynedd, United Kingdom. [email protected].
  8. School of Environment, Natural Resources and Geography, Bangor University, Bangor, Gwynedd, United Kingdom. [email protected].
  9. Virology Unit, Institut Pasteur of Madagascar, Ambatofotsikely, BP 1274, Antananarivo, Madagascar, Dummy_Only. [email protected].
PMID25888853 DOI10.1186/s12985-015-0271-y Year2015 Journal Virology journal Virol J Languageeng Statusepublish

Abstract

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. 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. 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. 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.

Supporting text Virus Host Location
Genetic Variation 127 Animals 1948 Chiroptera 371 Coronaviridae 13 Coronaviridae Infections 4 Genes, Viral 37 Geography 19 Madagascar 4 Phylogeny 805

Evidence records

4 total
Zoonotic Surveillance
3 records · 2 evidence types
Evidence type Viral Detection
2 records
OVE2005 Viral Detection
Key finding

Betacoronaviruses were detected in fecal and throat swabs from Pteropus rufus bats in Madagascar using RdRp gene amplification.

Virus
Betacoronavirus Coronaviridae
Host
Malagasy flying fox Pteropus rufus Natural host
Location
Madagascar
Supporting text

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. 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%.

Method
RNA-dependent RNA polymerase (RdRp) gene amplification
Sample type
fecal swabs | throat swabs
Geographic raw
Madagascar
Country inferred
MDG
OVE2006 Viral Detection
Key finding

Betacoronaviruses were detected in fecal and throat swabs from Eidolon dupreanum bats in Madagascar using RdRp gene amplification.

Virus
Betacoronavirus Coronaviridae
Host
Malagasy straw-colored fruit bat Eidolon dupreanum Natural host
Location
Madagascar
Supporting text

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. 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%.

Method
RNA-dependent RNA polymerase (RdRp) gene amplification
Sample type
fecal swabs | throat swabs
Geographic raw
Madagascar
Country inferred
MDG
Evidence type Reservoir Ecology
1 records
OVE2008 Reservoir Ecology
Key finding

Betacoronaviruses circulate among frugivorous bats in Madagascar, indicating these bats maintain natural viral circulation.

Virus
Betacoronavirus Coronaviridae
Host
flying foxes Pteropodidae Natural host
Location
Madagascar
Supporting text

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.

Method
field capture of bats | RNA extraction | RdRp gene amplification | phylogenetic analysis
Sample type
fecal swabs | throat swabs
Geographic raw
Madagascar
Country inferred
MDG
Genomic Evolution
1 records · 1 evidence types
Evidence type Phylogenetic Evolution
1 records
OVE2007 Phylogenetic Evolution
Key finding

Phylogenetic analysis showed that Malagasy Betacoronaviruses from frugivorous bats form three distinct clusters representing previously undescribed genetic lineages.

Virus
Betacoronavirus
Host
flying foxes Pteropodidae Natural host
Location
Not specified
Supporting text

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.

Genes or proteins
RNA-dependent RNA polymerase (RdRp) gene
Analysis methods
phylogenetic analysis