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Grant HE, Roy S, Williams R, Tutill H, Ferns B, Cane PA, Carswell JW, Ssemwanga D, Kaleebu P, Breuer J, Leigh Brown AJ. A large population sample of African HIV genomes from the 1980s reveals a reduction in subtype D over time associated with propensity for CXCR4 tropism. Retrovirology 2022; 19:28. [PMID: 36514107 PMCID: PMC9746199 DOI: 10.1186/s12977-022-00612-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 11/12/2022] [Indexed: 12/15/2022] Open
Abstract
We present 109 near full-length HIV genomes amplified from blood serum samples obtained during early 1986 from across Uganda, which to our knowledge is the earliest and largest population sample from the initial phase of the HIV epidemic in Africa. Consensus sequences were made from paired-end Illumina reads with a target-capture approach to amplify HIV material following poor success with standard approaches. In comparisons with a smaller 'intermediate' genome dataset from 1998 to 1999 and a 'modern' genome dataset from 2007 to 2016, the proportion of subtype D was significantly higher initially, dropping from 67% (73/109), to 57% (26/46) to 17% (82/465) respectively (p < 0.0001). Subtype D has previously been shown to have a faster rate of disease progression than other subtypes in East African population studies, and to have a higher propensity to use the CXCR4 co-receptor ("X4 tropism"); associated with a decrease in time to AIDS. Here we find significant differences in predicted tropism between A1 and D subtypes in all three sample periods considered, which is particularly striking the 1986 sample: 66% (53/80) of subtype D env sequences were predicted to be X4 tropic compared with none of the 24 subtype A1. We also analysed the frequency of subtype in the envelope region of inter-subtype recombinants, and found that subtype A1 is over-represented in env, suggesting recombination and selection have acted to remove subtype D env from circulation. The reduction of subtype D frequency over three decades therefore appears to be a result of selective pressure against X4 tropism and its higher virulence. Lastly, we find a subtype D specific codon deletion at position 24 of the V3 loop, which may explain the higher propensity for subtype D to utilise X4 tropism.
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Affiliation(s)
- Heather E Grant
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK.
| | - Sunando Roy
- Division of Infection and Immunity, University College London, London, UK
| | - Rachel Williams
- UCL Great Ormond Street Institute of Child Health, London, UK
| | - Helena Tutill
- Division of Infection and Immunity, University College London, London, UK
| | - Bridget Ferns
- Department of Virology, University College London Hospitals NHS Foundation Trust, London, UK
| | | | | | - Deogratius Ssemwanga
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
| | - Pontiano Kaleebu
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
| | - Judith Breuer
- Division of Infection and Immunity, University College London, London, UK
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Gore DJ, Schueler K, Ramani S, Uvin A, Phillips G, McNulty M, Fujimoto K, Schneider J. HIV Response Interventions that Integrate HIV Molecular Cluster and Social Network Analysis: A Systematic Review. AIDS Behav 2022; 26:1750-1792. [PMID: 34779940 PMCID: PMC9842229 DOI: 10.1007/s10461-021-03525-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/01/2021] [Indexed: 01/19/2023]
Abstract
Due to improved efficiency and reduced cost of viral sequencing, molecular cluster analysis can be feasibly utilized alongside existing human immunodeficiency virus (HIV) prevention strategies. The goal of this paper is to elucidate how HIV molecular cluster and social network analyses are being integrated to implement HIV response interventions. We searched PubMed, Scopus, PsycINFO, and Cochrane Library databases for studies incorporating both HIV molecular cluster and social network data. We identified 32 articles that combined analyses of HIV molecular sequences and social or sexual networks. All studies were descriptive. Six studies described network interventions informed by molecular and social data but did not fully evaluate their efficacy. There is no current standard for incorporating molecular and social network analyses to inform interventions or data demonstrating its utility. More research must be conducted to delineate benefits and best practices for leveraging molecular data for network-based interventions.
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Affiliation(s)
- Daniel J Gore
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Kellie Schueler
- Department of Obstetrics and Gynecology, University of California San Diego, San Diego, CA, USA
| | - Santhoshini Ramani
- The Chicago Center for HIV Elimination, University of Chicago, 5841 S Maryland Ave, MC5065, Chicago, IL, 60637, USA
| | - Arno Uvin
- The Chicago Center for HIV Elimination, University of Chicago, 5841 S Maryland Ave, MC5065, Chicago, IL, 60637, USA
| | - Gregory Phillips
- Department of Medical Social Sciences, Northwestern University, Chicago, IL, USA
| | - Moira McNulty
- The Chicago Center for HIV Elimination, University of Chicago, 5841 S Maryland Ave, MC5065, Chicago, IL, 60637, USA
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Kayo Fujimoto
- Department of Health Promotion & Behavioral Sciences, University of Texas Health Sciences Center, Houston, TX, USA
| | - John Schneider
- The Chicago Center for HIV Elimination, University of Chicago, 5841 S Maryland Ave, MC5065, Chicago, IL, 60637, USA.
- Department of Medicine, University of Chicago, Chicago, IL, USA.
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Musema GMA, Akilimali PZ, za Balega TKN, Tshala-Katumbay D, Lusamba PSD. Predictive Factors of HIV-1 Drug Resistance and Its Distribution among Female Sex Workers in the Democratic Republic of the Congo (DRC). INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19042021. [PMID: 35206211 PMCID: PMC8872192 DOI: 10.3390/ijerph19042021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 02/01/2022] [Accepted: 02/07/2022] [Indexed: 01/27/2023]
Abstract
The predictive factors of HIV-1 drug resistance and its distribution are poorly documented in female sex workers (FSWs) in the Democratic Republic of the Congo (DRC). However, the identification of predictive factors can lead to the development of improved and effective antiretroviral therapy (ART). The objective of the current study was to determine the predictive factors of HIV-1 drug resistance and its distribution based on FSWs in the studied regions in the Democratic Republic of the Congo (DRC). HIV-positive FSWs who were diagnosed as part of the DRC Integrated Biological and Behavioral Surveillance Survey (IBBS) were included in this study. A total of 325 FSWs participated. The HIV-1 viral load (VL) was measured according to the Abbott m2000sp and m2000rt protocols. The homogeneity chi-square test was conducted to determine the homogeneity of HIV-1 drug resistance distribution. Using a significance level of 0.05, multivariate analyses were performed to identify factors associated with HIV-1 drug resistance to ART. HIV drug resistance mutation (HIVDRM) distribution was homogeneous in the three study regions (p = 0.554) but differed based on the HIV-1 VLs of the FSWs. FSWs with high HIV-1 VLs harbored more HIVDRMs (p = 0.028) of predominantly pure HIV-1 strains compared with those that had low HIV-1 VLs. Sexually transmitted infection (STI) history (aOR [95%CI] = 8.51 [1.62, 44.74]), high HIV-1 VLs (aOR [95%CI] = 5.39 [1.09, 26.74]), and HIV-1-syphilis coinfection (aOR [95%CI] = 9.71 [1.84, 51.27]) were associated with HIV drug resistance among FSWs in the DRC. A history of STIs (e.g., abnormal fluid) in the 12 months prior to the survey, a high HIV-1 VL, and HIV-1-syphilis coinfection were associated with HIV-1 drug resistance among FSWs in the DRC. Efforts should be made to systematically test for other infections which increase the HIV-1 VL, in the case of HIV-1 coinfection, in order to maintain ART effectiveness across the DRC.
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Affiliation(s)
- Godefroid Mulakilwa Ali Musema
- Kinshasa School of Public Health, University of Kinshasa, Kinshasa P.O. Box 11850, Democratic Republic of the Congo; (G.M.A.M.); (P.-S.D.L.)
| | - Pierre Zalagile Akilimali
- Kinshasa School of Public Health, University of Kinshasa, Kinshasa P.O. Box 11850, Democratic Republic of the Congo; (G.M.A.M.); (P.-S.D.L.)
- Correspondence: ; Tel.: +24-38-1580-0288
| | | | - Désiré Tshala-Katumbay
- Department of Neurology, School of Medicine and School of Public Health, Oregon Health & Science University, Portland, OR 97239, USA;
- Department of Neurology, School of Medicine, University of Kinshasa, Kinshasa P.O. Box 11850, Democratic Republic of the Congo
- Institut National de Recherches Biomédicales, Kinshasa P.O. Box 11850, Democratic Republic of the Congo
| | - Paul-Samson Dikasa Lusamba
- Kinshasa School of Public Health, University of Kinshasa, Kinshasa P.O. Box 11850, Democratic Republic of the Congo; (G.M.A.M.); (P.-S.D.L.)
