HIV type 1 transmission networks among men having sex with men and heterosexuals in Kenya

AIDS Research and Human Retroviruses

Volumn 30, Issue 2, 2014, Pages 118-126

  Bezemer, Daniela ^a   Faria, Nuno Rodrigues ^b   Hassan, Amin ^c   Hamers, Raph L ^d   Mutua, Gaudensia ^e   Anzala, Omu ^e   Mandaliya, Kishor ^f   Cane, Patricia ^g   Berkley, James A ^c,h   De Wit, Tobias F Rinke ^d   Wallis, Carole ⁱ   Graham, Susan M ^c,j   Price, Matthew A ^k,l   Coutinho, Roel A ^m,n   Sanders, Eduard J ^c,h  

^a STICHTING HIV MONITORING   (Netherlands)

^b UNIVERSITY OF LEUVEN   (Belgium)

^c KENYA MEDICAL RESEARCH INSTITUTE   (Kenya)

^d ACADEMIC MEDICAL CENTER   (Netherlands)

^e UNIVERSITY OF NAIROBI   (Kenya)

^f Department of Obstetrics and Gynaecology   (Kenya)

^g PUBLIC HEALTH ENGLAND   (United Kingdom)

^h UNIVERSITY OF OXFORD   (United Kingdom)

ⁱ LANCET LABORATORIES   (South Africa)

^j UNIVERSITY OF WASHINGTON   (United States)

^k INTERNATIONAL AIDS VACCINE INITIATIVE   (United States)

^l UNIVERSITY OF CALIFORNIA   (United States)

^m NATIONAL INSTITUTE FOR PUBLIC HEALTH AND THE ENVIRONMENT   (Netherlands)

ⁿ UNIVERSITY MEDICAL CENTER UTRECHT   (Netherlands)

more..

Author keywords

[No Author keywords available]

Indexed keywords

PROTEINASE;

ADULT; ARTICLE; FEMALE; GENE SEQUENCE; HETEROSEXUALITY; HIGH RISK BEHAVIOR; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; KENYA; MAJOR CLINICAL STUDY; MALE; MEN WHO HAVE SEX WITH MEN; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; PROBABILITY; PROSPECTIVE STUDY; SEQUENCE ALIGNMENT; SEXUAL ORIENTATION; VIRUS TRANSMISSION; YOUNG ADULT;

ADOLESCENT; ADULT; CLUSTER ANALYSIS; DISEASE TRANSMISSION, INFECTIOUS; FEMALE; GENOTYPE; HETEROSEXUALITY; HIV INFECTIONS; HIV-1; HOMOSEXUALITY, MALE; HUMANS; KENYA; MALE; MIDDLE AGED; MOLECULAR EPIDEMIOLOGY; PHYLOGENY; POL GENE PRODUCTS, HUMAN IMMUNODEFICIENCY VIRUS; PROSPECTIVE STUDIES; SEQUENCE ANALYSIS, DNA; YOUNG ADULT;

EID: 84893464109     PISSN: 08892229     EISSN: 19318405     Source Type: Journal    
DOI: 10.1089/aid.2013.0171     Document Type: Article

References (48)

