1
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Katsuya H, Cook LBM, Rowan AG, Melamed A, Turpin J, Ito J, Islam S, Miyazato P, Jek Yang Tan B, Matsuo M, Miyakawa T, Nakata H, Matsushita S, Taylor GP, Bangham CRM, Kimura S, Satou Y. Clonality of HIV-1- and HTLV-1-Infected Cells in Naturally Coinfected Individuals. J Infect Dis 2022; 225:317-326. [PMID: 33844021 DOI: 10.1093/infdis/jiab202] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 04/11/2021] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Coinfection with human immunodeficiency virus type 1 (HIV-1) and human T-cell leukemia virus type 1 (HTLV-1) diminishes the value of the CD4+ T-cell count in diagnosing AIDS, and increases the rate of HTLV-1-associated myelopathy. It remains elusive how HIV-1/HTLV-1 coinfection is related to such characteristics. We investigated the mutual effect of HIV-1/HTLV-1 coinfection on their integration sites (ISs) and clonal expansion. METHODS We extracted DNA from longitudinal peripheral blood samples from 7 HIV-1/HTLV-1 coinfected, and 12 HIV-1 and 13 HTLV-1 monoinfected individuals. Proviral loads (PVL) were quantified using real-time polymerase chain reaction (PCR). Viral ISs and clonality were quantified by ligation-mediated PCR followed by high-throughput sequencing. RESULTS PVL of both HIV-1 and HTLV-1 in coinfected individuals was significantly higher than that of the respective virus in monoinfected individuals. The degree of oligoclonality of both HIV-1- and HTLV-1-infected cells in coinfected individuals was also greater than in monoinfected subjects. ISs of HIV-1 in cases of coinfection were more frequently located in intergenic regions and transcriptionally silent regions, compared with HIV-1 monoinfected individuals. CONCLUSIONS HIV-1/HTLV-1 coinfection makes an impact on the distribution of viral ISs and clonality of virus-infected cells and thus may alter the risks of both HTLV-1- and HIV-1-associated disease.
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Affiliation(s)
- Hiroo Katsuya
- Division of Hematology, Respiratory Medicine and Oncology, Department of Internal Medicine, Faculty of Medicine, Saga University, Saga, Japan.,Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Lucy B M Cook
- Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, UK
| | - Aileen G Rowan
- Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, UK
| | - Anat Melamed
- Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, UK
| | - Jocelyn Turpin
- Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, UK
| | - Jumpei Ito
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Saiful Islam
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan.,International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Paola Miyazato
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan.,International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Benjy Jek Yang Tan
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan.,International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Misaki Matsuo
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan.,International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Toshikazu Miyakawa
- Department of Hematology, Rheumatology and Infectious Diseases, Kumamoto University of Medicine, Kumamoto, Japan
| | - Hirotomo Nakata
- Department of Hematology, Rheumatology and Infectious Diseases, Kumamoto University of Medicine, Kumamoto, Japan
| | - Shuzo Matsushita
- Clinical Retrovirology, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Graham P Taylor
- Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, UK
| | - Charles R M Bangham
- Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, UK
| | - Shinya Kimura
- Division of Hematology, Respiratory Medicine and Oncology, Department of Internal Medicine, Faculty of Medicine, Saga University, Saga, Japan
| | - Yorifumi Satou
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan.,International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
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Thomas J, Ruggiero A, Paxton WA, Pollakis G. Measuring the Success of HIV-1 Cure Strategies. Front Cell Infect Microbiol 2020; 10:134. [PMID: 32318356 PMCID: PMC7154081 DOI: 10.3389/fcimb.2020.00134] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 03/13/2020] [Indexed: 01/10/2023] Open
Abstract
HIV-1 eradication strategies aim to achieve viral remission in the absence of antiretroviral therapy (ART). The development of an HIV-1 cure remains challenging due to the latent reservoir (LR): long-lived CD4 T cells that harbor transcriptionally silent HIV-1 provirus. The LR is stable despite years of suppressive ART and is the source of rebound viremia following therapy interruption. Cure strategies such as "shock and kill" aim to eliminate or reduce the LR by reversing latency, exposing the infected cells to clearance via the immune response or the viral cytopathic effect. Alternative strategies include therapeutic vaccination, which aims to prime the immune response to facilitate control of the virus in the absence of ART. Despite promising advances, these strategies have been unable to significantly reduce the LR or increase the time to viral rebound but have provided invaluable insight in the field of HIV-1 eradication. The development and assessment of an HIV-1 cure requires robust assays that can measure the LR with sufficient sensitivity to detect changes that may occur following treatment. The viral outgrowth assay (VOA) is considered the gold standard method for LR quantification due to its ability to distinguish intact and defective provirus. However, the VOA is time consuming and resource intensive, therefore several alternative assays have been developed to bridge the gap between practicality and accuracy. Whilst a cure for HIV-1 infection remains elusive, recent advances in our understanding of the LR and methods for its eradication have offered renewed hope regarding achieving ART free viral remission.