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Nduva GM, Nazziwa J, Hassan AS, Sanders EJ, Esbjörnsson J. The Role of Phylogenetics in Discerning HIV-1 Mixing among Vulnerable Populations and Geographic Regions in Sub-Saharan Africa: A Systematic Review. Viruses 2021; 13:1174. [PMID: 34205246 PMCID: PMC8235305 DOI: 10.3390/v13061174] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/09/2021] [Accepted: 06/10/2021] [Indexed: 12/19/2022] Open
Abstract
To reduce global HIV-1 incidence, there is a need to understand and disentangle HIV-1 transmission dynamics and to determine the geographic areas and populations that act as hubs or drivers of HIV-1 spread. In Sub-Saharan Africa (sSA), the region with the highest HIV-1 burden, information about such transmission dynamics is sparse. Phylogenetic inference is a powerful method for the study of HIV-1 transmission networks and source attribution. In this review, we assessed available phylogenetic data on mixing between HIV-1 hotspots (geographic areas and populations with high HIV-1 incidence and prevalence) and areas or populations with lower HIV-1 burden in sSA. We searched PubMed and identified and reviewed 64 studies on HIV-1 transmission dynamics within and between risk groups and geographic locations in sSA (published 1995-2021). We describe HIV-1 transmission from both a geographic and a risk group perspective in sSA. Finally, we discuss the challenges facing phylogenetic inference in mixed epidemics in sSA and offer our perspectives and potential solutions to the identified challenges.
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Affiliation(s)
- George M. Nduva
- Department of Translational Medicine, Lund University, 205 02 Malmö, Sweden; (G.M.N.); (J.N.); (A.S.H.)
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi 80108, Kenya;
| | - Jamirah Nazziwa
- Department of Translational Medicine, Lund University, 205 02 Malmö, Sweden; (G.M.N.); (J.N.); (A.S.H.)
| | - Amin S. Hassan
- Department of Translational Medicine, Lund University, 205 02 Malmö, Sweden; (G.M.N.); (J.N.); (A.S.H.)
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi 80108, Kenya;
| | - Eduard J. Sanders
- Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi 80108, Kenya;
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, The University of Oxford, Oxford OX1 2JD, UK
| | - Joakim Esbjörnsson
- Department of Translational Medicine, Lund University, 205 02 Malmö, Sweden; (G.M.N.); (J.N.); (A.S.H.)
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, The University of Oxford, Oxford OX1 2JD, UK
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Phylogenetic Networks and Parameters Inferred from HIV Nucleotide Sequences of High-Risk and General Population Groups in Uganda: Implications for Epidemic Control. Viruses 2021; 13:v13060970. [PMID: 34073846 PMCID: PMC8225143 DOI: 10.3390/v13060970] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 05/13/2021] [Accepted: 05/18/2021] [Indexed: 12/17/2022] Open
Abstract
Phylogenetic inference is useful in characterising HIV transmission networks and assessing where prevention is likely to have the greatest impact. However, estimating parameters that influence the network structure is still scarce, but important in evaluating determinants of HIV spread. We analyzed 2017 HIV pol sequences (728 Lake Victoria fisherfolk communities (FFCs), 592 female sex workers (FSWs) and 697 general population (GP)) to identify transmission networks on Maximum Likelihood (ML) phylogenetic trees and refined them using time-resolved phylogenies. Network generative models were fitted to the observed degree distributions and network parameters, and corrected Akaike Information Criteria and Bayesian Information Criteria values were estimated. 347 (17.2%) HIV sequences were linked on ML trees (maximum genetic distance ≤4.5%, ≥95% bootstrap support) and, of these, 303 (86.7%) that consisted of pure A1 (n = 168) and D (n = 135) subtypes were analyzed in BEAST v1.8.4. The majority of networks (at least 40%) were found at a time depth of ≤5 years. The waring and yule models fitted best networks of FFCs and FSWs respectively while the negative binomial model fitted best networks in the GP. The network structure in the HIV-hyperendemic FFCs is likely to be scale-free and shaped by preferential attachment, in contrast to the GP. The findings support the targeting of interventions for FFCs in a timely manner for effective epidemic control. Interventions ought to be tailored according to the dynamics of the HIV epidemic in the target population and understanding the network structure is critical in ensuring the success of HIV prevention programs.
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Ssemwanga D, Bbosa N, Nsubuga RN, Ssekagiri A, Kapaata A, Nannyonjo M, Nassolo F, Karabarinde A, Mugisha J, Seeley J, Yebra G, Leigh Brown A, Kaleebu P. The Molecular Epidemiology and Transmission Dynamics of HIV Type 1 in a General Population Cohort in Uganda. Viruses 2020; 12:v12111283. [PMID: 33182587 PMCID: PMC7697205 DOI: 10.3390/v12111283] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/01/2020] [Accepted: 10/02/2020] [Indexed: 12/13/2022] Open
Abstract
The General Population Cohort (GPC) in south-western Uganda has a low HIV-1 incidence rate (<1%). However, new infections continue to emerge. In this research, 3796 HIV-1 pol sequences (GPC: n = 1418, non-GPC sites: n = 1223, Central Uganda: n = 1010 and Eastern Uganda: n = 145) generated between 2003–2015 were analysed using phylogenetic methods with demographic data to understand HIV-1 transmission in this cohort and inform the epidemic response. HIV-1 subtype A1 was the most prevalent strain in the GPC area (GPC and non-GPC sites) (39.8%), central (45.9%) and eastern (52.4%) Uganda. However, in the GPC alone, subtype D was the predominant subtype (39.1%). Of the 524 transmission clusters identified by Cluster Picker, all large clusters (≥5 individuals, n = 8) involved individuals from the GPC. In a multivariate analysis, clustering was strongly associated with being female (adjusted Odds Ratio, aOR = 1.28; 95% CI, 1.06–1.54), being >25 years (aOR = 1.52; 95% CI, 1.16–2.0) and being a resident in the GPC (aOR = 6.90; 95% CI, 5.22–9.21). Phylogeographic analysis showed significant viral dissemination (Bayes Factor test, BF > 3) from the GPC without significant viral introductions (BF < 3) into the GPC. The findings suggest localized HIV-1 transmission in the GPC. Intensifying geographically focused combination interventions in the GPC would contribute towards controlling HIV-1 infections.
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Affiliation(s)
- Deogratius Ssemwanga
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe 256, Uganda; (N.B.); (R.N.N.); (A.K.); (M.N.); (F.N.); (A.K.); (J.M.); (J.S.); (P.K.)
- Department of General Virology, Uganda Virus Research Institute, Entebbe 256, Uganda;
- Correspondence: ; Tel.: +256-(0)-417-704000
| | - Nicholas Bbosa
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe 256, Uganda; (N.B.); (R.N.N.); (A.K.); (M.N.); (F.N.); (A.K.); (J.M.); (J.S.); (P.K.)
| | - Rebecca N. Nsubuga
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe 256, Uganda; (N.B.); (R.N.N.); (A.K.); (M.N.); (F.N.); (A.K.); (J.M.); (J.S.); (P.K.)
| | - Alfred Ssekagiri
- Department of General Virology, Uganda Virus Research Institute, Entebbe 256, Uganda;
| | - Anne Kapaata
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe 256, Uganda; (N.B.); (R.N.N.); (A.K.); (M.N.); (F.N.); (A.K.); (J.M.); (J.S.); (P.K.)
| | - Maria Nannyonjo
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe 256, Uganda; (N.B.); (R.N.N.); (A.K.); (M.N.); (F.N.); (A.K.); (J.M.); (J.S.); (P.K.)
| | - Faridah Nassolo
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe 256, Uganda; (N.B.); (R.N.N.); (A.K.); (M.N.); (F.N.); (A.K.); (J.M.); (J.S.); (P.K.)
| | - Alex Karabarinde
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe 256, Uganda; (N.B.); (R.N.N.); (A.K.); (M.N.); (F.N.); (A.K.); (J.M.); (J.S.); (P.K.)
| | - Joseph Mugisha
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe 256, Uganda; (N.B.); (R.N.N.); (A.K.); (M.N.); (F.N.); (A.K.); (J.M.); (J.S.); (P.K.)
| | - Janet Seeley
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe 256, Uganda; (N.B.); (R.N.N.); (A.K.); (M.N.); (F.N.); (A.K.); (J.M.); (J.S.); (P.K.)
