The Impact of Viral and Host Factors on the Influenza A Virus Transmission Bottleneck

BackgroundTransmission bottlenecks are defined by the number of unique virions or genotypes that establish an infection, and they restrict the viral diversity that passes from one infected host to another. They have a major impact on the spread of mutations in a population. Previous work has identified a tight transmission bottleneck for seasonal influenza A virus (IAV) based on an analysis of 43 household pairs, largely from a single A(H3N2) predominant season. While many viral and host factors are known to influence IAV transmission in households, their impact on the transmission bottleneck is not clear. MethodsNasal swabs were collected daily from IAV infected individuals enrolled in two case-ascertained U.S. household transmission studies, FluTES (2017/2018 through 2019/2020 seasons) and RVTN (2021/2022 season). Viruses were sequenced in duplicate, and intrahost single nucleotide variants (iSNV) were identified at a 0.5% frequency threshold using a benchmarked pipeline with >99.99% specificity for mutations present in both replicates. Transmission pairs were defined based on co-residence, test date, and genetic distance. For each possible transmission pair, the bottleneck was estimated using a beta binomial and a clonal mutation model. ResultsWe sequenced 567 samples from 319 individuals and 102 households in duplicate. Based on epidemiologic linkage and a sequence-based cut-off, we defined 56 transmission pairs for the beta binomial model and 60 transmission pairs for the clonal mutation model. Across all pairs, we identified a transmission bottleneck of 1 both using the beta-binomial model (CI 1, 1) and the clonal mutation model (exact estimate: 0.91, CI: 0.91, 0.97). In our cohort, influenza season, subtype, and host factors (influenza vaccination status, sex, and age) did not alter the transmission bottleneck. ConclusionsIAV is subject to a tight genetic bottleneck during transmission, which limits the onward propagation of newly arising nucleotide variants. Tight bottlenecks appear to be intrinsic to the transmission process, as host and viral factors within households do not affect its size.