Rabies remains a major public health problem in Burkina Faso, where epidemiological and molecular data are still limited. This study aimed to assess the prevalence of infection in biting animals and to compare the performance of direct immunofluorescence (DFA) and conventional RT-PCR. A total of 97 brain tissue samples from biting animals collected between 2018 and 2019 at the National Livestock Laboratory were analyzed. Direct immunofluorescence (DFA) was performed according to the standard reference method, and conventional RT-PCR was carried out using primers targeting a conserved region of the Lyssavirus N gene. Epidemiological data (species, age, vaccination status, number of people bitten, and origin) were associated with the diagnostic results. DFA revealed an overall infection rate of 88.6%, which was higher in dogs (90.2%) and in unvaccinated animals (92.6%). Infection was more frequent in animals aged three months or older and was systematic in those that had bitten at least twice. RT-PCR showed an overall infection rate of 36.1%, with no positivity detected in vaccinated animals. The agreement between the two methods was low (Kappa = 0.13), probably due to prolonged preservation and suboptimal storage conditions of the samples. This study confirms the central role of dogs in the transmission of rabies and highlights the need to strengthen the vaccination of domestic animals. DFA remains a reference method well suited to the local context, while the optimization of molecular techniques and the improvement of sample preservation conditions represent key perspectives for strengthening epidemiological surveillance and moving toward the elimination of human rabies by 2030.
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