Bat coronavirus phylogeography in the Western Indian Ocean

Léa Joffrin; Steven M. Goodman; David A. Wilkinson; Beza Ramasindrazana; Erwan Lagadec; Yann Gomard; Gildas Le Minter; Andréa Dos Santos; M. Corrie Schoeman; Rajendraprasad Sookhareea; Pablo Tortosa; Simon Julienne; Eduardo S. Gudo; Patrick Mavingui; Camille Lebarbenchon

The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/742866 doi: bioRxiv preprint 4 % are endemic to the island. The smaller studied islands of the WIO, Mauritius, Mayotte, Re-63 union Island, and Mahé (Seychelles), host reduced bat species diversity (e.g. three species on 64 Reunion Island), whereas SECA supports a wide range of bat species. To date, several studies 65 have identified bat-infecting CoVs in countries of continental Africa, including Zimbabwe (4), 66 South Africa (5), and Kenya (6). CoVs have also been reported in fruit bat (Pteropodidae) pop-67 ulations of Madagascar, where beta-coronaviruses belonging to the D-subgroup were identified 68 in the two bat species Eidolon dupreanum, and Pteropus rufus (7). 69 In this study, we investigated the presence of CoVs in over 1,000 individual bats be- Appendix Table S1 . 86 author/funder. All rights reserved. No reuse allowed without permission. The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/742866 doi: bioRxiv preprint 6 7: 5'-CCA-TCA-TCA-GAT-AGA-ATC-ATC-ATA-3' (14 119 We tested the effect of bat family, species, sex, as well as sampling location and roosting 120 habitat (caves, outdoor or buildings) on the probability for detecting CoV RNA using Pearson 121 χ² tests. The effect of bat age (adult vs juvenile) and female reproductive status (pregnant vs not