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Konno Y, Uriu K, Chikata T, Takada T, Kurita JI, Ueda MT, Islam S, Yang Tan BJ, Ito J, Aso H, Kumata R, Williamson C, Iwami S, Takiguchi M, Nishimura Y, Morita E, Satou Y, Nakagawa S, Koyanagi Y, Sato K. Two-step evolution of HIV-1 budding system leading to pandemic in the human population. Cell Rep 2024; 43:113697. [PMID: 38294901 DOI: 10.1016/j.celrep.2024.113697] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 11/19/2023] [Accepted: 01/05/2024] [Indexed: 02/02/2024] Open
Abstract
The pandemic HIV-1, HIV-1 group M, emerged from a single spillover event of its ancestral lentivirus from a chimpanzee. During human-to-human spread worldwide, HIV-1 diversified into multiple subtypes. Here, our interdisciplinary investigation mainly sheds light on the evolutionary scenario of the viral budding system of HIV-1 subtype C (HIV-1C), a most successfully spread subtype. Of the two amino acid motifs for HIV-1 budding, the P(T/S)AP and YPxL motifs, HIV-1C loses the YPxL motif. Our data imply that HIV-1C might lose this motif to evade immune pressure. Additionally, the P(T/S)AP motif is duplicated dependently of the level of HIV-1 spread in the human population, and >20% of HIV-1C harbored the duplicated P(T/S)AP motif. We further show that the duplication of the P(T/S)AP motif is caused by the expansion of the CTG triplet repeat. Altogether, our results suggest that HIV-1 has experienced a two-step evolution of the viral budding process during human-to-human spread worldwide.
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Affiliation(s)
- Yoriyuki Konno
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan
| | - Keiya Uriu
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan; Graduate School of Medicine, the University of Tokyo, Tokyo 1130033, Japan; Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Aomori 0368561, Japan
| | - Takayuki Chikata
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8608556, Japan
| | - Toru Takada
- Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka 8128581, Japan
| | - Jun-Ichi Kurita
- Graduate School of Medical Life Science, Yokohama City University, Kanagawa 2300045, Japan
| | - Mahoko Takahashi Ueda
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa 2591193, Japan
| | - Saiful Islam
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8608556, Japan
| | - Benjy Jek Yang Tan
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8608556, Japan
| | - Jumpei Ito
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan
| | - Hirofumi Aso
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan; Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 6068507, Japan; Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 6068501, Japan
| | - Ryuichi Kumata
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan
| | - Carolyn Williamson
- Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town 7925, South Africa
| | - Shingo Iwami
- Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka 8128581, Japan; MIRAI, Japan Science and Technology Agency, Kawaguchi 3320012, Japan
| | - Masafumi Takiguchi
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8608556, Japan
| | - Yoshifumi Nishimura
- Graduate School of Medical Life Science, Yokohama City University, Kanagawa 2300045, Japan
| | - Eiji Morita
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Aomori 0368561, Japan
| | - Yorifumi Satou
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8608556, Japan
| | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa 2591193, Japan
| | - Yoshio Koyanagi
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 6068507, Japan; Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 6068501, Japan
| | - Kei Sato
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan; Graduate School of Medicine, the University of Tokyo, Tokyo 1130033, Japan; International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan; International Vaccine Design Center, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan; Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 2778561, Japan; CREST, Japan Science and Technology Agency, Kawaguchi 3320012, Japan.
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Schulz VE, Tuff JF, Tough RH, Lewis L, Chimukangara B, Garrett N, Abdool Karim Q, Abdool Karim SS, McKinnon LR, Kharsany ABM, McLaren PJ. Host genetic variation at a locus near CHD1L impacts HIV sequence diversity in a South African population. J Virol 2023; 97:e0095423. [PMID: 37747237 PMCID: PMC10617395 DOI: 10.1128/jvi.00954-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [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: 07/05/2023] [Accepted: 08/04/2023] [Indexed: 09/26/2023] Open
Abstract
IMPORTANCE It has been previously shown that genetic variants near CHD1L on chromosome 1 are associated with reduced HIV VL in African populations. However, the impact of these variants on viral diversity and how they restrict viral replication are unknown. We report on a regional association analysis in a South African population and show evidence of selective pressure by variants near CHD1L on HIV RT and gag. Our findings provide further insight into how genetic variability at this locus contributes to host control of HIV in a South African population.
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Affiliation(s)
- Vanessa E. Schulz
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
- Sexually Transmitted and Bloodborne Infections Division, JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratories, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Jeffrey F. Tuff
- Sexually Transmitted and Bloodborne Infections Division, JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratories, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Riley H. Tough
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
- Sexually Transmitted and Bloodborne Infections Division, JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratories, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Lara Lewis
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
| | - Benjamin Chimukangara
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
- Department of Virology, University of KwaZulu-Natal, Durban, South Africa
| | - Nigel Garrett
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- Department of Public Health Medicine, School of Nursing and Public Health, University of KwaZulu-Natal, Durban, South Africa
| | - Quarraisha Abdool Karim
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Salim S. Abdool Karim
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Lyle R. McKinnon
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
| | - Ayesha B. M. Kharsany
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- Department of Medical Microbiology, School of Laboratory Medicine and Medical Science, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Paul J. McLaren
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
- Sexually Transmitted and Bloodborne Infections Division, JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratories, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
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3
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Madlala P, Mkhize Z, Naicker S, Khathi SP, Maikoo S, Gopee K, Dong KL, Ndung'u T. Genetic variation of the HIV-1 subtype C transmitted/founder viruses long terminal repeat elements and the impact on transcription activation potential and clinical disease outcomes. PLoS Pathog 2023; 19:e1011194. [PMID: 37307292 DOI: 10.1371/journal.ppat.1011194] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 05/04/2023] [Indexed: 06/14/2023] Open
Abstract
A genetic bottleneck is a hallmark of HIV-1 transmission such that only very few viral strains, termed transmitted/founder (T/F) variants establish infection in a newly infected host. Phenotypic characteristics of these variants may determine the subsequent course of disease. The HIV-1 5' long terminal repeat (LTR) promoter drives viral gene transcription and is genetically identical to the 3' LTR. We hypothesized that HIV-1 subtype C (HIV-1C) T/F virus LTR genetic variation is a determinant of transcriptional activation potential and clinical disease outcome. The 3'LTR was amplified from plasma samples of 41 study participants acutely infected with HIV-1C (Fiebig stages I and V/VI). Paired longitudinal samples were also available at one year post-infection for 31 of the 41 participants. 3' LTR amplicons were cloned into a pGL3-basic luciferase expression vector, and transfected alone or together with Transactivator of transcription (tat) into Jurkat cells in the absence or presence of cell activators (TNF-α, PMA, Prostratin and SAHA). Inter-patient T/F LTR sequence diversity was 5.7% (Renge: 2-12) with subsequent intrahost viral evolution observed in 48.4% of the participants analyzed at 12 months post-infection. T/F LTR variants exhibited differential basal transcriptional activity, with significantly higher Tat-mediated transcriptional activity compared to basal (p<0.001). Basal and Tat-mediated T/F LTR transcriptional activity showed significant positive correlation with contemporaneous viral loads and negative correlation with CD4 T cell counts (p<0.05) during acute infection respectively. Furthermore, Tat-mediated T/F LTR transcriptional activity significanly correlated positively with viral load set point and viral load; and negatively with CD4 T cell counts at one year post infection (all p<0.05). Lastly, PMA, Prostratin, TNF-α and SAHA cell stimulation resulted in enhanced yet heterologous transcriptional activation of different T/F LTR variants. Our data suggest that T/F LTR variants may influence viral transcriptional activity, disease outcomes and sensitivity to cell activation, with potential implications for therapeutic interventions.
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Affiliation(s)
- Paradise Madlala
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Zakithi Mkhize
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Shamara Naicker
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Samukelisiwe P Khathi
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Shreyal Maikoo
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Kasmira Gopee
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Krista L Dong
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, Massachusetts, United States of America
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
| | - Thumbi Ndung'u
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, Massachusetts, United States of America
- Africa Health Research Institute (AHRI), Durban, South Africa
- Division of Infection and Immunity, University College London, London, United Kingdom
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4
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Alves E, Al-Kaabi M, Keane NM, Leary S, Almeida CAM, Deshpande P, Currenti J, Chopra A, Smith R, Castley A, Mallal S, Kalams SA, Gaudieri S, John M. Adaptation to HLA-associated immune pressure over the course of HIV infection and in circulating HIV-1 strains. PLoS Pathog 2022; 18:e1010965. [PMID: 36525463 PMCID: PMC9803285 DOI: 10.1371/journal.ppat.1010965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 12/30/2022] [Accepted: 11/01/2022] [Indexed: 12/23/2022] Open
Abstract
Adaptation to human leukocyte antigen (HLA)-associated immune pressure represents a major driver of human immunodeficiency virus (HIV) evolution at both the individual and population level. To date, there has been limited exploration of the impact of the initial cellular immune response in driving viral adaptation, the dynamics of these changes during infection and their effect on circulating transmitting viruses at the population level. Capturing detailed virological and immunological data from acute and early HIV infection is challenging as this commonly precedes the diagnosis of HIV infection, potentially by many years. In addition, rapid initiation of antiretroviral treatment following a diagnosis is the standard of care, and central to global efforts towards HIV elimination. Yet, acute untreated infection is the critical period in which the diversity of proviral reservoirs is first established within individuals, and associated with greater risk of onward transmissions in a population. Characterizing the viral adaptations evident in the earliest phases of infection, coinciding with the initial cellular immune responses is therefore relevant to understanding which changes are of greatest impact to HIV evolution at the population level. In this study, we utilized three separate cohorts to examine the initial CD8+ T cell immune response to HIV (cross-sectional acute infection cohort), track HIV evolution in response to CD8+ T cell-mediated immunity over time (longitudinal chronic infection cohort) and translate the impact of HLA-driven HIV evolution to the population level (cross-sectional HIV sequence data spanning 30 years). Using next generation viral sequencing and enzyme-linked immunospot interferon-gamma recall responses to peptides representing HLA class I-specific HIV T cell targets, we observed that CD8+ T cell responses can select viral adaptations prior to full antibody seroconversion. Using the longitudinal cohort, we uncover that viral adaptations have the propensity to be retained over time in a non-selective immune environment, which reflects the increasing proportion of pre-adapted HIV strains within the Western Australian population over an approximate 30-year period.
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Affiliation(s)
- Eric Alves
- School of Human Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Marwah Al-Kaabi
- School of Human Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Niamh M. Keane
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Western Australia, Australia
| | - Shay Leary
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Western Australia, Australia
| | - Coral-Ann M. Almeida
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Western Australia, Australia
| | - Pooja Deshpande
- School of Human Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Western Australia, Australia
| | - Jennifer Currenti
- School of Human Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Abha Chopra
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Western Australia, Australia
| | - Rita Smith
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Alison Castley
- Department of Clinical Immunology, Royal Perth Hospital, Perth, Western Australia, Australia
| | - Simon Mallal
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Western Australia, Australia
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Spyros A. Kalams
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Silvana Gaudieri
- School of Human Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Western Australia, Australia
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Mina John
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Western Australia, Australia
- Department of Clinical Immunology, Royal Perth Hospital, Perth, Western Australia, Australia
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Ahmed RA, Adekoya KO, Onwuamah CK, Oboh BO, Iyer SS, Oluwatosin AS, Audu RA, Ezechi OC. Mechanism of Viral Suppression among HIV Elite Controllers and Long-Term Nonprogressors in Nigeria and South Africa. Viruses 2022; 14:1270. [PMID: 35746741 DOI: 10.3390/v14061270] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 06/01/2022] [Accepted: 06/07/2022] [Indexed: 12/30/2022] Open
Abstract
A subgroup among people living with HIV (PLHIV) experience viral suppression, sometimes to an undetectable level in the blood and/or are able to maintain a healthy CD4+ T-cell count without the influence of antiretroviral (ARV) therapy. One out of three hundred PLHIV fall into this category, and a large sample of this group can be found in areas with a high prevalence of HIV infection such as Nigeria and South Africa. Understanding the mechanism underpinning the nonprogressive phenotype in this subgroup may provide insights into the control of the global HIV epidemic. This work provides mechanisms of the elite control and nonprogressive phenotype among PLHIV in Nigeria and South Africa and identifies research gaps that will contribute to a better understanding on HIV controllers among PLHIV.
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Prathiviraj R, Saranya S, Bharathi M, Chellapandi P. A hijack mechanism of Indian SARS-CoV-2 isolates for relapsing contemporary antiviral therapeutics. Comput Biol Med 2021; 132:104315. [PMID: 33705994 DOI: 10.1016/j.compbiomed.2021.104315] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 03/02/2021] [Indexed: 12/16/2022]
Abstract
Coronavirus disease (COVID-19) rapidly expands to a global pandemic and its impact on public health varies from country to country. It is caused by a new virus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). It is imperative for relapsing current antiviral therapeutics owing to randomized genetic drift in global SARS-CoV-2 isolates. A molecular mechanism behind the emerging genomic variants is not yet understood for the prioritization of selective antivirals. The present computational study was aimed to repurpose existing antivirals for Indian SARS-CoV-2 isolates by uncovering a hijack mechanism based on structural and functional characteristics of protein variants. Forty-one protein mutations were identified in 12 Indian SARS-CoV-2 isolates by analysis of genome variations across 460 genome sequences obtained from 30 geographic sites in India. Two unique mutations such as W6152R and N5928H found in exonuclease of Surat (GBRC275b) and Gandhinagar (GBRC239) isolates. We report for the first time the impact of folding rate on stabilizing/retaining a sequence-structure-function-virulence link of emerging protein variants leading to accommodate hijack ability from current antivirals. Binding affinity analysis revealed the effect of point mutations on virus infectivity and the drug-escaping efficiency of Indian isolates. Emodin and artinemol suggested herein as repurposable antivirals for the treatment of COVID-19 patients infected with Indian isolates. Our study concludes that a protein folding rate is a key structural and evolutionary determinant to enhance the receptor-binding specificity and ensure hijack ability from the prevalent antiviral therapeutics.
