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

ABSTRACT 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.