Phylodynamic analysis reveals CRF01-AE dissemination between Japan and neighboring Asian countries and the role of intravenous drug use in transmission

PLoS ONE

Volumn 9, Issue 7, 2014, Pages

  Shiino, Teiichiro ^a   Hattori, Junko ^b   Yokomaku, Yoshiyuki ^b   Iwatani, Yasumasa ^b,c   Sugiura, Wataru ^b,c   Ajisawa, Atsushi ^d   Chiba, Hitoshi ^d   Fujii, Teruhisa ^d   Fujikawa, Yuko ^d   Fujita, Akira ^d   Fukutake, Katsuyuki ^d   Gatanaga, Hiroyuki ^d   Goto, Tetsushi ^d   Hatakeyama, Shuji ^d   Hongo, Igen ^d   Horiba, Masahide ^d   Kondo, Makiko ^d   Konishi, Mitsuru ^d   Matsushita, Shuzo ^d   Matsuura, Motoo ^d   Minami, Rumi ^d   Miyazaki, Naoko ^d   Mori, Haruyo ^d   Noda, Masaaki ^d   Otani, Chiho ^d   Sato, Takeyuki ^d   Shirahata, Satoshi ^d   Taki, Masashi ^d   Tamashima, Sadahiro ^d   Tateyma, Masap ^d   Tei, Masanori ^d   Uchida, Kazue ^d   Watanabe, Dai ^d   Yamamoto, Yasuyuki ^d   Yano, Kunio ^d   Yotsumoto, Mihoko ^d   Yoshida, Shigeru ^d   more..

^a NATIONAL INSTITUTE OF INFECTIOUS DISEASES   (Japan)

^b NATIONAL HOSPITAL ORGANIZATION NAGOYA MEDICAL CENTER   (Japan)

^c NAGOYA UNIVERSITY GRADUATE SCHOOL OF MEDICINE   (Japan)

^d NONE

Author keywords

[No Author keywords available]

Indexed keywords

RNA DIRECTED DNA POLYMERASE;

ADULT; AGE DISTRIBUTION; AGED; ARTICLE; BAYES THEOREM; CLUSTER ANALYSIS; CONTROLLED STUDY; DISEASE ASSOCIATION; FEMALE; GEOGRAPHIC DISTRIBUTION; HETEROSEXUALITY; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS 1 (STRAIN CRF01 AE); HUMAN IMMUNODEFICIENCY VIRUS 1 INFECTION; INTRAVENOUS DRUG ABUSE; JAPAN; MAJOR CLINICAL STUDY; MALE; MEN WHO HAVE SEX WITH MEN; MONTE CARLO METHOD; MORBIDITY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHENOTYPIC VARIATION; PHYLOGENY; PROBABILITY; RISK FACTOR; SEX RATIO; SOUTHEAST ASIA; UNINDEXED SEQUENCE; VIRUS STRAIN; VIRUS TRANSMISSION; COMPLICATION; GENETICS; HIGH RISK BEHAVIOR; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; MIDDLE AGED; SUBSTANCE ABUSE; TRANSMISSION; UNSAFE SEX; VIROLOGY; VIRUS GENE;

ADULT; ASIA, SOUTHEASTERN; FEMALE; GENES, VIRAL; HIV INFECTIONS; HIV-1; HUMANS; JAPAN; MALE; MIDDLE AGED; PHYLOGENY; RISK-TAKING; SUBSTANCE ABUSE, INTRAVENOUS; UNSAFE SEX;

EID: 84904264268     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0102633     Document Type: Article

References (51)

