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Analysis of HIV Diversity in HIV-Infected Black Men Who Have Sex with Men (HPTN 061). PLoS One 2016; 11:e0167629. [PMID: 27936098 PMCID: PMC5147928 DOI: 10.1371/journal.pone.0167629] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 11/17/2016] [Indexed: 01/01/2023] Open
Abstract
Background HIV populations often diversify in response to selective pressures, such as the immune response and antiretroviral drug use. We analyzed HIV diversity in Black men who have sex with men who were enrolled in the HIV Prevention Trials Network 061 study. Methods A high resolution melting (HRM) diversity assay was used to measure diversity in six regions of the HIV genome: two in gag, one in pol, and three in env. HIV diversity was analyzed for 146 men who were HIV infected at study enrollment, including three with acute infection and 13 with recent infection (identified using a multi-assay algorithm), and for 21 men who seroconverted during the study. HIV diversification was analyzed in a paired analysis for 62 HIV-infected men using plasma samples from the enrollment and 12-month (end of study) visits. Results Men with acute or recent infection at enrollment and seroconverters had lower median HRM scores (lower HIV diversity) than men with non-recent infection in all six regions analyzed. In univariate analyses, younger age, higher CD4 cell count, and HIV drug resistance were associated with lower median HRM scores in multiple regions; ARV drug detection was marginally associated with lower diversity in the pol region. In multivariate analysis, acute or recent infection (all six regions) and HIV drug resistance (both gag regions) were associated with lower median HRM scores. Diversification in the pol region over 12 months was greater for men with acute or recent infection, higher CD4 cell count, and lower HIV viral load at study enrollment. Conclusions HIV diversity was significantly associated with duration of HIV infection, and lower gag diversity was observed in men who had HIV drug resistance. HIV pol diversification was more pronounced in men with acute or recent infection, higher CD4 cell count, and lower HIV viral load.
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Chen I, Khaki L, Lindsey JC, Fry C, Cousins MM, Siliciano RF, Violari A, Palumbo P, Eshleman SH. Association of pol diversity with antiretroviral treatment outcomes among HIV-infected African children. PLoS One 2013; 8:e81213. [PMID: 24312277 PMCID: PMC3842253 DOI: 10.1371/journal.pone.0081213] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Accepted: 10/09/2013] [Indexed: 01/02/2023] Open
Abstract
Background In HIV-infected children, viral diversity tends to increase with age in the absence of antiretroviral treatment (ART). We measured HIV diversity in African children (ages 6–36 months) enrolled in a randomized clinical trial comparing two ART regimens (Cohort I of the P1060 trial). Children in this cohort were exposed to single dose nevirapine (sdNVP) at birth. Methods HIV diversity was measured retrospectively using a high resolution melting (HRM) diversity assay. Samples were obtained from 139 children at the enrollment visit prior to ART initiation. Six regions of the HIV genome were analyzed: two in gag, one in pol, and three in env. A single numeric HRM score that reflects HIV diversity was generated for each region; composite HRM scores were also calculated (mean and median for all six regions). Results In multivariable median regression models using backwards selection that started with demographic and clinical variables, older age was associated with higher HRM scores (higher HIV diversity) in pol (P = 0.005) and with higher mean (P = 0.014) and median (P<0.001) HRM scores. In multivariable models adjusted for age, pre-treatment HIV viral load, pre-treatment CD4%, and randomized treatment regimen, higher HRM scores in pol were associated with shorter time to virologic suppression (P = 0.016) and longer time to study endpoints (virologic failure [VF], VF/death, and VF/off study treatment; P<0.001 for all measures). Conclusions In this cohort of sdNVP-exposed, ART-naïve African children, higher levels of HIV diversity in the HIV pol region prior to ART initiation were associated with better treatment outcomes.
