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J Infect Dis. 2019 Mar 4. pii: jiz093. doi: 10.1093/infdis/jiz093. [Epub ahead of print]

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

Author information

1
Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.
2
Institute of Medical Virology, University of Zurich, Zurich, Switzerland.
3
Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University of Basel, Basel, Switzerland.
4
Division of Infectious Diseases, Regional Hospital Lugano, Lugano, Switzerland.
5
Laboratory of Virology and Division of Infectious Diseases, Geneva University Hospital, University of Geneva, Geneva, Switzerland.
6
Division of Infectious Diseases, Lausanne University Hospital, Lausanne, Switzerland.
7
Division of Infectious Diseases, Cantonal Hospital St Gallen, St. Gallen, Switzerland.
8
olecular Virology, Department of Biomedicine-Petersplatz, University of Basel, Basel, Switzerland.
9
University of Lausanne, Lausanne, Switzerland.
10
Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern, Switzerland.

Abstract

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.

KEYWORDS:

HIV; coinfections; comorbidities; opportunistic infections; phylogenetic analysis

PMID:
30835292
DOI:
10.1093/infdis/jiz093

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