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Mackelprang RD, Filali-Mouhim A, Richardson B, Lefebvre F, Katabira E, Ronald A, Gray G, Cohen KW, Klatt NR, Pecor T, Celum C, McElrath MJ, Hughes SM, Hladik F, Cameron MJ, Lingappa JR. Upregulation of IFN-stimulated genes persists beyond the transitory broad immunologic changes of acute HIV-1 infection. iScience 2023; 26:106454. [PMID: 37020953 PMCID: PMC10067744 DOI: 10.1016/j.isci.2023.106454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 09/15/2022] [Accepted: 03/15/2023] [Indexed: 04/03/2023] Open
Abstract
Chronic immune activation during HIV-1 infection contributes to morbidity and mortality in people living with HIV. To elucidate the underlying biological pathways, we evaluated whole blood gene expression trajectories from before, through acute, and into chronic HIV-1 infection. Interferon-stimulated genes, including MX1, IFI27 and ISG15, were upregulated during acute infection, remained elevated into chronic infection, and were strongly correlated with plasma HIV-1 RNA as well as TNF-α and CXCL10 cytokine levels. In contrast, genes involved in cellular immune responses, such as CD8A, were upregulated during acute infection before reaching a peak and returning to near pre-infection levels in chronic infection. Our results indicate that chronic immune activation during HIV-1 infection is characterized by persistent elevation of a narrow set of interferon-stimulated genes and innate cytokines. These findings raise the prospect of devising a targeted intervention to restore healthy immune homeostasis in people living with HIV-1.
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Li Y, Lefebvre F, Nakku-Joloba E, Ronald A, Gray G, de Bruyn G, Kiarie J, Celum C, Cameron MJ, Lingappa JR, Mackelprang RD. Upregulation of PTPRC and Interferon Response Pathways in HIV-1 Seroconverters Prior to Infection. J Infect Dis 2023; 227:714-719. [PMID: 36637125 PMCID: PMC9978315 DOI: 10.1093/infdis/jiac498] [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: 06/02/2022] [Revised: 12/16/2022] [Accepted: 12/27/2022] [Indexed: 01/14/2023] Open
Abstract
Human immunodeficiency virus 1 (HIV-1) exposed seronegative (HESN) individuals may have unique characteristics that alter susceptibility to HIV-1 infection. However, identifying truly exposed HESN is challenging. We utilized stored data and biospecimens from HIV-1 serodifferent couple cohorts, in which couples' HIV-1 exposures were quantified based on unprotected sex frequency and viral load of the partner with HIV-1. We compared peripheral blood gene expression between 15 HESN and 18 seroconverters prior to infection. We found PTPRC (encoding CD45 antigen) and interferon-response pathways had significantly higher expression among individuals who went on to become seropositive and thus may be a signature for increased acquisition risk.
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Affiliation(s)
- Yunqi Li
- Institute for Public Health Genetics, University of Washington, Seattle, Washington, USA
| | - Francois Lefebvre
- Canadian Centre for Computational Genomics-Montréal Node, Montreal, Quebec, Canada
| | | | - Allan Ronald
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
| | - Glenda Gray
- Perinatal HIV Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Guy de Bruyn
- Perinatal HIV Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - James Kiarie
- Department of Obstetrics and Gynecology, University of Nairobi, Nairobi, Kenya
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Connie Celum
- Department of Global Health, University of Washington, Seattle, Washington, USA
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
| | - Mark J Cameron
- Department of Population and Quantitative Health Science, Case Western Reserve University, Cleveland, Ohio, 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
| | - Romel D Mackelprang
- Department of Global Health, University of Washington, Seattle, Washington, USA
- Department of Obstetrics and Gynecology, University of Washington, Seattle, Washington, USA
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3
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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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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] [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, Oxford, UK
| | - Chris Wymant
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - François Blanquart
- Centre for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, PSL Research University, Paris, France
| | - Tanya Golubchik
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Astrid Gall
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Margreet Bakker
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | | | - Matthew Hall
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Swee Hoe Ong
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - 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, Department of Infectious Diseases, Robert Koch Institute, Berlin, Germany
| | - Jacques Fellay
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - M Kate Grabowski
- Department of Pathology, John Hopkins University, Baltimore, MD, USA
| | | | - 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 D Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | | | - Laurence Meyer
- INSERM CESP U1018, Université Paris Saclay, APHP, Service de Santé Publique, Hôpital de Bicêtre, Le Kremlin-Bicêtre, France
