Maintenance of viral diversity through influenza transmission bottlenecks: a within-host branching-process model

Viral populations can experience a dramatic reduction in population size and genetic diversity during transmission between donor and recipient hosts. Transmission bottlenecks can therefore decrease the evolutionary potential of viral populations, slowing adaptation by increasing the strength of genetic drift and decreasing the strength of selection. Recent barcoded influenza experiments in guinea pigs showed that recipient animals receive a diverse viral inoculum but lose most of that diversity within one to two days. The resulting bottleneck therefore arises not at physical transfer but during early viral growth in the recipient. We develop a branching-process framework to quantify how much of this loss follows from stochasticity in early growth alone. Each transmitted lineage is treated as an independent stochastic process governed by measurable viral parameters. We recover these parameters from viral growth rates estimated from observed viral load. A residual filter for each animal then captures any additional loss imposed by the recipient host. Applied to twenty-four recipient animals, the model reveals two distinct groups. For roughly half of the animals, the stochastic extinction during early growth already accounts for the observed loss. For the remaining animals, the additional host filter is severe. Only about one in a hundred free virions pass through. This decomposition offers a quantitative entry point for future work on immune contributions to transmission bottlenecks.