COVID-19 pandemic interventions reshaped the global dispersal of seasonal influenza viruses

Despite the availability of updated seasonal influenza vaccines and treatments, annual influenza epidemics continue to cause millions of hospitalizations and substantial burden on health care systems. The global circulation of seasonal influenza lineages depends on continued virus antigenic evolution and patterns of human travel from regions with year-round transmission to temperate regions. A clearer understanding of how human influenza and other respiratory pathogens were affected by COVID-19–related restrictions will help predict how future pandemics might influence infectious diseases and help inform more effective interventions.

 

During the COVID-19 pandemic, nonpharmaceutical interventions were introduced worldwide, which led to human behavioral changes on an unprecedented scale. This led to a decline in the global prevalence of endemic respiratory pathogens, including seasonal influenza subtypes H1N1pdm09 and H3N2 and lineages B/Victoria and B/Yamagata. The impact of changes in air travel connectivity among regions meant that the global circulation of seasonal influenza was perturbed. In this work, we assembled globally representative datasets to jointly analyze molecular, epidemiological, and international travel data to characterize how the global circulation of seasonal influenza was reshaped and when it returned to a pre-pandemic equilibrium.

 

Test positivity rates for influenza viruses dropped by >95% during the acute phase of the pandemic (April 2020 to March 2021) compared with the pre-pandemic period. We inferred that the locations where circulation of H1N1, H3N2, and B/Victoria influenza virus lineages was maintained during the acute phase were all in Asia. However, we also revealed that circulation continued in Africa, but with less influence on global circulation patterns, perhaps because of less frequent international travel. As pandemic-related restrictions weakened (albeit heterogeneously across the world), among-region virus lineage movements were detectable, and our statistical model showed strong support for association of international air travel with between-region influenza virus movements. In the post-pandemic period (after the World Health Organization’s International Health Regulations Emergency Committee declared the end of the global emergency in May 2023), the global circulation of seasonal influenza returned to pre-pandemic patterns characterized by continued viral movements and accumulation of genetic diversity—both important for maintaining transmission of seasonal influenza. The global lineage dynamics of seasonal influenza between May 2023 and March 2024 appears similar to that before the pandemic, albeit smaller in magnitude.

 

Our study revealed how seasonal influenza viruses are maintained during and reestablished after pandemic-related behavioral changes. The longer-term impact of the COVID-19 pandemic on influenza evolution and antigenicity will need continued monitoring through coordinated genomic surveillance and evaluation of the global transmission patterns. This is especially relevant as more regions become suitable for year-round circulation of influenza, including in Africa.