Comparative Analysis of the Evolutionary Dynamics of Seasonal Influenza Viruses in Madagascar Before and Since the Pandemic Period of COVID-19

Madagascar has maintained an influenza surveillance program for decades. Following the emergence of SARS-CoV-2 in 2020, the country implemented strict nonpharmaceutical interventions (NPIs) that disrupted influenza circulation. We studied the evolutionary dynamics of influenza viruses in Madagascar over a 5-year period, spanning both the pre-pandemic and COVID-19 pandemic periods: 2019–2023. We showed that global genetic evolution profiles for A(H1N1)pdm09, A(H3N2), and B/Victoria viruses occurred from the pre-pandemic to the pandemic period of COVID-19 in Madagascar. In addition, we observed distinct patterns of viral re-emergence following the relaxation of COVID-19 containment measures. This study underscores the importance of sustaining continuous surveillance of influenza virus circulation to monitor the emergence of new variants and identify clade-specific isolates. In addition, these results suggest that targeted NPIs could complement vaccination strategies in reducing influenza transmission and should be integrated into a comprehensive approach for effective influenza control.