Targeting HIV prevention based on molecular epidemiology among deeply sampled subnetworks of men who have sex with men

Clinical Infectious Diseases

Volumn 61, Issue 9, 2015, Pages 1462-1468

  Wang, Xicheng ^a   Wu, Yasong ^b   Mao, Lin ^a   Xia, Wei ^c   Zhang, Weiwei ^b   Dai, Lili ^c   Mehta, Sanjay R ^d,e   Wertheim, Joel O ^d   Dong, Xingqi ^a   Zhang, Tong ^c   Wu, Hao ^c   Smith, Davey M ^d,e  

^a Yunnan Provincial Hospital Infectious Disease   (China)

^b CHINESE CENTER FOR DISEASE CONTROL AND PREVENTION   (China)

^c CAPITAL MEDICAL UNIVERSITY   (China)

^d UNIVERSITY OF CALIFORNIA   (United States)

^e VA SAN DIEGO HEALTHCARE SYSTEM   (United States)

Author keywords

China; HIV; molecular epidemiology; MSM; targeted prevention

Indexed keywords

ANTI HUMAN IMMUNODEFICIENCY VIRUS AGENT; POL PROTEIN;

ADULT; AGED; ARTICLE; CD4 LYMPHOCYTE COUNT; COHORT ANALYSIS; ENZYME LINKED IMMUNOSORBENT ASSAY; GENETIC DISTANCE; HIV TEST; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 SUBTYPE B; HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 SUBTYPE C; INFECTION PREVENTION; MAJOR CLINICAL STUDY; MALE; MEN WHO HAVE SEX WITH MEN; MOLECULAR EPIDEMIOLOGY; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; VIRUS LOAD; VIRUS MUTATION; VIRUS RESISTANCE; VIRUS TRANSMISSION; CHINA; CLASSIFICATION; CLUSTER ANALYSIS; COMMUNICABLE DISEASE CONTROL; DISEASE TRANSMISSION; DNA SEQUENCE; GENETICS; GENOTYPE; HIV INFECTIONS; HUMAN IMMUNODEFICIENCY VIRUS 1; ISOLATION AND PURIFICATION; MALE HOMOSEXUALITY; MIDDLE AGED; PREVENTION AND CONTROL; PROCEDURES; TRANSMISSION; VIROLOGY; YOUNG ADULT;

ADULT; AGED; CHINA; CLUSTER ANALYSIS; COHORT STUDIES; COMMUNICABLE DISEASE CONTROL; DISEASE TRANSMISSION, INFECTIOUS; GENOTYPE; HIV INFECTIONS; HIV-1; HOMOSEXUALITY, MALE; HUMANS; MALE; MIDDLE AGED; MOLECULAR EPIDEMIOLOGY; POL GENE PRODUCTS, HUMAN IMMUNODEFICIENCY VIRUS; SEQUENCE ANALYSIS, DNA; YOUNG ADULT;

EID: 84946724557     PISSN: 10584838     EISSN: 15376591     Source Type: Journal    
DOI: 10.1093/cid/civ526     Document Type: Article

References (40)

