Epidemiological Dynamics of Influenza and SARS-CoV-2 Circulation in Burkina Faso in the Post-COVID-19

Influenza and COVID-19 remain major public health concerns due to their high morbidity, mortality, and epidemic potential. The COVID-19 pandemic notably disrupted health and economic systems worldwide in 2020. Despite reduced global attention, these pathogens continue to circulate, and emerging disease resurgence remains a constant threat, emphasizing the importance of ongoing epidemiological and virological surveillance. This study aimed to describe year-long surveillance of SARS-CoV-2 and influenza viruses in post-pandemic Burkina Faso. A prospective cross-sectional survey was conducted from January to December 2023 in sentinel surveillance sites across four regions. Patients with influenza-like illness (ILI), severe acute respiratory infection (SARI), and their contacts were recruited. Nasopharyngeal or oropharyngeal swabs were collected and tested for influenza and SARS-CoV-2 using real-time RT-PCR. Socio-demographic and clinical data were obtained from medical records or interviews. Among 3,311 samples, 11.41% tested positive for influenza and 6.07% for SARS-CoV-2. Influenza A viruses predominated (90.21%), followed by type B (7.79%). Of all participants, 68.4% were ILI and 31.6% SARI cases. Influenza A was more common among ILI patients. Two influenza waves were observed, during the dry/cold season (February–March) and the end of the rainy season (October). Children were most affected by influenza, while SARS-CoV-2 was more frequent among adolescents and adults. Influenza and SARS-CoV-2 were significantly present in ILI and SARI cases. Targeted vaccination for high-risk groups and during peak influenza seasons could enhance prevention and reduce disease burden.