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Lindquist L, Kilembe W, Karita E, Price MA, Kamali A, Kaleebu P, Tang J, Allen S, Hunter E, Gilmour J, Rowland-Jones SL, Sanders EJ, Hassan AS, Esbjörnsson J. HLA-A*23 Is Associated With Lower Odds of Acute Retroviral Syndrome in Human Immunodeficiency Virus Type 1 Infection: A Multicenter Sub-Saharan African Study. Open Forum Infect Dis 2024; 11:ofae129. [PMID: 38560608 PMCID: PMC10977907 DOI: 10.1093/ofid/ofae129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 03/11/2024] [Indexed: 04/04/2024] Open
Abstract
The role of human leukocyte antigen (HLA) class I and killer immunoglobulin-like receptor molecules in mediating acute retroviral syndrome (ARS) during human immunodeficiency virus type 1 (HIV-1) infection is unclear. Among 72 sub-Saharan African adults, HLA-A*23 was associated with lower odds of ARS (adjusted odds ratio, 0.10 [95% confidence interval, .01-.48]; P = .009), which warrants further studies to explore its role on HIV-1-specific immunopathogenesis.
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Affiliation(s)
- Lovisa Lindquist
- Lund University Centre, Lund University, Lund, Sweden
- Department of Translational Medicine, Lund University, Lund, Sweden
| | - William Kilembe
- Rwanda/Zambia HIV Research Group, Kigali, Rwanda and Lusaka, Zambia
| | - Etienne Karita
- Rwanda/Zambia HIV Research Group, Kigali, Rwanda and Lusaka, Zambia
| | - Matt A Price
- International AIDS Vaccine Initiative, New York, New York, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California, USA
| | | | - Pontiano Kaleebu
- Medical Research Council/Uganda Virus Centre Research Institute, Entebbe, Uganda
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Jianming Tang
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Susan Allen
- Rwanda/Zambia HIV Research Group, Kigali, Rwanda and Lusaka, Zambia
- Emory Vaccine Center, Emory University, Atlanta, Georgia, USA
| | - Eric Hunter
- Rwanda/Zambia HIV Research Group, Kigali, Rwanda and Lusaka, Zambia
- Emory Vaccine Center, Emory University, Atlanta, Georgia, USA
| | - Jill Gilmour
- International AIDS Vaccine Initiative, New York, New York, USA
- Human Immunology Laboratory, International AIDS Vaccine Initiative, London, United Kingdom
| | - Sarah L Rowland-Jones
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Eduard J Sanders
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
- Aurum Institute, Johannesburg, South Africa
| | - Amin S Hassan
- Lund University Centre, Lund University, Lund, Sweden
- Department of Translational Medicine, Lund University, Lund, Sweden
- Kenya Medical Research Institute/Wellcome Trust Research Programme, Kilifi, Kenya
| | - Joakim Esbjörnsson
- Lund University Centre, Lund University, Lund, Sweden
- Department of Translational Medicine, Lund University, Lund, Sweden
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
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2
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Cantor-Cutiva LC, Bottalico P, Webster J, Nudelman C, Hunter E. The Effect of Bilingualism on Production and Perception of Vocal Fry. J Voice 2023; 37:970.e1-970.e10. [PMID: 34301440 PMCID: PMC8770720 DOI: 10.1016/j.jvoice.2021.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 05/29/2021] [Accepted: 06/02/2021] [Indexed: 01/22/2023]
Abstract
AIMS (1) Determine the difference in vocal fry phonation in English and Spanish productions among bilingual young adults, (2) Characterize the effect of spoken language and native language on vocal fry production among English-Spanish bilingual speakers, (3) Identify the effect of first and second language knowledge of the listener in the voice perceptual assessment, and (4) Define the effect of the environment of the assessment (in situ vs. online), in the voice perceptual assessment. METHOD Exploratory cross-sectional study of 34 bilingual (Spanish-English) speakers and six inexperienced listeners. Participating speakers produced two speech samples (one in English and one in Spanish). Six inexperienced monolingual and bilingual listeners performed the voice perceptual assessment of vocal fry, General grade of hoarseness, and Roughness using a 4-point rating scale. RESULTS Bilingual speakers used vocal fry more often when they were speaking in English (around 3%) compared with their production in Spanish (around 2%). Bilingual native English speakers used vocal fry more often during their productions in both languages compared with bilingual native Spanish speakers. Bilingual listeners had the highest agreement when identifying vocal fry in both languages. CONCLUSIONS Differences in production of vocal fry between native speakers of American English and native speakers of Spanish may be evidence of transferring of vocal behavior (such as vocal fry) from one language to the second one. In addition, being a bilingual listener may have an important effect on the perceptual identification of voice quality in English and Spanish, as well as vocal fry in English.
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Affiliation(s)
| | | | | | | | - Eric Hunter
- Universidad Nacional de Colombia, Bogota, Colombia
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Bollimpelli VS, Reddy PBJ, Gangadhara S, Charles TP, Burton SL, Tharp GK, Styles TM, Labranche CC, Smith JC, Upadhyay AA, Sahoo A, Legere T, Shiferaw A, Velu V, Yu T, Tomai M, Vasilakos J, Kasturi SP, Shaw GM, Montefiori D, Bosinger SE, Kozlowski PA, Pulendran B, Derdeyn CA, Hunter E, Amara RR. Intradermal but not intramuscular modified vaccinia Ankara immunizations protect against intravaginal tier2 simian-human immunodeficiency virus challenges in female macaques. Nat Commun 2023; 14:4789. [PMID: 37553348 PMCID: PMC10409804 DOI: 10.1038/s41467-023-40430-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 07/28/2023] [Indexed: 08/10/2023] Open
Abstract
Route of immunization can markedly influence the quality of immune response. Here, we show that intradermal (ID) but not intramuscular (IM) modified vaccinia Ankara (MVA) vaccinations provide protection from acquisition of intravaginal tier2 simian-human immunodeficiency virus (SHIV) challenges in female macaques. Both routes of vaccination induce comparable levels of serum IgG with neutralizing and non-neutralizing activities. The protection in MVA-ID group correlates positively with serum neutralizing and antibody-dependent phagocytic activities, and envelope-specific vaginal IgA; while the limited protection in MVA-IM group correlates only with serum neutralizing activity. MVA-ID immunizations induce greater germinal center Tfh and B cell responses, reduced the ratio of Th1 to Tfh cells in blood and showed lower activation of intermediate monocytes and inflammasome compared to MVA-IM immunizations. This lower innate activation correlates negatively with induction of Tfh responses. These data demonstrate that the MVA-ID vaccinations protect against intravaginal SHIV challenges by modulating the innate and T helper responses.
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Affiliation(s)
- Venkata S Bollimpelli
- Emory Vaccine Center, Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, 30329, USA
| | - Pradeep B J Reddy
- Emory Vaccine Center, Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, 30329, USA
| | - Sailaja Gangadhara
- Emory Vaccine Center, Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, 30329, USA
| | - Tysheena P Charles
- Emory Vaccine Center, Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, 30329, USA
| | - Samantha L Burton
- Emory Vaccine Center, Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, 30329, USA
| | - Gregory K Tharp
- NHP Genomics Core Laboratory, Emory National Primate Research Center, Atlanta, GA, 30329, USA
| | - Tiffany M Styles
- Emory Vaccine Center, Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, 30329, USA
| | - Celia C Labranche
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Justin C Smith
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Amit A Upadhyay
- Emory Vaccine Center, Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, 30329, USA
| | - Anusmita Sahoo
- Emory Vaccine Center, Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, 30329, USA
| | - Traci Legere
- Emory Vaccine Center, Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, 30329, USA
| | - Ayalnesh Shiferaw
- Emory Vaccine Center, Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, 30329, USA
| | - Vijayakumar Velu
- Emory Vaccine Center, Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, 30329, USA
- Department of Pathology and Laboratory Medicine, Emory Vaccine Center, Emory National Primate Research Center, Atlanta, GA, USA
| | - Tianwei Yu
- Rollins School of Public Health, Emory University, Atlanta, GA, 30322, USA
| | - Mark Tomai
- 3M Corporate Research and Materials Lab, Saint Paul, MN, USA
| | | | - Sudhir P Kasturi
- Department of Pathology and Laboratory Medicine, Emory Vaccine Center, Emory National Primate Research Center, Atlanta, GA, USA
| | - George M Shaw
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - David Montefiori
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Steven E Bosinger
- Department of Pathology and Laboratory Medicine, Emory Vaccine Center, Emory National Primate Research Center, Atlanta, GA, USA
| | - Pamela A Kozlowski
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Bali Pulendran
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Cynthia A Derdeyn
- Department of Pathology and Laboratory Medicine, Emory Vaccine Center, Emory National Primate Research Center, Atlanta, GA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Eric Hunter
- Department of Pathology and Laboratory Medicine, Emory Vaccine Center, Emory National Primate Research Center, Atlanta, GA, USA
| | - Rama R Amara
- Emory Vaccine Center, Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, 30329, USA.
- Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA, 30322, USA.
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4
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Owens M, Ravi V, Hunter E. Digital Inclusion as a Lens for Equitable Parent Engagement. TechTrends 2023:1-11. [PMID: 37362590 PMCID: PMC10239715 DOI: 10.1007/s11528-023-00859-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 04/11/2023] [Indexed: 06/28/2023]
Abstract
Digital inclusion (DI) represents a framework for educational leaders to address ongoing digital access and participation divides for adult caretakers (e.g., parents) of school-aged children, as schools continue adopting new education technology tools. This preliminary research investigates teacher perceptions of different DI needs for parents during the pandemic. This research examines teacher perceptions of parents' knowledge and use of online tools in providing supervision to support home-based learning for their student children. A sample of K-12 teachers in the United States responded to open-ended survey questions relating to their observation and evaluation of student learning, parent involvement, and DI needs in their classes. The researchers used a framework drawn from Maslow's Hierarchy of Needs to categorize key DI components teachers identified, finding both digital access and digital participation needs existed in their students' homes. Ultimately, the framework of DI recognizes that household digital access alone does not create equitable opportunities for online instruction without holistic consideration of digital literacy training, technical support, and relevant online tools for parents and caretakers.
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Affiliation(s)
- Michael Owens
- Brigham Young University, 306-H MCKB-BYU, Provo, UT 84602 USA
| | - Vikram Ravi
- Brigham Young University, 1318 E Integra Court, Millcreek, UT 84106 USA
| | - Eric Hunter
- Michigan State University, 1026 Red Cedar Road, Room 113, Oyer Speech & Hearing Building, East Lansing, MI 48824 USA
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Nanjundeswaran C, van Mersbergen M, Banks R, Hunter E. Vocal Fatigue Index in Teachers Using Mokken Analysis. J Voice 2023; 37:298.e1-298.e9. [PMID: 33526304 PMCID: PMC8319213 DOI: 10.1016/j.jvoice.2020.12.053] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 12/15/2020] [Accepted: 12/21/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE Vocal fatigue (VF) is a primary vocal symptom experienced by professional voice users, such as teachers, whose voice is an occupational tool. The study determines the utilization of the Vocal Fatigue Index (VFI), a 19-item scale in identifying symptoms of VF and its severity in teachers. METHODS Using responses of 695 teachers who completed the VFI, Mokken scaling was conducted on the items to identify the experiences of VF and its associated hierarchical nature of VF symptoms in teachers. Mokken scaling was completed on a total of four groups: (a) Total teachers group, (b) No VF group, (c) Low VF group, and (d) High VF group. RESULTS Results revealed differences in item hierarchies between total teachers and across the separate groups of VF severity. Item hierarchy for teachers highlighted items from physical discomfort at the mild end of the hierarchy to items from symptom improvement with rest at the severe end of the hierarchy. Items related to avoidance presented as a separate scale for teachers presenting with high VF. DISCUSSION Mokken scaling in teachers provides insight into the underlying complexity of the experience of VF symptoms and reliance on differential behavioral strategies in its management, suggesting the heterogenous nature of latent trait for VF in this specific population.
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Affiliation(s)
- Chaya Nanjundeswaran
- Department of Audiology & Speech Language Pathology, East Tennessee State University, Johnson City, Tennessee.
| | - Miriam van Mersbergen
- School of Communication Sciences and Disorders; Institute for Intelligent Systems; University of Memphis, Memphis Tennessee
| | - Russell Banks
- Massachusetts General Hospital Institute of Health Professions, Boston, MA
| | - Eric Hunter
- Department of Communicative Sciences and Disorders, Michigan State University, Michigan
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6
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Gleason L, Hunter E, Cohen A, Suriano J, Nikbakht N. Atezolizumab-induced psoriasiform drug eruption successfully treated with ixekizumab: a case report and literature review. Dermatol Online J 2023; 29. [PMID: 37040912 DOI: 10.5070/d329160215] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 02/16/2023] [Indexed: 02/27/2023] Open
Abstract
Immune-related cutaneous adverse events (ircAE) are commonly seen with immune checkpoint inhibitors such as atezolizumab. Atezolizumab-induced psoriasis has been previously reported as an ircAE, especially in patients with pre-existing psoriasis. The severity of the reaction influences treatment of the cutaneous eruption. Biologics should be considered as a treatment option for severe refractory psoriasiform eruptions even in patients with complex medical conditions like chronic infections and malignancy. This is the first reported case of successful treatment of atezolizumab-induced psoriasiform eruption with ixekizumab, a neutralizing IL17A monoclonal antibody, to the best of our knowledge. Herein, we present a 63-year-old man with a history of human immunodeficiency virus and psoriasis who presented with atezolizumab-induced psoriasiform eruption while being treated for metastatic hepatocellular carcinoma. After initiating ixekizumab, atezolizumab was restarted without cutaneous eruption.
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Affiliation(s)
| | | | | | | | - N Nikbakht
- Department of Dermatology and Cutaneous Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA.
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7
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Michelo CM, Fiore-Gartland A, Dalel JA, Hayes P, Tang J, McGowan E, Kilembe W, Fernandez N, Gilmour J, Hunter E. Cohort-Specific Peptide Reagents Broaden Depth and Breadth Estimates of the CD8 T Cell Response to HIV-1 Gag Potential T Cell Epitopes. Vaccines (Basel) 2023; 11:vaccines11020472. [PMID: 36851349 PMCID: PMC9961105 DOI: 10.3390/vaccines11020472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/10/2023] [Accepted: 02/13/2023] [Indexed: 02/22/2023] Open
Abstract
An effective HIV vaccine will need to stimulate immune responses against the sequence diversity presented in circulating virus strains. In this study, we evaluate breadth and depth estimates of potential T-cell epitopes (PTEs) in transmitted founder virus sequence-derived cohort-specific peptide reagents against reagents representative of consensus and global sequences. CD8 T-cells from twenty-six HIV-1+ PBMC donor samples, obtained at 1-year post estimated date of infection, were evaluated. ELISpot assays compared responses to 15mer consensus (n = 121), multivalent-global (n = 320), and 10mer multivalent cohort-specific (n = 300) PTE peptides, all mapping to the Gag antigen. Responses to 38 consensus, 71 global, and 62 cohort-specific PTEs were confirmed, with sixty percent of common global and cohort-specific PTEs corresponding to consensus sequences. Both global and cohort-specific peptides exhibited broader epitope coverage compared to commonly used consensus reagents, with mean breadth estimates of 3.2 (global), 3.4 (cohort) and 2.2 (consensus) epitopes. Global or cohort peptides each identified unique epitope responses that would not be detected if these peptide pools were used alone. A peptide set designed around specific virologic and immunogenetic characteristics of a target cohort can expand the detection of CD8 T-cell responses to epitopes in circulating viruses, providing a novel way to better define the host response to HIV-1 with implications for vaccine development.
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Affiliation(s)
- Clive M. Michelo
- Center for Family Health Research Zambia, PostNet 412, P/Bag E891, B22/737 Bwembelelo, Emmasdale, Lusaka 10101, Zambia
| | - Andrew Fiore-Gartland
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Jama A. Dalel
- IAVI Human Immunology Laboratory, Imperial College, London SW10 9NH, UK
| | - Peter Hayes
- IAVI Human Immunology Laboratory, Imperial College, London SW10 9NH, UK
| | - Jianming Tang
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Edward McGowan
- IAVI Human Immunology Laboratory, Imperial College, London SW10 9NH, UK
| | - William Kilembe
- Center for Family Health Research Zambia, PostNet 412, P/Bag E891, B22/737 Bwembelelo, Emmasdale, Lusaka 10101, Zambia
| | - Natalia Fernandez
- IAVI Human Immunology Laboratory, Imperial College, London SW10 9NH, UK
| | - Jill Gilmour
- IAVI Human Immunology Laboratory, Imperial College, London SW10 9NH, UK
| | - Eric Hunter
- Center for Family Health Research Zambia, PostNet 412, P/Bag E891, B22/737 Bwembelelo, Emmasdale, Lusaka 10101, Zambia
- Emory Vaccine Center, Emory University, 954 Gatewood Road NE, Atlanta, GA 30329, USA
- Emory National Primate Research Center, Emory University, 954 Gatewood Road NE, Atlanta, GA 30329, USA
- Correspondence: ; Tel.: +1-404-727-8587; Fax: +1-404-727-9316
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Fernandez N, Hayes P, Makinde J, Hare J, King D, Xu R, Rehawi O, Mezzell AT, Kato L, Mugaba S, Serwanga J, Chemweno J, Nduati E, Price MA, Osier F, Ochsenbauer C, Yue L, Hunter E, Gilmour J. Assessment of a diverse panel of transmitted/founder HIV-1 infectious molecular clones in a luciferase based CD8 T-cell mediated viral inhibition assay. Front Immunol 2022; 13:1029029. [PMID: 36532063 PMCID: PMC9751811 DOI: 10.3389/fimmu.2022.1029029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 11/14/2022] [Indexed: 12/03/2022] Open
Abstract
Introduction Immunological protection against human immunodeficiency virus-1 (HIV-1) infection is likely to require both humoral and cell-mediated immune responses, the latter involving cytotoxic CD8 T-cells. Characterisation of CD8 T-cell mediated direct anti-viral activity would provide understanding of potential correlates of immune protection and identification of critical epitopes associated with HIV-1 control. Methods The present report describes a functional viral inhibition assay (VIA) to assess CD8 T-cell-mediated inhibition of replication of a large and diverse panel of 45 HIV-1 infectious molecular clones (IMC) engineered with a Renilla reniformis luciferase reporter gene (LucR), referred to as IMC-LucR. HIV-1 IMC replication in CD4 T-cells and CD8 T-cell mediated inhibition was characterised in both ART naive subjects living with HIV-1 covering a broad human leukocyte antigen (HLA) distribution and compared with uninfected subjects. Results & discussion CD4 and CD8 T-cell lines were established from subjects vaccinated with a candidate HIV-1 vaccine and provided standard positive controls for both assay quality control and facilitating training and technology transfer. The assay was successfully established across 3 clinical research centres in Kenya, Uganda and the United Kingdom and shown to be reproducible. This IMC-LucR VIA enables characterisation of functional CD8 T-cell responses providing a tool for rational T-cell immunogen design of HIV-1 vaccine candidates and evaluation of vaccine-induced T-cell responses in HIV-1 clinical trials.
