HIV-1 subtype distribution trends and evidence of transmission clusters among incident cases in a rural clinical cohort in Southwest Uganda, 2004-2010

AIDS Research and Human Retroviruses

Volumn 29, Issue 3, 2013, Pages 520-527

  Kapaata, Anne ^a   Lyagoba, Frederick ^a   Ssemwanga, Deogratius ^a   Magambo, Brian ^a   Nanyonjo, Maria ^a   Levin, Jonathan ^a   Mayanja, Billy N ^a   Mugasa, Claire ^b   Parry, Chris M ^a   Kaleebu, Pontiano ^a,c  

^a MEDICAL RESEARCH COUNCIL   (United Kingdom)

^b MAKERERE UNIVERSITY   (Uganda)

^c LONDON SCHOOL OF HYGIENE AND TROPICAL MEDICINE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

POL PROTEIN;

ADULT; AGE DISTRIBUTION; ARTICLE; CLINICAL ARTICLE; DISEASE COURSE; DNA SEQUENCE; FEMALE; HIGH RISK BEHAVIOR; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS 1 INFECTION; LOW RISK POPULATION; MALE; MEDICAL HISTORY; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; RURAL AREA; SEROCONVERSION; SEXUAL BEHAVIOR; SEXUAL TRANSMISSION; SEXUALITY; UGANDA; VIRUS TRANSMISSION;

ADULT; CLUSTER ANALYSIS; ENV GENE PRODUCTS, HUMAN IMMUNODEFICIENCY VIRUS; FEMALE; GAG GENE PRODUCTS, HUMAN IMMUNODEFICIENCY VIRUS; GENETIC VARIATION; GENOTYPE; HIV INFECTIONS; HIV-1; HUMANS; MALE; MOLECULAR EPIDEMIOLOGY; MOLECULAR SEQUENCE DATA; PHYLOGENY; POL GENE PRODUCTS, HUMAN IMMUNODEFICIENCY VIRUS; RNA, VIRAL; RURAL POPULATION; SEQUENCE ANALYSIS, DNA; UGANDA;

EID: 84874488731     PISSN: 08892229     EISSN: 19318405     Source Type: Journal    
DOI: 10.1089/aid.2012.0170     Document Type: Article

References (47)