| | - Kholoud Porter
- Institute for Global Health, University College London, London, UK
| | | | | | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Paul Kellam
- Kymab Ltd, Cambridge, UK
- Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, UK
| | - Marion Cornelissen
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
- Molecular Diagnostic Unit, Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Peter Reiss
- Stichting HIV Monitoring, Amsterdam, Netherlands
- Department of Global Health, Amsterdam University Medical Centers, University of Amsterdam and Amsterdam Institute for Global Health and Development, Amsterdam, Netherlands
| | - Christophe Fraser
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Luca Ferretti
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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Kageyama S, Amolong Hinay A, Telan EFO, Samonte GMJ, Leano PSA, Tsuneki-Tokunaga A, Kanai K. Intrinsic Replication Competences of HIV Strains After Zidovudine/Lamivudine/Nevirapine Treatment in the Philippines. J Int Assoc Provid AIDS Care 2020; 18:2325958219856579. [PMID: 31216920 PMCID: PMC6748504 DOI: 10.1177/2325958219856579] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Although drug-resistant HIV variants are considered to be less fit than drug-susceptible viruses, replication competence of these variants harbored by patients has not yet been elucidated in detail. We herein assessed the replication competence of strains obtained from individuals receiving antiretroviral therapy. Among 11 306 participants in a drug resistance surveillance in the Philippines, 2629 plasma samples were obtained from individuals after a 12-month treatment with zidovudine (ZDV)/lamivudine (3TC)/nevirapine (NVP). The replication competence of HIV isolates was then assessed by reinoculation into seronegative peripheral blood mononuclear cells in the absence of drugs in vitro. The drug resistance rate was estimated to be 9.2%. Drug-resistant strains were still a minority of closely related strains in a phylogenetic cluster. Among the available 295 samples, 37 HIV strains were successfully isolated. Progeny viruses were produced at a wide range (5.1 × 106 to 3.4 × 109 copies/mL) in primary culture of peripheral blood mononuclear cells. The viral yields were higher than the corresponding plasma viral load (1300 to 3.4 × 106 copies/mL) but correlated with those (r = 0.4). These results suggest that strains with higher intrinsic replication competence are one of the primary targets of newly selected drugs at the increasing phase of the plasma viral load during antiretroviral therapy.
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Affiliation(s)
- Seiji Kageyama
- 1 Division of Virology, Department of Microbiology and Immunology, Faculty of Medicine, Tottori University, Yonago, Japan
| | - Alfredo Amolong Hinay
- 1 Division of Virology, Department of Microbiology and Immunology, Faculty of Medicine, Tottori University, Yonago, Japan
| | | | | | - Prisca Susan Agustin Leano
- 2 National Reference Laboratory, STD AIDS Cooperative Central Laboratory, San Lazaro Hospital, Manila, Philippines
| | - Akeno Tsuneki-Tokunaga
- 1 Division of Virology, Department of Microbiology and Immunology, Faculty of Medicine, Tottori University, Yonago, Japan
| | - Kyosuke Kanai
- 1 Division of Virology, Department of Microbiology and Immunology, Faculty of Medicine, Tottori University, Yonago, Japan
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6
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Bochner AF, Secor WE, Baeten JM, van Dam GJ, Szpiro AA, Njenga SM, Corstjens PLAM, Mackelprang RD, Mugo NR, Overbaugh J, Celum C, Mujugira A, McClelland RS, Barnabas RV. Schistosomiasis was not associated with higher HIV-1 plasma or genital set point viral loads among HIV seroconverters from four cohort studies. PLoS Negl Trop Dis 2019; 13:e0007886. [PMID: 31747411 PMCID: PMC6867600 DOI: 10.1371/journal.pntd.0007886] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 10/27/2019] [Indexed: 01/08/2023] Open
Abstract
Background Many regions of sub-Saharan Africa experience a high prevalence of both schistosomiasis and HIV-1, leading to frequent coinfection. Higher plasma HIV-1 viral loads are associated with faster disease progression and genital HIV-1 loads are a primary determinant of HIV-1 transmission risk. We hypothesized that schistosome infection would be associated with higher HIV-1 viral loads in plasma and genital samples. Methods/Principal findings We utilized data from individuals who HIV-1 seroconverted while enrolled in one of four prospective cohort studies. Plasma and genital viral loads collected 4–24 months after the estimated date of HIV-1 acquisition, but prior to antiretroviral therapy initiation, were included. Detection of circulating anodic antigen in archived blood samples, collected prior to HIV-1 seroconversion, identified participants with active schistosomiasis; immunoblots determined the schistosome species causing infection. Our analysis included 370 HIV-1 seroconverters with plasma viral load results, of whom 82 (22%) had schistosomiasis. We did not find a statistically significant association between schistosomiasis and higher HIV-1 set point plasma viral loads (-0.17 log10 copies/ml, 95% CI -0.38 to 0.03); S. mansoni infection was associated with a lower set point (-0.34 log10 copies/ml, 95% CI -0.58 to -0.09). We found