- Department of Global Health and Development, London School of Hygiene and Tropical Medicine, 15-17 Tavistock Place, London WC1H 9SH, UK
| | - Gonzalo Yebra
- The Roslin Institute, Royal (Dick) School of Veterinary Medicine, University of Edinburgh, Easter Bush Campus, Edinburgh EH25 9RG, UK;
| | - Andrew Leigh Brown
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK;
| | - Pontiano Kaleebu
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe 256, Uganda; (N.B.); (R.N.N.); (A.K.); (M.N.); (F.N.); (A.K.); (J.M.); (J.S.); (P.K.)
- Department of General Virology, Uganda Virus Research Institute, Entebbe 256, Uganda;
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Grant HE, Hodcroft EB, Ssemwanga D, Kitayimbwa JM, Yebra G, Esquivel Gomez LR, Frampton D, Gall A, Kellam P, de Oliveira T, Bbosa N, Nsubuga RN, Kibengo F, Kwan TH, Lycett S, Kao R, Robertson DL, Ratmann O, Fraser C, Pillay D, Kaleebu P, Leigh Brown AJ. Pervasive and non-random recombination in near full-length HIV genomes from Uganda. Virus Evol 2020; 6:veaa004. [PMID: 32395255 PMCID: PMC7204518 DOI: 10.1093/ve/veaa004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Recombination is an important feature of HIV evolution, occurring both within and between the major branches of diversity (subtypes). The Ugandan epidemic is primarily composed of two subtypes, A1 and D, that have been co-circulating for 50 years, frequently recombining in dually infected patients. Here, we investigate the frequency of recombinants in this population and the location of breakpoints along the genome. As part of the PANGEA-HIV consortium, 1,472 consensus genome sequences over 5 kb have been obtained from 1,857 samples collected by the MRC/UVRI & LSHTM Research unit in Uganda, 465 (31.6 per cent) of which were near full-length sequences (>8 kb). Using the subtyping tool SCUEAL, we find that of the near full-length dataset, 233 (50.1 per cent) genomes contained only one subtype, 30.8 per cent A1 (n = 143), 17.6 per cent D (n = 82), and 1.7 per cent C (n = 8), while 49.9 per cent (n = 232) contained more than one subtype (including A1/D (n = 164), A1/C (n = 13), C/D (n = 9); A1/C/D (n = 13), and 33 complex types). K-means clustering of the recombinant A1/D genomes revealed a section of envelope (C2gp120-TMgp41) is often inherited intact, whilst a generalized linear model was used to demonstrate significantly fewer breakpoints in the gag-pol and envelope C2-TM regions compared with accessory gene regions. Despite similar recombination patterns in many recombinants, no clearly supported circulating recombinant form (CRF) was found, there was limited evidence of the transmission of breakpoints, and the vast majority (153/164; 93 per cent) of the A1/D recombinants appear to be unique recombinant forms. Thus, recombination is pervasive with clear biases in breakpoint location, but CRFs are not a significant feature, characteristic of a complex, and diverse epidemic.
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Affiliation(s)
- Heather E Grant
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Emma B Hodcroft
- Biozentrum, University of Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Deogratius Ssemwanga
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
- Uganda Virus Research Institute, Entebbe, Uganda
| | | | - Gonzalo Yebra
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | | | - Dan Frampton
- Division of Infection and Immunity, University College London, London, UK
| | - Astrid Gall
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - Paul Kellam
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - Tulio de Oliveira
- Nelson R. Mandela School of Medicine, Africa Health Research Institute, Durban, South Africa
| | - Nicholas Bbosa
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
| | - Rebecca N Nsubuga
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
| | - Freddie Kibengo
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
| | - Tsz Ho Kwan
- Stanley Ho Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Samantha Lycett
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Rowland Kao
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | | | - Oliver Ratmann
- Department of Mathematics, Imperial College London, London, UK
| | - Christophe Fraser
- Nuffield Department of Medicine, Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Deenan Pillay
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
- Nelson R. Mandela School of Medicine, Africa Health Research Institute, Durban, South Africa
| | - Pontiano Kaleebu
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
- Uganda Virus Research Institute, Entebbe, Uganda
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HIV controllers suppress viral replication and evolution and prevent disease progression following intersubtype HIV-1 superinfection. AIDS 2019; 33:399-410. [PMID: 30531316 DOI: 10.1097/qad.0000000000002090] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
OBJECTIVE The aim of this study was to investigate the impact of intersubtype HIV-1 superinfection on viremia, reservoir reseeding, viral evolution and disease progression in HIV controllers (HIC). DESIGN A longitudinal analysis of two Brazilian HIC individuals (EEC09 and VC32) previously identified as dually infected with subtypes B and F1 viruses. METHODS Changes in plasma viremia, total HIV-1 DNA levels, CD4+ T-cell counts and HIV-1 quasispecies composition were measured over time. HIV-1 env diversity in peripheral blood mononuclear cell (PBMC) and plasma samples was accessed by single genome amplification and next-generation sequencing approaches, respectively. Viral evolution was evaluated by estimating nucleotide diversity and divergence. RESULTS Individual EEC09 was probably initially infected with a CCR5-tropic subtype B strain and sequentially superinfected with a CXCR4-tropic subtype B strain and with a subtype F1 variant. Individual VC32 was infected with a subtype B strain and superinfected with a subtype F1 variant. The intersubtype superinfection events lead to a moderate increase in viremia and extensive turnover of viral population in plasma but exhibited divergent impact on the size and composition of cell-associated HIV DNA population. Both individuals maintained virologic control (<2000 copies/ml) and presented no evidence of viral evolution or immunologic progression for at least 2 years after the intersubtype superinfection event. CONCLUSION These data revealed that some HIC are able to repeatedly limit replication and evolution of superinfecting viral strains of a different subtype with no signs of disease progression.
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Prevalence and clinical impacts of HIV-1 intersubtype recombinants in Uganda revealed by near-full-genome population and deep sequencing approaches. AIDS 2017; 31:2345-2354. [PMID: 28832407 DOI: 10.1097/qad.0000000000001619] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
OBJECTIVES HIV-1 subtypes A1 and D cocirculate in a rural community in Mbarara, Uganda. This study examines HIV-1 intersubtype recombination in this community under a full-genome sequencing context. We aim to estimate prevalence, examine time trends, and test for clinical correlates and outcomes associated with intersubtype recombinants. METHODS Near-full-genome HIV-1 Sanger sequence data were collected from plasma samples of 504 treatment-naïve individuals, who then received protease inhibitor or nonnucleoside reverse transcriptase inhibitor-containing regimens and were monitored for up to 7.5 years. Subtypes were inferred by Los Alamos Recombinant Identification Program (RIP) 3.0 and compared with Sanger/REGA and MiSeq/RIP. 'Nonrecombinants' and 'recombinants' infections were compared in terms of pretherapy viral load, CD4 cell count, posttherapy time to virologic suppression, virologic rebound, first CD4 rise above baseline and sustained CD4 recovery. RESULTS Prevalence of intersubtype recombinants varied depending on the genomic region examined: gag (15%), prrt (11%), int (8%), vif (10%), vpr (2%), vpu (9%), GP120 (8%), GP41 (18%), and nef (4%). Of the 200 patients with near-full-genome data, prevalence of intersubtype recombination was 46%; the most frequently observed recombinant was A1-D (25%). Sanger/REGA and MiSeq/RIP yielded generally consistent results. Phylogenetic tree revealed most recombinants did not share common ancestors. No temporal trend was observed (all P > 0.1). Subsequent subtype switches were detected in 27 of 143 (19%) study participants with follow-up sequences. Nonrecombinant versus recombinants infections were not significantly different in any pre nor posttherapy clinical correlates examined (all P > 0.2). CONCLUSION Intersubtype recombination was highly prevalent (46%) in Uganda if the entire HIV genome was considered, but was neither associated with clinical correlates nor therapy outcomes.
