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Schulz VE, Tuff JF, Tough RH, Lewis L, Chimukangara B, Garrett N, Abdool Karim Q, Abdool Karim SS, McKinnon LR, Kharsany ABM, McLaren PJ. Host genetic variation at a locus near CHD1L impacts HIV sequence diversity in a South African population. J Virol 2023; 97:e0095423. [PMID: 37747237 PMCID: PMC10617395 DOI: 10.1128/jvi.00954-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 08/04/2023] [Indexed: 09/26/2023] Open
Abstract
IMPORTANCE It has been previously shown that genetic variants near CHD1L on chromosome 1 are associated with reduced HIV VL in African populations. However, the impact of these variants on viral diversity and how they restrict viral replication are unknown. We report on a regional association analysis in a South African population and show evidence of selective pressure by variants near CHD1L on HIV RT and gag. Our findings provide further insight into how genetic variability at this locus contributes to host control of HIV in a South African population.
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Affiliation(s)
- Vanessa E. Schulz
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
- Sexually Transmitted and Bloodborne Infections Division, JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratories, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Jeffrey F. Tuff
- Sexually Transmitted and Bloodborne Infections Division, JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratories, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Riley H. Tough
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
- Sexually Transmitted and Bloodborne Infections Division, JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratories, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Lara Lewis
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
| | - Benjamin Chimukangara
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
- Department of Virology, University of KwaZulu-Natal, Durban, South Africa
| | - Nigel Garrett
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- Department of Public Health Medicine, School of Nursing and Public Health, University of KwaZulu-Natal, Durban, South Africa
| | - Quarraisha Abdool Karim
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Salim S. Abdool Karim
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Lyle R. McKinnon
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
| | - Ayesha B. M. Kharsany
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- Department of Medical Microbiology, School of Laboratory Medicine and Medical Science, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Paul J. McLaren
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
- Sexually Transmitted and Bloodborne Infections Division, JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratories, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
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2
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Goodreau SM, Stansfield SE, Mittler JE, Murphy JT, Abernethy NF, Gottlieb GS, Reid MC, Burke JC, Pollock ED, Herbeck JT. Why does age at HIV infection correlate with set point viral load? An evolutionary hypothesis. Epidemics 2022; 41:100629. [PMID: 36162386 PMCID: PMC9807138 DOI: 10.1016/j.epidem.2022.100629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 07/29/2022] [Accepted: 09/20/2022] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Set-point viral load (SPVL) correlates with the age at which people acquire HIV. Although immunosenescence may seem like a parsimonious explanation for this, it does not easily explain the observation that the relationship between age and SPVL attenuates when accounting for source partner SPVL. Here we propose an alternative explanation that encompasses this latter finding: that decreasing risk of acquisition with older age generates a selection bottleneck that selects for more virulent strains with age. METHODS We adapted a previously published model of HIV transmission and evolution (EvoNetHIV), parameterized here for men who have sex with men (MSM). We conducted a series of simulation experiments that vary seven behavioral or clinical parameters that affect exposure risk as people age. We conducted regressions to determine the mean increase in SPVL per 10-year increase in seroconversion age, with and without source SPVL in the model. RESULTS All runs generated significant relationships between seroconversion age and SPVL when not including source SPVL. All saw attenuated relationships, most to near 0, with source SPVL included. Four of our behavioral measures (relational duration, age-related homophily, coital frequency, and mean age at relationship formation) had clear effects on this relationship, all in the hypothesized direction. Combining multiple forms of behavioral heterogeneity yielded an increase of 0.056 log10 copies/mL SPVL per 10-year increase in seroconversion age, nearly as large as that seen in two empirical studies of age-SPVL correlations in MSM. CONCLUSION The higher virulence of HIV among those infected later in life may be partly explained by a combination of selective bottlenecks and behavioral heterogeneity by age. Variation in the strength of this effect across populations may be in part due to different behavioral, epidemiological and clinical conditions, and not require assumptions about differences in patterns of immunosenescence among populations.
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Affiliation(s)
- Steven M Goodreau
- Departments of Anthropology & Epidemiology, University of Washington, Seattle, WA 98195, USA.
| | - Sarah E Stansfield
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - John E Mittler
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
| | - James T Murphy
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
| | - Neil F Abernethy
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA 98195, USA
| | - Geoffrey S Gottlieb
- Departments of Medicine & Global Health, Center for Emerging & Re-Emerging Infectious Diseases, University of Washington, Seattle, WA 98195, USA
| | - Molly C Reid
- Department of Epidemiology, University of Washington, Seattle, WA 98195, USA
| | - Juandalyn C Burke
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA 98195, USA
| | - Emily D Pollock
- Department of Anthropology, University of Washington, Seattle, WA 98195, USA
| | - Joshua T Herbeck
- Department of Global Health, University of Washington, Seattle, WA 98195, USA
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3
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Pérez-Yanes S, Pernas M, Marfil S, Cabrera-Rodríguez R, Ortiz R, Urrea V, Rovirosa C, Estévez-Herrera J, Olivares I, Casado C, Lopez-Galindez C, Blanco J, Valenzuela-Fernández A. The Characteristics of the HIV-1 Env Glycoprotein Are Linked With Viral Pathogenesis. Front Microbiol 2022; 13:763039. [PMID: 35401460 PMCID: PMC8988142 DOI: 10.3389/fmicb.2022.763039] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 01/31/2022] [Indexed: 12/17/2022] Open
Abstract
The understanding of HIV-1 pathogenesis and clinical progression is incomplete due to the variable contribution of host, immune, and viral factors. The involvement of viral factors has been investigated in extreme clinical phenotypes from rapid progressors to long-term non-progressors (LTNPs). Among HIV-1 proteins, the envelope glycoprotein complex (Env) has been concentrated on in many studies for its important role in the immune response and in the first steps of viral replication. In this study, we analyzed the contribution of 41 Envs from 24 patients with different clinical progression rates and viral loads (VLs), LTNP-Elite Controllers (LTNP-ECs); Viremic LTNPs (vLTNPs), and non-controller individuals contemporary to LTNPs or recent, named Old and Modern progressors. We studied the Env expression, the fusion and cell-to-cell transfer capacities, as well as viral infectivity. The sequence and phylogenetic analysis of Envs were also performed. In every functional characteristic, the Envs from subjects with viral control (LTNP-ECs and vLTNPs) showed significant lower performance compared to those from the progressor individuals (Old and Modern). Regarding sequence analysis, the variable loops of the gp120 subunit of the Env (i.e., V2, V4, and mainly V5) of the progressor individuals showed longer and more glycosylated sequences than controller subjects. Therefore, HIV-1 Envs from virus of patients presenting viremic control and the non-progressor clinical phenotype showed poor viral functions and shorter sequences, whereas functional Envs were associated with virus of patients lacking virological control and with progressor clinical phenotypes. These correlations support the role of Env genotypic and phenotypic characteristics in the in vivo HIV-1 infection and pathogenesis.
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Affiliation(s)
- Silvia Pérez-Yanes
- Unidad de Farmacología, Sección de Medicina, Laboratorio de Inmunología Celular y Viral, Facultad de Ciencias de la Salud de la Universidad de La Laguna (ULL), San Cristóbal de La Laguna, Spain
| | - María Pernas
- Unidad de Virologia Molecular, Laboratorio de Referencia e Investigación en Retrovirus, Centro Nacional de Microbiologia, Instituto de Salud Carlos III, Madrid, Spain
| | - Silvia Marfil
- Institut de Recerca de la Sida IrsiCaixa, Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Barcelona, Spain
| | - Romina Cabrera-Rodríguez
- Unidad de Farmacología, Sección de Medicina, Laboratorio de Inmunología Celular y Viral, Facultad de Ciencias de la Salud de la Universidad de La Laguna (ULL), San Cristóbal de La Laguna, Spain
| | - Raquel Ortiz
- Institut de Recerca de la Sida IrsiCaixa, Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Barcelona, Spain
| | - Víctor Urrea
- Institut de Recerca de la Sida IrsiCaixa, Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Barcelona, Spain
| | - Carla Rovirosa
- Institut de Recerca de la Sida IrsiCaixa, Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Barcelona, Spain
| | - Judith Estévez-Herrera
- Unidad de Farmacología, Sección de Medicina, Laboratorio de Inmunología Celular y Viral, Facultad de Ciencias de la Salud de la Universidad de La Laguna (ULL), San Cristóbal de La Laguna, Spain
| | - Isabel Olivares
- Unidad de Virologia Molecular, Laboratorio de Referencia e Investigación en Retrovirus, Centro Nacional de Microbiologia, Instituto de Salud Carlos III, Madrid, Spain
| | - Concepción Casado
- Unidad de Virologia Molecular, Laboratorio de Referencia e Investigación en Retrovirus, Centro Nacional de Microbiologia, Instituto de Salud Carlos III, Madrid, Spain
- Concepción Casado,
| | - Cecilio Lopez-Galindez
- Unidad de Virologia Molecular, Laboratorio de Referencia e Investigación en Retrovirus, Centro Nacional de Microbiologia, Instituto de Salud Carlos III, Madrid, Spain
- Cecilio Lopez-Galindez,
| | - Julià Blanco
- Institut de Recerca de la Sida IrsiCaixa, Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Barcelona, Spain
- Chair of Infectious Diseases and Immunity, Faculty of Medicine, Universitat de Vic-Universitat Central de Catalunya (UVic-UCC), Barcelona, Spain
- Julià Blanco,
| | - Agustín Valenzuela-Fernández
- Unidad de Farmacología, Sección de Medicina, Laboratorio de Inmunología Celular y Viral, Facultad de Ciencias de la Salud de la Universidad de La Laguna (ULL), San Cristóbal de La Laguna, Spain
- *Correspondence: Agustín Valenzuela-Fernández,
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4
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Zhao L, Wymant C, Blanquart F, Golubchik T, Gall A, Bakker M, Bezemer D, Hall M, Ong SH, Albert J, Bannert N, Fellay J, Grabowski MK, Gunsenheimer-Bartmeyer B, Günthard HF, Kivelä P, Kouyos RD, Laeyendecker O, Meyer L, Porter K, van Sighem A, van der Valk M, Berkhout B, Kellam P, Cornelissen M, Reiss P, Fraser C, Ferretti L. Phylogenetic estimation of the viral fitness landscape of HIV-1 set-point viral load. Virus Evol 2022; 8:veac022. [PMID: 35402002 PMCID: PMC8986633 DOI: 10.1093/ve/veac022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 02/25/2022] [Accepted: 03/15/2022] [Indexed: 11/16/2022] Open
Abstract
Set-point viral load (SPVL), a common measure of human immunodeficiency virus (HIV)-1 virulence, is partially determined by viral genotype. Epidemiological evidence suggests that this viral property has been under stabilising selection, with a typical optimum for the virus between 104 and 105 copies of viral RNA per ml. Here we aimed to detect transmission fitness differences between viruses from individuals with different SPVLs directly from phylogenetic trees inferred from whole-genome sequences. We used the local branching index (LBI) as a proxy for transmission fitness. We found that LBI is more sensitive to differences in infectiousness than to differences in the duration of the infectious state. By analysing subtype-B samples from the Bridging the Evolution and Epidemiology of HIV in Europe project, we inferred a significant positive relationship between SPVL and LBI up to approximately 105 copies/ml, with some evidence for a peak around this value of SPVL. This is evidence of selection against low values of SPVL in HIV-1 subtype-B strains, likely related to lower infectiousness, and perhaps a peak in the transmission fitness in the expected range of SPVL. The less prominent signatures of selection against higher SPVL could be explained by an inherent limit of the method or the deployment of antiretroviral therapy.
