Implementing a massively parallel sequencing workflow for the sequencing of serially passaged influenza A virus

Abstract

Influenza viruses are human and animal pathogens. Influenza viruses infect the respiratory tract of humans and can cause disease ranging from mild discomfort to death. In the United States roughly 30 million cases of seasonal influenza are reported yearly of which 500,000 require hospitalization. Host-to-host transmission of influenza viruses imposes a bottleneck wherein viral population size and diversity are dramatically reduced. Here, we evaluate how artificial serial bottleneck events of differing sizes affect the trajectory of influenza virus evolution. Previous work generated a panel of progeny lines by serially passaging A/Victoria/361/2011 (H3N2) in cell culture in which each subsequent round of growth was initiated by 1, 100, or 1000 viruses. I implemented a massively parallel sequencing workflow for the sequencing of serially passaged influenza A virus and characterized mutational patterns. We found that the amount of consensus sequence changes was not significantly different between the three passage conditions. Instead, the diversity of below consensus changes increased as the number of viruses used to initiate growth increased.