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Ssemwanga D, Lyagoba F, Magambo B, Kapaata A, Kirangwa J, Nannyonjo M, Nassolo F, Nsubuga R, Yebra G, Brown A, Kaleebu P. PHYLOGENETIC AND DEMOGRAPHIC CHARACTERISATION OF HIV-1 TRANSMISSION NETWORKS IN A GENERAL POPULATION COHORT IN UGANDA. BMJ Glob Health 2017. [DOI: 10.1136/bmjgh-2016-000260.23] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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Ssemwanga D, Nsubuga RN, Mayanja BN, Lyagoba F, Magambo B, Yirrell D, Van der Paal L, Grosskurth H, Kaleebu P. Effect of HIV-1 subtypes on disease progression in rural Uganda: a prospective clinical cohort study. PLoS One 2013; 8:e71768. [PMID: 23951241 PMCID: PMC3741119 DOI: 10.1371/journal.pone.0071768] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Accepted: 07/03/2013] [Indexed: 02/04/2023] Open
Abstract
Objective We examined the association of HIV-1 subtypes with disease progression based on three viral gene regions. Design A prospective HIV-1 clinical cohort study in rural Uganda. Methods Partial gag, env and pol genes were sequenced. Cox proportional hazard regression modelling was used to estimate adjusted hazard ratios (aHRs) of progression to: CD4≤250, AIDS onset and death, adjusted for sex, age and CD4 count at enrolment. Results Between 1990 and 2010, 292 incident cases were subtyped: 25% had subtype A, 45% had D, 26% had A/D recombinants, 1% had C and 4% were other recombinant forms. Of the 278 incident cases included in the disease progression analysis, 62% progressed to CD4≤250, 32% to AIDS, and 34% died with a higher proportion being among subtype D cases. The proportions of individuals progressing to the three endpoints were significantly higher among individuals infected with subtype D. Throughout the study period, individuals infected with subtype D progressed faster to CD4≤250, adjusted HR (aHR), (95% CI) = 1.72 (1.16–2.54), but this was mainly due to events in the period before antiretroviral therapy (ART) introduction, when individuals infected with subtype D significantly progressed faster to CD4≤250 than subtype A cases; aHR (95% CI) = 1.78 (1.01–3.14). Conclusions In this population, HIV-1 subtype D was the most prevalent and was associated with faster HIV-1 disease progression than subtype A. Further studies are needed to examine the effect of HIV-1 subtypes on disease progression in the ART period and their effect on the virological and immunological ART outcomes.
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Affiliation(s)
- Deogratius Ssemwanga
- Medical Research Council/Uganda Virus Research Institute Uganda Research Unit on AIDS, Entebbe, Uganda
| | - Rebecca N. Nsubuga
- Medical Research Council/Uganda Virus Research Institute Uganda Research Unit on AIDS, Entebbe, Uganda
| | - Billy N. Mayanja
- Medical Research Council/Uganda Virus Research Institute Uganda Research Unit on AIDS, Entebbe, Uganda
| | - Frederick Lyagoba
- Medical Research Council/Uganda Virus Research Institute Uganda Research Unit on AIDS, Entebbe, Uganda
| | - Brian Magambo
- Medical Research Council/Uganda Virus Research Institute Uganda Research Unit on AIDS, Entebbe, Uganda
| | - Dave Yirrell
- Department of Medical Microbiology, Ninewells Hospital, Dundee, United Kingdom
| | | | - Heiner Grosskurth
- Medical Research Council/Uganda Virus Research Institute Uganda Research Unit on AIDS, Entebbe, Uganda
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Pontiano Kaleebu
- Medical Research Council/Uganda Virus Research Institute Uganda Research Unit on AIDS, Entebbe, Uganda
- London School of Hygiene and Tropical Medicine, London, United Kingdom
- * E-mail:
