Résumé
The socio-ecological similarities between the tropical forest regions of Africa and those of South-East Asia, combined with the extraordinary propensity of SARS-CoV-2 to cross the species barrier and infect a wide variety of animals, suggest the risk of the virus being introduced into wildlife and adapted to new zoonotic reservoirs. To assess the occurrence of SARS-CoV-2 circulation in Congolese fauna, we conducted a two- year study in the frame of our PhD with EBO-SURSY Project support. This study first consisted of detecting SARS-CoV-2 genome by qPCR (quantitative polymerase chain reac- tion) in pets living in Covid-19-positive households in Brazzaville and its surroundings. Whole genome sequencing was then performed using a combined Ampliseq approach and MinION Nanopore technology. Of 100 pets included in this study, 14 tested positive. Sequencing analyses showed the simultaneous circulation of three SARS-CoV-2 variants and a putative recombinant variant between viruses from clades 20B and 20H. This also revealed long viral shedding times, reaching more than two weeks in a cat. At the end of the study, the animals studied were blood sampled and tested for antibodies against SARS-CoV-2 by Luminex™. We found a high seroprevalence of 38.6% in the 75 animals sampled.In the second step, we autopsied 96 rodents captured in three Brazzaville health facilities most visited by Covid-19 patients. Viral genome and antibodies were tested in faeces and blood samples, respectively. While we did not detect SARS-CoV-2 RNA using PCR, we found that 9.4% of the 96 rodents had specific antibodies, suggesting infection or at least exposure to SARS-CoV-2.Considering the interactions between humans, pets and wildlife from tropical forest regions of Africa, our results highlight the benefits of a One Health approach including SARS-CoV-2 diagnosis and surveillance of viral diversity in susceptible animals in order to quickly manage interspecies transmission and spillback events.