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Kiwuwa-Muyingo S, Nazziwa J, Ssemwanga D, Ilmonen P, Njai H, Ndembi N, Parry C, Kitandwe PK, Gershim A, Mpendo J, Neilsen L, Seeley J, Seppälä H, Lyagoba F, Kamali A, Kaleebu P. HIV-1 transmission networks in high risk fishing communities on the shores of Lake Victoria in Uganda: A phylogenetic and epidemiological approach. PLoS One 2017; 12:e0185818. [PMID: 29023474 PMCID: PMC5638258 DOI: 10.1371/journal.pone.0185818] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 09/20/2017] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Fishing communities around Lake Victoria in sub-Saharan Africa have been characterised as a population at high risk of HIV-infection. METHODS Using data from a cohort of HIV-positive individuals aged 13-49 years, enrolled from 5 fishing communities on Lake Victoria between 2009-2011, we sought to identify factors contributing to the epidemic and to understand the underlying structure of HIV transmission networks. Clinical and socio-demographic data were combined with HIV-1 phylogenetic analyses. HIV-1 gag-p24 and env-gp-41 sub-genomic fragments were amplified and sequenced from 283 HIV-1-infected participants. Phylogenetic clusters with ≥2 highly related sequences were defined as transmission clusters. Logistic regression models were used to determine factors associated with clustering. RESULTS Altogether, 24% (n = 67/283) of HIV positive individuals with sequences fell within 34 phylogenetically distinct clusters in at least one gene region (either gag or env). Of these, 83% occurred either within households or within community; 8/34 (24%) occurred within household partnerships, and 20/34 (59%) within community. 7/12 couples (58%) within households clustered together. Individuals in clusters with potential recent transmission (11/34) were more likely to be younger 71% (15/21) versus 46% (21/46) in un-clustered individuals and had recently become resident in the community 67% (14/21) vs 48% (22/46). Four of 11 (36%) potential transmission clusters included incident-incident transmissions. Independently, clustering was less likely in HIV subtype D (adjusted Odds Ratio, aOR = 0.51 [95% CI 0.26-1.00]) than A and more likely in those living with an HIV-infected individual in the household (aOR = 6.30 [95% CI 3.40-11.68]). CONCLUSIONS A large proportion of HIV sexual transmissions occur within house-holds and within communities even in this key mobile population. The findings suggest localized HIV transmissions and hence a potential benefit for the test and treat approach even at a community level, coupled with intensified HIV counselling to identify early infections.
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Affiliation(s)
- Sylvia Kiwuwa-Muyingo
- Medical Research Council/Uganda Virus Research Institute, Research Unit on AIDS, Entebbe, Uganda
| | - Jamirah Nazziwa
- Medical Research Council/Uganda Virus Research Institute, Research Unit on AIDS, Entebbe, Uganda
| | - Deogratius Ssemwanga
- Medical Research Council/Uganda Virus Research Institute, Research Unit on AIDS, Entebbe, Uganda
| | - Pauliina Ilmonen
- Aalto University, School of Science, Department of Mathematics and Systems Analysis, Espoo, Finland
| | - Harr Njai
- Medical Research Council/Uganda Virus Research Institute, Research Unit on AIDS, Entebbe, Uganda
| | - Nicaise Ndembi
- Medical Research Council/Uganda Virus Research Institute, Research Unit on AIDS, Entebbe, Uganda
| | - Chris Parry
- Medical Research Council/Uganda Virus Research Institute, Research Unit on AIDS, Entebbe, Uganda
| | | | - Asiki Gershim
- Medical Research Council/Uganda Virus Research Institute, Research Unit on AIDS, Entebbe, Uganda
| | | | - Leslie Neilsen
- International AIDS Vaccine Initiative, New York, United States of America
| | - Janet Seeley
- Medical Research Council/Uganda Virus Research Institute, Research Unit on AIDS, Entebbe, Uganda
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Heikki Seppälä
- Aalto University, School of Science, Department of Mathematics and Systems Analysis, Espoo, Finland
| | - Fred Lyagoba
- Medical Research Council/Uganda Virus Research Institute, Research Unit on AIDS, Entebbe, Uganda
| | - Anatoli Kamali
- Medical Research Council/Uganda Virus Research Institute, 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, Research Unit on AIDS, Entebbe, Uganda
- London School of Hygiene and Tropical Medicine, London, United Kingdom
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Muldoon KA. A systematic review of the clinical and social epidemiological research among sex workers in Uganda. BMC Public Health 2015; 15:1226. [PMID: 26652160 PMCID: PMC4674940 DOI: 10.1186/s12889-015-2553-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 12/01/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In response to the high burden of disease among sex workers and their position as a population heavily affected by the HIV epidemic, there has been a growing body of literature investigating the prevalence and risk factors associated with HIV risk among sex workers. To contextualize and summarize the existing research evidence base, a systematic review was conducted to synthesize the epidemiological literature on sex workers in Uganda. METHODS Database selection and search strategy development followed the Cochrane Collaboration's standards for conducting systematic review searches. All studies that included sex workers as the primary research participants were included in the review. The search was then geographically restricted to the country of Uganda. Items were identified from 18 databases (grey and peer-review) on March 10-11, 2015. RESULTS A total of 484 articles were retrieved from the database search. After removal of duplicates, a total of 353 articles were screened for eligibility and 64 full-text articles were assessed. The final review included 24 studies with quantitative methodology conducted among sex workers in Uganda. The HIV prevalence among female sex workers ranged from 32.4-52.0 % and between 8.2-9.0 % had multiple HIV infections. Both multi-drug resistance to antiretroviral therapy (2.6 %) and antibiotics (83.1 %) were observed. Between 33.3-55.1 % reported inconsistent condom use in the past month. In the previous 6 months, over 80 % of sex workers experienced client-perpetrated violence and 18 % experienced intimate partner violence. Over 30 % had a history of extreme war-related trauma. CONCLUSIONS There was limited information on socio-structural factors that affect sex workers' commercial working environments in Uganda, including the role of policing and criminalization, as well as the prevalence and factors associated with violence. The majority of the existing evidence is based in Kampala, highlighting a need for information on sex work in other regions of Uganda. Additionally, there is limited information on features of the non-commercial components of sex workers' lives as well as the services needed to reduce risks outside of the sex industry.
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Affiliation(s)
- Katherine A Muldoon
- School of Population and Public Health, Faculty of Medicine, University of British Columbia, 2206 East Mall, Vancouver, BC, V6T 1Z9, Canada.
- Ottawa Hospital Research Institute, University of Ottawa, 501 Smyth Road, Ottawa, ON, K1H 8L6, Canada.
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12
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Billings E, Sanders-Buell E, Bose M, Bradfield A, Lei E, Kijak GH, Arroyo MA, Kibaya RM, Scott PT, Wasunna MK, Sawe FK, Shaffer DN, Birx DL, McCutchan FE, Michael NL, Robb ML, Kim JH, Tovanabutra S. The Number and Complexity of Pure and Recombinant HIV-1 Strains Observed within Incident Infections during the HIV and Malaria Cohort Study Conducted in Kericho, Kenya, from 2003 to 2006. PLoS One 2015; 10:e0135124. [PMID: 26287814 PMCID: PMC4543584 DOI: 10.1371/journal.pone.0135124] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 07/18/2015] [Indexed: 11/18/2022] Open
Abstract
Characterization of HIV-1 subtype diversity in regions where vaccine trials are conducted is critical for vaccine development and testing. This study describes the molecular epidemiology of HIV-1 within a tea-plantation community cohort in Kericho, Kenya. Sixty-three incident infections were ascertained in the HIV and Malaria Cohort Study conducted in Kericho from 2003 to 2006. HIV-1 strains from 58 of those individuals were full genome characterized and compared to two previous Kenyan studies describing 41 prevalent infections from a blood bank survey (1999–2000) and 21 infections from a higher-risk cohort containing a mix of incident and prevalent infections (2006). Among the 58 strains from the community cohort, 43.1% were pure subtypes (36.2% A1, 5.2% C, and 1.7% G) and 56.9% were inter-subtype recombinants (29.3% A1D, 8.6% A1CD, 6.9% A1A2D, 5.2% A1C, 3.4% A1A2CD, and 3.4% A2D). This diversity and the resulting genetic distance between the observed strains will need to be addressed when vaccine immunogens are chosen. In consideration of current vaccine development efforts, the strains from these three studies were compared to five candidate vaccines (each of which are viral vectored, carrying inserts corresponding to parts of gag, pol, and envelope), which have been developed for possible use in sub-Saharan Africa. The sequence comparison between the observed strains and the candidate vaccines indicates that in the presence of diverse recombinants, a bivalent vaccine is more likely to provide T-cell epitope coverage than monovalent vaccines even when the inserts of the bivalent vaccine are not subtype-matched to the local epidemic.