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Affiliation(s)
- Natalia Fernandez
- IAVI Human Immunology Laboratory, Imperial College, London, United Kingdom,*Correspondence: Natalia Fernandez, ; Peter Hayes,
| | - Peter Hayes
- IAVI Human Immunology Laboratory, Imperial College, London, United Kingdom,*Correspondence: Natalia Fernandez, ; Peter Hayes,
| | - Julia Makinde
- IAVI Human Immunology Laboratory, Imperial College, London, United Kingdom
| | - Jonathan Hare
- IAVI Human Immunology Laboratory, Imperial College, London, United Kingdom,IAVI, New York, NY, United States
| | - Deborah King
- IAVI Human Immunology Laboratory, Imperial College, London, United Kingdom
| | - Rui Xu
- Emory Vaccine Center at Yerkes National Primate Research Center, Emory University, Atlanta, GA, United States
| | - Ola Rehawi
- University of Alabama at Birmingham, Birmingham, AL, United States
| | | | - Laban Kato
- Uganda Virus Research Institute, Entebbe, Uganda,Medical Research Council, Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine Uganda Research Unit, Entebbe, Uganda
| | - Susan Mugaba
- Uganda Virus Research Institute, Entebbe, Uganda,Medical Research Council, Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine Uganda Research Unit, Entebbe, Uganda
| | - Jennifer Serwanga
- Uganda Virus Research Institute, Entebbe, Uganda,Medical Research Council, Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine Uganda Research Unit, Entebbe, Uganda
| | - James Chemweno
- Kenya Medical Research Institute (KEMRI) Wellcome Trust Research Programme, Kilifi, Kenya
| | - Eunice Nduati
- Kenya Medical Research Institute (KEMRI) Wellcome Trust Research Programme, Kilifi, Kenya
| | - Matt A. Price
- IAVI, New York, NY, United States,Department of Epidemiology and Biostatistics, University of California at San Francisco, San Francisco, CA, United States
| | - Faith Osier
- IAVI Human Immunology Laboratory, Imperial College, London, United Kingdom
| | | | - Ling Yue
- Emory Vaccine Center at Yerkes National Primate Research Center, Emory University, Atlanta, GA, United States
| | - Eric Hunter
- Emory Vaccine Center at Yerkes National Primate Research Center, Emory University, Atlanta, GA, United States
| | - Jill Gilmour
- Department of Infectious Diseases, Imperial College, London, United Kingdom
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Solomon G, Suzuki S, Hathorne H, Barilla C, Wang B, Rab A, Manfredi C, Joshi D, Brewington J, Stecenko A, Driggers W, Bai S, Hunter E, Streby A, Hong J, Odem-Davis K, Davis B, Sorscher E, Linnemann R. 606 Focused clinical trials of modulator response for rare cystic fibrosis genotypes. J Cyst Fibros 2022. [DOI: 10.1016/s1569-1993(22)01296-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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DiFiglia S, Georgiopoulos A, Portenoy R, Berdella M, Friedman D, Kier C, Linnemann R, Middour-Oxler B, Walker P, Wang J, Buehler B, Chaudhary N, Esposito C, Henthorne K, Hunter E, Plachta A, Pollinger S, Stables-Carney T, Trentacoste J, Dhingra L. 242 Palliative care needs in cystic fibrosis: Baseline data from the Improving Life with Cystic Fibrosis Multi-site Implementation Trial for Primary Palliative Care Intervention. J Cyst Fibros 2022. [DOI: 10.1016/s1569-1993(22)00932-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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11
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Powles T, Sridhar S, Bellmunt J, Sternberg C, Grivas P, Hunter E, Dezfouli M, Salter M, Powell R, Dring A, Green J, Akoulitchev A, Amezquita R, Ching K, Pu J, Deng S, di Pietro A, Davis C. LBA74 Genomic biomarkers in peripheral blood (PB) from patients (pts) enrolled in the JAVELIN Bladder 100 trial of avelumab first-line (1L) maintenance in advanced urothelial carcinoma (aUC). Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.08.080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
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12
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Banks RE, Cantor-Cutiva LC, Hunter E. Factors Influencing Teachers' Experience of Vocal Fatigue and Classroom Voice Amplification. J Voice 2022:S0892-1997(22)00192-8. [PMID: 35999093 PMCID: PMC9939560 DOI: 10.1016/j.jvoice.2022.06.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/21/2022] [Accepted: 06/22/2022] [Indexed: 11/19/2022]
Abstract
BACKGROUND Voice disorders among teachers are widespread. Teachers' voice problems have been shown to influence the teaching-learning process, thereby impeding students' academic performance. Voice amplification has been used as a preventative strategy to avoid voice problems and as a means of augmenting student reception of a teacher's voice. However, the relationship between perceived vocal fatigue and amplification use has not been established, nor have factors been identified which may be associated with the use of voice amplification in the classroom. PURPOSE This research has two aims: (1) determine the relationship between self-reported vocal fatigue and self-reported teachers' use of sound field amplification in the classroom; and (2) identify which factors are related with the use of amplification systems among the participating teachers. METHODS Paper and online surveys were provided to teachers throughout the United States. These surveys contained the 19-question Vocal Fatigue Index (VFI), in addition to other questions regarding health-related conditions and lifestyle habits of respondents. Access to and use of amplification systems, as well as other work-related factors that might influence the use of such systems were detailed by the respondents. RESULTS Regardless of grades levels or measured factors, teachers who reported using amplification systems were more likely to report higher levels of vocal fatigue. Teachers who taught in lower grade levels or in larger capacity classrooms not only reported a greater likelihood of using the systems more frequently, but also reported a greater access to amplification systems. Overall, less than 40% of teachers had access to an amplification system. Teachers of lower grades reported having the least access. CONCLUSIONS Our results suggest an association between teachers' use of voice amplification systems and vocal fatigue. In addition, some work-related factors (eg, grade level, classroom capacity) were associated with the use of amplification systems. The results can be beneficial to teachers, school administrators, lawmakers and health professionals to more efficiently use diminishing educational resources in a targeted fashion to better train and potentially reduce the occurrence of voice problems among teachers.
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Affiliation(s)
- Russell E Banks
- Linus Health, Inc, Boston MA; Department of Communicative Sciences and Disorders, Michigan State University, East Lansing, MI.
| | - Lady C Cantor-Cutiva
- Department of Communicative Sciences and Disorders, Michigan State University, East Lansing, MI
| | - Eric Hunter
- Department of Communicative Sciences and Disorders, Michigan State University, East Lansing, MI
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13
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Umviligihozo G, Mann JK, Jin SW, Mwimanzi FM, Hsieh HSA, Sudderuddin H, Lee GQ, Byakwaga H, Muzoora C, Hunt PW, Martin JN, Haberer JE, Karita E, Allen S, Hunter E, Brumme ZL, Brockman MA. Attenuated HIV-1 Nef But Not Vpu Function in a Cohort of Rwandan Long-Term Survivors. Front Virol 2022; 2:917902. [PMID: 35982753 PMCID: PMC9383652 DOI: 10.3389/fviro.2022.917902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
HIV-1 accessory proteins Nef and Vpu enhance viral pathogenesis through partially overlapping immune evasion activities. Attenuated Nef or Vpu functions have been reported in individuals who display slower disease progression, but few studies have assessed the relative impact of these proteins in non-B HIV-1 subtypes or examined paired proteins from the same individuals. Here, we examined the sequence and function of matched Nef and Vpu clones isolated from 29 long-term survivors (LTS) from Rwanda living with HIV-1 subtype A and compared our results to those of 104 Nef and 62 Vpu clones isolated from individuals living with chronic untreated HIV-1 subtype A from the same geographic area. Nef and vpu coding regions were amplified from plasma HIV RNA and cloned. The function of one intact, phylogenetically-validated Nef and Vpu clone per individual was then quantified by flow cytometry following transient expression in an immortalized CD4+ T-cell line. We measured the ability of each Nef clone to downregulate CD4 and HLA class I, and of each Vpu clone to downregulate CD4 and Tetherin, from the cell surface. Results were normalized to reference clones (Nef-SF2 and Vpu-NL4.3). We observed that Nef-mediated CD4 and HLA downregulation functions were lower in LTS compared to the control cohort (Mann-Whitney p=0.03 and p<0.0001, respectively). Moreover, we found a positive correlation between Nef-mediated CD4 downregulation function and plasma viral load in LTS and controls (Spearman ρ= 0.59, p=0.03 and ρ=0.30, p=0.005, respectively). In contrast, Vpu-mediated functions were similar between groups and did not correlate with clinical markers. Further analyses identified polymorphisms at Nef codon 184 and Vpu codons 60-62 that were associated with function, which were confirmed through mutagenesis. Overall, our results support attenuated function of Nef, but not Vpu, as a contributor to slower disease progression in this cohort of long-term survivors with HIV-1 subtype A.
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Affiliation(s)
| | - Jaclyn K. Mann
- HIV Pathogenesis Programme, University of KwaZulu-Natal, Durban, South Africa
| | - Steven W. Jin
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | | | - Hua-Shiuan A. Hsieh
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Hanwei Sudderuddin
- British Columbia Centre for Excellence in HIV/AIDS, Vancover, BC, Canada
| | - Guinevere Q. Lee
- Department of Medicine, Weill Cornell Medical College, New York, NY, United States
| | - Helen Byakwaga
- Department of Community Health, Mbarara University of Science and Technology, Mbarara, Uganda,Department of Medicine, University of California, San Francisco, CA, United States
| | - Conrad Muzoora
- Department of Medicine, Weill Cornell Medical College, New York, NY, United States
| | - Peter W. Hunt
- Department of Community Health, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Jeff N. Martin
- Department of Community Health, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Jessica E. Haberer
- Center for Global Health, Massachusetts General Hospital, Boston, MA, United States,Department of Medicine, Harvard Medical School, Boston, MA, United States
| | | | - Susan Allen
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, United States
| | - Eric Hunter
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, United States,Emory Vaccine Center at Yerkes National Primate Research Center, Atlanta, GA, United States
| | - Zabrina L. Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada,British Columbia Centre for Excellence in HIV/AIDS, Vancover, BC, Canada
| | - Mark A. Brockman
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada,Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada,British Columbia Centre for Excellence in HIV/AIDS, Vancover, BC, Canada,Correspondence: Mark A. Brockman,
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14
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Joag V, Quarnstrom C, Soerens A, Stolley JM, Schenkel JM, Fraser K, Vezys V, Skinner PJ, Hunter E, Bimber B, Amara RR, Masopust D. Sensing and alarm function of vaccine-elicited SIV-gag specific CD8 TRM in the reproductive mucosa of rhesus macaques. The Journal of Immunology 2022. [DOI: 10.4049/jimmunol.208.supp.114.15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Abstract
TRM constitute a recently identified lymphocyte lineage that occupies non-lymphoid tissues (NLT) without recirculating. Experiments in mice demonstrated that TRM reactivation triggers antiviral responses in neighboring cells by promoting local stimulation of innate and adaptive immune cells, and by recruiting immune effectors. Collectively this is referred to as ‘sensing and alarm’ function. We wished to broadly identify TRM functions in non-human primates (NHP). Here we applied a prime-boost vaccine modality in rhesus macaques to generate abundant SIVgag-specific CD8 TRM in the female reproductive tract (FRT) and 14 other NLT. To assess sensing and alarm function, macaques were challenged intravaginally with CM9 peptide from the SIV gag protein and necropsied 24 or 48 hours later. CD8 TRM reactivation increased expression of CD69 and granzyme B in SIV-gag specific CD8 T cells throughout the FRT at 24h, in situ proliferation (Ki67 expression) by 48h, and rapid antiviral and IFN response gene expression in essentially all hematopoietic and non-hematopoietic cells by 24h. Upregulation of effector genes in CD8 T cells, CD4 T cells, NK cells, and ILCs peaked at 24h and persisted at 48h. Mucosal CD4 T cells expressed various HIV restriction factors, and had reduced expression of the HIV-coreceptor CCR5. Increased numbers of vaginal T and B cells coincided with increased expression of chemokines and VCAM-1 on endothelial and stromal cells and a concomitant reduction in circulating T cells, B cells and SIV-env-specific B cells. These data demonstrate that vaccine-elicited CD8 TRM rapidly trigger local activation and the recruitment of innate, cellular, and humoral immune responses to the site of antigen exposure.
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15
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Balinda SN, Kapaata A, Xu R, Salazar MG, Mezzell AT, Qin Q, Herard K, Dilernia D, Kamali A, Ruzagira E, Kibengo FM, Song H, Ochsenbauer C, Salazar-Gonzalez JF, Gilmour J, Hunter E, Yue L, Kaleebu P. Characterization of Near Full-Length Transmitted/Founder HIV-1 Subtype D and A/D Recombinant Genomes in a Heterosexual Ugandan Population (2006–2011). Viruses 2022; 14:v14020334. [PMID: 35215928 PMCID: PMC8874453 DOI: 10.3390/v14020334] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 01/01/2022] [Accepted: 01/10/2022] [Indexed: 12/04/2022] Open
Abstract
Detailed characterization of transmitted HIV-1 variants in Uganda is fundamentally important to inform vaccine design, yet studies on the transmitted full-length strains of subtype D viruses are limited. Here, we amplified single genomes and characterized viruses, some of which were previously classified as subtype D by sub-genomic pol sequencing that were transmitted in Uganda between December 2006 to June 2011. Analysis of 5′ and 3′ half genome sequences showed 73% (19/26) of infections involved single virus transmissions, whereas 27% (7/26) of infections involved multiple variant transmissions based on predictions of a model of random virus evolution. Subtype analysis of inferred transmitted/founder viruses showed a high transmission rate of inter-subtype recombinants (69%, 20/29) involving mainly A1/D, while pure subtype D variants accounted for one-third of infections (31%, 9/29). Recombination patterns included a predominance of subtype D in the gag/pol region and a highly recombinogenic envelope gene. The signal peptide-C1 region and gp41 transmembrane domain (Tat2/Rev2 flanking region) were hotspots for A1/D recombination events. Analysis of a panel of 14 transmitted/founder molecular clones showed no difference in replication capacity between subtype D viruses (n = 3) and inter-subtype mosaic recombinants (n = 11). However, individuals infected with high replication capacity viruses had a faster CD4 T cell loss. The high transmission rate of unique inter-subtype recombinants is striking and emphasizes the extraordinary challenge for vaccine design and, in particular, for the highly variable and recombinogenic envelope gene, which is targeted by rational designs aimed to elicit broadly neutralizing antibodies.
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Affiliation(s)
- Sheila N. Balinda
- Medical Research Council, UVRI & LSTHM Uganda Research Unit, Plot 51–59, Entebbe, Uganda; (A.K.); (M.G.S.); (E.R.); (F.M.K.); (J.F.S.-G.); (P.K.)
- Correspondence: ; Tel.: +25-675-466-0098
| | - Anne Kapaata
- Medical Research Council, UVRI & LSTHM Uganda Research Unit, Plot 51–59, Entebbe, Uganda; (A.K.); (M.G.S.); (E.R.); (F.M.K.); (J.F.S.-G.); (P.K.)
| | - Rui Xu
- Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA 30329, USA; (R.X.); (Q.Q.); (K.H.); (D.D.); (H.S.); (E.H.); (L.Y.)
| | - Maria G. Salazar
- Medical Research Council, UVRI & LSTHM Uganda Research Unit, Plot 51–59, Entebbe, Uganda; (A.K.); (M.G.S.); (E.R.); (F.M.K.); (J.F.S.-G.); (P.K.)
| | - Allison T. Mezzell
- Department of Molecular Genetics, Biochemistry, and Microbiology, University of Cincinnati College of Medicine, 3230, Eden Ave, Cincinnati, OH 45267, USA;
| | - Qianhong Qin
- Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA 30329, USA; (R.X.); (Q.Q.); (K.H.); (D.D.); (H.S.); (E.H.); (L.Y.)
| | - Kimberly Herard
- Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA 30329, USA; (R.X.); (Q.Q.); (K.H.); (D.D.); (H.S.); (E.H.); (L.Y.)
| | - Dario Dilernia
- Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA 30329, USA; (R.X.); (Q.Q.); (K.H.); (D.D.); (H.S.); (E.H.); (L.Y.)
| | - Anatoli Kamali
- International AIDS Vaccine Initiative (IAVI), Nairobi 00202, Kenya;
| | - Eugene Ruzagira
- Medical Research Council, UVRI & LSTHM Uganda Research Unit, Plot 51–59, Entebbe, Uganda; (A.K.); (M.G.S.); (E.R.); (F.M.K.); (J.F.S.-G.); (P.K.)
| | - Freddie M. Kibengo
- Medical Research Council, UVRI & LSTHM Uganda Research Unit, Plot 51–59, Entebbe, Uganda; (A.K.); (M.G.S.); (E.R.); (F.M.K.); (J.F.S.-G.); (P.K.)
| | - Heeyah Song
- Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA 30329, USA; (R.X.); (Q.Q.); (K.H.); (D.D.); (H.S.); (E.H.); (L.Y.)
| | - Christina Ochsenbauer
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA;
| | - Jesus F. Salazar-Gonzalez
- Medical Research Council, UVRI & LSTHM Uganda Research Unit, Plot 51–59, Entebbe, Uganda; (A.K.); (M.G.S.); (E.R.); (F.M.K.); (J.F.S.-G.); (P.K.)
| | - Jill Gilmour
- International AIDS Vaccine Initiative (IAVI), Imperial College London, London SW10 9NH, UK;
| | - Eric Hunter
- Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA 30329, USA; (R.X.); (Q.Q.); (K.H.); (D.D.); (H.S.); (E.H.); (L.Y.)
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA 30329, USA
| | - Ling Yue
- Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA 30329, USA; (R.X.); (Q.Q.); (K.H.); (D.D.); (H.S.); (E.H.); (L.Y.)
| | - Pontiano Kaleebu
- Medical Research Council, UVRI & LSTHM Uganda Research Unit, Plot 51–59, Entebbe, Uganda; (A.K.); (M.G.S.); (E.R.); (F.M.K.); (J.F.S.-G.); (P.K.)