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Kapaata A, Lyagoba F, Ssemwanga D, Magambo B, Nanyonjo M, Levin J, Mayanja BN, Mugasa C, Parry CM, Kaleebu P. HIV-1 subtype distribution trends and evidence of transmission clusters among incident cases in a rural clinical cohort in southwest Uganda, 2004-2010. AIDS Res Hum Retroviruses 2013; 29:520-7. [PMID: 23046049 DOI: 10.1089/aid.2012.0170] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The high diversity of HIV-1 has been shown to affect disease progression, transmission, and response to antiretroviral therapy and may influence HIV vaccine design. We describe the distribution trends of HIV-1 subtypes over a 7-year period among incident cases in a rural clinical cohort in Southwest Uganda and identify transmission clusters. Viral RNA was extracted from cryopreserved plasma samples from 94 participants who seroconverted and enrolled between 2004 and 2010. Partial gag (p24) and env (gp41) genes were directly sequenced to identify subtypes and transmission clusters with more than 95% bootstrap values. Direct sequencing of the partial pol gene and use of individual participant sexual life histories were also used to confirm these transmission clusters. The overall gag/env subtype distribution was A 28% (n=26), C 1% (n=1), and D 45% (n=42) and 27% (n=25) were intergene unique recombinant forms. The proportions of subtype A, D, or recombinants showed no significant increasing or decreasing trend over this time period (p=0.51). Phylogenetic analysis of the three genes confirmed 13 transmission clusters of which seven clusters were confirmed sexual partners using individual participants' sexual life histories. Subtype D has remained the predominant subtype in this population. From 2004 to 2010, there was no change in the proportions of these subtypes. Phylogenetic analysis and participants' sexual life histories revealed several transmission clusters. The high proportion of transmission clusters observed suggests continued high-risk sexual behavior and mixing in some individuals and possibly super transmitters in this presumed low-risk cohort, but also indicates that many transmissions occur in early HIV infection. This calls for early and targeted effective prevention and treatment intervention in this population.
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Affiliation(s)
- Anne Kapaata
- MRC/UVRI Uganda Research Unit on AIDS, Entebbe, Uganda
| | | | | | - Brian Magambo
- MRC/UVRI Uganda Research Unit on AIDS, Entebbe, Uganda
| | | | | | | | - Claire Mugasa
- Faculty of Veterinary Medicine, Makerere University, Kampala, Uganda
| | | | - Pontiano Kaleebu
- MRC/UVRI Uganda Research Unit on AIDS, Entebbe, Uganda
- London School of Hygiene and Tropical Medicine, London, United Kingdom
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Ssemwanga D, Kapaata A, Lyagoba F, Magambo B, Nanyonjo M, Mayanja BN, Parry CM, Kaleebu P. Low drug resistance levels among drug-naive individuals with recent HIV type 1 infection in a rural clinical cohort in southwestern Uganda. AIDS Res Hum Retroviruses 2012; 28:1784-7. [PMID: 22616647 DOI: 10.1089/aid.2012.0090] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
To investigate the prevalence of transmitted drug resistance (TDR) among individuals with recent HIV-1 infection between February 2004 and January 2010 in a rural clinical cohort, samples from 72 participants were analyzed. Results from the 72 participants showed no protease inhibitor and nucleoside reverse transcriptase inhibitor-associated mutations. One participant (1.4%, 95% CI: 0.04-7.5%) had two nonnucleoside reverse transcriptase inhibitor mutations (G190E and P225H). HIV-1 subtype frequencies were A 22 (30.6%), D 38 (52.8%), and C 1 (1.4%); 11 (15.3%) were A/D unique recombinant forms. Seven years after the scale up of antiretroviral therapy (ART) in a rural clinical cohort in Uganda, the prevalence of TDR among recently HIV-1-infected individuals was low at 1.4%. Since our findings from an HIV study cohort may not be generalizable to the general population, routine TDR surveys in specific populations may be necessary to inform policy on the magnitude and prevention strategies of TDR.