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Affiliation(s)
- Lele Zhao
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Headington, Oxford OX3 7LF, UK
| | - Chris Wymant
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Headington, Oxford OX3 7LF, UK
| | - François Blanquart
- Centre for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, PSL Research University, Cedex 05, Paris 75231, France
| | - Tanya Golubchik
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Headington, Oxford OX3 7LF, UK
| | - Astrid Gall
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge CB10 1SD, UK
| | - Margreet Bakker
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, MB 1007, Netherlands
| | - Daniela Bezemer
- Stichting HIV Monitoring, Amsterdam, Amsterdam, AZ 1105, Netherlands
| | - Matthew Hall
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Headington, Oxford OX3 7LF, UK
| | - Swee Hoe Ong
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Jan Albert
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Stockholm 171 77, Sweden
- Department of Clinical Microbiology, Karolinska University Hospital, Solna, Stockholm S-171 76, Sweden
| | - Norbert Bannert
- Division for HIV and Other Retroviruses, Department of Infectious Diseases, Robert Koch Institute, Berlin 13353, Germany
| | - Jacques Fellay
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
- Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
- Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne CH-1015, Switzerland
| | - M Kate Grabowski
- Department of Pathology, John Hopkins University, Baltimore, MD 21287, USA
| | | | - Huldrych F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich CH-8091, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich 8057, Switzerland
| | - Pia Kivelä
- Department of Infectious Diseases, Helsinki University Hospital, Helsinki FI-00029, Finland
| | - Roger D Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich CH-8091, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich 8057, Switzerland
| | | | - Laurence Meyer
- INSERM CESP U1018, Université Paris Saclay, APHP, Service de Santé Publique, Hôpital de Bicêtre, Le Kremlin-Bicêtre 94270, France
| | - Kholoud Porter
- Institute for Global Health, University College London, London WC1N 1EH, UK
| | - Ard van Sighem
- Stichting HIV Monitoring, Amsterdam, Amsterdam, AZ 1105, Netherlands
| | - Marc van der Valk
- Stichting HIV Monitoring, Amsterdam, Amsterdam, AZ 1105, Netherlands
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, MB 1007, Netherlands
| | - Paul Kellam
- Kymab Ltd, Babraham Research Campus, Cambridge CB22 3AT, UK
- Department of Infectious Diseases, Faculty of Medicine, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Marion Cornelissen
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, MB 1007, Netherlands
- Molecular Diagnostic Unit, Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, MB 1007, Netherlands
| | - Peter Reiss
- Stichting HIV Monitoring, Amsterdam, Amsterdam, AZ 1105, Netherlands
- Department of Global Health, Amsterdam University Medical Centers, University of Amsterdam and Amsterdam Institute for Global Health and Development, Amsterdam, DE 1100, Netherlands
| | - Christophe Fraser
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Headington, Oxford OX3 7LF, UK
| | - Luca Ferretti
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Headington, Oxford OX3 7LF, UK
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5
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Hendrickx DM, Delva W, Hens N. Influence of sexual risk behaviour and STI co-infection dynamics on the evolution of HIV set point viral load in MSM. Epidemics 2021; 36:100474. [PMID: 34153622 DOI: 10.1016/j.epidem.2021.100474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 03/17/2021] [Accepted: 06/07/2021] [Indexed: 11/27/2022] Open
Abstract
HIV viral load (VL) is an important predictor of HIV progression and transmission. Anti-retroviral therapy (ART) has been reported to reduce HIV transmission by lowering VL. However, apart from this beneficial effect, increased levels of population mean set-point viral load (SPVL), an estimator for HIV virulence, have been observed in men who have sex with men (MSM) in the decade following the introduction of ART in The Netherlands. Several studies have been devoted to explain these counter-intuitive trends in SPVL. However, to our knowledge, none of these studies has investigated an explanation in which it arises as the result of a sexually transmitted infection (STI) co-factor in detail. In this study, we adapted an event-based, individual-based model to investigate how STI co-infection and sexual risk behaviour affect the evolution of HIV SPVL in MSM before and after the introduction of ART. The results suggest that sexual risk behaviour has an effect on SPVL and indicate that more data are needed to test the effect of STI co-factors on SPVL. Furthermore, the observed trends in SPVL cannot be explained by sexual risk behaviour and STI co-factors only. We recommend to develop mathematical models including also factors related to viral evolution as reported earlier in the literature. However, this requires more complex models, and the collection of more data for parameter estimation than what is currently available.
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Affiliation(s)
- Diana M Hendrickx
- I-BioStat, Data Science Institute, Hasselt University, Hasselt, Belgium.
| | - Wim Delva
- I-BioStat, Data Science Institute, Hasselt University, Hasselt, Belgium; The South African Department of Science and Technology-National Research Foundation (DST-NRF) Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa; Department of Global Health, Faculty of Medicine and Health, Stellenbosch University, Stellenbosch, South Africa; International Centre for Reproductive Health, Ghent University, Ghent, Belgium; Rega Institute for Medical Research, KU Leuven, Leuven, Belgium; School for Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Niel Hens
- I-BioStat, Data Science Institute, Hasselt University, Hasselt, Belgium; Centre for Health Economics Research and Modelling Infectious Diseases, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
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6
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Makinde J, Nduati EW, Freni-Sterrantino A, Streatfield C, Kibirige C, Dalel J, Black SL, Hayes P, Macharia G, Hare J, McGowan E, Abel B, King D, Joseph S, Hunter E, Sanders EJ, Price M, Gilmour J. A Novel Sample Selection Approach to Aid the Identification of Factors That Correlate With the Control of HIV-1 Infection. Front Immunol 2021; 12:634832. [PMID: 33777023 PMCID: PMC7991997 DOI: 10.3389/fimmu.2021.634832] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 02/08/2021] [Indexed: 12/11/2022] Open
Abstract
Individuals infected with HIV display varying rates of viral control and disease progression, with a small percentage of individuals being able to spontaneously control infection in the absence of treatment. In attempting to define the correlates associated with natural protection against HIV, extreme heterogeneity in the datasets generated from systems methodologies can be further complicated by the inherent variability encountered at the population, individual, cellular and molecular levels. Furthermore, such studies have been limited by the paucity of well-characterised samples and linked epidemiological data, including duration of infection and clinical outcomes. To address this, we selected 10 volunteers who rapidly and persistently controlled HIV, and 10 volunteers each, from two control groups who failed to control (based on set point viral loads) from an acute and early HIV prospective cohort from East and Southern Africa. A propensity score matching approach was applied to control for the influence of five factors (age, risk group, virus subtype, gender, and country) known to influence disease progression on causal observations. Fifty-two plasma proteins were assessed at two timepoints in the 1st year of infection. We independently confirmed factors known to influence disease progression such as the B*57 HLA Class I allele, and infecting virus Subtype. We demonstrated associations between circulating levels of MIP-1α and IL-17C, and the ability to control infection. IL-17C has not been described previously within the context of HIV control, making it an interesting target for future studies to understand HIV infection and transmission. An in-depth systems analysis is now underway to fully characterise host, viral and immunological factors contributing to control.
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Affiliation(s)
- Julia Makinde
- IAVI Human Immunology Laboratory, Imperial College London, London, United Kingdom
| | - Eunice W Nduati
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Anna Freni-Sterrantino
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, Imperial College London, London, United Kingdom
| | - Claire Streatfield
- IAVI Human Immunology Laboratory, Imperial College London, London, United Kingdom
| | - Catherine Kibirige
- IAVI Human Immunology Laboratory, Imperial College London, London, United Kingdom
| | - Jama Dalel
- IAVI Human Immunology Laboratory, Imperial College London, London, United Kingdom
| | - S Lucas Black
- IAVI Human Immunology Laboratory, Imperial College London, London, United Kingdom
| | - Peter Hayes
- IAVI Human Immunology Laboratory, Imperial College London, London, United Kingdom
| | - Gladys Macharia
- IAVI Human Immunology Laboratory, Imperial College London, London, United Kingdom
| | - Jonathan Hare
- IAVI Human Immunology Laboratory, Imperial College London, London, United Kingdom
| | - Edward McGowan
- IAVI Human Immunology Laboratory, Imperial College London, London, United Kingdom
| | - Brian Abel
- IAVI Human Immunology Laboratory, Imperial College London, London, United Kingdom
| | - Deborah King
- IAVI Human Immunology Laboratory, Imperial College London, London, United Kingdom
| | - Sarah Joseph
- IAVI Human Immunology Laboratory, Imperial College London, London, United Kingdom
| | | | - Eric Hunter
- Emory Vaccine Centre, Yerkes National Primate Research Centre, Emory University, Atlanta, GA, United States.,Zambia-Emory HIV Research Project, Lusaka, Zambia
| | - Eduard J Sanders
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Matt Price
- IAVI, New York, NY, United States.,Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, United States
| | - Jill Gilmour
- IAVI Human Immunology Laboratory, Imperial College London, London, United Kingdom
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7
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Kapaata A, Balinda SN, Xu R, Salazar MG, Herard K, Brooks K, Laban K, Hare J, Dilernia D, Kamali A, Ruzagira E, Mukasa F, Gilmour J, Salazar-Gonzalez JF, Yue L, Cotten M, Hunter E, Kaleebu P. HIV-1 Gag-Pol Sequences from Ugandan Early Infections Reveal Sequence Variants Associated with Elevated Replication Capacity. Viruses 2021; 13:v13020171. [PMID: 33498793 PMCID: PMC7912664 DOI: 10.3390/v13020171] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 01/04/2021] [Accepted: 01/06/2021] [Indexed: 01/05/2023] Open
Abstract
The ability to efficiently establish a new infection is a critical property for human immunodeficiency virus type 1 (HIV-1). Although the envelope protein of the virus plays an essential role in receptor binding and internalization of the infecting virus, the structural proteins, the polymerase and the assembly of new virions may also play a role in establishing and spreading viral infection in a new host. We examined Ugandan viruses from newly infected patients and focused on the contribution of the Gag-Pol genes to replication capacity. A panel of Gag-Pol sequences generated using single genome amplification from incident HIV-1 infections were cloned into a common HIV-1 NL4.3 pol/env backbone and the influence of Gag-Pol changes on replication capacity was monitored. Using a novel protein domain approach, we then documented diversity in the functional protein domains across the Gag-Pol region and identified differences in the Gag-p6 domain that were frequently associated with higher in vitro replication.
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Affiliation(s)
- Anne Kapaata
- Medical Research Council, UVRI & LSTHM Uganda Research Unit, Plot 51–59, Entebbe, Uganda; (A.K.); (S.N.B.); (M.G.S.); (K.L.); (E.R.); (F.M.); (J.F.S.-G.); (P.K.)
| | - Sheila N. Balinda
- Medical Research Council, UVRI & LSTHM Uganda Research Unit, Plot 51–59, Entebbe, Uganda; (A.K.); (S.N.B.); (M.G.S.); (K.L.); (E.R.); (F.M.); (J.F.S.-G.); (P.K.)
| | - Rui Xu
- Emory University, Atlanta, GA 30322, USA; (R.X.); (K.H.); (K.B.); (D.D.); (L.Y.); (E.H.)
| | - Maria G. Salazar
- Medical Research Council, UVRI & LSTHM Uganda Research Unit, Plot 51–59, Entebbe, Uganda; (A.K.); (S.N.B.); (M.G.S.); (K.L.); (E.R.); (F.M.); (J.F.S.-G.); (P.K.)
| | - Kimberly Herard
- Emory University, Atlanta, GA 30322, USA; (R.X.); (K.H.); (K.B.); (D.D.); (L.Y.); (E.H.)
| | - Kelsie Brooks
- Emory University, Atlanta, GA 30322, USA; (R.X.); (K.H.); (K.B.); (D.D.); (L.Y.); (E.H.)
| | - Kato Laban
- Medical Research Council, UVRI & LSTHM Uganda Research Unit, Plot 51–59, Entebbe, Uganda; (A.K.); (S.N.B.); (M.G.S.); (K.L.); (E.R.); (F.M.); (J.F.S.-G.); (P.K.)
| | - Jonathan Hare
- Imperial College London, London SW7 2AZ, UK; (J.H.); (J.G.)
- International AIDS Vaccine Initiative (IAVI), New York, NY 10004, USA
| | - Dario Dilernia
- Emory University, Atlanta, GA 30322, USA; (R.X.); (K.H.); (K.B.); (D.D.); (L.Y.); (E.H.)
| | | | - Eugene Ruzagira
- Medical Research Council, UVRI & LSTHM Uganda Research Unit, Plot 51–59, Entebbe, Uganda; (A.K.); (S.N.B.); (M.G.S.); (K.L.); (E.R.); (F.M.); (J.F.S.-G.); (P.K.)
| | - Freddie Mukasa
- Medical Research Council, UVRI & LSTHM Uganda Research Unit, Plot 51–59, Entebbe, Uganda; (A.K.); (S.N.B.); (M.G.S.); (K.L.); (E.R.); (F.M.); (J.F.S.-G.); (P.K.)
| | - Jill Gilmour
- Imperial College London, London SW7 2AZ, UK; (J.H.); (J.G.)
- International AIDS Vaccine Initiative (IAVI), New York, NY 10004, USA
| | - Jesus F. Salazar-Gonzalez
- Medical Research Council, UVRI & LSTHM Uganda Research Unit, Plot 51–59, Entebbe, Uganda; (A.K.); (S.N.B.); (M.G.S.); (K.L.); (E.R.); (F.M.); (J.F.S.-G.); (P.K.)
| | - Ling Yue
- Emory University, Atlanta, GA 30322, USA; (R.X.); (K.H.); (K.B.); (D.D.); (L.Y.); (E.H.)
| | - Matthew Cotten
- Medical Research Council, UVRI & LSTHM Uganda Research Unit, Plot 51–59, Entebbe, Uganda; (A.K.); (S.N.B.); (M.G.S.); (K.L.); (E.R.); (F.M.); (J.F.S.-G.); (P.K.)
- Centre for Virus Research, MRC-University of Glasgow, Glasgow G61 1QH, UK
- Correspondence: ; Tel.: +25-6701-509-685
| | - Eric Hunter
- Emory University, Atlanta, GA 30322, USA; (R.X.); (K.H.); (K.B.); (D.D.); (L.Y.); (E.H.)
| | - Pontiano Kaleebu
- Medical Research Council, UVRI & LSTHM Uganda Research Unit, Plot 51–59, Entebbe, Uganda; (A.K.); (S.N.B.); (M.G.S.); (K.L.); (E.R.); (F.M.); (J.F.S.-G.); (P.K.)
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8
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Drug Repurposing Approaches to Combating Viral Infections. J Clin Med 2020; 9:jcm9113777. [PMID: 33238464 PMCID: PMC7700377 DOI: 10.3390/jcm9113777] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 11/18/2020] [Accepted: 11/19/2020] [Indexed: 12/14/2022] Open
Abstract
Development of novel antiviral molecules from the beginning costs an average of $350 million to $2 billion per drug, and the journey from the laboratory to the clinic takes about 10–15 years. Utilization of drug repurposing approaches has generated substantial interest in order to overcome these drawbacks. A drastic reduction in the failure rate, which otherwise is ~92%, is achieved with the drug repurposing approach. The recent exploration of the drug repurposing approach to combat the COVID-19 pandemic has further validated the fact that it is more beneficial to reinvestigate the in-practice drugs for a new application instead of designing novel drugs. The first successful example of drug repurposing is zidovudine (AZT), which was developed as an anti-cancer agent in the 1960s and was later approved by the US FDA as an anti-HIV therapeutic drug in the late 1980s after fast track clinical trials. Since that time, the drug repurposing approach has been successfully utilized to develop effective therapeutic strategies against a plethora of diseases. Hence, an extensive application of the drug repurposing approach will not only help to fight the current pandemics more efficiently but also predict and prepare for newly emerging viral infections. In this review, we discuss in detail the drug repurposing approach and its advancements related to viral infections such as Human Immunodeficiency Virus (HIV) and Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2).