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Affiliation(s)
- Erik Billings
- United States Military HIV Research Program/Henry M. Jackson Foundation, Rockville, Maryland, United States of America
| | - Eric Sanders-Buell
- United States Military HIV Research Program/Henry M. Jackson Foundation, Rockville, Maryland, United States of America
| | - Meera Bose
- United States Military HIV Research Program/Henry M. Jackson Foundation, Rockville, Maryland, United States of America
| | - Andrea Bradfield
- United States Military HIV Research Program/Henry M. Jackson Foundation, Rockville, Maryland, United States of America
| | - Esther Lei
- United States Military HIV Research Program/Henry M. Jackson Foundation, Rockville, Maryland, United States of America
| | - Gustavo H. Kijak
- United States Military HIV Research Program/Henry M. Jackson Foundation, Rockville, Maryland, United States of America
| | - Miguel A. Arroyo
- United States Military HIV Research Program/Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Rukia M. Kibaya
- The Kenya Medical Research Institute/Walter Reed Project Clinical Research Center, Kericho, Kenya
| | - Paul T. Scott
- United States Military HIV Research Program/Henry M. Jackson Foundation, Rockville, Maryland, United States of America
| | - Monique K. Wasunna
- The Kenya Medical Research Institute, Kericho, Kenya
- The Kenya Medical Research Institute, Nairobi, Kenya
| | - Frederick K. Sawe
- The Kenya Medical Research Institute/Walter Reed Project HIV Program, Kericho, Kenya
| | - Douglas N. Shaffer
- United States Army Medical Research Unit-Kenya/Walter Reed Project HIV Program, Kericho, Kenya
| | - Deborah L. Birx
- United States Military HIV Research Program/Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Francine E. McCutchan
- United States Military HIV Research Program/Henry M. Jackson Foundation, Rockville, Maryland, United States of America
| | - Nelson L. Michael
- United States Military HIV Research Program/Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Merlin L. Robb
- United States Military HIV Research Program/Henry M. Jackson Foundation, Rockville, Maryland, United States of America
| | - Jerome H. Kim
- International Vaccine Institute, Seoul, Republic of Korea
| | - Sodsai Tovanabutra
- United States Military HIV Research Program/Henry M. Jackson Foundation, Rockville, Maryland, United States of America
- * E-mail:
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13
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Yebra G, Ragonnet-Cronin M, Ssemwanga D, Parry CM, Logue CH, Cane PA, Kaleebu P, Brown AJL. Analysis of the history and spread of HIV-1 in Uganda using phylodynamics. J Gen Virol 2015; 96:1890-8. [PMID: 25724670 PMCID: PMC4635457 DOI: 10.1099/vir.0.000107] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
HIV prevalence has decreased in Uganda since the 1990s, but remains substantial within high-risk groups. Here, we reconstruct the history and spread of HIV subtypes A1 and D in Uganda and explore the transmission dynamics in high-risk populations. We analysed HIV pol sequences from female sex workers in Kampala (n = 42), Lake Victoria fisher-folk (n = 46) and a rural clinical cohort (n = 74), together with publicly available sequences from adjacent regions in Uganda (n = 412) and newly generated sequences from samples taken in Kampala in 1986 (n = 12). Of the sequences from the three Ugandan populations, 60 (37.1 %) were classified as subtype D, 54 (33.3 %) as subtype A1, 31 (19.1 %) as A1/D recombinants, six (3.7 %) as subtype C, one (0.6 %) as subtype G and 10 (6.2 %) as other recombinants. Among the A1/D recombinants we identified a new candidate circulating recombinant form. Phylodynamic and phylogeographic analyses using BEAST indicated that the Ugandan epidemics originated in 1960 (1950-1968) for subtype A1 and 1973 (1970-1977) for D, in rural south-western Uganda with subsequent spread to Kampala. They also showed extensive interconnection with adjacent countries. The sequence analysis shows both epidemics grew exponentially during the 1970s-1980s and decreased from 1992, which agrees with HIV prevalence reports in Uganda. Inclusion of sequences from the 1980s indicated the origin of both epidemics was more recent than expected and substantially narrowed the confidence intervals in comparison to previous estimates. We identified three transmission clusters and ten pairs, none of them including patients from different populations, suggesting active transmission within a structured transmission network.
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Affiliation(s)
- Gonzalo Yebra
- 1Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | | | | | - Chris M Parry
- 2MRC/UVRI, Uganda Research Unit on AIDS, Entebbe, Uganda
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Dennis AM, Herbeck JT, Brown AL, Kellam P, de Oliveira T, Pillay D, Fraser C, Cohen MS. Phylogenetic studies of transmission dynamics in generalized HIV epidemics: an essential tool where the burden is greatest? J Acquir Immune Defic Syndr 2014; 67:181-95. [PMID: 24977473 PMCID: PMC4304655 DOI: 10.1097/qai.0000000000000271] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Efficient and effective HIV prevention measures for generalized epidemics in sub-Saharan Africa have not yet been validated at the population level. Design and impact evaluation of such measures requires fine-scale understanding of local HIV transmission dynamics. The novel tools of HIV phylogenetics and molecular epidemiology may elucidate these transmission dynamics. Such methods have been incorporated into studies of concentrated HIV epidemics to identify proximate and determinant traits associated with ongoing transmission. However, applying similar phylogenetic analyses to generalized epidemics, including the design and evaluation of prevention trials, presents additional challenges. Here we review the scope of these methods and present examples of their use in concentrated epidemics in the context of prevention. Next, we describe the current uses for phylogenetics in generalized epidemics and discuss their promise for elucidating transmission patterns and informing prevention trials. Finally, we review logistic and technical challenges inherent to large-scale molecular epidemiological studies of generalized epidemics and suggest potential solutions.
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Affiliation(s)
- Ann M. Dennis
- Division of Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | - Andrew Leigh Brown
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Paul Kellam
- Wellcome Trust Sanger Institute, Cambridge, UK
- Division of Infection and Immunity, University College London, London, UK
| | - Tulio de Oliveira
- Wellcome Trust-Africa Centre for Health and Population Studies, University of Kwazula-Natal, ZA
| | - Deenan Pillay
- Division of Infection and Immunity, University College London, London, UK
| | - Christophe Fraser
- Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Myron S. Cohen
- Division of Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC
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15
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Tanser F, de Oliveira T, Maheu-Giroux M, Bärnighausen T. Concentrated HIV subepidemics in generalized epidemic settings. Curr Opin HIV AIDS 2014; 9:115-25. [PMID: 24356328 PMCID: PMC4228373 DOI: 10.1097/coh.0000000000000034] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
PURPOSE OF REVIEW A relatively neglected topic to date has been the occurrence of concentrated epidemics within generalized epidemic settings and the potential role of targeted interventions in such settings. We review recent studies in high-risk groups as well as findings relating to geographical heterogeneity and the potential for targeting 'high-transmission zones' in the 10 countries with highest HIV prevalence. RECENT FINDINGS Our review of recent studies confirmed earlier findings that, even in the context of generalized epidemics, MSM have a substantially higher prevalence than the general population. Estimates of prevalence of HIV among people who inject drugs (PWID) in sub-Saharan African countries are rarely available and, when they are, often outdated. We identified recent studies of sex workers in Kenya and Uganda. In all three cases - MSM, PWID, and sex workers - HIV prevalence estimates are mostly based on convenience. Moreover, good estimates of the total size of these populations are not available. Our review of recent studies of high-risk populations defined on the basis of geography showed high levels of both new and existing infections in Kenya (slums), South Africa (peri-urban communities), and Uganda (fishing villages). SUMMARY Recent empirical findings combined with evidence from phylogenetic studies and supported by mathematical models provide a clear rationale for testing the feasibility, acceptability, and effectiveness of targeted HIV prevention approaches in hyperendemic populations to supplement measures aimed at the general population.
