Inferring the sources of HIV infection in Africa from deep-sequence data with semi-parametric Bayesian Poisson flow models

Pathogen deep-sequencing is an increasingly routinely used technology in infectious disease surveillance. We present a semi-parametric Bayesian Poisson model to exploit these emerging data for inferring infectious disease transmission flows and the sources of infection at the population level. The framework is computationally scalable in high-dimensional flow spaces thanks to Hilbert Space Gaussian process approximations, allows for sampling bias adjustments, and estimation of gender- and age-specific transmission flows at finer resolution than previously possible. We apply the approach to densely sampled, population-based HIV deep-sequence data from Rakai, Uganda, and find substantive evidence that adolescent and young women were predominantly infected through age-disparate relationships in the study period 2009–2015.