Influenza A genomic diversity during human infections underscores the strength of genetic drift and the existence of tight transmission bottlenecks
Authors: Martin Michael A. , Berg Nick , Koelle Katia 
Published: June 2023

Influenza infections result in considerable public health and economic impacts each year. One of the contributing factors to the high annual incidence of human influenza is the virus’s ability to evade acquired immunity through continual antigenic evolution. Understanding the evolutionary forces that act within and between hosts is therefore critical to interpreting past trends in influenza virus evolution and in predicting future ones. Several studies have analyzed the longitudinal patterns of influenza A virus genetic diversity in natural human infections to assess the relative contributions of selection and genetic drift on within-host evolution. However, in these natural infections, within-host viral populations harbor very few single nucleotide variants, limiting our resolution in understanding the forces acting on these populations in vivo. Further, low levels of within host viral genetic diversity limit the ability to infer the extent of drift across transmission events. Here, we propose to use influenza virus genomic diversity as an alternative signal to better understand within and between host patterns of viral evolution. Specifically, we focus on the dynamics of defective viral genomes (DVGs) which harbor large internal deletions in one or more of influenza virus’s eight gene segments. Our longitudinal analyses of DVGs show that influenza A virus populations are highly dynamic within hosts, corroborating previous findings based on viral genetic diversity that point towards the importance of genetic drift in driving within-host viral evolution. Further, our analysis of DVG populations across transmission pairs indicate that DVGs rarely appeared to be shared, consistent with previous findings indicating the presence of tight transmission bottlenecks. Our analyses demonstrate that viral genomic diversity can be used to complement analyses based on viral genetic diversity to reveal processes that drive viral evolution within and between hosts.

Author summary

During viral replication within infected individuals, different types of mutation can occur. Point mutations introduce genetic diversity, with some sites in the viral genome becoming polymorphic at the viral population level. Structural mutations that result in deletions in the viral genome can also occur, contributing to genomic diversity in the viral population. Defective viral genomes (DVGs) are a particular type of this genomic diversity that are incapable of establishing productive infection on their own, but persist during infection through cellular coinfection with infectious virus. Here, we first identify DVGs in deep sequencing data from natural infections of influenza A virus subtype H3N2 and then use these DVGs to inform our understanding of within-host viral evolution and transmission dynamics. By analyzing DVG populations over time within infected individuals and between transmission pairs, we find that influenza A virus populations are shaped by genetic drift and tight transmission bottlenecks. Our results add to our understanding of influenza genomic diversity within-and between-hosts and demonstrate the possibility of considering the full suite of viral diversity to understand drivers of viral evolution.