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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].
PMID 25888853 2015 Virol J eng epublish
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Article

Publication summary

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.

Genetic Variation Animals Chiroptera Coronaviridae Coronaviridae Infections Genes, Viral Geography Madagascar Phylogeny

Structured evidence records

Evidence records

3 total
Genomic Evolution 1 records
Genomic Evolution Extraction confidence 0.90
Key finding

Phylogenetic analysis of RdRp gene sequences from Betacoronaviruses detected in endemic frugivorous bats of Madagascar revealed three distinct novel genetic lineages within the genus Betacoronavirus.

Location
Not specified
Supporting text

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. 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)
Analysis methods
gene amplification; phylogenetic analysis
Reservoir Ecology 1 records
Reservoir Ecology Extraction confidence 0.90
Key finding

Betacoronaviruses were found circulating in frugivorous bats, specifically Pteropus rufus and Eidolon dupreanum, in Madagascar, indicating these species act as natural reservoirs with potential human contact interfaces.

Location
Madagascar Madagascar
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%. Our findings suggest that CoVs circulate in frugivorous bats of Madagascar, demonstrating the need to evaluate spillover risk to human populations especially for individuals that hunt and consume infected bats.

Method
field sampling; RNA-dependent RNA polymerase gene amplification; phylogenetic analysis
Sample type
fecal swabs; throat swabs
Geographic raw
Madagascar
Country inferred
Madagascar
Zoonotic Surveillance 1 records
Zoonotic Surveillance Extraction confidence 0.95
Key finding

Surveillance of frugivorous bats in Madagascar identified new Betacoronavirus lineages in Pteropus rufus and Eidolon dupreanum based on RdRp gene detection.

Location
Madagascar 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... 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.

Method
PCR; phylogenetic analysis
Sample type
fecal swabs; throat swabs
Geographic raw
Madagascar
Country inferred
Madagascar