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Rashid A, Kang L, Yi F, Getaneh Y, Chu Q, Shah SA, Abidi SH, Shao Y. Identification of a novel first-generation HIV-1 circulating recombinant form (CRF152_DG) among people living with HIV in Karachi, Pakistan. Microbiol Spectr 2024; 12:e0052924. [PMID: 38771033 PMCID: PMC11218485 DOI: 10.1128/spectrum.00529-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 04/18/2024] [Indexed: 05/22/2024] Open
Abstract
The objective of this study was to characterize a novel circulating recombinant form of human immunodeficiency virus type 1 (HIV-1) among people living with HIV in Karachi, Pakistan. We conducted near-full-length genome (NFLG) sequencing on eight samples exhibiting D/G recombination signals in the pol gene region. We successfully obtained NFLG sequences (790-9,614; with reference to the HXB2 genome) from four of the eight samples and then conducted phylogenetic and recombination analyses on them. The four NFLG sequences from our study and one DG unique recombinant form previously identified in the United Kingdom (GenBank accession: MF109700) formed a distinct monophyletic cluster with an Shimodaira-Hasegawa approximate likelihood ratio test node support value of 100%. Bootscan analyses of the five NFLG sequences of DG recombinants showed that all five NFLGs shared the same unique mosaic pattern of recombination breakpoints between D and G clades, with two D fragments in the pol and vif regions inserted into a G backbone. Subregion phylogenetic analyses confirmed these sequences to be a novel circulating recombinant form (CRF) composed of subtypes D and G. The DG recombinant sequences were eventually designated as CRF152_DG by the Los Alamos HIV Sequence Database staff. IMPORTANCE In Pakistan, the genetic diversity of human immunodeficiency virus type 1 (HIV-1) is becoming increasingly complex, compared to the early years of the epidemic that started after the detection of the first cases of HIV-1 in 1987 in Karachi. Based on the available molecular studies, two dominant HIV-1 clades, sub-subtype A1 and CRF02_AG, have been found to co-circulate with other clades, namely B, C, D, G, CRF01_AE, CRF35_A1D, and CRF56_cpx, in various urban areas of Pakistan. Several novel recombinant forms have also been detected. This first report of CRF152_DG highlights the complex nature of the HIV epidemic in Pakistan and emphasizes the importance of continual molecular surveillance (ideally based on whole-genome sequences) of HIV.
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Affiliation(s)
- Abdur Rashid
- School of Medicine, Nankai University, Tianjin, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Li Kang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing, China
- College of Life Sciences, Nankai University, Tianjin, China
| | - Feng Yi
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yimam Getaneh
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Qingfei Chu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing, China
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | | | - Syed Hani Abidi
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi, Pakistan
- Department of Biomedical Sciences, School of Medicine, Nazarbayev University, Astana, Kazakhstan
| | - Yiming Shao
- School of Medicine, Nankai University, Tianjin, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing, China
- College of Life Sciences, Nankai University, Tianjin, China
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Changping Laboratory, Beijing, China
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Kuriakose Gift S, Wieczorek L, Sanders-Buell E, Zemil M, Molnar S, Donofrio G, Townsley S, Chenine AL, Bose M, Trinh HV, Barrows BM, Sriplienchan S, Kitsiripornchai S, Nitayapan S, Eller LA, Rao M, Ferrari G, Michael NL, Ake JA, Krebs SJ, Robb ML, Tovanabutra S, Polonis VR. Evolution of Antibody Responses in HIV-1 CRF01_AE Acute Infection: Founder Envelope V1V2 Impacts the Timing and Magnitude of Autologous Neutralizing Antibodies. J Virol 2023; 97:e0163522. [PMID: 36749076 PMCID: PMC9973046 DOI: 10.1128/jvi.01635-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 01/10/2023] [Indexed: 02/08/2023] Open
Abstract
Understanding the dynamics of early immune responses to HIV-1 infection, including the evolution of initial neutralizing and antibody-dependent cellular cytotoxicity (ADCC)-mediating antibodies, will inform HIV vaccine design. In this study, we assess the development of autologous neutralizing antibodies (ANAbs) against founder envelopes (Envs) from 18 participants with HIV-1 CRF01_AE acute infection. The timing of ANAb development directly associated with the magnitude of the longitudinal ANAb response. Participants that developed ANAbs within 6 months of infection had significantly higher ANAb responses at 1 year (50% inhibitory concentration [IC50] geometric mean titer [GMT] = 2,010 versus 184; P = 0.001) and 2 years (GMT = 3,479 versus 340; P = 0.015), compared to participants that developed ANAb responses after 6 months. Participants with later development of ANAb tended to develop an earlier, potent heterologous tier 1 (92TH023) neutralizing antibody (NAb) response (P = 0.049). CRF01_AE founder Env V1V2 loop lengths correlated indirectly with the timing (P = 0.002, r = -0.675) and directly with magnitude (P = 0.005, r = 0.635) of ANAb responses; Envs with longer V1V2 loop lengths elicited earlier and more potent ANAb responses. While ANAb responses did not associate with viral load, the viral load set point correlated directly with neutralization of the heterologous 92TH023 strain (P = 0.007, r = 0.638). In contrast, a striking inverse correlation was observed between viral load set point and peak ADCC against heterologous 92TH023 Env strain (P = 0.0005, r = -0.738). These data indicate that specific antibody functions can be differentially related to viral load set point and may affect HIV-1 pathogenesis. Exploiting Env properties, such as V1V2 length, could facilitate development of subtype-specific vaccines that elicit more effective immune responses and improved protection. IMPORTANCE Development of an effective HIV-1 vaccine will be facilitated by better understanding the dynamics between the founder virus and the early humoral responses. Variations between subtypes may influence the evolution of immune responses and should be considered as we strive to understand these dynamics. In this study, autologous founder envelope neutralization and heterologous functional humoral responses were evaluated after acute infection by HIV-1 CRF01_AE, a subtype that has not been thoroughly characterized. The evolution of these humoral responses was assessed in relation to envelope characteristics, magnitude of elicited immune responses, and viral load. Understanding immune parameters in natural infection will improve our understanding of protective responses and aid in the development of immunogens that elicit protective functional antibodies. Advancing our knowledge of correlates of positive clinical outcomes should lead to the design of more efficacious vaccines.
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Affiliation(s)
- Syna Kuriakose Gift
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA
| | - Lindsay Wieczorek
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA
| | - Eric Sanders-Buell
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA
| | - Michelle Zemil
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA
| | - Sebastian Molnar
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA
| | - Gina Donofrio
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA
| | - Samantha Townsley
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA
| | - Agnes L. Chenine
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA
| | - Meera Bose
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA
| | - Hung V. Trinh
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA
| | - Brittani M. Barrows
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA
| | - Somchai Sriplienchan
- Department of Retrovirology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Suchai Kitsiripornchai
- Department of Retrovirology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Sorachai Nitayapan
- Royal Thai Army, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Leigh-Anne Eller
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA
| | - Mangala Rao
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Guido Ferrari
- Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Surgery, Duke University School of Medicine, Durham, North Carolina, USA
| | - Nelson L. Michael
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Julie A. Ake
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Shelly J. Krebs
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA
| | - Merlin L. Robb
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA
| | - Sodsai Tovanabutra
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA
| | - Victoria R. Polonis
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
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Mode of HIV acquisition among adolescents living with HIV in resource-limited settings: A data-driven approach from South Africa. PLoS One 2023; 18:e0281298. [PMID: 36827268 PMCID: PMC9955664 DOI: 10.1371/journal.pone.0281298] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 01/19/2023] [Indexed: 02/25/2023] Open
Abstract
Adolescents living with HIV (ALHIV) face unique treatment and care challenges which may differ by how they acquired HIV, whether vertically (in-utero, perinatal or postnatal exposure during breastfeeding) or sexually (sexual exposure). Distinguishing and documenting the mode of HIV acquisition (MOHA) is crucial to further research on the different needs and outcomes for ALHIV and to tailor HIV services to their needs. Age-based cut-offs have been used to attribute MOHA but have not been validated. We analysed data from a three-wave cohort of n = 1107 ALHIV part of a longitudinal study in South Africa. Age-based MOHA was allocated using age at ART initiation, validated against a logic-tree model based on literature-hypothesised factors: self-reported HIV, sexual, and family history. After testing six ART initiation age cut-offs (10 to 15 years old), we determined the optimal MOHA cut-off age by calculating the sensitivity and specificity for each cut-off, measured against the final logic-tree allocation. Following validation using this longitudinal study, the methodology is extended to 214 additional third-wave participants-adolescent girls and young women living with HIV who became mothers before the age of 20. Finally, descriptive statistics of the final allocations are presented. Among the 1,063 (96.0%) cohort study participants classified, 68.7% acquired HIV vertically, following validation. ART initiation before cut-off age 10 had the highest sensitivity (58.9%) but cut-off age 12 had the largest area under the curve (AUC) (0.712). Among the additional young mothers living with HIV, 95.3% were estimated to have acquired it sexually, following the same algorithm. For this group, while cut-off ages 10 to 12 had the highest sensitivity (92.2%), age 14 had the highest AUC (0.703). ART initiation before 10 years old is strongly associated with vertical HIV acquisition. Therefore, a cut-off age of 10 would remain the recommendation in LMIC regions with similar epidemiology as South Africa for determining MOHA in research and clinic settings.