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9
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Novel association of genetic variants in non-coding regulatory regions with HIV-1 infection. INFECTION GENETICS AND EVOLUTION 2020; 85:104514. [PMID: 32861908 DOI: 10.1016/j.meegid.2020.104514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 07/23/2020] [Accepted: 08/22/2020] [Indexed: 11/22/2022]
Abstract
Host genetic variability interplays with the environment and variegating viral factors to determine the outcome in HIV-1/AIDS. Several GWAS studies have reported that genetic heterogeneity of individuals leads to differential HIV susceptibility. Proxy SNPs that are in Linkage Disequilibrium to the GWAS SNPs could be important targets in HIV pathogenesis and need to be analyzed further for their potential regulatory role. Current study thus aimed to identify novel proxy SNPs that may play a critical role in HIV susceptibility and disease progression. 372 SNPs, associated with HIV-1/AIDS pathogenesis, were retrieved via GWAS catalogue. 1854 proxy SNPs, in Linkage Disequilibrium (r2 = 0.8) to the GWAS reported SNPs, were identified using the SNAP web tool. Regulatory functions of aforementioned 1854 polymorphic sites (GWAS SNPs and their proxy SNPs) were acquired from RegulomeDB. 178 of the proxy SNPs showed evidence of strong regulatory potential returning a score of ≤3. Among these regulatory SNPs, 22 had already been reported for their association with HIV/AIDS while 156 SNPs showed novel association. Three of these novel SNPs (g.rs6457282T>C, g.rs17064977C>T and g.rs3130350G>T) were validated using sequence specific PCR (SSP-PCR) on HIV-infected patients. For g.rs6457282T>C and rs17064977C>T, CT genotype was determined to be significantly associated with increased risk of HIV-1 infection (rs6457282T>C: OR = 9.5, 95% CI = 3.0792-29.3099, p = 0.0001; rs17064977C>T: OR = 8.1077, 95% CI = 3.1125-21.119, p = 0.0001). Moreover, the association of interacting protein partners of affected genes with HIV-1 elucidates the significance of corresponding SNPs in HIV disease outcome that further needs to be functionally deciphered.
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10
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Clinical and evolutionary consequences of HIV adaptation to HLA: implications for vaccine and cure. Curr Opin HIV AIDS 2020; 14:194-204. [PMID: 30925534 DOI: 10.1097/coh.0000000000000541] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
PURPOSE OF REVIEW The purpose of this review is to summarize recent advances in our understanding of HIV adaptation to human leukocyte antigen (HLA)-associated immune pressures and its relevance to HIV prevention and cure research. RECENT FINDINGS Recent research has confirmed that HLA is a major driver of individual and population-level HIV evolution, that HIV strains are adapting to the immunogenetic profiles of the different human ethnic groups in which they circulate, and that HIV adaptation has substantial clinical and immunologic consequences. As such, adaptation represents a major challenge to HIV prevention and cure. At the same time, there are opportunities: Studies of HIV adaptation are revealing why certain HLA alleles are protective in some populations and not others; they are identifying immunogenic viral epitopes that harbor high mutational barriers to escape, and they may help illuminate novel, vaccine-relevant HIV epitopes in regions where circulating adaptation is extensive. Elucidation of HLA-driven adapted and nonadapted viral forms in different human populations and HIV subtypes also renders 'personalized' immunogen selection, as a component of HIV cure strategies, conceptually feasible. SUMMARY Though adaptation represents a major challenge to HIV prevention and cure, achieving an in-depth understanding of this phenomenon can help move the design of such strategies forward.
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11
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Partner HIV Serostatus Impacts Viral Load, Genital HIV Shedding, and Immune Activation in HIV-Infected Individuals. J Acquir Immune Defic Syndr 2020; 82:51-60. [PMID: 31169767 DOI: 10.1097/qai.0000000000002089] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Studies of seronegative individuals in HIV discordant relationships provide important insights into the effects of HIV exposure on the seronegative partner, but few have examined the impact of partner serostatus on disease progression in seropositive individuals. We investigated the impact of HIV serostatus on clinical and biological factors influencing HIV disease progression in 337 HIV-infected heterosexual individuals in stable long-term HIV-seroconcordant or HIV-serodiscordant relationships. Seroconcordant individuals had significantly higher plasma viral loads (pVLs) than HIV-infected partners in serodiscordant partnerships [4.4 log10 copies RNA/mL (interquartile range 3.7-5.0) versus 3.9 (3.3-4.5), P < 0.0001], irrespective of gender. pVLs correlated inversely with CD4 T-cell counts, although CD4 counts did not differ significantly between seroconcordant and serodiscordant individuals. HIV+ seroconcordant individuals had higher frequencies of CCR5 CD4 and CD8 T cells (P = 0.03 and P = 0.02, respectively) than HIV+ individuals in serodiscordant relationships and higher concentrations of plasma IL-1β (P = 0.04), TNF-α (P = 0.02), and IL-10 (P = 0.02). Activated CD4 T-cell frequencies and TNF-α were the most influential in determining variation in pVLs, independently of CD4 counts. In addition, HIV+ seroconcordant women had significantly higher genital VLs (gVLs) than HIV+ women in serodiscordant relationships (P < 0.001), with pVLs correlating significantly with gVLs (Rho = 0.65, P < 0.0001). Cervical and blood T-cell activation tended to correlate positively, although partner seroconcordance did not influence genital T-cell activation. We conclude that HIV+ seroconcordant individuals have higher frequencies of activated, CCR5-expressing T cells in blood and higher pVLs and gVLs than their HIV+ counterparts in discordant relationships, which could translate to faster disease progression or larger viral reservoir.
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12
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Price MA, Rida W, Kilembe W, Karita E, Inambao M, Ruzagira E, Kamali A, Sanders EJ, Anzala O, Hunter E, Allen S, Edward VA, Wall KM, Tang J, Fast PE, Kaleebu P, Lakhi S, Mutua G, Bekker LG, Abu-Baker G, Tichacek A, Chetty P, Latka MH, Maenetje P, Makkan H, Kibengo F, Priddy F, Gilmour J. Control of the HIV-1 Load Varies by Viral Subtype in a Large Cohort of African Adults With Incident HIV-1 Infection. J Infect Dis 2020; 220:432-441. [PMID: 30938435 PMCID: PMC6603968 DOI: 10.1093/infdis/jiz127] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 03/22/2019] [Indexed: 12/14/2022] Open
Abstract
Few human immunodeficiency virus (HIV)–infected persons can maintain low viral levels without therapeutic intervention. We evaluate predictors of spontaneous control of the viral load (hereafter, “viral control”) in a prospective cohort of African adults shortly after HIV infection. Viral control was defined as ≥2 consecutively measured viral loads (VLs) of ≤10 000 copies/mL after the estimated date of infection, followed by at least 4 subsequent measurements for which the VL in at least 75% was ≤10 000 copies/mL in the absence of ART. Multivariable logistic regression characterized predictors of viral control. Of 590 eligible volunteers, 107 (18.1%) experienced viral control, of whom 25 (4.2%) maintained a VL of 51–2000 copies/mL, and 5 (0.8%) sustained a VL of ≤50 copies/mL. The median ART-free follow-up time was 3.3 years (range, 0.3–9.7 years). Factors independently associated with control were HIV-1 subtype A (reference, subtype C; adjusted odds ratio [aOR], 2.1 [95% confidence interval {CI}, 1.3–3.5]), female sex (reference, male sex; aOR, 1.8 [95% CI, 1.1–2.8]), and having HLA class I variant allele B*57 (reference, not having this allele; aOR, 1.9 [95% CI, 1.0–3.6]) in a multivariable model that also controlled for age at the time of infection and baseline CD4+ T-cell count. We observed strong associations between infecting HIV-1 subtype, HLA type, and sex on viral control in this cohort. HIV-1 subtype is important to consider when testing and designing new therapeutic and prevention technologies, including vaccines.
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Affiliation(s)
- Matt A Price
- International AIDS Vaccine Initiative, New York, New York.,Department of Epidemiology and Biostatistics, University of California-San Francisco
| | | | - William Kilembe
- Rwanda Zambia HIV Research Group, Lusaka and Ndola.,Rwanda Zambia HIV Research Group, Zambia and Kigali.,Rwanda Zambia HIV Research Group, Rwanda
| | - Etienne Karita
- Rwanda Zambia HIV Research Group, Lusaka and Ndola.,Rwanda Zambia HIV Research Group, Zambia and Kigali.,Rwanda Zambia HIV Research Group, Rwanda
| | - Mubiana Inambao
- Rwanda Zambia HIV Research Group, Lusaka and Ndola.,Rwanda Zambia HIV Research Group, Zambia and Kigali.,Rwanda Zambia HIV Research Group, Rwanda
| | | | - Anatoli Kamali
- International AIDS Vaccine Initiative, New York, New York
| | - Eduard J Sanders
- Kenyan Medical Research Institute-Wellcome Trust, Kilifi, Nairobi, Kenya.,Nuffield Department of Clinical Medicine, Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford, Headington, London, United Kingdom
| | - Omu Anzala
- KAVI Institute of Clinical Research, Nairobi, Kenya
| | - Eric Hunter
- Rwanda Zambia HIV Research Group, Lusaka and Ndola.,Rwanda Zambia HIV Research Group, Zambia and Kigali.,Rwanda Zambia HIV Research Group, Rwanda.,Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia
| | - Susan Allen
- Rwanda Zambia HIV Research Group, Lusaka and Ndola.,Rwanda Zambia HIV Research Group, Zambia and Kigali.,Rwanda Zambia HIV Research Group, Rwanda.,Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia
| | - Vinodh A Edward
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, Connecticut.,The Aurum Institute, South Africa.,School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, South Africa.,Advancing Care and Treatment for TB/HIV, South African Medical Research Council, Johannesburg, South Africa
| | - Kristin M Wall
- Rwanda Zambia HIV Research Group, Lusaka and Ndola.,Rwanda Zambia HIV Research Group, Zambia and Kigali.,Rwanda Zambia HIV Research Group, Rwanda.,Department of Epidemiology, Emory University, Atlanta, Georgia
| | - Jianming Tang
- Department of Medicine, University of Alabama-Birmingham
| | | | | | - Shabir Lakhi
- Rwanda Zambia HIV Research Group, Lusaka and Ndola.,Rwanda Zambia HIV Research Group, Zambia and Kigali.,Rwanda Zambia HIV Research Group, Rwanda
| | | | | | | | - Amanda Tichacek
- Rwanda Zambia HIV Research Group, Lusaka and Ndola.,Rwanda Zambia HIV Research Group, Zambia and Kigali.,Rwanda Zambia HIV Research Group, Rwanda.,Department of Epidemiology, Emory University, Atlanta, Georgia
| | - Paramesh Chetty
- International AIDS Vaccine Initiative, New York, New York.,International AIDS Vaccine Initiative Human Immunology Laboratory, London, United Kingdom
| | | | | | | | | | - Fran Priddy
- International AIDS Vaccine Initiative, New York, New York
| | - Jill Gilmour
- International AIDS Vaccine Initiative Human Immunology Laboratory, London, United Kingdom
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13
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Wertheim JO, Oster AM, Switzer WM, Zhang C, Panneer N, Campbell E, Saduvala N, Johnson JA, Heneine W. Natural selection favoring more transmissible HIV detected in United States molecular transmission network. Nat Commun 2019; 10:5788. [PMID: 31857582 PMCID: PMC6923435 DOI: 10.1038/s41467-019-13723-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 11/22/2019] [Indexed: 01/10/2023] Open
Abstract
HIV molecular epidemiology can identify clusters of individuals with elevated rates of HIV transmission. These variable transmission rates are primarily driven by host risk behavior; however, the effect of viral traits on variable transmission rates is poorly understood. Viral load, the concentration of HIV in blood, is a heritable viral trait that influences HIV infectiousness and disease progression. Here, we reconstruct HIV genetic transmission clusters using data from the United States National HIV Surveillance System and report that viruses in clusters, inferred to be frequently transmitted, have higher viral loads at diagnosis. Further, viral load is higher in people in larger clusters and with increased network connectivity, suggesting that HIV in the United States is experiencing natural selection to be more infectious and virulent. We also observe a concurrent increase in viral load at diagnosis over the last decade. This evolutionary trajectory may be slowed by prevention strategies prioritized toward rapidly growing transmission clusters.
