High prevalence and phylogenetic diversity of coronaviruses in insectivorous cave-dwelling bats in the Republic of the Congo.

Authors

Aldi Fred Mandiangou, Léadisaelle Hosanna Lenguiya, Nicole Vidal, Matthieu Fritz, Illich Manfred Mombo, Deborah Garcia, Felix Koukouikila-Koussounda, Louis Régis Dossou-Yovo, Léa Gwladys Gangoué, Novy Charel Bobouaka Bonguili, Jordy Exaucé Demboux Lyelet, Amour Mouanda Sounda, Grâce Petula Urielle Fila-Fila, Pembe Issamou Mayengue, Eric Maurice Leroy, Fabien Roch Niama

Published in

Scientific reports. Jul 02, 2026. Epub Jul 02, 2026.

Abstract

The role of bats in hosting a wide variety of coronaviruses (CoVs) with complex viral evolution is well-established; additionally, they spread coronavirus species to other wildlife. Owing to the bioecological characteristics of bats, caves are effective models for studying coronavirus transmission. Little is known about the circulation of CoVs among cave-dwelling bats in Africa, particularly in the Republic of the Congo. In this study, the diversity of CoVs was investigated to understand possible associated variables driving coronavirus transmission among bats in Boundou and Mont-Belo caves. Fecal samples were screened for RNA using conventional pan-CoV PCR. Positive samples were sequenced, and phylogenetic analysis was performed on the RdRp gene fragment. Among the 1800 guano samples analyzed, 230 (12.78%) were positive for coronavirus, of which 107 (42.8%) were from Triaenops, 28 (40%) were from Miniopterus, 35 (7.38%) were from Rhinolophus, and 60 (5.96%) were from Hipposideros. Phylogenetic analyses revealed a wide range of Alphacoronavirus: 126 (54.78%), 60 (26.09%), and 26 (11.31%) samples were positive for Setracovirus, Minunacovirus, and Duvinacovirus, respectively, and two (0.87%) unclassified sequences were identified; samples were also positive for Betacoronavirus, with 11 (4.78%) and five (2.17%) being positive for Hibecovirus and Sarbecovirus, respectively. These results highlight the associations of Setracovirus and Minunacovirus with Triaenops and Miniopterus, respectively. Hipposideros carry multiple coronavirus subgenera of Alphacoronavirus and Betacoronavirus in both caves. Additionally, Sarbecovirus has also been found to infect Hipposideros.

PMID:
42393337
Bibliographic data and abstract were imported from PubMed on 03 Jul 2026.

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