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Nduva GM, Otieno F, Kimani J, Wahome E, McKinnon LR, Cholette F, Majiwa M, Masika M, Mutua G, Anzala O, Graham SM, Gelmon L, Price MA, Smith AD, Bailey RC, Baele G, Lemey P, Hassan AS, Sanders EJ, Esbjörnsson J. Quantifying rates of HIV-1 flow between risk groups and geographic locations in Kenya: A country-wide phylogenetic study. Virus Evol 2022; 8:veac016. [PMID: 35356640 PMCID: PMC8962731 DOI: 10.1093/ve/veac016] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 02/23/2022] [Accepted: 03/01/2022] [Indexed: 12/14/2022] Open
Abstract
In Kenya, HIV-1 key populations including men having sex with men (MSM), people who inject drugs (PWID) and female sex workers (FSW) are thought to significantly contribute to HIV-1 transmission in the wider, mostly heterosexual (HET) HIV-1 transmission network. However, clear data on HIV-1 transmission dynamics within and between these groups are limited. We aimed to empirically quantify rates of HIV-1 flow between key populations and the HET population, as well as between different geographic regions to determine HIV-1 'hotspots' and their contribution to HIV-1 transmission in Kenya. We used maximum-likelihood phylogenetic and Bayesian inference to analyse 4058 HIV-1 pol sequences (representing 0.3 per cent of the epidemic in Kenya) sampled 1986-2019 from individuals of different risk groups and regions in Kenya. We found 89 per cent within-risk group transmission and 11 per cent mixing between risk groups, cyclic HIV-1 exchange between adjoining geographic provinces and strong evidence of HIV-1 dissemination from (i) West-to-East (i.e. higher-to-lower HIV-1 prevalence regions), and (ii) heterosexual-to-key populations. Low HIV-1 prevalence regions and key populations are sinks rather than major sources of HIV-1 transmission in Kenya. Targeting key populations in Kenya needs to occur concurrently with strengthening interventions in the general epidemic.
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Affiliation(s)
- George M Nduva
- Department of Translational Medicine, Lund University, Faculty of Medicine, Lund University, Box 117 SE-221 00 Lund, Sweden
- Kenya Medical Research Institute-Wellcome Trust Research Programme, KEMRI-Center For Geographic Medicine Research, P.O. Box 230-80108, Kilifi, Kenya
| | - Frederick Otieno
- Nyanza Reproductive Health Society, United Mall, P.O. Box 1764, Kisumu, Kenya
| | - Joshua Kimani
- Department of Medical Microbiology, University of Nairobi, P.O. Box 30197-00100, Nairobi, Kenya
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Max Rady College of Medicine, Room 543-745 Bannatyne Avenue, University of Manitoba (Bannatyne campus), Winnipeg MB R3E 0J9, Canada
| | - Elizabeth Wahome
- Kenya Medical Research Institute-Wellcome Trust Research Programme, KEMRI-Center For Geographic Medicine Research, P.O. Box 230-80108, Kilifi, Kenya
| | - Lyle R McKinnon
- Department of Medical Microbiology, University of Nairobi, P.O. Box 30197-00100, Nairobi, Kenya
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Max Rady College of Medicine, Room 543-745 Bannatyne Avenue, University of Manitoba (Bannatyne campus), Winnipeg MB R3E 0J9, Canada
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Private Bag X7, Congella 4013, South Africa
| | - Francois Cholette
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Max Rady College of Medicine, Room 543-745 Bannatyne Avenue, University of Manitoba (Bannatyne campus), Winnipeg MB R3E 0J9, Canada
- National Microbiology Laboratory at the JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, 745 Logan Avenue, Winnipeg, Canada
| | - Maxwell Majiwa
- Kenya Medical Research Institute/Center for Global Health Research, KEMRI-CGHR, P.O. Box 20778-00202, Kisumu, Kenya
| | - Moses Masika
- Faculty of Health Sciences 3RD Floor Wing B, KAVI Institute of Clinical Research, University of Nairobi, P.O. Box 19676-00202, Nairobi, Kenya
| | - Gaudensia Mutua
- Faculty of Health Sciences 3RD Floor Wing B, KAVI Institute of Clinical Research, University of Nairobi, P.O. Box 19676-00202, Nairobi, Kenya
| | - Omu Anzala
- Faculty of Health Sciences 3RD Floor Wing B, KAVI Institute of Clinical Research, University of Nairobi, P.O. Box 19676-00202, Nairobi, Kenya
| | - Susan M Graham
- Kenya Medical Research Institute-Wellcome Trust Research Programme, KEMRI-Center For Geographic Medicine Research, P.O. Box 230-80108, Kilifi, Kenya
- Department of Epidemiology, University of Washington, Office of the Chair, UW Box # 351619, Seattle, DC, USA
| | - Larry Gelmon
- Department of Medical Microbiology, University of Nairobi, P.O. Box 30197-00100, Nairobi, Kenya
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Max Rady College of Medicine, Room 543-745 Bannatyne Avenue, University of Manitoba (Bannatyne campus), Winnipeg MB R3E 0J9, Canada
| | - Matt A Price
- IAVI Global Headquarters, 125 Broad Street, 9th Floor, New York, NY 10004, USA
- Department of Epidemiology and Biostatistics, University of California, Mission Hall: Global Health & Clinical Sciences Building, 550 16th Street, 2nd Floor, San Francisco, CA 94158-2549, USA
| | - Adrian D Smith
- Nuffield Department of Medicine, The University of Oxford, Old Road Campus, Headington, Oxford OX3 7BN, UK
| | - Robert C Bailey
- Nyanza Reproductive Health Society, United Mall, P.O. Box 1764, Kisumu, Kenya
- Division of Epidemiology and Biostatistics, University of Illinois at Chicago, 1603 W Taylor St, Chicago, IL 60612, USA
| | - Guy Baele
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Clinical and Evolutionary and Computational Virology, Rega-Herestraat 49-box 1040, Leuven 3000, Belgium
| | - Philippe Lemey
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Clinical and Evolutionary and Computational Virology, Rega-Herestraat 49-box 1040, Leuven 3000, Belgium
| | - Amin S Hassan
- Department of Translational Medicine, Lund University, Faculty of Medicine, Lund University, Box 117 SE-221 00 Lund, Sweden
- Kenya Medical Research Institute-Wellcome Trust Research Programme, KEMRI-Center For Geographic Medicine Research, P.O. Box 230-80108, Kilifi, Kenya
| | - Eduard J Sanders
- Kenya Medical Research Institute-Wellcome Trust Research Programme, KEMRI-Center For Geographic Medicine Research, P.O. Box 230-80108, Kilifi, Kenya
- Nuffield Department of Medicine, The University of Oxford, Old Road Campus, Headington, Oxford OX3 7BN, UK
| | - Joakim Esbjörnsson
- Department of Translational Medicine, Lund University, Faculty of Medicine, Lund University, Box 117 SE-221 00 Lund, Sweden
- Nuffield Department of Medicine, The University of Oxford, Old Road Campus, Headington, Oxford OX3 7BN, UK
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Gibson KM, Steiner MC, Rentia U, Bendall ML, Pérez-Losada M, Crandall KA. Validation of Variant Assembly Using HAPHPIPE with Next-Generation Sequence Data from Viruses. Viruses 2020; 12:E758. [PMID: 32674515 PMCID: PMC7412389 DOI: 10.3390/v12070758] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 07/03/2020] [Accepted: 07/06/2020] [Indexed: 01/04/2023] Open
Abstract
Next-generation sequencing (NGS) offers a powerful opportunity to identify low-abundance, intra-host viral sequence variants, yet the focus of many bioinformatic tools on consensus sequence construction has precluded a thorough analysis of intra-host diversity. To take full advantage of the resolution of NGS data, we developed HAplotype PHylodynamics PIPEline (HAPHPIPE), an open-source tool for the de novo and reference-based assembly of viral NGS data, with both consensus sequence assembly and a focus on the quantification of intra-host variation through haplotype reconstruction. We validate and compare the consensus sequence assembly methods of HAPHPIPE to those of two alternative software packages, HyDRA and Geneious, using simulated HIV and empirical HIV, HCV, and SARS-CoV-2 datasets. Our validation methods included read mapping, genetic distance, and genetic diversity metrics. In simulated NGS data, HAPHPIPE generated pol consensus sequences significantly closer to the true consensus sequence than those produced by HyDRA and Geneious and performed comparably to Geneious for HIV gp120 sequences. Furthermore, using empirical data from multiple viruses, we demonstrate that HAPHPIPE can analyze larger sequence datasets due to its greater computational speed. Therefore, we contend that HAPHPIPE provides a more user-friendly platform for users with and without bioinformatics experience to implement current best practices for viral NGS assembly than other currently available options.
