Wide diversity of coronaviruses in frugivorous and insectivorous bat species: a pilot study in Guinea, West Africa. coronaviruses in bats from Guinea

Zoonoses represent 60% of emerging infectious diseases and constitute a threat for public health than can have a global importance, as seen with the current pandemic of Severe Acute Respiratory Syndrome Coronavirus. Bats have been recognized as an important source of zoonotic viruses, and harbor a wide diversity of coronaviruses (CoVs). In West Africa, where there is a high diversity of bat species, a few is known on the circulation of coronaviruses in these hosts, especially at the interface with human populations. Thus, it is important to expand our knowledge of the presence of CoVs in bats which may represent a risk to humans. In this study in Guinea, we tested a total of 634 swabs and feces samples from 319 individuals belonging to 14 genera and 6 families of insectivorous and frugivorous bats across the country, for the presence of coronaviruses using a broadly reactive Reverse Transcription PCR assay. We found CoVs in 35 (11%) of the tested bats, in 3 insectivorous bat species belonging to 3 families (i.e. Hipposideridae, Rhinolophidae and Nycteridae) and 5 fruit bat species (Eidolon helvum, Rousettus aegyptiacus, Lissonycteris angolensis, Epomophorus gambianus, Nanonycteris sp.). Positivity rates varied from 5.7% to 100% depending on bat species, and a wide diversity of alpha and beta coronaviruses was found among the obtained sequences. This includes 3 sequences from insectivorous bats (Hipposideros sp. and Nycteris sp.) that clustered with ßCoVs from the sub-genera of SarbeCoVs and MerbeCoVs, known to harbor the highy pathogenic human coronaviruses SARS-CoVs and MERS-CoVs respectively. We also report for the fisrt time, infection in a Nanonycteris bat and a co-infection with α and ßCov in a frugivorous bat (R. aegyptiacus). This pilot study described a large diversity found in 13 of the 14 collection sites across the country suggesting that CoVs are widely spread in West Africa and their circulation should be assessed. This is even more relevant that positive bats were mostly captured (72%) close to human habitats, showing the importance of larger studies on the characterization of CoVs and to evaluate the risk of exposure of potential zoonotic CoVs to humans.