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Literature detail

Bat coronavirus phylogeography in the Western Indian Ocean.

Léa Joffrin1 Steven M Goodman2,3 David A Wilkinson4 Beza Ramasindrazana4,2,5 Erwan Lagadec4 Yann Gomard4 Gildas Le Minter4 Andréa Dos Santos6 M Corrie Schoeman7 Rajendraprasad Sookhareea8 Pablo Tortosa4 Simon Julienne9 Eduardo S Gudo10 Patrick Mavingui4 Camille Lebarbenchon11
Affiliations 11 institutions
  1. Université de La Réunion, UMR Processus Infectieux en Milieu Insulaire Tropical (PIMIT), INSERM 1187, CNRS 9192, IRD 249, Sainte-Clotilde, La Réunion, France. [email protected].
  2. Association Vahatra, Antananarivo, Madagascar.
  3. Field Museum of Natural History, Chicago, USA.
  4. Université de La Réunion, UMR Processus Infectieux en Milieu Insulaire Tropical (PIMIT), INSERM 1187, CNRS 9192, IRD 249, Sainte-Clotilde, La Réunion, France.
  5. Beza Ramasindrazana, Institut Pasteur de Madagascar, BP 1274, Ambatofotsikely, Antananarivo, 101, Madagascar.
  6. Veterinary Faculty, Eduardo Mondlane University, Maputo, Mozambique.
  7. School of Life Sciences, University of Kwa-Zulu Natal, Kwa-Zulu Natal, South Africa.
  8. National Parks and Conservation Service, Réduit, Mauritius.
  9. Seychelles Ministry of Health, Victoria, Mahe, Seychelles.
  10. Instituto Nacional de Saúde, Maputo, Mozambique.
  11. Université de La Réunion, UMR Processus Infectieux en Milieu Insulaire Tropical (PIMIT), INSERM 1187, CNRS 9192, IRD 249, Sainte-Clotilde, La Réunion, France. [email protected].
PMID 32327721 2020 Sci Rep eng epublish
PubMed DOI Browse context

Article

Publication summary

Bats provide key ecosystem services such as crop pest regulation, pollination, seed dispersal, and soil fertilization. Bats are also major hosts for biological agents responsible for zoonoses, such as coronaviruses (CoVs). The islands of the Western Indian Ocean are identified as a major biodiversity hotspot, with more than 50 bat species. In this study, we tested 1,013 bats belonging to 36 species from Mozambique, Madagascar, Mauritius, Mayotte, Reunion Island and Seychelles, based on molecular screening and partial sequencing of the RNA-dependent RNA polymerase gene. In total, 88 bats (8.7%) tested positive for coronaviruses, with higher prevalence in Mozambican bats (20.5% ± 4.9%) as compared to those sampled on islands (4.5% ± 1.5%). Phylogenetic analyses revealed a large diversity of α- and β-CoVs and a strong signal of co-evolution between CoVs and their bat host species, with limited evidence for host-switching, except for bat species sharing day roost sites. These results highlight that strong variation between islands does exist and is associated with the composition of the bat species community on each island. Future studies should investigate whether CoVs detected in these bats have a potential for spillover in other hosts.

Phylogeny Alphacoronavirus Animals Base Sequence Betacoronavirus Chiroptera Coronavirus Infections DNA, Viral Ecosystem Evolution, Molecular Genetic Variation Host Specificity Indian Ocean Islands Phylogeography Prevalence Real-Time Polymerase Chain Reaction RNA-Dependent RNA Polymerase Zoonoses

Structured evidence records

Evidence records

5 total
Reservoir Ecology 2 records
Reservoir Ecology Extraction confidence 0.90
Key finding

Coronavirus prevalence in bats varied geographically across the Western Indian Ocean, with higher rates in Mozambique than in island populations, indicating ecological variation in reservoir dynamics among bat communities.

Host
Chiroptera
Location
Mozambique Mozambique
Supporting text

We tested 1,013 bats belonging to 36 species from Mozambique, Madagascar, Mauritius, Mayotte, Reunion Island and Seychelles... 88 bats (8.7%) tested positive for coronaviruses, with higher prevalence in Mozambican bats (20.5%) compared to island bats (4.5%).

Method
molecular screening; partial sequencing
Geographic raw
Mozambique
Country inferred
Mozambique
Reservoir Ecology Extraction confidence 0.90
Key finding

Co-evolution between bat species and their associated α- and β-coronaviruses suggests stable reservoir relationships, with limited host-switching primarily at shared roosts.

Host
Chiroptera
Location
Western Indian Ocean
Supporting text

Phylogenetic analyses revealed a large diversity of α- and β-CoVs and a strong signal of co-evolution between CoVs and their bat host species, with limited evidence for host-switching, except for bat species sharing day roost sites.

Method
phylogenetic analysis
Geographic raw
Western Indian Ocean
Cross Species Transmission 1 records
Cross Species Transmission Extraction confidence 0.70
Key finding

Limited cross-species transmission of bat coronaviruses was detected, occurring between bat species that share day roost sites.

Location
Western Indian Ocean
Supporting text

Phylogenetic analyses revealed a large diversity of α- and β-CoVs and a strong signal of co-evolution between CoVs and their bat host species, with limited evidence for host-switching, except for bat species sharing day roost sites.

Method
molecular screening; partial sequencing; phylogenetic analysis
Study design
phylogenetic analysis
Transmission direction
animal-to-animal
Geographic raw
Western Indian Ocean
Genomic Evolution 1 records
Genomic Evolution Extraction confidence 0.90
Key finding

Phylogenetic analysis of partial RNA-dependent RNA polymerase sequences showed diverse bat α- and β-coronaviruses exhibiting co-evolution with their bat hosts and limited cross-species transmission.

Host
Chiroptera
Location
Not specified
Supporting text

Phylogenetic analyses revealed a large diversity of α- and β-CoVs and a strong signal of co-evolution between CoVs and their bat host species, with limited evidence for host-switching.

Genes or proteins
RNA-dependent RNA polymerase
Analysis methods
phylogenetic analysis; molecular screening; partial sequencing
Zoonotic Surveillance 1 records
Zoonotic Surveillance Extraction confidence 0.95
Key finding

Molecular surveillance detected alpha- and beta-coronaviruses in bats from multiple Western Indian Ocean islands and Mozambique, with higher prevalence in Mozambique.

Host
Chiroptera
Location
Madagascar Mozambique Seychelles Mauritius Mayotte, France Réunion, France
Supporting text

In this study, we tested 1,013 bats belonging to 36 species from Mozambique, Madagascar, Mauritius, Mayotte, Reunion Island and Seychelles, based on molecular screening and partial sequencing of the RNA-dependent RNA polymerase gene. In total, 88 bats (8.7%) tested positive for coronaviruses.

Method
molecular screening; partial sequencing; Real-Time Polymerase Chain Reaction
Geographic raw
Mozambique, Madagascar, Mauritius, Mayotte, Reunion Island and Seychelles