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16
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Umviligihozo G, Muok E, Nyirimihigo Gisa E, Xu R, Dilernia D, Herard K, Song H, Qin Q, Bizimana J, Farmer P, Hare J, Gilmour J, Allen S, Karita E, Hunter E, Yue L. Increased Frequency of Inter-Subtype HIV-1 Recombinants Identified by Near Full-Length Virus Sequencing in Rwandan Acute Transmission Cohorts. Front Microbiol 2021; 12:734929. [PMID: 34690973 PMCID: PMC8529237 DOI: 10.3389/fmicb.2021.734929] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 09/07/2021] [Indexed: 12/01/2022] Open
Abstract
Most studies of HIV-1 transmission have focused on subtypes B and C. In this study, we determined the genomic sequences of the transmitted founder (TF) viruses from acutely infected individuals enrolled between 2005 and 2011 into IAVI protocol C in Rwanda and have compared these isolates to viruses from more recent (2016–2019) acute/early infections in three at risk populations – MSM, high risk women (HRW), and discordant couples (DC). For the Protocol C samples, we utilized near full-length single genome (NFLG) amplification to generate 288 HIV-1 amplicons from 26 acutely infected seroconverters (SC), while for the 21 recent seroconverter samples (13 from HRW, two from DC, and six from MSM), we PCR amplified overlapping half-genomes. Using PacBio SMRT technology combined with the MDPseq workflow, we performed multiplex sequencing to obtain high accuracy sequences for each amplicon. Phylogenetic analyses indicated that the majority of recent transmitted viruses from DC and HRW clustered within those of the earlier Protocol C cohort. However, five of six sequences from the MSM cohort branched together and were greater than 97% identical. Recombination analyses revealed a high frequency (6/26; 23%) of unique inter-subtype recombination in Protocol C with 19% AC and 4% CD recombinant viruses, which contrasted with only 6.5% of recombinants defined by sequencing of the pol gene previously. The frequency of recombinants was significantly higher (12/21; 57%) in the more recent isolates, although, the five related viruses from the MSM cohort had identical recombination break points. While major drug resistance mutations were absent from Protocol C viruses, 4/21 of recent isolates exhibited transmitted nevirapine resistance. These results demonstrate the ongoing evolution and increased prevalence of recombinant and drug resistant transmitted viruses in Rwanda and highlight the importance of defining NFLG sequences to fully understand the nature of TF viruses and in particular the prevalence of unique recombinant forms (URFs) in transmission cohorts.
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Affiliation(s)
| | - Erick Muok
- Centre for Family Health Research, Kigali, Rwanda
| | | | - Rui Xu
- Emory Vaccine Center at Yerkes National Primate Research Center, Atlanta, GA, United States
| | - Dario Dilernia
- Emory Vaccine Center at Yerkes National Primate Research Center, Atlanta, GA, United States
| | - Kimberley Herard
- Emory Vaccine Center at Yerkes National Primate Research Center, Atlanta, GA, United States
| | - Heeyah Song
- Emory Vaccine Center at Yerkes National Primate Research Center, Atlanta, GA, United States
| | - Qianhong Qin
- Emory Vaccine Center at Yerkes National Primate Research Center, Atlanta, GA, United States
| | | | - Paul Farmer
- Emory Vaccine Center at Yerkes National Primate Research Center, Atlanta, GA, United States
| | | | - Jill Gilmour
- Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Susan Allen
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, United States
| | | | - Eric Hunter
- Emory Vaccine Center at Yerkes National Primate Research Center, Atlanta, GA, United States.,Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, United States
| | - Ling Yue
- Emory Vaccine Center at Yerkes National Primate Research Center, Atlanta, GA, United States
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17
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Brooks K, Omondi FH, Liang RH, Sudderuddin H, Jones BR, Joy JB, Brumme CJ, Hunter E, Brumme ZL. Proviral Turnover During Untreated HIV Infection Is Dynamic and Variable Between Hosts, Impacting Reservoir Composition on ART. Front Microbiol 2021; 12:719153. [PMID: 34489909 PMCID: PMC8417368 DOI: 10.3389/fmicb.2021.719153] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 07/30/2021] [Indexed: 12/25/2022] Open
Abstract
Human immunodeficiency virus (HIV) can persist as an integrated provirus, in a transcriptionally repressed state, within infected cells. This small yet enduring pool of cellular reservoirs that harbor replication-competent HIV is the main barrier to cure. Entry of viral sequences into cellular reservoirs begins shortly after infection, and cells containing integrated proviral DNA are extremely stable once suppressive antiretroviral therapy (ART) is initiated. During untreated HIV infection however, reservoir turnover is likely to be more dynamic. Understanding these dynamics is important because the longevity of the persisting proviral pool during untreated infection dictates reservoir composition at ART initiation. If the persisting proviral pool turns over slowly pre-ART, then HIV sequences seeded into it during early infection would have a high likelihood of persisting for long periods. However, if pre-ART turnover was rapid, the persisting proviral pool would rapidly shift toward recently circulating HIV sequences. One-way to estimate this turnover rate is from the age distributions of proviruses sampled shortly after therapy initiation: this is because, at the time of sampling, the majority of proviral turnover would have already occurred prior to ART. Recently, methods to estimate a provirus’ age from its sequence have made this possible. Using data from 12 individuals with HIV subtype C for whom proviral ages had been determined phylogenetically, we estimated that the average proviral half-life during untreated infection was 0.78 (range 0.45–2.38) years, which is >15 times faster than that of proviral DNA during suppressive ART. We further show that proviral turnover during untreated infection correlates with both viral setpoint and rate of CD4+ T-cell decline during this period. Overall, our results support dynamic proviral turnover pre-ART in most individuals, which helps explain why many individuals’ reservoirs are skewed toward younger HIV sequences. Broadly, our findings are consistent with the notion that active viral replication creates an environment less favorable to proviral persistence, while viral suppression creates conditions more favorable to persistence, where ART stabilizes the proviral pool by dramatically slowing its rate of decay. Strategies to inhibit this stabilizing effect and/or to enhance reservoir turnover during ART could represent additional strategies to reduce the HIV reservoir.
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Affiliation(s)
- Kelsie Brooks
- Emory Vaccine Center, Emory University, Atlanta, GA, United States
| | - F Harrison Omondi
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada.,British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Richard H Liang
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Hanwei Sudderuddin
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Bradley R Jones
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada.,Bioinformatics Program, University of British Columbia, Vancouver, BC, Canada
| | - Jeffrey B Joy
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada.,Bioinformatics Program, University of British Columbia, Vancouver, BC, Canada.,Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Chanson J Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada.,Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Eric Hunter
- Emory Vaccine Center, Emory University, Atlanta, GA, United States.,Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, United States
| | - 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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18
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Hassan AS, Hare J, Gounder K, Nazziwa J, Karlson S, Olsson L, Streatfield C, Kamali A, Karita E, Kilembe W, Price MA, Borrow P, Björkman P, Kaleebu P, Allen S, Hunter E, Ndung'u T, Gilmour J, Rowland-Jones S, Esbjörnsson J, Sanders EJ. A Stronger Innate Immune Response During Hyperacute Human Immunodeficiency Virus Type 1 (HIV-1) Infection Is Associated With Acute Retroviral Syndrome. Clin Infect Dis 2021; 73:832-841. [PMID: 33588436 PMCID: PMC8423478 DOI: 10.1093/cid/ciab139] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Acute retroviral syndrome (ARS) is associated with human immunodeficiency virus type 1 (HIV-1) subtype and disease progression, but the underlying immunopathological pathways are poorly understood. We aimed to elucidate associations between innate immune responses during hyperacute HIV-1 infection (hAHI) and ARS. METHODS Plasma samples obtained from volunteers (≥18.0 years) before and during hAHI, defined as HIV-1 antibody negative and RNA or p24 antigen positive, from Kenya, Rwanda, Uganda, Zambia, and Sweden were analyzed. Forty soluble innate immune markers were measured using multiplexed assays. Immune responses were differentiated into volunteers with stronger and comparatively weaker responses using principal component analysis. Presence or absence of ARS was defined based on 11 symptoms using latent class analysis. Logistic regression was used to determine associations between immune responses and ARS. RESULTS Of 55 volunteers, 31 (56%) had ARS. Volunteers with stronger immune responses (n = 36 [65%]) had increased odds of ARS which was independent of HIV-1 subtype, age, and risk group (adjusted odds ratio, 7.1 [95% confidence interval {CI}: 1.7-28.8], P = .003). Interferon gamma-induced protein (IP)-10 was 14-fold higher during hAHI, elevated in 7 of the 11 symptoms and independently associated with ARS. IP-10 threshold >466.0 pg/mL differentiated stronger immune responses with a sensitivity of 84.2% (95% CI: 60.4-96.6) and specificity of 100.0% (95% CI]: 90.3-100.0). CONCLUSIONS A stronger innate immune response during hAHI was associated with ARS. Plasma IP-10 may be a candidate biomarker of stronger innate immunity. Our findings provide further insights on innate immune responses in regulating ARS and may inform the design of vaccine candidates harnessing innate immunity.
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Affiliation(s)
- Amin S Hassan
- KEMRI/Wellcome Trust Research Programme, Kilifi, Kenya.,Department of Translational Medicine, Lund University, Sweden
| | - Jonathan Hare
- IAVI Human Immunology Laboratory, Imperial College, London, United Kingdom.,IAVI, New York, New York, USA, and Nairobi, Kenya
| | - Kamini Gounder
- Africa Health Research Institute, Durban, South Africa.,HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Jamirah Nazziwa
- Department of Translational Medicine, Lund University, Sweden
| | - Sara Karlson
- Department of Translational Medicine, Lund University, Sweden
| | - Linnéa Olsson
- Department of Internal Medicine, Helsingborg Hospital, Helsingborg, Sweden
| | | | | | - Etienne Karita
- Rwanda/Zambia HIV Research Group, Kigali, Rwanda and Lusaka, Zambia
| | - William Kilembe
- Rwanda/Zambia HIV Research Group, Kigali, Rwanda and Lusaka, Zambia
| | - Matt A Price
- IAVI, New York, New York, USA, and Nairobi, Kenya.,UCSF Department of Epidemiology and Biostatistics, San Francisco,California, USA
| | - Persephone Borrow
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Per Björkman
- Department of Translational Medicine, Lund University, Sweden
| | - Pontiano Kaleebu
- Medical Research Council/Uganda Virus Research Institute, Uganda, and London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Susan Allen
- Rwanda/Zambia HIV Research Group, Kigali, Rwanda and Lusaka, Zambia.,Emory Vaccine Center, Emory University, Atlanta, Georgia, USA
| | - Eric Hunter
- Rwanda/Zambia HIV Research Group, Kigali, Rwanda and Lusaka, Zambia.,Emory Vaccine Center, Emory University, Atlanta, Georgia, USA
| | - Thumbi Ndung'u
- Africa Health Research Institute, Durban, South Africa.,HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa.,Max Planck Institute for Infection Biology, Berlin, Germany.,Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, USA.,Division of Infection and Immunity, University College London, London, United Kingdom
| | - Jill Gilmour
- IAVI Human Immunology Laboratory, Imperial College, London, United Kingdom
| | - Sarah Rowland-Jones
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Joakim Esbjörnsson
- Department of Translational Medicine, Lund University, Sweden.,Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Eduard J Sanders
- KEMRI/Wellcome Trust Research Programme, Kilifi, Kenya.,Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
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19
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Hare J, Macharia G, Yue L, Streatfield CL, Hunter E, Purcell A, Ternette N, Gilmour J. Direct identification of HLA-presented CD8 T cell epitopes from transmitted founder HIV-1 variants. Proteomics 2021; 21:e2100142. [PMID: 34275180 DOI: 10.1002/pmic.202100142] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/13/2021] [Accepted: 07/13/2021] [Indexed: 11/09/2022]
Abstract
Cytotoxic T lymphocytes (CTLs) are a critical arm of the immune response to viral infections. The activation and expansion of antigen specific CTL requires recognition of peptide antigens presented on class I major histocompatibility complex molecules (MHC-1) of infected cells. Methods to identify presented peptide antigens that do not rely on the pre-existence of antigen specific CTL are critical to the development of new vaccines. We infected activated CD4+ T cells with two HIV-1 transmitted founder (TF) isolates and used high-resolution mass spectrometry (MS) to identify HIV peptides bound on MHC-1. Using this approach, we identified 14 MHC-1 bound peptides from across the two TF isolates. Assessment of predicted binding thresholds revealed good association of the identified peptides to the shared HLA alleles between the HIV+ donors and the naïve PBMC sample with three peptides identified through peptide sequencing inducing a CD8 T-cell response (p < 0.05). Direct infection of naïve CD4 cells by HIV TF isolates and sequencing of MHC-I presented peptides by HPLC-MS/MS enables identification of novel peptides that may be missed by alternative epitope mapping strategies and can provide valuable insight in to the first peptides presented by an HIV-infected CD4 cell in the first few days post infection.
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Affiliation(s)
- Jonathan Hare
- IAVI Human Immunology Laboratory, Imperial College London, London, UK.,IAVI, New York, New York, USA
| | - Gladys Macharia
- IAVI Human Immunology Laboratory, Imperial College London, London, UK.,Department of Infectious Disease, Imperial College London, London, UK
| | - Ling Yue
- Emory Vaccine Center, Emory University, Atlanta, Georgia, USA
| | - Claire L Streatfield
- IAVI Human Immunology Laboratory, Imperial College London, London, UK.,Department of Infectious Disease, Imperial College London, London, UK
| | - Eric Hunter
- Emory Vaccine Center, Emory University, Atlanta, Georgia, USA
| | - Anthony Purcell
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | | | - Jill Gilmour
- Department of Infectious Disease, Imperial College London, London, UK
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20
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Hare J, Fiore-Gartland A, McGowan E, Hunter E, Gilmour J, Nielsen M. Selective HLA restriction enables the evaluation and interpretation of immunogenic breadth at comparable levels to that observed with broader HLA distribution. Proteomics 2021; 21:e2100121. [PMID: 34275199 DOI: 10.1002/pmic.202100121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/07/2021] [Accepted: 07/14/2021] [Indexed: 11/06/2022]
Abstract
Existing approaches to identifying predictive T-cell epitopes have traditionally utilized either 2-digit HLA super-families or more commonly utilizing autologous HLA alleles to facilitate the predictions. However, the use of these criteria may not consider the HLA representation within any target population. Here we propose a modification to concept of utilizing autologous HLA whereby subsets of individuals are selected for their specific HLA allele profiles and the representation they provide within a given population. Using this selective approach to HLA selection and the linkages to specific individuals may enable the design of more targeted experimentalstrategies.
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Affiliation(s)
- Jonathan Hare
- International AIDS Vaccine Initiative, New York, New York, USA.,IAVI Human Immunology Laboratory, Imperial College, London, UK
| | - Andrew Fiore-Gartland
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Edward McGowan
- IAVI Human Immunology Laboratory, Imperial College, London, UK
| | - Eric Hunter
- Emory Vaccine Center, Emory University, Atlanta, Georgia, USA
| | - Jill Gilmour
- Department of Infectious Disease, Imperial College, London, UK
| | - Morten Nielsen
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
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21
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Wall KM, Karita E, Nyombayire J, Ingabire R, Mukamuyango J, Parker R, Brill I, Price M, Haddad LB, Tichacek A, Hunter E, Allen S. Genital Abnormalities, Hormonal Contraception, and Human Immunodeficiency Virus Transmission Risk in Rwandan Serodifferent Couples. J Infect Dis 2021; 224:81-91. [PMID: 33560366 PMCID: PMC8253127 DOI: 10.1093/infdis/jiab071] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 02/02/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND We explored the role of genital abnormalities and hormonal contraception in human immunodeficiency virus (HIV) transmission among heterosexual serodifferent couples in Rwanda. METHODS From 2002 to 2011, HIV-serodifferent couples who were not using antiretroviral treatment were followed up, and sociodemographic and clinical data were collected, family planning provided, and HIV-negative partners retested. Couples were assessed for genital ulcers; nonulcerative genital sexually transmitted infection (STIs), including gonorrhea, chlamydia, and trichomoniasis; and non-STI vaginal infections, including bacterial vaginosis and candida. Multivariable models evaluated associations between covariates and HIV transmission genetically linked to the index partner. RESULTS Among 877 couples in which the man was HIV positive, 37 linked transmissions occurred. Factors associated with women's HIV acquisition included genital ulceration in the female partner (adjusted hazard ratio, 14.1) and nonulcerative STI in the male partner (8.6). Among 955 couples in which the woman was HIV positive, 46 linked transmissions occurred. Factors associated with HIV acquisition in men included nonulcerative STI in the female partner (adjusted hazard ratio, 4.4), non-STI vaginal dysbiosis (7.1), and genital ulceration in the male partner (2.6). Hormonal contraception use was not associated with HIV transmission or acquisition. CONCLUSIONS Our findings underscore the need for integrating HIV services with care for genital abnormalities. Barriers (eg, cost of training, demand creation, advocacy, and client education; provider time; and clinic space) to joint HIV/STI testing need to be considered and addressed.
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Affiliation(s)
- Kristin M Wall
- Rwanda Zambia Health Research Group, Department of Pathology & Laboratory Medicine, School of Medicine and Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
- Department of Epidemiology, Rollins School of Public Health, Laney Graduate School, Emory University, Atlanta, Georgia, USA
| | - Etienne Karita
- Rwanda Zambia Health Research Group, Department of Pathology & Laboratory Medicine, School of Medicine and Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
- Projet San Francisco, Kigali, Rwanda
| | - Julien Nyombayire
- Rwanda Zambia Health Research Group, Department of Pathology & Laboratory Medicine, School of Medicine and Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
- Projet San Francisco, Kigali, Rwanda
| | - Rosine Ingabire
- Rwanda Zambia Health Research Group, Department of Pathology & Laboratory Medicine, School of Medicine and Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
- Projet San Francisco, Kigali, Rwanda
| | - Jeannine Mukamuyango
- Rwanda Zambia Health Research Group, Department of Pathology & Laboratory Medicine, School of Medicine and Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
- Projet San Francisco, Kigali, Rwanda
| | - Rachel Parker
- Rwanda Zambia Health Research Group, Department of Pathology & Laboratory Medicine, School of Medicine and Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Ilene Brill
- Department of Epidemiology, Ryals School of Public Health, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Matt Price
- IAVI, New York, New York, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California, USA
| | - Lisa B Haddad
- Center for Biomedical Research, Population Council, New York, New York, USA
| | - Amanda Tichacek
- Rwanda Zambia Health Research Group, Department of Pathology & Laboratory Medicine, School of Medicine and Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | | | - Susan Allen
- Rwanda Zambia Health Research Group, Department of Pathology & Laboratory Medicine, School of Medicine and Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
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22
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Nyombayire J, Ingabire R, Mukamuyango J, Karita E, Mazzei A, Wall KM, Parker R, Tichacek A, Allen S, Hunter E, Price MA. Antiretroviral Therapy Use and HIV Transmission Among Discordant Couples in Nonresearch Settings in Kigali, Rwanda. Sex Transm Dis 2021; 48:424-428. [PMID: 33433171 PMCID: PMC10881059 DOI: 10.1097/olq.0000000000001350] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
BACKGROUND Antiretroviral therapy (ART) efficacy for HIV prevention among discordant couples has been demonstrated in clinical trials. Effectiveness outside of research settings is less well understood. METHODS HIV-discordant couples were enrolled in couples' testing and follow-up at 20 government clinics in Kigali from 2010 to 2014. We performed viral linkage analysis on seroconverting couples to determine infection sources (intracouple vs. extracouple). Antiretroviral therapy use in index partners was collected at baseline and during follow-up by self-report with verification of government medical records. RESULTS A total of 3777 HIV-discordant couples were identified and followed up at government health clinics. Fifty-four incident HIV infections were identified, of which 36 were confirmed linked to the index partner, 4 were unlinked, and 14 were unknown. Among the 50 linked or unknown transmission pairs, 38% occurred among couples in which the index partner was on ART (HIV incidence rate of 0.63/100 person-years), whereas 62% occurred among couples in which the index partner was not on ART (HIV incidence rate of 5.51/100 person-years; adjusted rate ratio, 6.9). HIV acquisition was higher in women than in men with non-ART using index partners (P < 0.001). CONCLUSIONS Couples in a government clinic couples' HIV testing and follow-up program in Rwanda had an 89% reduction in HIV incidence when index partners were using ART, slightly lower than efficacy estimates from randomized trials. Antiretroviral therapy for prevention should be prioritized for key populations including discordant couples identified via couples' voluntary counseling and testing, with increased efforts to improve uptake, adherence, and viral load monitoring.
