Background: Influenza is a major cause of acute respiratory infections worldwide. In tropical regions such as Sub-Saharan Africa, influenza circulates year-round with irregular peaks, yet genomic data guiding prevention strategies remain limited. This study characterized the genetic diversity and seasonal dynamics of influenza A(H1N1)pdm09 and A(H3N2) viruses circulating in Burkina Faso in 2024.

Methods: A cross-sectional study was conducted from January to December 2024, including seven sentinel surveillance sites. Patients presenting with influenza-like illness or severe acute respiratory illness were enrolled. Respiratory specimens were tested by real-time RT-PCR. Influenza-positive samples with a cycle threshold ≤ 30 underwent whole-genome sequencing using Oxford Nanopore and Illumina platforms. Phylogenetic analyses and clade assignment were performed using MEGA Version 12.

Results: Out of 2951 samples tested, 6.74% were positive for influenza viruses. Females had higher odds of influenza positivity than males (OR = 1.48; 95% CI: 1.11-1.98). A significantly higher risk of positivity was observed in the age groups of 5-15 years (OR = 1.67; 95% CI: 1.07-2.52; p = 0.02) and 25-50 years (OR = 2.54; 95% CI: 1.53-4.03; p < 0.001). Influenza A(H3N2) peaked in July, while A(H1N1)pdm09 peaked in October. Phylogenetic analysis of 43 genomes revealed co-circulation of multiple clades within both subtypes.

Conclusion: Influenza A viruses circulating in Burkina Faso in 2024 showed substantial genetic diversity, underscoring the need for continuous genomic surveillance to inform vaccine strain selection and public health strategies in tropical Africa.