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Cao C, He J, Mak L, Perera D, Kwok D, Wang J, Li M, Mourier T, Gavriliuc S, Greenberg M, Morrissy AS, Sycuro LK, Yang G, Jeffares DC, Long Q. Reconstruction of Microbial Haplotypes by Integration of Statistical and Physical Linkage in Scaffolding. Mol Biol Evol 2021; 38:2660-2672. [PMID: 33547786 PMCID: PMC8136496 DOI: 10.1093/molbev/msab037] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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] [Indexed: 12/30/2022] Open
Abstract
DNA sequencing technologies provide unprecedented opportunities to analyze within-host evolution of microorganism populations. Often, within-host populations are analyzed via pooled sequencing of the population, which contains multiple individuals or "haplotypes." However, current next-generation sequencing instruments, in conjunction with single-molecule barcoded linked-reads, cannot distinguish long haplotypes directly. Computational reconstruction of haplotypes from pooled sequencing has been attempted in virology, bacterial genomics, metagenomics, and human genetics, using algorithms based on either cross-host genetic sharing or within-host genomic reads. Here, we describe PoolHapX, a flexible computational approach that integrates information from both genetic sharing and genomic sequencing. We demonstrated that PoolHapX outperforms state-of-the-art tools tailored to specific organismal systems, and is robust to within-host evolution. Importantly, together with barcoded linked-reads, PoolHapX can infer whole-chromosome-scale haplotypes from 50 pools each containing 12 different haplotypes. By analyzing real data, we uncovered dynamic variations in the evolutionary processes of within-patient HIV populations previously unobserved in single position-based analysis.
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Affiliation(s)
- Chen Cao
- Department of Biochemistry & Molecular Biology, Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, AB, Canada
| | - Jingni He
- Department of Biochemistry & Molecular Biology, Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, AB, Canada,Department of Cardiology, Xiangya Hospital, Central South University, Changsha, China
| | - Lauren Mak
- Department of Biochemistry & Molecular Biology, Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, AB, Canada,Present address: Tri-Institutional Computational Biology & Medicine Program, Weill Cornell Medicine of Cornell University, New York, NY, USA
| | - Deshan Perera
- Department of Biochemistry & Molecular Biology, Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, AB, Canada
| | - Devin Kwok
- Department of Mathematics & Statistics, University of Calgary, Calgary, AB, Canada
| | - Jia Wang
- Electrical and Computer Engineering, Illinois Institute of Technology, Chicago, IL, USA
| | - Minghao Li
- Department of Biochemistry & Molecular Biology, Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, AB, Canada
| | - Tobias Mourier
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Stefan Gavriliuc
- Department of Biochemistry & Molecular Biology, Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, AB, Canada
| | - Matthew Greenberg
- Department of Mathematics & Statistics, University of Calgary, Calgary, AB, Canada
| | - A Sorana Morrissy
- Department of Biochemistry & Molecular Biology, Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, AB, Canada
| | - Laura K Sycuro
- Department of Biochemistry & Molecular Biology, Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, AB, Canada,Department of Microbiology, Immunology, and Infectious Diseases, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada
| | - Guang Yang
- Department of Biochemistry & Molecular Biology, Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, AB, Canada,Department of Medical Genetics, University of Calgary, Calgary, AB, Canada
| | - Daniel C Jeffares
- Department of Biology, York Biomedical Research Institute, University of York, York, United Kingdom
| | - Quan Long
- Department of Biochemistry & Molecular Biology, Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, AB, Canada,Department of Mathematics & Statistics, University of Calgary, Calgary, AB, Canada,Department of Medical Genetics, University of Calgary, Calgary, AB, Canada,Hotchkiss Brain Institute, O’Brien Institute for Public Health, University of Calgary, Calgary, AB, Canada,Corresponding author: E-mail:
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Ellwanger JH, Veiga ABGD, Kaminski VDL, Valverde-Villegas JM, Freitas AWQD, Chies JAB. Control and prevention of infectious diseases from a One Health perspective. Genet Mol Biol 2021; 44:e20200256. [PMID: 33533395 PMCID: PMC7856630 DOI: 10.1590/1678-4685-gmb-2020-0256] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [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: 07/20/2020] [Accepted: 12/18/2020] [Indexed: 12/18/2022] Open
Abstract
The ongoing COVID-19 pandemic has caught the attention of the global community and rekindled the debate about our ability to prevent and manage outbreaks, epidemics, and pandemics. Many alternatives are suggested to address these urgent issues. Some of them are quite interesting, but with little practical application in the short or medium term. To realistically control infectious diseases, human, animal, and environmental factors need to be considered together, based on the One Health perspective. In this article, we highlight the most effective initiatives for the control and prevention of infectious diseases: vaccination; environmental sanitation; vector control; social programs that encourage a reduction in the population growth; control of urbanization; safe sex stimulation; testing; treatment of sexually and vertically transmitted infections; promotion of personal hygiene practices; food safety and proper nutrition; reduction of the human contact with wildlife and livestock; reduction of social inequalities; infectious disease surveillance; and biodiversity preservation. Subsequently, this article highlights the impacts of human genetics on susceptibility to infections and disease progression, using the SARS-CoV-2 infection as a study model. Finally, actions focused on mitigation of outbreaks and epidemics and the importance of conservation of ecosystems and translational ecology as public health strategies are also discussed.
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Affiliation(s)
- Joel Henrique Ellwanger
- Universidade Federal do Rio Grande do Sul - UFRGS, Departamento de Genética, Laboratório de Imunobiologia e Imunogenética, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul - UFRGS, Departamento de Genética, Programa de Pós-Graduação em Genética e Biologia Molecular - PPGBM, Porto Alegre, RS, Brazil
| | | | - Valéria de Lima Kaminski
- Universidade Federal de São Paulo - UNIFESP, Instituto de Ciência e Tecnologia - ICT, Laboratório de Imunologia Aplicada, Programa de Pós-Graduação em Biotecnologia, São José dos Campos, SP, Brazil
| | - Jacqueline María Valverde-Villegas
- Universidade Federal do Rio Grande do Sul - UFRGS, Departamento de Genética, Laboratório de Imunobiologia e Imunogenética, Porto Alegre, RS, Brazil
- Institut de Génétique Moléculaire de Montpellier (IGMM), Centre National de la Recherche Scientifique (CNRS), Laboratoire coopératif IGMM/ABIVAX, UMR 5535, Montpellier, France
| | - Abner Willian Quintino de Freitas
- Universidade Federal de Ciências da Saúde de Porto Alegre - UFCSPA, Programa de Pós-Graduação em Tecnologias da Informação e Gestão em Saúde, Porto Alegre, RS, Brazil
| | - José Artur Bogo Chies
- Universidade Federal do Rio Grande do Sul - UFRGS, Departamento de Genética, Laboratório de Imunobiologia e Imunogenética, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul - UFRGS, Departamento de Genética, Programa de Pós-Graduação em Genética e Biologia Molecular - PPGBM, Porto Alegre, RS, Brazil
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Avila-Rios S, Carlson JM, John M, Mallal S, Brumme ZL. Clinical and evolutionary consequences of HIV adaptation to HLA: implications for vaccine and cure. Curr Opin HIV AIDS 2019; 14:194-204. [PMID: 30925534 DOI: 10.1097/COH.0000000000000541] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
PURPOSE OF REVIEW The purpose of this review is to summarize recent advances in our understanding of HIV adaptation to human leukocyte antigen (HLA)-associated immune pressures and its relevance to HIV prevention and cure research. RECENT FINDINGS Recent research has confirmed that HLA is a major driver of individual and population-level HIV evolution, that HIV strains are adapting to the immunogenetic profiles of the different human ethnic groups in which they circulate, and that HIV adaptation has substantial clinical and immunologic consequences. As such, adaptation represents a major challenge to HIV prevention and cure. At the same time, there are opportunities: Studies of HIV adaptation are revealing why certain HLA alleles are protective in some populations and not others; they are identifying immunogenic viral epitopes that harbor high mutational barriers to escape, and they may help illuminate novel, vaccine-relevant HIV epitopes in regions where circulating adaptation is extensive. Elucidation of HLA-driven adapted and nonadapted viral forms in different human populations and HIV subtypes also renders 'personalized' immunogen selection, as a component of HIV cure strategies, conceptually feasible. SUMMARY Though adaptation represents a major challenge to HIV prevention and cure, achieving an in-depth understanding of this phenomenon can help move the design of such strategies forward.
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Jaumdally SZ, Liebenberg LJP, Gumbi PP, Little F, Jaspan HB, Gamieldien H, Tiemessen CT, Coetzee D, Martin DP, Williamson C, Williamson AL, Passmore JS. Partner HIV Serostatus Impacts Viral Load, Genital HIV Shedding, and Immune Activation in HIV-Infected Individuals. J Acquir Immune Defic Syndr 2019; 82:51-60. [PMID: 31169767 DOI: 10.1097/QAI.0000000000002089] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Studies of seronegative individuals in HIV discordant relationships provide important insights into the effects of HIV exposure on the seronegative partner, but few have examined the impact of partner serostatus on disease progression in seropositive individuals. We investigated the impact of HIV serostatus on clinical and biological factors influencing HIV disease progression in 337 HIV-infected heterosexual individuals in stable long-term HIV-seroconcordant or HIV-serodiscordant relationships. Seroconcordant individuals had significantly higher plasma viral loads (pVLs) than HIV-infected partners in serodiscordant partnerships [4.4 log10 copies RNA/mL (interquartile range 3.7-5.0) versus 3.9 (3.3-4.5), P < 0.0001], irrespective of gender. pVLs correlated inversely with CD4 T-cell counts, although CD4 counts did not differ significantly between seroconcordant and serodiscordant individuals. HIV+ seroconcordant individuals had higher frequencies of CCR5 CD4 and CD8 T cells (P = 0.03 and P = 0.02, respectively) than HIV+ individuals in serodiscordant relationships and higher concentrations of plasma IL-1β (P = 0.04), TNF-α (P = 0.02), and IL-10 (P = 0.02). Activated CD4 T-cell frequencies and TNF-α were the most influential in determining variation in pVLs, independently of CD4 counts. In addition, HIV+ seroconcordant women had significantly higher genital VLs (gVLs) than HIV+ women in serodiscordant relationships (P < 0.001), with pVLs correlating significantly with gVLs (Rho = 0.65, P < 0.0001). Cervical and blood T-cell activation tended to correlate positively, although partner seroconcordance did not influence genital T-cell activation. We conclude that HIV+ seroconcordant individuals have higher frequencies of activated, CCR5-expressing T cells in blood and higher pVLs and gVLs than their HIV+ counterparts in discordant relationships, which could translate to faster disease progression or larger viral reservoir.
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Currenti J, Chopra A, John M, Leary S, McKinnon E, Alves E, Pilkinton M, Smith R, Barnett L, McDonnell WJ, Lucas M, Noel F, Mallal S, Conrad JA, Kalams SA, Gaudieri S. Deep sequence analysis of HIV adaptation following vertical transmission reveals the impact of immune pressure on the evolution of HIV. PLoS Pathog 2019; 15:e1008177. [PMID: 31821379 PMCID: PMC6924686 DOI: 10.1371/journal.ppat.1008177] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [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: 08/05/2019] [Revised: 12/20/2019] [Accepted: 10/31/2019] [Indexed: 12/25/2022] Open
Abstract
Human immunodeficiency virus (HIV) can adapt to an individual’s T cell immune response via genomic mutations that affect antigen recognition and impact disease outcome. These viral adaptations are specific to the host’s human leucocyte antigen (HLA) alleles, as these molecules determine which peptides are presented to T cells. As HLA molecules are highly polymorphic at the population level, horizontal transmission events are most commonly between HLA-mismatched donor/recipient pairs, representing new immune selection environments for the transmitted virus. In this study, we utilised a deep sequencing approach to determine the HIV quasispecies in 26 mother-to-child transmission pairs where the potential for founder viruses to be pre-adapted is high due to the pairs being haplo-identical at HLA loci. This scenario allowed the assessment of specific HIV adaptations following transmission in either a non-selective immune environment, due to recipient HLA mismatched to original selecting HLA, or a selective immune environment, mediated by matched donor/recipient HLA. We show that the pattern of reversion or fixation of HIV adaptations following transmission provides insight into the replicative cost, and likely compensatory networks, associated with specific adaptations in vivo. Furthermore, although transmitted viruses were commonly heavily pre-adapted to the child’s HLA genotype, we found evidence of de novo post-transmission adaptation, representing new epitopes targeted by the child’s T cell response. High-resolution analysis of HIV adaptation is relevant when considering vaccine and cure strategies for individuals exposed to adapted viruses via transmission or reactivated from reservoirs. Highly mutable pathogens utilise genetic variations within T cell epitopes as a mechanism of immune escape (viral adaptation). The diversity of the human leucocyte antigen (HLA) molecules that present viral targets to T cells in human populations partially protects against rapid population-level accumulation of human immunodeficiency virus (HIV) adaptations through horizontal transmissions. In contrast, vertical transmissions occur between haplo-identical mother/child pairs, and potentially include adaptive changes through father-mother-child transmission, representing a pathway to complete pre-adaptation to HLA alleles in child hosts over only two transmission events. We utilised next-generation sequencing to examine HIV evolution in the unique setting of vertical HIV transmission. We predict the in vivo replicative cost and immune benefit of specific HIV adaptations that could be used to inform vaccine design and cure strategies to combat viral immune adaptation.
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Affiliation(s)
- Jennifer Currenti
- School of Human Sciences, University of Western Australia, Crawley, Western Australia, Australia
| | - Abha Chopra
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Western Australia, Australia
| | - Mina John
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Western Australia, Australia
- Department of Clinical Immunology, Royal Perth Hospital, Perth, Western Australia, Australia
| | - Shay Leary
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Western Australia, Australia
| | - Elizabeth McKinnon
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Western Australia, Australia
| | - Eric Alves
- School of Human Sciences, University of Western Australia, Crawley, Western Australia, Australia
| | - Mark Pilkinton
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Rita Smith
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Louise Barnett
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Wyatt J. McDonnell
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Michaela Lucas
- School of Medicine, University of Western Australia, Crawley, Western Australia, Australia
| | | | - Simon Mallal
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Western Australia, Australia
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Joseph A. Conrad
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Spyros A. Kalams
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Silvana Gaudieri
- School of Human Sciences, University of Western Australia, Crawley, Western Australia, Australia
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Western Australia, Australia
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- * E-mail:
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12
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Wang C, Liu D, Zuo T, Hora B, Cai F, Ding H, Kappes J, Ochsenbauer C, Kong W, Yu X, Bhattacharya T, Perelson AS, Gao F. Accumulated mutations by 6 months of infection collectively render transmitted/founder HIV-1 significantly less fit. J Infect 2019; 80:210-218. [PMID: 31812703 DOI: 10.1016/j.jinf.2019.12.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 11/22/2019] [Accepted: 12/01/2019] [Indexed: 01/16/2023]
Abstract
OBJECTIVE Viral fitness plays an important role in HIV-1 evolution, transmission and pathogenesis. However, how mutations accumulated during early infection affect viral fitness has not been well studied. METHODS Paired infectious molecular clones (IMCs) for transmitted/founder (T/F) and 6-month (6-mo) viruses post infection were generated from 10 infected individuals to investigate the impact of accumulated mutations on viral fitness by comparing 6-mo viruses to their cognate T/F viruses. RESULTS All ten 6-mo viruses were less fit than their cognate T/F viruses. Moreover, the fitness losses of the 6-mo viruses correlated with the decrease in viral loads from the peak of viremia. CONCLUSION These results show that the mutations accumulated during half a year post infection collectively reduce viral fitness and thereby contribute to lowering viral loads.