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Affiliation(s)
- Keylie M. Gibson
- Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Washington, DC 20052, USA; (M.C.S.); (U.R.); (M.L.B.); (M.P.-L.); (K.A.C.)
| | - Margaret C. Steiner
- Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Washington, DC 20052, USA; (M.C.S.); (U.R.); (M.L.B.); (M.P.-L.); (K.A.C.)
| | - Uzma Rentia
- Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Washington, DC 20052, USA; (M.C.S.); (U.R.); (M.L.B.); (M.P.-L.); (K.A.C.)
| | - Matthew L. Bendall
- Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Washington, DC 20052, USA; (M.C.S.); (U.R.); (M.L.B.); (M.P.-L.); (K.A.C.)
| | - Marcos Pérez-Losada
- Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Washington, DC 20052, USA; (M.C.S.); (U.R.); (M.L.B.); (M.P.-L.); (K.A.C.)
- Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, The George Washington University, Washington, DC 20052, USA
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4169-007 Vairão, Portugal
| | - Keith A. Crandall
- Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Washington, DC 20052, USA; (M.C.S.); (U.R.); (M.L.B.); (M.P.-L.); (K.A.C.)
- Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, The George Washington University, Washington, DC 20052, USA
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Nduva GM, Hassan AS, Nazziwa J, Graham SM, Esbjörnsson J, Sanders EJ. HIV-1 Transmission Patterns Within and Between Risk Groups in Coastal Kenya. Sci Rep 2020; 10:6775. [PMID: 32317722 PMCID: PMC7174422 DOI: 10.1038/s41598-020-63731-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 03/30/2020] [Indexed: 11/09/2022] Open
Abstract
HIV-1 transmission patterns within and between populations at different risk of HIV-1 acquisition in Kenya are not well understood. We investigated HIV-1 transmission networks in men who have sex with men (MSM), injecting drug users (IDU), female sex workers (FSW) and heterosexuals (HET) in coastal Kenya. We used maximum-likelihood and Bayesian phylogenetics to analyse new (N = 163) and previously published (N = 495) HIV-1 polymerase sequences collected during 2005-2019. Of the 658 sequences, 131 (20%) were from MSM, 58 (9%) IDU, 109 (17%) FSW, and 360 (55%) HET. Overall, 206 (31%) sequences formed 61 clusters. Most clusters (85%) consisted of sequences from the same risk group, suggesting frequent within-group transmission. The remaining clusters were mixed between HET/MSM (7%), HET/FSW (5%), and MSM/FSW (3%) sequences. One large IDU-exclusive cluster was found, indicating an independent sub-epidemic among this group. Phylodynamic analysis of this cluster revealed a steady increase in HIV-1 infections among IDU since the estimated origin of the cluster in 1987. Our results suggest mixing between high-risk groups and heterosexual populations and could be relevant for the development of targeted HIV-1 prevention programmes in coastal Kenya.
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Affiliation(s)
- George M Nduva
- Lund University, Lund, Sweden
- KEMRI/Wellcome Trust Research Programme, Kilifi, Kenya
| | - Amin S Hassan
- Lund University, Lund, Sweden
- KEMRI/Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Susan M Graham
- KEMRI/Wellcome Trust Research Programme, Kilifi, Kenya
- University of Washington, Seattle, WA, USA
| | - Joakim Esbjörnsson
- Lund University, Lund, Sweden.
- The University of Oxford, Oxford, United Kingdom.
| | - Eduard J Sanders
- KEMRI/Wellcome Trust Research Programme, Kilifi, Kenya
- The University of Oxford, Oxford, United Kingdom
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Understanding disclosed and cryptic HIV transmission risk via genetic analysis: what are we missing and when does it matter? Curr Opin HIV AIDS 2020; 14:205-212. [PMID: 30946142 DOI: 10.1097/coh.0000000000000537] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
PURPOSE OF REVIEW To discuss the recent HIV phylogenetic analyses examining HIV transmission patterns among and within risk groups. RECENT FINDINGS Phylodynamic analysis has recently been applied to multiple HIV outbreaks among people who inject drugs to determine whether HIV transmission is ongoing. Large-scale analyses of datasets of HIV sequences collected for drug-resistance testing provide population-level insights into transmission patterns. One focus across world regions has been to investigate whether age-disparity is a driver of HIV transmission. In sub-Saharan Africa, researchers have examined transmission between heterosexuals and MSM and between high prevalence fishing communities and inland communities. In the US and the UK, cryptic risk groups such as nondisclosed MSM and the partners of transgender women are increasingly being uncovered based on their position in densely sampled molecular transmission networks. SUMMARY Analysis of HIV genetic sequence can resolve viral transmission patterns between risk groups at unprecedented scales and levels of detail. Future research should focus on understanding the effect of missing data on inferences and the biases of different methods. Uncovering groups and patterns obscured from traditional epidemiolocal analyses is exciting but should not compromise the privacy of the groups in question.
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Mochache V, Richardson BA, Masese LN, Graham SM, Mandaliya K, Kinuthia J, Jaoko W, Overbaugh J, McClelland RS. Older age at infection and nulliparity are associated with long-term non-progression in female sex workers infected with non-subtype B HIV-1. Int J STD AIDS 2020; 31:510-516. [PMID: 32295475 DOI: 10.1177/0956462419898324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Studies have reported on HIV-infected, antiretroviral therapy (ART)-naïve individuals who show minimal disease progression despite prolonged infection. The characteristics of these long-term non-progressors (LTNPs) are not well-characterized in populations predominantly infected with non-subtype B HIV-1. Female sex workers in Mombasa, Kenya who acquired HIV-1 were studied to ascertain immunologic disease progression. Long-term non-progression was defined as an ART-naïve duration of infection ≥7 years and a majority of CD4+ cell counts ≥600 cells/µl with a non-declining CD4+ trend. Correlates of long-term non-progression were determined using multivariable logistic regression. Between February 1993 and March 2014, 332 women acquired HIV-1. Of these, 77 (23%) had ≥7 years of follow-up and 13 (17%) were categorized as LTNPs. Factors associated with long-term non-progression included age >30 years at infection (aOR = 9.41, 95% CI: 1.48–59.86, P = 0.005) and nulliparity (aOR = 20.19, 95% CI: 1.36–299.90, P = 0.03). Each log10 copies/ml increase in viral load (VL) set point was associated with a lower likelihood of being a LTNP (aOR = 0.31, 95% CI: 0.12–0.79, P = 0.01). These findings suggest that age and parity may influence the likelihood of long-term non-progression through mechanisms that are not mediated by the effects of these variables on VL. Future studies should seek to determine whether the associations presented are reproducible.
