Whole genome sequencing of Influenza isolates from a prospective household cohort

A complete understanding of influenza virus evolution requires studies at all levels, as viral evolutionary dynamics may differ across spatial and temporal scales. The relative contribution of deterministic processes, such as selection, and stochastic processes, such as genetic drift, is influenced by viral effective population size. While the global evolution of influenza A virus (IAV) is dominated by the positive selection of novel antigenic variants that circulate in the tropics, much less is known about influenza virus evolution within and between human hosts. With few exceptions, most of the available data derive from studies of chronically infected, immunocompromised hosts, experimental infections with attenuated viruses, or animal models. Here we define the evolutionary dynamics of IAV in human hosts through next generation sequencing of 249 upper respiratory specimens from 200 individuals collected over 6290 person-seasons of observation. Because these viruses were collected over 5 seasons from individuals in a prospective community-based cohort, they are broadly representative of natural human infections with seasonal viruses. Within host genetic diversity was low, and we found little evidence for positive selection of minority variants. We used viral sequence data from 35 serially sampled individuals to estimate a within host effective population size of 30-50. This estimate is consistent across several models and robust to their underlying assumptions. We also identified 43 epidemiologically linked and genetically validated transmission pairs. Maximum likelihood optimization of multiple transmission models estimates an effective transmission bottleneck of 1-2 distinct genomes. Our data suggest that positive selection of novel viral variants is inefficient at the level of the individual host and that genetic drift and other stochastic processes dominate the within and between host evolution of influenza A viruses.