Assessing the danger of self-sustained HIV epidemics in heterosexuals by population based phylogenetic cluster analysis

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 determi...

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Bibliographic Details
Published in:eLife 2017-09, Vol.6
Main Authors: Turk, Teja, Bachmann, Nadine, Kadelka, Claus, Böni, Jürg, Yerly, Sabine, Aubert, Vincent, Klimkait, Thomas, Battegay, Manuel, Bernasconi, Enos, Calmy, Alexandra, Cavassini, Matthias, Furrer, Hansjakob, Hoffmann, Matthias, Günthard, Huldrych F, Kouyos, Roger D
Format: Article
Language:English
Subjects:
Analysis
Bacteria
Basic Reproduction Number
basic reproductive number
Case studies
Cluster Analysis
concentrated vs. generalised epidemic
Disease transmission
Disease Transmission, Infectious
Diseases
Epidemics
Epidemiology
Epidemiology and Global Health
Female
Genetic research
Health aspects
heterosexual
Heterosexuality
HIV
HIV Infections - epidemiology
HIV Infections - transmission
HIV Infections - virology
HIV tests
Human immunodeficiency virus
Humans
Infection
Male
Microbiology and Infectious Disease
Models, Statistical
Molecular Epidemiology
Phylogeny
Public health
Public health movements
Switzerland - epidemiology
transmission
Zoonoses
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Summary: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.
ISSN:2050-084X
2050-084X
DOI:10.7554/eLife.28721