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Affiliation(s)
- Vernon Mochache
- University of Maryland, Center for International Health, Education and Biosecurity, Nairobi, Kenya
| | - Barbra A Richardson
- University of Maryland, Center for International Health, Education and Biosecurity, Nairobi, Kenya
| | - Linnet N Masese
- University of Maryland, Center for International Health, Education and Biosecurity, Nairobi, Kenya
| | - Susan M Graham
- University of Maryland, Center for International Health, Education and Biosecurity, Nairobi, Kenya
| | - Kishorchandra Mandaliya
- University of Maryland, Center for International Health, Education and Biosecurity, Nairobi, Kenya
| | - John Kinuthia
- Kenyatta National Hospital, Department of Research, Nairobi, Kenya.,University of Nairobi, Faculty of Medicine, Nairobi, Kenya
| | - Walter Jaoko
- University of Nairobi, Faculty of Medicine, Nairobi, Kenya
| | - Julie Overbaugh
- Fred Hutchison Cancer Research Center, Seattle, Washington, USA
| | - R Scott McClelland
- University of Washington, Department of Epidemiology, Seattle, Washington, USA
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9
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Hebberecht L, Vancoillie L, Schauvliege M, Staelens D, Demecheleer E, Hardy J, Mortier V, Verhofstede C. Single genome sequencing of near full-length HIV-1 RNA using a limiting dilution approach. J Virol Methods 2019; 274:113737. [PMID: 31562885 DOI: 10.1016/j.jviromet.2019.113737] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 09/20/2019] [Accepted: 09/22/2019] [Indexed: 11/18/2022]
Abstract
Sequencing very long stretches of the HIV-1 genome can advance studies on virus evolution and in vivo recombination but remains technically challenging. We developed an efficient procedure to sequence near full-length HIV-1 RNA using a two-amplicon approach. The whole genome was successfully amplified for 107 (88%) of 121 plasma samples including samples from patients infected with HIV-1 subtype A1, B, C, D, F1, G, H, CRF01_AE and CRF02_AG. For the 17 samples with a viral load below 1000 c/ml and the 104 samples with a viral load above 1000 c/ml, the amplification efficiency was respectively 53% and 94%. The sensitivity of the method was further evaluated using limiting dilution of RNA extracted from a plasma pool containing an equimolar mixture of three HIV-1 subtypes (B, C and CRF02_AG) and diluted before and after cDNA generation. Both RNA and cDNA dilution showed comparable sensitivity and equal accuracy in reflecting the subtype distribution of the plasma pool. One single event of in vitro recombination was detected amongst the 41 sequences obtained after cDNA dilution but no indications for in vitro recombination were found after RNA dilution. In conclusion, a two-amplicon strategy and limiting dilution of viral RNA followed by reverse transcription, nested PCR and Sanger sequencing, allows near full genome sequencing of individual HIV-1 RNA molecules. This method will be a valuable tool in the study of virus evolution and recombination.
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Affiliation(s)
- Laura Hebberecht
- Aids Reference Laboratory, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Leen Vancoillie
- Aids Reference Laboratory, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Marlies Schauvliege
- Aids Reference Laboratory, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Delfien Staelens
- Aids Reference Laboratory, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Els Demecheleer
- Aids Reference Laboratory, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Jarryt Hardy
- Aids Reference Laboratory, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Virginie Mortier
- Aids Reference Laboratory, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Chris Verhofstede
- Aids Reference Laboratory, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium.
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10
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Kijak GH, Sanders-Buell E, Pham P, Harbolick EA, Oropeza C, O'Sullivan AM, Bose M, Beckett CG, Milazzo M, Robb ML, Peel SA, Scott PT, Michael NL, Armstrong AW, Kim JH, Brett-Major DM, Tovanabutra S. Next-generation sequencing of HIV-1 single genome amplicons. BIOMOLECULAR DETECTION AND QUANTIFICATION 2019; 17:100080. [PMID: 30923677 PMCID: PMC6423504 DOI: 10.1016/j.bdq.2019.01.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Revised: 01/18/2019] [Accepted: 01/29/2019] [Indexed: 12/14/2022]
Abstract
The analysis of HIV-1 sequences has helped understand the viral molecular epidemiology, monitor the development of antiretroviral drug resistance, and design candidate vaccines. The introduction of single genome amplification (SGA) has been a major advancement in the field, allowing for the characterization of multiple sequences per patient while preserving linkage among polymorphisms in the same viral genome copy. Sequencing of SGA amplicons is performed by capillary Sanger sequencing, which presents low throughput, requires a high amount of template, and is highly sensitive to template/primer mismatching. In order to meet the increasing demand for HIV-1 SGA amplicon sequencing, we have developed a platform based on benchtop next-generation sequencing (NGS) (IonTorrent) accompanied by a bioinformatics pipeline capable of running on computer resources commonly available at research laboratories. During assay validation, the NGS-based sequencing of 10 HIV-1 env SGA amplicons was fully concordant with Sanger sequencing. The field test was conducted on plasma samples from 10 US Navy and Marine service members with recent HIV-1 infection (sampling interval: 2005–2010; plasma viral load: 5,884–194,984 copies/ml). The NGS analysis of 101 SGA amplicons (median: 10 amplicons/individual) showed within-individual viral sequence profiles expected in individuals at this disease stage, including individuals with highly homogeneous quasispecies, individuals with two highly homogeneous viral lineages, and individuals with heterogeneous viral populations. In a scalability assessment using the Ion Chef automated system, 41/43 tested env SGA amplicons (95%) multiplexed on a single Ion 318 chip showed consistent gene-wide coverage >50×. With lower sample requirements and higher throughput, this approach is suitable to support the increasing demand for high-quality and cost-effective HIV-1 sequences in fields such as molecular epidemiology, and development of preventive and therapeutic strategies.
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Affiliation(s)
- Gustavo H Kijak
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States
| | - Eric Sanders-Buell
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States
| | - Phuc Pham
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States
| | - Elizabeth A Harbolick
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States
| | - Celina Oropeza
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States
| | - Anne Marie O'Sullivan
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States
| | - Meera Bose
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States
| | | | - Mark Milazzo
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States
| | - Merlin L Robb
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States
| | - Sheila A Peel
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States
| | - Paul T Scott
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States
| | - Nelson L Michael
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States
| | | | - Jerome H Kim
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States
| | - David M Brett-Major
- Department of Preventive Medicine and Biostatistics, F. Edward Hébert School of Medicine, Uniformed Services University, Bethesda, MD, United States
| | - Sodsai Tovanabutra
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States
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11
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Hassan AS, Esbjörnsson J, Wahome E, Thiong’o A, Makau GN, Price MA, Sanders EJ. HIV-1 subtype diversity, transmission networks and transmitted drug resistance amongst acute and early infected MSM populations from Coastal Kenya. PLoS One 2018; 13:e0206177. [PMID: 30562356 PMCID: PMC6298690 DOI: 10.1371/journal.pone.0206177] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 10/08/2018] [Indexed: 11/21/2022] Open
Abstract
Background HIV-1 molecular epidemiology amongst men who have sex with men (MSM) in sub-Saharan Africa remains not well characterized. We aimed to determine HIV-1 subtype distribution, transmission clusters and transmitted drug resistance (TDR) in acute and early infected MSM from Coastal Kenya. Methods Analysis of HIV-1 partial pol sequences from MSM recruited 2005–2017 and sampled within six months of the estimated date of infection. Volunteers were classified as men who have sex with men exclusively (MSME) or with both men and women (MSMW). HIV-1 subtype and transmission clusters were determined by maximum-likelihood phylogenetics. TDR mutations were determined using the Stanford HIV drug resistance database. Results Of the 97 volunteers, majority (69%) were MSMW; 74%, 16%, 9% and 1% had HIV-1 subtypes A1, D, C or G, respectively. Overall, 65% formed transmission clusters, with substantial mixing between MSME and MSMW. Majority of volunteer sequences were either not linked to any reference sequence (56%) or clustered exclusively with sequences of Kenyan origin (19%). Eight (8% [95% CI: 4–16]) had at least one TDR mutation against nucleoside (n = 2 [2%]) and/or non-nucleoside (n = 7 [7%]) reverse transcriptase inhibitors. The most prevalent TDR mutation was K103N (n = 5), with sequences forming transmission clusters of two and three taxa each. There were no significant differences in HIV-1 subtype distribution and TDR between MSME and MSMW. Conclusions This HIV-1 MSM epidemic was predominantly sub-subtype A1, of Kenyan origin, with many transmission clusters and having intermediate level of TDR. Targeted HIV-1 prevention, early identification and care interventions are warranted to break the transmission cycle amongst MSM from Coastal Kenya.