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Affiliation(s)
| | - Anne Kapaata
- MRC/UVRI Uganda Research Unit on AIDS, Entebbe, Uganda
| | | | - Brian Magambo
- MRC/UVRI Uganda Research Unit on AIDS, Entebbe, Uganda
| | | | | | | | - Pontiano Kaleebu
- MRC/UVRI Uganda Research Unit on AIDS, Entebbe, Uganda
- London School of Hygiene and Tropical Medicine, London, United Kingdom
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Ssemwanga D, Ndembi N, Lyagoba F, Magambo B, Kapaata A, Bukenya J, Lubega GW, Bertagnolio S, Vandepitte J, Grosskurth H, Kaleebu P. Transmitted antiretroviral drug resistance among drug-naive female sex workers with recent infection in Kampala, Uganda. Clin Infect Dis 2012; 54 Suppl 4:S339-42. [PMID: 22544200 DOI: 10.1093/cid/cir937] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
During 2006-2007, transmitted human immunodeficiency virus (HIV) drug resistance (TDR) among drug-naive women with newly diagnosed HIV infection and likely to be recently infected when attending antenatal clinics in Entebbe was found to be <5% with use of the World Health Organization (WHO) survey method. Using the same method, we attempted to classify TDR among women who seroconverted during 2008-2010 and who were identified from a cohort of recently infected sex workers in Kampala, Uganda. TDR mutations were identified using the 2009 WHO TDR mutations list. The WHO survey method could not be used to classify TDR because the necessary sample size was not reached during the survey period. However, a point prevalence estimate of 2.6% (95% confidence interval, 0.07%-13.8%) nonnucleoside reverse-transcriptase inhibitor TDR was determined.
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Sigaloff KC, Mandaliya K, Hamers RL, Otieno F, Jao IM, Lyagoba F, Magambo B, Kapaata A, Ndembi N, Rinke de Wit TF. Short communication: High prevalence of transmitted antiretroviral drug resistance among newly HIV type 1 diagnosed adults in Mombasa, Kenya. AIDS Res Hum Retroviruses 2012; 28:1033-7. [PMID: 22149307 DOI: 10.1089/aid.2011.0348] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Abstract In view of the recent antiretroviral therapy (ART) scale-up in Kenya, surveillance of transmitted HIV drug resistance (TDR) is important. A cross-sectional survey was conducted among newly HIV-1 diagnosed, antiretroviral-naive adults in Mombasa, Kenya. Surveillance drug resistance mutations (SDRMs) were identified according to the 2009 WHO list. HIV-1 subtypes were determined using REGA and SCUEAL subtyping tools. Genotypic test results were obtained for 68 of 81 participants, and SDRMs were identified in 9 samples. Resistance to nonnucleoside reverse transcriptase inhibitors (K103N) occurred in five participants, yielding a TDR prevalence of 7.4% (95% confidence interval 2.4-16.3%). Frequencies of HIV-1 subtypes were A (70.6%), C (5.9%), D (2.9%), and unique recombinant forms (20.6%). The TDR prevalence found in this survey is higher than previously reported in different regions in Kenya. These findings justify increased vigilance with respect to TDR surveillance in African regions where ART programs are scaled-up in order to inform treatment guidelines.