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Affiliation(s)
- Joel O Wertheim
- Department of Medicine, University of California, San Diego, CA, USA.
| | - Alexandra M Oster
- Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - William M Switzer
- Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Chenhua Zhang
- ICF International, Atlanta, GA, USA
- SciMetrika LLC, Atlanta, GA, USA
| | - Nivedha Panneer
- Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Ellsworth Campbell
- Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Jeffrey A Johnson
- Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Walid Heneine
- Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
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14
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Stansfield SE, Mittler JE, Gottlieb GS, Murphy JT, Hamilton DT, Detels R, Wolinsky SM, Jacobson LP, Margolick JB, Rinaldo CR, Herbeck JT, Goodreau SM. Sexual role and HIV-1 set point viral load among men who have sex with men. Epidemics 2019; 26:68-76. [PMID: 30193771 PMCID: PMC6538391 DOI: 10.1016/j.epidem.2018.08.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 07/12/2018] [Accepted: 08/28/2018] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND HIV-1 set point viral load (SPVL) is a highly variable trait that influences disease progression and transmission risk. Men who are exclusively insertive (EI) during anal intercourse require more sexual contacts to become infected than exclusively receptive (ER) men. Thus, we hypothesize that EIs are more likely to acquire their viruses from highly infectious partners (i.e., with high SPVLs) and to have higher SPVLs than infected ERs. METHODS We used a one-generation Bernoulli model, a dynamic network model, and data from the Multicenter AIDS Cohort Study (MACS) to examine whether and under what circumstances MSM differ in SPVL by sexual role. RESULTS Both models predicted higher SPVLs in EIs than role versatile (RV) or ER men, but only in scenarios where longer-term relationships predominated. ER and RV men displayed similar SPVLs. EI men remained far less likely than ER men to become infected, however. When the MACS data were limited by some estimates of lower sex partner counts (a proxy for longer relationships), EI men had higher SPVLs; these differences were clinically relevant (>0.3 log10 copies/mL) and statistically significant (p < 0.05). CONCLUSIONS Mode of acquisition may be an important aspect of SPVL evolution in MSM, with clinical implications.
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Affiliation(s)
- Sarah E Stansfield
- Departments of Anthropology & Epidemiology, University of Washington, 314 Denny Hall, Box 353100, Seattle, WA 98195-3100, USA.
| | - John E Mittler
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
| | - Geoffrey S Gottlieb
- Departments of Medicine & Global Health, University of Washington, Seattle, WA 98195, USA
| | - James T Murphy
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
| | - Deven T Hamilton
- Center for Studies in Demography and Ecology, University of Washington, Seattle, WA 98195, USA
| | - Roger Detels
- Department of Epidemiology, University of California School of Public Health, Los Angeles, CA, 90024, USA
| | - Steven M Wolinsky
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Lisa P Jacobson
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Joseph B Margolick
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Charles R Rinaldo
- Department of Infectious Diseases and Microbiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, 15261, USA
| | - Joshua T Herbeck
- Department of Global Health, University of Washington, Seattle, WA 98195, USA
| | - Steven M Goodreau
- Department of Anthropology, University of Washington, Seattle, WA 98195, USA
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15
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Alteri C, Fabeni L, Scutari R, Berno G, Di Carlo D, Gori C, Bertoli A, Vergori A, Mastrorosa I, Bellagamba R, Mussini C, Colafigli M, Montella F, Pennica A, Mastroianni CM, Girardi E, Andreoni M, Antinori A, Svicher V, Ceccherini-Silberstein F, Perno CF, Santoro MM. Genetic divergence of HIV-1 B subtype in Italy over the years 2003-2016 and impact on CTL escape prevalence. Sci Rep 2018; 8:15739. [PMID: 30356083 PMCID: PMC6200748 DOI: 10.1038/s41598-018-34058-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 10/04/2018] [Indexed: 12/05/2022] Open
Abstract
HIV-1 is characterized by high genetic variability, with implications for spread, and immune-escape selection. Here, the genetic modification of HIV-1 B subtype over time was evaluated on 3,328 pol and 1,152 V3 sequences belonging to B subtype and collected from individuals diagnosed in Italy between 2003 and 2016. Sequences were analyzed for genetic-distance from consensus-B (Tajima-Nei), non-synonymous and synonymous rates (dN and dS), CTL escapes, and intra-host evolution over four time-spans (2003–2006, 2007–2009, 2010–2012, 2013–2016). Genetic-distance increased over time for both pol and V3 sequences (P < 0.0001 and 0.0003). Similar results were obtained for dN and dS. Entropy-value significantly increased at 16 pol and two V3 amino acid positions. Seven of them were CTL escape positions (protease: 71; reverse-transcriptase: 35, 162, 177, 202, 207, 211). Sequences with ≥3 CTL escapes increased from 36.1% in 2003–2006 to 54.0% in 2013–2016 (P < 0.0001), and showed better intra-host adaptation than those containing ≤2 CTL escapes (intra-host evolution: 3.0 × 10−3 [2.9 × 10−3–3.1 × 10−3] vs. 4.3 × 10−3 [4.0 × 10−3–5.0 × 10−3], P[LRT] < 0.0001[21.09]). These data provide evidence of still ongoing modifications, involving CTL escape mutations, in circulating HIV-1 B subtype in Italy. These modifications might affect the process of HIV-1 adaptation to the host, as suggested by the slow intra-host evolution characterizing viruses with a high number of CTL escapes.
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Affiliation(s)
- Claudia Alteri
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Rome, 00133, Italy.
| | - Lavinia Fabeni
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Rome, 00133, Italy
| | - Rossana Scutari
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Rome, 00133, Italy
| | - Giulia Berno
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, 00161, Italy
| | - Domenico Di Carlo
- Department of Biomedical and Clinical Sciences "L. Sacco", University of Milan, Pediatric Clinical Research Center "Romeo and Enrica Invernizzi", Milan, 20133, Italy
| | - Caterina Gori
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, 00161, Italy
| | - Ada Bertoli
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Rome, 00133, Italy
| | - Alessandra Vergori
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, 00161, Italy
| | - Ilaria Mastrorosa
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, 00161, Italy
| | - Rita Bellagamba
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, 00161, Italy
| | | | | | | | | | | | - Enrico Girardi
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, 00161, Italy
| | | | - Andrea Antinori
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, 00161, Italy
| | - Valentina Svicher
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Rome, 00133, Italy
| | | | - Carlo Federico Perno
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, 00161, Italy.,Department of Oncology, University of Milan, Milan, 20122, Italy
| | - Maria Mercedes Santoro
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Rome, 00133, Italy
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16
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HLA Class I Downregulation by HIV-1 Variants from Subtype C Transmission Pairs. J Virol 2018; 92:JVI.01633-17. [PMID: 29321314 DOI: 10.1128/jvi.01633-17] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 12/23/2017] [Indexed: 02/08/2023] Open
Abstract
HIV-1 downregulates human leukocyte antigen A (HLA-A) and HLA-B from the surface of infected cells primarily to evade CD8 T cell recognition. HLA-C was thought to remain on the cell surface and bind inhibitory killer immunoglobulin-like receptors, preventing natural killer (NK) cell-mediated suppression. However, a recent study found HIV-1 primary viruses have the capacity to downregulate HLA-C. The goal of this study was to assess the heterogeneity of HLA-A, HLA-B, and HLA-C downregulation among full-length primary viruses from six chronically infected and six newly infected individuals from transmission pairs and to determine whether transmitted/founder variants exhibit common HLA class I downregulation characteristics. We measured HLA-A, HLA-B, HLA-C, and total HLA class I downregulation by flow cytometry of primary CD4 T cells infected with 40 infectious molecular clones. Primary viruses mediated a range of HLA class I downregulation capacities (1.3- to 6.1-fold) which could differ significantly between transmission pairs. Downregulation of HLA-C surface expression on infected cells correlated with susceptibility to in vitro NK cell suppression of virus release. Despite this, transmitted/founder variants did not share a downregulation signature and instead were more similar to the quasispecies of matched donor partners. These data indicate that a range of viral abilities to downregulate HLA-A, HLA-B, and HLA-C exist within and between individuals that can have functional consequences on immune recognition.IMPORTANCE Subtype C HIV-1 is the predominant subtype involved in heterosexual transmission in sub-Saharan Africa. Authentic subtype C viruses that contain natural sequence variations throughout the genome often are not used in experimental systems due to technical constraints and sample availability. In this study, authentic full-length subtype C viruses, including transmitted/founder viruses, were examined for the ability to disrupt surface expression of HLA class I molecules, which are central to both adaptive and innate immune responses to viral infections. We found that the HLA class I downregulation capacity of primary viruses varied, and HLA-C downregulation capacity impacted viral suppression by natural killer cells. Transmitted viruses were not distinct in the capacity for HLA class I downregulation or natural killer cell evasion. These results enrich our understanding of the phenotypic variation existing among natural HIV-1 viruses and how that might impact the ability of the immune system to recognize infected cells in acute and chronic infection.
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17
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Abstract
Pathogen traits, such as the virulence of an infection, can vary significantly between patients. A major challenge is to measure the extent to which genetic differences between infecting strains explain the observed variation of the trait. This is quantified by the trait’s broad-sense heritability, H2. A recent discrepancy between estimates of the heritability of HIV-virulence has opened a debate on the estimators’ accuracy. Here, we show that the discrepancy originates from model limitations and important lifecycle differences between sexually reproducing organisms and transmittable pathogens. In particular, current quantitative genetics methods, such as donor–recipient regression of surveyed serodiscordant couples and the phylogenetic mixed model (PMM), are prone to underestimate H2, because they neglect or do not fit to the loss of resemblance between transmission partners caused by within-host evolution. In a phylogenetic analysis of 8,483 HIV patients from the United Kingdom, we show that the phenotypic correlation between transmission partners decays with the amount of within-host evolution of the virus. We reproduce this pattern in toy-model simulations and show that a phylogenetic Ornstein–Uhlenbeck model (POUMM) outperforms the PMM in capturing this correlation pattern and in quantifying H2. In particular, we show that POUMM outperforms PMM even in simulations without selection—as it captures the mentioned correlation pattern—which has not been appreciated until now. By cross-validating the POUMM estimates with ANOVA on closest phylogenetic pairs, we obtain H2 ≈ 0.2, meaning ∼20% of the variation in HIV-virulence is explained by the virus genome both for European and African data.
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Affiliation(s)
- Venelin Mitov
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.,Swiss Institute of Bioinformatics, Switzerland
| | - Tanja Stadler
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.,Swiss Institute of Bioinformatics, Switzerland
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What Is the most Important for Elite Control: Genetic Background of Patient, Genetic Background of Partner, both or neither? Description of Complete Natural History within a Couple of MSM. EBioMedicine 2017; 27:51-60. [PMID: 29273355 PMCID: PMC5828297 DOI: 10.1016/j.ebiom.2017.12.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 11/23/2017] [Accepted: 12/05/2017] [Indexed: 11/23/2022] Open
Abstract
Background We describe a homosexual man who strongly controlled HIV-1 for ten years despite lack of protective genetic background. Methods HIV-1 DNA was measured in blood and other tissues. Cell susceptibility was evaluated with various strains. HIV-1-specific (CD4 and CD8 activation markers and immune check points) and NK cells responses were assessed; KIRs haplotypes and HLA alleles were determined. Findings Two HIV-1 RNA copies/mL of plasma were detected in 2009, using an ultra-sensitive assay. HIV-DNA was detected at 1.1 and 2 copies/106 PBMCs in 2009 and 2015 respectively, at 1.2 copies/106 cells in rectal cells in 2011. WBs showed weak reactivity with antibodies to gp160, p55 and p25 from 2007 to 2014, remaining incomplete in 2017. CD4 T cells were susceptible to various strains including HIVKON, a primary isolate of his own CRF02_AG variant. CD8 T cells showed a strong poly-functional response against HIV-Gag, producing mainly IFN-γ; a robust capacity of antibody-dependant cell cytotoxicity (ADCC) was observed in NK cells. Case patient was group B KIR haplotype. Neutralizing antibodies were not detected. CD4 and CD8 blood T cells showed normal proportions without increased activation markers. Phylogenetic analyses identified the same CRF02_AG variant in his partner. The patient and his partner were heterozygous for the CCR5ΔD32 deletion and shared HLA-B*07, C*07 non-protective alleles. Interpretation This thorough description of the natural history of an individual controlling HIV-1 in various compartments for ten years despite lack of protective alleles, and of his partner, may have implications for strategies to cure HIV-1 infection. We described a MSM, elite controller despite pejorative genetic background. The patient had two HLA pejoratives alleles and no protective alleles. The partner was infected by the same strain. The genetic backgrounds of the patient and partner, and the virus could interact with each other to lead to elite control.
We considered all the evidence about elite control, HLA, ADCC and NK, using Medline/PubMed. We described a MSM, elite controller despite non-protective genetic background, explored extensively the patient: sequential WBs, RNA in plasma (ultrasensitive assay), DNA in PBMC/GALT, cell susceptibility, HIV-1 responses in PBMC/LNMC, neutralizing antibodies, CD3-CD56 + NK, ADCC, KIRs. He had one HLA pejorative and no protective alleles. The partner was infected by the same strain, his genetic background was studied. The genetic background of the exposed person, of the source, and the viral strain could interact with each other to lead to elite control.