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Affiliation(s)
- Frank Tanser
- Africa Centre for Health and Population Studies, University of KwaZulu-Natal, SA
| | - Tulio de Oliveira
- Africa Centre for Health and Population Studies, University of KwaZulu-Natal, SA
| | - Mathieu Maheu-Giroux
- Department of Global Health and Population, Harvard School of Public Health, USA
| | - Till Bärnighausen
- Africa Centre for Health and Population Studies, University of KwaZulu-Natal, SA
- Department of Global Health and Population, Harvard School of Public Health, USA
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Kaleebu P, Njai HF, Wang L, Jones N, Ssewanyana I, Richardson P, Kintu K, Emel L, Musoke P, Fowler MG, Ou SS, Guay L, Andrew P, Baglyos L, team HC. Immunogenicity of ALVAC-HIV vCP1521 in infants of HIV-1-infected women in Uganda (HPTN 027): the first pediatric HIV vaccine trial in Africa. J Acquir Immune Defic Syndr 2014; 65:268-77. [PMID: 24091694 PMCID: PMC4171956 DOI: 10.1097/01.qai.0000435600.65845.31] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE Maternal-to-child-transmission of HIV-1 infection remains a significant cause of HIV-1 infection despite successful prevention strategies. Testing protective HIV-1 vaccines remains a critical priority. The immunogenicity of ALVAC-HIV vCP1521 (ALVAC) in infants born to HIV-1-infected women in Uganda was evaluated in the first pediatric HIV-1 vaccine study in Africa. DESIGN HIV Prevention Trials Network 027 was a randomized, double-blind, placebo-controlled phase I trial to evaluate the safety and immunogenicity of ALVAC in 60 infants born to HIV-1-infected mothers with CD4 counts of >500 cells per microliter, which were randomized to the ALVAC vaccine or placebo. ALVAC-HIV vCP1521 is an attenuated recombinant canarypox virus expressing HIV-1 clade E env, clade B gag, and protease gene products. METHODS Infants were vaccinated at birth and 4, 8, and 12 weeks of age with ALVAC or placebo. Cellular and humoral immune responses were evaluated using interferon-γ enzyme-linked immunosorbent spot, carboxyfluorescein diacetate succinimidyl ester proliferation, intracellular cytokine staining, and binding and neutralizing antibody assays. Fisher exact test was used to compare positive responses between the study arms. RESULTS Low levels of antigen-specific CD4 and CD8 T-cell responses (intracellular cytokine assay) were detected at 24 months (CD4-6/36 vaccine vs. 1/9 placebo; CD8-5/36 vaccine vs. 0/9 placebo) of age. There was a nonsignificant trend toward higher cellular immune response rates in vaccine recipients compared with placebo. There were minimal binding antibody responses and no neutralizing antibodies detected. CONCLUSIONS HIV-1-exposed infants are capable of generating low levels of cellular immune responses to ALVAC vaccine, similar to responses seen in adults.
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Affiliation(s)
- Pontiano Kaleebu
- Medical Research Council/Uganda Virus Research Institute, Nakiwogo Road, PO Box 49 Entebbe, Uganda
| | - Harr Freeya Njai
- Medical Research Council/Uganda Virus Research Institute, Nakiwogo Road, PO Box 49 Entebbe, Uganda
| | - Lei Wang
- SCHARP, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, LE-400, PO Box 19024, Seattle, WA, USA 98109
| | - Norman Jones
- Viral and Rickettsial Disease Laboratory, 850 Marina Bay Parkway, Richmond, CA, USA 94804
| | - Isaac Ssewanyana
- Joint Clinical Research Center, Plot 101, Upper Lubowa Estates, PO Box 10005, Kampala, Uganda
| | - Paul Richardson
- Johns Hopkins University School of Medicine, 600 North Wolfe Street, Pathology 313, Baltimore, MD, USA 21287
| | - Kenneth Kintu
- Makerere University-Johns Hopkins University Research Collaboration, PO Box 7072, Kampala, Uganda
| | - Lynda Emel
- SCHARP, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, LE-400, PO Box 19024, Seattle, WA, USA 98109
| | - Philippa Musoke
- Makerere University-Johns Hopkins University Research Collaboration, PO Box 7072, Kampala, Uganda
- Department of Paediatrics and Child Health, College of Health Sciences, Makerere University, PO Box 7072, Kampala, Uganda
| | - Mary Glenn Fowler
- Johns Hopkins University School of Medicine, 600 North Wolfe Street, Pathology 313, Baltimore, MD, USA 21287
| | - San-San Ou
- SCHARP, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, LE-400, PO Box 19024, Seattle, WA, USA 98109
| | - Laura Guay
- George Washington University School of Public Health and Health Services, 2100 W. Pennsylvania Avenue N.W., 8th Floor, Washington DC, USA 20037
| | | | - Lynn Baglyos
- Sanofi Pasteur, Discovery Drive, Swiftwater, PA, USA 18370
| | - Huyen Cao team
- Viral and Rickettsial Disease Laboratory, 850 Marina Bay Parkway, Richmond, CA, USA 94804
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Njai HF, Ewings FM, Lyimo E, Foulongne V, Ngerageza D, Mongi A, Ssemwanga D, Andreasen A, Nyombi B, Ao T, Michael D, Urassa M, Todd J, Zaba B, Changalucha J, Hayes R, Kapiga SH. Deciphering the complex distribution of human immunodeficiency virus type 1 subtypes among different cohorts in Northern Tanzania. PLoS One 2013; 8:e81848. [PMID: 24349139 PMCID: PMC3859540 DOI: 10.1371/journal.pone.0081848] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 10/17/2013] [Indexed: 11/19/2022] Open
Abstract
Background Increased understanding of the genetic diversity of HIV-1 is challenging but important in the development of an effective vaccine. We aimed to describe the distribution of HIV-1 subtypes in northern Tanzania among women enrolled in studies preparing for HIV-1 prevention trials (hospitality facility-worker cohorts), and among men and women in an open cohort demographic surveillance system (Kisesa cohort). Methods The polymerase encompassing partial reverse transcriptase was sequenced and phylogenetic analysis performed and subtype determined. Questionnaires documented demographic data. We examined factors associated with subtype using multinomial logistic regression, adjusted for study, age, and sex. Results Among 140 individuals (125 women and 15 men), subtype A1 predominated (54, 39%), followed by C (46, 33%), D (25, 18%) and unique recombinant forms (URFs) (15, 11%). There was weak evidence to suggest different subtype frequencies by study (for example, 18% URFs in the Kisesa cohort versus 5–9% in the hospitality facility-worker cohorts; adjusted relative-risk ratio (aRR) = 2.35 [95% CI 0.59,9.32]; global p = 0.09). Compared to men, women were less likely to have subtype D versus A (aRR = 0.12 [95% CI 0.02,0.76]; global p = 0.05). There was a trend to suggest lower relative risk of subtype D compared to A with older age (aRR = 0.44 [95% CI 0.23,0.85] per 10 years; global p = 0.05). Conclusions We observed multiple subtypes, confirming the complex genetic diversity of HIV-1 strains circulating in northern Tanzania, and found some differences between cohorts and by age and sex. This has important implications for vaccine design and development, providing opportunity to determine vaccine efficacy in diverse HIV-1 strains.