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Affiliation(s)
- Kim C.E. Sigaloff
- PharmAccess Foundation, Amsterdam, The Netherlands
- Department of Global Health, Academic Medical Centre of the University of Amsterdam, Amsterdam Institute for Global Health and Development, Amsterdam, The Netherlands
| | - Kishor Mandaliya
- Coast Province General Hospital, International Center for Reproductive Health, Mombasa, Kenya
| | - Raph L. Hamers
- PharmAccess Foundation, Amsterdam, The Netherlands
- Department of Global Health, Academic Medical Centre of the University of Amsterdam, Amsterdam Institute for Global Health and Development, Amsterdam, The Netherlands
| | - Francis Otieno
- Coast Province General Hospital, International Center for Reproductive Health, Mombasa, Kenya
| | - Irene M. Jao
- Coast Province General Hospital, International Center for Reproductive Health, Mombasa, Kenya
| | - Frederick Lyagoba
- Medical Research Council/Uganda Virus Research Institute, Uganda Research Unit on AIDS, Entebbe, Uganda
| | - Brian Magambo
- Medical Research Council/Uganda Virus Research Institute, Uganda Research Unit on AIDS, Entebbe, Uganda
| | - Anne Kapaata
- Medical Research Council/Uganda Virus Research Institute, Uganda Research Unit on AIDS, Entebbe, Uganda
| | | | - Tobias F. Rinke de Wit
- PharmAccess Foundation, Amsterdam, The Netherlands
- Department of Global Health, Academic Medical Centre of the University of Amsterdam, Amsterdam Institute for Global Health and Development, Amsterdam, The Netherlands
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Pillay D, Goodall R, Gilks CF, Yirrell D, Gibb D, Spyer M, Kaleebu P, Munderi P, Kityo C, McCormick A, Nkalubo J, Lyagoba F, Chirara M, Hakim J. Virological findings from the SARA trial: boosted PI monotherapy as maintenance second-line ART in Africa. J Int AIDS Soc 2010. [PMCID: PMC3112833 DOI: 10.1186/1758-2652-13-s4-o20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Mugyenyi P, Walker AS, Hakim J, Munderi P, Gibb DM, Kityo C, Reid A, Grosskurth H, Darbyshire JH, Ssali F, Bray D, Katabira E, Babiker AG, Gilks CF, Grosskurth H, Munderi P, Kabuye G, Nsibambi D, Kasirye R, Zalwango E, Nakazibwe M, Kikaire B, Nassuna G, Massa R, Fadhiru K, Namyalo M, Zalwango A, Generous L, Khauka P, Rutikarayo N, Nakahima W, Mugisha A, Todd J, Levin J, Muyingo S, Ruberantwari A, Kaleebu P, Yirrell D, Ndembi N, Lyagoba F, Hughes P, Aber M, Lara AM, Foster S, Amurwon J, Wakholi BN, Whitworth J, Wangati K, Amuron B, Kajungu D, Nakiyingi J, Omony W, Fadhiru K, Nsibambi D, Khauka P, Mugyenyi P, Kityo C, Ssali F, Tumukunde D, Otim T, Kabanda J, Musana H, Akao J, Kyomugisha H, Byamukama A, Sabiiti J, Komugyena J, Wavamunno P, Mukiibi S, Drasiku A, Byaruhanga R, Labeja O, Katundu P, Tugume S, Awio P, Namazzi A, Bakeinyaga GT, Katabira H, Abaine D, Tukamushaba J, Anywar W, Ojiambo W, Angweng E, Murungi S, Haguma W, Atwiine S, Kigozi J, Namale L, Mukose A, Mulindwa G, Atwiine D, Muhwezi A, Nimwesiga E, Barungi G, Takubwa J, Murungi S, Mwebesa D, Kagina G, Mulindwa M, Ahimbisibwe F, Mwesigwa P, Akuma S, Zawedde C, Nyiraguhirwa D, Tumusiime C, Bagaya L, Namara W, Kigozi J, Karungi J, Kankunda R, Enzama R, Latif A, Hakim J, Robertson V, Reid A, Chidziva E, Bulaya-Tembo R, Musoro G, Taziwa F, Chimbetete C, Chakonza L, Mawora A, Muvirimi C, Tinago G, Svovanapasis P, Simango M, Chirema O, Machingura J, Mutsai S, Phiri M, Bafana T, Chirara M, Muchabaiwa L, Muzambi M, Mutowo J, Chivhunga T, Chigwedere E, Pascoe M, Warambwa C, Zengeza E, Mapinge F, Makota S, Jamu A, Ngorima N, Chirairo H, Chitsungo S, Chimanzi J, Maweni C, Warara R, Matongo M, Mudzingwa S, Jangano M, Moyo K, Vere L, Mdege N, Machingura I, Katabira E, Ronald A, Kambungu A, Lutwama F, Mambule I, Nanfuka A, Walusimbi J, Nabankema E, Nalumenya R, Namuli T, Kulume R, Namata I, Nyachwo L, Florence A, Kusiima A, Lubwama E, Nairuba R, Oketta F, Buluma E, Waita R, Ojiambo H, Sadik F, Wanyama J, Nabongo P, Oyugi J, Sematala F, Muganzi