1. Beyrer C, Baral SD, Walker D, Wirtz AL, Johns B, and Sifakis F: The expanding epidemics of HIV type 1 among men who have sex with men in low-And middle-income countries: Diversity and consistency. Epidemiol Rev 2010;32(1):137-151.
2. Lewis F, Hughes GJ, Rambaut A, Pozniak A, and Leigh Brown AJ: Episodic sexual transmission of HIV revealed by molecular phylodynamics. PLoS Med 2008;18;5(3):e50.
3. Bezemer D, van Sighem AI, Lukashov V, et al.: Transmission networks of HIV-1 among men having sex with men in the Netherlands. AIDS 2010;24(2):271-282.
4. Holmes EC, Zhang LQ, Robertson P, et al.: The molecular epidemiology of human immunodeficiency virus type 1 in Edinburgh. J Infect Dis 1995;171(1):45-53.
5. Kouyos RD, von W, 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.
6. Tovanabutra S, Sanders EJ, Graham SM, et al.: Evaluation of HIV type 1 strains in men having sex with men and in female sex workers in Mombasa, Kenya. AIDS Res Hum Retroviruses 2010;26(2):123-131.
7. Sanders EJ, Graham SM, Okuku HS, et al.: HIV-1 infection in high risk men who have sex with men in Mombasa, Kenya. AIDS 2007;21(18):2513-2520.
8. Price MA, Rida W, Mwangome M, et al.: Identifying at-risk populations in Kenya and South Africa: HIV incidence in cohorts of men who report sex with men, sex workers, and youth. J Acquir Immune Defic Syndr 2012;59(2):185-193.
9. Sanders EJ, Okuku HS, Smith AD, et al.: High HIV-1 incidence, correlates of HIV-1 acquisition, and high viral loads following seroconversion among MSM. AIDS 2013;27(3): 437-446.
10. Mannava P, Geibel S, King'ola N, Temmerman M, and Luchters S: Male sex workers who sell sex to men also engage in anal intercourse with women: Evidence from Mombasa, Kenya. PLoS One 2013;8(1):e52547.
11. Resik S, Lemey P, Ping LH, et al.: Limitations to contact tracing and phylogenetic analysis in establishing HIV type 1 transmission networks in Cuba. AIDS Res Hum Retroviruses 2007;23(3):347-356.
12. Fisher M, Pao D, Brown AE, et al.: Determinants of HIV-1 transmission in men who have sex with men: A combined clinical, epidemiological and phylogenetic approach. AIDS 2010;24(11):1739-1747.
13. Gifford RJ, de OT, Rambaut A, et al.: Phylogenetic surveillance of viral genetic diversity and the evolving molecular epidemiology of human immunodeficiency virus type 1. J Virol 2007;81(23):13050-13056.
14. Hue S, Gifford RJ, Dunn D, Fernhill E, and Pillay D: Demonstration of sustained drug-resistant human immunodeficiency virus type 1 lineages circulating among treatment-naive individuals. J Virol 2009;83(6):2645-2654.
15. Hue S, Clewley JP, Cane PA, and Pillay D: HIV-1 pol gene variation is sufficient for reconstruction of transmissions in the era of antiretroviral therapy. AIDS 2004;18(5): 719-728.
16. Hue S, Pillay D, Clewley JP, and Pybus OG: Genetic analysis reveals the complex structure of HIV-1 transmission within defined risk groups. Proc Natl Acad Sci USA 2005;102(12): 4425-4429.
17. Bahl J, Nelson MI, Chan KH, et al.: Temporally structured metapopulation dynamics and persistence of influenza A H3N2 virus in humans. Proc Natl Acad Sci USA 2011; 108(48):19359-19364.
18. Faria NR, Hodges-Mameletzis I, Silva JC, et al.: The phylogeographic footprint of colonial history in the global dispersal of HIV-2 group A. J Gen Virol 2012;93:889-899.
19. Faria NR, Suchard MA, Abecasis A, et al.: Phylodynamics of the HIV-1 CRF02-AG clade in Cameroon. Infect Genet Evol 2012;12(2):453-460.
20. de Oliveira T., Pillay D, and Gifford RJ: The HIV-1 subtype C epidemic in South America is linked to the United Kingdom. PLoS One 2010;5(2):e9311.
21. Junqueira DM, de Medeiros RM, Matte MC, et al.: Reviewing the history of HIV-1: Spread of subtype B in the Americas. PLoS One 2011;6(11):e27489.
22. Gray RR, Tatem AJ, Lamers S, et al.: Spatial phylodynamics of HIV-1 epidemic emergence in east Africa. AIDS 2009; 23(14):F9-F17.
23. Worobey M, Gemmel M, Teuwen DE, et al.: Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960. Nature 2008;455(7213):661-664.
