Global dispersal pattern of HIV type 1 subtype CRF01-AE: A genetic trace of human mobility related to heterosexual sexual activities centralized in southeast Asia

Journal of Infectious Diseases

Volumn 211, Issue 11, 2015, Pages 1735-1744

  Angelis, Konstantinos ^a   Albert, Jan ^b   Mamais, Ioannis ^a   Magiorkinis, Gkikas ^a,c   Hatzakis, Angelos ^a   Hamouda, Osamah ^d   Struck, Daniel ^e   Vercauteren, Jurgen ^f   Wensing, Annemarie M J ^g   Alexiev, Ivailo ⁱ   Åsjö, Birgitta ^j   Balotta, Claudia ^k   Camacho, Ricardo J ^l   Coughlan, Suzie ^m   Griskevicius, Algirdas ⁿ   Grossman, Zehava ^o   Horban, Andrzej ^p   Kostrikis, Leondios G ^q   Lepej, Snjezana ^r   Liitsola, Kirsi ^s   Linka, Marek ^t   Nielsen, Claus ^u   Otelea, Dan ^v   Paredes, Roger ^w   Poljak, Mario ^x   Puchhammer Stöckl, Elisabeth ^b   Schmit, Jean Claude ^e   Sönnerborg, Anders ^b   Staneková, Danica ^y   Stanojevic, Maja ^z   Boucher, Charles A B ^h   Kaplan, Lauren ^aa   Vandamme, Anne Mieke ^f,l   Paraskevis, Dimitrios ^a   more..

^a UNIVERSITY OF ATHENS MEDICAL SCHOOL   (Greece)

^b KAROLINSKA UNIVERSITY HOSPITAL   (Sweden)

^c UNIVERSITY OF OXFORD   (United Kingdom)

^d ROBERT KOCH INSTITUTE   (Germany)

^e LUXEMBOURG INSTITUTE OF HEALTH   (Luxembourg)

^f REGA INSTITUTE FOR MEDICAL RESEARCH   (Belgium)

^g UNIVERSITY MEDICAL CENTER UTRECHT   (Netherlands)

^h ERASMUS MEDICAL CENTER   (Netherlands)

ⁱ NATIONAL CENTER OF INFECTIOUS AND PARASITIC DISEASES   (Bulgaria)

^j UNIVERSITY OF BERGEN   (Norway)

^k UNIVERSITY OF MILAN   (Italy)

^l INSTITUTO DE HIGIENE E MEDICINA TROPICAL   (Portugal)

^m UNIVERSITY COLLEGE DUBLIN   (Ireland)

ⁿ Lithuanian AIDS Center   (Lithuania)

^o TEL AVIV UNIVERSITY   (Israel)

^p SP ZOZ Wojewodzki Szpital Zakazny Centrum Diagnostyki i Terapii AIDS Warszawa   (Poland)

^q UNIVERSITY OF CYPRUS   (Cyprus)

^r Croatia   (Croatia)

^s NATIONAL PUBLIC HEALTH INSTITUTE   (Finland)

^t NATIONAL INSTITUTES OF HEALTH   (United States)

^u STATENS SERUM INSTITUT   (Denmark)

^v IrsiCaixa Foundation ^*  (Romania)

^w IrsiCaixa Foundation   (Spain)

^x UNIVERSITY OF LJUBLJANA   (Slovenia)

^y SLOVAK MEDICAL UNIVERSITY   (Slovakia)

^z UNIVERSITY OF BELGRADE   (Serbia)

^aa UNIVERSITY OF CALIFORNIA   (United States)

more..