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Affiliation(s)
- Iris Chen
- Dept. of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- * E-mail: (SHE); (IC)
| | - Leila Khaki
- Dept. of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Jane C. Lindsey
- Center for Biostatistics in AIDS Research, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Carrie Fry
- Frontier Science and Technology Research Foundation, Amherst, New York, United States of America
| | - Matthew M. Cousins
- Dept. of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Robert F. Siliciano
- Dept. of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Avy Violari
- PHRU, Chris Baragwanath Hospital, Soweto, South Africa
| | - Paul Palumbo
- Depts. of Pediatrics and Medicine, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, United States of America
| | - Susan H. Eshleman
- Dept. of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- * E-mail: (SHE); (IC)
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Comparison of a high-resolution melting assay to next-generation sequencing for analysis of HIV diversity. J Clin Microbiol 2012; 50:3054-9. [PMID: 22785188 DOI: 10.1128/jcm.01460-12] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Next-generation sequencing (NGS) has recently been used for analysis of HIV diversity, but this method is labor-intensive, costly, and requires complex protocols for data analysis. We compared diversity measures obtained using NGS data to those obtained using a diversity assay based on high-resolution melting (HRM) of DNA duplexes. The HRM diversity assay provides a single numeric score that reflects the level of diversity in the region analyzed. HIV gag and env from individuals in Rakai, Uganda, were analyzed in a previous study using NGS (n = 220 samples from 110 individuals). Three sequence-based diversity measures were calculated from the NGS sequence data (percent diversity, percent complexity, and Shannon entropy). The amplicon pools used for NGS were analyzed with the HRM diversity assay. HRM scores were significantly associated with sequence-based measures of HIV diversity for both gag and env (P < 0.001 for all measures). The level of diversity measured by the HRM diversity assay and NGS increased over time in both regions analyzed (P < 0.001 for all measures except for percent complexity in gag), and similar amounts of diversification were observed with both methods (P < 0.001 for all measures except for percent complexity in gag). Diversity measures obtained using the HRM diversity assay were significantly associated with those from NGS, and similar increases in diversity over time were detected by both methods. The HRM diversity assay is faster and less expensive than NGS, facilitating rapid analysis of large studies of HIV diversity and evolution.
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Cousins MM, Laeyendecker O, Beauchamp G, Brookmeyer R, Towler WI, Hudelson SE, Khaki L, Koblin B, Chesney M, Moore RD, Kelen GD, Coates T, Celum C, Buchbinder SP, Seage GR, Quinn TC, Donnell D, Eshleman SH. Use of a high resolution melting (HRM) assay to compare gag, pol, and env diversity in adults with different stages of HIV infection. PLoS One 2011; 6:e27211. [PMID: 22073290 PMCID: PMC3206918 DOI: 10.1371/journal.pone.0027211] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2011] [Accepted: 10/11/2011] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Cross-sectional assessment of HIV incidence relies on laboratory methods to discriminate between recent and non-recent HIV infection. Because HIV diversifies over time in infected individuals, HIV diversity may serve as a biomarker for assessing HIV incidence. We used a high resolution melting (HRM) diversity assay to compare HIV diversity in adults with different stages of HIV infection. This assay provides a single numeric HRM score that reflects the level of genetic diversity of HIV in a sample from an infected individual. METHODS HIV diversity was measured in 203 adults: 20 with acute HIV infection (RNA positive, antibody negative), 116 with recent HIV infection (tested a median of 189 days after a previous negative HIV test, range 14-540 days), and 67 with non-recent HIV infection (HIV infected >2 years). HRM scores were generated for two regions in gag, one region in pol, and three regions in env. RESULTS Median HRM scores were higher in non-recent infection than in recent infection for all six regions tested. In multivariate models, higher HRM scores in three of the six regions were independently associated with non-recent HIV infection. CONCLUSIONS The HRM diversity assay provides a simple, scalable method for measuring HIV diversity. HRM scores, which reflect the genetic diversity in a viral population, may be useful biomarkers for evaluation of HIV incidence, particularly if multiple regions of the HIV genome are examined.