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Affiliation(s)
- Amin S. Hassan
- KEMRI/Wellcome Trust Research Programme, Kilifi, Kenya
- Lund University, Lund, Sweden
- * E-mail:
| | | | | | | | - George N. Makau
- KEMRI/Wellcome Trust Research Programme, Kilifi, Kenya
- Lund University, Lund, Sweden
| | - Mathew A. Price
- International AIDS Vaccine Initiative, New York, New York, United States of America
- Department of Epidemiology and Biostatistics, University of California at San Francisco, San Francisco, California, United States of America
| | - Eduard J. Sanders
- KEMRI/Wellcome Trust Research Programme, Kilifi, Kenya
- Oxford University, Oxford, United Kingdom
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12
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Esra RT, Olivier AJ, Passmore JAS, Jaspan HB, Harryparsad R, Gray CM. Does HIV Exploit the Inflammatory Milieu of the Male Genital Tract for Successful Infection? Front Immunol 2016; 7:245. [PMID: 27446076 PMCID: PMC4919362 DOI: 10.3389/fimmu.2016.00245] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 06/10/2016] [Indexed: 12/16/2022] Open
Abstract
In many parts of the World, medical male circumcision (MMC) is used as standard prevention of care against HIV infection. This is based on seminal reports made over 10 years ago that removal of the foreskin provides up to 60% protection against HIV infection in males and seems currently the best antiretroviral-free prevention strategy yet against the global epidemic. We explore the potential mechanisms by which MMC protects against HIV-1 acquisition and that one of the oldest, albeit re-invented, rituals of removing a foreskin underscores the exploitative nature of HIV on the anatomy and tissue of the uncircumcised penis. Furthermore, foreskin removal also reveals how males acquire HIV, and in reality, the underlying mechanisms of MMC are not known. We argue that the normal sequelae of inflammation in the male genital tract (MGT) for protection from sexually transmitted infections (STI)-induced pathology represents a perfect immune and microbial ecosystem for HIV acquisition. The accumulation of HIV-1 target cells in foreskin tissue and within the urethra in response to STIs, both during and after resolution of infection, suggests that acquisition of HIV-1, through sexual contact, makes use of the natural immune milieu of the MGT. Understanding immunity in the MGT, the movement of HIV-1 target cells to the urethra and foreskin tissue upon encounter with microbial signals would provide more insight into viral acquisition and lay the foundation for further prevention strategies in males that would be critical to curb the epidemic in all sexual partners at risk of infection. The global female-centric focus of HIV-1 transmission and acquisition research has tended to leave gaps in our knowledge of what determines HIV-1 acquisition in men and such understanding would provide a more balanced and complete view of viral acquisition.
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Affiliation(s)
- Rachel T. Esra
- Department of Pathology, Division of Immunology, Faculty of Health Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Abraham J. Olivier
- Department of Pathology, Division of Immunology, Faculty of Health Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Jo-Ann S. Passmore
- Department of Pathology, Division of Virology, Faculty of Health Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- National Health Laboratory Services, Cape Town, South Africa
| | - Heather B. Jaspan
- Department of Pathology, Division of Immunology, Faculty of Health Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Rushil Harryparsad
- Department of Pathology, Division of Immunology, Faculty of Health Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Clive M. Gray
- Department of Pathology, Division of Immunology, Faculty of Health Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- National Health Laboratory Services, Cape Town, South Africa
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13
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Resilience among gay/bisexual young men in Western Kenya: psychosocial and sexual health outcomes. AIDS 2015; 29 Suppl 3:S261-9. [PMID: 26562815 DOI: 10.1097/qad.0000000000000905] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
OBJECTIVE To explore associations between intrapersonal and interpersonal factors and both sexual and psychosocial resilient outcomes among young gay, bisexual, and other men who have sex with men (GBMSM) in Western Kenya. DESIGN Cross-sectional observational study. METHODS Five hundred and eleven GBMSM ages 18-29 were recruited from nine communities in Western Kenya using community-based mobilization strategies. Participants completed an audio computer-assisted self-interview survey in English or Duhluo. We estimated four three-step hierarchical linear regression models to examine associations between predictors (intrapersonal and interpersonal factors) and four resilient outcomes (psychological well-being, self-esteem, condom use, HIV testing). RESULTS Psychosocial well-being model (modeled conversely as depression/anxiety) was significant (F(13,424) = 106.41, P < 0.001, R = 0.765) with loneliness, lesbian/gay/bisexual (LGB) difficult process, LGB identity superiority, and reactions to trauma as predictors. Self-esteem model was significant (F(12,425) = 6.40, P < 0.001, R = 0.153) with known HIV-seropositivity, perceived social support, internalized homonegativity, and LGB difficult process as predictors. Condom use model was significant (F(13,379) = 4.30, P < 0.001, R = 0.128) with perceived social support, self-esteem, and reactions to trauma as predictors. HIV testing model was significant (F(12,377) = 4.75, P < 0.001, R = 0.131) with loneliness, LGB identity uncertainty, LGB difficult process, and LGB identity superiority as predictors. CONCLUSION This study demonstrates the variety of ways in which intrapersonal and interpersonal factors are associated with HIV-related resilient outcomes for young GBMSM in Western Kenya. HIV prevention programs for this population should be developed in collaboration with GBMSM and include intervention components that promote resilience.
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14
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Smith AD, Muhaari AD, Agwanda C, Kowuor D, van der Elst E, Davies A, Graham SM, Jaffe HW, Sanders EJ. Heterosexual behaviours among men who sell sex to men in coastal Kenya. AIDS 2015; 29 Suppl 3:S201-10. [PMID: 26565965 PMCID: PMC4706370 DOI: 10.1097/qad.0000000000000889] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
OBJECTIVE African men who have sex with men often sell sex to men, and MSM who sell sex (MSM-SW) often also have female partners. We compared sexual risk behaviour of MSM-SW who were sexually active with female partners (bisexual MSW) to MSM-SW with only male partners (exclusive MSW). DESIGN Descriptive behavioural study METHODS : A novel, validated daily event and partner diary self-completed by 82 MSM who sold sex over a follow-up period of 42 days with weekly review. Cumulative individual counts of sex and condomless sex were compiled by partner characteristics. The incidence of specific partnerships and sex acts were compared within and between bisexual and exclusive MSW. RESULTS Most (59%) MSM-SW reported female partners during follow-up. The majority of both male and female partners were cash-paying clients originating locally. Bisexual MSW reported a similar rate of condomless sex with male and female partners, but significantly fewer male partners than exclusive MSW. Bisexual MSW had lower HIV prevalence, were more likely to only report insertive anal sex roles, and reported lower frequencies of condomless receptive anal sex than exclusive MSW. CONCLUSION Bisexually active male sex workers in coastal Kenya create HIV and other sexually transmitted infection transmission pathways to partners and clients in both MSM and heterosexual networks, but differed from exclusive MSW in having lower HIV acquisition and transmission risks. Epidemiological projection methods are liable to overestimate bridging potential of MSM-SW and MSM populations without account for systematic differences in risk within these populations.
