Intracellular replication dynamics of influenza A virus impose strong bottleneck effects

Understanding the sources of genetic diversity in Influenza A Virus (IAV) infections is crucial for understanding the mechanisms of viral evolution and immune escape. Whereas prior studies have characterized the effects of population bottlenecks during host-to-host transmission and intrahost tissue-to-tissue dissemination, the role of intracellular replication processes on IAV genetic diversity remains largely unexplored. In this study, we used stochastic mathematical modeling to simulate the replication of genetically distinct IAV strains within individual cells and tissues. Our results reveal significant bottleneck effects within a single infection cycle of individual cells. Intracellular bottleneck effects are driven by stochastic molecular processes and lead to the expansion or elimination of neutral variants creating large-scale differences between the initial and final frequencies of genetic variants in individual cells. By expanding our findings to a population-level tissue model, we show that IAV intracellular replication reduces the effective population size, thereby diminishing the impact of selection and increasing the role of genetic drift. Our findings highlight the important contribution of intracellular replication processes to the generation of genetic diversity in IAV.