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Affiliation(s)
- Chu Wang
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, Jilin, China; Department of Medicine and Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Donglai Liu
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, Jilin, China; Department of Medicine and Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA; Division of the Second in Vitro Diagnostic, National Institute for Food and Drug Control, Beijing 100050, China
| | - Tao Zuo
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, Jilin, China; Department of Medicine and Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Bhavna Hora
- Department of Medicine and Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Fangping Cai
- Department of Medicine and Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Haitao Ding
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - John Kappes
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Christina Ochsenbauer
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Wei Kong
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, Jilin, China
| | - Xianghui Yu
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, Jilin, China
| | - Tanmoy Bhattacharya
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Alan S Perelson
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Feng Gao
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, Jilin, China; Department of Medicine and Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA.
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13
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Abstract
The accessory protein Nef of human immunodeficiency virus (HIV) is a primary determinant of viral pathogenesis. Nef is abundantly expressed during infection and reroutes a variety of cell surface proteins to disrupt host immunity and promote the viral replication cycle. Nef counteracts host defenses by sequestering and/or degrading its targets via the endocytic and secretory pathways. Nef does this by physically engaging a number of host trafficking proteins. Substantial progress has been achieved in identifying the targets of Nef, and a structural and mechanistic understanding of Nef's ability to command the protein trafficking machinery has recently started to coalesce. Comparative analysis of HIV and simian immunodeficiency virus (SIV) Nef proteins in the context of recent structural advances sheds further light on both viral evolution and the mechanisms whereby trafficking is hijacked. This review describes how advances in cell and structural biology are uncovering in growing detail how Nef subverts the host immune system, facilitates virus release, and enhances viral infectivity.
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14
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Boppana S, Sterrett S, Files J, Qin K, Fiore-Gartland A, Cohen KW, De Rosa SC, Bansal A, Goepfert PA. HLA-I Associated Adaptation Dampens CD8 T-Cell Responses in HIV Ad5-Vectored Vaccine Recipients. J Infect Dis 2019; 220:1620-1628. [PMID: 31301135 PMCID: PMC6782105 DOI: 10.1093/infdis/jiz368] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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: 03/29/2019] [Accepted: 07/10/2019] [Indexed: 01/08/2023] Open
Abstract
HLA-I-associated human immunodeficiency virus (HIV) adaptation is known to negatively affect disease progression and CD8 T-cell responses. We aimed to assess how HLA-I-associated adaptation affects HIV vaccine-induced CD8 T-cell responses in 2 past vaccine efficacy trials. We found that vaccine-encoded adapted epitopes were less immunogenic than vaccine-encoded nonadapted epitopes, and adapted epitope-specific responses were less polyfunctional than nonadapted epitope-specific responses. Along those lines, vaccine recipients with higher HLA-I adaptation to the Gag vaccine insert mounted less polyfunctional CD8 T-cell responses at the protein level. Breadth of response, which correlated with viral control in recipients who became infected, is also dampened by HLA-I adaptation. These findings suggest that HLA-I-associated adaptation is an important consideration for strategies aiming to induce robust CD8 T-cell responses.
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Affiliation(s)
- Sushma Boppana
- Division of Infectious Diseases, Department of Medicine, University of Alabama at Birmingham
| | - Sarah Sterrett
- Division of Infectious Diseases, Department of Medicine, University of Alabama at Birmingham
| | - Jacob Files
- Division of Infectious Diseases, Department of Medicine, University of Alabama at Birmingham
| | - Kai Qin
- Division of Infectious Diseases, Department of Medicine, University of Alabama at Birmingham
| | - Andrew Fiore-Gartland
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Kristen W Cohen
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Stephen C De Rosa
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Anju Bansal
- Division of Infectious Diseases, Department of Medicine, University of Alabama at Birmingham
| | - Paul A Goepfert
- Division of Infectious Diseases, Department of Medicine, University of Alabama at Birmingham
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15
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Abstract
The course of Human Immunodeficiency Virus type 1 (HIV) infection is a dynamic interplay in which both host and viral genetic variation, among other factors, influence disease susceptibility and rate of progression. HIV set-point viral load (spVL), a key indicator of HIV disease progression, has an estimated 30% of variance attributable to common heritable effects and roughly 70% attributable to environmental factors and/or additional non-genetic factors. Genome-wide genotyping and sequencing studies have allowed for large-scale association testing studying host and viral genetic variants associated with infection and disease progression. Host genomics of HIV infection has been studied predominantly in Caucasian populations consistently identifying human leukocyte antigen (HLA) genes and C-C motif chemokine receptor 5 as key factors of HIV susceptibility and progression. However, these studies don’t fully assess all classes of genetic variation (e.g., very rare polymorphisms, copy number variants etc.) and do not inform on non-European ancestry groups. Additionally, viral sequence variability has been demonstrated to influence disease progression independently of host genetic variation. Viral sequence variation can be attributed to the rapid evolution of the virus within the host due to the selective pressure of the host immune response. As the host immune system responds to the virus, e.g., through recognition of HIV antigens, the virus is able to mitigate this response by evolving HLA-specific escape mutations. Diversity of viral genotypes has also been correlated with moderate to strong effects on CD4+ T cell decline and some studies showing weak to no correlation with spVL. There is evidence to support these viral genetic factors being heritable between individuals and the evolution of these factors having important consequences in the genetic epidemiology of HIV infection on a population level. This review will discuss the host-pathogen interaction of HIV infection, explore the importance of host and viral genetics for a better understanding of pathogenesis and identify opportunities for additional genetic studies.
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Affiliation(s)
- Riley H Tough
- JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, MB, Canada.,Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
| | - Paul J McLaren
- JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, MB, Canada.,Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
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16
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Liu D, Wang C, Hora B, Zuo T, Goonetilleke N, Liu MKP, Berrong M, Ferrari G, McMichael AJ, Bhattacharya T, Perelson AS, Gao F. A strongly selected mutation in the HIV-1 genome is independent of T cell responses and neutralizing antibodies. Retrovirology 2017; 14:46. [PMID: 29017536 PMCID: PMC5634943 DOI: 10.1186/s12977-017-0371-4] [Citation(s) in RCA: 2] [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: 06/23/2017] [Accepted: 10/03/2017] [Indexed: 01/19/2023] Open
Abstract
Background Mutations rapidly accumulate in the HIV-1 genome after infection. Some of those mutations are selected by host immune responses and often cause viral fitness losses. This study is to investigate whether strongly selected mutations that are not associated with immune responses result in fitness losses. Results Strongly selected mutations were identified by analyzing 5′-half HIV-1 genome (gag/pol) sequences from longitudinal samples of subject CH0131. The K43R mutation in the gag gene was first detected at day 91 post screening and was fixed in the viral population at day 273 while the synonymous N323tc mutation was first detected at day 177 and fixed at day 670. No conventional or cryptic T cell responses were detected against either mutation sites by ELISpot analysis. However, when fitness costs of both mutations were measured by introducing each mutation into their cognate transmitted/founder (T/F) viral genome, the K43R mutation caused a significant fitness loss while the N323tc mutation had little impact on viral fitness. Conclusions The rapid fixation, the lack of detectable immune responses and the significant fitness cost of the K43R mutation suggests that it was strongly selected by host factors other than T cell responses and neutralizing antibodies.
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Affiliation(s)
- Donglai Liu
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin, China.,Department of Medicine, Duke Human Vaccine Institute, Duke University Medical Center, 303 Research Dr., 244 Sands Building, DUMC 102359, Durham, NC, 27710, USA.,Division II of In Vitro Diagnostics for Infectious Diseases, Institute for In Vitro Diagnostics Control, National Institutes for Food and Drug Control, Beijing, China
| | - Chu Wang
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin, China.,Department of Medicine, Duke Human Vaccine Institute, Duke University Medical Center, 303 Research Dr., 244 Sands Building, DUMC 102359, Durham, NC, 27710, USA
| | - Bhavna Hora
- Department of Medicine, Duke Human Vaccine Institute, Duke University Medical Center, 303 Research Dr., 244 Sands Building, DUMC 102359, Durham, NC, 27710, USA
| | - Tao Zuo
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin, China.,Department of Medicine, Duke Human Vaccine Institute, Duke University Medical Center, 303 Research Dr., 244 Sands Building, DUMC 102359, Durham, NC, 27710, USA
| | - Nilu Goonetilleke
- Department of Microbiology, Immunology and Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Michael K P Liu
- Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, England, UK
| | - Mark Berrong
- Department of Surgery, Duke University Medical Center, Durham, NC, USA
| | - Guido Ferrari
- Department of Surgery, Duke University Medical Center, Durham, NC, USA
| | - Andrew J McMichael
- Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, England, UK
| | | | - Alan S Perelson
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Feng Gao
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin, China. .,Department of Medicine, Duke Human Vaccine Institute, Duke University Medical Center, 303 Research Dr., 244 Sands Building, DUMC 102359, Durham, NC, 27710, USA.
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17
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Sundaramurthi JC, Ashokkumar M, Swaminathan S, Hanna LE. HLA based selection of epitopes offers a potential window of opportunity for vaccine design against HIV. Vaccine 2017; 35:5568-5575. [PMID: 28888341 DOI: 10.1016/j.vaccine.2017.08.070] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 08/18/2017] [Accepted: 08/24/2017] [Indexed: 12/21/2022]
Abstract
The pace of progression to AIDS after HIV infection varies from individual to individual. While some individuals develop AIDS quickly, others are protected from the onset of disease for more than a decade (elite controllers and long term non-progressors). The mechanisms of protection are not yet clearly understood, though various factors including host genetics, immune components and virus attenuation have been elucidated partly. The influence of HLA alleles on HIV-1 infection and disease outcome has been studied extensively. Several HLA alleles are known to be associated with resistance to infection or delayed progression to AIDS after infection. Similarly, certain HLA alleles are reported to be associated with rapid progression to disease. Since HLA alleles influence the outcome of HIV infection differentially, selection of epitopes specifically recognized by protective alleles could serve asa rational means for HIV vaccine design. In this review article, we discuss existing knowledge on HLA alleles and their association with resistance/susceptibility to HIV and its relevance to vaccine design.
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Affiliation(s)
- Jagadish Chandrabose Sundaramurthi
- National Institute for Research in Tuberculosis (ICMR), (Formerly Tuberculosis Research Centre), Chetpet, Chennai 600031, Tamil Nadu, India
| | - Manickam Ashokkumar
- National Institute for Research in Tuberculosis (ICMR), (Formerly Tuberculosis Research Centre), Chetpet, Chennai 600031, Tamil Nadu, India
| | - Soumya Swaminathan
- National Institute for Research in Tuberculosis (ICMR), (Formerly Tuberculosis Research Centre), Chetpet, Chennai 600031, Tamil Nadu, India
| | - Luke Elizabeth Hanna
- National Institute for Research in Tuberculosis (ICMR), (Formerly Tuberculosis Research Centre), Chetpet, Chennai 600031, Tamil Nadu, India.
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18
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Selhorst P, Combrinck C, Ndabambi N, Ismail SD, Abrahams MR, Lacerda M, Samsunder N, Garrett N, Abdool Karim Q, Abdool Karim SS, Williamson C. Replication Capacity of Viruses from Acute Infection Drives HIV-1 Disease Progression. J Virol 2017; 91:e01806-16. [PMID: 28148791 DOI: 10.1128/JVI.01806-16] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 01/19/2017] [Indexed: 01/09/2023] Open
Abstract
The viral genotype has been shown to play an important role in HIV pathogenesis following transmission. However, the viral phenotypic properties that contribute to disease progression remain unclear. Most studies have been limited to the evaluation of Gag function in the context of a recombinant virus backbone. Using this approach, important biological information may be lost, making the evaluation of viruses obtained during acute infection, representing the transmitted virus, a more biologically relevant model. Here, we evaluate the roles of viral infectivity and the replication capacity of viruses from acute infection in disease progression in women who seroconverted in the CAPRISA 004 tenofovir microbicide trial. We show that viral replication capacity, but not viral infectivity, correlates with the set point viral load (Spearman r = 0.346; P = 0.045) and that replication capacity (hazard ratio [HR] = 4.52; P = 0.01) can predict CD4 decline independently of the viral load (HR = 2.9; P = 0.004) or protective HLA alleles (HR = 0.61; P = 0.36). We further demonstrate that Gag-Pro is not the main driver of this association, suggesting that additional properties of the transmitted virus play a role in disease progression. Finally, we find that although viruses from the tenofovir arm were 2-fold less infectious, they replicated at rates similar to those of viruses from the placebo arm. This indicates that the use of tenofovir gel did not select for viral variants with higher replication capacity. Overall, this study supports a strong influence of the replication capacity in acute infection on disease progression, potentially driven by interaction of multiple genes rather than a dominant role of the major structural gene gagIMPORTANCE HIV disease progression is known to differ between individuals, and defining which fraction of this variation can be attributed to the virus is important both clinically and epidemiologically. In this study, we show that the replication capacity of viruses isolated during acute infection predicts subsequent disease progression and drives CD4 decline independently of the viral load. This provides further support for the hypothesis that the replication capacity of the transmitted virus determines the initial damage to the immune system, setting the pace for later disease progression. However, we did not find evidence that the major structural gene gag drives this correlation, highlighting the importance of other genes in determining disease progression.
