Longitudinal phylogenetic surveillance identifies distinct patterns of cluster dynamics

Journal of Acquired Immune Deficiency Syndromes

Volumn 55, Issue 1, 2010, Pages 102-108

  Ragonnet Cronin, Manon ^a   Ofner Agostini, Marianna ^a   Merks, Harriet ^a   Pilon, Richard ^b   Rekart, Michael ^a   Archibald, Chris P ^a   Sandstrom, Paul A ^a   Brooks, James I ^a  

^a PUBLIC HEALTH AGENCY OF CANADA   (Canada)

^b BRITISH COLUMBIA CENTRE FOR DISEASE CONTROL   (Canada)

Author keywords

Cluster dynamics; HIV; Phylogenetic; Public health; Transmission dynamics

Indexed keywords

ADOLESCENT; ADULT; ARTICLE; BOOTSTRAPPING; CANADA; CLUSTER ANALYSIS; CONTROLLED STUDY; CROSS-SECTIONAL STUDY; DISEASE CLASSIFICATION; DISEASE SURVEILLANCE; ETHNICITY; FEMALE; GENE AMPLIFICATION; GENE CLUSTER; GENE SEQUENCE; GENETIC ANALYSIS; GENOMIC FRAGMENT; GENOTYPE; GEOGRAPHIC DISTRIBUTION; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS INFECTED PATIENT; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; INTRAVENOUS DRUG ABUSE; MAJOR CLINICAL STUDY; MALE; PHYLOGENY; POPULATION; PRIORITY JOURNAL; SAMPLE SIZE; STRUCTURAL GENE; VIRUS TRANSMISSION; ANTIVIRAL RESISTANCE; CLASSIFICATION; DISEASE TRANSMISSION; DNA SEQUENCE; GENETICS; GROWTH, DEVELOPMENT AND AGING; HUMAN IMMUNODEFICIENCY VIRUS; ISOLATION AND PURIFICATION; MIDDLE AGED; MOLECULAR EPIDEMIOLOGY; MOLECULAR GENETICS; SEQUENCE HOMOLOGY; VIROLOGY;

POL PROTEIN; VIRUS RNA;

ADOLESCENT; BRITISH COLUMBIA; CLUSTER ANALYSIS; CROSS-SECTIONAL STUDIES; DRUG RESISTANCE, VIRAL; FEMALE; GENOTYPE; HIV; HIV INFECTIONS; HUMANS; MALE; MIDDLE AGED; MOLECULAR EPIDEMIOLOGY; MOLECULAR SEQUENCE DATA; POL GENE PRODUCTS, HUMAN IMMUNODEFICIENCY VIRUS; RNA, VIRAL; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY; YOUNG ADULT;

EID: 77956638123     PISSN: 15254135     EISSN: 10779450     Source Type: Journal    
DOI: 10.1097/QAI.0b013e3181e8c7b0     Document Type: Article

References (37)

