Evolutionary History of HIV-1 Subtype B and CRF01_AE Transmission Clusters among Men Who Have Sex with Men (MSM) in Kuala Lumpur, Malaysia

PLoS ONE

Volumn 8, Issue 6, 2013, Pages

  Ng, Kim Tien ^a   Ong, Lai Yee ^a   Lim, Sin How ^a   Takebe, Yutaka ^a,b   Kamarulzaman, Adeeba ^a   Tee, Kok Keng ^a  

^a UNIVERSITY OF MALAYA   (Malaysia)

^b NATIONAL INSTITUTE OF INFECTIOUS DISEASES   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

NONNUCLEOSIDE REVERSE TRANSCRIPTASE INHIBITOR; PROTEINASE INHIBITOR; RNA DIRECTED DNA POLYMERASE INHIBITOR;

ANTIBIOTIC RESISTANCE; ARTICLE; BAYES THEOREM; CLUSTER ANALYSIS; EVOLUTION; GENE; GENE MUTATION; GENOTYPE; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS 1 B; HUMAN IMMUNODEFICIENCY VIRUS 1 CRF01 AE; HUMAN IMMUNODEFICIENCY VIRUS 1 INFECTION; MALE; MEN WHO HAVE SEX WITH MEN; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; POPULATION GROWTH; POPULATION SIZE; PRO RT GENE; RISK ASSESSMENT; UNINDEXED SEQUENCE; VIRUS TRANSMISSION;

BAYES THEOREM; CLUSTER ANALYSIS; EVOLUTION, MOLECULAR; GENOTYPE; HIV INFECTIONS; HIV-1; HOMOSEXUALITY, MALE; HUMANS; LIKELIHOOD FUNCTIONS; MALAYSIA; MALE; MODELS, GENETIC; PHYLOGENY;

HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 84879256201     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0067286     Document Type: Article

References (39)

