COVID-19 pandemic interventions reshaped the global dispersal of seasonal influenza viruses
Zhiyuan Chen, Joseph L.-H. Tsui, Bernardo Gutiérrez, Simón Busch Moreno, Louis du Plessis, Xiaowei Deng, Jun Cai, Sumali Bajaj, Marc A. Suchard, Oliver G. Pybus, Philippe Lemey, Moritz U. G. Kraemer, Hongjie Yu
Abstract
The global dynamics of seasonal influenza viruses inform the design of surveillance, intervention, and vaccination strategies. The COVID-19 pandemic provided a singular opportunity to evaluate how influenza circulation worldwide was perturbed by human behavioral changes. We combine molecular, epidemiological, and international travel data and find that the pandemic's onset led to a shift in the intensity and structure of international influenza lineage movement. During the pandemic, South Asia played an important role as a phylogenetic trunk location of influenza A viruses, whereas West Asia maintained the circulation of influenza B/Victoria. We explore drivers of influenza lineage dynamics across the pandemic period and reasons for the possible extinction of the B/Yamagata lineage. After a period of 3 years, the intensity of among-region influenza lineage movements returned to pre-pandemic levels, with the exception of B/Yamagata, after the recovery of global air traffic, highlighting the robustness of global lineage dispersal patterns to substantial perturbation.