1. Infectious Diseases Surveillance Center (2011) HIV/AIDS in Japan, 2010. IASR 32: 282-283.
2. Yamanaka T, Fujimura Y, Ishimoto S, Yoshioka A, Konishi M, et al. (1997) Correlation of titer of antibody to principal neutralizing domain of HIVMN strain with disease progression in Japanese hemophiliacs seropositive for HIV type 1. AIDS Res Hum Retroviruses 13: 317-326. (Pubitemid 27117944)
3. Kato S, Saito R, Hiraishi Y, Kitamura N, Matsumoto T, et al. (2003) Differential prevalence of HIV type 1 subtype B and CRF01-AE among different sexual transmission groups in Tokyo, Japan, as revealed by subtypespecific PCR. AIDS Res Hum Retroviruses 19: 1057-1063. (Pubitemid 37476036)
4. Weniger BG, Takebe Y, Ou CY, Yamazaki S (1994) The molecular epidemiology of HIV in Asia. AIDS 8 Suppl 2: S13-S28.
5. Ou CY, Takebe Y, Luo CC, Kalish M, Auwanit W, et al. (1992) Wide distribution of two subtypes of HIV-1 in Thailand. AIDS Res Hum Retroviruses 8: 1471-1472.
6. Ou CY, Takebe Y, Weniger BG, Luo CC, Kalish ML, et al. (1993) Independent introduction of two major HIV-1 genotypes into distinct high-risk populations in Thailand. Lancet 341: 1171-1174. (Pubitemid 23137112)
7. Lau KA, Wang B, Saksena NK (2007) Emerging trends of HIV epidemiology in Asia. AIDS Rev 9: 218-229. (Pubitemid 351192646)
8. Beyrer C, Vancott TC, Peng NK, Artenstein A, Duriasamy G, et al. (1998) HIV type 1 subtypes in Malaysia, determined with serologic assays: 1992-1996. AIDS Res Hum Retroviruses 14: 1687-1691. (Pubitemid 28563860)
9. Kusagawa S, Sato H, Kato K, Nohtomi K, Shiino T, et al. (1999) HIV type 1 env subtype E in Cambodia. AIDS Res Hum Retroviruses 15: 91-94. (Pubitemid 29038331)
10. Menu E, Truong TX, Lafon ME, Nguyen TH, Müller-Trutwin MC, et al. (1996) HIV type 1 Thai subtype E is predominant in South Vietnam. AIDS Res Hum Retroviruses 12: 629-633. (Pubitemid 26120295)
11. Nerurkar VR, Nguyen HT, Woodward CL, Hoffmann PR, Dashwood WM, et al. (1997) Sequence and phylogenetic analyses of HIV-1 infection in Vietnam: subtype E in commercial sex workers (CSW) and injection drug users (IDU). Cell Mol Biol (Noisy-le-grand) 43: 959-968.
12. Porter KR, Mascola JR, Hupudio H, Ewing D, VanCott TC, et al. (1997) Genetic, antigenic and serologic characterization of human immunodeficiency virus type 1 from Indonesia. J Acquir Immune Defic Syndr Hum Retrovirol 14: 1-6.
13. Wang W, Jiang S, Li S, Yang K, Ma L, et al. (2008) Identification of subtype B, multiple circulating recombinant forms and unique recombinants of HIV type 1 in an MSM cohort in China. AIDS Res Hum Retroviruses 24: 1245-1254.
14. Wang W, Xu J, Jiang S, Yang K, Meng Z, et al. (2011) The dynamic face of HIV-1 subtypes among men who have sex with men in Beijing, China. Curr HIV Res 9: 136-139.
15. Zhang X, Li S, Li X, Li X, Xu J, et al. (2007) Characterization of HIV-1 subtypes and viral antiretroviral drug resistance in men who have sex with men in Beijing, China. AIDS 21 Suppl 8: S59-S65.
16. Hattori J, Shiino T, Gatanaga H, Yoshida S, Watanabe D, et al. (2010) Trends in transmitted drug-resistant HIV-1 and demographic characteristics of newly diagnosed patients: nationwide surveillance from 2003 to 2008 in Japan. Antiviral Res 88: 72-79.
17. Kihara M, Ichikawa S, Kihara M, Yamasaki S (1997) Descriptive epidemiology of HIV/AIDS in Japan, 1985-1994. J Acquir Immune Defic Syndr Hum Retrovirol 14 Suppl 2:S3-12.
18. Grenfell BT, Pybus OG, Gog JR, Wood JL, Daly JM, et al. (2004) Unifying the epidemiological and evolutionary dynamics of pathogens. Science 303: 327-332. (Pubitemid 38095764)
19. Nelson MI, Holmes EC (2007) The evolution of epidemic influenza. Nat Rev Genet 8: 196-205.
20. Nelson MI, Simonsen L, Viboud C, Miller MA, Holmes EC (2007) Phylogenetic analysis reveals the global migration of seasonal influenza A viruses. PLoS Pathog 3: 1220-1228. (Pubitemid 47510275)
21. Shiino T, Okabe N, Yasui Y, Sunagawa T, Ujike M, et al. (2010) Molecular evolutionary analysis of the influenza A(H1N1)pdm, May-September, 2009: temporal and spatial spreading profile of the viruses in Japan. PLoS One 5: e11057.
22. Magiorkinis G, Magiorkinis E, Paraskevis D, Ho SY, Shapiro B, et al. (2009) The global spread of hepatitis C virus 1a and 1b: a phylodynamic and phylogeographic analysis. PLoS Med 6: e1000198.
23. Pybus OG, Drummond AJ, Nakano T, Robertson BH, Rambaut A (2003) The epidemiology and iatrogenic transmission of hepatitis C virus in Egypt: a Bayesian coalescent approach. Mol Biol Evol 20: 381-387. (Pubitemid 36427172)