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Affiliation(s)
- Julien Nyombayire
- From the Projet San Francisco, Rwanda Zambia HIV Research Group, Kigali, Rwanda
| | - Rosine Ingabire
- From the Projet San Francisco, Rwanda Zambia HIV Research Group, Kigali, Rwanda
| | | | - Etienne Karita
- From the Projet San Francisco, Rwanda Zambia HIV Research Group, Kigali, Rwanda
| | - Amelia Mazzei
- From the Projet San Francisco, Rwanda Zambia HIV Research Group, Kigali, Rwanda
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23
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Tong O, Duette G, O’Neil TR, Royle CM, Rana H, Johnson B, Popovic N, Dervish S, Brouwer MAE, Baharlou H, Patrick E, Ctercteko G, Palmer S, Lee E, Hunter E, Harman AN, Cunningham AL, Nasr N. Plasmacytoid dendritic cells have divergent effects on HIV infection of initial target cells and induce a pro-retention phenotype. PLoS Pathog 2021; 17:e1009522. [PMID: 33872331 PMCID: PMC8084337 DOI: 10.1371/journal.ppat.1009522] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 04/29/2021] [Accepted: 04/01/2021] [Indexed: 01/12/2023] Open
Abstract
Although HIV infection inhibits interferon responses in its target cells in vitro, interferon signatures can be detected in vivo soon after sexual transmission, mainly attributed to plasmacytoid dendritic cells (pDCs). In this study, we examined the physiological contributions of pDCs to early HIV acquisition using coculture models of pDCs with myeloid DCs, macrophages and the resting central, transitional and effector memory CD4 T cell subsets. pDCs impacted infection in a cell-specific manner. In myeloid cells, HIV infection was decreased via antiviral effects, cell maturation and downregulation of CCR5 expression. In contrast, in resting memory CD4 T cells, pDCs induced a subset-specific increase in intracellular HIV p24 protein expression without any activation or increase in CCR5 expression, as measured by flow cytometry. This increase was due to reactivation rather than enhanced viral spread, as blocking HIV entry via CCR5 did not alter the increased intracellular p24 expression. Furthermore, the load and proportion of cells expressing HIV DNA were restricted in the presence of pDCs while reverse transcriptase and p24 ELISA assays showed no increase in particle associated reverse transcriptase or extracellular p24 production. In addition, pDCs also markedly induced the expression of CD69 on infected CD4 T cells and other markers of CD4 T cell tissue retention. These phenotypic changes showed marked parallels with resident memory CD4 T cells isolated from anogenital tissue using enzymatic digestion. Production of IFNα by pDCs was the main driving factor for all these results. Thus, pDCs may reduce HIV spread during initial mucosal acquisition by inhibiting replication in myeloid cells while reactivating latent virus in resting memory CD4 T cells and retaining them for immune clearance. IFNs constitute one of the first and most important innate immune controls to restrict initial viral replication and spread. As HIV has evolved mechanisms to block IFN-I induction in its target cells, but not in infiltrating pDCs, understanding how pDCs influence HIV infection of target cells upon initial transmission is critical to prevent or control initial infection. Therefore, we modelled the early events occurring immediately as HIV enters the human genital mucosa. We showed that IFNα secreting pDC compensated for HIV inhibition of IFN-I production in its target cells in two different ways: i) reduced infection in DCs and macrophages which would limit viral spread to resident or newly infiltrating memory CD4 T cells; ii) reactivation of latent HIV in all subsets of resting memory CD4 T cell subsets, accompanied by limited viral spread, upregulation of MHC-I and induction of a tissue retention phenotype. The increased HIV protein, MHC-I expression and retention may enhance exposure to CD8 T cell surveillance. This model suggests that IFNα reactivation of latent HIV combined with adoptive immunotherapy using CD8 T cells or those expressing chimeric antigen receptors (CAR) could provide a novel ‘kick and kill’ approach to eradicate HIV reservoirs.
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Affiliation(s)
- Orion Tong
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, New South Wales, Australia
- The University of Sydney, Faculty of Medicine and Health, Sydney, New South Wales, Australia
| | - Gabriel Duette
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, New South Wales, Australia
| | - Thomas R. O’Neil
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, New South Wales, Australia
- The University of Sydney, Faculty of Medicine and Health, Sydney, New South Wales, Australia
| | - Caroline M. Royle
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, New South Wales, Australia
| | - Hafsa Rana
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, New South Wales, Australia
- The University of Sydney, Faculty of Medicine and Health, Sydney, New South Wales, Australia
| | - Blake Johnson
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, New South Wales, Australia
- The University of Sydney, Faculty of Medicine and Health, Sydney, New South Wales, Australia
| | - Nicole Popovic
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, New South Wales, Australia
- The University of Sydney, Faculty of Medicine and Health, Sydney, New South Wales, Australia
| | - Suat Dervish
- Westmead research Hub, The Westmead Institute for Medical Research, Westmead, New South Wales, Australia
| | - Michelle A. E. Brouwer
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, New South Wales, Australia
- Department of Internal Medicine, Radboud Centre for Infectious Diseases, Radboud Institute of Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Heeva Baharlou
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, New South Wales, Australia
- The University of Sydney, Faculty of Medicine and Health, Sydney, New South Wales, Australia
| | - Ellis Patrick
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, New South Wales, Australia
- The University of Sydney, School of Mathematics and Statistics, Faculty of Science, Sydney, New South Wales, Australia
| | - Grahame Ctercteko
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, New South Wales, Australia
- Westmead Hospital, Westmead, New South Wales, Australia
| | - Sarah Palmer
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, New South Wales, Australia
- The University of Sydney, Faculty of Medicine and Health, Sydney, New South Wales, Australia
| | - Eunok Lee
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, New South Wales, Australia
| | - Eric Hunter
- Emory Vaccine Centre, Atlanta, Georgia, United States of America
| | - Andrew N. Harman
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, New South Wales, Australia
- The University of Sydney, School of Medical Sciences, Faculty of Medicine and Health, Sydney, New South Wales, Australia
| | - Anthony L. Cunningham
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, New South Wales, Australia
- The University of Sydney, Faculty of Medicine and Health, Sydney, New South Wales, Australia
- * E-mail: (ALC); (NN)
| | - Najla Nasr
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, New South Wales, Australia
- The University of Sydney, School of Medical Sciences, Faculty of Medicine and Health, Sydney, New South Wales, Australia
- * E-mail: (ALC); (NN)
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24
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Rhodes JW, Botting RA, Bertram KM, Vine EE, Rana H, Baharlou H, Vegh P, O'Neil TR, Ashhurst AS, Fletcher J, Parnell GP, Graham JD, Nasr N, Lim JJK, Barnouti L, Haertsch P, Gosselink MP, Di Re A, Reza F, Ctercteko G, Jenkins GJ, Brooks AJ, Patrick E, Byrne SN, Hunter E, Haniffa MA, Cunningham AL, Harman AN. Human anogenital monocyte-derived dendritic cells and langerin+cDC2 are major HIV target cells. Nat Commun 2021; 12:2147. [PMID: 33846309 PMCID: PMC8042121 DOI: 10.1038/s41467-021-22375-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 03/12/2021] [Indexed: 02/06/2023] Open
Abstract
Tissue mononuclear phagocytes (MNP) are specialised in pathogen detection and antigen presentation. As such they deliver HIV to its primary target cells; CD4 T cells. Most MNP HIV transmission studies have focused on epithelial MNPs. However, as mucosal trauma and inflammation are now known to be strongly associated with HIV transmission, here we examine the role of sub-epithelial MNPs which are present in a diverse array of subsets. We show that HIV can penetrate the epithelial surface to interact with sub-epithelial resident MNPs in anogenital explants and define the full array of subsets that are present in the human anogenital and colorectal tissues that HIV may encounter during sexual transmission. In doing so we identify two subsets that preferentially take up HIV, become infected and transmit the virus to CD4 T cells; CD14+CD1c+ monocyte-derived dendritic cells and langerin-expressing conventional dendritic cells 2 (cDC2).
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Affiliation(s)
- Jake W Rhodes
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, NSW, Australia.,Westmead Clinical School, Faculty of Medicine and Health Sydney, The University of Sydney, Westmead, NSW, Australia
| | - Rachel A Botting
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, NSW, Australia.,Westmead Clinical School, Faculty of Medicine and Health Sydney, The University of Sydney, Westmead, NSW, Australia.,Biosciences Institute, The University of Newcastle, Newcastle upon Tyne, UK
| | - Kirstie M Bertram
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, NSW, Australia.,Westmead Clinical School, Faculty of Medicine and Health Sydney, The University of Sydney, Westmead, NSW, Australia
| | - Erica E Vine
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, NSW, Australia.,Westmead Clinical School, Faculty of Medicine and Health Sydney, The University of Sydney, Westmead, NSW, Australia
| | - Hafsa Rana
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, NSW, Australia.,Westmead Clinical School, Faculty of Medicine and Health Sydney, The University of Sydney, Westmead, NSW, Australia
| | - Heeva Baharlou
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, NSW, Australia.,Westmead Clinical School, Faculty of Medicine and Health Sydney, The University of Sydney, Westmead, NSW, Australia
| | - Peter Vegh
- Biosciences Institute, The University of Newcastle, Newcastle upon Tyne, UK
| | - Thomas R O'Neil
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, NSW, Australia.,Westmead Clinical School, Faculty of Medicine and Health Sydney, The University of Sydney, Westmead, NSW, Australia
| | - Anneliese S Ashhurst
- School of Medical Sciences, Faculty of Medicine and Health Sydney, The University of Sydney, Westmead, NSW, Australia
| | - James Fletcher
- Biosciences Institute, The University of Newcastle, Newcastle upon Tyne, UK
| | - Grant P Parnell
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, NSW, Australia.,Westmead Clinical School, Faculty of Medicine and Health Sydney, The University of Sydney, Westmead, NSW, Australia
| | - J Dinny Graham
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, NSW, Australia.,Westmead Clinical School, Faculty of Medicine and Health Sydney, The University of Sydney, Westmead, NSW, Australia
| | - Najla Nasr
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, NSW, Australia.,School of Medical Sciences, Faculty of Medicine and Health Sydney, The University of Sydney, Westmead, NSW, Australia
| | | | | | - Peter Haertsch
- Burns Unit, Concord Repatriation General Hospital, Sydney, Australia
| | - Martijn P Gosselink
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, NSW, Australia.,Department of Colorectal Surgery, Westmead Hospital, Westmead, NSW, Australia
| | - Angelina Di Re
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, NSW, Australia.,Department of Colorectal Surgery, Westmead Hospital, Westmead, NSW, Australia
| | - Faizur Reza
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, NSW, Australia.,Department of Colorectal Surgery, Westmead Hospital, Westmead, NSW, Australia
| | - Grahame Ctercteko
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, NSW, Australia.,Department of Colorectal Surgery, Westmead Hospital, Westmead, NSW, Australia
| | - Gregory J Jenkins
- Department of Obstetrics and Gynaecology, Westmead Hospital, Westmead, NSW, Australia
| | - Andrew J Brooks
- Department of Urology, Westmead Hospital, Westmead, NSW, Australia
| | - Ellis Patrick
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, NSW, Australia.,School of Maths and Statistics, Faculty of Science, The University of Sydney, Camperdown, NSW, Australia
| | - Scott N Byrne
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, NSW, Australia.,School of Medical Sciences, Faculty of Medicine and Health Sydney, The University of Sydney, Westmead, NSW, Australia
| | | | - Muzlifah A Haniffa
- Biosciences Institute, The University of Newcastle, Newcastle upon Tyne, UK.,Wellcome Sanger Institute, Hinxton, UK.,Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Anthony L Cunningham
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, NSW, Australia.,Westmead Clinical School, Faculty of Medicine and Health Sydney, The University of Sydney, Westmead, NSW, Australia
| | - Andrew N Harman
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, NSW, Australia. .,School of Medical Sciences, Faculty of Medicine and Health Sydney, The University of Sydney, Westmead, NSW, Australia.
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25
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Baker CJ, Bertsche W, Capra A, Carruth C, Cesar CL, Charlton M, Christensen A, Collister R, Mathad AC, Eriksson S, Evans A, Evetts N, Fajans J, Friesen T, Fujiwara MC, Gill DR, Grandemange P, Granum P, Hangst JS, Hardy WN, Hayden ME, Hodgkinson D, Hunter E, Isaac CA, Johnson MA, Jones JM, Jones SA, Jonsell S, Khramov A, Knapp P, Kurchaninov L, Madsen N, Maxwell D, McKenna JTK, Menary S, Michan JM, Momose T, Mullan PS, Munich JJ, Olchanski K, Olin A, Peszka J, Powell A, Pusa P, Rasmussen CØ, Robicheaux F, Sacramento RL, Sameed M, Sarid E, Silveira DM, Starko DM, So C, Stutter G, Tharp TD, Thibeault A, Thompson RI, van der Werf DP, Wurtele JS. Laser cooling of antihydrogen atoms. Nature 2021; 592:35-42. [PMID: 33790445 PMCID: PMC8012212 DOI: 10.1038/s41586-021-03289-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 01/26/2021] [Indexed: 11/08/2022]
Abstract
The photon-the quantum excitation of the electromagnetic field-is massless but carries momentum. A photon can therefore exert a force on an object upon collision1. Slowing the translational motion of atoms and ions by application of such a force2,3, known as laser cooling, was first demonstrated 40 years ago4,5. It revolutionized atomic physics over the following decades6-8, and it is now a workhorse in many fields, including studies on quantum degenerate gases, quantum information, atomic clocks and tests of fundamental physics. However, this technique has not yet been applied to antimatter. Here we demonstrate laser cooling of antihydrogen9, the antimatter atom consisting of an antiproton and a positron. By exciting the 1S-2P transition in antihydrogen with pulsed, narrow-linewidth, Lyman-α laser radiation10,11, we Doppler-cool a sample of magnetically trapped antihydrogen. Although we apply laser cooling in only one dimension, the trap couples the longitudinal and transverse motions of the anti-atoms, leading to cooling in all three dimensions. We observe a reduction in the median transverse energy by more than an order of magnitude-with a substantial fraction of the anti-atoms attaining submicroelectronvolt transverse kinetic energies. We also report the observation of the laser-driven 1S-2S transition in samples of laser-cooled antihydrogen atoms. The observed spectral line is approximately four times narrower than that obtained without laser cooling. The demonstration of laser cooling and its immediate application has far-reaching implications for antimatter studies. A more localized, denser and colder sample of antihydrogen will drastically improve spectroscopic11-13 and gravitational14 studies of antihydrogen in ongoing experiments. Furthermore, the demonstrated ability to manipulate the motion of antimatter atoms by laser light will potentially provide ground-breaking opportunities for future experiments, such as anti-atomic fountains, anti-atom interferometry and the creation of antimatter molecules.
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Affiliation(s)
- C J Baker
- Department of Physics, College of Science, Swansea University, Swansea, UK
| | - W Bertsche
- School of Physics and Astronomy, University of Manchester, Manchester, UK
- Cockcroft Institute, Sci-Tech Daresbury, Warrington, UK
| | - A Capra
- TRIUMF, Vancouver, British Columbia, Canada
| | - C Carruth
- Department of Physics, University of California at Berkeley, Berkeley, CA, USA
| | - C L Cesar
- Instituto de Fisica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - M Charlton
- Department of Physics, College of Science, Swansea University, Swansea, UK
| | - A Christensen
- Department of Physics, University of California at Berkeley, Berkeley, CA, USA
| | | | - A Cridland Mathad
- Department of Physics, College of Science, Swansea University, Swansea, UK
| | - S Eriksson
- Department of Physics, College of Science, Swansea University, Swansea, UK
| | - A Evans
- Department of Physics and Astronomy, University of Calgary, Calgary, Alberta, Canada
| | - N Evetts
- Department of Physics and Astronomy, University of British Columbia, Vancouver, British Columbia, Canada
| | - J Fajans
- Department of Physics, University of California at Berkeley, Berkeley, CA, USA
| | - T Friesen
- Department of Physics and Astronomy, University of Calgary, Calgary, Alberta, Canada
| | | | - D R Gill
- TRIUMF, Vancouver, British Columbia, Canada
| | - P Grandemange
- TRIUMF, Vancouver, British Columbia, Canada
- Department of Physics and Astronomy, University of Calgary, Calgary, Alberta, Canada
| | - P Granum
- Department of Physics and Astronomy, Aarhus University, Aarhus, Denmark
| | - J S Hangst
- Department of Physics and Astronomy, Aarhus University, Aarhus, Denmark.
| | - W N Hardy
- Department of Physics and Astronomy, University of British Columbia, Vancouver, British Columbia, Canada
| | - M E Hayden
- Department of Physics, Simon Fraser University, Burnaby, British Columbia, Canada
| | - D Hodgkinson
- School of Physics and Astronomy, University of Manchester, Manchester, UK
| | - E Hunter
- Department of Physics, University of California at Berkeley, Berkeley, CA, USA
| | - C A Isaac
- Department of Physics, College of Science, Swansea University, Swansea, UK
| | - M A Johnson
- School of Physics and Astronomy, University of Manchester, Manchester, UK
- Cockcroft Institute, Sci-Tech Daresbury, Warrington, UK
| | - J M Jones
- Department of Physics, College of Science, Swansea University, Swansea, UK
| | - S A Jones
- Department of Physics and Astronomy, Aarhus University, Aarhus, Denmark
| | - S Jonsell
- Department of Physics, Stockholm University, Stockholm, Sweden
| | - A Khramov
- TRIUMF, Vancouver, British Columbia, Canada
- Department of Physics and Astronomy, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Physics, British Columbia Institute of Technology, Burnaby, British Columbia, Canada
| | - P Knapp
- Department of Physics, College of Science, Swansea University, Swansea, UK
| | | | - N Madsen
- Department of Physics, College of Science, Swansea University, Swansea, UK
| | - D Maxwell
- Department of Physics, College of Science, Swansea University, Swansea, UK
| | - J T K McKenna
- TRIUMF, Vancouver, British Columbia, Canada
- Department of Physics and Astronomy, Aarhus University, Aarhus, Denmark
| | - S Menary
- Department of Physics and Astronomy, York University, Toronto, Ontario, Canada
| | - J M Michan
- TRIUMF, Vancouver, British Columbia, Canada
- Department of Physics and Astronomy, University of British Columbia, Vancouver, British Columbia, Canada
| | - T Momose
- TRIUMF, Vancouver, British Columbia, Canada.
- Department of Physics and Astronomy, University of British Columbia, Vancouver, British Columbia, Canada.