A, Twijukye C, Byakwaga H, Ochai R, Muhweezi D, Coutinho A, Etukoit B, Gilks C, Boocock K, Puddephatt C, Grundy C, Bohannon J, Winogron D, Gibb DM, Burke A, Bray D, Babiker A, Walker AS, Wilkes H, Rauchenberger M, Sheehan S, Spencer-Drake C, Taylor K, Spyer M, Ferrier A, Naidoo B, Dunn D, Goodall R, Darbyshire JH, Peto L, Nanfuka R, Mufuka-Kapuya C, Kaleebu P, Pillay D, Robertson V, Yirrell D, Tugume S, Chirara M, Katundu P, Ndembi N, Lyagoba F, Dunn D, Goodall R, McCormick A, Lara AM, Foster S, Amurwon J, Wakholi BN, Kigozi J, Muchabaiwa L, Muzambi M, Weller I, Babiker A, Bahendeka S, Bassett M, Wapakhabulo AC, Darbyshire JH, Gazzard B, Gilks C, Grosskurth H, Hakim J, Latif A, Mapuchere C, Mugurungi O, Mugyenyi P, Burke C, Jones S, Newland C, Pearce G, Rahim S, Rooney J, Smith M, Snowden W, Steens JM, Breckenridge A, McLaren A, Hill C, Matenga J, Pozniak A, Serwadda D, Peto T, Palfreeman A, Borok M, Katabira E. Routine versus clinically driven laboratory monitoring of HIV antiretroviral therapy in Africa (DART): a randomised non-inferiority trial. Lancet 2010; 375:123-31. [PMID: 20004464 PMCID: PMC2805723 DOI: 10.1016/s0140-6736(09)62067-5] [Citation(s) in RCA: 220] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
BACKGROUND HIV antiretroviral therapy (ART) is often managed without routine laboratory monitoring in Africa; however, the effect of this approach is unknown. This trial investigated whether routine toxicity and efficacy monitoring of HIV-infected patients receiving ART had an important long-term effect on clinical outcomes in Africa. METHODS In this open, non-inferiority trial in three centres in Uganda and one in Zimbabwe, 3321 symptomatic, ART-naive, HIV-infected adults with CD4 counts less than 200 cells per microL starting ART were randomly assigned to laboratory and clinical monitoring (LCM; n=1659) or clinically driven monitoring (CDM; n=1662) by a computer-generated list. Haematology, biochemistry, and CD4-cell counts were done every 12 weeks. In the LCM group, results were available to clinicians; in the CDM group, results (apart from CD4-cell count) could be requested if clinically indicated and grade 4 toxicities were available. Participants switched to second-line ART after new or recurrent WHO stage 4 events in both groups, or CD4 count less than 100 cells per microL (LCM only). Co-primary endpoints were new WHO stage 4 HIV events or death, and serious adverse events. Non-inferiority was defined as the upper 95% confidence limit for the hazard ratio (HR) for new WHO stage 4 events or death being no greater than 1.18. Analyses were by intention to treat. This study is registered, number ISRCTN13968779. FINDINGS Two participants assigned to CDM and three to LCM were excluded from analyses. 5-year survival was 87% (95% CI 85-88) in the CDM group and 90% (88-91) in the LCM group, and 122 (7%) and 112 (7%) participants, respectively, were lost to follow-up over median 4.9 years' follow-up. 459 (28%) participants receiving CDM versus 356 (21%) LCM had a new WHO stage 4 event or died (6.94 [95% CI 6.33-7.60] vs 5.24 [4.72-5.81] per 100 person-years; absolute difference 1.70 per 100 person-years [0.87-2.54]; HR 1.31 [1.14-1.51]; p=0.0001). Differences in disease progression occurred from the third year on ART, whereas higher rates of switch to second-line treatment occurred in LCM from the second year. 283 (17%) participants receiving CDM versus 260 (16%) LCM had a new serious adverse event (HR 1.12 [0.94-1.32]; p=0.19), with anaemia the most common (76 vs 61 cases). INTERPRETATION ART can be delivered safely without routine laboratory monitoring for toxic effects, but differences in disease progression suggest a role for monitoring of CD4-cell count from the second year of ART to guide the switch to second-line treatment. FUNDING UK Medical Research Council, the UK Department for International Development, the Rockefeller Foundation, GlaxoSmithKline, Gilead Sciences, Boehringer-Ingelheim, and Abbott Laboratories.