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19
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Chopera DR, Ntale R, Ndabambi N, Garrett N, Gray CM, Matten D, Abdool Karim Q, Abdool Karim S, Williamson C. Early evolution of human leucocyte antigen-associated escape mutations in variable Gag proteins predicts CD4+ decline in HIV-1 subtype C-infected women. AIDS 2017; 31:191-7. [PMID: 27755110 DOI: 10.1097/QAD.0000000000001298] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
OBJECTIVE HIV-1 escape from cytotoxic T-lymphocytes results in the accumulation of human leucocyte antigen (HLA)-associated mutations in the viral genome. To understand the contribution of early escape to disease progression, this study investigated the evolution and pathogenic implications of cytotoxic T-lymphocyte escape in a cohort followed from infection for 5 years. METHODS Viral loads and CD4 cell counts were monitored in 78 subtype C-infected individuals from onset of infection until CD4 cell count decline to less than 350 cells/μl or 5 years postinfection. The gag gene was sequenced and HLA-associated changes between enrolment and 12 months postinfection were mapped. RESULTS HLA-associated escape mutations were identified in 48 (62%) of the participants and were associated with CD4 decline to less than 350 cells/μl (P = 0.05). Escape mutations in variable Gag proteins (p17 and p7p6) had a greater impact on disease progression than escape in more conserved regions (p24) (P = 0.03). The association between HLA-associated escape mutations and CD4 decline was independent of protective HLA allele (B57, B58 : 01 and B81) expression. CONCLUSION The high frequency of escape contributed to rapid disease progression in this cohort. Although HLA-adaption in both conserved and variable Gag domains in the first year of infection was detrimental to long-term clinical outcome, escape in variable domains had greater impact.
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20
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Abstract
In this chapter, we will review recent research on the virology of HIV-1 transmission and the impact of the transmitted virus genotype on subsequent disease progression. In most instances of HIV-1 sexual transmission, a single genetic variant, or a very limited number of variants from the diverse viral quasi-species present in the transmitting partner establishes systemic infection. Transmission involves both stochastic and selective processes, such that in general a minority variant in the donor is transmitted. While there is clear evidence for selection, the biological properties that mediate transmission remain incompletely defined. Nevertheless, the genotype of the transmitted founder virus, which reflects prior exposure to and escape from host immune responses, clearly influences disease progression. Some escape mutations impact replicative capacity, while others effectively cloak the virus from the newly infected host's immune response by preventing recognition. It is the balance between the impact of escape mutations on viral fitness and susceptibility to the host immunogenetics that defines HIV-1 disease progression.
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Carlson JM, Du VY, Pfeifer N, Bansal A, Tan VY, Power K, Brumme CJ, Kreimer A, DeZiel CE, Fusi N, Schaefer M, Brockman MA, Gilmour J, Price MA, Kilembe W, Haubrich R, John M, Mallal S, Shapiro R, Frater J, Harrigan PR, Ndung'u T, Allen S, Heckerman D, Sidney J, Allen TM, Goulder PJ, Brumme ZL, Hunter E, Goepfert PA. Impact of pre-adapted HIV transmission. Nat Med 2016; 22:606-13. [PMID: 27183217 DOI: 10.1038/nm.4100] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 04/07/2016] [Indexed: 12/17/2022]
Abstract
Human leukocyte antigen class I (HLA)-restricted CD8(+) T lymphocyte (CTL) responses are crucial to HIV-1 control. Although HIV can evade these responses, the longer-term impact of viral escape mutants remains unclear, as these variants can also reduce intrinsic viral fitness. To address this, we here developed a metric to determine the degree of HIV adaptation to an HLA profile. We demonstrate that transmission of viruses that are pre-adapted to the HLA molecules expressed in the recipient is associated with impaired immunogenicity, elevated viral load and accelerated CD4(+) T cell decline. Furthermore, the extent of pre-adaptation among circulating viruses explains much of the variation in outcomes attributed to the expression of certain HLA alleles. Thus, viral pre-adaptation exploits 'holes' in the immune response. Accounting for these holes may be key for vaccine strategies seeking to elicit functional responses from viral variants, and to HIV cure strategies that require broad CTL responses to achieve successful eradication of HIV reservoirs.
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Van Tran G, Chikata T, Carlson JM, Murakoshi H, Nguyen DH, Tamura Y, Akahoshi T, Kuse N, Sakai K, Sakai S, Cobarrubias K, Oka S, Brumme ZL, Van Nguyen K, Takiguchi M; NHTD Treatment-Naive Cohort Study Group. A strong association of human leukocyte antigen-associated Pol and Gag mutations with clinical parameters in HIV-1 subtype A/E infection. AIDS 2016; 30:681-9. [PMID: 26595539 DOI: 10.1097/QAD.0000000000000969] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVES Identification of human leukocyte antigen-associated HIV-1 polymorphisms (HLA-APs) in different global populations furthers our understanding of HIV-1 pathogenesis and may help identify candidate immunogens for HIV vaccines targeted to these populations. Although numerous population-based studies identifying HLA-APs have been conducted in HIV-1 subtype B- and subtype C-infected cohorts, few have focused on subtype A/E. DESIGN We investigated HLA-APs in a cohort of chronically HIV-1 subtype A/E-infected Vietnamese individuals. METHODS HLA-APs in HIV-1 Gag, Pol, and Nef regions from 388 treatment-naive individuals chronically infected with HIV-1 subtype A/E were analyzed using phylogenetically informed approaches. RESULTS A total of 303 HLA-APs were identified. HLA-APs occurring at six positions in Gag and six positions in Pol were significantly associated with higher plasma viral load (pVL), whereas HLA-APs occurring at two positions in Gag and 13 positions in Pol were significantly associated with lower CD4 T-cell counts. Furthermore, the proportion of Pol codons harboring an HLA-AP specific to the host's HLA correlated positively with HIV-1 pVL (R = 0.22; P < 0.0001) and inversely with CD4 T-cell counts (R = -0.32; P < 0.0001). Similarly, the proportion of HLA-associated Gag codons harboring host-specific HLA-AP correlated inversely with CD4 T-cell counts (R = -0.13; P = 0.01). CONCLUSION These significant associations between HIV-1 amino acids adapted to Vietnamese HLA alleles and higher pVL and lower CD4 T-cell counts suggests that accumulation of cytotoxic T cells escape mutations may influence clinical outcomes in HIV-1 subtype A/E-infected Vietnamese individuals.
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Nagaraja P, Alexander HK, Bonhoeffer S, Dixit NM. Influence of recombination on acquisition and reversion of immune escape and compensatory mutations in HIV-1. Epidemics 2016; 14:11-25. [DOI: 10.1016/j.epidem.2015.09.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Revised: 09/11/2015] [Accepted: 09/11/2015] [Indexed: 11/28/2022] Open
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Sakai K, Chikata T, Brumme ZL, Brumme CJ, Gatanaga H, Gatanag H, Oka S, Takiguchi M. Lack of a significant impact of Gag-Protease-mediated HIV-1 replication capacity on clinical parameters in treatment-naive Japanese individuals. Retrovirology 2015; 12:98. [PMID: 26585907 PMCID: PMC4653850 DOI: 10.1186/s12977-015-0223-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [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: 04/30/2015] [Accepted: 11/08/2015] [Indexed: 01/29/2023] Open
Abstract
Background HLA class I-associated escape mutations in HIV-1 Gag can reduce viral replication, suggesting that associated fitness costs could impact HIV-1 disease progression. Previous studies in North American and African cohorts have reported reduced Gag-Protease mediated viral replication capacity (Gag-Pro RC) in individuals expressing protective HLA class I alleles including HLA-B*57:01, B*27:05, and B*81:01. These studies also reported significant positive associations between Gag-Pro RCs and plasma viral load (pVL). However, these HLA alleles are virtually absent in Japan, and the importance of Gag as an immune target is not clearly defined in this population. Results We generated chimeric NL4-3 viruses carrying patient-derived Gag-Protease from 306 treatment-naive Japanese individuals chronically infected with HIV-1 subtype B. We analyzed associations between Gag-Pro RC and clinical markers of HIV-1 infection and host HLA expression. We observed no significant correlation between Gag-Pro RC and pVL in Japan in the overall cohort. However, upon exclusion of individuals expressing Japanese protective alleles HLA-B*52:01 and B*67:01, Gag-Pro RC correlated positively with pVL and negatively with CD4 T-cell count. Our results thus contrast with studies from other global cohorts reporting significantly lower Gag-Pro RC among persons expressing protective HLA alleles, and positive relationships between Gag-Pro RC and pVL in the overall study populations. We also identified five amino acids in Gag-Protease significantly associated with Gag-Pro RC, whose effects on RC were confirmed by site-directed mutagenesis. However, of the four mutations that decreased Gag-Pro RC, none were associated with reductions in pVL in Japan though two were associated with lower pVL in North America. Conclusions These data indicate that Gag fitness does not affect clinical outcomes in subjects with protective HLA class I alleles as well as the whole Japanese population. Moreover, the impact of Gag fitness costs on HIV-1 clinical parameters in chronic infection is likely low in Japan compared to other global populations. Electronic supplementary material The online version of this article (doi:10.1186/s12977-015-0223-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Keiko Sakai
- Center for AIDS Research, Kumamoto University, Kumamoto, 860-0811, Japan.
| | - Takayuki Chikata
- Center for AIDS Research, Kumamoto University, Kumamoto, 860-0811, Japan.
| | - Zabrina L Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada. .,Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada.
| | - Chanson J Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada.
| | - Hiroyuki Gatanaga
- Center for AIDS Research, Kumamoto University, Kumamoto, 860-0811, Japan.
| | | | - Shinichi Oka
- Center for AIDS Research, Kumamoto University, Kumamoto, 860-0811, Japan. .,National Center for Global Health and Medicine, Tokyo, 162-8655, Japan.
| | - Masafumi Takiguchi
- Center for AIDS Research, Kumamoto University, Kumamoto, 860-0811, Japan. .,International Research Center for Medical Sciences, Kumamoto University, Kumamoto, 860-0811, Japan. .,Nuffield Department of Medicine, University of Oxford, Oxford, UK.
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Gadhamsetty S, Beltman JB, de Boer RJ. What do mathematical models tell us about killing rates during HIV-1 infection? Immunol Lett 2015; 168:1-6. [PMID: 26279491 DOI: 10.1016/j.imlet.2015.07.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 07/15/2015] [Accepted: 07/31/2015] [Indexed: 10/23/2022]
Abstract
Over the past few decades the extent to which cytotoxic T lymphocytes (CTLs) control human immunodeficiency virus (HIV) replication has been studied extensively, yet their role and mode of action remain controversial. In some studies, CTLs were found to kill a large fraction of the productively infected cells relative to the viral cytopathicity, whereas in others CTLs were suggested to kill only a small fraction of infected cells. In this review, we compile published estimates of CTL-mediated death rates, and examine whether these studies permit determining the rate at which CTLs kill HIV-1 infected cells. We highlight potential misinterpretations of the CTL-killing rates from the escape rates of mutants, and from perturbations of the steady state viral load during chronic infection. Our major conclusion is that CTL-mediated killing rates remain unknown. But contrary to current consensus, we argue that killing rates higher than one per day are perfectly consistent with the experimental data, which would imply that the majority of the productively infected cells could still die from CTL-mediated killing rather than from viral cytopathicity.
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Affiliation(s)
- Saikrishna Gadhamsetty
- Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
| | - Joost B Beltman
- Division of Toxicology, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Rob J de Boer
- Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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Gounder K, Padayachi N, Mann JK, Radebe M, Mokgoro M, van der Stok M, Mkhize L, Mncube Z, Jaggernath M, Reddy T, Walker BD, Ndung'u T. High frequency of transmitted HIV-1 Gag HLA class I-driven immune escape variants but minimal immune selection over the first year of clade C infection. PLoS One 2015; 10:e0119886. [PMID: 25781986 DOI: 10.1371/journal.pone.0119886] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 02/03/2015] [Indexed: 11/19/2022] Open
Abstract
In chronic HIV infection, CD8+ T cell responses to Gag are associated with lower viral loads, but longitudinal studies of HLA-restricted CD8+ T cell-driven selection pressure in Gag from the time of acute infection are limited. In this study we examined Gag sequence evolution over the first year of infection in 22 patients identified prior to seroconversion. A total of 310 and 337 full-length Gag sequences from the earliest available samples (median = 14 days after infection [Fiebig stage I/II]) and at one-year post infection respectively were generated. Six of 22 (27%) individuals were infected with multiple variants. There was a trend towards early intra-patient viral sequence diversity correlating with viral load set point (p = 0.07, r = 0.39). At 14 days post infection, 59.7% of Gag CTL epitopes contained non-consensus polymorphisms and over half of these (35.3%) comprised of previously described CTL escape variants. Consensus and variant CTL epitope proportions were equally distributed irrespective of the selecting host HLA allele and most epitopes remained unchanged over 12 months post infection. These data suggest that intrapatient diversity during acute infection is an indicator of disease outcome. In this setting, there is a high rate of transmitted CTL escape variants and limited immune selection in Gag during the first year of infection. These data have relevance for vaccine strategies designed to elicit effective CD8+ T cell immune responses.
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Williamson C, Swanstrom R. HIV-1 replication capacity: Setting the pace of disease. Proc Natl Acad Sci U S A 2015; 112:3591-2. [PMID: 25775570 DOI: 10.1073/pnas.1502208112] [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: 11/18/2022] Open
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28
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Serwanga J, Nakiboneka R, Mugaba S, Magambo B, Ndembi N, Gotch F, Kaleebu P. Frequencies of Gag-restricted T-cell escape "footprints" differ across HIV-1 clades A1 and D chronically infected Ugandans irrespective of host HLA B alleles. Vaccine 2015; 33:1664-72. [PMID: 25728323 PMCID: PMC4374673 DOI: 10.1016/j.vaccine.2015.02.037] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [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: 09/17/2014] [Revised: 01/29/2015] [Accepted: 02/16/2015] [Indexed: 01/05/2023]
Abstract
A and D infected subjects even though they bear the same presenting HLA alleles, and live in the same environment. Escape mutations that are known to confer survival advantage were more frequent in clade A-infected subjects irrespective of host HLA alleles. There was no evidence to link this difference in outcome to the evaluated adaptive T-Cell responses (IFN-γ responses and polyfunctional responses) to those key structurally constrained Gag epitopes. However, we have demonstrated that there was significantly greater selective pressure on the Gag protein of clade A than that of clade D. The data are in line with the known faster disease progression in clade D than clade A infected individuals. The data also highlight that the current difficulties in formulating a global HIV vaccine design will be further challenged by clade associated differences in outcome.
