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

Kusejko, Katharina; Bachmann, Nadine; Chaudron, Sandra Elisabeth; Nguyen, Huyen Tran; Braun, Dominique L; Hampel, Benjamin; Battegay, Manuel; Bernasconi, Enos; Calmy, Alexandra; Cavassini, Matthias; Hoffmann, Matthias; Böni, Jürg; Yerly Ferrillo, Sabine; Klimkait, Thomas; Perreau, Matthieu; Rauch, Andri; Günthard, Huldrych F; Kouyos, Roger D

doi:10.1093/infdis/jiz093

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Title		A systematic phylogenetic approach to study the interaction of HIV-1 with coinfections, noncommunicable diseases, and opportunistic diseases
Authors		Kusejko, Katharina Bachmann, Nadine Chaudron, Sandra Elisabeth Nguyen, Huyen Tran Braun, Dominique L Hampel, Benjamin Battegay, Manuel Bernasconi, Enos Calmy, Alexandra Cavassini, Matthias Hoffmann, Matthias Böni, Jürg Yerly Ferrillo, Sabine Klimkait, Thomas Perreau, Matthieu Rauch, Andri Günthard, Huldrych F Kouyos, Roger D show all authors [1 - 18]
Collaboration		Swiss HIV Cohort Study
Published in		The Journal of Infectious Diseases. 2019, vol. 220, no. 2, p. 244-253
Abstract		To systematically test whether coinfections spread along the HIV-1 transmission network and whether similarities in 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 sarcoma, clustered significantly, suggesting transmission of these infections along the HIV-1 transmission network. The clustering of patients with neurocognitive complaints 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 coinfections and comorbidities 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.
Keywords		HIV — Coinfections — Comorbidities — Opportunistic infections — Phylogenetic analysis
Identifiers		DOI: 10.1093/infdis/jiz093 PMID: 30835292
Full text		Article (Published version) (287 Kb) - Limited access to UNIGE Supplemental data (640 Kb) - Limited access to UNIGE
Structures		Faculté de médecine / Section de médecine clinique / Département de médecine
Research groups		Groupe Laurent Kaiser (virologie clinique) (668) VIH/SIDA (930)
Projects		FNS: BSSGI0_155851, 179571 FNS: 177499
Citation (ISO format)		KUSEJKO, Katharina et al. A systematic phylogenetic approach to study the interaction of HIV-1 with coinfections, noncommunicable diseases, and opportunistic diseases. In: The Journal of Infectious Diseases, 2019, vol. 220, n° 2, p. 244-253. doi: 10.1093/infdis/jiz093 https://archive-ouverte.unige.ch/unige:136094