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada.
| | - P S Mullan
- Department of Physics, College of Science, Swansea University, Swansea, UK
| | - J J Munich
- Department of Physics, Simon Fraser University, Burnaby, British Columbia, Canada
| | | | - A Olin
- TRIUMF, Vancouver, British Columbia, Canada
- Department of Physics and Astronomy, University of Victoria, Victoria, British Columbia, Canada
| | - J Peszka
- Department of Physics, College of Science, Swansea University, Swansea, UK
| | - A Powell
- Department of Physics, College of Science, Swansea University, Swansea, UK
- Department of Physics and Astronomy, University of Calgary, Calgary, Alberta, Canada
| | - P Pusa
- Department of Physics, University of Liverpool, Liverpool, UK
| | - C Ø Rasmussen
- Experimental Physics Department, CERN, Geneva, Switzerland
| | - F Robicheaux
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN, USA
| | - R L Sacramento
- Instituto de Fisica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - M Sameed
- School of Physics and Astronomy, University of Manchester, Manchester, UK
| | - E Sarid
- Soreq NRC, Yavne, Israel
- Department of Physics, Ben Gurion University, Beer Sheva, Israel
| | - D M Silveira
- TRIUMF, Vancouver, British Columbia, Canada
- Instituto de Fisica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - D M Starko
- Department of Physics and Astronomy, York University, Toronto, Ontario, Canada
| | - C So
- TRIUMF, Vancouver, British Columbia, Canada
| | - G Stutter
- Department of Physics and Astronomy, Aarhus University, Aarhus, Denmark
| | - T D Tharp
- Physics Department, Marquette University, Milwaukee, WI, USA
| | - A Thibeault
- TRIUMF, Vancouver, British Columbia, Canada
- Faculté de Génie, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - R I Thompson
- TRIUMF, Vancouver, British Columbia, Canada
- Department of Physics and Astronomy, University of Calgary, Calgary, Alberta, Canada
| | - D P van der Werf
- Department of Physics, College of Science, Swansea University, Swansea, UK
| | - J S Wurtele
- Department of Physics, University of California at Berkeley, Berkeley, CA, USA
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26
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McInally S, Wall K, Yu T, Tirouvanziam R, Kilembe W, Gilmour J, Allen SA, Hunter E. Elevated levels of inflammatory plasma biomarkers are associated with risk of HIV infection. Retrovirology 2021; 18:8. [PMID: 33731158 PMCID: PMC7968240 DOI: 10.1186/s12977-021-00552-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 03/06/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND To determine if individuals, from HIV-1 serodiscordant couple cohorts from Rwanda and Zambia, who become HIV-positive have a distinct inflammatory biomarker profile compared to individuals who remain HIV-negative, we compared levels of biomarkers in plasma of HIV-negative individuals who either seroconverted (pre-infection) and became HIV-positive or remained HIV-negative (uninfected). RESULTS We observed that individuals in the combined cohort, as well as those in the individual country cohorts, who later became HIV-1 infected had significantly higher baseline levels of multiple inflammatory cytokines/chemokines compared to individuals who remained HIV-negative. Genital inflammation/ulceration or schistosome infections were not associated with this elevated profile. Defined levels of ITAC and IL-7 were significant predictors of later HIV acquisition in ROC predictive analyses, whereas the classical Th1 and Th2 inflammatory cytokines such as IL-12 and interferon-γ or IL-4, IL-5 and Il-13 were not. CONCLUSIONS Overall, the data show a significant association between increased plasma biomarkers linked to inflammation and immune activation and HIV acquisition and suggests that pre-existing conditions that increase systemic biomarkers represent a factor for increased risk of HIV infection.
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Affiliation(s)
- Samantha McInally
- Emory Vaccine Center at Yerkes National Primate Research Center, Atlanta, GA, USA
| | - Kristin Wall
- Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Tianwei Yu
- School of Data Science, The Chinese University of Hong Kong, Shenzhen, Shenzhen, Guangdong Province, China
| | - Rabindra Tirouvanziam
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA.,Center of CF and Airways Disease Research, Children's Healthcare of Atlanta, Atlanta, GA, USA
| | | | - Jill Gilmour
- Faculty of Medicine, Imperial College, London, SW7 2AZ, UK
| | - Susan A Allen
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA
| | - Eric Hunter
- Emory Vaccine Center at Yerkes National Primate Research Center, Atlanta, GA, USA. .,Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA.
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27
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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28
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Price MA, Kilembe W, Ruzagira E, Karita E, Inambao M, Sanders EJ, Anzala O, Allen S, Edward VA, Kaleebu P, Fast PE, Rida W, Kamali A, Hunter E, Tang J, Lakhi S, Mutua G, Bekker LG, Abu-Baker G, Tichacek A, Chetty P, Latka MH, Maenetje P, Makkan H, Hare J, Kibengo F, Priddy F, Landais E, Chinyenze K, Gilmour J. Cohort Profile: IAVI's HIV epidemiology and early infection cohort studies in Africa to support vaccine discovery. Int J Epidemiol 2021; 50:29-30. [PMID: 32879950 PMCID: PMC7938500 DOI: 10.1093/ije/dyaa100] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/06/2020] [Indexed: 12/20/2022] Open
Affiliation(s)
- Matt A Price
- IAVI, New York, USA & Nairobi, Kenya
- Department of Epidemiology and Biostatistics, University of California at San Francisco, San Francisco, CA, USA
| | - William Kilembe
- Rwanda Zambia Emory HIV Research Group, Lusaka & Ndola, Zambia; Kigali, Rwanda
- Emory University, Atlanta, GA, USA
| | - Eugene Ruzagira
- Medical Research Council, Uganda Virus Research Institute, and London School of Hygiene and Tropical Medicine Uganda Research Unit (MULS), Entebbe & Masaka, Uganda
| | - Etienne Karita
- Rwanda Zambia Emory HIV Research Group, Lusaka & Ndola, Zambia; Kigali, Rwanda
- Emory University, Atlanta, GA, USA
| | - Mubiana Inambao
- Rwanda Zambia Emory HIV Research Group, Lusaka & Ndola, Zambia; Kigali, Rwanda
- Emory University, Atlanta, GA, USA
| | - Eduard J Sanders
- Kenyan Medical Research Institute-Wellcome Trust, Kilifi, Kenya
- Nuffield Department of Clinical Medicine, Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford, Headington, UK
| | - Omu Anzala
- KAVI-Institute of Clinical Research, Nairobi, Kenya
| | - Susan Allen
- Rwanda Zambia Emory HIV Research Group, Lusaka & Ndola, Zambia; Kigali, Rwanda
- Emory University, Atlanta, GA, USA
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA
| | - Vinodh A Edward
- The Aurum Institute, Johannesburg and Rustenburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Advancing Care and Treatment for TB/HIV, A Collaborating Centre of the South African Medical Research Council, Cape Town, South Africa
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, CT, USA
| | - Pontiano Kaleebu
- Medical Research Council, Uganda Virus Research Institute, and London School of Hygiene and Tropical Medicine Uganda Research Unit (MULS), Entebbe & Masaka, Uganda
| | - Patricia E Fast
- IAVI, New York, USA & Nairobi, Kenya
- Pediatric Infectious Diseases, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Wasima Rida
- Biostatistics Consultant, Arlington, VA, USA
| | | | - Eric Hunter
- Rwanda Zambia Emory HIV Research Group, Lusaka & Ndola, Zambia; Kigali, Rwanda
- Emory University, Atlanta, GA, USA
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA
| | - Jianming Tang
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Shabir Lakhi
- Rwanda Zambia Emory HIV Research Group, Lusaka & Ndola, Zambia; Kigali, Rwanda
- Emory University, Atlanta, GA, USA
| | | | - Linda Gail Bekker
- Desmond Tutu HIV Centre, University of Cape Town, Cape Town, South Africa
| | - Ggayi Abu-Baker
- Medical Research Council, Uganda Virus Research Institute, and London School of Hygiene and Tropical Medicine Uganda Research Unit (MULS), Entebbe & Masaka, Uganda
| | - Amanda Tichacek
- Rwanda Zambia Emory HIV Research Group, Lusaka & Ndola, Zambia; Kigali, Rwanda
- Emory University, Atlanta, GA, USA
- Department of Epidemiology, Emory University, Atlanta, GA, USA
| | | | - Mary H Latka
- The Aurum Institute, Johannesburg and Rustenburg, South Africa
| | - Pholo Maenetje
- The Aurum Institute, Johannesburg and Rustenburg, South Africa
| | - Heeran Makkan
- The Aurum Institute, Johannesburg and Rustenburg, South Africa
| | - Jonathan Hare
- IAVI Human Immunology Laboratory, Imperial College, London, UK
| | - Freddie Kibengo
- Medical Research Council, Uganda Virus Research Institute, and London School of Hygiene and Tropical Medicine Uganda Research Unit (MULS), Entebbe & Masaka, Uganda
| | | | - Elise Landais
- IAVI, New York, USA & Nairobi, Kenya
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | | | - Jill Gilmour
- IAVI Human Immunology Laboratory, Imperial College, London, UK
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29
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McGowan E, Rosenthal R, Fiore-Gartland A, Macharia G, Balinda S, Kapaata A, Umviligihozo G, Muok E, Dalel J, Streatfield CL, Coutinho H, Dilernia D, Monaco DC, Morrison D, Yue L, Hunter E, Nielsen M, Gilmour J, Hare J. Utilizing Computational Machine Learning Tools to Understand Immunogenic Breadth in the Context of a CD8 T-Cell Mediated HIV Response. Front Immunol 2021; 12:609884. [PMID: 33679745 PMCID: PMC7930081 DOI: 10.3389/fimmu.2021.609884] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 01/28/2021] [Indexed: 11/13/2022] Open
Abstract
Predictive models are becoming more and more commonplace as tools for candidate antigen discovery to meet the challenges of enabling epitope mapping of cohorts with diverse HLA properties. Here we build on the concept of using two key parameters, diversity metric of the HLA profile of individuals within a population and consideration of sequence diversity in the context of an individual's CD8 T-cell immune repertoire to assess the HIV proteome for defined regions of immunogenicity. Using this approach, analysis of HLA adaptation and functional immunogenicity data enabled the identification of regions within the proteome that offer significant conservation, HLA recognition within a population, low prevalence of HLA adaptation and demonstrated immunogenicity. We believe this unique and novel approach to vaccine design as a supplement to vitro functional assays, offers a bespoke pipeline for expedited and rational CD8 T-cell vaccine design for HIV and potentially other pathogens with the potential for both global and local coverage.
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Affiliation(s)
- Ed McGowan
- IAVI Human Immunology Laboratory, Imperial College, London, United Kingdom
| | - Rachel Rosenthal
- Cancer Evolution and Genome Instability Laboratory, Francis Crick Institute, London, United Kingdom
| | - Andrew Fiore-Gartland
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Gladys Macharia
- IAVI Human Immunology Laboratory, Imperial College, London, United Kingdom
| | - Sheila Balinda
- Medical Research Council/Uganda Virus Research Institute (MRC/UVRI) and London School of Health and Tropical Medicine (LSHTM), Uganda Research Unit, Entebbe, Uganda
| | - Anne Kapaata
- Medical Research Council/Uganda Virus Research Institute (MRC/UVRI) and London School of Health and Tropical Medicine (LSHTM), Uganda Research Unit, Entebbe, Uganda
| | - Gisele Umviligihozo
- Project San Francisco (PSF) Center for Family Health Research (CFHR), Kigali, Rwanda
| | - Erick Muok
- Project San Francisco (PSF) Center for Family Health Research (CFHR), Kigali, Rwanda
| | - Jama Dalel
- IAVI Human Immunology Laboratory, Imperial College, London, United Kingdom
| | | | - Helen Coutinho
- IAVI Human Immunology Laboratory, Imperial College, London, United Kingdom
| | - Dario Dilernia
- Emory Vaccine Center, Emory University, Atlanta, GA, United States
| | | | | | - Ling Yue
- Emory Vaccine Center, Emory University, Atlanta, GA, United States
| | - Eric Hunter
- Emory Vaccine Center, Emory University, Atlanta, GA, United States
| | - Morten Nielsen
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Jill Gilmour
- IAVI Human Immunology Laboratory, Imperial College, London, United Kingdom
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30
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Charles TP, Burton SL, Arunachalam PS, Cottrell CA, Sewall LM, Bollimpelli VS, Gangadhara S, Dey AK, Ward AB, Shaw GM, Hunter E, Amara RR, Pulendran B, van Gils MJ, Derdeyn CA. The C3/465 glycan hole cluster in BG505 HIV-1 envelope is the major neutralizing target involved in preventing mucosal SHIV infection. PLoS Pathog 2021; 17:e1009257. [PMID: 33556148 PMCID: PMC7895394 DOI: 10.1371/journal.ppat.1009257] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 02/19/2021] [Accepted: 12/23/2020] [Indexed: 01/08/2023] Open
Abstract
Stabilized HIV-1 envelope (Env) trimers elicit tier 2 autologous neutralizing antibody (nAb) responses in immunized animals. We previously demonstrated that BG505 SOSIP.664.T332N gp140 (BG505 SOSIP) immunization of rhesus macaques (RM) provided robust protection against autologous intra-vaginal simian-human immunodeficiency virus (SHIV) challenge that was predicted by high serum nAb titers. Here, we show that nAb in these protected RM targeted a glycan hole proximal to residue 465 in gp120 in all cases. nAb also targeted another glycan hole at residues 241/289 and an epitope in V1 at varying frequencies. Non-neutralizing antibodies directed at N611-shielded epitopes in gp41 were also present but were more prevalent in RM with low nAb titers. Longitudinal analysis demonstrated that nAb broadened in some RM during sequential immunization but remained focused in others, the latter being associated with increases in nAb titer. Thirty-eight monoclonal antibodies (mAbs) isolated from a protected RM with an exceptionally high serum neutralization titer bound to the trimer in ELISA, and four of the mAbs potently neutralized the BG505 Env pseudovirus (PV) and SHIV. The four neutralizing mAbs were clonally related and targeted the 465 glycan hole to varying degrees, mimicking the serum. The data demonstrate that the C3/465 glycan hole cluster was the dominant neutralization target in high titer protected RM, despite other co-circulating neutralizing and non-neutralizing specificities. The isolation of a neutralizing mAb family argues that clonotype expansion occurred during BG505 SOSIP immunization, leading to high titer, protective nAb and setting a desirable benchmark for HIV vaccines.
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Affiliation(s)
- Tysheena P. Charles
- Emory Vaccine Center, Emory University, Atlanta, Georgia, United States of America
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Samantha L. Burton
- Emory Vaccine Center, Emory University, Atlanta, Georgia, United States of America
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Prabhu S. Arunachalam
- Departments of Pathology, and Microbiology and Immunology, Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, California, United States of America
| | - Christopher A. Cottrell
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Leigh M. Sewall
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Venkata S. Bollimpelli
- Emory Vaccine Center, Emory University, Atlanta, Georgia, United States of America
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Sailaja Gangadhara
- Emory Vaccine Center, Emory University, Atlanta, Georgia, United States of America
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Antu K. Dey
- International AIDS Vaccine Initiative, New York, New York, United States of America
| | - Andrew B. Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - George M. Shaw
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Eric Hunter
- Emory Vaccine Center, Emory University, Atlanta, Georgia, United States of America
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Rama R. Amara
- Emory Vaccine Center, Emory University, Atlanta, Georgia, United States of America
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
- Department of Microbiology and Immunology, Emory University, Atlanta, Georgia, United States of America
| | - Bali Pulendran
- Departments of Pathology, and Microbiology and Immunology, Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, California, United States of America
| | - Marit J. van Gils
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- * E-mail: (MJVG); (CAD)
| | - Cynthia A. Derdeyn
- Emory Vaccine Center, Emory University, Atlanta, Georgia, United States of America
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, United States of America
- * E-mail: (MJVG); (CAD)
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31
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Michelo CM, Dalel JA, Hayes P, Fernandez N, Fiore-Gartland A, Kilembe W, Tang J, Streatfield C, Gilmour J, Hunter E. Comprehensive epitope mapping using polyclonally expanded human CD8 T cells and a two-step ELISpot assay for testing large peptide libraries. J Immunol Methods 2021; 491:112970. [PMID: 33529681 DOI: 10.1016/j.jim.2021.112970] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 11/30/2020] [Accepted: 01/18/2021] [Indexed: 02/01/2023]
Abstract
The genetic diversity of circulating HIV-1 strains poses a major barrier to the design, development and evaluation of HIV-1 vaccines. The assessment of both vaccine- and natural infection-elicited T cell responses is commonly done with multivalent peptides that are designed to maximally capture the diversity of potential T cell epitopes (PTEs) observed in natural circulating sequences. However, depending on the sequence diversity of viral subtypes and number of the HIV immunogens under investigation, PTE estimates, including HLA-guided computational methods, can easily generate enormous peptide libraries. Evaluation of T cell epitope specificity using such extensive peptide libraries is usually limited by sample availability, even for high-throughput and robust epitope mapping techniques like ELISpot assays. Here we describe a novel, two-step protocol for in-vitro polyclonal expansion of CD8 T cells from a single vial of frozen PBMC, which facilitated the screening 441 HIV-1 Gag peptides for immune responses among 32 HIV-1 positive subjects and 40 HIV-1 negative subjects for peptide qualification. Using a pooled-peptide mapping strategy, epitopes were mapped in two sequential ELISpot assays; the first ELISpot screened 33 large peptide pools using CD8 T cells expanded for 7 days, while the second step tested pool-matrix peptides to identify individual peptides using CD8 T cells expanded for 10 days. This comprehensive epitope screening established the breadth and magnitude of HIV-1 Gag-specific CD8 T cells and further revealed the extent of immune responses to variable/polymorphic epitopes.
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Affiliation(s)
- Clive M Michelo
- Zambia Emory HIV Research Project, B22/737 Mwembelelo, Emmasdale, Lusaka, Zambia
| | - Jama A Dalel
- Human Immunology Laboratory, International AIDS Vaccine Initiative, Imperial College London, London, United Kingdom
| | - Peter Hayes
- Human Immunology Laboratory, International AIDS Vaccine Initiative, Imperial College London, London, United Kingdom
| | - Natalia Fernandez
- Human Immunology Laboratory, International AIDS Vaccine Initiative, Imperial College London, London, United Kingdom
| | - Andrew Fiore-Gartland
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - William Kilembe
- Zambia Emory HIV Research Project, B22/737 Mwembelelo, Emmasdale, Lusaka, Zambia
| | - Jianming Tang
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Claire Streatfield
- Human Immunology Laboratory, International AIDS Vaccine Initiative, Imperial College London, London, United Kingdom
| | - Jill Gilmour
- Human Immunology Laboratory, International AIDS Vaccine Initiative, Imperial College London, London, United Kingdom
| | - Eric Hunter
- Zambia Emory HIV Research Project, B22/737 Mwembelelo, Emmasdale, Lusaka, Zambia; Emory Vaccine Center, Yerkes National Primate Research Center, 954 Gatewood Road NE, Atlanta, GA 30329, USA.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Monaco DC, Zapata L, Hunter E, Salomon H, Dilernia DA. Resistance profile of HIV-1 quasispecies in patients under treatment failure using single molecule, real-time sequencing. AIDS 2020; 34:2201-2210. [PMID: 33196493 DOI: 10.1097/qad.0000000000002697] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
OBJECTIVE Short-read next-generation sequencing (NGS) has been implemented to study the resistance profile of HIV as it provides a higher sensitivity than Sanger sequencing. However, short-reads only generates a consensus view of the viral population rather than a reconstruction of the viral haplotypes. In this study, we evaluated the resistance profile of HIV quasispecies in patients undergoing treatment failure using SMRT sequencing. DESIGN Whole-pol RT-PCR was performed on viral RNA extracted from plasma samples of 38 HIV-positive individuals undergoing treatment failure, and sequenced in the RSII instrument. Error correction and viral haplotype phasing was performed with the Multilayer Directed Phasing and Sequencing (MDPSeq) algorithm. Presence of resistance mutations reported by the IAS-USA in 2017 was assessed using an in-house script. RESULTS The SMRT sequencing-based test detected 131/134 resistance mutations previously detected using a Sanger sequencing-based test. However, the SMRT test also identified seven additional mutations present at an estimated frequency lower than 30%. The intra-host phylogenetic analysis showed that seven samples harbored at least one resistance variant at 20--80% frequency. The haplotype-resolved sequencing revealed viral diversification and selection of new resistance during suboptimal treatment, an overall trend toward selection and accumulation of new resistance mutations, as well as the co-existence of resistant and susceptible variants. CONCLUSION Our results validate the SMRT sequencing-based test for detection of HIV drug resistance. In addition, this method unraveled the complex dynamic of HIV quasispecies during treatment failure, which might have several implications on clinical management.
