Timing of the emergence of new successful viral strains in seasonal influenza

•We develop a mathematical model that describes co-evolution between host and virus.•We clarify how emergence time and epidemic peak timing depend on parameters.•Strains that trigger epidemic emerge in early phase of epidemic season.•Epidemic peak timing of the strain is more than 1 year later since its emergence time.•Time lag between emergence and epidemic peak shows predictability of future strains.

High evolvability of influenza virus and the complex nature of its antagonistic interaction with the host immune system make it difficult to predict which strain of virus will become epidemic next and when it will emerge. To investigate the most likely time at which a new successful strain emerges every year in seasonal influenza, we use an individual-based model that takes into account the seasonality in transmission rate and host cross-immunity against a current viral strain due to previous infections with other strains. Our model deals with antigenic evolution of influenza virus that originated by point mutations at amino acid sites that constitute epitope and is driven by host immune response. Under the range of parameters by which influenza virus shows a “trunk” shape in its phylogenetic tree, as is typical in influenza A virus evolution, we find that most successful mutant strains emerge in an early part of the epidemic season, and that the time when the number of infected hosts reaches a maximum tends to be more than one season after viral emergence. This carryover of the epidemic peak timing implies that we can predict the strain that will become dominant in the epidemic in the following year.