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The evolution of influenza viruses is fundamentally shaped by within-host processes. However, the within-host evolutionary dynamics of influenza viruses remain incompletely understood, in part because most studies have focused on infections in healthy adults based on single timepoint data. Here, we analyzed the within-host evolution of 82 longitudinally sampled individuals, mostly young children, infected with A/H1N1pdm09 or A/H3N2 viruses between 2007 and 2009. For A/H1N1pdm09 infections during the 2009 pandemic, nonsynonymous minority variants were more prevalent than synonymous ones. For A/H3N2 viruses in young children, early infection was dominated by purifying selection. As these infections progressed, nonsynonymous variants typically increased in frequency even when within-host virus titers decreased. Unlike the short-lived infections of adults where de novo within-host variants are rare, longer infections in young children allow for the maintenance of virus diversity via mutation-selection balance creating potentially important opportunities for within-host virus evolution.

We initiated the Vietnam Initiative on Zoonotic Infections (VIZIONS) research program to better understand the epidemiology of disease transmission at the human–animal interface in Vietnamese rural communities and to integrate One Health approaches to disease surveillance. We established a longitudinal community cohort study of individuals with occupational exposure to animals, which involves concurrent targeted sampling from domestic livestock species and follow-up monitoring of human clinical cases. The project was implemented by government agencies at the provincial and district levels of the public health and animal health sectors in Vietnam. Engaging with rural communities builds response capacity at the grassroots level, and has improved dialogue between local stakeholders responsible for monitoring human and animal health. Here we describe the process of initiating participatory research and cohort field implementation over the first year in two study sites in Vietnam. Keywords: Vietnam, participatory research, zoonoses, field epidemiology