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Affiliation(s)
| | - Lucas Zapata
- Institute of Biomedical Investigations in Retrovirus and AIDS (INBIRS), School of Medicine, University of Buenos Aires, Buenos Aires, Argentina
| | - Eric Hunter
- Emory Vaccine Center, Emory University, Atlanta, Georgia, USA
- Department of Pathology, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Horacio Salomon
- Institute of Biomedical Investigations in Retrovirus and AIDS (INBIRS), School of Medicine, University of Buenos Aires, Buenos Aires, Argentina
| | - Dario A Dilernia
- Emory Vaccine Center, Emory University, Atlanta, Georgia, USA
- Department of Pathology, School of Medicine, Emory University, Atlanta, Georgia, USA
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34
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Hunter E, Stander M, Kossmann J, Chakraborty S, Prince S, Peters S, Loedolff B. Toward the identification of a phytocannabinoid-like compound in the flowers of a South African medicinal plant (Leonotis leonurus). BMC Res Notes 2020; 13:522. [PMID: 33172494 PMCID: PMC7653773 DOI: 10.1186/s13104-020-05372-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 10/31/2020] [Indexed: 01/01/2023] Open
Abstract
OBJECTIVE Current global trends on natural therapeutics suggest an increasing market interest toward the use and discovery of new plant-derived therapeutic compounds, often referred to as traditional medicine (TM). The Cannabis industry is currently one such focal area receiving attention, owing to the occurrence of phytocannabinoids (pCBs) which have shown promise in health-promotion and disease prevention. However, the occurrence of pCBs in other plant species are often overlooked and rarely studied. Leonotis leonurus (L.) R. Br. is endemic to South Africa with a rich history of use in TM practices amongst indigenous people and, has been recorded to induce mild psychoactive effects akin to Cannabis. While the leaves have been well-reported to contain therapeutic phytochemicals, little information exists on the flowers. Consequently, as part of a larger research venture, we targeted the flowers of L. leonurus for the identification of potential pCB or pCB-like compounds. RESULTS Flower extracts were separated and analyzed using high performance thin layer chromatography (HPTLC). A single pCB candidate was isolated from HPTLC plates and, using liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS), we could successfully group this compound as a fatty amide and tentatively identified as 7,10,13,16-Docosatetraenoylethanolamine (adrenoyl-EA), a known bioactive compound.
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Affiliation(s)
- E. Hunter
- Department of Genetics, Institute of Plant Biotechnology, Faculty of AgriSciences, Stellenbosch University, Stellenbosch, South Africa
| | - M. Stander
- Central Analytical Facilities, Stellenbosch University, Stellenbosch, South Africa
| | - J. Kossmann
- Department of Genetics, Institute of Plant Biotechnology, Faculty of AgriSciences, Stellenbosch University, Stellenbosch, South Africa
| | - S. Chakraborty
- Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - S. Prince
- Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - S. Peters
- Department of Genetics, Institute of Plant Biotechnology, Faculty of AgriSciences, Stellenbosch University, Stellenbosch, South Africa
| | - Bianke Loedolff
- Department of Genetics, Institute of Plant Biotechnology, Faculty of AgriSciences, Stellenbosch University, Stellenbosch, South Africa
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Chamcha V, Reddy PBJ, Kannanganat S, Wilkins C, Gangadhara S, Velu V, Green R, Law GL, Chang J, Bowen JR, Kozlowski PA, Lifton M, Santra S, Legere T, Chea LS, Chennareddi L, Yu T, Suthar MS, Silvestri G, Derdeyn CA, Gale M, Villinger F, Hunter E, Amara RR. Strong T H1-biased CD4 T cell responses are associated with diminished SIV vaccine efficacy. Sci Transl Med 2020; 11:11/519/eaav1800. [PMID: 31748228 DOI: 10.1126/scitranslmed.aav1800] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 04/07/2019] [Accepted: 09/13/2019] [Indexed: 12/18/2022]
Abstract
Activated CD4 T cells are a major target of HIV infection. Results from the STEP HIV vaccine trial highlighted a potential role for total activated CD4 T cells in promoting HIV acquisition. However, the influence of vaccine insert-specific CD4 T cell responses on HIV acquisition is not known. Here, using the data obtained from four macaque studies, we show that the DNA prime/modified vaccinia Ankara boost vaccine induced interferon γ (IFNγ+) CD4 T cells [T helper 1 (TH1) cells] rapidly migrate to multiple tissues including colon, cervix, and vaginal mucosa. These mucosal TH1 cells persisted at higher frequencies and expressed higher density of CCR5, a viral coreceptor, compared to cells in blood. After intravaginal or intrarectal simian immunodeficiency virus (SIV)/simian-human immunodeficiency virus (SHIV) challenges, strong vaccine protection was evident only in animals that had lower frequencies of vaccine-specific TH1 cells but not in animals that had higher frequencies of TH1 cells, despite comparable vaccine-induced humoral and CD8 T cell immunity in both groups. An RNA transcriptome signature in blood at 7 days after priming immunization from one study was associated with induction of fewer TH1-type CD4 cells and enhanced protection. These results demonstrate that high and persisting frequencies of HIV vaccine-induced TH1-biased CD4 T cells in the intestinal and genital mucosa can mitigate beneficial effects of protective antibodies and CD8 T cells, highlighting a critical role of priming immunization and vaccine adjuvants in modulating HIV vaccine efficacy.
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Affiliation(s)
- Venkateswarlu Chamcha
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA.,Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Pradeep B J Reddy
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA.,Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Sunil Kannanganat
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA.,Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Courtney Wilkins
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington School of Medicine, Seattle, WA 981909, USA
| | - Sailaja Gangadhara
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA.,Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Vijayakumar Velu
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA.,Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Richard Green
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington School of Medicine, Seattle, WA 981909, USA
| | - G Lynn Law
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington School of Medicine, Seattle, WA 981909, USA
| | - Jean Chang
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington School of Medicine, Seattle, WA 981909, USA
| | - James R Bowen
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA.,Division of Infectious Diseases, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Pamela A Kozlowski
- Department of Microbiology, Immunology and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
| | - Michelle Lifton
- Harvard Medical School, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Sampa Santra
- Harvard Medical School, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Traci Legere
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Lynette S Chea
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA.,Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Lakshmi Chennareddi
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA.,Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Tianwei Yu
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA 30322, USA
| | - Mehul S Suthar
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA.,Division of Infectious Diseases, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Guido Silvestri
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA.,Department of Pathology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Cynthia A Derdeyn
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA.,Department of Pathology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Michael Gale
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington School of Medicine, Seattle, WA 981909, USA
| | - Francois Villinger
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA.,Department of Pathology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Eric Hunter
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA.,Department of Pathology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Rama Rao Amara
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA. .,Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
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Macharia GN, Yue L, Staller E, Dilernia D, Wilkins D, Song H, McGowan E, King D, Fast P, Imami N, Price MA, Sanders EJ, Hunter E, Gilmour J. Infection with multiple HIV-1 founder variants is associated with lower viral replicative capacity, faster CD4+ T cell decline and increased immune activation during acute infection. PLoS Pathog 2020; 16:e1008853. [PMID: 32886726 PMCID: PMC7498102 DOI: 10.1371/journal.ppat.1008853] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 09/17/2020] [Accepted: 08/03/2020] [Indexed: 02/07/2023] Open
Abstract
HIV-1 transmission is associated with a severe bottleneck in which a limited number of variants from a pool of genetically diverse quasispecies establishes infection. The IAVI protocol C cohort of discordant couples, female sex workers, other heterosexuals and men who have sex with men (MSM) present varying risks of HIV infection, diverse HIV-1 subtypes and represent a unique opportunity to characterize transmitted/founder viruses (TF) where disease outcome is known. To identify the TF, the HIV-1 repertoire of 38 MSM participants' samples was sequenced close to transmission (median 21 days post infection, IQR 18-41) and assessment of multivariant infection done. Patient derived gag genes were cloned into an NL4.3 provirus to generate chimeric viruses which were characterized for replicative capacity (RC). Finally, an evaluation of how the TF virus predicted disease progression and modified the immune response at both acute and chronic HIV-1 infection was done. There was higher prevalence of multivariant infection compared with previously described heterosexual cohorts. A link was identified between multivariant infection and replicative capacity conferred by gag, whereby TF gag tended to be of lower replicative capacity in multivariant infection (p = 0.02) suggesting an overall lowering of fitness requirements during infection with multiple variants. Notwithstanding, multivariant infection was associated with rapid CD4+ T cell decline and perturbances in the CD4+ T cell and B cell compartments compared to single variant infection, which were reversible upon control of viremia. Strategies aimed at identifying and mitigating multivariant infection could contribute toward improving HIV-1 prognosis and this may involve strategies that tighten the stringency of the transmission bottleneck such as treatment of STI. Furthermore, the sequences and chimeric viruses help with TF based experimental vaccine immunogen design and can be used in functional assays to probe effective immune responses against TF.
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Affiliation(s)
- Gladys N. Macharia
- Department of Medicine, Imperial College London, London, United Kingdom
- IAVI Human Immunology Laboratory, London, United Kingdom
| | - Ling Yue
- Emory Vaccine Centre, Yerkes National Primate Research Centre, Emory University, Atlanta, GA, United States of America
| | - Ecco Staller
- Department of Medicine, Imperial College London, London, United Kingdom
- IAVI Human Immunology Laboratory, London, United Kingdom
| | - Dario Dilernia
- Emory Vaccine Centre, Yerkes National Primate Research Centre, Emory University, Atlanta, GA, United States of America
| | - Daniel Wilkins
- Emory Vaccine Centre, Yerkes National Primate Research Centre, Emory University, Atlanta, GA, United States of America
| | - Heeyah Song
- Emory Vaccine Centre, Yerkes National Primate Research Centre, Emory University, Atlanta, GA, United States of America
| | - Edward McGowan
- Department of Medicine, Imperial College London, London, United Kingdom
- IAVI Human Immunology Laboratory, London, United Kingdom
| | - Deborah King
- Department of Medicine, Imperial College London, London, United Kingdom
- IAVI Human Immunology Laboratory, London, United Kingdom
| | - Pat Fast
- IAVI, New York, NY, United States of America
| | - Nesrina Imami
- Department of Medicine, Imperial College London, London, United Kingdom
| | - Matthew A. Price
- IAVI, New York, NY, United States of America
- Department of Epidemiology and Biostatistics, University of California at San Francisco, San Francisco, CA, United States of America
| | - Eduard J. Sanders
- Kenya Medical Research Institute-Wellcome Trust, Kilifi, Kenya
- Nuffield Department of Clinical Medicine, Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford, Headington, United Kingdom
| | - Eric Hunter
- Emory Vaccine Centre, Yerkes National Primate Research Centre, Emory University, Atlanta, GA, United States of America
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, United States of America
| | - Jill Gilmour
- Department of Medicine, Imperial College London, London, United Kingdom
- IAVI Human Immunology Laboratory, London, United Kingdom
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Connolly S, Wall KM, Parker R, Kilembe W, Inambao M, Visoiu AM, Sharkey T, Hunter E, Allen S. Sociodemographic factors and STIs associated with Chlamydia trachomatis and Neisseria gonorrhoeae infections in Zambian female sex workers and single mothers. Int J STD AIDS 2020; 31:364-374. [PMID: 32126947 DOI: 10.1177/0956462419894453] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Sexually transmitted infections (STIs) in women caused by Chlamydia trachomatis (CT) and/or Neisseria gonorrhoeae (NG) are epidemiologically distinct. In this study, associations with sociodemographic and clinical risk factors are explored separately for CT and NG. Multivariate logistic regression (MLR) models quantify associations between potential CT and/or NG risk factors within a cross-sectional study of high-risk women in two Zambian cities, Lusaka and Ndola. CT was associated with living in Lusaka, younger age, and literacy. Long-acting reversible contraception (LARC) was predictive of CT in Ndola, but protective in Lusaka. In Lusaka only, CT was associated with lower education and reported unprotected sex. NG was associated with younger age, lower education, concurrent Trichomonas vaginalis, bacterial vaginosis, and incident syphilis infection. Signs and symptoms were rare and not associated with either infection. CT was more prevalent, nearly 11%, compared to NG, 6.8%. The higher prevalence of CT could explain the lack of association with other STIs. The associations observed with NG could be the result of high-risk sexual networks or lack of protective immunity. Risk factors for CT and NG are distinct and may differ geographically, which should be considered when developing diagnostic tools or guiding presumptive treatment in specific populations.
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Affiliation(s)
- Sarah Connolly
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA.,Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Kristin M Wall
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA.,Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA
| | - Rachel Parker
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA.,Zambia-Emory HIV Research Project, Lusaka, Zambia
| | | | | | | | | | - Eric Hunter
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA.,Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA
| | - Susan Allen
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA.,Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA.,Zambia-Emory HIV Research Project, Lusaka, Zambia
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38
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El-Badry E, Macharia G, Claiborne D, Brooks K, Dilernia DA, Goepfert P, Kilembe W, Allen S, Gilmour J, Hunter E. Better Viral Control despite Higher CD4 + T Cell Activation during Acute HIV-1 Infection in Zambian Women Is Linked to the Sex Hormone Estradiol. J Virol 2020; 94:e00758-20. [PMID: 32461316 PMCID: PMC7394904 DOI: 10.1128/jvi.00758-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 05/19/2020] [Indexed: 02/06/2023] Open
Abstract
The influence of biological sex on disease progression in HIV-1-infected individuals has been focused on the chronic stage of infection, but little is known about how sex differences influence acute HIV-1 infection. We observed profound differences in viral load and CD4+ T cell activation from the earliest time points in men and women in a Zambian heterosexual acute infection cohort. Women exhibited a >2-fold higher rate of CD4+ T cell loss despite significantly lower viral loads (VL) than men. The importance of studying acute infection was highlighted by the observation that very early in infection, women exhibited significantly higher levels of CD4+ T cell activation, a difference that was lost over the first 3 years of infection as activation in men increased. In women, activation of CD4+ T cells in the acute phase was significantly correlated with plasma levels of 17β-estradiol (E2). However, unlike in men, higher CD4+ T cell activation in women was not associated with higher VL. In contrast, a higher E2 level in early infection was associated with lower early and set-point VL in women. We attribute this to an inhibitory effect of estradiol on virus replication, which we were able to observe with relevant transmitted/founder viruses in vitro Thus, estradiol plays a key role in defining major differences between men and women during early HIV-1 infection by contributing to both viral control and CD4+ T cell loss, an effect that extends into the chronic phase of the disease.IMPORTANCE Previous studies have identified sex-specific differences during chronic HIV-1 infection, but little is known about sex differences in the acute phase, or how disparities in the initial response to the virus may affect disease. We demonstrate that restriction of viral load in women begins during acute infection and is maintained into chronic infection. Despite this, women exhibit more rapid CD4+ T cell loss than men. These profound differences are influenced by 17β-estradiol, which contributes both to T cell activation and to reduced viral replication. Thus, we conclude that estradiol plays a key role in shaping responses to early HIV-1 infection that influence the chronic phase of disease.
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Affiliation(s)
- Elina El-Badry
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - Gladys Macharia
- Department of Medicine, Imperial College London, London, United Kingdom
- International AIDS Vaccine Initiative Human Immunology Laboratory, London, United Kingdom
| | - Daniel Claiborne
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - Kelsie Brooks
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - Darío A Dilernia
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - Paul Goepfert
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | | | - Susan Allen
- Zambia-Emory HIV Research Project, Lusaka, Zambia
- Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, USA
| | - Jill Gilmour
- Department of Medicine, Imperial College London, London, United Kingdom
- International AIDS Vaccine Initiative Human Immunology Laboratory, London, United Kingdom
| | - Eric Hunter
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, USA
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Kasprowicz VO, Chopera D, Waddilove KD, Brockman MA, Gilmour J, Hunter E, Kilembe W, Karita E, Gaseitsiwe S, Sanders EJ, Ndung'u T. African-led health research and capacity building- is it working? BMC Public Health 2020; 20:1104. [PMID: 32664891 PMCID: PMC7359480 DOI: 10.1186/s12889-020-08875-3] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 05/07/2020] [Indexed: 12/29/2022] Open
Abstract
Background Africa bears a disproportionately high burden of globally significant disease but has lagged in knowledge production to address its health challenges. In this contribution, we discuss the challenges and approaches to health research capacity strengthening in sub-Saharan Africa and propose that the recent shift to an African-led approach is the most optimal. Methods and findings We introduce several capacity building approaches and recent achievements, explore why African-led research on the continent is a potentially paradigm-shifting and innovative approach, and discuss the advantages and challenges thereof. We reflect on the approaches used by the African Academy of Sciences (AAS)-funded Sub-Saharan African Network for TB/HIV Research Excellence (SANTHE) consortium as an example of an effective African-led science and capacity building programme. We recommend the following as crucial components of future efforts: 1. Directly empowering African-based researchers, 2. Offering quality training and career development opportunities to large numbers of junior African scientists and support staff, and 3. Effective information exchange and collaboration. Furthermore, we argue that long-term investment from international donors and increasing funding commitments from African governments and philanthropies will be needed to realise a critical mass of local capacity and to create and sustain world-class research hubs that will be conducive to address Africa’s intractable health challenges. Conclusions Our experiences so far suggest that African-led research has the potential to overcome the vicious cycle of brain-drain and may ultimately lead to improvement of health and science-led economic transformation of Africa into a prosperous continent.