Objective(s) We evaluated relationships between critical Gag T-cell escape mutations and concomitant T-cell responses to determine whether HLA-restricted Gag mutations that confer protection, occur at similar rates in a population infected with mixed HIV-1 clades A1 and D viruses. Methods Assessment of Gag selective pressure, and adaptive T-cell functions to KAFSPEVIPMF (KF11), ISPRTLNAW (ISW9) and TSTLQEQIGW (TW10) Gag epitopes were combined with host HLA to assess correlations with rates of critical epitope escape mutations in clades A1- (n = 23) and D- (n = 21) infected, untreated subjects. Infecting clades and selection pressure were determined from the gag sequences. Results Overall, Gag escape mutations A163X in KF11 were detected in 61% (14/23) A1- infected compared to 5% (1/21) in D-infected subjects (p = 0.00015). Gag mutations I147X in the ISW9 epitope were seen in 43%: (10/23) clade A compared to 5%: (1/21) clade D infected subjects, p = 0.007, Fisher's Exact test. Both mutations were more frequent in clade A1 infection. Frequencies of the measured epitope-specific T-cell responses were comparable across clades. Peptide binding affinities for the restricting HLA alleles did not differ across clades. Overall, selection pressure on the Gag protein was significantly greater in clade A than in clade D sequences. Conclusions These findings imply that HIV-1 vaccine strategies designed to target structurally constrained T-cell epitopes may be further challenged by clade-driven outcomes in specific HLA-restricted Gag epitopes. Equally, the data are line with slower HIV-1 disease progression in clade A infection; and raise hope that increased selective pressure on Gag may be protective irrespective of host HLA alleles.
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Affiliation(s)
| | | | - Susan Mugaba
- MRC/UVRI Uganda Research Unit on AIDS, Entebbe, Uganda
| | - Brian Magambo
- MRC/UVRI Uganda Research Unit on AIDS, Entebbe, Uganda
| | | | - Frances Gotch
- Department of Immunology, Imperial College, Chelsea & Westminster Hospital, London, United Kingdom
| | - Pontiano Kaleebu
- MRC/UVRI Uganda Research Unit on AIDS, Entebbe, Uganda; London School of Hygiene and Tropical Medicine, United Kingdom
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Carlson JM, Le AQ, Shahid A, Brumme ZL. HIV-1 adaptation to HLA: a window into virus-host immune interactions. Trends Microbiol 2015; 23:212-24. [PMID: 25613992 DOI: 10.1016/j.tim.2014.12.008] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 12/04/2014] [Accepted: 12/16/2014] [Indexed: 11/26/2022]
Abstract
HIV-1 develops specific mutations within its genome that allow it to escape detection by human leukocyte antigen (HLA) class I-restricted immune responses, notably those of CD8(+) cytotoxic T lymphocytes (CTL). HLA thus represents a major force driving the evolution and diversification of HIV-1 within individuals and at the population level. Importantly, the study of HIV-1 adaptation to HLA also represents an opportunity to identify what qualities constitute an effective immune response, how the virus in turn adapts to these pressures, and how we may harness this information to design HIV-1 vaccines that stimulate effective cellular immunity.
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Affiliation(s)
| | - Anh Q Le
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Aniqa Shahid
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada; British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada.
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Yue L, Pfafferott KJ, Baalwa J, Conrod K, Dong CC, Chui C, Rong R, Claiborne DT, Prince JL, Tang J, Ribeiro RM, Cormier E, Hahn BH, Perelson AS, Shaw GM, Karita E, Gilmour J, Goepfert P, Derdeyn CA, Allen SA, Borrow P, Hunter E. Transmitted virus fitness and host T cell responses collectively define divergent infection outcomes in two HIV-1 recipients. PLoS Pathog 2015; 11:e1004565. [PMID: 25569444 DOI: 10.1371/journal.ppat.1004565] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2014] [Accepted: 11/10/2014] [Indexed: 12/27/2022] Open
Abstract
Control of virus replication in HIV-1 infection is critical to delaying disease progression. While cellular immune responses are a key determinant of control, relatively little is known about the contribution of the infecting virus to this process. To gain insight into this interplay between virus and host in viral control, we conducted a detailed analysis of two heterosexual HIV-1 subtype A transmission pairs in which female recipients sharing three HLA class I alleles exhibited contrasting clinical outcomes: R880F controlled virus replication while R463F experienced high viral loads and rapid disease progression. Near full-length single genome amplification defined the infecting transmitted/founder (T/F) virus proteome and subsequent sequence evolution over the first year of infection for both acutely infected recipients. T/F virus replicative capacities were compared in vitro, while the development of the earliest cellular immune response was defined using autologous virus sequence-based peptides. The R880F T/F virus replicated significantly slower in vitro than that transmitted to R463F. While neutralizing antibody responses were similar in both subjects, during acute infection R880F mounted a broad T cell response, the most dominant components of which targeted epitopes from which escape was limited. In contrast, the primary HIV-specific T cell response in R463F was focused on just two epitopes, one of which rapidly escaped. This comprehensive study highlights both the importance of the contribution of the lower replication capacity of the transmitted/founder virus and an associated induction of a broad primary HIV-specific T cell response, which was not undermined by rapid epitope escape, to long-term viral control in HIV-1 infection. It underscores the importance of the earliest CD8 T cell response targeting regions of the virus proteome that cannot mutate without a high fitness cost, further emphasizing the need for vaccines that elicit a breadth of T cell responses to conserved viral epitopes.
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Radebe M, Gounder K, Mokgoro M, Ndhlovu ZM, Mncube Z, Mkhize L, van der Stok M, Jaggernath M, Walker BD, Ndung'u T. Broad and persistent Gag-specific CD8+ T-cell responses are associated with viral control but rarely drive viral escape during primary HIV-1 infection. AIDS 2015; 29:23-33. [PMID: 25387316 DOI: 10.1097/QAD.0000000000000508] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE We characterized protein-specific CD8 T-cell immunodominance patterns during the first year of HIV-1 infection, and their impact on viral evolution and immune control. METHODS We analyzed CD8 T-cell responses to the full HIV-1 proteome during the first year of infection in 18 antiretroviral-naïve individuals with acute HIV-1 subtype C infection, all identified prior to seroconversion. Ex-vivo and cultured interferon-γ ELISPOT assays were performed and viruses from plasma were sequenced within defined CTL Gag epitopes. RESULTS Nef-specific CD8 T-cell responses were dominant during the first 4 weeks after infection and made up 40% of the total responses at this time; yet, by 1 year, responses against this region had declined and Gag responses made up to 47% of all T-cell responses measured. An inverse correlation between the breadth of Gag-specific responses and viral load set point was evident at 26 weeks after infection (P = 0.0081, r = -0.60) and beyond. An inverse correlation between the number of persistent responses targeting Gag and viral set point was also identified (P = 0.01, r = -0.58). Gag-specific responses detectable by the cultured ELISPOT assay correlated negatively with viral load set point (P = 0.0013, r = -0.91). Sequence evolution in targeted and nontargeted Gag epitopes in this cohort was infrequent. CONCLUSIONS These data underscore the importance of HIV-specific CD8 T-cell responses, particularly to the Gag protein, in the maintenance of low viral load levels during primary infection, and show that these responses are initially poorly elicited by natural infection. These data have implications for vaccine design strategies.
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Mackelprang RD, Carrington M, Thomas KK, Hughes JP, Baeten JM, Wald A, Farquhar C, Fife K, Campbell MS, Kapiga S, Gao X, Mullins JI, Lingappa JR. Host genetic and viral determinants of HIV-1 RNA set point among HIV-1 seroconverters from sub-saharan Africa. J Virol 2015; 89:2104-11. [PMID: 25473042 DOI: 10.1128/JVI.01573-14] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
UNLABELLED We quantified the collective impact of source partner HIV-1 RNA levels, human leukocyte antigen (HLA) alleles, and innate responses through Toll-like receptor (TLR) alleles on the HIV-1 set point. Data came from HIV-1 seroconverters in African HIV-1 serodiscordant couple cohorts. Linear regression was used to determine associations with set point and R(2) to estimate variation explained by covariates. The strongest predictors of set point were HLA alleles (B*53:01, B*14:01, and B*27:03) and plasma HIV-1 levels of the transmitting partner, which explained 13% and 10% of variation in set point, respectively. HLA-A concordance between partners and TLR polymorphisms (TLR2 rs3804100 and TLR7 rs179012) also were associated with set point, explaining 6% and 5% of the variation, respectively. Overall, these factors and genital factors of the transmitter (i.e., male circumcision, bacterial vaginosis, and use of acyclovir) explained 46% of variation in set point. We found that both innate and adaptive immune responses, together with plasma HIV-1 levels of the transmitting partner, explain almost half of the variation in viral load set point. IMPORTANCE After HIV-1 infection, uncontrolled virus replication leads to a rapid increase in HIV-1 concentrations. Once host immune responses develop, however, HIV-1 levels reach a peak and subsequently decline until they reach a stable level that may persist for years. This stable HIV-1 set point represents an equilibrium between the virus and host responses and is predictive of later disease progression and transmission potential. Understanding how host and virus factors interact to determine HIV-1 set point may elucidate novel mechanisms or biological pathways for treating HIV-1 infection. We identified host and virus factors that predict HIV-1 set point in people who recently acquired HIV-1, finding that both innate and adaptive immune responses, along with factors that likely influence HIV-1 virulence and inoculum, explain ∼46% of the variation in HIV-1 set point.
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Liu D, Zuo T, Hora B, Song H, Kong W, Yu X, Goonetilleke N, Bhattacharya T, Perelson AS, Haynes BF, McMichael AJ, Gao F. Preexisting compensatory amino acids compromise fitness costs of a HIV-1 T cell escape mutation. Retrovirology 2014; 11:101. [PMID: 25407514 PMCID: PMC4264250 DOI: 10.1186/s12977-014-0101-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [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: 06/19/2014] [Accepted: 10/28/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Fitness costs and slower disease progression are associated with a cytolytic T lymphocyte (CTL) escape mutation T242N in Gag in HIV-1-infected individuals carrying HLA-B*57/5801 alleles. However, the impact of different context in diverse HIV-1 strains on the fitness costs due to the T242N mutation has not been well characterized. To better understand the extent of fitness costs of the T242N mutation and the repair of fitness loss through compensatory amino acids, we investigated its fitness impact in different transmitted/founder (T/F) viruses. RESULTS The T242N mutation resulted in various levels of fitness loss in four different T/F viruses. However, the fitness costs were significantly compromised by preexisting compensatory amino acids in (Isoleucine at position 247) or outside (glutamine at position 219) the CTL epitope. Moreover, the transmitted T242N escape mutant in subject CH131 was as fit as the revertant N242T mutant and the elimination of the compensatory amino acid I247 in the T/F viral genome resulted in significant fitness cost, suggesting the fitness loss caused by the T242N mutation had been fully repaired in the donor at transmission. Analysis of the global circulating HIV-1 sequences in the Los Alamos HIV Sequence Database showed a high prevalence of compensatory amino acids for the T242N mutation and other T cell escape mutations. CONCLUSIONS Our results show that the preexisting compensatory amino acids in the majority of circulating HIV-1 strains could significantly compromise the fitness loss due to CTL escape mutations and thus increase challenges for T cell based vaccines.
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Affiliation(s)
- Donglai Liu
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, 27710, USA. .,National Engineering Laboratory For AIDS Vaccine, College of Life Science, Jilin University, Changchun, 130012, Jilin, China.
| | - Tao Zuo
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, 27710, USA. .,National Engineering Laboratory For AIDS Vaccine, College of Life Science, Jilin University, Changchun, 130012, Jilin, China.
| | - Bhavna Hora
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, 27710, USA.
| | - Hongshuo Song
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, 27710, USA.
| | - Wei Kong
- National Engineering Laboratory For AIDS Vaccine, College of Life Science, Jilin University, Changchun, 130012, Jilin, China.
| | - Xianghui Yu
- National Engineering Laboratory For AIDS Vaccine, College of Life Science, Jilin University, Changchun, 130012, Jilin, China.
| | - Nilu Goonetilleke
- Department of Microbiology, Immunology and Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
| | - Tanmoy Bhattacharya
- Theoretical Division, Los Alamos National laboratory, Los Alamos, NM, 87545, USA.
| | - Alan S Perelson
- Theoretical Division, Los Alamos National laboratory, Los Alamos, NM, 87545, USA.
| | - Barton F Haynes
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, 27710, USA.
| | - Andrew J McMichael
- Weatherall Institute of molecular Medicine, University of Oxford, Oxford, OX3 9DS, England, UK.
| | - Feng Gao
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, 27710, USA. .,National Engineering Laboratory For AIDS Vaccine, College of Life Science, Jilin University, Changchun, 130012, Jilin, China.
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Kharsany AB, Buthelezi TJ, Frohlich JA, Yende-Zuma N, Samsunder N, Mahlase G, Williamson C, Travers SA, Marais JC, Dellar R, Karim SSA, Karim QA. HIV infection in high school students in rural South Africa: role of transmissions among students. AIDS Res Hum Retroviruses 2014; 30:956-65. [PMID: 25077861 DOI: 10.1089/aid.2014.0110] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In South Africa, adolescents constitute a key population at high risk of HIV acquisition. However, little is known about HIV transmission among students within schools. This study was undertaken to assess the risk factors for HIV infection and the extent of transmission among rural high school students. Between February and May 2012, consenting students from five randomly selected public sector high schools in rural KwaZulu-Natal participated in an anonymous cross-sectional survey. Dried blood spot samples were collected and tested for HIV. β-Human chorionic gonadotropin (βHCG) levels were measured in females for pregnancy. Family circumstances as well as sociodemographic and behavioral factors were assessed as potential risk factors. A subset (106/148, 72%) of HIV-positive samples underwent gag p17p24 sequencing for phylogenetic analysis. A total of 3,242 students (81.7% of enrolled students) participated. HIV prevalence was 6.8% [95% confidence interval (CI) 3.9-9.8%] in girls and 2.7% (CI 1.6-3.8%) in boys [adjusted odds ratio (aOR)=3.0, CI 2.4-3.8; p<0.001]. HIV prevalence increased from 4.6% (95% CI 1.9-7.3) in the 12- to 15-year-old girls to 23.1% (95% CI 7.7-38.5) in girls over 20 years, while in boys HIV prevalence increased from 2.7% (95% CI 0.6-4.9) in the 12- to15-year-old boys to 11.1% (95% CI 2.7-19.4) in those over 20 years. Sequencing of samples obtained from students revealed only two clusters, suggesting within-school transmission and three interschool clusters, while the remainder was most likely acquired from sources other than those currently found in students attending the school concerned. HIV prevalence in both girls (aOR=3.6, CI 2.9-4.5; p<0.001) and boys (aOR=2.8, CI 1.2-6.2; p=0.01) was higher in those without a living biological mother. The high burden of HIV infection among students was not associated with intraschool transmission in this rural setting. Lack of a living parent is an important factor defining high risk in this group of adolescents.
