Dispersion of the HIV-1 Epidemic in Men Who Have Sex with Men in the Netherlands: A Combined Mathematical Model and Phylogenetic Analysis

Daniela Bezemer and colleagues investigate the extent to which the resurgent HIV epidemic in the Netherlands is the result of newly introduced strains, or of growth of already circulating strains.

Vyšlo v časopise: Dispersion of the HIV-1 Epidemic in Men Who Have Sex with Men in the Netherlands: A Combined Mathematical Model and Phylogenetic Analysis. PLoS Med 12(11): e32767. doi:10.1371/journal.pmed.1001898
Kategorie: Research Article
prolekare.web.journal.doi_sk: 10.1371/journal.pmed.1001898


Daniela Bezemer and colleagues investigate the extent to which the resurgent HIV epidemic in the Netherlands is the result of newly introduced strains, or of growth of already circulating strains.


1. Bezemer D, de Wolf F, Boerlijst MC, van Sighem A, Hollingsworth TD, et al. (2008) A resurgent HIV-1 epidemic among men who have sex with men in the era of potent antiretroviral therapy. AIDS 22: 1071–1077. doi: 10.1097/QAD.0b013e3282fd167c 18520351

2. Bezemer D, de Wolf F, Boerlijst MC, vanSighem A, Hollingsworth TD, et al. (2010) 27 years of the HIV epidemic amongst men having sex with men in the Netherlands: an in depth mathematical model-based analysis. Epidemics 2: 66–79. doi: 10.1016/j.epidem.2010.04.001 21352777

3. van Sighem A, Vidondo B, Glass TR, Bucher HC, Vernazza P, et al. (2012) Resurgence of HIV infection among men who have sex with men in Switzerland: mathematical modelling study. PLoS ONE 7: e44819. doi: 10.1371/journal.pone.0044819 23024766

4. Sullivan PS, Hamouda O, Delpech V, Geduld JE, Prejean J, et al. (2009) Reemergence of the HIV epidemic among men who have sex with men in North America, Western Europe, and Australia, 1996–2005. Ann Epidemiol 19: 423–431. doi: 10.1016/j.annepidem.2009.03.004 19460672

5. Phillips AN, Cambiano V, Nakagawa F, Brown AE, Lampe F, et al. (2013) Increased HIV incidence in men who have sex with men despite high levels of ART-induced viral suppression: analysis of an extensively documented epidemic. PLoS ONE 8: e55312. doi: 10.1371/journal.pone.0055312 23457467

6. van Sighem AI, Gras LA, Reiss P, Brinkman K, de Wolf F (2010) Life expectancy of recently diagnosed asymptomatic HIV-infected patients approaches that of uninfected individuals. AIDS 24: 1527–1535. doi: 10.1097/QAD.0b013e32833a3946 20467289

7. Attia S, Egger M, Muller M, Zwahlen M, Low N (2009) Sexual transmission of HIV according to viral load and antiretroviral therapy: systematic review and meta-analysis. AIDS 23: 1397–1404. doi: 10.1097/QAD.0b013e32832b7dca 19381076

8. Kelley CF, Haaland RE, Patel P, Evans-Strickfaden T, Farshy C, et al. (2011) HIV-1 RNA rectal shedding is reduced in men with low plasma HIV-1 RNA viral loads and is not enhanced by sexually transmitted bacterial infections of the rectum. J Infect Dis 204: 761–767. doi: 10.1093/infdis/jir400 21844302

9. Jansen IA, Geskus RB, Davidovich U, Jurriaans S, Coutinho RA, et al. (2011) Ongoing HIV-1 transmission among men who have sex with men in Amsterdam: a 25-year prospective cohort study. AIDS 25: 493–501. doi: 10.1097/QAD.0b013e328342fbe9 21192230

10. van Sighem A, Jansen I, Bezemer D, de Wolf F, Prins M, et al. (2012) Increasing sexual risk behaviour among Dutch men who have sex with men: mathematical models versus prospective cohort data. AIDS 26: 1840–1843. doi: 10.1097/QAD.0b013e3283574df9 22781219

11. Bezemer D, van Sighem AI, Lukashov V, van der Hoek L, Back N, et al. (2010) Transmission networks of HIV-1 among men having sex with men in the Netherlands. AIDS 24: 271–282. doi: 10.1097/QAD.0b013e328333ddee 20010072

12. Kouyos RD, von Wyl V, Yerly S, Boni J, Taffe P, et al. (2010) Molecular epidemiology reveals long-term changes in HIV type 1 subtype B transmission in Switzerland. J Infect Dis 201: 1488–1497. doi: 10.1086/651951 20384495

13. Stadler T, Kouyos R, von Wyl V, Yerly S, Boni J, et al. (2012) Estimating the basic reproductive number from viral sequence data. Mol Biol Evol 29: 347–357. doi: 10.1093/molbev/msr217 21890480

14. Leventhal GE, Gunthard HF, Bonhoeffer S, Stadler T (2014) Using an epidemiological model for phylogenetic inference reveals density dependence in HIV transmission. Mol Biol Evol 31: 6–17. doi: 10.1093/molbev/mst172 24085839

15. Wallinga J, Teunis P (2004) Different epidemic curves for severe acute respiratory syndrome reveal similar impacts of control measures. Am J Epidemiol 160: 509–516. doi: 10.1093/aje/kwh255 15353409

16. Gras L, van Sighem A, Smit C, Zaheri S, Prins M, de Wolf F Monitoring of human immunodeficiency virus (HIV) infection in the Netherlands. Amsterdam: Stichting HIV Monitoring; 2010. Available: http://www.hiv-monitoring.nl/files/9313/0164/8920/EN-HIVM-RPRT10-WEB.pdf. Accessed 6 October 2015.