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Serwanga J, Ndembi N, Nanteza B, Mugaba S, Pimego E, Pala P, Auma B, Lyagoba F, Kaleebu P. P20-10. Differences in patterns of Gag-induced immunogenetic pressure occur between clades A and D chronic HIV-1 infection in a Ugandan population. Retrovirology 2009. [PMCID: PMC2767893 DOI: 10.1186/1742-4690-6-s3-p380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Ndembi N, Lyagoba F, Nanteza B, Kushemererwa G, Serwanga J, Katongole-Mbidde E, Grosskurth H, Kaleebu P. Transmitted antiretroviral drug resistance surveillance among newly HIV type 1-diagnosed women attending an antenatal clinic in Entebbe, Uganda. AIDS Res Hum Retroviruses 2008; 24:889-95. [PMID: 18544019 DOI: 10.1089/aid.2007.0317] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
To evaluate transmitted HIV-1 drug resistance and study the natural polymorphism in pol of HIV-1 strains of newly diagnosed women attending an antenatal clinic in Uganda we sequenced the protease and reverse transcriptase genes for 46 HIV-1 strains from the threshold surveillance. Of the 46 sequences analyzed, 48.0% were subtype A1 (n 22), 39.0% subtype D (n 18), 2.0% subtype A2 (n 1), 2.0% subtype C (n 1), and 9.0% intersubtype recombinant A1/D (n 4). Overall, many minor mutations were identified in the protease sequences. None of the strains had major associated mutations to any RTI drug or drug class interest after genotyping 37 samples of our cohort. The HIV drug resistance prevalence estimate in Entebbe following the HIVDR-TS methodology is less than 5% as set out by WHO guidelines.
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Affiliation(s)
- N Ndembi
- MRC/UVR1/Uganda Research Unit on AIDS, Entebbe, Uganda
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Herbeck JT, Lyagoba F, Moore SW, Shindo N, Biryahwaho B, Kaleebu P, Mullins JI. Prevalence and genetic diversity of HIV type 1 subtypes A and D in women attending antenatal clinics in Uganda. AIDS Res Hum Retroviruses 2007; 23:755-60. [PMID: 17531003 DOI: 10.1089/aid.2006.0237.a] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
To monitor the relative prevalence and evolutionary trends of HIV-1 in Uganda, we conducted a retrospective study of pregnant women over the time period 1989-2000. From a total of 300 women sampled, we defined subtypes by heteroduplex mobility assay for 230 subjects and by partial sequencing and phylogenetic analyses of the env gene for 216 subjects. Subtypes A and D were most prevalent, and there were no significant trends in relative frequencies of subtypes A (45%), D (41%), C (5%), or recombinants (9%) over the 11 years sampled. There was also no phylogenetic clustering of subtypes related to geography (clinic location) or year of collection. Mean pairwise nucleotide diversity of subtype A (pi = 0.163) and subtype D (pi =0.156) samples did not differ significantly between subtypes, nor did these levels change over the period of the study. This report suggests that among pregnant women in Uganda A and D subtypes are transmitted without geographic constraints, and are not associated with significantly different transmission rates.