no association between schistosomiasis and cervical (+0.07 log10 copies/swab, 95% CI -0.20 to 0.34) or vaginal (+0.11 log10 copies/swab, 95% CI -0.17 to 0.39) set point viral loads; S. haematobium infection was associated with lower cervical viral loads (-0.59 log10 copies/swab, 95% CI -1.11 to -0.06). Conclusions/Significance These results do not support the hypotheses that schistosome coinfection increases plasma or genital HIV-1 viral loads. Schistosomiasis is a parasitic disease that is common in many parts of sub-Saharan Africa most affected by the HIV-1 epidemic. Schistosomiasis causes genital damage when schistosome ova become lodged in the female genital tract, inducing inflammation that may elevate HIV-1 genital viral loads and increase the risk of HIV-1 transmission. Schistosomiasis may also promote viral replication by facilitating cell-to-cell transmission of HIV-1, elevating HIV-1 plasma viral load levels. Using data from 370 individuals residing in Kenya or Uganda who acquired HIV-1 while participating in one of four prospective cohort studies, we tested the hypotheses that schistosomiasis increases plasma and genital viral load levels. We found no evidence that individuals with schistosomiasis had higher set point plasma viral load levels, a measure of viral replication obtained during the set point period 4–24 months after HIV-1 acquisition when viral load levels remain relatively stable. Additionally, we found no evidence that schistosomiasis was associated with higher female set point genital viral loads measured from vaginal or cervical swabs. Unexpectedly, we found that S. mansoni infection was associated with a decline in plasma viral load levels while S. haematobium infection was associated with a decline in cervical viral load levels. Thus, our results do not support the hypotheses that schistosomiasis increases plasma and genital HIV-1 viral loads.
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Affiliation(s)
- Aaron F. Bochner
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
- * E-mail:
| | - W. Evan Secor
- Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Jared M. Baeten
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
- School of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Govert J. van Dam
- Department of Parasitology, Leiden University Medical Center, Leiden, the Netherlands
| | - Adam A. Szpiro
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | | | - Paul L. A. M. Corstjens
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Romel D. Mackelprang
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
| | | | - Julie Overbaugh
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Connie Celum
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
- School of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Andrew Mujugira
- Infectious Diseases Institute, College of Health Sciences, Makerere University, Kampala, Uganda
| | - R. Scott McClelland
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
- School of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Ruanne V. Barnabas
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
- School of Medicine, University of Washington, Seattle, Washington, United States of America
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7
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Heffron R, Stalter R, Pyra M, Nanda K, Erikson DW, Hladik F, Blue SW, Davis NL, Mugo N, Kourtis AP, Lingappa JR, Baeten JM. HIV risk associated with serum medroxyprogesterone acetate levels among women in East and southern Africa. AIDS 2019; 33:735-744. [PMID: 30585845 PMCID: PMC6399047 DOI: 10.1097/qad.0000000000002123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND Some observational studies have found increased HIV risk associated with self-reported use of injectable depot medroxyprogesterone acetate. Testing blood samples for medroxyprogesterone acetate (MPA), the progestin in depot medroxyprogesterone acetate, permits validation of self-reported data, and exploration of whether potential HIV risk is correlated with MPA levels, which are highest soon after injection. METHODS We conducted a case-control study testing archived serum from women who participated in three longitudinal studies of HIV prevention in East and southern Africa. Case samples, from women who acquired HIV, were from visits that occurred at or immediately prior to the first evidence of HIV infection. Secondary analyses restricted to case samples collected within 15 and 30 days of the estimated date of HIV infection. Matched control samples were from women who remained HIV uninfected. We used multivariable conditional logistic regression to compare exogenous hormone levels, quantified through mass spectrometry, among cases and controls. RESULTS When restricted to cases with samples collected within 15 days or less of estimated date of HIV infection, MPA detection was more frequent among women who acquired HIV (adjusted odds ratio = 2.75, 95% confidence interval 1.22-6.19). In this subset, the increase in HIV risk was only among samples with MPA detected at a low level of 0.02-0.50 ng/ml: 36.7% of cases and 9.4% of controls, adjusted odds ratio = 6.03, 95% confidence interval 2.50-14.54. CONCLUSION Detection of MPA at low levels close to the estimated time of HIV acquisition was significantly more frequent among women who acquired HIV. Studies are needed that explore biological mechanisms elicited by any MPA level and HIV risk.
