Social meets molecular: Combining phylogenetic and latent class analyses to understand HIV-1 transmission in Switzerland

American Journal of Epidemiology

Volumn 179, Issue 12, 2014, Pages 1514-1525

  Avila, Dorita ^a,b   Keiser, Olivia ^a   Egger, Matthias ^a,c   Kouyos, Roger ^j   Böni, Jürg ^d   Yerly, Sabine ^e   Klimkait, Thomas ^f   Vernazza, Pietro L ^g   Aubert, Vincent ^h   Rauch, Andri ⁱ   Bonhoeffer, Sebastian ^b   Günthard, Huldrych F ^j   Stadler, Tanja ^b   Spycher, Ben D ^a   Aubert, V ^k   Barth, J ^k   Battegay, M ^k   Bernasconi, E ^k   Boni J ^k   Bucher, H C ^k   Burton Jeangros, C ^k   Calmy, A ^k   Cavassini, M ^k   Egger, M ^k   Elzi, L ^k   Fehr, J ^k   Fellay, J ^k   Furrer, H ^k   Fux, C A ^k   Gorgievski, M ^k   Gunthard H ^k   Haerry, D ^k   Hasse, B ^k   Hirsch, H H ^k   Hosli I ^k   Kahlert, C ^k   Kaiser, L ^k   Keiser, O ^k   Klimkait, T ^k   Kouyos, R ^k   Kovari, H ^k   Ledergerber, B ^k   Martinetti, G ^k   Martinez De Tejada, B ^k   Metzner, K ^k   Muller N ^k   Nadal, D ^k   Pantaleo, G ^k   Regenass, S ^k   Rickenbach, M ^k   Rudin, C ^k   Schoni Affolter F ^k   Schmid, P ^k   Schultze, D ^k   Schupbach J ^k   Speck, R ^k   Staehelin, C ^k   Tarr, P ^k   Telenti, A ^k   Trkola, A ^k   Vernazza, P ^k   Weber, R ^k   Yerly, S ^k   more..

^a UNIVERSITY OF BERN   (Switzerland)

^b ETH ZURICH   (Switzerland)

^c UNIVERSITY OF CAPE TOWN   (South Africa)

^d UNIVERSITY OF ZURICH   (Switzerland)

^e GENEVA UNIVERSITY HOSPITALS   (Switzerland)

^f UNIVERSITY OF BASEL   (Switzerland)

^g CANTONAL HOSPITAL ST GALLEN   (Switzerland)

^h LAUSANNE UNIVERSITY HOSPITAL   (Switzerland)

ⁱ UNIVERSITY OF BERN   (Switzerland)

^j UNIVERSITY HOSPITAL ZURICH   (Switzerland)

^k NONE

more..

Author keywords

HIV; HIV 1 transmission; injection drug use; latent class analysis; phylogenetics; sexual orientation; socioeconomic position; Switzerland

Indexed keywords

POL PROTEIN;

COHORT ANALYSIS; DISEASE TRANSMISSION; EPIDEMIOLOGY; HUMAN IMMUNODEFICIENCY VIRUS; MOLECULAR ANALYSIS; PHYLOGENETICS; SPATIOTEMPORAL ANALYSIS;

ADULT; ARTICLE; DISEASE TRANSMISSION; FEMALE; HETEROSEXUALITY; HOMOSEXUAL MALE; HOMOSEXUALITY; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS 1 INFECTION; INTRAVENOUS DRUG ABUSE; MAJOR CLINICAL STUDY; MALE; MIGRANT; MOLECULAR EPIDEMIOLOGY; PHYLOGENY; SOCIAL BEHAVIOR; SOCIAL STATUS; SWITZERLAND; UNPROTECTED SEX; VIRUS TRANSMISSION;

SWITZERLAND;

HUMAN IMMUNODEFICIENCY VIRUS; HUMAN IMMUNODEFICIENCY VIRUS 1;

HIV; HIV-1 TRANSMISSION; INJECTION DRUG USE; LATENT CLASS ANALYSIS; PHYLOGENETICS; SEXUAL ORIENTATION; SOCIOECONOMIC POSITION; SWITZERLAND;

ADULT; FEMALE; HETEROSEXUALITY; HIV INFECTIONS; HIV-1; HOMOSEXUALITY; HUMANS; MALE; MIDDLE AGED; PHYLOGENY; SOCIAL BEHAVIOR; SOCIOLOGY, MEDICAL; SWITZERLAND;

EID: 84902491302     PISSN: 00029262     EISSN: 14766256     Source Type: Journal    
DOI: 10.1093/aje/kwu076     Document Type: Article

References (26)