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Affiliation(s)
- Adrian D. Smith
- Nuffield Department of Population Health, University of
Oxford, Oxford, UK
| | - Allan D. Muhaari
- Kenya Medical Research Institute-Wellcome Trust Research
Programme, Kilifi, Kenya
| | - Carole Agwanda
- Kenya Medical Research Institute-Wellcome Trust Research
Programme, Kilifi, Kenya
| | - Dickens Kowuor
- Kenya Medical Research Institute-Wellcome Trust Research
Programme, Kilifi, Kenya
| | - Elise van der Elst
- Kenya Medical Research Institute-Wellcome Trust Research
Programme, Kilifi, Kenya
| | - Alun Davies
- Kenya Medical Research Institute-Wellcome Trust Research
Programme, Kilifi, Kenya
| | - Susan M. Graham
- Kenya Medical Research Institute-Wellcome Trust Research
Programme, Kilifi, Kenya
- Department of Medicine, Global Health and Epidemiology,
University of Washington, Seattle, Washington, USA
| | - Harold W. Jaffe
- Nuffield Department of Population Health, University of
Oxford, Oxford, UK
| | - Eduard J. Sanders
- Kenya Medical Research Institute-Wellcome Trust Research
Programme, Kilifi, Kenya
- Centre for Topical Medicine and Global Health, Nuffield
Department of Medicine, University of Oxford, Oxford, UK
- Department of Global Health, Academic Medical Centre,
University of Amsterdam, Amsterdam, the Netherlands
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15
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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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16
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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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Wirtz AL, Pretorius C, Beyrer C, Baral S, Decker MR, Sherman SG, Sweat M, Poteat T, Butler J, Oelrichs R, Semini I, Kerrigan D. Epidemic impacts of a community empowerment intervention for HIV prevention among female sex workers in generalized and concentrated epidemics. PLoS One 2014; 9:e88047. [PMID: 24516580 PMCID: PMC3916392 DOI: 10.1371/journal.pone.0088047] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Accepted: 12/20/2013] [Indexed: 11/19/2022] Open
Abstract
Introduction Sex workers have endured a high burden of HIV infection in and across HIV epidemics. A comprehensive, community empowerment-based HIV prevention intervention emphasizes sex worker organization and mobilization to address HIV risk and often includes community-led peer education, condom distribution, and other activities. Meta-analysis of such interventions suggests a potential 51% reduction in inconsistent condom use. Mathematical modeling exercises provide theoretical insight into potential impacts of the intervention on HIV incidence and burden in settings where interventions have not yet been implemented. Methods We used a deterministic model, Goals, to project the impact on HIV infections when the community empowerment interventions were scaled up among female sex workers in Kenya, Thailand, Brazil, and Ukraine. Modeling scenarios included expansion of the comprehensive community empowerment-based HIV prevention intervention from baseline coverage over a 5-year period (5–65% in Kenya and Ukraine; 10–70% in Thailand and Brazil), while other interventions were held at baseline levels. A second exercise increased the intervention coverage simultaneously with equitable access to ART for sex workers. Impacts on HIV outcomes among sex workers and adults are observed from 2012–2016 and, compared to status quo when all interventions are held constant. Results Optimistic but feasible coverage (65%–70%) of the intervention demonstrated a range of impacts on HIV: 220 infections averted over 5 yrs. among sex workers in Thailand, 1,830 in Brazil, 2,220 in Ukraine, and 10,800 infections in Kenya. Impacts of the intervention for female sex workers extend to the adult population, cumulatively averting 730 infections in Thailand to 20,700 adult infections in Kenya. Impacts vary by country, influenced by HIV prevalence in risk groups, risk behaviors, intervention use, and population size. Discussion A community empowerment approach to HIV prevention and access to universal ART for female sex workers is a promising human rights-based solution to overcoming the persistent burden of HIV among female sex workers across epidemic settings.
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Affiliation(s)
- Andrea L. Wirtz
- Center for Public Health and Human Rights, Department of Epidemiology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
- Department of Emergency Medicine, Johns Hopkins Medical Institute, Baltimore, Maryland, United States of America
- * E-mail:
| | - Carel Pretorius
- Futures Institute, Glastonbury, Connecticut, United States of America
| | - Chris Beyrer
- Center for Public Health and Human Rights, Department of Epidemiology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Stefan Baral
- Center for Public Health and Human Rights, Department of Epidemiology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Michele R. Decker
- Center for Public Health and Human Rights, Department of Epidemiology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
- Department of Population, Family, and Reproductive Health, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Susan G. Sherman
- Center for Public Health and Human Rights, Department of Epidemiology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Michael Sweat
- Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - Tonia Poteat
- Center for Public Health and Human Rights, Department of Epidemiology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Jennifer Butler
- HIV and Key Populations, United Nations Population Fund, New York, New York, United States of America
| | - Robert Oelrichs
- Human Development Network, The World Bank, Washington, District of Columbia, United States of America
| | - Iris Semini
- Human Development Network, The World Bank, Washington, District of Columbia, United States of America
| | - Deanna Kerrigan
- Center for Public Health and Human Rights, Department of Epidemiology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
- Department of Health, Behavior & Society, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
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Bezemer D, Faria NR, Hassan A, Hamers RL, Mutua G, Anzala O, Mandaliya K, Cane P, Berkley JA, Rinke de Wit TF, Wallis C, Graham SM, Price MA, Coutinho RA, Sanders EJ. HIV Type 1 transmission networks among men having sex with men and heterosexuals in Kenya. AIDS Res Hum Retroviruses 2014; 30:118-26. [PMID: 23947948 DOI: 10.1089/aid.2013.0171] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
We performed a molecular phylogenetic study on HIV-1 polymerase sequences of men who have sex with men (MSM) and heterosexual patient samples in Kenya to characterize any observed HIV-1 transmission networks. HIV-1 polymerase sequences were obtained from samples in Nairobi and coastal Kenya from 84 MSM, 226 other men, and 364 women from 2005 to 2010. Using Bayesian phylogenetics, we tested whether sequences clustered by sexual orientation and geographic location. In addition, we used trait diffusion analyses to identify significant epidemiological links and to quantify the number of transmissions between risk groups. Finally, we compared 84 MSM sequences with all HIV-1 sequences available online at GenBank. Significant clustering of sequences from MSM at both coastal Kenya and Nairobi was found, with evidence of HIV-1 transmission between both locations. Although a transmission pair between a coastal MSM and woman was confirmed, no significant HIV-1 transmission was evident between MSM and the comparison population for the predominant subtype A (60%). However, a weak but significant link was evident when studying all subtypes together. GenBank comparison did not reveal other important transmission links. Our data suggest infrequent intermingling of MSM and heterosexual HIV-1 epidemics in Kenya.
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Affiliation(s)
| | - Nuno Rodrigues Faria
- Department of Microbiology and Immunology, University of Leuven, Leuven, Belgium
| | - Amin Hassan
- Kenya Medical Research Institute, Centre for Geographic Medicine Research–Coast, Kilifi, Kenya
| | - Raph L. Hamers
- PharmAccess Foundation, Department of Global Health, Academic Medical Center of the University of Amsterdam, Amsterdam Institute for Global Health and Development, Amsterdam, The Netherlands
| | - Gaudensia Mutua
- Kenya AIDS Vaccine Initiative, University of Nairobi, Nairobi, Kenya
| | - Omu Anzala
- Kenya AIDS Vaccine Initiative, University of Nairobi, Nairobi, Kenya
| | | | | | - James A. Berkley
- Kenya Medical Research Institute, Centre for Geographic Medicine Research–Coast, Kilifi, Kenya
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Tobias F. Rinke de Wit
- PharmAccess Foundation, Department of Global Health, Academic Medical Center of the University of Amsterdam, Amsterdam Institute for Global Health and Development, Amsterdam, The Netherlands
| | | | - Susan M. Graham
- Kenya Medical Research Institute, Centre for Geographic Medicine Research–Coast, Kilifi, Kenya
- University of Washington, Seattle, Washington
| | - Matthew A. Price
- International AIDS Vaccine Initiative, New York, New York
- Department of Epidemiology and Biostatistics, University of California at San Francisco, San Francisco, California
| | - Roel A. Coutinho
- Centre for Infectious Disease Control, RIVM, Utrecht, The Netherlands
- Julius Center for Health Science and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Eduard J. Sanders
- Kenya Medical Research Institute, Centre for Geographic Medicine Research–Coast, Kilifi, Kenya
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
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Decker MR, Wirtz AL, Pretorius C, Sherman SG, Sweat MD, Baral SD, Beyrer C, Kerrigan DL. Estimating the impact of reducing violence against female sex workers on HIV epidemics in Kenya and Ukraine: a policy modeling exercise. Am J Reprod Immunol 2013; 69 Suppl 1:122-32. [PMID: 23387931 DOI: 10.1111/aji.12063] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Accepted: 11/19/2012] [Indexed: 11/29/2022] Open
Abstract
PROBLEM Female sex workers (FSWs) worldwide suffer disproportionate burdens of HIV and gender-based violence. Despite evidence linking these threats, little is known about the potential HIV epidemic impact of reducing abuse. METHOD OF STUDY The Goals model approximated the impact of reducing violence against FSWs on HIV epidemics in Ukraine and Kenya, measured by reductions in new infections among FSWs and adults. Cumulative infections averted over a 5-year period, in which violence declined was calculated, relative to a status quo with no reduction. Projections held HIV interventions constant at baseline levels; subsequently, scenarios adjusted for planned expansion of antiretroviral therapy (ART) coverage. RESULTS An approximate 25% reduction in incident HIV infections among FSWs was observed when physical or sexual violence was reduced; cumulative infections averted were 21,200 and 4700 in Kenya and Ukraine, respectively. Similar percent reductions were observed assuming ART coverage expansion, with approximately 18,200 and 4400 infections averted among FSWs in Kenya and Ukraine. New infections were also averted in the general population. CONCLUSION Reducing violence against FSWs appears to impart significant reductions in new infections among FSWs and in the general adult population in both generalized and concentrated epidemics. Limitations provide direction to improve the precision of future estimates.
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Affiliation(s)
- Michele R Decker
- Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe Street, Baltimore, MD 21205, USA.