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Affiliation(s)
| | | | - Maria Pyra
- University of Washington, Seattle, Washington
| | - Kavita Nanda
- Global Health, Population and Nutrition, FHI360, Durham, North Carolina
| | - David W Erikson
- Endocrine Technologies Core, Oregon National Primate Research Center, Hillsboro, Oregon
| | - Florian Hladik
- Department of Obstetrics and Gynecology, University of Washington, Seattle, Washington
| | - Steven W Blue
- Endocrine Technologies Core, Oregon National Primate Research Center, Hillsboro, Oregon
| | - Nicole L Davis
- Division of Reproductive Health, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Nelly Mugo
- University of Washington, Seattle, Washington
- Center for Clinical Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Athena P Kourtis
- Division of Reproductive Health, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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8
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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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9
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Davis SM, Pals S, Yang C, Odoyo-June E, Chang J, Walters MS, Jaoko W, Bock N, Westerman L, Toledo C, Bailey RC. Circumcision status at HIV infection is not associated with plasma viral load in men: analysis of specimens from a randomized controlled trial. BMC Infect Dis 2018; 18:350. [PMID: 30055581 PMCID: PMC6064164 DOI: 10.1186/s12879-018-3257-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 07/17/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Male circumcision provides men with approximately 60% protection from acquiring HIV infection via heterosexual sex, and has become a key component of HIV prevention efforts in sub-Saharan Africa. Possible mechanisms for this protection include removal of the inflammatory anaerobic sub-preputial environment and the high concentration of Langerhans cells on the inside of the foreskin, both believed to promote local vulnerability to HIV infection. In people who do acquire HIV, viral load is partially determined by infecting partner viral load, potentially mediated by size of infecting inoculum. By removing a portal for virion entry, prior male circumcision could decrease infecting inoculum and thus viral load in men who become HIV-infected, conferring the known associated benefits of slower progression to disease and decreased infectiousness. METHODS We performed an as-treated analysis of plasma samples collected under a randomized controlled trial of male circumcision for HIV prevention, comparing men based on their circumcision status at the time of HIV acquisition, to determine whether circumcision is associated with lower viral load. Eligible men were seroconverters who had at least one plasma sample available drawn at least 6 months after infection, reported no potential exposures other than vaginal sex and, for those who were circumcised, were infected more than 6 weeks after circumcision, to eliminate the open wound as a confounder. Initial viral load testing indicated that quality of pre-2007 samples might have been compromised during storage and they were excluded, as were those with undetectable or unquantifiable results. Log viral loads were compared between groups using univariable and multivariable linear regression, adjusting for sample age and sexually transmitted infection diagnosis with 3.5 months of seroconversion, with a random effect for intra-individual clustering for samples from the same man. A per-protocol analysis was also performed. RESULTS There were no viral load differences between men who were circumcised and uncircumcised at the time of HIV infection (means 4.00 and 4.03 log10 copies/mL respectively, p = .88) in any analysis. CONCLUSION Circumcision status at the time of HIV infection does not affect viral load in men. TRIAL REGISTRATION The original RCT which provided the samples was ClinicalTrials.gov trial NCT00059371 .