1. Taylor BS, Sobieszczyk ME, McCutchan FE, and Hammer SM: The challenge of HIV-1 subtype diversity. N Engl J Med 2008;358(15):1590-1602.
2. Plantier JC, Leoz M, Dickerson JE, et al.: A new human immunodeficiency virus derived from gorillas. Nat Med 2009; 15(8):871-872.
3. Vallari A, Holzmayer V, Harris B, et al.: Confirmation of putative HIV-1 group P in Cameroon. J Virol 2011;85(3): 1403-1407.
4. LANL: HIV Circulating Recombinant Forms (CRFs). http://www.hiv.lanl.gov/ content/sequence/HIV/CRFs/CRFs.html. Accessed January 2012.
5. Yirrell DL, Kaleebu P, Morgan D, Hutchinson S, and Whitworth JA: HIV-1 subtype dynamics over 10 years in a rural Ugandan cohort. Int J STD AIDS 2004; 15(2):103-106.
6. Hu DJ, Baggs J, Downing RG, et al.: Predominance of HIV-1 subtype A and D infections in Uganda. Emerg Infect Dis 2000;6(6):609-615.
7. Kaleebu P, Whitworth J, Hamilton L, et al.: Molecular epidemiology of HIV type 1 in a rural community in southwest Uganda. AIDS Res Hum Retroviruses 2000; 16(5):393-401.
8. Bruce C, Clegg C, Featherstone A, et al.: Presence of multiple genetic subtypes of human immunodeficiency virus type 1 proviruses in Uganda. AIDS Res Hum Retroviruses 1994; 10(11):1543-1550.
9. Senkaali D, Muwonge R, Morgan D, Yirrell D, Whitworth J, and Kaleebu P: The relationship between HIV type 1 disease progression and V3 serotype in a rural Ugandan cohort. AIDS Res Hum Retroviruses 2004;20(9):932-937.
10. Yirrell DL, Kaleebu P, Morgan D, et al.: Inter- and intra-genic intersubtype HIV-1 recombination in rural and semi-urban Uganda. AIDS 2002;16(2):279-286.
11. Gale CV, Yirrell DL, Campbell E, Van der Paal L, Grosskurth H, and Kaleebu P: Genotypic variation in the pol gene of HIV type 1 in an antiretroviral treatment-naive population in rural southwestern Uganda. AIDS Res Hum Retroviruses 2006;22(10):985-992.
12. Kaleebu P, Bobkov A, Cheingsong-Popov R, Bieniasz P, Garaev M, and Weber J: Identification of HIV-1 subtype G from Uganda. AIDS Res Hum Retroviruses 1995;11(5): 657-659.
13. Eshleman SH, Gonzales MJ, Becker-Pergola G, et al.: Identification of Ugandan HIV type 1 variants with unique patterns of recombination in pol involving subtypes A and D. AIDS Res Hum Retroviruses 2002;18(7):507-511.
14. Ssemwanga D, Lyagoba F, Ndembi N, et al.: Multiple HIV-1 infections with evidence of recombination in heterosexual partnerships in a low risk rural clinical cohort in Uganda. Virology 2011;411(1):113-131.
15. Baeten JM, Chohan B, Lavreys L, et al.: HIV-1 subtype D infection is associated with faster disease progression than subtype A in spite of similar plasma HIV-1 loads. J Infect Dis 2007;195(8):1177-1180.
16. Kaleebu P, French N, Mahe C, et al.: Effect of human immunodeficiency virus (HIV) type 1 envelope subtypes A and D on disease progression in a large cohort of HIV-1-positive persons in Uganda. J Infect Dis 2002;185(9):1244-1250.
17. Kaleebu P, Ross A, Morgan D, et al.: Relationship between HIV-1 Env subtypes A and D and disease progression in a rural Ugandan cohort. AIDS 2001;15(3):293-299.
18. Kiwanuka N, Laeyendecker O, Robb M, et al.: Effect of human immunodeficiency virus Type 1 (HIV-1) subtype on disease progression in persons from Rakai, Uganda, with incident HIV-1 infection. J Infect Dis 2008;197(5):707-713.
19. Vasan A, Renjifo B, Hertzmark E, et al.: Different rates of disease progression of HIV type 1 infection in Tanzania based on infecting subtype. Clin Infect Dis 2006;42(6): 843-852.
20. Kiwanuka N, Laeyendecker O, Quinn TC, et al.: HIV-1 subtypes and differences in heterosexual HIV transmission among HIV-discordant couples in Rakai, Uganda. AIDS 2009;23(18):2479-2484.
21. Conroy SA, Laeyendecker O, Redd AD, et al.: Changes in the distribution of HIV type 1 subtypes D and A in Rakai District, Uganda between 1994 and 2002. AIDS Res Hum Retroviruses 2010;26(10):1087-1091.
22. Easterbrook PJ, Smith M, Mullen J, et al.: Impact of HIV-1 viral subtype on disease progression and response to antiretroviral therapy. J Int AIDS Soc 2010;13:4.