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Muraguri N, Temmerman M, Geibel S. A decade of research involving men who have sex with men in sub-Saharan Africa: current knowledge and future directions. SAHARA J 2013; 9:137-47. [PMID: 23237068 DOI: 10.1080/17290376.2012.744176] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
It has been just over 10 years since the first large behavioral survey of men who have sex with men (MSM) was implemented in Senegal in 2001. Since then, behavioral and/or HIV prevalence surveys have been conducted in over 14 other countries in sub-Saharan Africa. Current available evidence and review have established that HIV prevalence among MSM in these countries are significantly higher than corresponding general populations, that MSM engage in sexual risk behaviors that place them and sexual partners at higher risk, and that issues of discrimination and stigmatization inhibit HIV interventions for MSM. This paper summarizes the existing knowledge, describes limitations of this evidence, and proposes new and enhanced research approaches to fulfill needed gaps to inform national HIV responses for MSM populations.
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Molecular evolution of the HIV-1 Thai epidemic between the time of RV144 immunogen selection to the execution of the vaccine efficacy trial. J Virol 2013; 87:7265-81. [PMID: 23576510 DOI: 10.1128/jvi.03070-12] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The RV144 HIV-1 vaccine trial (Thailand, 2003 to 2009), using immunogens genetically matched to the regional epidemic, demonstrated the first evidence of efficacy for an HIV-1 vaccine. Here we studied the molecular evolution of the HIV-1 epidemic from the time of immunogen selection to the execution of the efficacy trial. We studied HIV-1 genetic diversity among 390 volunteers who were deferred from enrollment in RV144 due to preexisting HIV-1 infection using a multiregion hybridization assay, full-genome sequencing, and phylogenetic analyses. The subtype distribution was 91.7% CRF01_AE, 3.5% subtype B, 4.3% B/CRF01_AE recombinants, and 0.5% dual infections. CRF01_AE strains were 31% more diverse than the ones from the 1990s Thai epidemic. Sixty-nine percent of subtype B strains clustered with the cosmopolitan Western B strains. Ninety-three percent of B/CRF01_AE recombinants were unique; recombination breakpoint analysis showed that these strains were highly embedded within the larger network that integrates recombinants from East/Southeast Asia. Compared to Thai sequences from the early 1990s, the distance to the RV144 immunogens increased 52% to 68% for CRF01_AE Env immunogens and 12% to 29% for subtype B immunogens. Forty-three percent to 48% of CRF01_AE sequences differed from the sequence of the vaccine insert in Env variable region 2 positions 169 and 181, which were implicated in vaccine sieve effects in RV144. In conclusion, compared to the molecular picture at the early stages of vaccine development, our results show an overall increase in the genetic complexity of viruses in the Thai epidemic and in the distance to vaccine immunogens, which should be considered at the time of the analysis of the trial results.
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High HIV-1 incidence, correlates of HIV-1 acquisition, and high viral loads following seroconversion among MSM. AIDS 2013; 27:437-46. [PMID: 23079811 DOI: 10.1097/qad.0b013e32835b0f81] [Citation(s) in RCA: 133] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
BACKGROUND HIV-1 incidence estimates and correlates of HIV-1 acquisition in African MSM are largely unknown. METHODS Since 2005, HIV-1-uninfected men who reported sex with men and women (MSMW) or sex with men exclusively (MSME) were followed at scheduled visits for collection of behavioural and clinical examination data and plasma for HIV-1 testing. Urethral or rectal secretions were collected from symptomatic men to screen for gonorrhoea. Poisson regression methods were used to estimate adjusted incidence rate ratios to explore associations between risk factors and incident HIV-1 infection. Plasma viral loads (PVLs) were assessed over 2 years following seroconversion. RESULTS Overall HIV-1 incidence in 449 men was 8.6 [95% confidence interval (CI) 6.7-11.0] per 100 person-years. Incidence was 5.8 (95% CI 4.2-7.9) per 100 person-years among MSMW, and 35.2 (95% CI 23.8-52.1) per 100 person-years among MSME. Unprotected sex, receptive anal intercourse, exclusive sex with men, group sex, and gonorrhoea in the past 6 months were strongly associated with HIV-1 acquisition, adjusted for confounders. PVL in seroconverters was more than 4 log10 copies/ml at 230 (73.4%) of 313 visits in MSMW and 153 (75.0%) of 204 visits in MSME. CONCLUSION HIV-1 incidence is very high among MSM in coastal Kenya, and many seroconverters maintain high PVL for up to 2 years after infection. Effective HIV-1 prevention interventions, including treatment as prevention, are urgently needed in this population.
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HIV-1 subtypes and recombinants in Northern Tanzania: distribution of viral quasispecies. PLoS One 2012; 7:e47605. [PMID: 23118882 PMCID: PMC3485255 DOI: 10.1371/journal.pone.0047605] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Accepted: 09/13/2012] [Indexed: 11/25/2022] Open
Abstract
This study analyzed the distribution and prevalence of HIV-1 subtypes, multiplicity of HIV-1 infection, and frequency of inter-subtype recombination among HIV-1-infected female bar and hotel workers in Moshi, Kilimanjaro Region, Tanzania, from 2004 to 2007. The HIV-1 viral sequences spanning the V1-C5 region of HIV-1 env gp120 were analyzed from 50 subjects by single genome amplification and sequencing (SGA/S) technique. A total of 1740 sequences were amplified and sequenced from the HIV-1 proviral DNA template. The median env sequences analyzed per subject per two time points was 38 (IQR 28–50) over one year of HIV infection. In a subset of 14 subjects, a total of 239 sequences were obtained from HIV-1 RNA template at the baseline visit. The most prevalent HIV-1 subtypes were A1 (56%) and C (30%), while HIV-1 subtype D and inter-subtype recombinant viruses were found in 6% and 8% of subjects respectively. Transmission of multiple HIV-1 variants was evident in 27% of the subjects infected with pure HIV-1 subtypes A1, C, or D. The HIV-1 inter-subtype recombinants were found in 8% including HIV-1 C/A, D/A, and complex mosaic recombinants. Multiple viral variants were found in two subjects infected with inter-subtype recombinants. One subject harbored quasispecies of both pure HIV-1 A1 and C/A recombinant. The other subject was infected with two complex mosaic inter-subtype recombinant variants belonging to subtype D. HIV-1 multiple infections and ongoing recombination contribute significantly to the genetic diversity of circulating HIV-1 in Tanzania and have important implications for vaccine design and the development of therapeutic strategies.
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Millett GA, Jeffries WL, Peterson JL, Malebranche DJ, Lane T, Flores SA, Fenton KA, Wilson PA, Steiner R, Heilig CM. Common roots: a contextual review of HIV epidemics in black men who have sex with men across the African diaspora. Lancet 2012; 380:411-23. [PMID: 22819654 DOI: 10.1016/s0140-6736(12)60722-3] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Pooled estimates from across the African diaspora show that black men who have sex with men (MSM) are 15 times more likely to be HIV positive compared with general populations and 8·5 times more likely compared with black populations. Disparities in the prevalence of HIV infection are greater in African and Caribbean countries that criminalise homosexual activity than in those that do not criminalise such behaviour. With the exception of US and African epidemiological studies, most studies of black MSM mainly focus on outcomes associated with HIV behavioural risk rather than on prevalence, incidence, or undiagnosed infection. Nevertheless, black MSM across the African diaspora share common experiences such as discrimination, cultural norms valuing masculinity, concerns about confidentiality during HIV testing or treatment, low access to HIV drugs, threats of violence or incarceration, and few targeted HIV prevention resources.
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Affiliation(s)
- Gregorio A Millett
- National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA 20201, USA.