1. Estimates for the HIV/AIDS Epidemic in China. In: Ministry of Health PsRoC. Beijing, China: Joint United Nations Programme on HIV/AIDS, World Health Organization, 2011.
2. Dai L, Li N, Wei F, et al. Transmitted antiretroviral drug resistance in the men who have sex with men HIV patient cohort, Beijing, China, 2008-2011. Viral Immunol 2014; 27:392-7.
3. Little SJ, Kosakovsky Pond SL, Anderson CM, et al. Using HIV networks to inform real time prevention interventions. PLoS ONE 2014; 9:e98443.
4. Wertheim JO, Leigh Brown AJ, Hepler NL, et al. The global transmission network of HIV-1. J Infect Dis 2014; 209:304-13.
5. Smith DM, May SJ, Tweeten S, et al. A public health model for the molecular surveillance of HIV transmission in San Diego, California. AIDS 2009; 23:225-32.
6. Aldous JL, Pond SK, Poon A, et al. Characterizing HIV transmission networks across the United States. Clin Infect Dis 2012; 55:1135-43.
7. Huang X, Chen H, Li W, et al. Precise determination of time to reach viral load set point after acute HIV-1 infection. J Acquir Immune Defic Syndr 2012; 61:448-54.
8. Yang C, Liu S, Zhang T, et al. Transmitted antiretroviral drug resistance and thumb subdomain polymorphisms among newly HIV type 1 diagnosed patients infected with CRF01-AE and CRF07-BC virus in Guangdong Province, China. AIDS Res Hum Retroviruses 2012; 28:1723-8.
9. Gifford RJ, Liu TF, Rhee SY, et al. The calibrated population resistance tool: standardized genotypic estimation of transmitted HIV-1 drug resistance. Bioinformatics 2009; 25:1197-8.
10. Rose PP, Korber BT. Detecting hypermutations in viral sequences with an emphasis on G-A hypermutation. Bioinformatics 2000; 16:400-1.
11. 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:e1000581.
12. Kosakovsky Pond SL, Frost SDW, Muse SV. HyPhy: hypothesis testing using phylogenies. Bioinformatics 2005; 21:676-9.
13. Tamura K, Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial-Dna in humans and chimpanzees. Mol Biol Evol 1993; 10:512-26.
14. Hightower GK, May SJ, Perez-Santiago J, et al. HIV-1 clade B pol evolution following primary infection. PLoS One 2013; 8:e68188.
15. Frost SD, Volz EM. Viral phylodynamics and the search for an ?effective number of infections?. Philos Trans R Soc Lond B Biol Sci 2010; 365:1879-90.
16. Volz EM, Koelle K, Bedford T. Viral phylodynamics. PLoS Comput Biol 2013; 9:e1002947.
17. Guindon S, Dufayard JF, Lefort V, Anisimova M, HordijkW, Gascuel O. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 2010; 59:307-21.
18. Gouy M, Guindon S, Gascuel O. SeaView version 4: A multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol Biol Evol 2010; 27:221-4.
19. Drummond AJ, Suchard MA, Xie D, Rambaut A. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol 2012; 29:1969-73.
20. Wertheim JO, Fourment M, Kosakovsky Pond SL. Inconsistencies in estimating the age of HIV-1 subtypes due to heterotachy. Mol Biol Evol 2012; 29:451-6.
21. Su Y, Zhang F, Liu H, et al. The prevalence of HIV-1 drug resistance among antiretroviral treatment naive individuals in mainland China: a meta-Analysis. PLoS One 2014; 9:e110652.
22. Vergne L, Stuyver L, Van Houtte M, Butel C, Delaporte E, Peeters M. Natural polymorphism in protease and reverse transcriptase genes and in vitro antiretroviral drug susceptibilities of non-B HIV-1 strains from treatment-naive patients. J Clin Virol 2006; 36:43-9.
23. Leigh Brown AJ, Lycett SJ, Weinert L, Hughes GJ, Fearnhill E, Dunn DT. Transmission network parameters estimated from HIV sequences for a nationwide epidemic. J Infect Dis 2011; 204:1463-9.
24. Schneeberger A, Mercer CH, Gregson SA, et al. Scale-free networks and sexually transmitted diseases: a description of observed patterns of sexual contacts in Britain and Zimbabwe. Sex Transm Dis 2004; 31:380-7.
25. Granich RM, Gilks CF, Dye C, De Cock KM, Williams BG. Universal voluntary HIV testing with immediate antiretroviral therapy as a strategy for elimination of HIV transmission: a mathematical model. Lancet 2009; 373:48-57.
26. Quinn TC, Wawer MJ, Sewankambo N, et al. Viral load and heterosexual transmission of human immunodeficiency virus type 1. Rakai Project Study Group. N Engl J Med 2000; 342:921-9.
27. Cohen MS, Chen YQ, McCauley M, et al. Prevention of HIV-1 infection with early antiretroviral therapy. N Engl J Med 2011; 365:493-505.
28. Attia S, Egger M, Muller M, Zwahlen M, Low N. Sexual transmission of HIV according to viral load and antiretroviral therapy: systematic review and meta-Analysis. AIDS 2009; 23:1397-404.
29. Stadeli KM, Richman DD. Rates of emergence of HIV drug resistance in resource-limited settings: a systematic review. Antivir Ther 2013; 18:115-23.
30. Bennett DE, Camacho RJ, Otelea D, et al. Drug resistance mutations for surveillance of transmitted HIV-1 drug-resistance: 2009 update. PLoS One 2009; 4:e4724.
31. Ma Y, Zhao D, Yu L, et al. Predictors of virologic failure in HIV-1-infected adults receiving first-line antiretroviral therapy in 8 provinces in China. Clin Infect Dis 2010; 50:264-71.
32. Zhang F, Dou Z, Ma Y, et al. Five-year outcomes of the China National Free Antiretroviral Treatment Program. Ann Intern Med 2009; 151: 241-51, W-52.
33. Takebe Y, Naito Y, Raghwani J, et al. Intercontinental dispersal of HIV-1 subtype B associated with transmission among men who have sex with men in Japan. J Virol 2014; 88:9864-76.
34. Brenner BG, Roger M, Routy JP, et al. High rates of forward transmission events after acute/early HIV-1 infection. J Infect Dis 2007; 195: 951-9.
35. Chen JH, Wong KH, Chan KC, To SW, Chen Z, Yam WC. Phylodynamics of HIV-1 subtype B among the men-having-sex-with-men (MSM) population in Hong Kong. PLoS One 2011; 6:e25286.
36. Hue S, Brown AE, Ragonnet-Cronin M, et al. Phylogenetic analyses reveal HIV-1 infections between men misclassified as heterosexual transmissions. AIDS 2014; 28:1967-75.
37. Hue S, Pillay D, Clewley JP, Pybus OG. Genetic analysis reveals the complex structure of HIV-1 transmission within defined risk groups. Proc Natl Acad Sci U S A 2005; 102:4425-9.
38. Grinsztejn B, Hosseinipour MC, Ribaudo HJ, et al. Effects of early versus delayed initiation of antiretroviral treatment on clinical outcomes of HIV-1 infection: results from the phase 3 HPTN 052 randomised controlled trial. Lancet Infect Dis 2014; 14:281-90.
39. Meghan Rothenberger AH, Khoruts A, Beilman G, et al. Brief interruption of HIV antiretroviral therapy in patients with preserved CD4 count and virologic suppression is safe and well tolerated. In: Infectious Disease Society Association. San Diego, 2012.
40. Sigaloff KC, Lange JM, Montaner J. Global response to HIV: treatment as prevention, or treatment for treatment? Clin Infect Dis 2014; 59(suppl 1): S7-11.