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Affiliation(s)
- Joshua T Herbeck
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington 98195-8070, USA
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Yirrell DL, Kaleebu P, Morgan D, Watera C, Magambo B, Lyagoba F, Whitworth J. Inter- and intra-genic intersubtype HIV-1 recombination in rural and semi-urban Uganda. AIDS 2002; 16:279-86. [PMID: 11807313 DOI: 10.1097/00002030-200201250-00018] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVE To investigate the number and variety of viruses with discrepant subtypes between env and gag and within gag in two cohorts in Uganda. METHODS Sequences were generated from PCR products amplified directly (without cloning) from patient blood and compared in the v3/v4 region of env and the p17 and p24 regions of gag to reference subtype strains by phylogenetic analysis. Gag sequences with a discrepant subtype between p17 and p24 were analysed further to indicate approximate sites of recombination. RESULTS Envelope subtypes D and A were predominant, but subtypes B, C and G were also found. From analysis of three short regions of the HIV genome we found 15 different combinations of subtype assortment, including 11 different recombinant permutations. Approximately 30% of viruses (29/104) in this part of Uganda appear to be recombinants between the env and gag genes and 10% (11/104) are recombinant within the gag gene. There was no clear pattern of crossover points within the gag gene. There seems to be no evidence of new circulating recombinant forms. CONCLUSION Both inter-genic and intra-genic inter-subtype recombination appear to be a relatively common occurrence in this geographical region where two subtypes of virus co-circulate. These results have implications for cross-clade vaccine design.
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Affiliation(s)
- David L Yirrell
- Centre for HIV Research, ICAPB, University of Edinburgh, Edinburgh, UK
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Kaleebu P, Ross A, Morgan D, Yirrell D, Oram J, Rutebemberwa A, Lyagoba F, Hamilton L, Biryahwaho B, Whitworth J. Relationship between HIV-1 Env subtypes A and D and disease progression in a rural Ugandan cohort. AIDS 2001; 15:293-9. [PMID: 11273208 DOI: 10.1097/00002030-200102160-00001] [Citation(s) in RCA: 86] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE To investigate the role of HIV-1 envelope subtypes on disease progression in a rural cohort of Ugandan adults where two major HIV-1 subtypes (A and D) exist. METHODS Participants of a clinical cohort seen between December 1995 and December 1998 had blood collected for HIV-1 subtyping. These included prevalent cases (people already infected with HIV at the start of the study in 1990) and incident cases (those who seroconverted between 1990 and December 1998). HIV-1 subtyping was carried out by heteroduplex mobility assay and DNA sequencing in the V3 env region. Disease progression was measured by the rate of CD4 lymphocyte count decline, clinical progression for the incident cases as time from seroconversion to AIDS or death, to first CD4 lymphocyte count < 200 x 10(6)/l and to the World Health Organization clinical stage 3. All analyses were adjusted for age and sex. RESULTS One hundred and sixty-four individuals, including 47 prevalent and 117 incident cases, had V3 env subtype data of which 65 (40%) were subtyped as A and 99 as D. In the incident cases, 44 (38%) were subtyped as A and 73 as D. There was a suggestion that for most end-points A had a slower progression than D. The cumulative probability of remaining free from AIDS or death at 6 years post-seroconversion was 0.72 [95% confidence interval (CI), 0.50 to 0.85] for A and 0.58 (95% CI, 0.42 to 0.71) for D, and the adjusted hazard ratio of subtype D compared to A was estimated to be 1.39 (95% CI, 0.66 to 2.94; P = 0.39). The estimated difference in rates of decline in square root CD4 lymphocyte counts was -0.41 per year (95% CI, -0.98 to 0.15; P = 0.15). CONCLUSION This study suggests that although subtype A may have a slower progression than D, HIV-1 envelope subtype is not a major factor in determining the progression of HIV-1 disease in a rural population in Uganda.