1. Malim MH, Emerman M, (2001) HIV-1 sequence variation: drift, shift, and attenuation. Cell 104: 469-472.
2. Beyrer C, Baral SD, van Griensven F, Goodreau SM, Chariyalertsak S, et al. (2012) Global epidemiology of HIV infection in men who have sex with men. Lancet 380: 367-377.
3. Baral S, Sifakis F, Cleghorn F, Beyrer C, (2007) Elevated risk for HIV infection among men who have sex with men in low- and middle-income countries 2000-2006: a systematic review. PLoS Med 4: e339.
4. Ananworanich J, Phanuphak N, de Souza M, Paris R, Arroyo M, et al. (2008) Incidence and characterization of acute HIV-1 infection in a high-risk Thai population. J Acquir Immune Defic Syndr 49: 151-155.
5. Kanter J, Koh C, Razali K, Tai R, Izenberg J, et al. (2011) Risk behaviour and HIV prevalence among men who have sex with men in a multiethnic society: a venue-based study in Kuala Lumpur, Malaysia. Int J STD AIDS 22: 30-37.
6. Nguyen TA, Nguyen HT, Le GT, Detels R, (2008) Prevalence and risk factors associated with HIV infection among men having sex with men in Ho Chi Minh City, Vietnam. AIDS Behav 12: 476-482.
7. Tee KK, Li XJ, Nohtomi K, Ng KP, Kamarulzaman A, et al. (2006) Identification of a novel circulating recombinant form (CRF33_01B) disseminating widely among various risk populations in Kuala Lumpur, Malaysia. J Acquir Immune Defic Syndr 43: 523-529.
8. Cohen MS, Chen YQ, McCauley M, Gamble T, Hosseinipour MC, et al. (2011) Prevention of HIV-1 infection with early antiretroviral therapy. N Engl J Med 365: 493-505.
9. Granich RM, Gilks CF, Dye C, De Cock KM, Williams BG, (2009) Universal voluntary HIV testing with immediate antiretroviral therapy as a strategy for elimination of HIV transmission: a mathematical model. Lancet 373: 48-57.
10. Li J, Lu JF, Dong HH, Bao ZY, Liu SY, et al. (2006) Phenotypic resistance of resistant strains of HIV type-1 subtype B in China. Chin Med J (Engl) 119: 1972-1977.
11. Tee KK, Kamarulzaman A, Ng KP, (2006) Short communication: low prevalence of genotypic drug resistance mutations among antiretroviral-naive HIV type 1 patients in Malaysia. AIDS Res Hum Retroviruses 22: 121-124.
12. Wang YM, Dyer WB, Workman C, Wang B, Sullivan JS, et al. (2000) Molecular evidence for drug-induced compartmentalization of HIV-1 quasispecies in a patient with periodic changes to HAART. AIDS 14: 2265-2272.
13. Bennett DE, Camacho RJ, Otelea D, Kuritzkes DR, Fleury H, et al. (2009) Drug resistance mutations for surveillance of transmitted HIV-1 drug-resistance: 2009 update. PLoS One 4: e4724.
14. Saitou N, Nei M, (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4: 406-425.
15. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, et al. (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28: 2731-2739.
16. Swofford DL (2003) PAUP*: Phylogenetic analysis using parsimony (*and other methods), version 4 beta. Sinauer Associates, Sunderland, MA.
17. Drummond AJ, Rambaut A, (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 7: 214.
18. Aldous JL, Pond SK, Poon A, Jain S, Qin H, et al. (2012) Characterizing HIV transmission networks across the United States. Clin Infect Dis 55: 1135-1143.
19. Chalmet K, Staelens D, Blot S, Dinakis S, Pelgrom J, et al. (2010) Epidemiological study of phylogenetic transmission clusters in a local HIV-1 epidemic reveals distinct differences between subtype B and non-B infections. BMC Infect Dis 10: 262.
20. Zehender G, Ebranati E, Lai A, Santoro MM, Alteri C, et al. (2010) Population dynamics of HIV-1 subtype B in a cohort of men-having-sex-with-men in Rome, Italy. J Acquir Immune Defic Syndr 55: 156-160.
21. Drummond AJ, Ho SY, Phillips MJ, Rambaut A, (2006) Relaxed phylogenetics and dating with confidence. PLoS Biol 4: e88.
22. Rodriguez F, Oliver JL, Marin A, Medina JR, (1990) The general stochastic model of nucleotide substitution. J Theor Biol 142: 485-501.
23. Yang Z, (1994) Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J Mol Evol 39: 306-314.
24. Suchard MA, Weiss RE, Sinsheimer JS, (2001) Bayesian selection of continuous-time Markov chain evolutionary models. Mol Biol Evol 18: 1001-1013.
25. Drummond AJ, Nicholls GK, Rodrigo AG, Solomon W, (2002) Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data. Genetics 161: 1307-1320.
26. Deng X, Liu H, Shao Y, Rayner S, Yang R, (2008) The epidemic origin and molecular properties of B': a founder strain of the HIV-1 transmission in Asia. AIDS 22: 1851-1858.
27. Li Z, He X, Wang Z, Xing H, Li F, et al. (2012) Tracing the origin and history of HIV-1 subtype B' epidemic by near full-length genome analyses. AIDS 26: 877-884.
28. Hue S, Pillay D, Clewley JP, Pybus OG, (2005) Genetic analysis reveals the complex structure of HIV-1 transmission within defined risk groups. Proc Natl Acad Sci U S A 102: 4425-4429.
29. Li Y, Uenishi R, Hase S, Liao H, Li XJ, et al. (2010) Explosive HIV-1 subtype B' epidemics in Asia driven by geographic and risk group founder events. Virology 402: 223-227.
30. Brenner BG, Roger M, Moisi DD, Oliveira M, Hardy I, et al. (2008) Transmission networks of drug resistance acquired in primary/early stage HIV infection. AIDS 22: 2509-2515.
31. 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.
32. Smith DM, May SJ, Tweeten S, Drumright L, Pacold ME, et al. (2009) A public health model for the molecular surveillance of HIV transmission in San Diego, California. AIDS 23: 225-232.
33. Giuliani M, Di Carlo A, Palamara G, Dorrucci M, Latini A, et al. (2005) Increased HIV incidence among men who have sex with men in Rome. AIDS 19: 1429-1431.
34. 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.
35. Brenner BG, Roger M, Stephens D, Moisi D, Hardy I, et al. (2011) Transmission clustering drives the onward spread of the HIV epidemic among men who have sex with men in Quebec. J Infect Dis 204: 1115-1119.
36. Ng OT, Munshaw S, Lamers SL, Chew KK, Lin L, et al. (2011) Molecular epidemiology of HIV type 1 in Singapore and identification of novel CRF01_AE/B recombinant forms. AIDS Res Hum Retroviruses 27: 1135-1137.
37. Baral S, Burrell E, Scheibe A, Brown B, Beyrer C, et al. (2011) HIV risk and associations of HIV infection among men who have sex with men in peri-urban Cape Town, South Africa. BMC Public Health 11: 766.
38. Fay H, Baral SD, Trapence G, Motimedi F, Umar E, et al. (2011) Stigma, health care access, and HIV knowledge among men who have sex with men in Malawi, Namibia, and Botswana. AIDS Behav 15: 1088-1097.
39. Poteat T, Diouf D, Drame FM, Ndaw M, Traore C, et al. (2011) HIV risk among MSM in Senegal: a qualitative rapid assessment of the impact of enforcing laws that criminalize same sex practices. PLoS One 6: e28760.