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Affiliation(s)
- Ayesha B.M. Kharsany
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Congella, Durban, South Africa
| | - Thulasizwe John Buthelezi
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Congella, Durban, South Africa
| | - Janet A. Frohlich
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Congella, Durban, South Africa
| | - Nonhlanhla Yende-Zuma
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Congella, Durban, South Africa
| | - Natasha Samsunder
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Congella, Durban, South Africa
| | | | - Carolyn Williamson
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Congella, Durban, South Africa
- Division of Medical Virology, Clinical Laboratory Sciences and Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- National Health Laboratory Service, Durban, South Africa
| | - Simon A. Travers
- South African National Bioinformatics Institute, South African Medical Research Council Bioinformatics Unit, University of the Western Cape, Bellville, South Africa
| | - Jinny C. Marais
- Division of Medical Virology, Clinical Laboratory Sciences and Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Rachael Dellar
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Congella, Durban, South Africa
| | - Salim S. Abdool Karim
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Congella, Durban, South Africa
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York
| | - Quarraisha Abdool Karim
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Congella, Durban, South Africa
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York
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Claiborne DT, Prince JL, Hunter E. A restriction enzyme based cloning method to assess the in vitro replication capacity of HIV-1 subtype C Gag-MJ4 chimeric viruses. J Vis Exp 2014:51506. [PMID: 25225725 PMCID: PMC4364379 DOI: 10.3791/51506] [Citation(s) in RCA: 10] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
The protective effect of many HLA class I alleles on HIV-1 pathogenesis and disease progression is, in part, attributed to their ability to target conserved portions of the HIV-1 genome that escape with difficulty. Sequence changes attributed to cellular immune pressure arise across the genome during infection, and if found within conserved regions of the genome such as Gag, can affect the ability of the virus to replicate in vitro. Transmission of HLA-linked polymorphisms in Gag to HLA-mismatched recipients has been associated with reduced set point viral loads. We hypothesized this may be due to a reduced replication capacity of the virus. Here we present a novel method for assessing the in vitro replication of HIV-1 as influenced by the gag gene isolated from acute time points from subtype C infected Zambians. This method uses restriction enzyme based cloning to insert the gag gene into a common subtype C HIV-1 proviral backbone, MJ4. This makes it more appropriate to the study of subtype C sequences than previous recombination based methods that have assessed the in vitro replication of chronically derived gag-pro sequences. Nevertheless, the protocol could be readily modified for studies of viruses from other subtypes. Moreover, this protocol details a robust and reproducible method for assessing the replication capacity of the Gag-MJ4 chimeric viruses on a CEM-based T cell line. This method was utilized for the study of Gag-MJ4 chimeric viruses derived from 149 subtype C acutely infected Zambians, and has allowed for the identification of residues in Gag that affect replication. More importantly, the implementation of this technique has facilitated a deeper understanding of how viral replication defines parameters of early HIV-1 pathogenesis such as set point viral load and longitudinal CD4+ T cell decline.
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Affiliation(s)
- Daniel T Claiborne
- Emory Vaccine Center at Yerkes National Primate Research Center, Emory University
| | - Jessica L Prince
- Emory Vaccine Center at Yerkes National Primate Research Center, Emory University
| | - Eric Hunter
- Emory Vaccine Center at Yerkes National Primate Research Center, Emory University; Department of Pathology and Laboratory Medicine, Emory University;
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Song H, Hora B, Bhattacharya T, Goonetilleke N, Liu MKP, Wiehe K, Li H, Iyer SS, McMichael AJ, Perelson AS, Gao F. Reversion and T cell escape mutations compensate the fitness loss of a CD8+ T cell escape mutant in their cognate transmitted/founder virus. PLoS One 2014; 9:e102734. [PMID: 25028937 PMCID: PMC4100905 DOI: 10.1371/journal.pone.0102734] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 06/23/2014] [Indexed: 11/18/2022] Open
Abstract
Immune escape mutations that revert back to the consensus sequence frequently occur in newly HIV-1-infected individuals and have been thought to render the viruses more fit. However, their impact on viral fitness and their interaction with other immune escape mutations have not been evaluated in the background of their cognate transmitted/founder (T/F) viral genomes. To precisely determine the role of reversion mutations, we introduced reversion mutations alone or together with CD8+ T cell escape mutations in their unmodified cognate T/F viral genome and determined their impact on viral fitness in primary CD4+ T cells. Two reversion mutations, V247I and I64T, were identified in Gag and Tat, respectively, but neither had measurable effect on the fitness of their cognate T/F virus. The V247I and G248A mutations that were detected before and concurrently with the potent T cell escape mutation T242N, respectively, were selected by early T cell responses. The V247I or the G248A mutation alone partially restored the fitness loss caused by the T242N mutation. Together they could fully restore the fitness of the T242N mutant to the T/F level. These results demonstrate that the fitness loss caused by a T cell escape mutation could be compensated by preexisting or concurrent reversion and other T cell escape mutations. Our findings indicate that the overall viral fitness is modulated by the complex interplay among T cell escape, compensatory and reversion mutations to maintain the balance between immune escape and viral replication capacity.
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Affiliation(s)
- Hongshuo Song
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Bhavna Hora
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Tanmoy Bhattacharya
- Theoretical Division, Los Alamos National laboratory, Los Alamos, New Mexico, United States of America
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
| | - Nilu Goonetilleke
- Weatherall Institute of molecular Medicine, University of Oxford, Oxford, England, United Kingdom
| | - Michael K. P. Liu
- Weatherall Institute of molecular Medicine, University of Oxford, Oxford, England, United Kingdom
| | - Kevin Wiehe
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Hui Li
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Shilpa S. Iyer
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Andrew J. McMichael
- Weatherall Institute of molecular Medicine, University of Oxford, Oxford, England, United Kingdom
| | - Alan S. Perelson
- Theoretical Division, Los Alamos National laboratory, Los Alamos, New Mexico, United States of America
| | - Feng Gao
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
- * E-mail:
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Carlson JM, Schaefer M, Monaco DC, Batorsky R, Claiborne DT, Prince J, Deymier MJ, Ende ZS, Klatt NR, DeZiel CE, Lin TH, Peng J, Seese AM, Shapiro R, Frater J, Ndung'u T, Tang J, Goepfert P, Gilmour J, Price MA, Kilembe W, Heckerman D, Goulder PJR, Allen TM, Allen S, Hunter E. HIV transmission. Selection bias at the heterosexual HIV-1 transmission bottleneck. Science 2014; 345:1254031. [PMID: 25013080 DOI: 10.1126/science.1254031] [Citation(s) in RCA: 195] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Heterosexual transmission of HIV-1 typically results in one genetic variant establishing systemic infection. We compared, for 137 linked transmission pairs, the amino acid sequences encoded by non-envelope genes of viruses in both partners and demonstrate a selection bias for transmission of residues that are predicted to confer increased in vivo fitness on viruses in the newly infected, immunologically naïve recipient. Although tempered by transmission risk factors, such as donor viral load, genital inflammation, and recipient gender, this selection bias provides an overall transmission advantage for viral quasispecies that are dominated by viruses with high in vivo fitness. Thus, preventative or therapeutic approaches that even marginally reduce viral fitness may lower the overall transmission rates and offer long-term benefits even upon successful transmission.
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Affiliation(s)
| | - Malinda Schaefer
- Emory Vaccine Center at Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Daniela C Monaco
- Emory Vaccine Center at Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Rebecca Batorsky
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02114, USA
| | - Daniel T Claiborne
- Emory Vaccine Center at Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Jessica Prince
- Emory Vaccine Center at Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Martin J Deymier
- Emory Vaccine Center at Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Zachary S Ende
- Emory Vaccine Center at Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Nichole R Klatt
- Emory Vaccine Center at Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | | | | | - Jian Peng
- Microsoft Research, Redmond, WA 98052, USA
| | - Aaron M Seese
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02114, USA
| | - Roger Shapiro
- Division of Infectious Diseases, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - John Frater
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX1 7BN, UK. National Institute of Health Research, Oxford Biomedical Research Centre, Oxford OX3 7LE, UK. Oxford Martin School, University of Oxford, Oxford OX1 3BD, UK
| | - Thumbi Ndung'u
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02114, USA. HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban 4013, South Africa. KwaZulu-Natal Research Institute for Tuberculosis and HIV (K-RITH), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa. Max Planck Institute for Infection Biology, D-10117 Berlin, Germany
| | - Jianming Tang
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Paul Goepfert
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Jill Gilmour
- International AIDS Vaccine Initiative, London SW10 9NH, UK. Imperial College of Science Technology and Medicine, London SW10 9NH, UK
| | - Matt A Price
- International AIDS Vaccine Initiative, San Francisco, CA 94105, USA. Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA 94105, USA
| | - William Kilembe
- Rwanda-Zambia HIV Research Group: Zambia-Emory HIV Research Project, Lusaka, Zambia
| | | | - Philip J R Goulder
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban 4013, South Africa. Department of Paediatrics, University of Oxford, Oxford OX1 3SY, UK
| | - Todd M Allen
- Rwanda-Zambia HIV Research Group: Zambia-Emory HIV Research Project, Lusaka, Zambia. Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA 30322, USA. Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Susan Allen
- International AIDS Vaccine Initiative, San Francisco, CA 94105, USA. Microsoft Research, Los Angeles, CA 98117, USA. Department of Paediatrics, University of Oxford, Oxford OX1 3SY, UK
| | - Eric Hunter
- Emory Vaccine Center at Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA. Rwanda-Zambia HIV Research Group: Zambia-Emory HIV Research Project, Lusaka, Zambia. Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA 30322, USA.
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Juarez-Molina CI, Payne R, Soto-Nava M, Avila-Rios S, Valenzuela-Ponce H, Adland E, Leitman E, Brener J, Muenchhoff M, Branch S, Landis C, Reyes-Teran G, Goulder P. Impact of HLA selection pressure on HIV fitness at a population level in Mexico and Barbados. J Virol 2014; 88:10392-8. [PMID: 25008926 DOI: 10.1128/JVI.01162-14] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Previous studies have demonstrated that effective cytotoxic T lymphocyte (CTL) responses drive the selection of escape mutations that reduce viral replication capacity (VRC). Escape mutations, including those with reduced VRC, can be transmitted and accumulate in a population. Here we compared two antiretroviral therapy (ART)-naive HIV clade B-infected cohorts, in Mexico and Barbados, in which the most protective HLA alleles (HLA-B*27/57/58:01/81:01) are differentially expressed, at 8% and 34%, respectively. Viral loads were significantly higher in Mexico than in Barbados (median, 40,774 versus 14,200; P < 0.0001), and absolute CD4+ T-cell counts were somewhat lower (median, 380/mm3 versus 403/mm3; P = 0.007). We tested the hypothesis that the disparate frequencies of these protective HLA alleles would be associated with a higher VRC at the population level in Mexico. Analysis of VRC in subjects in each cohort, matched for CD4+ T-cell count, revealed that the VRC was indeed higher in the Mexican cohort (mean, 1.13 versus 1.03; P = 0.0025). Although CD4 counts were matched, viral loads remained significantly higher in the Mexican subjects (P = 0.04). This VRC difference was reflected by a significantly higher frequency in the Barbados cohort of HLA-B*27/57/58:01/81:01-associated Gag escape mutations previously shown to incur a fitness cost on the virus (P = 0.004), a difference between the two cohorts that remained statistically significant even in subjects not expressing these protective alleles (P = 0.01). These data suggest that viral set points and disease progression rates at the population level may be significantly influenced by the prevalence of protective HLA alleles such as HLA-B*27/57/58:01/81:01 and that CD4 count-based guidelines to initiate antiretroviral therapy may need to be modified accordingly, to optimize the effectiveness of treatment-for-prevention strategies and reduce HIV transmission rates to the absolute minimum. IMPORTANCE Immune control of HIV at an individual level is strongly influenced by the HLA class I genotype. HLA class I molecules mediating effective immune control, such as HLA-B*27 and HLA-B*57, are associated with the selection of escape mutants that reduce viral replicative capacity. The escape mutants selected in infected patients can be transmitted and affect the viral load and CD4 count in the recipient. These findings prompt the hypothesis that the frequency of protective alleles in a population may affect viral set points and rates of disease progression in that population. These studies in Mexico and Barbados, where the prevalence rates of protective HLA alleles are 8% and 34%, respectively, support this hypothesis. These data suggest that antiretroviral therapy (ART) treatment-for-prevention strategies will be less successful in populations such as those in Mexico, where viral loads are higher for a given CD4 count. Consideration may therefore usefully be given to ART initiation at higher absolute CD4 counts in such populations to optimize the impact of ART for prevention.
