Recherche Fondamentale (basic research) - Prevalence, diversité génétique et distribution géographique des coronavirus chez les chauves souris sauvages afin d'évaluer le risk pour de futur transmissions zoonotiques Prevalence, genetic diversity and geographic distribution of coronaviruses in wild bat populations in their natural habitat to evaluate risk for futur cross-species transmissions to humans.

The majority of EID are dominated by zoonoses and >70% of zoonotic EID events are caused by pathogens from wildlife origin. The actual COVID-19 epidemic with the SARS-CoV2 virus clearly illustrates the global damage of a single cross-species transmission from an animal coronavirus leading to a lock down of 4 billion people across the globe in a few months only. Bats have been confirmed to be the origin of human CoVs, either directly or by an intermediate host. Contacts between humans and bats are diverse, and range from direct exposure to infected blood or tissues through hunting and butchering, or indirect exposure to bat guano or fruit contaminated by their saliva, urine or faeces. A wide diversity of bat species are hunted for food or medicine, and bushmeat hunting is increasingly recognized inWest and Central Africa. Therefore, documenting the prevalence and genetic diversity of coronaviruses in bats is now more than crucial. The general objective of the project is to provide new on coronaviruses in bats in African countries with high likelihood for emergence of zoonotic infections from bats. Overall we will (i) document the genetic diversity and evolution of coronaviruses in African bats; (ii) develop a high throughput serological assay to study antibodies to different coronaviruses and estimate prevalence of coronaviruses in different bat species and (iii) study seasonality of coronavirus shedding in bats. From previous studies in Guinea, Cameroon, the Democratic Republic of Congo (DRC) and Zimbabwe, we have already samples from >10,000 bats in their natural habitat available (Dried blood spots, oral and anal swabs, and fecal samples). Retrospective screening for presence of coronaviruses will be done by amplifying and sequencing of a 440bp fragment of RdRp. On a subset of samples, additional sequence efforts will be done to obtain sequences from larger genomic fragments (especially in genes that are important for serological assays (S and/or N genes) or near full-length genomes using MinION technology. We will use a high throughput serological assay (Luminex approach) to detect antibodies to coronaviruses (SARS-CoV1, SARS-CoV2, MERSV, ..) to screen bat samples in which no viral RNA could be amplified for the presence of antibodies. Like other pathogens, it is possible that coronaviruses also exhibit highly seasonal circulation patterns and occasional sampling may not be sufficient for detecting coronavirus RNA or antibodies. Samples from bat colonies in Cameroon and Guinea, collected during monthly follow-up over a one year period will be analyzed for presence of viral RNA in shedding and for antibodies to document seasonality of viral shedding in different species. Overall, this study will rapidly provide key informations on the genetic diversity of coronaviruses in bats in Africa and estimates on their prevalence. This is the first study to look for coronavirus infection rates at a large scale in bats across Africa and using the same technologies for molecular and serological screening allowing thus comparison of results between geographic areas and species. The study will provide information on proportions of bats that are shedding virus, have been infected with the virus and on seasons when viral shedding is highest for zoonotic transmissions. The information obtained by this project will also contribute to development of an appropriate diagnostic platform that can include a large panel of broadly reactive and specific antigens covering as much as possible the diversity of coronaviruses to rapidly identify circulation of new coronaviruses in humans as well as development of broad-spectrum vaccines. Similarly, additional information on targets of antiviral drugs for a wide diversity of coronaviruses with zoonotic potential will be useful to identify eventual activity of existing and new drugs.