17. Bezemer D, Jurriaans S, Prins M, van der Hoek L, Prins JM, et al. (2004) Declining trend in transmission of drug-resistant HIV-1 in Amsterdam. AIDS 18: 1571–1577. 15238775

18. Los Alamos National Laboratory (2015) HIV Se quence Database [database]. Available: http://www.hiv.lanl.gov/content/sequence/HIV/mainpage.html. Accessed 15 March 2013.

19. Kramer MA, Cornelissen M, Paraskevis D, Prins M, Coutinho RA, et al. (2011) HIV transmission patterns among The Netherlands, Suriname, and The Netherlands Antilles: a molecular epidemiological study. AIDS Res Hum Retroviruses 27: 123–130. doi: 10.1089/aid.2010.0115 20929384

20. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, et al. (2009) BLAST+: architecture and applications. BMC Bioinformatics 10: 421. doi: 10.1186/1471-2105-10-421 20003500

21. Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, et al. (2011) Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol 7: 539. doi: 10.1038/msb.2011.75 21988835

22. Castresana J (2000) Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 17: 540–552. 10742046

23. Johnson VA, Calvez V, Gunthard HF, Paredes R, Pillay D, et al. (2013) Update of the drug resistance mutations in HIV-1: March 2013. Top Antivir Med 21: 6–14. 23596273

24. Price MN, Dehal PS, Arkin AP (2010) FastTree 2—approximately maximum-likelihood trees for large alignments. PLoS ONE 5: e9490. doi: 10.1371/journal.pone.0009490 20224823

25. Prosperi MC, Ciccozzi M, Fanti I, Saladini F, Pecorari M, et al. (2011) A novel methodology for large-scale phylogeny partition. Nat Commun 2: 321. doi: 10.1038/ncomms1325 21610724

26. Drummond AJ, Suchard MA, Xie D, Rambaut A (2012) Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol 29: 1969–1973. doi: 10.1093/molbev/mss075 22367748

27. Drummond AJ, Ho SY, Phillips MJ, Rambaut A (2006) Relaxed phylogenetics and dating with confidence. PLoS Biol 4: e88. 16683862

28. Minin VN, Bloomquist EW, Suchard MA (2008) Smooth skyride through a rough skyline: Bayesian coalescent-based inference of population dynamics. Mol Biol Evol 25: 1459–1471. doi: 10.1093/molbev/msn090 18408232

29. Molecular Evolution, Phylogenetics and Epidemiology (2015) FigTree and Tracer [computer programs]. Availabe: http://tree.bio.ed.ac.uk/software. Accessed 25 September 2015.

30. Junqueira DM, de Medeiros RM, Matte MC, Araujo LA, Chies JA, et al. (2011) Reviewing the history of HIV-1: spread of subtype B in the Americas. PLoS ONE 6: e27489. doi: 10.1371/journal.pone.0027489 22132104

31. Cabello M, Junqueira DM, Bello G (2015) Dissemination of nonpandemic Caribbean HIV-1 subtype B clades in Latin America. AIDS 29: 483–492. doi: 10.1097/QAD.0000000000000552 25630042

32. Cabello M, Mendoza Y, Bello G (2014) Spatiotemporal dynamics of dissemination of non-pandemic HIV-1 subtype B clades in the Caribbean region. PLoS ONE 9: e106045. doi: 10.1371/journal.pone.0106045 25148215

33. Grassly NC, Fraser C (2008) Mathematical models of infectious disease transmission. Nat Rev Microbiol 6: 477–487. doi: 10.1038/nrmicro1845 18533288

34. Lewis F, Hughes GJ, Rambaut A, Pozniak A, Leigh Brown AJ (2008) Episodic sexual transmission of HIV revealed by molecular phylodynamics. PLoS Med 5: e50. doi: 10.1371/journal.pmed.0050050 18351795

35. Volz EM, Ionides E, Romero-Severson EO, Brandt MG, Mokotoff E, et al. (2013) HIV-1 transmission during early infection in men who have sex with men: a phylodynamic analysis. PLoS Med 10: e1001568. doi: 10.1371/journal.pmed.1001568 24339751

36. Powers KA, Ghani AC, Miller WC, Hoffman IF, Pettifor AE, et al. (2011) The role of acute and early HIV infection in the spread of HIV and implications for transmission prevention strategies in Lilongwe, Malawi: a modelling study. Lancet 378: 256–268. doi: 10.1016/S0140-6736(11)60842-8 21684591

37. Cohen MS, Dye C, Fraser C, Miller WC, Powers KA, et al. (2012) HIV treatment as prevention: debate and commentary—will early infection compromise treatment-as-prevention strategies? PLoS Med 9: e1001232. doi: 10.1371/journal.pmed.1001232 22802728

38. Op de Coul EL, Schreuder I, Conti S, van SA, Xiridou M, et al. (2015) Changing patterns of undiagnosed HIV infection in the Netherlands: who benefits most from intensified HIV test and treat policies? PLoS ONE 10: e0133232. doi: 10.1371/journal.pone.0133232 26185998

39. Parker J, Rambaut A, Pybus OG (2008) Correlating viral phenotypes with phylogeny: accounting for phylogenetic uncertainty. Infect Genet Evol 8: 239–246. 17921073

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