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Affiliation(s)
- Harr F. Njai
- Mwanza Intervention Trials Unit, National Institute for Medical Research, Mwanza, Tanzania
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Fiona M. Ewings
- Mwanza Intervention Trials Unit, National Institute for Medical Research, Mwanza, Tanzania
- MRC Tropical Epidemiology Group, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Eric Lyimo
- National Institute for Medical Research, Mwanza, Tanzania
| | - Vincent Foulongne
- Laboratoire de Virologie, University of Montpellier, Montpellier, France
| | | | - Aika Mongi
- Mwanza Intervention Trials Unit, National Institute for Medical Research, Mwanza, Tanzania
| | | | - Aura Andreasen
- Mwanza Intervention Trials Unit, National Institute for Medical Research, Mwanza, Tanzania
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | | | - Tony Ao
- Mwanza Intervention Trials Unit, National Institute for Medical Research, Mwanza, Tanzania
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Denna Michael
- National Institute for Medical Research, Mwanza, Tanzania
| | - Mark Urassa
- National Institute for Medical Research, Mwanza, Tanzania
| | - Jim Todd
- London School of Hygiene and Tropical Medicine, London, United Kingdom
- National Institute for Medical Research, Mwanza, Tanzania
- Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | - Basia Zaba
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | | | - Richard Hayes
- MRC Tropical Epidemiology Group, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Saidi H. Kapiga
- Mwanza Intervention Trials Unit, National Institute for Medical Research, Mwanza, Tanzania
- London School of Hygiene and Tropical Medicine, London, United Kingdom
- * E-mail:
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High frequency of HIV-1 infections with multiple HIV-1 strains in men having sex with men (MSM) in Senegal. INFECTION GENETICS AND EVOLUTION 2013; 20:206-14. [DOI: 10.1016/j.meegid.2013.09.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 08/28/2013] [Accepted: 09/02/2013] [Indexed: 02/01/2023]
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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] [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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20
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Treatment failure and drug resistance is more frequent in HIV-1 subtype D versus subtype A-infected Ugandans over a 10-year study period. AIDS 2013; 27:1899-909. [PMID: 23727942 DOI: 10.1097/qad.0b013e3283610ec7] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVES To determine the impact of HIV-1 subtype on treatment outcomes and the emergence of drug resistance in the resource limited setting of Kampala, Uganda. DESIGN The Joint Clinical Research Centre (JCRC) in Kampala, Uganda has provided over 2000 drug-resistant genotypes (DRGs) over the past 10 years as standard of care for patients failing therapy and 1403 from treatment-naive and experienced patients over the past 10 years have been analyzed for this study. METHOD Viral loads, CD4 cell count, treatment histories and other relevant clinical data was compared with the infecting HIV-1 subtype and DRGs of Ugandan patients failing treatment. RESULTS Patients failing HAART with DRGs (n = 937) were more frequently infected with subtype D than expected on the basis of the subtype distribution in the treatment-naive population (n = 655) in Kampala (P < 0.001). Higher proportions of treatment failures among subtype D-infected patients were driven by resistance to nucleoside reverse transcriptase inhibitors (NRTI) (P < 0.0002) more than to non-NRTIs (P > 0.04) or protease inhibitors. CONCLUSION Higher rates of treatment failure among subtype D as compared with subtype A-infected Ugandans was analogous to the faster disease progression in subtype D-infected patients. The mechanism(s) by which drug resistance may emerge faster in subtype D HIV-1 may relate to higher replicative fitness and increased propensity for a CXCR4 tropism.
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21
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Nazziwa J, Njai HF, Ndembi N, Birungi J, Lyagoba F, Gershim A, Nakiyingi-Miiro J, Nielsen L, Mpendo J, Nanvubya A, Debont J, Grosskurth H, Kamali A, Seeley J, Kaleebu, and the CHIVTUM Study Team P. Short communication: HIV type 1 transmitted drug resistance and evidence of transmission clusters among recently infected antiretroviral-naive individuals from Ugandan fishing communities of Lake Victoria. AIDS Res Hum Retroviruses 2013; 29:788-95. [PMID: 23173702 DOI: 10.1089/aid.2012.0123] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) prevalence and incidence in the fishing communities on Lake Victoria in Uganda are high. This population may play a role in driving the HIV epidemic in Uganda including the spread of transmitted drug resistance (TDR). We report data on TDR in this population among antiretroviral (ARV)-naive, recently infected individuals about 5 years after ARV scaling-up in Uganda. We identified phylogenetic transmission clusters and combined these with volunteer life histories in order to understand the sexual networks within this population. From a prospective cohort of 1,000 HIV-negative individuals recruited from five communities, 51 seroconverters were identified over a period of 2 years. From these, whole blood was collected and population sequencing of the HIV-1 pol gene (protease/reverse transcriptase) was performed from plasma. Drug resistance mutations (DRMs) were scored using the 2009 WHO list for surveillance of TDR. TDR prevalence categories were estimated using the WHO recommended truncated sampling technique for the surveillance of TDR for use in resource-limited settings (RLS). Of the samples 92% (47/51) were successfully genotyped. HIV-1 subtype frequencies were 15/47 (32%) A1, 20/47 (43%) D, 1/47 (2%) C, 1/47 (2%) G, and 10/47 (21%) unique recombinant forms. Nonnucleoside reverse transcriptase inhibitor (NNRTI) drug resistance mutation K103N was identified in two individuals and V106A in one (6%) suggesting that the level of TDR was moderate in this population. No nucleoside/tide reverse transcriptase inhibitor (NRTI) or protease inhibitor (PI) DRMs were detected. In this study, we identified five transmission clusters supported by high bootstrap values and low genetic distances. Of these, one pair included the two individuals with K103N. Two of the genotypic clusters corresponded with reported sexual partnerships as detected through prior in-depth interviews. The level of TDR to NNRTIs in these ARV-naive individuals was moderate by WHO threshold survey categorization. The transmission clusters suggest a high degree of sexual partner mixing between members of these communities.
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Affiliation(s)
- Jamirah Nazziwa
- MRC/UVRI Uganda Research Unit on AIDS, Entebbe, Uganda
- Uganda Virus Research Institute/IAVI HIV Vaccine Program, Entebbe, Uganda
| | - Harr Freeya Njai
- MRC/UVRI Uganda Research Unit on AIDS, Entebbe, Uganda
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | | | - Josephine Birungi
- Uganda Virus Research Institute/IAVI HIV Vaccine Program, Entebbe, Uganda
| | - Fred Lyagoba
- MRC/UVRI Uganda Research Unit on AIDS, Entebbe, Uganda
| | - Asiki Gershim
- MRC/UVRI Uganda Research Unit on AIDS, Entebbe, Uganda
| | | | - Leslie Nielsen
- International AIDS Vaccine Initiative, New York, New York
| | - Juliet Mpendo
- Uganda Virus Research Institute/IAVI HIV Vaccine Program, Entebbe, Uganda
| | - Annet Nanvubya
- Uganda Virus Research Institute/IAVI HIV Vaccine Program, Entebbe, Uganda
| | - Jan Debont
- International AIDS Vaccine Initiative, New York, New York
| | - Heiner Grosskurth
- MRC/UVRI Uganda Research Unit on AIDS, Entebbe, Uganda
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Anatoli Kamali
- MRC/UVRI Uganda Research Unit on AIDS, Entebbe, Uganda
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Janet Seeley
- MRC/UVRI Uganda Research Unit on AIDS, Entebbe, Uganda
- London School of Hygiene and Tropical Medicine, London, United Kingdom
- School of International Development, University of East Anglia, Norwich, United Kingdom
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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] [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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Baalwa J, Wang S, Parrish NF, Decker JM, Keele BF, Learn GH, Yue L, Ruzagira E, Ssemwanga D, Kamali A, Amornkul PN, Price MA, Kappes JC, Karita E, Kaleebu P, Sanders E, Gilmour J, Allen S, Hunter E, Montefiori DC, Haynes BF, Cormier E, Hahn BH, Shaw GM. Molecular identification, cloning and characterization of transmitted/founder HIV-1 subtype A, D and A/D infectious molecular clones. Virology 2012; 436:33-48. [PMID: 23123038 DOI: 10.1016/j.virol.2012.10.009] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2012] [Revised: 09/25/2012] [Accepted: 10/05/2012] [Indexed: 11/18/2022]
Abstract
We report the molecular identification, cloning and initial biological characterization of 12 full-length HIV-1 subtype A, D and A/D recombinant transmitted/founder (T/F) genomes. T/F genomes contained intact canonical open reading frames and all T/F viruses were replication competent in primary human T-cells, although subtype D virus replication was more efficient (p<0.05). All 12 viruses utilized CCR5 but not CXCR4 as a co-receptor for entry and exhibited a neutralization profile typical of tier 2 primary virus strains, with significant differences observed between subtype A and D viruses with respect to sensitivity to monoclonal antibodies VRC01, PG9 and PG16 and polyclonal subtype C anti-HIV IgG (p<0.05 for each). The present report doubles the number of T/F HIV-1 clones available for pathogenesis and vaccine research and extends their representation to include subtypes A, B, C and D.
