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Little research on coronaviruses has been conducted on wild animals in Africa. Here, we screened a wide range of wild animals collected in six provinces and five caves of Gabon between 2009 and 2015. We collected a total of 1867 animal samples (cave-dwelling bats, rodents, non-human primates and other wild animals). We explored the diversity of CoVs and determined the factors driving the infection of CoVs in wild animals. Based on a nested reverse transcription-polymerase chain reaction, only bats, belonging to the  Hipposideros gigas  (4/156),  Hipposideros  cf.  ruber  (13/262) and  Miniopterus inflatus  (1/249) species, were found infected with CoVs. We identified alphacoronaviruses in  H. gigas  and  H . cf . ruber  and betacoronaviruses in  H. gigas . All  Alphacoronavirus  sequences grouped with  Human coronavirus 229E  (HCoV-229E). Ecological analyses revealed that CoV infection was significantly found in July and October in  H. gigas  and in October and November in  H . cf  ruber . The prevalence in the Faucon cave was significantly higher. Our findings suggest that insectivorous bats harbor potentially zoonotic CoVs; highlight a probable seasonality of the infection in cave-dwelling bats from the North-East of Gabon and pointed to an association between the disturbance of the bats’ habitat by human activities and CoV infection.

Genetic diversity and ecology of coronaviruses hosted by cave-dwelling bats in Gabon