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Affiliation(s)
- Victoria O Kasprowicz
- Africa Health Research Institute, Durban, South Africa.,HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Denis Chopera
- Africa Health Research Institute, Durban, South Africa
| | | | - Mark A Brockman
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada.,Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada.,British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | | | - Eric Hunter
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA.,Rwanda Zambia Emory HIV Research Group, Zambia; Kigali, Rwanda and Emory University, Atlanta, USA
| | - William Kilembe
- Rwanda Zambia Emory HIV Research Group, Zambia; Kigali, Rwanda and Emory University, Atlanta, USA
| | - Etienne Karita
- Rwanda Zambia Emory HIV Research Group, Zambia; Kigali, Rwanda and Emory University, Atlanta, USA
| | - Simani Gaseitsiwe
- Botswana-Harvard AIDS Institute Partnership, Gaborone, Botswana.,Department of Immunology & Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Eduard J Sanders
- Kenyan Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya.,Nuffield Department of Clinical Medicine, Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford, Headington, UK
| | - Thumbi Ndung'u
- Africa Health Research Institute, Durban, South Africa. .,HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa. .,Ragon Institute of MGH, MIT and Harvard University, Cambridge, MA, USA. .,Max Planck Institute for Infection Biology, Berlin, Germany. .,Division of Infection and Immunity, University College London, London, UK.
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Umviligihozo G, Cobarrubias KD, Chandrarathna S, Jin SW, Reddy N, Byakwaga H, Muzoora C, Bwana MB, Lee GQ, Hunt PW, Martin JN, Brumme CJ, Bangsberg DR, Karita E, Allen S, Hunter E, Ndung'u T, Brumme ZL, Brockman MA. Differential Vpu-Mediated CD4 and Tetherin Downregulation Functions among Major HIV-1 Group M Subtypes. J Virol 2020; 94:e00293-20. [PMID: 32376625 PMCID: PMC7343213 DOI: 10.1128/jvi.00293-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Accepted: 04/30/2020] [Indexed: 12/12/2022] Open
Abstract
Downregulation of BST-2/tetherin and CD4 by HIV-1 viral protein U (Vpu) promotes viral egress and allows infected cells to evade host immunity. Little is known however about the natural variability in these Vpu functions among the genetically diverse viral subtypes that contribute to the HIV-1 pandemic. We collected Vpu isolates from 332 treatment-naive individuals living with chronic HIV-1 infection in Uganda, Rwanda, South Africa, and Canada. Together, these Vpu isolates represent four major HIV-1 group M subtypes (A [n = 63], B [n = 84], C [n = 94], and D [n = 59]) plus intersubtype recombinants and uncommon strains (n = 32). The ability of each Vpu clone to downregulate endogenous CD4 and tetherin was quantified using flow cytometry following transfection into an immortalized T-cell line and compared to that of a reference Vpu clone derived from HIV-1 subtype B NL4.3. Overall, the median CD4 downregulation function of natural Vpu isolates was similar to that of NL4.3 (1.01 [interquartile range {IQR}, 0.86 to 1.18]), while the median tetherin downregulation function was moderately lower than that of NL4.3 (0.90 [0.79 to 0.97]). Both Vpu functions varied significantly among HIV-1 subtypes (Kruskal-Wallis P < 0.0001). Specifically, subtype C clones exhibited the lowest CD4 and tetherin downregulation activities, while subtype D and B clones were most functional for both activities. We also identified Vpu polymorphisms associated with CD4 or tetherin downregulation function and validated six of these using site-directed mutagenesis. Our results highlight the marked extent to which Vpu function varies among global HIV-1 strains, raising the possibility that natural variation in this accessory protein may contribute to viral pathogenesis and/or spread.IMPORTANCE The HIV-1 accessory protein Vpu enhances viral spread by downregulating CD4 and BST-2/tetherin on the surface of infected cells. Natural variability in these Vpu functions may contribute to HIV-1 pathogenesis, but this has not been investigated among the diverse viral subtypes that contribute to the HIV-1 pandemic. In this study, we found that Vpu function differs significantly among HIV-1 subtypes A, B, C, and D. On average, subtype C clones displayed the lowest ability to downregulate both CD4 and tetherin, while subtype B and D clones were more functional. We also identified Vpu polymorphisms that associate with functional differences among HIV-1 isolates and subtypes. Our study suggests that genetic diversity in Vpu may play an important role in the differential pathogenesis and/or spread of HIV-1.
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Affiliation(s)
- Gisele Umviligihozo
- Faculty of Health Sciences, Simon Fraser University, Vancouver, British Columbia, Canada
| | - Kyle D Cobarrubias
- Faculty of Health Sciences, Simon Fraser University, Vancouver, British Columbia, Canada
| | - Sandali Chandrarathna
- Faculty of Health Sciences, Simon Fraser University, Vancouver, British Columbia, Canada
| | - Steven W Jin
- Faculty of Health Sciences, Simon Fraser University, Vancouver, British Columbia, Canada
| | - Nicole Reddy
- University of KwaZulu-Natal, Durban, South Africa
- Africa Health Research Institute, Durban, South Africa
| | - Helen Byakwaga
- Mbarara University of Science and Technology, Mbarara, Uganda
- University of California, San Francisco, California, USA
| | - Conrad Muzoora
- Mbarara University of Science and Technology, Mbarara, Uganda
| | - Mwebesa B Bwana
- Mbarara University of Science and Technology, Mbarara, Uganda
| | - Guinevere Q Lee
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Peter W Hunt
- University of California, San Francisco, California, USA
| | - Jeff N Martin
- University of California, San Francisco, California, USA
| | - Chanson J Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- University of British Columbia, Vancouver, British Columbia, Canada
| | - David R Bangsberg
- Oregon Health and Science University-Portland State University School of Public Health, Portland, Oregon, USA
| | - Etienne Karita
- Rwanda Zambia HIV Research Group-Projet San Francisco, Kigali, Rwanda
| | - Susan Allen
- Rwanda Zambia HIV Research Group-Projet San Francisco, Kigali, Rwanda
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, USA
- Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Eric Hunter
- Rwanda Zambia HIV Research Group-Projet San Francisco, Kigali, Rwanda
- Emory Vaccine Center at Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - Thumbi Ndung'u
- University of KwaZulu-Natal, Durban, South Africa
- Africa Health Research Institute, Durban, South Africa
- Max Planck Institute for Infection Biology, Berlin, Germany
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Vancouver, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Mark A Brockman
- Faculty of Health Sciences, Simon Fraser University, Vancouver, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
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Brooks K, Jones BR, Dilernia DA, Wilkins DJ, Claiborne DT, McInally S, Gilmour J, Kilembe W, Joy JB, Allen SA, Brumme ZL, Hunter E. HIV-1 variants are archived throughout infection and persist in the reservoir. PLoS Pathog 2020; 16:e1008378. [PMID: 32492044 PMCID: PMC7295247 DOI: 10.1371/journal.ppat.1008378] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 06/15/2020] [Accepted: 02/03/2020] [Indexed: 01/23/2023] Open
Abstract
The HIV-1 reservoir consists of latently infected cells that persist despite antiretroviral therapy (ART). Elucidating the proviral genetic composition of the reservoir, particularly in the context of pre-therapy viral diversity, is therefore important to understanding reservoir formation and the persistence of latently infected cells. Here we investigate reservoir proviral variants from 13 Zambian acutely-infected individuals with additional pre-therapy sampling for a unique comparison to the ART-naïve quasispecies. We identified complete transmitted/founder (TF) viruses from seroconversion plasma samples, and additionally amplified and sequenced HIV-1 from plasma obtained one year post-infection and just prior to ART initiation. While the majority of proviral variants in the reservoir were most closely related to viral variants from the latest pre-therapy time point, we also identified reservoir proviral variants dating to or near the time of infection, and to intermediate time points between infection and treatment initiation. Reservoir proviral variants differing by five or fewer nucleotide changes from the TF virus persisted during treatment in five individuals, including proviral variants that exactly matched the TF in two individuals, one of whom had remained ART-naïve for more than six years. Proviral variants during treatment were significantly less divergent from the TF virus than plasma variants present at the last ART-naïve time point. These findings indicate that reservoir proviral variants are archived throughout infection, recapitulating much of the viral diversity that arises throughout untreated HIV-1 infection, and strategies to target and reduce the reservoir must therefore permit for the clearance of proviruses encompassing this extensive diversity. Despite reducing viremia to levels below the limit of detection in standard assays, effective antiretroviral therapy (ART) does not eradicate cells latently infected with HIV-1. These cells serve as a reservoir for viral rebound if therapy is interrupted; thus, understanding the composition of the reservoir may yield further targets for HIV-1 cure strategies. We have taken a genetic approach to elucidating the reservoir in 13 Zambian subtype C seroconvertors who were followed longitudinally through ART initiation and virologic suppression. In five of the 13 individuals, provirus sequences identical to or differing by five or fewer nucleotides from the transmitted/founder virus were detected, indicating archiving and persistence of early infection variants for more than six years following infection. While the majority of proviral variants in latently infected cells were most closely related to plasma virus circulating immediately prior to treatment initiation, additional variants dating to intermediate time points in the infection were also observed. These findings demonstrate that virus is archived during all stages of ART-naïve infection, and these variants persist throughout ART. HIV-1 cure strategies to eliminate the reservoir must address the broad genetic diversity of a within-host proviral quasispecies including variants archived from acute through chronic infection.
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Affiliation(s)
- Kelsie Brooks
- Emory Vaccine Center, Emory University, Atlanta, Georgia, United States of America
| | - Bradley R. Jones
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Dario A. Dilernia
- Emory Vaccine Center, Emory University, Atlanta, Georgia, United States of America
| | - Daniel J. Wilkins
- Emory Vaccine Center, Emory University, Atlanta, Georgia, United States of America
| | - Daniel T. Claiborne
- Emory Vaccine Center, Emory University, Atlanta, Georgia, United States of America
| | - Samantha McInally
- Emory Vaccine Center, Emory University, Atlanta, Georgia, United States of America
| | - Jill Gilmour
- Human Immunology Lab, International AIDS Vaccine Initiative, London, England, United Kingdom
| | | | - Jeffrey B. Joy
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Susan A. Allen
- Zambia-Emory HIV Research Project, Lusaka, Zambia
- Department of Pathology & Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Zabrina L. Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Eric Hunter
- Emory Vaccine Center, Emory University, Atlanta, Georgia, United States of America
- Department of Pathology & Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, United States of America
- * E-mail:
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Wall KM, Inambao M, Kilembe W, Karita E, Chomba E, Vwalika B, Mulenga J, Parker R, Sharkey T, Tichacek A, Hunter E, Yohnka R, Streeb G, Corso PS, Allen S. Cost-effectiveness of couples' voluntary HIV counselling and testing in six African countries: a modelling study guided by an HIV prevention cascade framework. J Int AIDS Soc 2020; 23 Suppl 3:e25522. [PMID: 32602618 PMCID: PMC7325504 DOI: 10.1002/jia2.25522] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 03/17/2020] [Accepted: 04/23/2020] [Indexed: 11/07/2022] Open
Abstract
INTRODUCTION Couples' voluntary HIV counselling and testing (CVCT) is a high-impact HIV prevention intervention in Rwanda and Zambia. Our objective was to model the cost-per-HIV infection averted by CVCT in six African countries guided by an HIV prevention cascade framework. The HIV prevention cascade as yet to be applied to evaluating CVCT effectiveness or cost-effectiveness. METHODS We defined a priority population for CVCT in Africa as heterosexual adults in stable couples. Based on our previous experience nationalizing CVCT in Rwanda and scaling-up CVCT in 73 clinics in Zambia, we estimated HIV prevention cascade domains of motivation for use, access and effectiveness of CVCT as model parameters. Costs-per-couple tested were also estimated based on our previous studies. We used these parameters as well as country-specific inputs to model the impact of CVCT over a five-year time horizon in a previously developed and tested deterministic compartmental model. We consider six countries across Africa with varied HIV epidemics (South Africa, Zimbabwe, Kenya, Tanzania, Ivory Coast and Sierra Leone). Outcomes of interest were the proportion of HIV infections averted by CVCT, nationwide CVCT implementation costs and costs-per-HIV infection averted by CVCT. We applied 3%/year discounting to costs and outcomes. Univariate and Monte Carlo multivariate sensitivity analyses were conducted. RESULTS We estimated that CVCT could avert between 54% (Sierra Leone) and 62% (South Africa) of adult HIV infections. Average costs-per-HIV infection averted were lowest in Zimbabwe ($550) and highest in South Africa ($1272). Nationwide implementations would cost between 7% (Kenya) and 21% (Ivory Coast) of a country's President's Emergency Plan for AIDS Relief (PEPFAR) budget over five years. In sensitivity analyses, model outputs were most sensitive to estimates of cost-per-couple tested; the proportion of adults in heterosexual couples and HIV prevention cascade domains of CVCT motivation and access. CONCLUSIONS Our model indicates that nationalized CVCT could prevent over half of adult HIV infections for 7% to 21% of the modelled countries' five-year PEPFAR budgets. While other studies have indicated that CVCT motivation is high given locally relevant promotional and educational efforts, without required indicators, targets and dedicated budgets, access remains low.
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Affiliation(s)
- Kristin M Wall
- Rwanda Zambia HIV Research GroupDepartment of Pathology & Laboratory MedicineSchool of Medicine and Hubert Department of Global HealthRollins School of Public HealthLaney Graduate SchoolEmory UniversityAtlantaGAUSA
- Department of EpidemiologyRollins School of Public HealthLaney Graduate SchoolEmory UniversityAtlantaGAUSA
| | - Mubiana Inambao
- Rwanda Zambia HIV Research GroupDepartment of Pathology & Laboratory MedicineSchool of Medicine and Hubert Department of Global HealthRollins School of Public HealthLaney Graduate SchoolEmory UniversityAtlantaGAUSA
- Department of Obstetrics and GynecologyNdola Central HospitalNdolaZambia
| | - William Kilembe
- Rwanda Zambia HIV Research GroupDepartment of Pathology & Laboratory MedicineSchool of Medicine and Hubert Department of Global HealthRollins School of Public HealthLaney Graduate SchoolEmory UniversityAtlantaGAUSA
| | - Etienne Karita
- Rwanda Zambia HIV Research GroupDepartment of Pathology & Laboratory MedicineSchool of Medicine and Hubert Department of Global HealthRollins School of Public HealthLaney Graduate SchoolEmory UniversityAtlantaGAUSA
| | | | - Bellington Vwalika
- Rwanda Zambia HIV Research GroupDepartment of Pathology & Laboratory MedicineSchool of Medicine and Hubert Department of Global HealthRollins School of Public HealthLaney Graduate SchoolEmory UniversityAtlantaGAUSA
- Department of Obstetrics and GynecologySchool of MedicineUniversity of ZambiaLusakaZambia
| | - Joseph Mulenga
- Rwanda Zambia HIV Research GroupDepartment of Pathology & Laboratory MedicineSchool of Medicine and Hubert Department of Global HealthRollins School of Public HealthLaney Graduate SchoolEmory UniversityAtlantaGAUSA
| | - Rachel Parker
- Rwanda Zambia HIV Research GroupDepartment of Pathology & Laboratory MedicineSchool of Medicine and Hubert Department of Global HealthRollins School of Public HealthLaney Graduate SchoolEmory UniversityAtlantaGAUSA
| | - Tyronza Sharkey
- Rwanda Zambia HIV Research GroupDepartment of Pathology & Laboratory MedicineSchool of Medicine and Hubert Department of Global HealthRollins School of Public HealthLaney Graduate SchoolEmory UniversityAtlantaGAUSA
| | - Amanda Tichacek
- Rwanda Zambia HIV Research GroupDepartment of Pathology & Laboratory MedicineSchool of Medicine and Hubert Department of Global HealthRollins School of Public HealthLaney Graduate SchoolEmory UniversityAtlantaGAUSA
| | - Eric Hunter
- Rwanda Zambia HIV Research GroupDepartment of Pathology & Laboratory MedicineSchool of Medicine and Hubert Department of Global HealthRollins School of Public HealthLaney Graduate SchoolEmory UniversityAtlantaGAUSA
- Department of Pathology & Laboratory MedicineSchool of MedicineEmory UniversityAtlantaGAUSA
- Emory Vaccine CenterYerkes National Primate Research CenterEmory UniversityAtlantaGAUSA
| | - Robert Yohnka
- Rwanda Zambia HIV Research GroupDepartment of Pathology & Laboratory MedicineSchool of Medicine and Hubert Department of Global HealthRollins School of Public HealthLaney Graduate SchoolEmory UniversityAtlantaGAUSA
| | - Gordon Streeb
- Departments of Economics and Political ScienceEmory UniversityAtlantaGAUSA
| | | | - Susan Allen
- Rwanda Zambia HIV Research GroupDepartment of Pathology & Laboratory MedicineSchool of Medicine and Hubert Department of Global HealthRollins School of Public HealthLaney Graduate SchoolEmory UniversityAtlantaGAUSA
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Galloway M, Hunter E, Akoulitchev A, Vigneswaran S, Abdi B, Denton C, Abraham D, Stratton R. OP0254 CHROMATIN CONFORMATION SIGNATURE ANALYSIS IN EARLY VS LATE SCLERODERMA PHENOTYPES. Ann Rheum Dis 2020. [DOI: 10.1136/annrheumdis-2020-eular.6323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Background:Systemic sclerosis (scleroderma, SSc) is a heterogeneous disease in which clinical outcomes vary widely. Predicting outcomes on an individual basis remains challenging despite progress made through autoantibody analysis and gene expression profiling. Effective targeted therapies are evolving and accurately predicting outcomes is important to enable patient stratification for therapy.Chromatin Conformation Signature (CCS) profiling of peripheral blood for systemic epigenetic deregulations could be used for such a purpose. The EpiSwitch platform offering high throughput and resolution chromosome conformation (3C) capture detects significant regulatory changes in 3D genome architecture and maps long range interaction between distant genomic locations. This then reveals the spatial disposition and physical properties of the chromosome, such as chromatin loops and inter-chromosomal connections, which have a role in network organization and genetic epistasis controlling gene expression. EpiSwitch automated platform has been successfully utilised in patient stratification in RA, MS and other indications.This methodology could be applied to patients with SSc to identify CCS associated with different phenotypes and may ultimately be used to stratify and identify patients into pathogenic subtypes.Objectives:We aimed to determine significant CCSs associated with early and late phenotypes of SSc.Methods:The EpiSwitch-based chromosome conformation capture (3C) method was applied to blood samples from early phenotype, and late phenotype SSc patients. Intact nuclei were isolated from peripheral blood mononuclear cells and subjected to formaldehyde fixation resulting in crosslinking between physically touching segments of the genome via contacts between their DNA bound proteins. For quantification of cross-linking frequencies, the cross linked DNA was digested and then subjected to ligation. Cross-linking was then reversed and individual ligation products detected and quantified by EpiSwitch custom oligo array annotated across the whole genome to the anchoring sites of 3D genome architecture.Results:7 significant CCSs were found over the HLA-C, HLA-B and TNF regions on Chromosome 6 in the early phenotype. The top 8 pathways for genetic locations associated to the CCSs are shown in Table 1.Table 1.Top 8 pathways for genetic locations associated to significant CCS for the early phenotype.GeneSet1Natural Killer cell mediated cytotoxicity2Immunoregulatory interations between a lymphoid cell and a non-lymphoid cell3Antigen Processing & presentation4Phagosome5Graft versus host disease6Type 1 diabetes mellitus7Osteoclast differentiation8Class 1 MHC mediated antigen processing & presentation2 significant CCSs were found centred around the IFNG region of chromosome 12 in the late phenotype. The top 8 pathways for genetic locations associated to significant CCSs are shown in Table 2.Table 2.Top 8 pathways for genetic locations associated to significant CCS for the late phenotype.GeneSet1Surfactant metabolism2IL12 signalling mediated by STAT43Protein digestion & absorption4Calcineruin regulated NFAT dependent transcription in lymphocytes5Transcriptional misregulation in cancer6Kaposi’s sarcoma associated herpes virus infection7IL2 mediated signalling events8Inflammatory bowel diseaseConclusion:Significant CCSs, as part of 3D genomic regulatory control, and their associated pathways for the genetic locations, were identified in both late and early phenotypes. There were distinct CCSs in the early phenotype compared to the late suggesting the CCSs change as the disease progresses and varies between phenotypes. If CCSs could be linked to each clinically defined subgroup across a SSc cohort they could be used as a biomarker tool to predict outcome and progression in patients.Disclosure of Interests:Megan Galloway: None declared, Ewan Hunter: None declared, Alexandre Akoulitchev: None declared, Shivanee Vigneswaran: None declared, Bahja Abdi: None declared, Christopher Denton Grant/research support from: GlaxoSmithKline, Inventiva, CSF Behring, Consultant of: Roche-Genentech, Actelion, GlaxoSmithKline, Sanofi Aventis, Inventiva, CSL Behring, Boehringer Ingelheim, Bayer, David Abraham: None declared, Richard Stratton: None declared
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Arunachalam PS, Charles TP, Joag V, Bollimpelli VS, Scott MKD, Wimmers F, Burton SL, Labranche CC, Petitdemange C, Gangadhara S, Styles TM, Quarnstrom CF, Walter KA, Ketas TJ, Legere T, Jagadeesh Reddy PB, Kasturi SP, Tsai A, Yeung BZ, Gupta S, Tomai M, Vasilakos J, Shaw GM, Kang CY, Moore JP, Subramaniam S, Khatri P, Montefiori D, Kozlowski PA, Derdeyn CA, Hunter E, Masopust D, Amara RR, Pulendran B. T cell-inducing vaccine durably prevents mucosal SHIV infection even with lower neutralizing antibody titers. Nat Med 2020; 26:932-940. [PMID: 32393800 PMCID: PMC7303014 DOI: 10.1038/s41591-020-0858-8] [Citation(s) in RCA: 109] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 03/27/2020] [Indexed: 01/05/2023]
Abstract
Recent efforts toward an HIV vaccine focus on inducing broadly neutralizing antibodies, but eliciting both neutralizing antibodies (nAbs) and cellular responses may be superior. Here, we immunized macaques with an HIV envelope trimer, either alone to induce nAbs, or together with a heterologous viral vector regimen to elicit nAbs and cellular immunity, including CD8+ tissue-resident memory T cells. After ten vaginal challenges with autologous virus, protection was observed in both vaccine groups at 53.3% and 66.7%, respectively. A nAb titer >300 was generally associated with protection but in the heterologous viral vector + nAb group, titers <300 were sufficient. In this group, protection was durable as the animals resisted six more challenges 5 months later. Antigen stimulation of T cells in ex vivo vaginal tissue cultures triggered antiviral responses in myeloid and CD4+ T cells. We propose that cellular immune responses reduce the threshold of nAbs required to confer superior and durable protection.