1. Joint United Nations Programme on HIV/AIDS. Global Report: UNAIDS Report on the Global AIDS Epidemic 2010. Geneva, Switzerland: Joint United Nations Programme on HIV/ AIDS; 2010.
2. van Sighem A, Vidondo B, Glass TR, et al. Resurgence of HIV infection among men who have sex with men in Switzerland: mathematical modelling study. PLoS One. 2012; 7(9):e44819.
3. Yerly S, von Wyl V, Ledergerber B, et al. Transmission of HIV-1 drug resistance in Switzerland: a 10-year molecular epidemiology survey. AIDS. 2007;21(16): 2223-2229.
4. von Wyl V, Kouyos RD, Yerly S, et al. The role of migration and domestic transmission in the spread of HIV-1 non-B subtypes in Switzerland. J Infect Dis. 2011;204(7): 1095-1103.
5. Leventhal GE, Kouyos R, Stadler T, et al. Inferring epidemic contact structure from phylogenetic trees. PLoS Comput Biol. 2012;8(3):e1002413.
6. Hue S, Pillay D, Clewley JP, et al. Genetic analysis reveals the complex structure of HIV-1 transmission within defined risk groups. Proc Natl Acad Sci U S A. 2005;102(12): 4425-4429.
7. Schoeni-Affolter F, Ledergerber B, Rickenbach M, et al. Cohort profile: the Swiss HIV Cohort Study. Int J Epidemiol. 2010; 39(5): 1179-1189.
8. Kouyos RD, von Wyl V, Yerly S, et al. Molecular epidemiology reveals long-term changes in HIV type 1 subtype B transmission in Switzerland. J Infect Dis. 2010;201(10): 1488-1497.
9. Lazarsfeld PF, Henry NW. Latent Structure Analysis. Boston, MA: Houghton Mifflin Company; 1968.
10. Keiser O, Spycher B, Rauch A, et al. Outcomes of antiretroviral therapy in the Swiss HIV Cohort Study: latent class analysis. AIDS Behav. 2012;16(2): 245-255.
11. Gebhardt M, Rickenbach M, Egger M. Impact of antiretroviral combination therapies on AIDS surveillance reports in Switzerland. Swiss HIV Cohort Study. AIDS. 1998;12(10): 1195-1201.
12. McLachlan G, Peel D. Finite Mixture Models. New York, NY: John Wiley & Sons, Inc.; 2000.
13. World Health Organization. Comparative Quantification of Health Risks - Global and Regional Burden of Disease Attribution to Selected Major Risk Factors. Geneva, Switzerland: World Health Organization; 2004.
14. Muthén BO, Muthén LK. Mplus. Los Angeles, CA: Muthén & Muthén; 1998.
15. von Wyl V, Yerly S, Böni J, et al. Emergence of HIV-1 drug resistance in previously untreated patients initiating combination antiretroviral treatment: a comparison of different regimen types. Arch Intern Med. 2007;167(16): 1782-1790.
16. Yerly S, Vora S, Rizzardi P, et al. Acute HIV infection: impact on the spread of HIV and transmission of drug resistance. AIDS. 2001;15(17): 2287-2292.
17. Los Alamos National Laboratory. HIV Databases. Los Alamos, NM: Los Alamos National Laboratory; 2011. (http://www.hiv. lanl.gov/). (Accessed November 3, 2011).
18. Hirsch MS, Günthard HF, Schapiro JM, et al. Antiretroviral drug resistance testing in adult HIV-1 infection: 2008 recommendations of an International AIDS Society-USA panel. Clin Infect Dis. 2008;47(2): 266-285.
19. Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics. 2006;22(21): 2688-2690.
20. R Core Team. R: A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing; 2012.
21. Greenacre M. Theory and Applications of Correspondence Analysis. London, United Kingdom: Academic Press Ltd.; 1984.
22. Johnson AM, Mercer CH, Erens B, et al. Sexual behaviour in Britain: partnerships, practices, and HIV risk behaviours. Lancet. 2001;358(9296): 1835-1842.
23. Wang J, Häusermann M, Wydler H, et al. Suicidality and sexual orientation among men in Switzerland: findings from 3 probability surveys. J Psychiatr Res. 2012;46(8): 980-986.
24. Sankar A, Nevedal A, Neufeld S, et al. What do we know about older adults and HIV? A review of social and behavioral literature. AIDS Care. 2011;23(10): 1187-1207.
25. Slater LZ, Moneyham L, Vance DE, et al. Support, stigma, health, coping, and quality of life in older gay men with HIV. J Assoc Nurses AIDS Care. 2013;24(1): 38-49.
26. Valdiserri RO. HIV/AIDS stigma: an impediment to public health. Am J Public Health. 2002;92(3): 341-342.