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Affiliation(s)
- Stephanie M Davis
- Division of Global HIV/AIDS and Tuberculosis, US Centers for Disease Control, Atlanta, GA, USA. .,Division of Global HIV and TB, HIV Prevention Branch US Centers for Disease Control and Prevention, 1600 Clifton Rd. NE Mail Stop E-04, Atlanta, GA, 30329, USA.
| | - Sherri Pals
- Division of Global HIV/AIDS and Tuberculosis, US Centers for Disease Control, Atlanta, GA, USA
| | - Chunfu Yang
- Division of Global HIV/AIDS and Tuberculosis, US Centers for Disease Control, Atlanta, GA, USA
| | - Elijah Odoyo-June
- Division of Global HIV/AIDS and Tuberculosis, US Centers for Disease Control, Kisumu, Kenya
| | - Joy Chang
- Division of Global HIV/AIDS and Tuberculosis, US Centers for Disease Control, Atlanta, GA, USA
| | - Maroya Spalding Walters
- Division of Global HIV/AIDS and Tuberculosis, US Centers for Disease Control, Atlanta, GA, USA
| | - Walter Jaoko
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
| | - Naomi Bock
- Division of Global HIV/AIDS and Tuberculosis, US Centers for Disease Control, Atlanta, GA, USA
| | - Larry Westerman
- Division of Global HIV/AIDS and Tuberculosis, US Centers for Disease Control, Atlanta, GA, USA
| | - Carlos Toledo
- Division of Global HIV/AIDS and Tuberculosis, US Centers for Disease Control, Atlanta, GA, USA
| | - Robert C Bailey
- Division of Epidemiology and Biostatistics, University of Illinois Chicago School of Public Health, Chicago, IL, USA
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10
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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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11
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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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12
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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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13
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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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14
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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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15
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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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16
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Pintye J, Baeten JM, Manhart LE, Celum C, Ronald A, Mugo N, Mujugira A, Cohen C, Were E, Bukusi E, Kiarie J, Heffron R. Association between male circumcision and incidence of syphilis in men and women: a prospective study in HIV-1 serodiscordant heterosexual African couples. LANCET GLOBAL HEALTH 2014; 2:e664-71. [PMID: 25442691 DOI: 10.1016/s2214-109x(14)70315-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
BACKGROUND Male circumcision is a primary HIV-1 prevention intervention for men, but whether the procedure reduces the risk of syphilis among men and their female partners is uncertain. We aimed to assess whether male circumcision was associated with incident syphilis in men and in their female partners. METHODS In this large prospective cohort study, participants were members of Kenyan and Ugandan HIV-1 serodiscordant heterosexual couples enrolled in a randomised safety and efficacy clinical trial of pre-exposure prophylaxis for HIV-1 prevention (the Partners PrEP Study). Participants attended monthly or quarterly follow-up visits for up to 36 months. Annually, syphilis serology testing was done and male circumcision status was assessed. We used multivariate Andersen-Gill survival methods, adjusted for age, sexual behaviour, and plasma HIV RNA levels of the HIV-infected partner. FINDINGS 4716 HIV-1 serodiscordant couples (38%) with a man with HIV were followed for a median of 2·75 years. At enrolment, 1575 (53%) men with HIV and 560 (32%) men without HIV were circumcised; an additional 69 (4%) men with HIV and 132 (5%) men without HIV were circumcised during study follow-up. 221 incident syphilis infections were reported: 46 (21%) in men with HIV (incidence 1·10 per 100 person-years), 76 (34%) in men without HIV (1·09), 54 (24%) in women with HIV (0·77), and 45 (24%) in women without HIV (1·11). Male circumcision was associated with a 42% reduction in incident syphilis in men (adjusted hazard ratio [aHR] 0·58, 95% CI 0·37-0·91) including a 62% reduction in men with HIV (0·38, 0·18-0·81), and a non-significant reduction in incident syphilis in men without HIV (0·64, 0·36-1·11). In women, circumcision of their male partners was associated with a 59% reduction in incident syphilis (aHR 0·41, 95% CI 0·25-0·69), including a 75% reduction in women without HIV (0·25, 0·08-0·76) and a 48% reduction in women with HIV (0·52, 0·27-0·97). INTERPRETATION Male circumcision was associated with decreased risk of incident syphilis in men and women. If confirmed, these results suggest that medical male circumcision could substantially reduce incidence of syphilis and its sequelae. FUNDING Bill & Melinda Gates Foundation and the Eunice Kennedy Shriver National Institute of Child Health and Human Development.
