1. Epidemiology and Global Health
  2. Microbiology and Infectious Disease
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Assessing the danger of self-sustained HIV epidemics in heterosexuals by population based phylogenetic cluster analysis

  1. Teja Turk
  2. Nadine Bachmann
  3. Claus Kadelka
  4. Jürg Böni
  5. Sabine Yerly
  6. Vincent Aubert
  7. Thomas Klimkait
  8. Manuel Battegay
  9. Enos Bernasconi
  10. Alexandra Calmy
  11. Matthias Cavassini
  12. Hansjakob Furrer
  13. Matthias Hoffmann
  14. Huldrych F Günthard
  15. Roger D Kouyos Is a corresponding author
  1. University Hospital Zurich, Switzerland
  2. University of Hospital Zurich, Switzerland
  3. University of Zurich, Switzerland
  4. Geneva University Hospitals, Switzerland
  5. University Hospital Lausanne, Switzerland
  6. University of Basel, Switzerland
  7. University Hospital Basel, Switzerland
  8. Regional Hospital of Lugano, Switzerland
  9. Geneva University Hospital, Switzerland
  10. Lausanne University Hospital, Switzerland
  11. University of Bern, Switzerland
  12. Cantonal Hospital St. Gallen, Switzerland
  13. University Hospital Zürich, Switzerland
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Cite as: eLife 2017;6:e28721 doi: 10.7554/eLife.28721

Abstract

Assessing the danger of transition of HIV transmission from a concentrated to a generalized epidemic is of major importance for public health. In this study, we develop a phylogeny-based statistical approach to address this question. As a case study, we use this to investigate the trends and determinants of HIV transmission among Swiss heterosexuals. We extract the corresponding transmission clusters from a phylogenetic tree. To capture the incomplete sampling, the delayed introduction of imported infections to Switzerland, and potential factors associated with basic reproductive number R0, we extend the branching process model to infer transmission parameters. Overall, the R0 is estimated to be 0.44 (95%-confidence interval 0.42-0.46) and it is decreasing by 11% per 10 years (4%-17%). Our findings indicate rather diminishing HIV transmission among Swiss heterosexuals far below the epidemic threshold. Generally, our approach allows to assess the danger of self-sustained epidemics from any viral sequence data.

Article and author information

Author details

  1. Teja Turk

    Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
    Competing interests
    No competing interests declared.
    ORCID icon 0000-0003-3065-8578
  2. Nadine Bachmann

    Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
    Competing interests
    No competing interests declared.
    ORCID icon 0000-0002-7303-9542
  3. Claus Kadelka

    Division of Infectious Diseases and Hospital Epidemiology, University of Hospital Zurich, Zurich, Switzerland
    Competing interests
    No competing interests declared.
  4. Jürg Böni

    Institute of Medical Virology, University of Zurich, Zurich, Switzerland
    Competing interests
    No competing interests declared.
  5. Sabine Yerly

    Laboratory of Virology, Geneva University Hospitals, Geneva, Switzerland
    Competing interests
    No competing interests declared.
  6. Vincent Aubert

    Divisions of Immunology and Allergy, University Hospital Lausanne, Lausanne, Switzerland
    Competing interests
    No competing interests declared.
  7. Thomas Klimkait

    Department of Biomedicine, University of Basel, Basel, Switzerland
    Competing interests
    No competing interests declared.
  8. Manuel Battegay

    Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
    Competing interests
    No competing interests declared.
  9. Enos Bernasconi

    Division of Infectious Diseases, Regional Hospital of Lugano, Lugano, Switzerland
    Competing interests
    Enos Bernasconi, E.B. has been a consultant for BMS, Gilead, ViiV Healthcare, Pfizer, MSD, and Janssen; has received unrestricted research grants from Gilead, Abbott, Roche, and MSD; and has received travel grants from BMS, Boehringer Ingelheim, Gilead, MSD, and Janssen..
  10. Alexandra Calmy

    Division of Infectious Diseases, Geneva University Hospital, Geneva, Switzerland
    Competing interests
    No competing interests declared.
  11. Matthias Cavassini

    Service of Infectious Diseases, Department of Medicine, Lausanne University Hospital, Lausanne, Switzerland
    Competing interests
    No competing interests declared.
  12. Hansjakob Furrer

    Department of Infectious Diseases, University of Bern, Bern, Switzerland
    Competing interests
    Hansjakob Furrer, The institution of H.F. has received unrestricted grant support from ViiV, Gilead, Abbott, Janssen, Roche, Bristol-Myers Squibb (BMS), Merck Sharp & Dohme (MSD), and Boehringer Ingelheim..
    ORCID icon 0000-0002-1375-3146
  13. Matthias Hoffmann

    Division of Infectious Diseases, Cantonal Hospital St. Gallen, St. Gallen, Switzerland
    Competing interests
    No competing interests declared.
  14. Huldrych F Günthard

    Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, Zürich, Switzerland
    Competing interests
    Huldrych F Günthard, H.F.G. has been an adviser and/or consultant for GlaxoSmithKline, Abbott, Gilead, Novartis, Boehringer Ingelheim, Roche, Tibotec, Pfizer, and BMS and has received unrestricted research and educational grants from Roche, Abbott, BMS, Gilead, Astra-Zeneca, GlaxoSmithKline, and MSD (all money to the institution)..
  15. Roger D Kouyos

    Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
    For correspondence
    roger.kouyos@usz.ch
    Competing interests
    Roger D Kouyos, RDK has received speaker honoraria and travel grants from Gilead Sciences. None if these are in relation with the submitted manuscript..
    ORCID icon 0000-0002-9220-8348

Funding

Swiss National Science Foundation (33CS30-148522 and 159868)

  • Huldrych F Günthard

Swiss National Science Foundation (PZ00P3-142411)

  • Roger D Kouyos

Yvonne-Jacob Foundation

  • Huldrych F Günthard

University of Zurich's Clinical Research Priority Program's ZPHI

  • Huldrych F Günthard

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Ethics

Human subjects: The SHCS was approved by the ethics committees of the participating institutions (Kantonale Ethikkommission Bern, Ethikkommission des Kantons St. Gallen, Comite Departemental d'Ethique des Specialites Medicales et de Medicine Communataire et de Premier Recours, Kantonale Ethikkommission Zürich, Repubblica e Cantone Ticino-Comitato Ethico Cantonale, Commission Cantonale d'Étique de la Recherche sur l'Être Humain, Ethikkommission beiderBasel; all approvals are available on http://www.shcs.ch/206-ethic-committee-approval-and-informed-consent), and written informed consent was obtained from all participants.

Reviewing Editor

  1. Ryosuke Omori, Reviewing Editor

Publication history

  1. Received: May 17, 2017
  2. Accepted: August 28, 2017
  3. Accepted Manuscript published: September 12, 2017 (version 1)

Copyright

© 2017, Turk et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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