23. Brenner BG, Oliveira M, Doualla-Bell F, et al.: HIV-1 subtype C viruses rapidly develop K65R resistance to tenofovir in cell culture. AIDS 2006;20(9):F9-13.
24. Wawer MJ, Gray RH, Sewankambo NK, et al.: Rates of HIV-1 transmission per coital act, by stage of HIV-1 infection, in Rakai, Uganda. J Infect Dis 2005;191(9):1403-1409.
25. 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(10):1785- 1792.
26. Leynaert B, Downs AM, and de Vincenzi I: Heterosexual transmission of human immunodeficiency virus: Variability of infectivity throughout the course of infection. European Study Group on Heterosexual Transmission of HIV. Am J Epidemiol 1998;148(1):88-96.
27. 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(13):921-929.
28. Cohen MS and Pilcher CD: Amplified HIV transmission and new approaches to HIV prevention. J Infect Dis 2005;191(9): 1391-1393.
29. Hollingsworth TD, Anderson RM, and Fraser C: HIV-1 transmission, by stage of infection. J Infect Dis 2008;198(5): 687-693.
30. Shafer LA, Biraro S, Nakiyingi-Miiro J, et al.: HIV prevalence and incidence are no longer falling in southwest Uganda: Evidence from a rural population cohort 1989-2005. AIDS 2008;22(13):1641-1649.
31. Yerly S, Jost S, Telenti A, et al.: Infrequent transmission of HIV-1 drug-resistant variants. Antivir Ther 2004;9(3): 375-384.
32. Mulder DW, Nunn AJ, Wagner HU, Kamali A, and Kengeya-Kayondo JF: HIV-1 incidence and HIV-1-Associated mortality in a rural Ugandan population cohort. AIDS 1994;8(1):87-92.
33. Mbulaiteye SM, Mahe C, Ruberantwari A, and Whitworth JA: Generalizability of population-based studies on AIDS: A comparison of newly and continuously surveyed villages in rural southwest Uganda. Int J Epidemiol 2002;31(5): 961-967.
34. Morgan D, Malamba SS, Maude GH, et al.: An HIV-1 natural history cohort and survival times in rural Uganda. AIDS 1997;11(5):633-640.
35. Uganda MoHaRo: National Antiretroviral Treatment and Care Guidelines for Adults and children, Kampala, 2003.
36. Ssemwanga D, Ndembi N, Lyagoba F, et al.: HIV type 1 subtype distribution, multiple infections, sexual networks, and partnership histories in female sex workers in Kampala, Uganda. AIDS Res Hum Retroviruses 2012;28(4): 357-365.
37. Ndembi N, Hamers RL, Sigaloff KC, et al.: Transmitted antiretroviral drug resistance among newly HIV-1 diagnosed young individuals in Kampala. AIDS 2011;25(7): 905-910.
38. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, and Kumar S: MEGA5: Molecular Evolutionary Genetics Analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011; 28(10):2731-2739.
39. Kimura M: A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980;16(2):111-120.
40. Saitou N and Nei M: The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol Biol Evol 1987;4(4):406-425.
41. de Oliveira T, Deforche K, Cassol S, et al.: An automated genotyping system for analysis of HIV-1 and other microbial sequences. Bioinformatics 2005;21(19):3797-3800.
42. Lole KS, Bollinger RC, Paranjape RS, et al.: Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination. J Virol 1999;73(1):152-160.
43. Collinson-Streng AN, Redd AD, Sewankambo NK, et al.: Geographic HIV type 1 subtype distribution in Rakai district, Uganda. AIDS Res Hum Retroviruses 2009;25(10):1045-1048.
44. Kiwanuka N, Robb M, Laeyendecker O, et al.: HIV-1 viral subtype differences in the rate of CD4 + T-cell decline among HIV seroincident antiretroviral naive persons in Rakai district, Uganda. J Acquir Immune Defic Syndr 2010;54(2):180-184.
45. Herbeck JT, Lyagoba F, Moore SW, et al.: Prevalence and genetic diversity of HIV type 1 subtypes A and D in women attending antenatal clinics in Uganda. AIDS Res Hum Retroviruses 2007;23(5):755-760.
46. Rainwater S, DeVange S, Sagar M, et al.: No evidence for rapid subtype C spread within an epidemic in which multiple subtypes and intersubtype recombinants circulate. AIDS Res Hum Retroviruses 2005;21(12):1060-1065.
47. Geretti AM, Harrison L, Green H, et al.: Effect of HIV-1 subtype on virologic and immunologic response to starting highly active antiretroviral therapy. Clin Infect Dis 2009; 48(9):1296-1305.