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

Kusejko, Katharina; Bachmann, Nadine; Chaudron, Sandra E; Nguyen, Huyen; Braun, Dominique L; Hampel, Benjamin; Battegay, Manuel; Bernasconi, Enos; Calmy, Alexandra; Cavassini, Matthias; Hoffmann, Matthias; Böni, Jürg; Yerly, Sabine; Klimkait, Thomas; Perreau, Matthieu; Rauch, Andri; Günthard, Huldrych F; Kouyos, Roger D (2019). A systematic phylogenetic approach to study the interaction of HIV-1 with coinfections, non-communicable and opportunistic diseases. The journal of infectious diseases, 220(2), pp. 244-253. Oxford University Press 10.1093/infdis/jiz093

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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.

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