Author keywords

CRF01 AE; dispersal pattern; HIV 1; migration; phylogeography

Indexed keywords

AFRICA; ARTICLE; ASIAN; CHINA; CLADISTICS; CONTROLLED STUDY; EUROPE; FEMALE; GENE SEQUENCE; GENETIC ANALYSIS; HETEROSEXUALITY; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS 1 SUBTYPE CRF01_AE; JAPAN; MAJOR CLINICAL STUDY; MALE; MAXIMUM LIKELIHOOD METHOD; MIGRATION; NORTH AMERICA; PHYLOGENY; PHYLOGEOGRAPHY; PRIORITY JOURNAL; SEQUENCE ALIGNMENT; SEX TOURISM; SEXUAL BEHAVIOR; SINGAPORE; SOUTHEAST ASIA; TAIWAN; THAILAND; VIET NAM; VIRUS STRAIN; CLASSIFICATION; CLUSTER ANALYSIS; FACTUAL DATABASE; GENETICS; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; POPULATION DYNAMICS; TRANSMISSION; VIROLOGY;

ASIA, SOUTHEASTERN; CLUSTER ANALYSIS; DATABASES, FACTUAL; EUROPE; HETEROSEXUALITY; HIV INFECTIONS; HIV-1; HUMANS; PHYLOGENY; PHYLOGEOGRAPHY; POPULATION DYNAMICS;

EID: 84930451658     PISSN: 00221899     EISSN: 15376613     Source Type: Journal    
DOI: 10.1093/infdis/jiu666     Document Type: Article

References (41)