1. Pilcher CD, Wong JK, Pillai SK. Inferring HIV transmission dynamics from phylogenetic sequence relationships. PLoS Med. 2008;5:e69.
2. Pillay D, Rambaut A, Geretti AM, et al. HIV phylogenetics. BMJ. 2007;335:460-461. (Pubitemid 47401594)
3. Brenner BG, Roger M, Routy JP, et al. High rates of forward transmission events after acute/early HIV-1 infection. J Infect Dis. 2007;195:951-959. (Pubitemid 46452099)
4. Pao D, Fisher M, Hue S, et al. Transmission of HIV-1 during primary infection: relationship to sexual risk and sexually transmitted infections. AIDS. 2005;19:85-90. (Pubitemid 40111022)
5. Pilcher CD, Tien HC, Eron JJ Jr, et al. Brief but efficient: acute HIV infection and the sexual transmission of HIV. J Infect Dis. 2004;189:1785-1792. (Pubitemid 38657214)
6. Pinkerton SD. Probability of HIV transmission during acute infection in Rakai, Uganda. AIDS Behav. 2008;12:677-684.
7. Yerly S, von Wyl V, Ledergerber B, et al. Transmission of HIV-1 drug resistance in Switzerland: a 10-year molecular epidemiology survey. AIDS. 2007;21:2223-2229. (Pubitemid 350287221)
8. Kaye M, Chibo D, Birch C. Phylogenetic investigation of transmission pathways of drug-resistant HIV-1 utilizing pol sequences derived from resistance genotyping. J Acquir Immune Defic Syndr. 2008;49:9-16.
9. Pillay D, Bhaskaran K, Jurriaans S, et al. The impact of transmitted drug resistance on the natural history of HIV infection and response to first-line therapy. AIDS. 2006;20:21-28. (Pubitemid 41818110)
10. Torian LV, Blank S, Kellerman SE, et al. Investigation of a New Diagnosis of Multidrug-Resistant, Dual-Tropic HIV-1 Infection-New York City, 2005. MMWR Morb Mortal Wkly Rep. 2006;55:793-796.
11. Boulos D, Yan P, Schanzer D, et al. Estimates of HIV prevalence and incidence in Canada, 2005. Can Commun Dis Rep. 2006;32:165-174.
12. Hue S, Clewley JP, Cane PA, et al. HIV-1 pol gene variation is sufficient for reconstruction of transmissions in the era of antiretroviral therapy. AIDS. 2004;18:719-728. (Pubitemid 38541542)
13. Hue S, Clewley JP, Cane PA, et al. Investigation of HIV-1 transmission events by phylogenetic methods: requirement for scientific rigour. AIDS. 2005;19:449-450. (Pubitemid 40446195)
14. EuroGUidelines Group for HIV resistance. Clinical and laboratory guidelines for the use of HIV-1 drug resistance testing as part of treatment management: recommendations for the European setting. The Euro-GUidelines Group for HIV resistance. AIDS. 2001;15:309-320.
15. Gazzard BG. British HIV Association guidelines for the treatment of HIV-1-infected adults with antiretroviral therapy 2008. HIV Med. 2008;9:563-608.
16. Hirsch MS, Gunthard HF, Schapiro JM, et al. Antiretroviral drug resistance testing in adult HIV-1 infection: 2008 recommendations of an International AIDS Society-USA panel. Clin Infect Dis. 2008;47:266-285. (Pubitemid 351920631)
17. Panel on Antiretroviral Guidelines for Adults and Adolescents. Guidelines for the use of antiretroviral agents in HIV-1-infected adults and adolescents. Department of Health and Human Services. December 1, 2009;1-161, p 9-15. Available at http://www.aidsinfo.nih.gov/ContentFiles/AdultandAdolescentGL.pdf. Accessed July 6, 2010.
18. Haag D, Kim P, Spencer D, et al. HIV/AIDS Update Year End 2005. Vancouver, BC: British Columbia Centre for Disease Control STI/HIV Prevention and Control; 2006.
19. Jayaraman GC, Archibald CP, Lior L, et al. Integrating laboratory and epidemiological techniques for population-based surveillance of HIV strains and drug resistance in Canada. Can J Infect Dis. 2000;11:74-80. (Pubitemid 30318136)
20. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser. 1999;41:95-98.
21. Johnson VA, Brun-Vezinet F, Clotet B, et al. Update of the drug resistance mutations in HIV-1: Fall 2005. Top HIV Med. 2005;13:125-131.
22. Parekh BS, Kennedy MS, Dobbs T, et al. Quantitative detection of increasing HIV type 1 antibodies after seroconversion: a simple assay for detecting recent HIV infection and estimating incidence. AIDS Res Hum Retroviruses. 2002;18:295-307. (Pubitemid 34253148)
23. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987;4:406-425.
24. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol. 1980;16:111-120. (Pubitemid 11166431)
25. Kumar S, Tamura K, Nei M. MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 2004;5:150-163.
26. Public Health Agency of Canada. HIV and AIDS in Canada: Selected Surveillance Tables to June 30, 2008. Surveillance and Risk Assessment Division, Centre for Communicable Diseases and Infection Control. Ottawa, ON: Public Health Agency of Canada; 2009.
27. Woolhouse ME, Dye C, Etard JF, et al. Heterogeneities in the transmission of infectious agents: implications for the design of control programs. Proc Natl Acad Sci U S A. 1997;94:338-342. (Pubitemid 27027211)
28. Lloyd-Smith JO, Schreiber SJ, Kopp PE, et al. Superspreading and the effect of individual variation on disease emergence. Nature. 2005;438:355-359. (Pubitemid 41643951)
29. Galvani AP, May RM. Epidemiology: dimensions of superspreading. Nature. 2005;438:293-295. (Pubitemid 41643933)
30. Loschen S, Batzing-Feigenbaum J, Poggensee G, et al. Comparison of the human immunodeficiency virus (HIV) type 1-specific immunoglobulin G capture enzyme-linked immunosorbent assay and the avidity index method for identification of recent HIV infections. J Clin Microbiol. 2008;46:341-345.
31. Lewis F, Hughes GJ, Rambaut A, et al. Episodic sexual transmission of HIV revealed by molecular phylodynamics. PLoS Med. 2008;5:e50.
32. Hughes GJ, Fearnhill E, Dunn D, et al. Molecular phylodynamics of the heterosexual HIV epidemic in the United Kingdom. PLoS Pathog. 2009;5:e1000590.
33. Sturmer M, Preiser W, Gute P, et al. Phylogenetic analysis of HIV-1 transmission: pol gene sequences are insufficient to clarify true relationships between patient isolates. AIDS. 2004;18:2109-2113. (Pubitemid 39463675)
34. Leitner T, Escanilla D, Franzen C, et al. Accurate reconstruction of a known HIV-1 transmission history by phylogenetic tree analysis. Proc Natl Acad Sci U S A. 1996;93:10864-10869. (Pubitemid 26333082)
35. 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;23:225-232.
36. Cuevas M, Fernandez-Garcia A, Sanchez-Garcia A, et al. Incidence of non-B subtypes of HIV-1 in Galicia, Spain: high frequency and diversity of HIV-1 among men who have sex with men. Euro Surveill. 2009;14(47):Article 3.
37. Nguyen L, Hu DJ, Choopanya K, et al. Genetic analysis of incident HIV-1 strains among injection drug users in Bangkok: evidence for multiple transmission clusters during a period of high incidence. J Acquir Immune Defic Syndr. 2002;30:248-256. (Pubitemid 34664422)