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Blanquart F, Wymant C, Cornelissen M, Gall A, Bakker M, Bezemer D, Hall M, Hillebregt M, Ong SH, Albert J, Bannert N, Fellay J, Fransen K, Gourlay AJ, Grabowski MK, Gunsenheimer-Bartmeyer B, Günthard HF, Kivelä P, Kouyos R, Laeyendecker O, Liitsola K, Meyer L, Porter K, Ristola M, van Sighem A, Vanham G, Berkhout B, Kellam P, Reiss P, Fraser C. Viral genetic variation accounts for a third of variability in HIV-1 set-point viral load in Europe. PLoS Biol 2017; 15:e2001855. [PMID: 28604782 PMCID: PMC5467800 DOI: 10.1371/journal.pbio.2001855] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 05/09/2017] [Indexed: 12/20/2022] Open
Abstract
HIV-1 set-point viral load-the approximately stable value of viraemia in the first years of chronic infection-is a strong predictor of clinical outcome and is highly variable across infected individuals. To better understand HIV-1 pathogenesis and the evolution of the viral population, we must quantify the heritability of set-point viral load, which is the fraction of variation in this phenotype attributable to viral genetic variation. However, current estimates of heritability vary widely, from 6% to 59%. Here we used a dataset of 2,028 seroconverters infected between 1985 and 2013 from 5 European countries (Belgium, Switzerland, France, the Netherlands and the United Kingdom) and estimated the heritability of set-point viral load at 31% (CI 15%-43%). Specifically, heritability was measured using models of character evolution describing how viral load evolves on the phylogeny of whole-genome viral sequences. In contrast to previous studies, (i) we measured viral loads using standardized assays on a sample collected in a strict time window of 6 to 24 months after infection, from which the viral genome was also sequenced; (ii) we compared 2 models of character evolution, the classical "Brownian motion" model and another model ("Ornstein-Uhlenbeck") that includes stabilising selection on viral load; (iii) we controlled for covariates, including age and sex, which may inflate estimates of heritability; and (iv) we developed a goodness of fit test based on the correlation of viral loads in cherries of the phylogenetic tree, showing that both models of character evolution fit the data well. An overall heritability of 31% (CI 15%-43%) is consistent with other studies based on regression of viral load in donor-recipient pairs. Thus, about a third of variation in HIV-1 virulence is attributable to viral genetic variation.
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Affiliation(s)
- François Blanquart
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Chris Wymant
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Marion Cornelissen
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, the Netherlands
| | - Astrid Gall
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Margreet Bakker
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, the Netherlands
| | | | - Matthew Hall
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | | | - Swee Hoe Ong
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Jan Albert
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Norbert Bannert
- Division for HIV and other Retroviruses, Robert Koch Institute, Berlin, Germany
| | - Jacques Fellay
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Katrien Fransen
- HIV/STI reference laboratory, WHO collaborating centre, Institute of Tropical Medicine, Department of Clinical Science, Antwerpen, Belgium
| | - Annabelle J. Gourlay
- Department of Infection and Population Health, University College London, London, United Kingdom
| | - M. Kate Grabowski
- Department of Epidemiology, John Hopkins University, Baltimore, Maryland, United States of America
| | | | - Huldrych F. Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Pia Kivelä
- Department of Infectious Diseases, Helsinki University Hospital, Helsinki, Finland
| | - Roger Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Oliver Laeyendecker
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Kirsi Liitsola
- Department of Health Security, National Institute for Health and Welfare, Helsinki, Finland
| | - Laurence Meyer
- INSERM CESP U1018, Université Paris Sud, Université Paris Saclay, APHP, Service de Santé Publique, Hôpital de Bicêtre, Le Kremlin-Bicêtre, France
| | - Kholoud Porter
- Department of Infection and Population Health, University College London, London, United Kingdom
| | - Matti Ristola
- Department of Health Security, National Institute for Health and Welfare, Helsinki, Finland
| | | | - Guido Vanham
- Virology Unit, Immunovirology Research Pole, Biomedical Sciences Department, Institute of Tropical Medicine, Antwerpen, Belgium
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, the Netherlands
| | - Paul Kellam
- Kymab Ltd, Cambridge, United Kingdom
- Division of Infectious Diseases, Department of Medicine, Imperial College London, London, United Kingdom
| | - Peter Reiss
- Stichting HIV Monitoring, Amsterdam, the Netherlands
- Department of Global Health, Academic Medical Center, Amsterdam, the Netherlands
| | - Christophe Fraser
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
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Replication Capacity of Viruses from Acute Infection Drives HIV-1 Disease Progression. J Virol 2017; 91:JVI.01806-16. [PMID: 28148791 DOI: 10.1128/jvi.01806-16] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 01/19/2017] [Indexed: 01/09/2023] Open
Abstract
The viral genotype has been shown to play an important role in HIV pathogenesis following transmission. However, the viral phenotypic properties that contribute to disease progression remain unclear. Most studies have been limited to the evaluation of Gag function in the context of a recombinant virus backbone. Using this approach, important biological information may be lost, making the evaluation of viruses obtained during acute infection, representing the transmitted virus, a more biologically relevant model. Here, we evaluate the roles of viral infectivity and the replication capacity of viruses from acute infection in disease progression in women who seroconverted in the CAPRISA 004 tenofovir microbicide trial. We show that viral replication capacity, but not viral infectivity, correlates with the set point viral load (Spearman r = 0.346; P = 0.045) and that replication capacity (hazard ratio [HR] = 4.52; P = 0.01) can predict CD4 decline independently of the viral load (HR = 2.9; P = 0.004) or protective HLA alleles (HR = 0.61; P = 0.36). We further demonstrate that Gag-Pro is not the main driver of this association, suggesting that additional properties of the transmitted virus play a role in disease progression. Finally, we find that although viruses from the tenofovir arm were 2-fold less infectious, they replicated at rates similar to those of viruses from the placebo arm. This indicates that the use of tenofovir gel did not select for viral variants with higher replication capacity. Overall, this study supports a strong influence of the replication capacity in acute infection on disease progression, potentially driven by interaction of multiple genes rather than a dominant role of the major structural gene gagIMPORTANCE HIV disease progression is known to differ between individuals, and defining which fraction of this variation can be attributed to the virus is important both clinically and epidemiologically. In this study, we show that the replication capacity of viruses isolated during acute infection predicts subsequent disease progression and drives CD4 decline independently of the viral load. This provides further support for the hypothesis that the replication capacity of the transmitted virus determines the initial damage to the immune system, setting the pace for later disease progression. However, we did not find evidence that the major structural gene gag drives this correlation, highlighting the importance of other genes in determining disease progression.
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Estimating the Respective Contributions of Human and Viral Genetic Variation to HIV Control. PLoS Comput Biol 2017; 13:e1005339. [PMID: 28182649 PMCID: PMC5300119 DOI: 10.1371/journal.pcbi.1005339] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 01/03/2017] [Indexed: 02/02/2023] Open
Abstract
We evaluated the fraction of variation in HIV-1 set point viral load attributable to viral or human genetic factors by using joint host/pathogen genetic data from 541 HIV infected individuals. We show that viral genetic diversity explains 29% of the variation in viral load while host factors explain 8.4%. Using a joint model including both host and viral effects, we estimate a total of 30% heritability, indicating that most of the host effects are reflected in viral sequence variation. Viral loads of Human Immunodeficiency Virus infections are correlated between the donor and the recipient of the transmission pair. Similarly, human genetic factors may modulate viral load. In this study we estimate the extents to which viral load is heritable either via the viral genotype (from donor to recipient) or via the host’s Human Leukocyte Antigen (HLA) genotype. We find that a major fraction of inter individual variability is explained by the similarity of the viral genotypes, and that human genetic variation in the HLA region provide little additional explanatory power.
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22
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Abstract
In this chapter, we will review recent research on the virology of HIV-1 transmission and the impact of the transmitted virus genotype on subsequent disease progression. In most instances of HIV-1 sexual transmission, a single genetic variant, or a very limited number of variants from the diverse viral quasi-species present in the transmitting partner establishes systemic infection. Transmission involves both stochastic and selective processes, such that in general a minority variant in the donor is transmitted. While there is clear evidence for selection, the biological properties that mediate transmission remain incompletely defined. Nevertheless, the genotype of the transmitted founder virus, which reflects prior exposure to and escape from host immune responses, clearly influences disease progression. Some escape mutations impact replicative capacity, while others effectively cloak the virus from the newly infected host's immune response by preventing recognition. It is the balance between the impact of escape mutations on viral fitness and susceptibility to the host immunogenetics that defines HIV-1 disease progression.
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23
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Diversification in the HIV-1 Envelope Hyper-variable Domains V2, V4, and V5 and Higher Probability of Transmitted/Founder Envelope Glycosylation Favor the Development of Heterologous Neutralization Breadth. PLoS Pathog 2016; 12:e1005989. [PMID: 27851829 PMCID: PMC5112890 DOI: 10.1371/journal.ppat.1005989] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 10/11/2016] [Indexed: 11/19/2022] Open
Abstract
A recent study of plasma neutralization breadth in HIV-1 infected individuals at nine International AIDS Vaccine Initiative (IAVI) sites reported that viral load, HLA-A*03 genotype, and subtype C infection were strongly associated with the development of neutralization breadth. Here, we refine the findings of that study by analyzing the impact of the transmitted/founder (T/F) envelope (Env), early Env diversification, and autologous neutralization on the development of plasma neutralization breadth in 21 participants identified during recent infection at two of those sites: Kigali, Rwanda (n = 9) and Lusaka, Zambia (n = 12). Single-genome analysis of full-length T/F Env sequences revealed that all 21 individuals were infected with a highly homogeneous population of viral variants, which were categorized as subtype C (n = 12), A1 (n = 7), or recombinant AC (n = 2). An extensive amino acid sequence-based analysis of variable loop lengths and glycosylation patterns in the T/F Envs revealed that a lower ratio of NXS to NXT-encoded glycan motifs correlated with neutralization breadth. Further analysis comparing amino acid sequence changes, insertions/deletions, and glycan motif alterations between the T/F Env and autologous early Env variants revealed that extensive diversification focused in the V2, V4, and V5 regions of gp120, accompanied by contemporaneous viral escape, significantly favored the development of breadth. These results suggest that more efficient glycosylation of subtype A and C T/F Envs through fewer NXS-encoded glycan sites is more likely to elicit antibodies that can transition from autologous to heterologous neutralizing activity following exposure to gp120 diversification. This initiates an Env-antibody co-evolution cycle that increases neutralization breadth, and is further augmented over time by additional viral and host factors. These findings suggest that understanding how variation in the efficiency of site-specific glycosylation influences neutralizing antibody elicitation and targeting could advance the design of immunogens aimed at inducing antibodies that can transition from autologous to heterologous neutralizing activity.
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24
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Mónaco DC, Dilernia DA, Fiore-Gartland A, Yu T, Prince JL, Dennis KK, Qin K, Schaefer M, Claiborne DT, Kilembe W, Tang J, Price MA, Farmer P, Gilmour J, Bansal A, Allen S, Goepfert P, Hunter E. Balance between transmitted HLA preadapted and nonassociated polymorphisms is a major determinant of HIV-1 disease progression. J Exp Med 2016; 213:2049-63. [PMID: 27551154 PMCID: PMC5030801 DOI: 10.1084/jem.20151984] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2015] [Accepted: 07/25/2016] [Indexed: 11/05/2022] Open
Abstract
In a cohort of Zambian heterosexual transmission pairs, the authors show that HIV-1–transmitted variants already exhibit a significant degree of preadaptation to the new host's HLA alleles, which, modulated by polymorphisms that decrease viral fitness, determines early set-point VL and the rate of disease progression in the newly infected individual. HIV-1 adapts to a new host through mutations that facilitate immune escape. Here, we evaluate the impact on viral control and disease progression of transmitted polymorphisms that were either preadapted to or nonassociated with the new host’s HLA. In a cohort of 169 Zambian heterosexual transmission pairs, we found that almost one-third of possible HLA-linked target sites in the transmitted virus Gag protein are already adapted, and that this transmitted preadaptation significantly reduced early immune recognition of epitopes. Transmitted preadapted and nonassociated polymorphisms showed opposing effects on set-point VL and the balance between the two was significantly associated with higher set-point VLs in a multivariable model including other risk factors. Transmitted preadaptation was also significantly associated with faster CD4 decline (<350 cells/µl) and this association was stronger after accounting for nonassociated polymorphisms, which were linked with slower CD4 decline. Overall, the relative ratio of the two classes of polymorphisms was found to be the major determinant of CD4 decline in a multivariable model including other risk factors. This study reveals that, even before an immune response is mounted in the new host, the balance of these opposing factors can significantly influence the outcome of HIV-1 infection.
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Affiliation(s)
| | | | - Andrew Fiore-Gartland
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
| | - Tianwei Yu
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA 30322
| | | | | | - Kai Qin
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35233
| | | | | | | | - Jianming Tang
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35233
| | - Matt A Price
- International AIDS Vaccine Initiative (IAVI), San Francisco, CA 94105 Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA 94105
| | - Paul Farmer
- Emory Vaccine Center, Emory University, Atlanta, GA 30322
| | | | - Anju Bansal
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35233
| | - Susan Allen
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA 30322
| | - Paul Goepfert
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35233
| | - Eric Hunter
- Emory Vaccine Center, Emory University, Atlanta, GA 30322 Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA 30322
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Abstract
Human leukocyte antigen class I (HLA)-restricted CD8(+) T lymphocyte (CTL) responses are crucial to HIV-1 control. Although HIV can evade these responses, the longer-term impact of viral escape mutants remains unclear, as these variants can also reduce intrinsic viral fitness. To address this, we here developed a metric to determine the degree of HIV adaptation to an HLA profile. We demonstrate that transmission of viruses that are pre-adapted to the HLA molecules expressed in the recipient is associated with impaired immunogenicity, elevated viral load and accelerated CD4(+) T cell decline. Furthermore, the extent of pre-adaptation among circulating viruses explains much of the variation in outcomes attributed to the expression of certain HLA alleles. Thus, viral pre-adaptation exploits 'holes' in the immune response. Accounting for these holes may be key for vaccine strategies seeking to elicit functional responses from viral variants, and to HIV cure strategies that require broad CTL responses to achieve successful eradication of HIV reservoirs.