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Kuang XT, Li X, Anmole G, Mwimanzi P, Shahid A, Le AQ, Chong L, Qian H, Miura T, Markle T, Baraki B, Connick E, Daar ES, Jessen H, Kelleher AD, Little S, Markowitz M, Pereyra F, Rosenberg ES, Walker BD, Ueno T, Brumme ZL, Brockman MA. Impaired Nef function is associated with early control of HIV-1 viremia. J Virol 2014; 88:10200-13. [PMID: 24965469 DOI: 10.1128/JVI.01334-14] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
UNLABELLED Host and viral factors influence the HIV-1 infection course. Reduced Nef function has been observed in HIV-1 controllers during the chronic phase, but the kinetics and mechanisms of Nef attenuation in such individuals remain unclear. We examined plasma RNA-derived Nef clones from 10 recently infected individuals who subsequently suppressed viremia to less than 2,000 RNA copies/ml within 1 year postinfection (acute controllers) and 50 recently infected individuals who did not control viremia (acute progressors). Nef clones from acute controllers displayed a lesser ability to downregulate CD4 and HLA class I from the cell surface and a reduced ability to enhance virion infectivity compared to those from acute progressors (all P<0.01). HLA class I downregulation activity correlated inversely with days postinfection (Spearman's R=-0.85, P=0.004) and positively with baseline plasma viral load (Spearman's R=0.81, P=0.007) in acute controllers but not in acute progressors. Nef polymorphisms associated with functional changes over time were identified in follow-up samples from six controllers. For one such individual, mutational analyses indicated that four polymorphisms selected by HLA-A*31 and B*37 acted in combination to reduce Nef steady-state protein levels and HLA class I downregulation activity. Our results demonstrate that relative control of initial HIV-1 viremia is associated with Nef clones that display reduced function, which in turn may influence the course of HIV-1 infection. Transmission of impaired Nef sequences likely contributed in part to this observation; however, accumulation of HLA-associated polymorphisms in Nef that impair function also suggests that CD8+ T-cell pressures play a role in this phenomenon. IMPORTANCE Rare individuals can spontaneously control HIV-1 viremia in the absence of antiretroviral treatment. Understanding the host and viral factors that contribute to the controller phenotype may identify new strategies to design effective vaccines or therapeutics. The HIV-1 Nef protein enhances viral pathogenesis through multiple mechanisms. We examined the function of plasma HIV-1 RNA-derived Nef clones isolated from 10 recently infected individuals who subsequently controlled HIV viremia compared to the function of those from 50 individuals who failed to control viremia. Our results demonstrate that early Nef clones from HIV controllers displayed lower HLA class I and CD4 downregulation activity, as well as a reduced ability to enhance virion infectivity. The accumulation of HLA-associated polymorphisms in Nef during the first year postinfection was associated with impaired protein function in some controllers. This report highlights the potential for host immune responses to modulate HIV pathogenicity and disease outcome by targeting cytotoxic T lymphocyte (CTL) epitopes in Nef.
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Chikata T, Carlson JM, Tamura Y, Borghan MA, Naruto T, Hashimoto M, Murakoshi H, Le AQ, Mallal S, John M, Gatanaga H, Oka S, Brumme ZL, Takiguchi M. Host-specific adaptation of HIV-1 subtype B in the Japanese population. J Virol 2014; 88:4764-75. [PMID: 24522911 DOI: 10.1128/JVI.00147-14] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The extent to which HIV-1 clade B strains exhibit population-specific adaptations to host HLA alleles remains incompletely known, in part due to incomplete characterization of HLA-associated HIV-1 polymorphisms (HLA-APs) in different global populations. Moreover, it remains unknown to what extent the same HLA alleles may drive significantly different escape pathways across populations. As the Japanese population exhibits distinctive HLA class I allele distributions, comparative analysis of HLA-APs between HIV-1 clade B-infected Japanese and non-Asian cohorts could shed light on these questions. However, HLA-APs remain incompletely mapped in Japan. In a cohort of 430 treatment-naive Japanese with chronic HIV-1 clade B infection, we identified 284 HLA-APs in Gag, Pol, and Nef using phylogenetically corrected methods. The number of HLA-associated substitutions in Pol, notably those restricted by HLA-B*52:01, was weakly inversely correlated with the plasma viral load (pVL), suggesting that the transmission and persistence of B*52:01-driven Pol mutations could modulate the pVL. Differential selection of HLA-APs between HLA subtype members, including those differing only with respect to substitutions outside the peptide-binding groove, was observed, meriting further investigation as to their mechanisms of selection. Notably, two-thirds of HLA-APs identified in Japan had not been reported in previous studies of predominantly Caucasian cohorts and were attributable to HLA alleles unique to, or enriched in, Japan. We also identified 71 cases where the same HLA allele drove significantly different escape pathways in Japan versus predominantly Caucasian cohorts. Our results underscore the distinct global evolution of HIV-1 clade B as a result of host population-specific cellular immune pressures. IMPORTANCE Cytotoxic T lymphocyte (CTL) escape mutations in HIV-1 are broadly predictable based on the HLA class I alleles expressed by the host. Because HLA allele distributions differ among worldwide populations, the pattern and diversity of HLA-associated escape mutations are likely to be somewhat distinct to each race and region. HLA-associated polymorphisms (HLA-APs) in HIV-1 have previously been identified at the population level in European, North American, Australian, and African cohorts; however, large-scale analyses of HIV-1 clade B-specific HLA-APs in Asians are lacking. Differential intraclade HIV-1 adaptation to global populations can be investigated via comparative analyses of HLA-associated polymorphisms across ethnic groups, but such studies are rare. Here, we identify HLA-APs in a large Japanese HIV-1 clade B cohort using phylogenetically informed methods and observe that the majority of them had not been previously characterized in predominantly Caucasian populations. The results highlight HIV's unique adaptation to cellular immune pressures imposed by different global populations.
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Payne RP, Branch S, Kløverpris H, Matthews PC, Koofhethile CK, Strong T, Adland E, Leitman E, Frater J, Ndung'u T, Hunter E, Haubrich R, Mothe B, Edwards A, Riddell L, Chen F, Harrigan PR, Brumme ZL, Mallal S, John M, Jooste JP, Shapiro R, Deeks SG, Walker BD, Brander C, Landis C, Carlson JM, Prado JG, Goulder PJ. Differential escape patterns within the dominant HLA-B*57:03-restricted HIV Gag epitope reflect distinct clade-specific functional constraints. J Virol 2014; 88:4668-78. [PMID: 24501417 DOI: 10.1128/JVI.03303-13] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED HLA-B*57:01 and HLA-B*57:03, the most prevalent HLA-B*57 subtypes in Caucasian and African populations, respectively, are the HLA alleles most protective against HIV disease progression. Understanding the mechanisms underlying this immune control is of critical importance, yet they remain unclear. Unexplained differences are observed in the impact of the dominant cytotoxic T lymphocyte (CTL) response restricted by HLA-B*57:01 and HLA-B*57:03 in chronic infection on the Gag epitope KAFSPEVIPMF (KF11; Gag 162 to 172). We previously showed that the HLA-B*57:03-KF11 response is associated with a >1-log-lower viral setpoint in C clade virus infection and that this response selects escape mutants within the epitope. We first examined the relationship of KF11 responses in B clade virus-infected subjects with HLA-B*57:01 to immune control and observed that a detectable KF11 response was associated with a >1-log-higher viral load (P = 0.02). No evidence of HLA-B*57:01-KF11-associated selection pressure was identified in previous comprehensive analyses of >1,800 B clade virus-infected subjects. We then studied a B clade virus-infected cohort in Barbados, where HLA-B*57:03 is highly prevalent. In contrast to findings for B clade virus-infected subjects expressing HLA-B*57:01, we observed strong selection pressure driven by the HLA-B*57:03-KF11 response for the escape mutation S173T. This mutation reduces recognition of virus-infected cells by HLA-B*57:03-KF11 CTLs and is associated with a >1-log increase in viral load in HLA-B*57:03-positive subjects (P = 0.009). We demonstrate functional constraints imposed by HIV clade relating to the residue at Gag 173 that explain the differential clade-specific escape patterns in HLA-B*57:03 subjects. Further studies are needed to evaluate the role of the KF11 response in HLA-B*57:01-associated HIV disease protection. IMPORTANCE HLA-B*57 is the HLA class I molecule that affords the greatest protection against disease progression in HIV infection. Understanding the key mechanism(s) underlying immunosuppression of HIV is of importance in guiding therapeutic and vaccine-related approaches to improve the levels of HIV control occurring in nature. Numerous mechanisms have been proposed to explain the HLA associations with differential HIV disease outcome, but no consensus exists. These studies focus on two subtypes of HLA-B*57 prevalent in Caucasian and African populations, HLA-B*57:01 and HLA-B*57:03, respectively. These alleles appear equally protective against HIV disease progression. The CTL epitopes presented are in many cases identical, and the dominant response in chronic infection in each case is to the Gag epitope KF11. However, there the similarity ends. This study sought to better understand the reasons for these differences and what they teach us about which immune responses contribute to immune control of HIV infection.
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Gijsbers EF, Feenstra KA, van Nuenen AC, Navis M, Heringa J, Schuitemaker H, Kootstra NA. HIV-1 replication fitness of HLA-B*57/58:01 CTL escape variants is restored by the accumulation of compensatory mutations in gag. PLoS One 2013; 8:e81235. [PMID: 24339913 PMCID: PMC3855271 DOI: 10.1371/journal.pone.0081235] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Accepted: 10/10/2013] [Indexed: 11/30/2022] Open
Abstract
Expression of HLA-B*57 and the closely related HLA-B*58:01 are associated with prolonged survival after HIV-1 infection. However, large differences in disease course are observed among HLA-B*57/58:01 patients. Escape mutations in CTL epitopes restricted by these HLA alleles come at a fitness cost and particularly the T242N mutation in the TW10 CTL epitope in Gag has been demonstrated to decrease the viral replication capacity. Additional mutations within or flanking this CTL epitope can partially restore replication fitness of CTL escape variants. Five HLA-B*57/58:01 progressors and 5 HLA-B*57/58:01 long-term nonprogressors (LTNPs) were followed longitudinally and we studied which compensatory mutations were involved in the restoration of the viral fitness of variants that escaped from HLA-B*57/58:01-restricted CTL pressure. The Sequence Harmony algorithm was used to detect homology in amino acid composition by comparing longitudinal Gag sequences obtained from HIV-1 patients positive and negative for HLA-B*57/58:01 and from HLA-B*57/58:01 progressors and LTNPs. Although virus isolates from HLA-B*57/58:01 individuals contained multiple CTL escape mutations, these escape mutations were not associated with disease progression. In sequences from HLA-B*57/58:01 progressors, 5 additional mutations in Gag were observed: S126N, L215T, H219Q, M228I and N252H. The combination of these mutations restored the replication fitness of CTL escape HIV-1 variants. Furthermore, we observed a positive correlation between the number of escape and compensatory mutations in Gag and the replication fitness of biological HIV-1 variants isolated from HLA-B*57/58:01 patients, suggesting that the replication fitness of HLA-B*57/58:01 escape variants is restored by accumulation of compensatory mutations.
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Affiliation(s)
- Esther F. Gijsbers
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory, and Center for Infectious Diseases and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - K. Anton Feenstra
- Centre for Integrative Bioinformatics (IBIVU) and Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), VU University, Amsterdam, The Netherlands
- Netherlands Bioinformatics Centre (NBIC), Nijmegen, The Netherlands
| | - Ad C. van Nuenen
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory, and Center for Infectious Diseases and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Marjon Navis
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory, and Center for Infectious Diseases and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Jaap Heringa
- Centre for Integrative Bioinformatics (IBIVU) and Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), VU University, Amsterdam, The Netherlands
- Netherlands Bioinformatics Centre (NBIC), Nijmegen, The Netherlands
| | - Hanneke Schuitemaker
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory, and Center for Infectious Diseases and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Neeltje A. Kootstra
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory, and Center for Infectious Diseases and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
- * E-mail:
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Chopera DR, Mann JK, Mwimanzi P, Omarjee S, Kuang XT, Ndabambi N, Goodier S, Martin E, Naranbhai V, Karim SA, Karim QA, Brumme ZL, Ndung'u T, Williamson C, Brockman MA; CAPRISA 004 TRAPS Team. No evidence for selection of HIV-1 with enhanced gag-protease or Nef function among breakthrough infections in the CAPRISA 004 tenofovir microbicide trial. PLoS One 2013; 8:e71758. [PMID: 24015191 DOI: 10.1371/journal.pone.0071758] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Accepted: 07/02/2013] [Indexed: 11/29/2022] Open
Abstract
Background Use of antiretroviral-based microbicides for HIV-1 prophylaxis could introduce a transmission barrier that inadvertently facilitates the selection of fitter viral variants among incident infections. To investigate this, we assessed the in vitro function of gag-protease and nef sequences from participants who acquired HIV-1 during the CAPRISA 004 1% tenofovir microbicide gel trial. Methods and Results We isolated the earliest available gag-protease and nef gene sequences from 83 individuals and examined their in vitro function using recombinant viral replication capacity assays and surface protein downregulation assays, respectively. No major phylogenetic clustering and no significant differences in gag-protease or nef function were observed in participants who received tenofovir gel versus placebo gel prophylaxis. Conclusion Results indicate that the partial protective effects of 1% tenofovir gel use in the CAPRISA 004 trial were not offset by selection of transmitted/early HIV-1 variants with enhanced Gag-Protease or Nef fitness.
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van Deutekom HWM, Wijnker G, de Boer RJ. The rate of immune escape vanishes when multiple immune responses control an HIV infection. J Immunol 2013; 191:3277-86. [PMID: 23940274 DOI: 10.4049/jimmunol.1300962] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
During the first months of HIV infection, the virus typically evolves several immune escape mutations. These mutations are found in epitopes in viral proteins and reduce the impact of the CD8⁺ T cells specific for these epitopes. Recent data show that only a subset of the epitopes escapes, that most of these escapes evolve early, and that the rate of immune escape slows down considerably. To investigate why the evolution of immune escape slows down over the time of infection, we have extended a consensus mathematical model to allow several immune responses to control the virus together. In the extended model, most escapes also occur early, and the immune escape rate becomes small later, and typically only a minority of the epitopes escape. We show that escaping one of the many immune responses provides little advantage after viral setpoint has been approached because the total killing rate hardly depends on the breadth of the immune response. If the breadth of the immune response slowly wanes during disease progression, the model predicts an increase in the rate of immune escape at late stages of infection. Overall, the most striking prediction of the model is that HIV evolves a small number of immune escapes, in both relative and absolute terms, when the CTL immune response is broad.