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Affiliation(s)
- P Kaleebu
- Medical Research Council Programme on AIDS in Uganda, Uganda Virus Research Institute, Entebbe
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Kaleebu P, Yirrell D, French N, Lyagoba F, Rutebemberwa A, Cheingsong-Popov R, Gilks C, Biryahwaho B, Weber J, Whitworth J. An improved algorithm for determining HIV type 1 subtypes in a primary laboratory in Uganda. AIDS Res Hum Retroviruses 2000; 16:621-5. [PMID: 10791872 DOI: 10.1089/088922200308846] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A pilot study was undertaken with the objective of developing a simple, economical, and efficient algorithm through which to subtype HIV-1 in a large epidemiological cohort study in Uganda. A peptide enzyme immunoassay (PEIA) employing both V3 and gp41 regions and a heteroduplex mobility assay (HMA) were evaluated in comparison with DNA sequencing. Of 146 samples selected, 115 (79%) were successfully sequenced. Taking sequence data as the "gold standard," other assays were compared with these data. The HMA correctly identified 95 (83%) of the samples, and only 1 sample was wrongly identified. The V3 PEIA alone and in combination with gp41 peptides correctly identified 76 and 78% of the samples, respectively; however, the number of wrongly identified samples was four times less with the combination compared with V3 peptides alone (4 versus 16%). The sensitivity, specificity, and positive and negative predictive values for serotype A and D samples were greater for the combination than V3 peptides alone. We have described a new algorithm to segregate subtypes A and D. This algorithm uses the two peptide assays followed by HMA and then DNA sequencing for untypable samples, giving an accuracy of 95% at a cost of 37 and 21% for consumables compared with subtyping all the samples by HMA or DNA sequencing, respectively. This proposed approach is suitable for epidemiological studies in Uganda and other regions with a predominance of A and D subtypes.
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Affiliation(s)
- P Kaleebu
- Medical Research Council Programme on AIDS in Uganda, Uganda Virus Research Institute, Entebbe.
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Kaleebu P, Whitworth J, Hamilton L, Rutebemberwa A, Lyagoba F, Morgan D, Duffield M, Biryahwaho B, Magambo B, Oram J. Molecular epidemiology of HIV type 1 in a rural community in southwest Uganda. AIDS Res Hum Retroviruses 2000; 16:393-401. [PMID: 10772525 DOI: 10.1089/088922200309052] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The molecular epidemiology of a population-based cohort in a cluster of 15 villages in southwestern Uganda was investigated by sequencing part of the p24 gag gene and performing heteroduplex mobility assays (HMAs) of the V3 region of the env gene. Sequence and HMA data, obtained for 69 and 88 proviruses, respectively, showed that the clade A and D viruses were present at a ratio of about 0.67:1. No other clades were detected. Thirteen (22%) of 59 proviruses for which both gag and env data were obtained appeared to be recombinants. Although both clade A and D viruses were present in 13 of the villages, their distribution was unequal: for example, from env data 59% of clade A viruses were found in the eastern villages, compared with only 27% of clade D viruses. Phylogenetic (maximum likelihood) analysis of the p24 gag sequences showed a total of five clusters supported by bootstrap resampling values above or close to 75%. Four clusters were sexual partners, but there was no known sexual contact between the persons in the other cluster. The DNA sequences showed between 0.5 and 8.3% divergence from the cohort clade A or D consensus sequences. The sequences were not closely related to those published for other clade A or D proviruses.
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Affiliation(s)
- P Kaleebu
- Medical Research Council Programme for AIDS in Uganda/Uganda Virus Research Institute, Entebbe.
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Ali S, Lyagoba F, Biryawaho B, Nunn A, Wagner HV, Malamba S, Whitworth J, Mulder D, Hill A. MHC polymorphisms associated with HIV infection in Uganda. Hum Immunol 1996. [DOI: 10.1016/0198-8859(96)85349-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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