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Potential Pitfalls in Estimating Viral Load Heritability. Trends Microbiol 2016; 24:687-698. [PMID: 27185643 DOI: 10.1016/j.tim.2016.04.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 04/14/2016] [Accepted: 04/15/2016] [Indexed: 01/08/2023]
Abstract
In HIV patients, the set-point viral load (SPVL) is the most widely used predictor of disease severity. Yet SPVL varies over several orders of magnitude between patients. The heritability of SPVL quantifies how much of the variation in SPVL is due to transmissible viral genetics. There is currently no clear consensus on the value of SPVL heritability, as multiple studies have reported apparently discrepant estimates. Here we illustrate that the discrepancies in estimates are most likely due to differences in the estimation methods, rather than the study populations. Importantly, phylogenetic estimates run the risk of being strongly confounded by unrealistic model assumptions. Care must be taken when interpreting and comparing the different estimates to each other.
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27
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Pananghat AN, Aggarwal H, Prakash SS, Makhdoomi MA, Singh R, Lodha R, Ali S, Srinivas M, Das BK, Pandey RM, Kabra SK, Luthra K. IL-8 Alterations in HIV-1 Infected Children With Disease Progression. Medicine (Baltimore) 2016; 95:e3734. [PMID: 27227934 PMCID: PMC4902358 DOI: 10.1097/md.0000000000003734] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Disease progression in HIV-1 infected children is faster than in adults. Less than 5% of the infected children maintain stable CD4 counts beyond 7 years of infection and are termed long-term nonprogressors (LTNPs). Delineating the host immune response in antiretroviral naïve (ART) and treated HIV-1 infected children at different disease stages will help in understanding the immunopathogenesis of the disease.A total of 79 asymptomatic, perinatally HIV-1 infected children (50 ART naïve and 29 ART treated) and 8 seronegative donors were recruited in this study. T- and B-cell activation PCR arrays were performed from the cDNA, using total RNA extracted from the peripheral blood mononuclear cells (PBMCs) of 14 HIV-1 infected children at different stages of the disease. The differentially expressed genes were identified. Quantitative RT-PCR was performed for the (interleukin-8) IL-8 gene and its transcriptional mediators, that is, SHP2, GRB2, and IL-8R (IL-8 receptor/CXCR1). Plasma levels of IL-8 were measured by flow cytometry.Gene array data revealed a higher expression of IL-8 in the ART naïve HIV-1 infected progressors and in ART nonresponders than LTNPs and ART responders, respectively. Quantitative RT-PCR analysis demonstrated a significant higher expression of IL-8 (P < 0.001), its receptor CXCR1 (P = 0.03) and the upstream signaling molecule SHP2 (P = 0.04) in the progressors versus LTNPs. Plasma levels of IL-8 were significantly higher in progressors versus LTNPs (P < 0.001), and ART nonresponders versus ART responders (P < 0.001). A significant negative correlation of plasma levels of IL-8 with CD4 counts (cells/μL) was observed in HIV-1 infected ART naïve subjects (r = -0.488; P < 0.001), while the IL-8 levels positively correlated with viral load in the ART treated children (r = 0.5494; P < 0.001). ART naïve progressors on follow up demonstrated a significant reduction in the mRNA expression (P = 0.05) and plasma levels of IL-8 (P = 0.05) post 6 months of ART initiation suggesting the beneficial role of ART therapy in reducing inflammation in infected children.Our data suggest that IL-8 may serve as a potential prognostic marker in adjunct with CD4 counts to monitor disease progression in the HIV-1 infected children and the efficacy of ART.
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Affiliation(s)
- Ambili Nair Pananghat
- From the Department of Biochemistry (ANP, HA, SSP, MAM, KL), Department of Pediatrics (RS, RL, SKK), Department of Microbiology (BKD), Department of Pediatrics Surgery (MS), Department of Biostatistics (RMP), All India Institute of Medical Sciences (RMP), and Department of Biochemistry, Jamia Hamdard University, New Delhi, India (ANP, SA)
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28
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Kinloch NN, MacMillan DR, Le AQ, Cotton LA, Bangsberg DR, Buchbinder S, Carrington M, Fuchs J, Harrigan PR, Koblin B, Kushel M, Markowitz M, Mayer K, Milloy MJ, Schechter MT, Wagner T, Walker BD, Carlson JM, Poon AFY, Brumme ZL. Population-Level Immune-Mediated Adaptation in HIV-1 Polymerase during the North American Epidemic. J Virol 2016; 90:1244-58. [PMID: 26559841 PMCID: PMC4719594 DOI: 10.1128/jvi.02353-15] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 11/06/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Human leukocyte antigen (HLA) class I-associated polymorphisms in HIV-1 that persist upon transmission to HLA-mismatched hosts may spread in the population as the epidemic progresses. Transmission of HIV-1 sequences containing such adaptations may undermine cellular immune responses to the incoming virus in future hosts. Building upon previous work, we investigated the extent of HLA-associated polymorphism accumulation in HIV-1 polymerase (Pol) through comparative analysis of linked HIV-1/HLA class I genotypes sampled during historic (1979 to 1989; n = 338) and modern (2001 to 2011; n = 278) eras from across North America (Vancouver, BC, Canada; Boston, MA; New York, NY; and San Francisco, CA). Phylogenies inferred from historic and modern HIV-1 Pol sequences were star-like in shape, with an inferred most recent common ancestor (epidemic founder virus) sequence nearly identical to the modern North American subtype B consensus sequence. Nevertheless, modern HIV-1 Pol sequences exhibited roughly 2-fold-higher patristic (tip-to-tip) genetic distances than historic sequences, with HLA pressures likely driving ongoing diversification. Moreover, the frequencies of published HLA-associated polymorphisms in individuals lacking the selecting HLA class I allele was on average ∼2.5-fold higher in the modern than in the historic era, supporting their spread in circulation, though some remained stable in frequency during this time. Notably, polymorphisms restricted by protective HLA alleles appear to be spreading to a greater relative extent than others, though these increases are generally of modest absolute magnitude. However, despite evidence of polymorphism spread, North American hosts generally remain at relatively low risk of acquiring an HIV-1 polymerase sequence substantially preadapted to their HLA profiles, even in the present era. IMPORTANCE HLA class I-restricted cytotoxic T-lymphocyte (CTL) escape mutations in HIV-1 that persist upon transmission may accumulate in circulation over time, potentially undermining host antiviral immunity to the transmitted viral strain. We studied >600 experimentally collected HIV-1 polymerase sequences linked to host HLA information dating back to 1979, along with phylogenetically reconstructed HIV-1 sequences dating back to the virus' introduction into North America. Overall, our results support the gradual spread of many-though not all-HIV-1 polymerase immune escape mutations in circulation over time. This is consistent with recent observations from other global regions, though the extent of polymorphism accumulation in North America appears to be lower than in populations with high seroprevalence, older epidemics, and/or limited HLA diversity. Importantly, the risk of acquiring an HIV-1 polymerase sequence at transmission that is substantially preadapted to one's HLA profile remains relatively low in North America, even in the present era.
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Affiliation(s)
- Natalie N Kinloch
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Daniel R MacMillan
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Anh Q Le
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Laura A Cotton
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - David R Bangsberg
- Massachusetts General Hospital, Boston, Massachusetts, USA Harvard Medical School, Cambridge, Massachusetts, USA
| | - Susan Buchbinder
- San Francisco Department of Public Health, San Francisco, California, USA University of California, San Francisco, San Francisco, California, USA
| | - Mary Carrington
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA Ragon Institute of Massachusetts General Hospital, MIT, and Harvard University, Cambridge, Massachusetts, USA
| | - Jonathan Fuchs
- San Francisco Department of Public Health, San Francisco, California, USA University of California, San Francisco, San Francisco, California, USA
| | - P Richard Harrigan
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | | | - Margot Kushel
- University of California, San Francisco, San Francisco, California, USA
| | | | - Kenneth Mayer
- Harvard Medical School, Cambridge, Massachusetts, USA Fenway Community Health, Boston, Massachusetts, USA
| | - M J Milloy
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Martin T Schechter
- Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Theresa Wagner
- San Francisco Department of Public Health, San Francisco, California, USA
| | - Bruce D Walker
- Ragon Institute of Massachusetts General Hospital, MIT, and Harvard University, Cambridge, Massachusetts, USA
| | | | - Art F Y Poon
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
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Broadly Neutralizing Antibody Responses in a Large Longitudinal Sub-Saharan HIV Primary Infection Cohort. PLoS Pathog 2016; 12:e1005369. [PMID: 26766578 PMCID: PMC4713061 DOI: 10.1371/journal.ppat.1005369] [Citation(s) in RCA: 204] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 12/07/2015] [Indexed: 11/19/2022] Open
Abstract
Broadly neutralizing antibodies (bnAbs) are thought to be a critical component of a protective HIV vaccine. However, designing vaccines immunogens able to elicit bnAbs has proven unsuccessful to date. Understanding the correlates and immunological mechanisms leading to the development of bnAb responses during natural HIV infection is thus critical to the design of a protective vaccine. The IAVI Protocol C program investigates a large longitudinal cohort of primary HIV-1 infection in Eastern and South Africa. Development of neutralization was evaluated in 439 donors using a 6 cross-clade pseudo-virus panel predictive of neutralization breadth on larger panels. About 15% of individuals developed bnAb responses, essentially between year 2 and year 4 of infection. Statistical analyses revealed no influence of gender, age or geographical origin on the development of neutralization breadth. However, cross-clade neutralization strongly correlated with high viral load as well as with low CD4 T cell counts, subtype-C infection and HLA-A*03(-) genotype. A correlation with high overall plasma IgG levels and anti-Env IgG binding titers was also found. The latter appeared not associated with higher affinity, suggesting a greater diversity of the anti-Env responses in broad neutralizers. Broadly neutralizing activity targeting glycan-dependent epitopes, largely the N332-glycan epitope region, was detected in nearly half of the broad neutralizers while CD4bs and gp41-MPER bnAb responses were only detected in very few individuals. Together the findings suggest that both viral and host factors are critical for the development of bnAbs and that the HIV Env N332-glycan supersite may be a favorable target for vaccine design.
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Replicative fitness of transmitted HIV-1 drives acute immune activation, proviral load in memory CD4+ T cells, and disease progression. Proc Natl Acad Sci U S A 2015; 112:E1480-9. [PMID: 25730868 DOI: 10.1073/pnas.1421607112] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
HIV-1 infection is characterized by varying degrees of chronic immune activation and disruption of T-cell homeostasis, which impact the rate of disease progression. A deeper understanding of the factors that influence HIV-1-induced immunopathology and subsequent CD4(+) T-cell decline is critical to strategies aimed at controlling or eliminating the virus. In an analysis of 127 acutely infected Zambians, we demonstrate a dramatic and early impact of viral replicative capacity (vRC) on HIV-1 immunopathogenesis that is independent of viral load (VL). Individuals infected with high-RC viruses exhibit a distinct inflammatory cytokine profile as well as significantly elevated T-cell activation, proliferation, and CD8(+) T-cell exhaustion, during the earliest months of infection. Moreover, the vRC of the transmitted virus is positively correlated with the magnitude of viral burden in naive and central memory CD4(+) T-cell populations, raising the possibility that transmitted viral phenotypes may influence the size of the initial latent viral reservoir. Taken together, these findings support an unprecedented role for the replicative fitness of the founder virus, independent of host protective genes and VL, in influencing multiple facets of HIV-1-related immunopathology, and that a greater focus on this parameter could provide novel approaches to clinical interventions.
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31
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Mackelprang RD, Carrington M, Thomas KK, Hughes JP, Baeten JM, Wald A, Farquhar C, Fife K, Campbell MS, Kapiga S, Gao X, Mullins JI, Lingappa JR. Host genetic and viral determinants of HIV-1 RNA set point among HIV-1 seroconverters from sub-saharan Africa. J Virol 2015; 89:2104-11. [PMID: 25473042 PMCID: PMC4338863 DOI: 10.1128/jvi.01573-14] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 11/25/2014] [Indexed: 12/20/2022] Open
Abstract
UNLABELLED We quantified the collective impact of source partner HIV-1 RNA levels, human leukocyte antigen (HLA) alleles, and innate responses through Toll-like receptor (TLR) alleles on the HIV-1 set point. Data came from HIV-1 seroconverters in African HIV-1 serodiscordant couple cohorts. Linear regression was used to determine associations with set point and R(2) to estimate variation explained by covariates. The strongest predictors of set point were HLA alleles (B*53:01, B*14:01, and B*27:03) and plasma HIV-1 levels of the transmitting partner, which explained 13% and 10% of variation in set point, respectively. HLA-A concordance between partners and TLR polymorphisms (TLR2 rs3804100 and TLR7 rs179012) also were associated with set point, explaining 6% and 5% of the variation, respectively. Overall, these factors and genital factors of the transmitter (i.e., male circumcision, bacterial vaginosis, and use of acyclovir) explained 46% of variation in set point. We found that both innate and adaptive immune responses, together with plasma HIV-1 levels of the transmitting partner, explain almost half of the variation in viral load set point. IMPORTANCE After HIV-1 infection, uncontrolled virus replication leads to a rapid increase in HIV-1 concentrations. Once host immune responses develop, however, HIV-1 levels reach a peak and subsequently decline until they reach a stable level that may persist for years. This stable HIV-1 set point represents an equilibrium between the virus and host responses and is predictive of later disease progression and transmission potential. Understanding how host and virus factors interact to determine HIV-1 set point may elucidate novel mechanisms or biological pathways for treating HIV-1 infection. We identified host and virus factors that predict HIV-1 set point in people who recently acquired HIV-1, finding that both innate and adaptive immune responses, along with factors that likely influence HIV-1 virulence and inoculum, explain ∼46% of the variation in HIV-1 set point.