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Affiliation(s)
- Matthew M. Cousins
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Oliver Laeyendecker
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Geetha Beauchamp
- Statistical Center for HIV/AIDS Research and Prevention, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Ronald Brookmeyer
- Department of Biostatistics, University of California Los Angeles, Los Angeles, California, United States of America
| | - William I. Towler
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Sarah E. Hudelson
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Leila Khaki
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Beryl Koblin
- Laboratory of Infectious Disease Prevention, New York Blood Center, New York, New York, United States of America
| | - Margaret Chesney
- University of California San Francisco, San Francisco, California, United States of America
| | - Richard D. Moore
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Gabor D. Kelen
- Department of Emergency Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Thomas Coates
- Program in Global Health, University of California Los Angeles, Los Angeles, California, United States of America
| | - Connie Celum
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Susan P. Buchbinder
- University of California San Francisco, San Francisco, California, United States of America
- San Francisco Department of Public Health, San Francisco, California, United States of America
| | - George R. Seage
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Thomas C. Quinn
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Deborah Donnell
- Statistical Center for HIV/AIDS Research and Prevention, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Susan H. Eshleman
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
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Barsov EV, Trivett MT, Minang JT, Sun H, Ohlen C, Ott DE. Transduction of SIV-specific TCR genes into rhesus macaque CD8+ T cells conveys the ability to suppress SIV replication. PLoS One 2011; 6:e23703. [PMID: 21886812 PMCID: PMC3160320 DOI: 10.1371/journal.pone.0023703] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2011] [Accepted: 07/22/2011] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND The SIV/rhesus macaque model for HIV/AIDS is a powerful system for examining the contribution of T cells in the control of AIDS viruses. To better our understanding of CD8(+) T-cell control of SIV replication in CD4(+) T cells, we asked whether TCRs isolated from rhesus macaque CD8(+) T-cell clones that exhibited varying abilities to suppress SIV replication could convey their suppressive properties to CD8(+) T cells obtained from an uninfected/unvaccinated animal. PRINCIPAL FINDINGS We transferred SIV-specific TCR genes isolated from rhesus macaque CD8(+) T-cell clones with varying abilities to suppress SIV replication in vitro into CD8(+) T cells obtained from an uninfected animal by retroviral transduction. After sorting and expansion, transduced CD8(+) T-cell lines were obtained that specifically bound their cognate SIV tetramer. These cell lines displayed appropriate effector function and specificity, expressing intracellular IFNγ upon peptide stimulation. Importantly, the SIV suppression properties of the transduced cell lines mirrored those of the original TCR donor clones: cell lines expressing TCRs transferred from highly suppressive clones effectively reduced wild-type SIV replication, while expression of a non-suppressing TCR failed to reduce the spread of virus. However, all TCRs were able to suppress the replication of an SIV mutant that did not downregulate MHC-I, recapitulating the properties of their donor clones. CONCLUSIONS Our results show that antigen-specific SIV suppression can be transferred between allogenic T cells simply by TCR gene transfer. This advance provides a platform for examining the contributions of TCRs versus the intrinsic effector characteristics of T-cell clones in virus suppression. Additionally, this approach can be applied to develop non-human primate models to evaluate adoptive T-cell transfer therapy for AIDS and other diseases.
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Affiliation(s)
- Eugene V. Barsov
- AIDS and Cancer Virus Program, SAIC-Frederick Inc., National Cancer Institute at Frederick, Frederick, Maryland, United States of America
| | - Matthew T. Trivett
- AIDS and Cancer Virus Program, SAIC-Frederick Inc., National Cancer Institute at Frederick, Frederick, Maryland, United States of America
| | - Jacob T. Minang
- AIDS and Cancer Virus Program, SAIC-Frederick Inc., National Cancer Institute at Frederick, Frederick, Maryland, United States of America
| | - Haosi Sun
- AIDS and Cancer Virus Program, SAIC-Frederick Inc., National Cancer Institute at Frederick, Frederick, Maryland, United States of America
| | - Claes Ohlen
- AIDS and Cancer Virus Program, SAIC-Frederick Inc., National Cancer Institute at Frederick, Frederick, Maryland, United States of America
| | - David E. Ott
- AIDS and Cancer Virus Program, SAIC-Frederick Inc., National Cancer Institute at Frederick, Frederick, Maryland, United States of America
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James MM, Wang L, Musoke P, Donnell D, Fogel J, Towler WI, Khaki L, Nakabiito C, Jackson JB, Eshleman SH. Association of HIV diversity and survival in HIV-infected Ugandan infants. PLoS One 2011; 6:e18642. [PMID: 21533179 PMCID: PMC3077388 DOI: 10.1371/journal.pone.0018642] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2010] [Accepted: 03/13/2011] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The level of viral diversity in an HIV-infected individual can change during the course of HIV infection, reflecting mutagenesis during viral replication and selection of viral variants by immune and other selective pressures. Differences in the level of viral diversity in HIV-infected infants may reflect differences in viral dynamics, immune responses, or other factors that may also influence HIV disease progression. We used a novel high resolution melting (HRM) assay to measure HIV diversity in Ugandan infants and examined the relationship between diversity and survival through 5 years of age. METHODS Plasma samples were obtained from 31 HIV-infected infants (HIVNET 012 trial). The HRM assay was used to measure diversity in two regions in the gag gene (Gag1 and Gag2) and one region in the pol gene (Pol). RESULTS HRM scores in all three regions increased with age from 6-8 weeks to 12-18 months (for Gag1: P = 0.005; for Gag2: P = 0.006; for Pol: P = 0.016). Higher HRM scores at 6-8 weeks of age (scores above the 75(th) percentile) were associated with an increased risk of death by 5 years of age (for Pol: P = 0.005; for Gag1/Gag2 (mean of two scores): P = 0.003; for Gag1/Gag2/Pol (mean of three scores): P = 0.002). We did not find an association between HRM scores and other clinical and laboratory variables. CONCLUSIONS Genetic diversity in HIV gag and pol measured using the HRM assay was typically low near birth and increased over time. Higher HIV diversity in these regions at 6-8 weeks of age was associated with a significantly increased risk of death by 5 years of age.