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Affiliation(s)
- Joshua Baalwa
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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Soares de Oliveira AC, Pessôa de Farias R, da Costa AC, Sauer MM, Bassichetto KC, Oliveira SMS, Costa PR, Tomiyama C, Tomiyama HTI, Sabino EC, Kallas EG, Sanabani SS. Frequency of subtype B and F1 dual infection in HIV-1 positive, Brazilian men who have sex with men. Virol J 2012; 9:223. [PMID: 23021203 PMCID: PMC3499372 DOI: 10.1186/1743-422x-9-223] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Accepted: 09/27/2012] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Because various HIV vaccination studies are in progress, it is important to understand how often inter- and intra-subtype co/superinfection occurs in different HIV-infected high-risk groups. This knowledge would aid in the development of future prevention programs. In this cross-sectional study, we report the frequency of subtype B and F1 co-infection in a clinical group of 41 recently HIV-1 infected men who have sex with men (MSM) in São Paulo, Brazil. METHODOLOGY Proviral HIV-1 DNA was isolated from subject's peripheral blood polymorphonuclear leukocytes that were obtained at the time of enrollment. Each subject was known to be infected with a subtype B virus as determined in a previous study. A small fragment of the integrase gene (nucleotide 4255-4478 of HXB2) was amplified by nested polymerase chain reaction (PCR) using subclade F1 specific primers. The PCR results were further confirmed by phylogenetic analysis. Viral load (VL) data were extrapolated from the medical records of each patient. RESULTS For the 41 samples from MSM who were recently infected with subtype B virus, it was possible to detect subclade F1 proviral DNA in five patients, which represents a co-infection rate of 12.2%. In subjects with dual infection, the median VL was 5.3 × 10(4) copies/ML, whereas in MSM that were infected with only subtype B virus the median VL was 3.8 × 10(4) copies/ML (p > 0.8). CONCLUSIONS This study indicated that subtype B and F1 co-infection occurs frequently within the HIV-positive MSM population as suggested by large number of BF1 recombinant viruses reported in Brazil. This finding will help us track the epidemic and provide support for the development of immunization strategies against the HIV.
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Rusine J, Jurriaans S, van de Wijgert J, Cornelissen M, Kateera B, Boer K, Karita E, Mukabayire O, de Jong M, Ondoa P. Molecular and phylogeographic analysis of human immuno-deficiency virus type 1 strains infecting treatment-naive patients from Kigali, Rwanda. PLoS One 2012; 7:e42557. [PMID: 22905148 PMCID: PMC3419187 DOI: 10.1371/journal.pone.0042557] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Accepted: 07/09/2012] [Indexed: 01/18/2023] Open
Abstract
This study aimed at describing the genetic subtype distribution of HIV-1 strains circulating in Kigali and their epidemiological link with the HIV-1 strains from the five countries surrounding Rwanda. One hundred and thirty eight pol (RT and PR) sequences from 116 chronically- and 22 recently-infected antiretroviral therapy (ART)-naïve patients from Kigali were generated and subjected to HIV drug resistance (HIV-DR), phylogenetic and recombinant analyses in connection with 366 reference pol sequences from Rwanda, Burundi, Kenya, Democratic Republic of Congo, Tanzania and Uganda (Los Alamos database). Among the Rwandan samples, subtype A1 predominated (71.7%), followed by A1/C recombinants (18.1%), subtype C (5.8%), subtype D (2.9%), one A1/D recombinant (0.7%) and one unknown subtype (0.7%). Thirteen unique and three multiple A1/C recombinant forms were identified. No evidence for direct transmission events was found within the Rwandan strains. Molecular characteristics of HIV-1 were similar between chronically and recently-infected individuals and were not significantly associated with demographic or social factors. Our report suggests that the HIV-1 epidemic in Kigali is characterized by the emergence of A1/C recombinants and is not phylogenetically connected with the HIV-1 epidemic in the five neighboring countries. The relatively low level of transmitted HIV-DR mutations (2.9%) reported here indicates the good performance of the ART programme in Rwanda. However, the importance of promoting couples' counseling, testing and disclosure during HIV prevention strategies is highlighted.
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Affiliation(s)
- John Rusine
- National Reference Laboratory, Kigali, Rwanda
| | - Suzanne Jurriaans
- Laboratory of Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam Institute for Global Health and Development (AIGHD), Amsterdam, The Netherlands
| | - Janneke van de Wijgert
- Department of Global Health, Academic Medical Center, University of Amsterdam, Amsterdam Institute for Global Health and Development (AIGHD), Amsterdam, The Netherlands
| | - Marion Cornelissen
- Laboratory of Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam Institute for Global Health and Development (AIGHD), Amsterdam, The Netherlands
| | - Brenda Kateera
- Department of Global Health, Academic Medical Center, University of Amsterdam, Amsterdam Institute for Global Health and Development (AIGHD), Amsterdam, The Netherlands
- The Infectious Diseases Network for Treatment and Research in Africa (INTERACT) Project, Kigali, Rwanda
- Royal Tropical Institute (KIT), Biomedical Research, Epidemiology Unit, Amsterdam Institute for Global Health and Development (AIGHD), Amsterdam, The Netherlands
| | - Kimberly Boer
- Department of Global Health, Academic Medical Center, University of Amsterdam, Amsterdam Institute for Global Health and Development (AIGHD), Amsterdam, The Netherlands
- The Infectious Diseases Network for Treatment and Research in Africa (INTERACT) Project, Kigali, Rwanda
- Royal Tropical Institute (KIT), Biomedical Research, Epidemiology Unit, Amsterdam Institute for Global Health and Development (AIGHD), Amsterdam, The Netherlands
| | | | | | - Menno de Jong
- Laboratory of Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam Institute for Global Health and Development (AIGHD), Amsterdam, The Netherlands
| | - Pascale Ondoa
- Department of Global Health, Academic Medical Center, University of Amsterdam, Amsterdam Institute for Global Health and Development (AIGHD), Amsterdam, The Netherlands
- * E-mail:
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Delatorre EO, Bello G. Phylodynamics of HIV-1 subtype C epidemic in east Africa. PLoS One 2012; 7:e41904. [PMID: 22848653 PMCID: PMC3407063 DOI: 10.1371/journal.pone.0041904] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Accepted: 06/27/2012] [Indexed: 11/18/2022] Open
Abstract
The HIV-1 subtype C accounts for an important fraction of HIV infections in east Africa, but little is known about the genetic characteristics and evolutionary history of this epidemic. Here we reconstruct the origin and spatiotemporal dynamics of the major HIV-1 subtype C clades circulating in east Africa. A large number (n = 1,981) of subtype C pol sequences were retrieved from public databases to explore relationships between strains from the east, southern and central African regions. Maximum-likelihood phylogenetic analysis of those sequences revealed that most (>70%) strains from east Africa segregated in a single regional-specific monophyletic group, here called CEA. A second major Ethiopian subtype C lineage and a large collection of minor Kenyan and Tanzanian subtype C clades of southern African origin were also detected. A Bayesian coalescent-based method was then used to reconstruct evolutionary parameters and migration pathways of the CEA African lineage. This analysis indicates that the CEA clade most probably originated in Burundi around the early 1960s, and later spread to Ethiopia, Kenya, Tanzania and Uganda, giving rise to major country-specific monophyletic sub-clusters between the early 1970s and early 1980s. The results presented here demonstrate that a substantial proportion of subtype C infections in east Africa resulted from dissemination of a single HIV local variant, probably originated in Burundi during the 1960s. Burundi was the most important hub of dissemination of that subtype C clade in east Africa, fueling the origin of new local epidemics in Ethiopia, Kenya, Tanzania and Uganda. Subtype C lineages of southern African origin have also been introduced in east Africa, but seem to have had a much more restricted spread.
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Affiliation(s)
| | - Gonzalo Bello
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz, Rio de Janeiro, Brazil
- * E-mail:
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Brewer DD, Potterat JJ, Brody S. Comprehensive assessment of blood and sexual exposures needed for rigorous investigation of HIV transmission. AIDS Res Hum Retroviruses 2012; 28:435-6. [PMID: 21806487 DOI: 10.1089/aid.2011.0237] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
| | | | - Stuart Brody
- School of Social Sciences, University of the West of Scotland, Paisley, United Kingdom
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