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Affiliation(s)
- Romel D Mackelprang
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Mary Carrington
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, Leidos Biomedical Research, Inc., Frederick National Laboratories for Cancer Research, Frederick, Maryland, USA Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, USA
| | - Katherine K Thomas
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - James P Hughes
- Department of Biostatistics, University of Washington, Seattle, Washington, USA Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Jared M Baeten
- Department of Global Health, University of Washington, Seattle, Washington, USA Department of Epidemiology, University of Washington, Seattle, Washington, USA Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Anna Wald
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA Department of Epidemiology, University of Washington, Seattle, Washington, USA Department of Medicine, University of Washington, Seattle, Washington, USA Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
| | - Carey Farquhar
- Department of Global Health, University of Washington, Seattle, Washington, USA Department of Epidemiology, University of Washington, Seattle, Washington, USA Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Kenneth Fife
- Department of Medicine, Indiana University, Indianapolis, Indiana, USA Department of Microbiology and Immunology, Indiana University, Indianapolis, Indiana, USA Department of Pathology, Indiana University, Indianapolis, Indiana, USA
| | - Mary S Campbell
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Saida Kapiga
- Mwanza Intervention Trials Unit, National Institute for Medical Research, Mwanza, Tanzania Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Xiaojiang Gao
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, Leidos Biomedical Research, Inc., Frederick National Laboratories for Cancer Research, Frederick, Maryland, USA
| | - James I Mullins
- Department of Medicine, University of Washington, Seattle, Washington, USA Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA Department of Microbiology, University of Washington, Seattle, Washington, USA
| | - Jairam R Lingappa
- Department of Global Health, University of Washington, Seattle, Washington, USA Department of Medicine, University of Washington, Seattle, Washington, USA Department of Pediatrics, University of Washington, Seattle, Washington, USA
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32
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Carlson JM, Le AQ, Shahid A, Brumme ZL. HIV-1 adaptation to HLA: a window into virus-host immune interactions. Trends Microbiol 2015; 23:212-24. [PMID: 25613992 DOI: 10.1016/j.tim.2014.12.008] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 12/04/2014] [Accepted: 12/16/2014] [Indexed: 11/26/2022]
Abstract
HIV-1 develops specific mutations within its genome that allow it to escape detection by human leukocyte antigen (HLA) class I-restricted immune responses, notably those of CD8(+) cytotoxic T lymphocytes (CTL). HLA thus represents a major force driving the evolution and diversification of HIV-1 within individuals and at the population level. Importantly, the study of HIV-1 adaptation to HLA also represents an opportunity to identify what qualities constitute an effective immune response, how the virus in turn adapts to these pressures, and how we may harness this information to design HIV-1 vaccines that stimulate effective cellular immunity.
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Affiliation(s)
| | - Anh Q Le
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Aniqa Shahid
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada; British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada.
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33
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Transmitted virus fitness and host T cell responses collectively define divergent infection outcomes in two HIV-1 recipients. PLoS Pathog 2015; 11:e1004565. [PMID: 25569444 PMCID: PMC4287535 DOI: 10.1371/journal.ppat.1004565] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2014] [Accepted: 11/10/2014] [Indexed: 12/27/2022] Open
Abstract
Control of virus replication in HIV-1 infection is critical to delaying disease progression. While cellular immune responses are a key determinant of control, relatively little is known about the contribution of the infecting virus to this process. To gain insight into this interplay between virus and host in viral control, we conducted a detailed analysis of two heterosexual HIV-1 subtype A transmission pairs in which female recipients sharing three HLA class I alleles exhibited contrasting clinical outcomes: R880F controlled virus replication while R463F experienced high viral loads and rapid disease progression. Near full-length single genome amplification defined the infecting transmitted/founder (T/F) virus proteome and subsequent sequence evolution over the first year of infection for both acutely infected recipients. T/F virus replicative capacities were compared in vitro, while the development of the earliest cellular immune response was defined using autologous virus sequence-based peptides. The R880F T/F virus replicated significantly slower in vitro than that transmitted to R463F. While neutralizing antibody responses were similar in both subjects, during acute infection R880F mounted a broad T cell response, the most dominant components of which targeted epitopes from which escape was limited. In contrast, the primary HIV-specific T cell response in R463F was focused on just two epitopes, one of which rapidly escaped. This comprehensive study highlights both the importance of the contribution of the lower replication capacity of the transmitted/founder virus and an associated induction of a broad primary HIV-specific T cell response, which was not undermined by rapid epitope escape, to long-term viral control in HIV-1 infection. It underscores the importance of the earliest CD8 T cell response targeting regions of the virus proteome that cannot mutate without a high fitness cost, further emphasizing the need for vaccines that elicit a breadth of T cell responses to conserved viral epitopes.
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34
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van Dorp CH, van Boven M, de Boer RJ. Immuno-epidemiological modeling of HIV-1 predicts high heritability of the set-point virus load, while selection for CTL escape dominates virulence evolution. PLoS Comput Biol 2014; 10:e1003899. [PMID: 25522184 PMCID: PMC4270429 DOI: 10.1371/journal.pcbi.1003899] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 09/07/2014] [Indexed: 02/07/2023] Open
Abstract
It has been suggested that HIV-1 has evolved its set-point virus load to be optimized for transmission. Previous epidemiological models and studies into the heritability of set-point virus load confirm that this mode of adaptation within the human population is feasible. However, during the many cycles of replication between infection of a host and transmission to the next host, HIV-1 is under selection for escape from immune responses, and not transmission. Here we investigate with computational and mathematical models how these two levels of selection, within-host and between-host, are intertwined. We find that when the rate of immune escape is comparable to what has been observed in patients, immune selection within hosts is dominant over selection for transmission. Surprisingly, we do find high values for set-point virus load heritability, and argue that high heritability estimates can be caused by the 'footprints' left by differing hosts' immune systems on the virus.
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Affiliation(s)
- Christiaan H. van Dorp
- Theoretical Biology and Bioinformatics, Universiteit Utrecht, Utrecht, The Netherlands
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- * E-mail:
| | - Michiel van Boven
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Rob J. de Boer
- Theoretical Biology and Bioinformatics, Universiteit Utrecht, Utrecht, The Netherlands
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35
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Carlson JM, Schaefer M, Monaco DC, Batorsky R, Claiborne DT, Prince J, Deymier MJ, Ende ZS, Klatt NR, DeZiel CE, Lin TH, Peng J, Seese AM, Shapiro R, Frater J, Ndung'u T, Tang J, Goepfert P, Gilmour J, Price MA, Kilembe W, Heckerman D, Goulder PJR, Allen TM, Allen S, Hunter E. HIV transmission. Selection bias at the heterosexual HIV-1 transmission bottleneck. Science 2014; 345:1254031. [PMID: 25013080 DOI: 10.1126/science.1254031] [Citation(s) in RCA: 195] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Heterosexual transmission of HIV-1 typically results in one genetic variant establishing systemic infection. We compared, for 137 linked transmission pairs, the amino acid sequences encoded by non-envelope genes of viruses in both partners and demonstrate a selection bias for transmission of residues that are predicted to confer increased in vivo fitness on viruses in the newly infected, immunologically naïve recipient. Although tempered by transmission risk factors, such as donor viral load, genital inflammation, and recipient gender, this selection bias provides an overall transmission advantage for viral quasispecies that are dominated by viruses with high in vivo fitness. Thus, preventative or therapeutic approaches that even marginally reduce viral fitness may lower the overall transmission rates and offer long-term benefits even upon successful transmission.
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Affiliation(s)
| | - Malinda Schaefer
- Emory Vaccine Center at Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Daniela C Monaco
- Emory Vaccine Center at Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Rebecca Batorsky
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02114, USA
| | - Daniel T Claiborne
- Emory Vaccine Center at Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Jessica Prince
- Emory Vaccine Center at Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Martin J Deymier
- Emory Vaccine Center at Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Zachary S Ende
- Emory Vaccine Center at Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Nichole R Klatt
- Emory Vaccine Center at Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | | | | | - Jian Peng
- Microsoft Research, Redmond, WA 98052, USA
| | - Aaron M Seese
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02114, USA
| | - Roger Shapiro
- Division of Infectious Diseases, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - John Frater
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX1 7BN, UK. National Institute of Health Research, Oxford Biomedical Research Centre, Oxford OX3 7LE, UK. Oxford Martin School, University of Oxford, Oxford OX1 3BD, UK
| | - Thumbi Ndung'u
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02114, USA. HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban 4013, South Africa. KwaZulu-Natal Research Institute for Tuberculosis and HIV (K-RITH), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa. Max Planck Institute for Infection Biology, D-10117 Berlin, Germany
| | - Jianming Tang
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Paul Goepfert
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Jill Gilmour
- International AIDS Vaccine Initiative, London SW10 9NH, UK. Imperial College of Science Technology and Medicine, London SW10 9NH, UK
| | - Matt A Price
- International AIDS Vaccine Initiative, San Francisco, CA 94105, USA. Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA 94105, USA
| | - William Kilembe
- Rwanda-Zambia HIV Research Group: Zambia-Emory HIV Research Project, Lusaka, Zambia
| | | | - Philip J R Goulder
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban 4013, South Africa. Department of Paediatrics, University of Oxford, Oxford OX1 3SY, UK
| | - Todd M Allen
- Rwanda-Zambia HIV Research Group: Zambia-Emory HIV Research Project, Lusaka, Zambia. Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA 30322, USA. Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Susan Allen
- International AIDS Vaccine Initiative, San Francisco, CA 94105, USA. Microsoft Research, Los Angeles, CA 98117, USA. Department of Paediatrics, University of Oxford, Oxford OX1 3SY, UK
| | - Eric Hunter
- Emory Vaccine Center at Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA. Rwanda-Zambia HIV Research Group: Zambia-Emory HIV Research Project, Lusaka, Zambia. Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA 30322, USA.
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36
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Li X, Price MA, He D, Kamali A, Karita E, Lakhi S, Sanders EJ, Anzala O, Amornkul PN, Allen S, Hunter E, Kaslow RA, Gilmour J, Tang J. Host genetics and viral load in primary HIV-1 infection: clear evidence for gene by sex interactions. Hum Genet 2014; 133:1187-97. [PMID: 24969460 PMCID: PMC4127002 DOI: 10.1007/s00439-014-1465-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 06/16/2014] [Indexed: 01/09/2023]
Abstract
Research in the past two decades has generated unequivocal evidence that host genetic variations substantially account for the heterogeneous outcomes following human immunodeficiency virus type 1 (HIV-1) infection. In particular, genes encoding human leukocyte antigens (HLA) have various alleles, haplotypes, or specific motifs that can dictate the set-point (a relatively steady state) of plasma viral load (VL), although rapid viral evolution driven by innate and acquired immune responses can obscure the long-term relationships between HLA genotypes and HIV-1-related outcomes. In our analyses of VL data from 521 recent HIV-1 seroconverters enrolled from eastern and southern Africa, HLA-A*03:01 was strongly and persistently associated with low VL in women (frequency = 11.3 %, P < 0.0001) but not in men (frequency = 7.7 %, P = 0.66). This novel sex by HLA interaction (P = 0.003, q = 0.090) did not extend to other frequent HLA class I alleles (n = 34), although HLA-C*18:01 also showed a weak association with low VL in women only (frequency = 9.3 %, P = 0.042, q > 0.50). In a reduced multivariable model, age, sex, geography (clinical sites), previously identified HLA factors (HLA-B*18, B*45, B*53, and B*57), and the interaction term for female sex and HLA-A*03:01 collectively explained 17.0 % of the overall variance in geometric mean VL over a 3-year follow-up period (P < 0.0001). Multiple sensitivity analyses of longitudinal and cross-sectional VL data yielded consistent results. These findings can serve as a proof of principle that the gap of "missing heritability" in quantitative genetics can be partially bridged by a systematic evaluation of sex-specific associations.