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Affiliation(s)
- Jillian Pintye
- Department of Global Health, University of Washington, Seattle, WA, USA; Department of Nursing, University of Washington, Seattle, WA, USA
| | - Jared M Baeten
- Department of Global Health, University of Washington, Seattle, WA, USA; Department of Medicine, University of Washington, Seattle, WA, USA; Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Lisa E Manhart
- Department of Global Health, University of Washington, Seattle, WA, USA; Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Connie Celum
- Department of Global Health, University of Washington, Seattle, WA, USA; Department of Medicine, University of Washington, Seattle, WA, USA; Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Allan Ronald
- Departments of Medicine and Medical Microbiology, University of Manitoba, Winnipeg, MB, Canada; Infectious Disease Institute, Makerere University, Kampala, Uganda
| | - Nelly Mugo
- Department of Global Health, University of Washington, Seattle, WA, USA; Center for Microbiology Research and Center for Clinical Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Andrew Mujugira
- Department of Global Health, University of Washington, Seattle, WA, USA; Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Craig Cohen
- Center for Microbiology Research and Center for Clinical Research, Kenya Medical Research Institute, Nairobi, Kenya; Department of Obstetrics, Gynecology and Reproductive Sciences University of California-San Francisco, San Francisco, CA, USA
| | - Edwin Were
- Department of Reproductive Health, Moi University, Eldoret, Kenya
| | - Elizabeth Bukusi
- Department of Global Health, University of Washington, Seattle, WA, USA; Department of Obstetrics and Gynecology, University of Washington, Seattle, WA, USA; Center for Microbiology Research and Center for Clinical Research, Kenya Medical Research Institute, Nairobi, Kenya; Department of Obstetrics, Gynecology and Reproductive Sciences University of California-San Francisco, San Francisco, CA, USA
| | - James Kiarie
- Department of Global Health, University of Washington, Seattle, WA, USA; Department of Obstetrics and Gynaecology, University of Nairobi, Nairobi, Kenya
| | - Renee Heffron
- Department of Global Health, University of Washington, Seattle, WA, USA.
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17
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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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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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Graham LS, Krass L, Zariffard MR, Spear GT, Mirmonsef P. Effects of Succinic Acid and Other Microbial Fermentation Products on HIV Expression in Macrophages. Biores Open Access 2013; 2:385-91. [PMID: 24083094 PMCID: PMC3776615 DOI: 10.1089/biores.2013.0013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Bacterial vaginosis (BV), a common condition in women, is associated with increased shedding of HIV in the female genital tract. While the Lactobacillus species that comprise a healthy vaginal microbiota produce lactic acid, the bacteria common in BV produce high concentrations of short chain fatty acids (SCFAs) and succinic acid. Macrophages are abundant in the lower genital tract mucosa and are thought to play an important role in HIV infection. In this study, we investigated whether SCFAs and succinic acid impacted HIV expression in monocyte-derived macrophages. Monocytes differentiated with either granulocyte-macrophage colony-stimulating factor (GM-CSF) or macrophage colony-stimulating factor (M-CSF) were infected with either HIVBal or an HIV-luciferase reporter virus and treated with SCFAs, succinic acid, or lactic acid. Butyric acid suppressed HIV expression while succinic acid significantly increased expression in macrophages differentiated with either GM-CSF or M-CSF. Acetic, propionic, and lactic acids had no effect on HIV expression. Only succinic acid resulted in a significant increase in interleukin-8 production by infected macrophages. Our results suggest that succinic acid present in increased concentrations in the genital tract of women with BV plays a pro-inflammatory role and increases HIV expression. This could be one factor contributing to increased virus shedding seen in women with BV.
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Affiliation(s)
- Laura S Graham
- Department of Immunology/Microbiology, Rush University Medical Center , Chicago, Illinois
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Campbell MS, Kahle EM, Celum C, Lingappa JR, Kapiga S, Mujugira A, Mugo NR, Fife KH, Mullins JI, Baeten JM. Plasma viral loads during early HIV-1 infection are similar in subtype C- and non-subtype C-infected African seroconverters. J Infect Dis 2013; 207:1166-70. [PMID: 23315322 DOI: 10.1093/infdis/jit015] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Recent data suggest that infection with human immunodeficiency virus type 1 (HIV-1) subtype C results in prolonged high-level viremia (>5 log10 copies/mL) during early infection. We examined the relationship between HIV-1 subtype and plasma viremia among 153 African seroconverters. Mean setpoint viral loads were similar for C and non-C subtypes: 4.36 vs 4.42 log10 copies/mL (P = .61). The proportion of subtype C-infected participants with viral loads >5 log10 copies/mL was not greater than the proportion for those with non-C infection. Our data do not support the hypothesis that higher early viral load accounts for the rapid spread of HIV-1 subtype C in southern Africa.
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Affiliation(s)
- Mary S Campbell
- Department of Medicine, University of Washington, Seattle, WA 98195, USA.
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