Influenza A virus undergoes compartmentalized replication in vivo dominated by stochastic bottlenecks

• Authors: Katherine A Amato, University of Wisconsin-Madison; Luis A Haddock III, University of Wisconsin-Madison; Katarina M Bruan, University of Wisconsin-Madison; Victoria Meliopoulos, St. Jude Children’s Research Hospital; Brandi Livingston, St. Jude Children’s Research Hospital; Rebekah Honce, St. Jude Children’s Research Hospital; Grace A Schaack, University of Wisconsin-Madison; Emma Boehm, University of Wisconsin-Madison; Christina A Higgins, University of Wisconsin-Madison; Gabrielle L Barry, University of Wisconsin-Madison; Katharina Koelle, Emory University; Stacey Schultz-Cherry, St. Jude Children’s Research Hospital; Thomas C Friedrich, University of Wisconsin-Madison; Andrew Mehle, University of Wisconsin-Madison
• Journal Title: Nature Communications
• Volume: Volume 13
• Publisher: Nature Research (part of Springer Nature) | 2022-06-14
• Type of Work: Article | Final Publisher PDF
• Publisher DOI: http://doi.org/10.1038/s41467-022-31147-0
• Subjects: Health Sciences, Immunology; Biology, Microbiology
• Keywords: Viral evolution; Influenza virus

Abstract

Transmission of influenza A viruses (IAV) between hosts is subject to numerous physical and biological barriers that impose genetic bottlenecks, constraining viral diversity and adaptation. The bottlenecks within hosts and their potential impacts on evolutionary pathways taken during infection are poorly understood. To address this, we created highly diverse IAV libraries bearing molecular barcodes on two gene segments, enabling high-resolution tracking and quantification of unique virus lineages within hosts. Here we show that IAV infection in lungs is characterized by multiple within-host bottlenecks that result in “islands” of infection in lung lobes, each with genetically distinct populations. We perform site-specific inoculation of barcoded IAV in the upper respiratory tract of ferrets and track viral diversity as infection spreads to the trachea and lungs. We detect extensive compartmentalization of discrete populations within lung lobes. Bottleneck events and localized replication stochastically sample individual viruses from the upper respiratory tract or the trachea that become the dominant genotype in a particular lobe. These populations are shaped strongly by founder effects, with limited evidence for positive selection. The segregated sites of replication highlight the jackpot-style events that contribute to within-host influenza virus evolution and may account for low rates of intrahost adaptation.