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Social Meets Molecular: Combining Phylogenetic and Latent Class Analyses to Understand HIV-1 Transmission in Switzerland


Avila, Dorita; Keiser, Olivia; Egger, Matthias; Kouyos, Roger; Böni, Juerg; Yerly, Sabine; Klimkait, Thomas; Vernazza, Pietro L; Aubert, Vincent; Rauch, Andri; Bonhoeffer, Sebastian; Guenthard, Huldrych F; Stadler, Tanja; Spycher, Ben D (2014). Social Meets Molecular: Combining Phylogenetic and Latent Class Analyses to Understand HIV-1 Transmission in Switzerland. American Journal of Epidemiology, 179(12):1514-1525.

Abstract

Switzerland has a complex human immunodeficiency virus (HIV) epidemic involving several populations. We examined transmission of HIV type 1 (HIV-1) in a national cohort study. Latent class analysis was used to identify
socioeconomic and behavioral groups among 6,027 patients enrolled in the Swiss HIV Cohort Study between 2000 and 2011. Phylogenetic analysis of sequence data, available for 4,013 patients, was used to identify transmission clusters. Concordance between sociobehavioral groups and transmission clusters was assessed in correlation and multiple correspondence analyses. A total of 2,696 patients were infected with subtype B, 203 with subtype C, 196 with subtype A, and 733 with recombinant subtypes (mainly CRF02_AG and CRF01_AE). Latent class analysis identified 8 patient groups. Most transmission clusters of subtype B were shared between groups of gay men(groups 1–3) or between the heterosexual groups “heterosexual people of lower socioeconomic position”(group 4) and “injection drug users” (group 8). Clusters linking homosexual and heterosexual groups were associated with “older heterosexual and gay people on welfare” (group 5). “Migrant women in heterosexual partnerships” (group 6)and “heterosexual migrants on welfare” (group 7) shared non-B clusters with groups 4 and 5. Combining approaches from social and molecular epidemiology can provide insights into HIV-1 transmission and inform the design of prevention strategies.

Abstract

Switzerland has a complex human immunodeficiency virus (HIV) epidemic involving several populations. We examined transmission of HIV type 1 (HIV-1) in a national cohort study. Latent class analysis was used to identify
socioeconomic and behavioral groups among 6,027 patients enrolled in the Swiss HIV Cohort Study between 2000 and 2011. Phylogenetic analysis of sequence data, available for 4,013 patients, was used to identify transmission clusters. Concordance between sociobehavioral groups and transmission clusters was assessed in correlation and multiple correspondence analyses. A total of 2,696 patients were infected with subtype B, 203 with subtype C, 196 with subtype A, and 733 with recombinant subtypes (mainly CRF02_AG and CRF01_AE). Latent class analysis identified 8 patient groups. Most transmission clusters of subtype B were shared between groups of gay men(groups 1–3) or between the heterosexual groups “heterosexual people of lower socioeconomic position”(group 4) and “injection drug users” (group 8). Clusters linking homosexual and heterosexual groups were associated with “older heterosexual and gay people on welfare” (group 5). “Migrant women in heterosexual partnerships” (group 6)and “heterosexual migrants on welfare” (group 7) shared non-B clusters with groups 4 and 5. Combining approaches from social and molecular epidemiology can provide insights into HIV-1 transmission and inform the design of prevention strategies.

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Item Type:Journal Article, refereed, original work
Communities & Collections:04 Faculty of Medicine > Institute of Medical Virology
04 Faculty of Medicine > University Hospital Zurich > Clinic for Infectious Diseases
Dewey Decimal Classification:570 Life sciences; biology
610 Medicine & health
Uncontrolled Keywords:HIV;HIV-1 transmission; injectiondruguse; latentclassanalysis;phylogenetics;sexualorientation; socioeconomic position; Switzerland
Language:English
Date:11 March 2014
Deposited On:20 Nov 2014 12:21
Last Modified:05 Apr 2016 18:31
Publisher:Oxford University Press
ISSN:0002-9262
Funders:Swiss HIV Cohort Study (SHCS), Swiss National Science Foundation (grants 33CS30-134277, 33CS30- 148522, and PZ00P3-136820 to T.S., grant 324730-130865 to H.F.G., and SHCS projects 470, 528, 569, and 687), SHCS Research Foundation, European Community ’ s Seventh Framework Program (grant FP7/2007 – 2013), Collaborative HIV and Anti-HIV Drug Resistance Network (grant 223131 to H.F.G., Yvonne-Jacob Foundation (grant A/B1113 to H.F.G.), Anonymous research grant from the Union Bankof Switzerland (grant DRDB8910 to H.F.G., Research grant to the SHCS Research Foundation from Gilead Sciences Switzerland Sàrl (Zug, Switzerland, University of Zurich ’ s Clinical Research Priority Program: Viral Infectious Diseases — ZPHI Study, O.K., R.K., and B.D.S. were supported by Swiss National Science Foundation fellowships (grants 32333B_131629/1, PZ00P3_142411, PZ00P3_ 147987/1, and PZ00P3_136820, respectively
Additional Information:This is a pre-copy-editing, author-produced PDF of an article accepted for publication in American Journal of Epidemiology following peer review. The definitive publisher-authenticated version is available online at: DOI : 10.1093/aje/kwu076
Free access at:Publisher DOI. An embargo period may apply.
Publisher DOI:https://doi.org/10.1093/aje/kwu076
PubMed ID:24821749

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