Assessing the danger of self-sustained HIV epidemics in heterosexuals by population based phylogenetic cluster analysis

Assessing the danger of transition of HIV transmission from a concentrated to a generalized epidemic is of major importance for public health. In this study, we develop a phylogeny-based statistical approach to address this question. As a case study, we use this to investigate the trends and determinants of HIV transmission among Swiss heterosexuals. We extract the corresponding transmission clusters from a phylogenetic tree. To capture the incomplete sampling, the delayed introduction of imported infections to Switzerland, and potential factors associated with basic reproductive number [Formula: see text], we extend the branching process model to infer transmission parameters. Overall, the [Formula: see text] is estimated to be [Formula: see text] ([Formula: see text]-confidence interval [Formula: see text]—[Formula: see text]) and it is decreasing by [Formula: see text] per [Formula: see text] years ([Formula: see text]—[Formula: see text]). Our findings indicate rather diminishing HIV transmission among Swiss heterosexuals far below the epidemic threshold. Generally, our approach allows to assess the danger of self-sustained epidemics from any viral sequence data.