1. Sharp PM, Hahn BH. Origins of HIV and the AIDS pandemic. Cold Spring Harb Perspect Med 2011; 1:a006841.
2. Sharp PM, Hahn BH. The evolution of HIV-1 and the origin of AIDS. Philos Trans R Soc Lond B Biol Sci 2010; 365:2487-94.
3. Vidal N, Peeters M, Mulanga-Kabeya C, et al. Unprecedented degree of human immunodeficiency virus type 1 (HIV-1) group M genetic diversity in the Democratic Republic of Congo suggests that the HIV-1 pandemic originated in Central Africa. J Virol 2000; 74:10498-507.
4. Gao F, Robertson DL, Morrison SG, et al. The heterosexual human immunodeficiency virus type 1 epidemic in Thailand is caused by an intersubtype (A/E) recombinant of African origin. J Virol 1996; 70:7013-29.
5. World Health Organization (WHO) Regional Office for the Western Pacific. Sex work in Asia. Geneva: WHO, 2001.
6. Robertson DL, Sharp PM, McCutchan FE, Hahn BH. Recombination in HIV-1. Nature 1995; 374:124-6.
7. Carr JK, Salminen MO, Koch C, et al. Full-length sequence and mosaic structure of a human immunodeficiency virus type 1 isolate from Thailand. J Virol 1996; 70:5935-43.
8. McCutchan FE, Hegerich PA, Brennan TP, et al. Genetic variants of HIV-1 in Thailand. AIDS Res Hum Retroviruses 1992; 8:1887-95.
9. Nelson KE, Celentano DD, Suprasert S, et al. Risk factors for HIV infection among young adult men in northern Thailand. JAMA 1993; 270:955-60.
10. McCutchan FE, Artenstein AW, Sanders-Buell E, et al. Diversity of the envelope glycoprotein among human immunodeficiency virus type 1 isolates of clade E from Asia and Africa. J Virol 1996; 70:3331-8.
11. Hemelaar J, Gouws E, Ghys PD, Osmanov S. WHO-UNAIDS Network for HIV Isolation and Characterisation. Global trends in molecular epidemiology of HIV-1 during 2000-2007. AIDS 2011; 25:679-89.
12. Vanichseni S, Kitayaporn D, Mastro TD, et al. Continued high HIV-1 incidence in a vaccine trial preparatory cohort of injection drug users in Bangkok, Thailand. AIDS 2001; 15:397-405.
13. Wasi C, Herring B, Raktham S, et al. Determination of HIV-1 subtypes in injecting drug users in Bangkok, Thailand, using peptide-binding enzyme immunoassay and heteroduplex mobility assay: evidence of increasing infection with HIV-1 subtype E. AIDS 1995; 9:843-9.
14. UNAIDS. Evaluation of the 100% condom programme in Thailand. UNAIDS case study. Geneva: UNAIDS, 2000.
15. 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.
16. Tourism Authority of Thailand. Tourism statistics. http://www2.tat.or. th/stat/web/static-tsi-detail.php?L=&TsiID=1. Accessed 22 March 2014.
17. Liao H, Tee KK, Hase S, et al. Phylodynamic analysis of the dissemination of HIV-1 CRF01-AE in Vietnam. Virology 2009; 391:51-6.
18. Ng KT, Ng KY, Khong WX, et al. Phylodynamic profile of HIV-1 subtype B, CRF01-AE and the recently emerging CRF51-01B among men who have sex with men (MSM) in Singapore. PLoS One 2013; 8:e80884.
19. Abubakar YF, Meng Z, Zhang X, Xu J. Multiple independent introductions of HIV-1 CRF01-AE identified in China: what are the implications for prevention? PLoS One 2013; 8:e80487.
20. Ng KT, Ong LY, Lim SH, Takebe Y, Kamarulzaman A, Tee KK. 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 2013; 8:e67286.
21. Ye J, Xin R, Yu S, et al. Phylogenetic and temporal dynamics of human immunodeficiency virus type 1 CRF01-AE in China. PLoS One 2013; 8: e54238.
22. Los Alamos National Laboratory. HIV databases. http://www.hiv.lanl. gov/content/index. Accessed 2 November 2012.
23. Los Alamos National Laboratory. HCV sequence database. http://hcv. lanl.gov/content/sequence/ELIMDUPES/elimdupes.html. Accessed 4 December 2012.
24. Wensing AMJ, Vercauteren J, Van De Vijver DA, et al. Bouche, CAB, Spread programme. Transmission of drug-resistant HIV-1 in Europe remains limited to single classes. AIDS 2008; 22:625-35.
25. Paraskevis D, Pybus O, Magiorkinis G, et al. Tracing the HIV-1 subtype B mobility in Europe: a phylogeographic approach. Retrovirology 2009; 6:49.
26. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011; 28:2731-9.
27. Yang Z. Estimating the pattern of nucleotide substitution. J Mol Evol 1994; 39:105-11.
28. Yang Z. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J Mol Evol 1994; 39:306-14.
29. Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006; 22:2688-90.
30. Stamatakis A, Hoover P, Rougemont J. A rapid bootstrap algorithm for the RAxML Web servers. Syst Biol 2008; 57:758-71.
31. CIPRES Cyberinfrastructure for Phylogenetic Research. The CIPRES Science Gateway V. 3.3. http://www.phylo.org/index.php/portal/. Accessed 13 May 2013.
32. Slatkin M, Maddison WP. A cladistic measure of gene flow inferred from the phylogenies of alleles. Genetics 1989; 123:603-13.
33. Swofford DL. PAUP∗. phylogenetic analysis using parsimony (and other methods). Version 4. Sunderland, MA: Sinauer Associates, 2003.
34. 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; 85:510-8.
35. Skar H, Sylvan S, Hansson HB, et al. Multiple HIV-1 introductions into the Swedish intravenous drug user population. Infect Genet Evol 2008; 8:545-52.
36. Thailand's new condom crusade. Bull World Health Organ 2010; 88:404-5.
37. Kalish ML, Korber BT, Pillai S, et al. The sequential introduction of HIV-1 subtype B and CRF01AE in Singapore by sexual transmission: accelerated V3 region evolution in a subpopulation of Asian CRF01 viruses. Virology 2002; 304:311-29.
38. Nerurkar VR, Nguyen HT, Dashwood WM, et al. HIV type 1 subtype E in commercial sex workers and injection drug users in southern Vietnam. AIDS Res Hum Retroviruses 1996; 12:841-3.
39. Drummond AJ, Rambaut A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 2007; 7:214.
40. Ou CY, Takebe Y, Luo CC, et al. Wide distribution of two subtypes of HIV-1 in Thailand. AIDS Res Hum Retroviruses 1992; 8:1471-2.
41. Ubolyam S, Ruxrungtham , Sirivichayakul S, Okuda K, Phanuphak P. Evidence of three HIV-1 subtypes in subgroups of individuals in Thailand. Lancet 1994; 344:485-6.