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Baral S, Beyrer C, Muessig K, Poteat T, Wirtz AL, Decker MR, Sherman SG, Kerrigan D. Burden of HIV among female sex workers in low-income and middle-income countries: a systematic review and meta-analysis. THE LANCET. INFECTIOUS DISEASES 2012; 12:538-49. [PMID: 22424777 DOI: 10.1016/s1473-3099(12)70066-x] [Citation(s) in RCA: 861] [Impact Index Per Article: 71.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
BACKGROUND Female sex workers are a population who are at heightened risk of HIV infection secondary to biological, behavioural, and structural risk factors. However, three decades into the HIV pandemic, understanding of the burden of HIV among these women remains limited. We aimed to assess the burden of HIV in this population compared with that of other women of reproductive age. METHODS We searched PubMed, Embase, Global Health, SCOPUS, PsycINFO, Sociological Abstracts, CINAHL (Cumulative Index to Nursing and Allied Health Literature), Web of Science, and POPLine for studies of female sex workers in low-income and middle-income countries published between Jan 1, 2007, and June 25, 2011. Studies of any design that measured the prevalence or incidence of HIV among female sex workers, even if sex workers were not the main focus of the study, were included. Meta-analyses were done with the Mantel-Haenszel method with a random-effects model characterising an odds ratio for the prevalence of HIV among female sex workers compared with that for all women of reproductive age. FINDINGS Of 434 selected articles and surveillance reports, 102 were included in the analyses, representing 99,878 female sex workers in 50 countries. The overall HIV prevalence was 11·8% (95% CI 11·6-12·0) with a pooled odds ratio for HIV infection of 13·5 (95% CI 10·0-18·1) with wide intraregional ranges in the pooled HIV prevalence and odds ratios for HIV infection. In 26 countries with medium and high background HIV prevalence, 30·7% (95% CI 30·2-31·3; 8627 of 28,075) of sex workers were HIV-positive and the odds ratio for infection was 11·6 (95% CI 9·1-14·8). INTERPRETATION Although data characterising HIV risk among female sex workers is scarce, the burden of disease is disproportionately high. These data suggest an urgent need to scale up access to quality HIV prevention programmes. Considerations of the legal and policy environments in which sex workers operate and actions to address the important role of stigma, discrimination, and violence targeting female sex workers is needed. FUNDING The World Bank, UN Population Fund.
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Affiliation(s)
- Stefan Baral
- Johns Hopkins School of Public Health, Baltimore, MD 21205, USA.
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Hué S, Hassan AS, Nabwera H, Sanders EJ, Pillay D, Berkley JA, Cane PA. HIV type 1 in a rural coastal town in Kenya shows multiple introductions with many subtypes and much recombination. AIDS Res Hum Retroviruses 2012; 28:220-4. [PMID: 21770741 DOI: 10.1089/aid.2011.0048] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The extent of HIV-1 diversity was examined among patients attending a rural district hospital in a coastal area of Kenya. The pol gene was sequenced in samples from 153 patients. Subtypes were designated using the REGA, SCUEAL, and jpHMM programs. The most common subtype was A1, followed by C and D; A2 and G were also detected. However, a large proportion of the samples was found to be recombinants, which clustered within the pure subtype branches. Phylogeographic analysis of Kilifi sequences compared with those from other regions of Africa showed that while many sequences were closely related to sequences from Kenya, others were most closely related to known sequences from other parts of Africa, including West Africa. Overall, these data indicate that there have been multiple introductions of HIV-1 into this small rural town and surroundings with ongoing diversity being generated by recombination.
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Affiliation(s)
- Stéphane Hué
- Centre for Medical Molecular Virology, University College, London, United Kingdom
| | - Amin S. Hassan
- Kenya Medical Research Institute, Centre for Geographic Medicine Research–Coast, Kilifi, Kenya
| | - Helen Nabwera
- Kenya Medical Research Institute, Centre for Geographic Medicine Research–Coast, Kilifi, Kenya
| | - Eduard J. Sanders
- Kenya Medical Research Institute, Centre for Geographic Medicine Research–Coast, Kilifi, Kenya
| | - Deenan Pillay
- Centre for Medical Molecular Virology, University College, London, United Kingdom
- Health Protection Agency, London, United Kingdom
| | - James A. Berkley
- Kenya Medical Research Institute, Centre for Geographic Medicine Research–Coast, Kilifi, Kenya
- Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford, Oxford, United Kingdom
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Oyaro M, Mbithi J, Oyugi F, Laten A, Anzala O, Engelbrecht S. Molecular characterization of HIV type 1 among HIV-infected respondents in a cohort being prepared for HIV Phase III vaccine clinical trials, Western Kenya. AIDS Res Hum Retroviruses 2011; 27:257-64. [PMID: 20950148 DOI: 10.1089/aid.2010.0061] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Kenya is one of the sub-Saharan African countries affected by HIV-1 infection and AIDS. We investigated HIV-1 genetic diversity in 130 individuals from Busia, Bungoma, and Kakamega in western Kenya as part of an HIV-1 vaccine feasibility study in preparation for Phase III efficacy clinical trials. After RNA extraction the partial gag (484 bp) and env (1297 bp) regions were amplified and directly sequenced. Phylogenetic analysis was done using MEGA version 4 and recombinants were identified using the jpHMM tool and phylogenetic analysis. HIV-1 sequences were amplified from 122 of the 130 samples, 118 (90.8%) from the gag region and 78 (60 %) from the env region and 74 samples (56.9%) from both the gag and env regions. Of these sequenced on both regions, 51.4% were subtype A, 9.4% subtype D, 1.4% subtype C, 4.1% subtype G, and 33.7% were discordant and thus possible recombinants, including A1/C, A1/D, A1/A2, and A2/C. The jpHMM tool indicated a further two samples with CD and BD breakpoints within the env gene and one within the gag gene (A1C). An additional sample had an A1D breakpoint in the gag gene, but the envelope was not amplified. HIV-1 subtype diversity in western Kenya should be considered in vaccines designed for clinical trials in this region and this genetic diversity should be continuously monitored.
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Affiliation(s)
- Micah Oyaro
- Kenyatta University, Department of Biological Sciences, Nairobi, Kenya
- Kenya Aids Vaccine Initiative (KAVI), Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
| | - John Mbithi
- Kenyatta University, Department of Biological Sciences, Nairobi, Kenya
| | - Fred Oyugi
- Kenya Aids Vaccine Initiative (KAVI), Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
| | - Annette Laten
- Division of Medical Virology, National Health Laboratory Services (NHLS) and University of Stellenbosch, Tygerberg, South Africa
| | - Omu Anzala
- Kenya Aids Vaccine Initiative (KAVI), Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
| | - Susan Engelbrecht
- Division of Medical Virology, National Health Laboratory Services (NHLS) and University of Stellenbosch, Tygerberg, South Africa
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Kijak GH, Tovanabutra S, Beyrer C, Sanders–Buell EE, Arroyo MA, Robb ML, Michael NL, McCutchan FE, Kim JH. RecDraw: a software package for the representation of HIV-1 recombinant structures. AIDS Res Hum Retroviruses 2010; 26:1317-21. [PMID: 20961275 DOI: 10.1089/aid.2010.0127] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The crucial role of recombination in HIV-1 biology is being increasingly recognized. In vitro studies have shown that up to 30 strand-transfer events may occur per viral replication cycle. Thus, recombination may surpass mutation as a major mechanism driving HIV-1 evolution. Currently, recombinant strains comprise 37% of the full-genome HIV-1 sequence database, including sequences representing 47 Circulating Recombinant Forms (CRFs) and more than 250 different Unique Recombinant Forms (URFs). Mapping of recombination breakpoints helps establish relationships among strains that are related by descent, such as CRF07_BC and CRF08_BC in China, and sheds light on their origin and epidemic spread. Additionally, unrelated recombinants sharing common breakpoints may reflect recombination hotspots within the viral genome. Here we present a software tool, RecDraw, for the graphical representation and efficient comparison of recombinant HIV-1 structures and breakpoints. RecDraw is a platform-flexible, Java stand-alone application available through http://www.hivresearch.org/research.php?ServiceID = 5&SubServiceID = 6 .
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Affiliation(s)
- Gustavo H. Kijak
- US Military HIV Research Program, Rockville, Maryland
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Rockville, Maryland
| | - Sodsai Tovanabutra
- US Military HIV Research Program, Rockville, Maryland
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Rockville, Maryland
| | - Chris Beyrer
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Eric E. Sanders–Buell
- US Military HIV Research Program, Rockville, Maryland
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Rockville, Maryland
| | - Miguel A. Arroyo
- US Military HIV Research Program, Rockville, Maryland
- Division of Retrovirology, Walter Reed Army Institute of Research, Rockville, Maryland
| | - Merlin L. Robb
- US Military HIV Research Program, Rockville, Maryland
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Rockville, Maryland
| | - Nelson L. Michael
- US Military HIV Research Program, Rockville, Maryland
- Division of Retrovirology, Walter Reed Army Institute of Research, Rockville, Maryland
| | - Francine E. McCutchan
- US Military HIV Research Program, Rockville, Maryland
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Rockville, Maryland
| | - Jerome H. Kim
- US Military HIV Research Program, Rockville, Maryland
- Division of Retrovirology, Walter Reed Army Institute of Research, Rockville, Maryland
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