24. Hughes GJ, Fearnhill E, Dunn D, Lycett SJ, Rambaut A, et al. (2009) Molecular phylodynamics of the heterosexual HIV epidemic in the United Kingdom. PLoS Pathog 5: e1000590.
25. Leigh Brown AJ, Lycett SJ, Weinert L, Hughes GJ, Fearnhill E, et al. (2011) Transmission Network Parameters Estimated From HIV Sequences for a Nationwide Epidemic. J Infect Dis 204: 1463-1469.
26. 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.
27. Gatanaga H, Ibe S, Matsuda M, Yoshida S, Asagi T, et al. (2007) Drug-resistant HIV-1 prevalence in patients newly diagnosed with HIV/AIDS in Japan. Antiviral Res 75: 75-82. (Pubitemid 46610525)
28. UNGASS (2012) National Commitments and Policies Instrument (NCPI). Available: http://www.unaids.org/en/dataanalysis/knowyourresponse/ncpi/ 2012countries/Japan NCPI 2012.pdf. Accessed 20 June 2012.
29. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, et al. (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23: 2947-2948. (Pubitemid 350162903)
30. Lloyd AL, May RM (2001) Epidemiology. How viruses spread among computers and people. Science 292: 1316-1317. (Pubitemid 32476209)
31. Romano CM, de Carvalho-Mello IM, Jamal LF, de Melo FL, Iamarino A, et al. (2010) Social networks shape the transmission dynamics of hepatitis C virus. PLoS One 5: e11170.
32. Barabasi AL, Albert R (1999) Emergence of scaling in random networks. Science 286: 509-512.
33. R Development Core Team (2010) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing. Available: http://www.r-project.org/.
34. Tamura K, Nei M, Kumar S (2004) Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc Natl Acad Sci U S A 101: 11030-11035. (Pubitemid 38989579)
35. 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.
36. Swofford DL (2003) PAUP. Phylogenetic Analysis Using Parsimony (and Other Methods). Version 4. Sunderland, Massachusetts: Sinauer Associates.
37. Nylander JAA (2004) MrModeltest v2. Program distributed by the author. Uppsala University: Evolutionary Biology Centre.
38. Drummond AJ, Rambaut A (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 7: 214.
39. Suchard MA (2001) Bayesian selection of continuous-time Markov chain evolutionary models. Mol Biol Evol 18: 1001-1013. (Pubitemid 32520473)
40. Baele G, Li WL, Drummond AJ, Suchard MA, Lemey P (2013) Accurate model selection of relaxed molecular clocks in bayesian phylogenetics. Mol Biol Evol 30: 239-243.
41. Xie W, Lewis PO, Fan Y, Kuo L, Chen MH (2011) Improving marginal likelihood estimation for Bayesian phylogenetic model selection. Syst Biol 60: 150-160.
42. 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.
43. Drummond A, Forsberg R, Rodrigo AG (2001) The inference of stepwise changes in substitution rates using serial sequence samples. Mol Biol Evol 18: 1365-1371. (Pubitemid 32660680)
44. Drummond A, Rodrigo AG (2000) Reconstructing genealogies of serial samples under the assumption of a molecular clock using serial-sample UPGMA. Mol Biol Evol 17: 1807-1815.
45. Shankarappa R, Margolick JB, Gange SJ, Rodrigo AG, Upchurch D, et al. (1999) Consistent viral evolutionary changes associated with the progression of human immunodeficiency virus type 1 infection. J Virol 73: 10489-10502.
46. Liao H, Tee KK, Hase S, Uenishi R, Li XJ, et al. (2009) Phylodynamic analysis of the dissemination of HIV-1 CRF01-AE in Vietnam. Virology 391: 51-56.
47. Li L, Liang S, Chen L, Liu W, Li H, et al. (2010) Genetic characterization of 13 subtype CRF01-AE near full-length genomes in Guangxi, China. AIDS Res Hum Retroviruses 26: 699-704.
48. An M, Han X, Xu J, Chu Z, Jia M, et al. (2012) Reconstituting the epidemic history of HIV strain CRF01-AE among men who have sex with men (MSM) in Liaoning, northeastern China: implications for the expanding epidemic among MSM in China. J Virol 86: 12402-12406.
49. Feng Y, He X, Hsi JH, Li F, Li X, et al. (2013) The rapidly expanding CRF01-AE epidemic in China is driven by multiple lineages of HIV-1 viruses introduced in the 1990s. AIDS 27: 1793-1802.
50. Ye J, Xin R, Yu S, Bai L, Wang W, et al. (2013) Phylogenetic and temporal dynamics of human immunodeficiency virus type 1 CRF01-AE in China. PLoS One 8: e54238.
51. Kondo M, Lemey P, Sano T, Itoda I, Yoshimura Y, et al. (2013) Emergence in Japan of an HIV-1 variant associated with transmission among men who have sex with men (MSM) in China: first indication of the International Dissemination of the Chinese MSM lineage. J Virol 87: 5351-5361.