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MESH Headings
- Animals
- Antibodies, Neutralizing/drug effects
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/drug effects
- Antibodies, Viral/immunology
- CD4-Positive T-Lymphocytes/drug effects
- CD4-Positive T-Lymphocytes/immunology
- CD8-Positive T-Lymphocytes/drug effects
- CD8-Positive T-Lymphocytes/immunology
- Female
- Gene Products, gag/genetics
- Gene Products, gag/immunology
- Genetic Vectors
- Immunity, Cellular/drug effects
- Immunity, Cellular/immunology
- Immunity, Heterologous
- Immunogenicity, Vaccine
- Immunologic Memory/immunology
- Macaca mulatta
- Mucous Membrane
- SAIDS Vaccines/pharmacology
- Simian Acquired Immunodeficiency Syndrome/prevention & control
- Simian Immunodeficiency Virus/immunology
- Vagina
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Affiliation(s)
- Prabhu S Arunachalam
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Tysheena P Charles
- Department of Pathology and Laboratory Medicine, Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA, USA
| | - Vineet Joag
- Department of Microbiology and Immunology, Center for Immunology, University of Minnesota, Minneapolis, MN, USA
| | - Venkata S Bollimpelli
- Department of Microbiology and Immunology, Emory Vaccine Center, Yerkes National Primate Research Center at Emory University, Atlanta, GA, USA
| | - Madeleine K D Scott
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
- Center for Biomedical Informatics, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Florian Wimmers
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Samantha L Burton
- Department of Pathology and Laboratory Medicine, Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA, USA
| | - Celia C Labranche
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Caroline Petitdemange
- Department of Microbiology and Immunology, Emory Vaccine Center, Yerkes National Primate Research Center at Emory University, Atlanta, GA, USA
- HIV Inflammation and Persistence Unit, Institut Pasteur, Paris, France
| | - Sailaja Gangadhara
- Department of Microbiology and Immunology, Emory Vaccine Center, Yerkes National Primate Research Center at Emory University, Atlanta, GA, USA
| | - Tiffany M Styles
- Department of Microbiology and Immunology, Emory Vaccine Center, Yerkes National Primate Research Center at Emory University, Atlanta, GA, USA
| | - Clare F Quarnstrom
- Department of Microbiology and Immunology, Center for Immunology, University of Minnesota, Minneapolis, MN, USA
| | - Korey A Walter
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Thomas J Ketas
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY, USA
| | - Traci Legere
- Department of Microbiology and Immunology, Emory Vaccine Center, Yerkes National Primate Research Center at Emory University, Atlanta, GA, USA
| | - Pradeep Babu Jagadeesh Reddy
- Department of Microbiology and Immunology, Emory Vaccine Center, Yerkes National Primate Research Center at Emory University, Atlanta, GA, USA
- Pfizer, Andover, MA, USA
| | - Sudhir Pai Kasturi
- Department of Pathology and Laboratory Medicine, Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA, USA
- Department of Microbiology and Immunology, Emory Vaccine Center, Yerkes National Primate Research Center at Emory University, Atlanta, GA, USA
| | | | | | - Shakti Gupta
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Mark Tomai
- 3M Corporate Research and Materials Lab, Saint Paul, MN, USA
| | | | - George M Shaw
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Chil-Yong Kang
- Department of Microbiology and Immunology, Schulich School of Medicine & Dentistry, The University of Western Ontario, London, Ontario, Canada
| | - John P Moore
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY, USA
| | - Shankar Subramaniam
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Purvesh Khatri
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
- Center for Biomedical Informatics, Department of Medicine, Stanford University, Stanford, CA, USA
| | - David Montefiori
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Pamela A Kozlowski
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Cynthia A Derdeyn
- Department of Pathology and Laboratory Medicine, Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA, USA.
| | - Eric Hunter
- Department of Pathology and Laboratory Medicine, Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA, USA.
| | - David Masopust
- Department of Microbiology and Immunology, Center for Immunology, University of Minnesota, Minneapolis, MN, USA.
| | - Rama R Amara
- Department of Microbiology and Immunology, Emory Vaccine Center, Yerkes National Primate Research Center at Emory University, Atlanta, GA, USA.
| | - Bali Pulendran
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford University, Stanford, CA, USA.
- Department of Pathology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA.
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA.
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46
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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47
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Connolly S, Kilembe W, Inambao M, Visoiu AM, Sharkey T, Parker R, Hunter E, Allen S. 422. Pooling Strategy for Chlamydia trachomatis and Neisseria gonorrhoeae Reduces Cost of GeneXpert Molecular STI Screening in Two Limited-Resource Clinics in Zambia. Open Forum Infect Dis 2019. [PMCID: PMC6809951 DOI: 10.1093/ofid/ofz360.495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Background Risk of heterosexual HIV-1 transmission is elevated in the presence of sexually transmitted infections (STIs) such as chlamydia (CT) and gonorrhea (NG). Syndromic management is a common, low-resource, approach to detecting STIs. However, CT and/or NG infections in women are often asymptomatic and therefore missed by syndromic management. Molecular testing for STIs is highly sensitive, but time and cost restraints preclude implementation of these technologies in resource-limited settings. Pooling samples for testing together in GeneXpert cartridges is one strategy for reducing the cost per individual tested. Methods This project describes the development of a pooling strategy based on social and demographic factors associated with CT/NG prevalence rates in a cohort of high-risk women in Zambia. Logistic regression modeling was used to predict the probability of a positive CT/NG test result in the presence of various factors. Data from a 2016 cross-sectional sub-study on intra-vaginal practices in 509 women was examined and an easy-to-use diagnostic screening checklist was created to categorize women by probability of testing positive on the GeneXpert. An algorithm considering cost of each test and prevalence of disease in each group determined the optimal pool size for each risk category. Results Logistic regression identified CT/NG to be associated with: city, age, education, long-acting reversible contraception usage, and laboratory results for bacterial vaginosis, Trichomonas vaginalis, and incident syphilis on the day of CT/NG testing. Signs and symptoms were not found to be associated. The overall prevalence of either CT and/or NG infection in this population was 17%. Low, middle, and high-risk groups could be separated based on checklist score with 7.52%, 18.30%, and 46.51% CT/NG prevalence, respectively. Conclusion Pooling women with similar CT/NG predictive factors together, or testing those at highest risk individually, reduces the cost per test. Further implementation of this tool to guide presumptive treatment, in lieu of molecular testing, increases the cost-saving potential. The strategies described in this study are applicable to other low-resource clinical settings seeking to provide the accuracy of molecular testing with a reduced financial burden. Disclosures All authors: No reported disclosures.
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48
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Dale GA, Wilkins DJ, Bohannon CD, Dilernia D, Hunter E, Bedford T, Antia R, Sanz I, Jacob J. Clustered Mutations at the Murine and Human IgH Locus Exhibit Significant Linkage Consistent with Templated Mutagenesis. J Immunol 2019; 203:1252-1264. [PMID: 31375545 PMCID: PMC6702052 DOI: 10.4049/jimmunol.1801615] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 06/18/2019] [Indexed: 01/21/2023]
Abstract
Somatic hypermutation generates a myriad of Ab mutants in Ag-specific B cells, from which high-affinity mutants are selected. Chickens, sheep, and rabbits use nontemplated point mutations and templated mutations via gene conversion to diversify their expressed Ig loci, whereas mice and humans rely solely on untemplated somatic point mutations. In this study, we demonstrate that, in addition to untemplated point mutations, templated mutagenesis readily occurs at the murine and human Ig loci. We provide two distinct lines of evidence that are not explained by the Neuberger model of somatic hypermutation: 1) across multiple data sets there is significant linkage disequilibrium between individual mutations, especially among close mutations, and 2) among those mutations, those <8 bp apart are significantly more likely to match microhomologous regions in the IgHV repertoire than predicted by the mutation profiles of somatic hypermutation. Together, this supports the role of templated mutagenesis during somatic diversification of Ag-activated B cells.
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Affiliation(s)
- Gordon A Dale
- Emory Vaccine Center, Yerkes National Primate Center, Emory University, Atlanta, GA 30329
| | - Daniel J Wilkins
- Emory Vaccine Center, Yerkes National Primate Center, Emory University, Atlanta, GA 30329
| | - Caitlin D Bohannon
- Emory Vaccine Center, Yerkes National Primate Center, Emory University, Atlanta, GA 30329
| | - Dario Dilernia
- Emory Vaccine Center, Yerkes National Primate Center, Emory University, Atlanta, GA 30329
| | - Eric Hunter
- Emory Vaccine Center, Yerkes National Primate Center, Emory University, Atlanta, GA 30329
| | - Trevor Bedford
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA 98195
| | - Rustom Antia
- Department of Biology, Emory University, Atlanta, GA 30322; and
| | - Ignacio Sanz
- Lowance Center for Human Immunology, Department of Medicine, Emory University, Atlanta, GA 30322
| | - Joshy Jacob
- Emory Vaccine Center, Yerkes National Primate Center, Emory University, Atlanta, GA 30329;
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49
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Claiborne DT, Scully EP, Palmer CD, Prince JL, Macharia GN, Kopycinski J, Michelo CM, Wiener HW, Parker R, Nganou-Makamdop K, Douek D, Altfeld M, Gilmour J, Price MA, Tang J, Kilembe W, Allen SA, Hunter E. Protective HLA alleles are associated with reduced LPS levels in acute HIV infection with implications for immune activation and pathogenesis. PLoS Pathog 2019; 15:e1007981. [PMID: 31449552 PMCID: PMC6730937 DOI: 10.1371/journal.ppat.1007981] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 09/06/2019] [Accepted: 07/14/2019] [Indexed: 12/12/2022] Open
Abstract
Despite extensive research on the mechanisms of HLA-mediated immune control of HIV-1 pathogenesis, it is clear that much remains to be discovered, as exemplified by protective HLA alleles like HLA-B*81 which are associated with profound protection from CD4+ T cell decline without robust control of early plasma viremia. Here, we report on additional HLA class I (B*1401, B*57, B*5801, as well as B*81), and HLA class II (DQB1*02 and DRB1*15) alleles that display discordant virological and immunological phenotypes in a Zambian early infection cohort. HLA class I alleles of this nature were also associated with enhanced immune responses to conserved epitopes in Gag. Furthermore, these HLA class I alleles were associated with reduced levels of lipopolysaccharide (LPS) in the plasma during acute infection. Elevated LPS levels measured early in infection predicted accelerated CD4+ T cell decline, as well as immune activation and exhaustion. Taken together, these data suggest novel mechanisms for HLA-mediated immune control of HIV-1 pathogenesis that do not necessarily involve significant control of early viremia and point to microbial translocation as a direct driver of HIV-1 pathogenesis rather than simply a consequence. During acute HIV infection, there exists a complex interplay between the host immune response and the virus, and the balance of these interactions dramatically affects disease trajectory in infected individuals. Variations in Human Leukocyte Antigen (HLA) alleles dictate the potency of the cellular immune response to HIV, and certain well-studied alleles (HLA-B*57, B*27) are associated with control of HIV viremia. However, though plasma viral load is indicative of disease progression, the number of CD4+ T cells in the blood is a better measurement of disease severity. Through analysis of a large Zambian acute infection cohort, we identified HLA alleles that were associated with protection for CD4+ T cell loss, without dramatic affect on early plasma viremia. We further link these favorable HLA alleles to reduction in a well-known contributor to HIV pathogenesis, the presence of microbial products in the blood, which is indicative of damage to the gastrointestinal tract, a process which accelerates disease progression in HIV infected individuals. Ultimately, these results suggest a new mechanism by which the cellular immune response can combat HIV-associated pathogenesis, and further highlight the contribution of gut damage and microbial translocation to accelerating disease progression, even at early stages in HIV infection.
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Affiliation(s)
- Daniel T. Claiborne
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Eileen P. Scully
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Christine D. Palmer
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Jessica L. Prince
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Gladys N. Macharia
- Human Immunology Laboratory, International AIDS Vaccine Initiative, London, United Kingdom
| | - Jakub Kopycinski
- Human Immunology Laboratory, International AIDS Vaccine Initiative, London, United Kingdom
| | | | - Howard W. Wiener
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Rachel Parker
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Krystelle Nganou-Makamdop
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Daniel Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Marcus Altfeld
- Virus Immunology Unit, Heinrich-Pette-Institut, Hamburg, Germany
| | - Jill Gilmour
- Human Immunology Laboratory, International AIDS Vaccine Initiative, London, United Kingdom
| | - Matt A. Price
- International AIDS Vaccine Initiative, New York, New York, United States of America
- Department of Epidemiology and Biostatistics, University of California at San Francisco, San Francisco, California, United States of America
| | - Jianming Tang
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | | | - Susan A. Allen
- Zambia-Emory HIV Research Project, Lusaka, Zambia
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Eric Hunter
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, United States of America
- * E-mail:
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50
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Qin K, Boppana S, Du VY, Carlson JM, Yue L, Dilernia DA, Hunter E, Mailliard RB, Mallal SA, Bansal A, Goepfert PA. CD8 T cells targeting adapted epitopes in chronic HIV infection promote dendritic cell maturation and CD4 T cell trans-infection. PLoS Pathog 2019; 15:e1007970. [PMID: 31398241 PMCID: PMC6703693 DOI: 10.1371/journal.ppat.1007970] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 08/21/2019] [Accepted: 07/08/2019] [Indexed: 11/18/2022] Open
Abstract
HIV-1 frequently escapes from CD8 T cell responses via HLA-I restricted adaptation, leading to the accumulation of adapted epitopes (AE). We previously demonstrated that AE compromise CD8 T cell responses during acute infection and are associated with poor clinical outcomes. Here, we examined the impact of AE on CD8 T cell responses and their biological relevance in chronic HIV infection (CHI). In contrast to acute infection, the majority of AE are immunogenic in CHI. Longitudinal analyses from acute to CHI showed an increased frequency and magnitude of AE-specific IFNγ responses compared to NAE-specific ones. These AE-specific CD8 T cells also were more cytotoxic to CD4 T cells. In addition, AE-specific CD8 T cells expressed lower levels of PD1 and CD57, as well as higher levels of CD28, suggesting a more activated and less exhausted phenotype. During CHI, viral sequencing identified AE-encoding strains as the dominant quasispecies. Despite increased CD4 T cell cytotoxicity, CD8 T cells responding to AE promoted dendritic cell (DC) maturation and CD4 T cell trans-infection perhaps explaining why AE are predominant in CHI. Taken together, our data suggests that the emergence of AE-specific CD8 T cell responses in CHI confers a selective advantage to the virus by promoting DC-mediated CD4 T cell trans-infection. HIV-1 infection remains a critical public health threat across the world. Over the past two decades, CD8 T cells have been clearly shown to exert immune pressure on HIV and drive viral adaptation. Previously, our group reported that such HLA-I associated adaptations can predict clinical outcomes and are beneficial to HIV-1 as CD8 T cells are unable to recognize epitopes with adaptation in acute HIV infection. However, it is still unclear how HIV-1 adaptation impacts CD8 T cells during chronic HIV infection. In this study, we observed an enhancement of CD8 T cell responses targeting adapted epitopes in chronic infection. Although these responses were cytotoxic, they also exhibited a “helper” effect by promoting viral infection of CD4 T cells via interaction with dendritic cells. This phenomenon may contribute to the persistence of adapted viruses. In summary, these findings present a novel mechanism of CD8 T cell driven HIV-1 adaptation.
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Affiliation(s)
- Kai Qin
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Sushma Boppana
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Victor Y. Du
- The Salk Institute for Biological Studies, La Jolla, California, United States of America
| | | | - Ling Yue
- Emory Vaccine Center at Yerkes National Primate Research Center and Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Dario A. Dilernia
- Emory Vaccine Center at Yerkes National Primate Research Center and Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Eric Hunter
- Emory Vaccine Center at Yerkes National Primate Research Center and Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Robbie B. Mailliard
- Department of Infectious Diseases and Microbiology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Simon A. Mallal
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Anju Bansal
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- * E-mail: (AB); (PAG)
| | - Paul A. Goepfert
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- * E-mail: (AB); (PAG)
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