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Affiliation(s)
- Maria M. James
- Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Lei Wang
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Philippa Musoke
- Makerere University-Johns Hopkins University Research Collaboration (MU-JHU), Baltimore, Maryland, United States of America, and Kampala, Uganda
- Makerere University School of Medicine, Kampala, Uganda
| | - Deborah Donnell
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Jessica Fogel
- Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - William I. Towler
- Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Leila Khaki
- Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Clemensia Nakabiito
- Makerere University-Johns Hopkins University Research Collaboration (MU-JHU), Baltimore, Maryland, United States of America, and Kampala, Uganda
- Makerere University School of Medicine, Kampala, Uganda
| | - J. Brooks Jackson
- Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Susan H. Eshleman
- Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
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Cafaro A, Macchia I, Maggiorella MT, Titti F, Ensoli B. Innovative approaches to develop prophylactic and therapeutic vaccines against HIV/AIDS. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2010; 655:189-242. [PMID: 20047043 DOI: 10.1007/978-1-4419-1132-2_14] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The acquired immunodeficiency syndrome (AIDS) emerged in the human population in the summer of 1981. According to the latest United Nations estimates, worldwide over 33 million people are infected with human immunodeficiency virus (HIV) and the prevalence rates continue to rise globally. To control the alarming spread of HIV, an urgent need exists for developing a safe and effective vaccine that prevents individuals from becoming infected or progressing to disease. To be effective, an HIV/AIDS vaccine should induce broad and long-lasting humoral and cellular immune responses, at both mucosal and systemic level. However, the nature of protective immune responses remains largely elusive and this represents one of the major roadblocks preventing the development of an effective vaccine. Here we summarize our present understanding of the factors responsible for resistance to infection or control of progression to disease in human and monkey that may be relevant to vaccine development and briefly review recent approaches which are currently being tested in clinical trials. Finally, the rationale and the current status of novel strategies based on nonstructural HIV-1 proteins, such as Tat, Nef and Rev, used alone or in combination with modified structural HIV-1 Env proteins are discussed.
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Affiliation(s)
- Aurelio Cafaro
- National AIDS Center, Istituto Superiore di Sanità, V.le Regina Elena 299, 00161, Rome, Italy
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Frahm N, Kaufmann DE, Yusim K, Muldoon M, Kesmir C, Linde CH, Fischer W, Allen TM, Li B, McMahon BH, Faircloth KL, Hewitt HS, Mackey EW, Miura T, Khatri A, Wolinsky S, McMichael A, Funkhouser RK, Walker BD, Brander C, Korber BT. Increased sequence diversity coverage improves detection of HIV-specific T cell responses. THE JOURNAL OF IMMUNOLOGY 2007; 179:6638-50. [PMID: 17982054 DOI: 10.4049/jimmunol.179.10.6638] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The accurate identification of HIV-specific T cell responses is important for determining the relationship between immune response, viral control, and disease progression. HIV-specific immune responses are usually measured using peptide sets based on consensus sequences, which frequently miss responses to regions where test set and infecting virus differ. In this study, we report the design of a peptide test set with significantly increased coverage of HIV sequence diversity by including alternative amino acids at variable positions during the peptide synthesis step. In an IFN-gamma ELISpot assay, these "toggled" peptides detected HIV-specific CD4(+) and CD8(+) T cell responses of significantly higher breadth and magnitude than matched consensus peptides. The observed increases were explained by a closer match of the toggled peptides to the autologous viral sequence. Toggled peptides therefore afford a cost-effective and significantly more complete view of the host immune response to HIV and are directly applicable to other variable pathogens.
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Affiliation(s)
- Nicole Frahm
- Partners AIDS Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02129, USA
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