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Affiliation(s)
- Xuelin Li
- Department of Medicine, University of Alabama at Birmingham, 1665 University Boulevard, Birmingham, AL 35294 USA
| | - Matthew A. Price
- International AIDS Vaccine Initiative, New York City, NY USA
- Department of Epidemiology and Biostatistics, UCSF, San Francisco, CA USA
| | - Dongning He
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL USA
| | - Anatoli Kamali
- MRC/UVRI Uganda Virus Research Unit on AIDS, Masaka Site, Masaka, Uganda
| | | | - Shabir Lakhi
- Zambia-Emory HIV-1 Research Project, Lusaka, Zambia
| | - Eduard J. Sanders
- Centre for Geographic Medicine Research, Kenya Medical Research Institute (KEMRI), Kilifi, Kenya
- Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford, Headington, UK
| | - Omu Anzala
- Kenya AIDS Vaccine Initiative (KAVI), Nairobi, Kenya
| | - Pauli N. Amornkul
- International AIDS Vaccine Initiative, New York City, NY USA
- Department of Epidemiology and Biostatistics, UCSF, San Francisco, CA USA
| | - Susan Allen
- Projet San Francisco, Kigali, Rwanda
- Zambia-Emory HIV-1 Research Project, Lusaka, Zambia
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA USA
| | - Eric Hunter
- Vaccine Research Center, Emory University, Atlanta, GA USA
| | - Richard A. Kaslow
- International AIDS Vaccine Initiative, New York City, NY USA
- Present Address: Department of Veterans Affairs, Washington, DC, 20420 USA
| | - Jill Gilmour
- International AIDS Vaccine Initiative, Human Immunology Laboratory, Chelsea and Westminster Hospital, London, UK
| | - Jianming Tang
- Department of Medicine, University of Alabama at Birmingham, 1665 University Boulevard, Birmingham, AL 35294 USA
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL USA
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37
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Prentice HA, Pajewski NM, He D, Zhang K, Brown EE, Kilembe W, Allen S, Hunter E, Kaslow RA, Tang J. Host genetics and immune control of HIV-1 infection: fine mapping for the extended human MHC region in an African cohort. Genes Immun 2014; 15:275-81. [PMID: 24784026 PMCID: PMC4111776 DOI: 10.1038/gene.2014.16] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2014] [Revised: 03/28/2014] [Accepted: 03/28/2014] [Indexed: 12/31/2022]
Abstract
Multiple MHC loci encoding human leukocyte antigens (HLA) have allelic variants unequivocally associated with differential immune control of HIV-1 infection. Fine mapping based on single nucleotide polymorphisms (SNPs) in the extended MHC (xMHC) region is expected to reveal causal or novel factors and to justify a search for functional mechanisms. We have tested the utility of a custom fine-mapping platform (the ImmunoChip) for 172 HIV-1 seroconverters (SCs) and 449 seroprevalent individuals (SPs) from Lusaka, Zambia, with a focus on more than 6,400 informative xMHC SNPs. When conditioned on HLA and non-genetic factors previously associated with HIV-1 viral load (VL) in the study cohort, penalized approaches (HyperLasso models) identified an intergenic SNP (rs3094626 between RPP21 and HLA-E) and an intronic SNP (rs3134931 in NOTCH4) as novel correlates of early set-point VL in SCs. The minor allele of rs2857114 (downstream from HLA-DOB) was an unfavorable factor in SPs. Joint models based on demographic features, HLA alleles and the newly identified SNP variants could explain 29% and 15% of VL variance in SCs and SPs, respectively. These findings and bioinformatics strongly suggest that both classic and non-classic MHC genes deserve further investigation, especially in Africans with relatively short haplotype blocks.
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Affiliation(s)
- H A Prentice
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - N M Pajewski
- Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - D He
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - K Zhang
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - E E Brown
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - W Kilembe
- Zambia-Emory HIV-1 Research Project, Lusaka, Zambia
| | - S Allen
- 1] Zambia-Emory HIV-1 Research Project, Lusaka, Zambia [2] Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA
| | - E Hunter
- Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - R A Kaslow
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - J Tang
- 1] Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA [2] Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
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38
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Fraser C, Lythgoe K, Leventhal GE, Shirreff G, Hollingsworth TD, Alizon S, Bonhoeffer S. Virulence and pathogenesis of HIV-1 infection: an evolutionary perspective. Science 2014; 343:1243727. [PMID: 24653038 PMCID: PMC5034889 DOI: 10.1126/science.1243727] [Citation(s) in RCA: 166] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Why some individuals develop AIDS rapidly whereas others remain healthy without treatment for many years remains a central question of HIV research. An evolutionary perspective reveals an apparent conflict between two levels of selection on the virus. On the one hand, there is rapid evolution of the virus in the host, and on the other, new observations indicate the existence of virus factors that affect the virulence of infection whose influence persists over years in infected individuals and across transmission events. Here, we review recent evidence that shows that viral genetic factors play a larger role in modulating disease severity than anticipated. We propose conceptual models that reconcile adaptive evolution at both levels of selection. Evolutionary analysis provides new insight into HIV pathogenesis.
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Affiliation(s)
- Christophe Fraser
- Medical Research Council Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK
| | - Katrina Lythgoe
- Medical Research Council Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK
| | | | - George Shirreff
- Institute for Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - T. Déirdre Hollingsworth
- Warwick Mathematics Institute, University of Warwick, Coventry, UK
- School of Life Sciences, University of Warwick, Coventry, UK
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Samuel Alizon
- Laboratoire MIVEGEC (UMR CNRS 5290, IRD, UM1, UM2), Montpellier, France
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Kaslow RA, Stanberry LR, Le Duc JW. Viral Dynamics and Mathematical Models. VIRAL INFECTIONS OF HUMANS 2014. [PMCID: PMC7119994 DOI: 10.1007/978-1-4899-7448-8_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
Mathematical tools have been widely applied in understanding the dynamics and control of viral infections. Here we present some fundamental aspects of infection dynamics, starting with acute immunising infections as a case study for herd immunity and other important factors in the spread and control of infection. We then discuss the dynamics of infections with more complex life histories, including chronic infections, and those showing evolution for immune escape. We conclude with a discussion of important gaps in our current understanding of viral dynamics, along with future research needs.
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Affiliation(s)
- Richard A. Kaslow
- Department of Epidemiology, University of Alabama, Birmingham School of Public Health, Birmingham, Alabama USA
| | - Lawrence R. Stanberry
- Departmant of Pediatrics, Columbia University College of Physicians and Surgeons, New York, New York USA
| | - James W. Le Duc
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas USA
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Abstract
Purpose of review To review recent published literature around three areas: long-term nonprogression/viral control; predictors of viral load set point/disease progression; and the potential impact of antiretroviral therapy (ART) in early HIV infection. Recent findings The natural course of untreated HIV infection varies widely with some HIV-positive individuals able to maintain high CD4 cell counts and/or suppressed viral load in the absence of ART. Although similar, the underlying mechanistic processes leading to long-term nonprogression and viral control are likely to differ. Concerted ongoing research efforts will hopefully identify host factors that are causally related to these phenotypes, thus providing opportunities for the development of novel treatment or preventive strategies. Although there is increasing evidence that initiation of ART during primary infection may prevent the immunological deterioration which would otherwise be seen in untreated HIV infection, recent studies do not address the longer term clinical benefits of ART at this very early stage. Summary A better understanding of the relative influences of viral, host, and environmental factors on the natural course of HIV infection has the potential to identify novel targets for intervention to prevent and treat HIV-infected persons.
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Prentice HA, Price MA, Porter TR, Cormier E, Mugavero MJ, Kamali A, Karita E, Lakhi S, Sanders EJ, Anzala O, Amornkul PN, Allen S, Hunter E, Kaslow RA, Gilmour J, Tang J. Dynamics of viremia in primary HIV-1 infection in Africans: insights from analyses of host and viral correlates. Virology 2013; 449:254-62. [PMID: 24418560 DOI: 10.1016/j.virol.2013.11.024] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 10/11/2013] [Accepted: 11/14/2013] [Indexed: 12/15/2022]
Abstract
In HIV-1 infection, plasma viral load (VL) has dual implications for pathogenesis and public health. Based on well-known patterns of HIV-1 evolution and immune escape, we hypothesized that VL is an evolving quantitative trait that depends heavily on duration of infection (DOI), demographic features, human leukocyte antigen (HLA) genotypes and viral characteristics. Prospective data from 421 African seroconverters with at least four eligible visits did show relatively steady VL beyond 3 months of untreated infection, but host and viral factors independently associated with cross-sectional and longitudinal VL often varied by analytical approaches and sliding time windows. Specifically, the effects of age, HLA-B(⁎)53 and infecting HIV-1 subtypes (A1, C and others) on VL were either sporadic or highly sensitive to time windows. These observations were strengthened by the addition of 111 seroconverters with 2-3 eligible VL results, suggesting that DOI should be a critical parameter in epidemiological and clinical studies.
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Affiliation(s)
- Heather A Prentice
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Matthew A Price
- International AIDS Vaccine Initiative, New York City, NY, USA; Department of Epidemiology & Biostatistics, UCSF, San Francisco, CA, USA
| | - Travis R Porter
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Emmanuel Cormier
- International AIDS Vaccine Initiative, Human Immunology Laboratory, Chelsea and Westminster Hospital, London, UK
| | - Michael J Mugavero
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Anatoli Kamali
- MRC/UVRI Uganda Virus Research Unit on AIDS, Masaka Site, Masaka, Uganda
| | | | - Shabir Lakhi
- Zambia-Emory HIV Research Project, Lusaka, Zambia
| | - Eduard J Sanders
- Centre for Geographic Medicine Research, Kenya Medical Research Institute (KEMRI), Kilifi, Kenya; Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford, Headington, UK
| | - Omu Anzala
- Kenya AIDS Vaccine Initiative (KAVI), Nairobi, Kenya
| | | | - Susan Allen
- Zambia-Emory HIV Research Project, Lusaka, Zambia; Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA
| | - Eric Hunter
- Vaccine Research Center, Emory University, Atlanta, GA, USA
| | - Richard A Kaslow
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Jill Gilmour
- International AIDS Vaccine Initiative, Human Immunology Laboratory, Chelsea and Westminster Hospital, London, UK
| | - Jianming Tang
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA; Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA.
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Porter TR, Li X, Stephensen CB, Mulligan K, Rutledge B, Flynn PM, Lujan-Zilbermann J, Hazra R, Wilson CM, Havens PL, Tang J. Genetic associations with 25-hydroxyvitamin D deficiency in HIV-1-infected youth: fine-mapping for the GC/DBP gene that encodes the vitamin D-binding protein. Front Genet 2013; 4:234. [PMID: 24294218 PMCID: PMC3827582 DOI: 10.3389/fgene.2013.00234] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Accepted: 10/22/2013] [Indexed: 01/08/2023] Open
Abstract
Serum 25-hydroxyvitamin D [25(OH)D] is often deficient (<12 ng/ml) or insufficient (<20 ng/ml) in youth living with human immunodeficiency virus type 1 infection (YLH). Based on evidence from multiple genome-wide association studies, we hypothesized that genetic factors associated with 25(OH)D deficiency should be readily detectable in YLH even when controlling for other known factors, including use of the antiretroviral drug efavirenz (EFV). Genotyping by bi-directional sequencing targeted 15 single nucleotide polymorphisms (SNPs) at the GC/DBP locus, with a focus on coding and regulatory variants, as well as those repeatedly reported in the literature. Three intronic SNPs (rs222016, rs222020, and rs222029) in a conserved haplotype block had unequivocal association signals (false discovery rate ≤ 0.006). In particular, the minor allele G for rs222020 was highly unfavorable among 192 YLH (99 African–Americans and 93 others), as gauged by relatively low likelihood for 25(OH)D sufficiency at enrollment (odds ratio = 0.31, p = 9.0 × 10-4). In a reduced multivariable model, race, season, latitude, body mass index, exposure to EFV, and rs222020-G were independent factors that collectively accounted for 38% of variance in the log10-transformed 25(OH)D concentration (p < 0.0001). Interaction terms were evident for rs222020-G × season (p < 0.001), latitude × season (especially fall and winter; p < 0.01), and race × EFV use (p = 0.024). Overall, variance in serum 25(OH)D is substantially attributable to multiple factors, but the exact contribution of genetic and non-genetic factors can be obscured by partial overlaps and frequent interactions.
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Affiliation(s)
- Travis R Porter
- Department of Epidemiology, University of Alabama at Birmingham Birmingham, AL, USA
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Ng OT, Laeyendecker O, Redd AD, Munshaw S, Grabowski MK, Paquet AC, Evans MC, Haddad M, Huang W, Robb ML, Reynolds SJ, Gray RH, Wawer MJ, Serwadda D, Eshleman SH, Quinn TC. HIV type 1 polymerase gene polymorphisms are associated with phenotypic differences in replication capacity and disease progression. J Infect Dis 2013; 209:66-73. [PMID: 23922373 DOI: 10.1093/infdis/jit425] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Determinants of intersubtype differences in human immunodeficiency virus type 1 (HIV-1) clinical disease progression remain unknown. METHODS HIV-1 subtype was independently determined for 5 separate genomic regions in 396 HIV-1 seroconverters from Rakai, Uganda, using a multiregion hybridization assay. Replication capacities (RC) in samples from a subset of 145 of these subjects were determined. HIV-1 genomic regions and pol RC were examined for association with disease progression. Amino acid polymorphisms were examined for association with pol RC. RESULTS In multivariate analyses, the hazard for progression to the composite end point (defined as a CD4(+) T-cell count <250 cells/mm(3), antiretroviral therapy initiation, or death) among patients with subtype D pol infection was 2.4 times the hazard for those infected with subtype A pol infection (P = .001). Compared with subtype A pol (the reference group), the hazard for progression to the composite end point for subtype D pol infection with a pol RC >67% (ie, the median pol RC) was significantly greater (HR, 4.6; 95% confidence interval [CI], 1.9-11.0; P = .001), whereas the hazard for progression to the composite end point for subtype D pol infection with a pol RC ≤67% was not significantly different (HR, 2.2; 95% CI, 1.0-4.9; P = .051). Amino acid substitutions at protease positions 62 and 64 and at reverse transcriptase position 272 were associated with significant differences in pol RC. CONCLUSIONS HIV-1 pol gene intersubtype and RC differences are associated with disease progression and may be influenced by amino acid polymorphisms.
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