OmniVira

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].
PMID32327721 DOI10.1038/s41598-020-63799-7 Year2020 Journal Scientific reports Sci Rep Languageeng Statusepublish

Abstract

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.

Supporting text Virus Host Location
Phylogeny 805 Alphacoronavirus 29 Animals 1948 Base Sequence 52 Betacoronavirus 78 Chiroptera 371 Coronavirus Infections 171 DNA, Viral 39 Ecosystem 36 Evolution, Molecular 176 Genetic Variation 127 Host Specificity 132 Indian Ocean Islands 1 Phylogeography 30 Prevalence 62 Real-Time Polymerase Chain Reaction 18 RNA-Dependent RNA Polymerase 49 Zoonoses 397

Evidence records

2 total
Zoonotic Surveillance
1 records · 1 evidence types
Evidence type Viral Detection
1 records
OVE3752 Viral Detection
Key finding

Coronaviruses were detected in bats sampled across the Western Indian Ocean region, with 88 of 1,013 bats testing positive.

Virus
Coronaviridae
Host
bats Chiroptera Natural host
Location
Mozambique Madagascar Mauritius France Seychelles
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 of the RNA-dependent RNA polymerase gene
Geographic raw
Mozambique | Madagascar | Mauritius | Mayotte | Reunion Island | Seychelles
Country inferred
MOZ | MDG | MUS | FRA | SYC
Genomic Evolution
1 records · 1 evidence types
Evidence type Phylogenetic Evolution
1 records
OVE3753 Phylogenetic Evolution
Key finding

Phylogenetic analyses showed a large diversity of α- and β-coronaviruses and indicated co-evolution with bat host species, with limited host-switching except among bat species sharing day roosts.

Virus
Coronaviridae
Host
bats Chiroptera Natural host
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, except for bat species sharing day roost sites.

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