A systematic phylogenetic approach to study the interaction of HIV-1 with coinfections, non-communicable and opportunistic diseases.

To systematically test whether coinfections spread along the HIV-1 transmission network and whether similarities of HIV-1 genomes predict AIDS-defining illnesses and comorbidities, we analyzed the distribution of these variables on the HIV-phylogeny of the densely sampled Swiss HIV Cohort Study. By combining different statistical methods, we could detect, quantify and explain the clustering of diseases: Infectious conditions such as hepatitis C, but also Kaposi's sarcoma, clustered significantly, suggesting transmission of these infections along the HIV-1 transmission network. The clustering of patients with neurocognitive complaints, however, could not be completely explained by the clustering of patients with similar demographic risk factors, which suggests a potential impact of viral genetics. In summary, the consistent and robust signal for infectious conditions highlights the strong interaction of HIV-1 and other infections and shows the potential of combining phylogenetic methods to identify disease traits that are likely to be related to virus genetic factors.