Recherche Fondamentale (basic research) - AFRICoV - Veille génomique des virus SARS-CoV-2(-like) sur les marchés de viande de brousse africains, et perceptions des risques sanitaires liés au COVID-19 et à la consommation de viande de brousse AFRICoV-- Genomic surveillance of SARS-CoV-2(-like) viruses in African bushmeat markets, and perceptions of health risks related to COVID-19 and bushmeat consumption

Because the COVID-19 outbreak originated from a Chinese "wet market", the illegal wildlife trade has been hold for the prime responsible of the current pandemic. SARS-CoV-2-like strains have so far been isolated in two Asian mammals, a bat and a pangolin. Given the diversity of SARS-CoV viruses and their acknowledged ability to jump the species barrier, it is reasonable to consider that most of the SARS-CoV-2-like diversity spectrum remains to be described. Such knowledge gap could explain the current incapacity to describe the transmission pathway that allowed the infection of humans, the most privileged scenario being that of multiple recombinations among SARS-CoV-2-like strains in (unknown) intermediary hosts. Because the unsustainable harvesting of wildlife has a direct impact on the propagation of emerging diseases, wildlife trade surveys constitute crucial sentinels for the surveillance of future SARSCoV- 2-related outbreaks. Bushmeat (wild game) consumption is a major cultural practice in tropical Africa and has been the source of deadly zoonotic diseases such as HIV, Ebola and Lassa fever. Although SARS-CoV- 2-like viruses are yet unknown in tropical Africa, we posit that available evidence supports the hypothesis that SARS-CoV-2-like virus diversity has remained largely unscreened in mammals and that a huge knowledge gap in tropical Africa remains to be filled. All the more since the only mammals so far screened positive to SARS-CoV-2-like in Asia also have representatives in tropical Africa (pangolin and horseshoe bat). Because in the context of the COVID-19 pandemic surveying reservoirs and wildlife trade practices is a prerequisite to efficient health surveillance, AFRICoV tackles the issue of SARSCoV- 2 infection from the original prism of the reservoirs as part of the wildlife (bushmeat) trade established in Africa - and recently linking the African continent to Asia (through pangolin trafficking). Our general objective is to conduct health surveillance and risk assessment for a potential next SARS-CoV-2-related pandemic in tropical Africa linked to bushmeat consumption and trade. This is especially relevant in the African context given the general lack of awareness of populations regarding health issues linked to bushmeat consumption. AFRICoV aims to understand the pathways of infection between animals to humans through four main objectives: (i) assessing the prevalence of SARS-CoV-2-like viruses in mammals from tropical Africa, Specific objectives: - Systematic screening of SARS-CoV-2-like viruses in the widest possible spectrum of African mammals sold in the bushmeat market - Intensive screening of the African counterparts of the known Asian hosts (pangolins and horseshoe bats) (ii) characterizing the evolution of SARS-CoV-2, Specific objectives: - Genome assembly of SARS-CoV-2-like viruses - Phylogenomic analysis and datation among SARS-CoV-2-like strains - Characterization of evolutionary rates and recombination events (iii) anticipating a new SARS-CoV-2 reservoir in sub-Saharan Africa, Specific objectives: - Patterns of species-to-species infection during the evolution of SARS-CoV-2-like viruses (among wild mammals) and in the recent time (SARS-CoV-2; from humans to domestic / captive animals) - Detection of putative recombination in the recent time (between humans and domestic / captive animals) (iv) implementing efficient measures protecting African people from new zoonotic diseases. Through AFRICoV, we propose a multi-disciplinary approach linking genomic characterization of new SARS-CoV-2-like viruses, health surveillance of mammalian reservoirs and the study of bushmeat stakeholders' perceptions on the COVID-19 pandemic and its link with wildlife consumption, through an unprecedented comparative approach among three countries (Cote d'Ivoire, Benin and Cameroon). Members of the AFRICoV project have a demonstrated, longterm expertise in wildlife trade surveys, involving genetic / genomic surveys of mammalian hosts and their pathogens and the study of bushmeat stakeholders' representations and awareness on zoonoses linked to the wildlife trade. Such long-term upstream work provides an exceptional opportunity to access the bushmeat market network in Africa and assess the health risks associated to SARS-CoV-2-like viruses and bushmeat consumption. The main outputs from AFRICoV will include a better understanding of SARS-CoV-2-like virus evolution in mammals, an unprecedented estimation of SARS-CoV-2 reservoirs in Africa, the validation of an RT-PCR assay for screening SARS-CoV-2(-like) viruses in mammalian reservoirs, South-to-South training in the rapid diagnostic of SARS-CoV-2(-like) viruses (RT-PCR), educative material associated to bushmeat consumption and public health (leaflet and diffusion to national Medias), and a regional restitution workshop in western Africa including policy makers.