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Huang CJ, Wu CF, Lan CY, Sung FY, Lin CL, Liu CJ, Liu HF, Yu MW. Impact of genetic heterogeneity in polymerase of hepatitis B virus on dynamics of viral load and hepatitis B progression. PLoS One. 2013;8:e70169. [PMID: 23936156 PMCID: PMC3728348 DOI: 10.1371/journal.pone.0070169] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Accepted: 06/17/2013] [Indexed: 12/14/2022] Open
Abstract
Objective The hepatitis B virus (HBV)-polymerase region overlaps pre-S/S genes with high epitope density and plays an essential role in viral replication. We investigated whether genetic variation in the polymerase region determined long-term dynamics of viral load and the risk of hepatitis B progression in a population-based cohort study. Methods We sequenced the HBV-polymerase region using baseline plasma from treatment-naïve individuals with HBV-DNA levels≥1000 copies/mL in a longitudinal viral-load study of participants with chronic HBV infection followed-up for 17 years, and obtained sequences from 575 participants (80% with HBV genotype Ba and 17% with Ce). Results Patterns of viral sequence diversity across phases (i.e., immune-tolerant, immune-clearance, non/low replicative, and hepatitis B e antigen (HBeAg)-negative hepatitis phases) of HBV-infection, which were associated with viral and clinical features at baseline and during follow-up, were similar between HBV genotypes, despite greater diversity for genotype Ce vs. Ba. Irrespective of genotypes, however, HBeAg-negative participants had 1.5-to-2-fold higher levels of sequence diversity than HBeAg-positive participants (P<0.0001). Furthermore, levels of viral genetic divergence from the population consensus sequence, estimated by numbers of nucleotide substitutions, were inversely associated with long-term viral load even in HBeAg-negative participants. A mixed model developed through analysis of the entire HBV-polymerase region identified 153 viral load-associated single nucleotide polymorphisms in overall and 136 in HBeAg-negative participants, with distinct profiles between HBV genotypes. These polymorphisms were most evident at sites within or flanking T-cell epitopes. Seven polymorphisms revealed associations with both enhanced viral load and a more than 4-fold increased risk of hepatocellular carcinoma and/or liver cirrhosis. Conclusions The data highlight a role of viral genetic divergence in the natural course of HBV-infection. Interindividual differences in the long-term dynamics of viral load is not only associated with accumulation of mutations in HBV-polymerase region, but differences in specific viral polymorphisms which differ between genotypes.
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Abrahams MR, Treurnicht FK, Ngandu NK, Goodier SA, Marais JC, Bredell H, Thebus R, de Assis Rosa D, Mlisana K, Seoighe C, Karim SA, Gray CM, Williamson C. Rapid, complex adaptation of transmitted HIV-1 full-length genomes in subtype C-infected individuals with differing disease progression. AIDS 2013; 27:507-18. [PMID: 23370465 DOI: 10.1097/QAD.0b013e32835cab64] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
OBJECTIVE(S) There is limited information on full-length genome sequences and the early evolution of transmitted HIV-1 subtype C viruses, which constitute the majority of viruses spread in Africa. The purpose of this study was to characterize the earliest changes across the genome of subtype C viruses following transmission, to better understand early control of viremia. DESIGN We derived the near full-length genome sequence responsible for clinical infection from five HIV subtype C-infected individuals with different disease progression profiles and tracked adaptation to immune responses in the first 6 months of infection. METHODS Near full-length genomes were generated by single genome amplification and direct sequencing. Sequences were analyzed for amino acid mutations associated with cytotoxic T lymphocyte (CTL) or antibody-mediated immune pressure, and for reversion. RESULTS Fifty-five sequence changes associated with adaptation to the new host were identified, with 38% attributed to CTL pressure, 35% to antibody pressure, 16% to reversions and the remainder were unclassified. Mutations in CTL epitopes were most frequent in the first 5 weeks of infection, with the frequency declining over time with the decline in viral load. CTL escape predominantly occurred in nef, followed by pol and env. Shuffling/toggling of mutations was identified in 81% of CTL epitopes, with only 7% reaching fixation within the 6-month period. CONCLUSION There was rapid virus adaptation following transmission, predominantly driven by CTL pressure, with most changes occurring during high viremia. Rapid escape and complex escape pathways provide further challenges for vaccine protection.
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Boutwell CL, Carlson JM, Lin TH, Seese A, Power KA, Peng J, Tang Y, Brumme ZL, Heckerman D, Schneidewind A, Allen TM. Frequent and variable cytotoxic-T-lymphocyte escape-associated fitness costs in the human immunodeficiency virus type 1 subtype B Gag proteins. J Virol 2013; 87:3952-65. [PMID: 23365420 DOI: 10.1128/JVI.03233-12] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Cytotoxic-T-lymphocyte (CTL) escape mutations undermine the durability of effective human immunodeficiency virus type 1 (HIV-1)-specific CD8(+) T cell responses. The rate of CTL escape from a given response is largely governed by the net of all escape-associated viral fitness costs and benefits. The observation that CTL escape mutations can carry an associated fitness cost in terms of reduced virus replication capacity (RC) suggests a fitness cost-benefit trade-off that could delay CTL escape and thereby prolong CD8 response effectiveness. However, our understanding of this potential fitness trade-off is limited by the small number of CTL escape mutations for which a fitness cost has been quantified. Here, we quantified the fitness cost of the 29 most common HIV-1B Gag CTL escape mutations using an in vitro RC assay. The majority (20/29) of mutations reduced RC by more than the benchmark M184V antiretroviral drug resistance mutation, with impacts ranging from 8% to 69%. Notably, the reduction in RC was significantly greater for CTL escape mutations associated with protective HLA class I alleles than for those associated with nonprotective alleles. To speed the future evaluation of CTL escape costs, we also developed an in silico approach for inferring the relative impact of a mutation on RC based on its computed impact on protein thermodynamic stability. These data illustrate that the magnitude of CTL escape-associated fitness costs, and thus the barrier to CTL escape, varies widely even in the conserved Gag proteins and suggest that differential escape costs may contribute to the relative efficacy of CD8 responses.
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Liu MKP, Hawkins N, Ritchie AJ, Ganusov VV, Whale V, Brackenridge S, Li H, Pavlicek JW, Cai F, Rose-Abrahams M, Treurnicht F, Hraber P, Riou C, Gray C, Ferrari G, Tanner R, Ping LH, Anderson JA, Swanstrom R, Cohen M, Karim SSA, Haynes B, Borrow P, Perelson AS, Shaw GM, Hahn BH, Williamson C, Korber BT, Gao F, Self S, McMichael A, Goonetilleke N. Vertical T cell immunodominance and epitope entropy determine HIV-1 escape. J Clin Invest 2012; 123:380-93. [PMID: 23221345 DOI: 10.1172/jci65330] [Citation(s) in RCA: 137] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Accepted: 10/05/2012] [Indexed: 12/26/2022] Open
Abstract
HIV-1 accumulates mutations in and around reactive epitopes to escape recognition and killing by CD8+ T cells. Measurements of HIV-1 time to escape should therefore provide information on which parameters are most important for T cell-mediated in vivo control of HIV-1. Primary HIV-1-specific T cell responses were fully mapped in 17 individuals, and the time to virus escape, which ranged from days to years, was measured for each epitope. While higher magnitude of an individual T cell response was associated with more rapid escape, the most significant T cell measure was its relative immunodominance measured in acute infection. This identified subject-level or "vertical" immunodominance as the primary determinant of in vivo CD8+ T cell pressure in HIV-1 infection. Conversely, escape was slowed significantly by lower population variability, or entropy, of the epitope targeted. Immunodominance and epitope entropy combined to explain half of all the variability in time to escape. These data explain how CD8+ T cells can exert significant and sustained HIV-1 pressure even when escape is very slow and that within an individual, the impacts of other T cell factors on HIV-1 escape should be considered in the context of immunodominance.
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Affiliation(s)
- Michael K P Liu
- Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
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Manigart O, Boeras DI, Karita E, Hawkins PA, Vwalika C, Makombe N, Mulenga J, Derdeyn CA, Allen S, Hunter E. A gp41-based heteroduplex mobility assay provides rapid and accurate assessment of intrasubtype epidemiological linkage in HIV type 1 heterosexual transmission Pairs. AIDS Res Hum Retroviruses 2012; 28:1745-55. [PMID: 22587371 DOI: 10.1089/aid.2012.0023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A critical step in HIV-1 transmission studies is the rapid and accurate identification of epidemiologically linked transmission pairs. To date, this has been accomplished by comparison of polymerase chain reaction (PCR)-amplified nucleotide sequences from potential transmission pairs, which can be cost-prohibitive for use in resource-limited settings. Here we describe a rapid, cost-effective approach to determine transmission linkage based on the heteroduplex mobility assay (HMA), and validate this approach by comparison to nucleotide sequencing. A total of 102 HIV-1-infected Zambian and Rwandan couples, with known linkage, were analyzed by gp41-HMA. A 400-base pair fragment within the envelope gp41 region of the HIV proviral genome was PCR amplified and HMA was applied to both partners' amplicons separately (autologous) and as a mixture (heterologous). If the diversity between gp41 sequences was low (<5%), a homoduplex was observed upon gel electrophoresis and the transmission was characterized as having occurred between partners (linked). If a new heteroduplex formed, within the heterologous migration, the transmission was determined to be unlinked. Initial blind validation of gp-41 HMA demonstrated 90% concordance between HMA and sequencing with 100% concordance in the case of linked transmissions. Following validation, 25 newly infected partners in Kigali and 12 in Lusaka were evaluated prospectively using both HMA and nucleotide sequences. Concordant results were obtained in all but one case (97.3%). The gp41-HMA technique is a reliable and feasible tool to detect linked transmissions in the field. All identified unlinked results should be confirmed by sequence analyses.
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Affiliation(s)
- Olivier Manigart
- Rwanda Zambia HIV Research Group (RZHRG), Projet San Francisco (PSF), Kigali, Rwanda
- Emory University, Atlanta, Georgia
- RZHRG, Zambia Emory University HIV Research Project (ZEHRP), Lusaka, Zambia
| | | | - Etienne Karita
- Rwanda Zambia HIV Research Group (RZHRG), Projet San Francisco (PSF), Kigali, Rwanda
| | | | - Cheswa Vwalika
- RZHRG, Zambia Emory University HIV Research Project (ZEHRP), Lusaka, Zambia
| | - Nathan Makombe
- Rwanda Zambia HIV Research Group (RZHRG), Projet San Francisco (PSF), Kigali, Rwanda
| | - Joseph Mulenga
- RZHRG, Zambia Emory University HIV Research Project (ZEHRP), Lusaka, Zambia
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Prince JL, Claiborne DT, Carlson JM, Schaefer M, Yu T, Lahki S, Prentice HA, Yue L, Vishwanathan SA, Kilembe W, Goepfert P, Price MA, Gilmour J, Mulenga J, Farmer P, Derdeyn CA, Tang J, Heckerman D, Kaslow RA, Allen SA, Hunter E. Role of transmitted Gag CTL polymorphisms in defining replicative capacity and early HIV-1 pathogenesis. PLoS Pathog 2012; 8:e1003041. [PMID: 23209412 PMCID: PMC3510241 DOI: 10.1371/journal.ppat.1003041] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [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: 06/18/2012] [Accepted: 10/03/2012] [Indexed: 11/30/2022] Open
Abstract
Initial studies of 88 transmission pairs in the Zambia Emory HIV Research Project cohort demonstrated that the number of transmitted HLA-B associated polymorphisms in Gag, but not Nef, was negatively correlated to set point viral load (VL) in the newly infected partners. These results suggested that accumulation of CTL escape mutations in Gag might attenuate viral replication and provide a clinical benefit during early stages of infection. Using a novel approach, we have cloned gag sequences isolated from the earliest seroconversion plasma sample from the acutely infected recipient of 149 epidemiologically linked Zambian transmission pairs into a primary isolate, subtype C proviral vector, MJ4. We determined the replicative capacity (RC) of these Gag-MJ4 chimeras by infecting the GXR25 cell line and quantifying virion production in supernatants via a radiolabeled reverse transcriptase assay. We observed a statistically significant positive correlation between RC conferred by the transmitted Gag sequence and set point VL in newly infected individuals (p = 0.02). Furthermore, the RC of Gag-MJ4 chimeras also correlated with the VL of chronically infected donors near the estimated date of infection (p = 0.01), demonstrating that virus replication contributes to VL in both acute and chronic infection. These studies also allowed for the elucidation of novel sites in Gag associated with changes in RC, where rare mutations had the greatest effect on fitness. Although we observed both advantageous and deleterious rare mutations, the latter could point to vulnerable targets in the HIV-1 genome. Importantly, RC correlated significantly (p = 0.029) with the rate of CD4+ T cell decline over the first 3 years of infection in a manner that is partially independent of VL, suggesting that the replication capacity of HIV-1 during the earliest stages of infection is a determinant of pathogenesis beyond what might be expected based on set point VL alone. In the majority of HIV-1 cases, a single virus establishes infection. However, mutations in the viral genome accumulate over time in order to avoid recognition by the host immune response. Certain mutations in the main structural protein, Gag, driven by cytotoxic T lymphocytes are detrimental to viral replication, and we showed previously that, upon transmission, viruses with higher numbers of escape mutations in Gag were associated with lower early set point viral loads. We hypothesized that this could be attributed to attenuation of the transmitted virus. Here, we have cloned the gag gene from 149 newly infected individuals from linked transmission pairs into a clade C proviral vector and determined the replicative capacity in vitro. We found that the replicative capacity conferred by the transmitted Gag correlated with set point viral loads in newly infected individuals, as well as with the viral load of the transmitting partner, and we identified previously unrecognized residues associated with increasing and decreasing replicative capacity. Importantly, we demonstrate that transmitted viruses with high replicative capacity cause more rapid CD4+ decline over the first three years, independent of viral load. This suggests that the trajectory of pathogenesis may be affected very early in infection, before adaptive immunity can respond.
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Affiliation(s)
- Jessica L. Prince
- Emory Vaccine Center at Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Daniel T. Claiborne
- Emory Vaccine Center at Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | | | - Malinda Schaefer
- Emory Vaccine Center at Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Tianwei Yu
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, Georgia, United States of America
| | - Shabir Lahki
- Zambia-Emory HIV Research Project, Lusaka, Zambia
| | - Heather A. Prentice
- Department of Epidemiology, University of Alabama, Birmingham, Alabama, United States of America
| | - Ling Yue
- Emory Vaccine Center at Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Sundaram A. Vishwanathan
- Emory Vaccine Center at Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | | | - Paul Goepfert
- Department of Medicine, University of Alabama, Birmingham, Alabama, United States of America
| | - Matthew A. Price
- International AIDS Vaccine Initiative, San Francisco, California, United States of America
| | - Jill Gilmour
- International AIDS Vaccine Initiative, London, England
| | | | - Paul Farmer
- Emory Vaccine Center at Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Cynthia A. Derdeyn
- Emory Vaccine Center at 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
| | - Jiaming Tang
- Department of Medicine, University of Alabama, Birmingham, Alabama, United States of America
| | - David Heckerman
- Microsoft Research, Los Angeles, California, United States of America
| | - Richard A. Kaslow
- Department of Epidemiology, University of Alabama, 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
- Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, United States of America
| | - Eric Hunter
- Emory Vaccine Center at 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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