Thomas Leitner: Reconstructing HIV epidemics from HIV phylogenetics -- a multi-scale problem

Despite ongoing prevention campaigns, the HIV-1 epidemic persists on a global scale. New intervention campaigns may be promising, but a large fraction of infections occur between persons who are unaware of their infection. To monitor the effects of such campaigns, and more generally, to estimate incidence and prevalence in human populations, patterns of disease spread must be accurately reconstructed. The use of HIV genetic data to reconstruct HIV epidemics is a powerful method to reveal how a pathogen has spread when traditional epidemiological methods are not sufficient. For example, phylogenetic analyses of HIV-1 have been used to reconstruct transmission chains on the individual level to aid in criminal investigations. However, traditional epidemiology relies on case narratives that are often incapable of resolving transmission histories. Molecular epidemiologic methods also excel when subjects are unavailable as in deceased cases or with anonymous data. As phylogenetic and phylodynamic studies become more popular, a correct understanding of the limitations of what phylogenetics can and cannot reconstruct is crucial. Yet, there are several outstanding gaps in our current knowledge, e.g., the effect of the pre-transmission interval. In this talk I will introduce the multi-scale scene at which we need to model HIV epidemics, and present recent advances that identifies and deals with some of the fundamental issues in phylogenetic reconstruction of HIV epidemics.