24. Price MA, Wallis CL, Lakhi S, et al.: Transmitted HIV type 1 drug resistance among individuals with recent HIV infection in East and Southern Africa. AIDS Res Hum Retroviruses 2011;27(1):5-12.
25. Hamers RL, Oyomopito R, Kityo C, et al.: Cohort profile: The PharmAccess African (PASER-M) and the TREAT Asia (TASER-M) monitoring studies to evaluate resistance-HIV drug resistance in sub-Saharan Africa and the Asia-Pacific. Int J Epidemiol 2012;41(1):43-54.
26. Hamers RL, Wallis CL, Kityo C, et al.: HIV-1 drug resistance in antiretroviral-naive individuals in sub-Saharan Africa after rollout of antiretroviral therapy: A multicentre observational study. Lancet Infect Dis 2011;11(10):750-759.
27. Hue S, Hassan AS, Nabwera H, et al.: HIV type 1 in a rural coastal town in Kenya shows multiple introductions with many subtypes and much recombination. AIDS Res Hum Retroviruses 2012;28(2):220-224.
28. Gouy M, Guindon S, and Gascuel O: SeaView version 4: A multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol Biol Evol 2010; 27(2):221-224.
29. Kosakovsky Pond SL, Posada D, Stawiski E, et al.: An evolutionary model-based algorithm for accurate phylogenetic breakpoint mapping and subtype prediction in HIV-1. PLoS Comput Biol 2009;5(11):e1000581.
30. Johnson VA, Brun-Vezinet F, Clotet B, et al.: Update of the drug resistance mutations in HIV-1: December 2010. Top HIV Med 2010;18(5):156-163.
31. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, and Kumar S: MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011;28(10): 2731-2739.
32. Felsenstein J: Confidence limits on phylogenies: An approach using the bootstrap. Evolution 1985;39:783-791.
33. Bezemer D, van Sighem A, de Wolf F, et al.: Combination antiretroviral therapy failure and HIV super-infection. AIDS 2008;22(2):309-311.
34. Drummond AJ, Suchard MA, Xie D, and Rambaut A: Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol 2012;29(8):1969-1973.
35. Drummond AJ, Ho SY, Phillips MJ, and Rambaut A: Relaxed phylogenetics and dating with confidence. PLoS Biol 2006;4(5):e88.
36. Drummond AJ, Rambaut A, Shapiro B, and Pybus OG: Bayesian coalescent inference of past population dynamics from molecular sequences. Mol Biol Evol 2005;22(5):1185-1192.
37. Abecasis AB, Vandamme AM, and Lemey P: Quantifying differences in the tempo of human immunodeficiency virus type 1 subtype evolution. J Virol 2009;83(24):12917-12924.
38. FigTree and Tracer: Http://tree.bio.ed.ac.uk/software, 2012.
39. Parker J, Rambaut A, and Pybus OG: Correlating viral phenotypes with phylogeny: Accounting for phylogenetic uncertainty. Infect Genet Evol 2008;8(3):239-246.
40. Lemey P, Rambaut A, Drummond AJ, and Suchard MA: Bayesian phylogeography finds its roots. PLoS Comput Biol 2009;5(9):e1000520.
41. Faria NR, Suchard MA, Rambaut A, and Lemey P: Toward a quantitative understanding of viral phylogeography. Curr Opin Virol 2011;1(5):423-429.
42. O'Brien JD, Minin VN, and Suchard MA: Learning to count: Robust estimates for labeled distances between molecular sequences. Mol Biol Evol 2009;26(4):801-814.
43. Minin VN and Suchard MA: Counting labeled transitions in continuous-Time Markov models of evolution. J Math Biol 2008;56(3):391-412.
44. Skar H, Axelsson M, Berggren I, et al.: Dynamics of two separate but linked HIV-1 CRF01-AE outbreaks among injection drug users in Stockholm, Sweden, and Helsinki, Finland. J Virol 2011;85(1):510-518.
45. Sanders EJ, Thiong'o AN, Okuku HS, et al.: High prevalence of Chlamydia trachomatis and Neisseria gonorrhoeae infections among HIV-1 negative men who have sex with men in coastal Kenya. Sex Transm Infect 2010;86(6):440-441.
46. Kramer MA, Cornelissen M, Paraskevis D, et al.: HIV transmission patterns among The Netherlands, Suriname, and The Netherlands Antilles: A molecular epidemiological study. AIDS Res Hum Retroviruses 2011;27(2):123-130.
47. Geibel S, Luchters S, King'ola N, Esu-Williams E, Rinyiru A, and Tun W: Factors associated with self-reported unprotected anal sex among male sex workers in Mombasa, Kenya. Sex Transmitt Dis 2008;35(8):746-752.
48. UNAIDS: 2011 Report on the global AIDS epidemic. www.unaids.org/en/, 2011.