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Affiliation(s)
- Jordan Thomas
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Alessandra Ruggiero
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom.,Immune and Infectious Disease Division, Academic Department of Pediatrics (DPUO), Bambino Gesù Children's Hospital, Rome, Italy
| | - William A Paxton
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Georgios Pollakis
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
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3
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Total HIV-1 DNA, a Marker of Viral Reservoir Dynamics with Clinical Implications. Clin Microbiol Rev 2017; 29:859-80. [PMID: 27559075 DOI: 10.1128/cmr.00015-16] [Citation(s) in RCA: 153] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
HIV-1 DNA persists in infected cells despite combined antiretroviral therapy (cART), forming viral reservoirs. Recent trials of strategies targeting latent HIV reservoirs have rekindled hopes of curing HIV infection, and reliable markers are thus needed to evaluate viral reservoirs. Total HIV DNA quantification is simple, standardized, sensitive, and reproducible. Total HIV DNA load influences the course of the infection and is therefore clinically relevant. In particular, it is predictive of progression to AIDS and death, independently of HIV RNA load and the CD4 cell count. Baseline total HIV DNA load is predictive of the response to cART. It declines during cART but remains quantifiable, at a level that reflects both the history of infection (HIV RNA zenith, CD4 cell count nadir) and treatment efficacy (residual viremia, cumulative viremia, immune restoration, immune cell activation). Total HIV DNA load in blood is also predictive of the presence and severity of some HIV-1-associated end-organ disorders. It can be useful to guide individual treatment, notably, therapeutic de-escalation. Although it does not distinguish between replication-competent and -defective latent viruses, the total HIV DNA load in blood, tissues, and cells provides insights into HIV pathogenesis, probably because all viral forms participate in host cell activation and HIV pathogenesis. Total HIV DNA is thus a biomarker of HIV reservoirs, which can be defined as all infected cells and tissues containing all forms of HIV persistence that participate in pathogenesis. This participation may occur through the production of new virions, creating new cycles of infection and disseminating infected cells; maintenance or amplification of reservoirs by homeostatic cell proliferation; and viral transcription and synthesis of viral proteins without new virion production. These proteins can induce immune activation, thus participating in the vicious circle of HIV pathogenesis.
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4
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Molecular Detection and Characterization of HIV‐1. Mol Microbiol 2011. [DOI: 10.1128/9781555816834.ch35] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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5
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Masquelier B, Taieb A, Reigadas S, Marchou B, Cheneau C, Spire B, Charpentier C, Leport C, Raffi F, Chene G, Descamps D, Leport C, Raffi F, Chene G, Salamon R, Moatti JP, Pierret J, Spire B, Brun-Vezinet F, Fleury H, Masquelier B, Peytavin G, Garraffo R, Costagliola D, Dellamonica P, Katlama C, Meyer L, Salmon D, Sobel A, Cuzin L, Dupon M, Duval X, Le Moing V, Marchou B, May T, Morlat P, Rabaud C, Waldner-Combernoux A, Reboud P, Couffin-Cadiergues S, Marchand L, Bouteloup V, Bouhnik AD, Brunet-Francois C, Caron V, Carrieri MP, Courcoul M, Couturier F, Hardel L, Iordache L, Kurkdji P, Martiren S, Preau M, Protopopescu C, Surzyn J, Taieb A, Villes V, Schmit JL, Chennebault JM, Faller JP, Mgy-Bertrand N, Hoen B, Drobachef, Bouchaud O, Dupon M, Longy-Boursier, Morlat P, Ragnaud JM, Granier P, Garre M, Verdon R, Merrien D, Devidas A, Sobel A, Piroth L, Perronne C, Froguel E, Ceccaldi J, Peyramond D, Allard C, Reynes J, May T, Raffi F, Fuzibet JG, Dellamonica P, Arsac P, Bouvet E, Bricaire F, Bergmann P, Cabane J, Monsonego J, Girard PM, Guillevin L, Herson S, Leport C, Meyohas MC, Molina JM, Pialoux G, Salmon D, Roblot P, Jaussaud R, Michelet C, Lucht F, Debord T, Rey D, De Jaureguiberry JP, Marchou B, Bernard L. Cellular HIV-1 DNA quantification and short-term and long-term response to antiretroviral therapy. J Antimicrob Chemother 2011; 66:1582-9. [DOI: 10.1093/jac/dkr153] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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6
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Weidner J, Cassens U, Göhde W, Sibrowski W, Odaibo G, Olaleye D, Reichelt D, Greve B. An improved PCR method for detection of HIV-1 proviral DNA of a wide range of subtypes and recombinant forms circulating globally. J Virol Methods 2010; 172:22-6. [PMID: 21182872 DOI: 10.1016/j.jviromet.2010.12.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2009] [Revised: 12/02/2010] [Accepted: 12/13/2010] [Indexed: 10/18/2022]
Abstract
Proviral DNAs are being measured increasingly as a marker of the efficacy of highly active anti-retroviral therapy (HAART) and is accepted for the early diagnosis of perinatal HIV-1 infections. This requires a standardized test which enables the detection of a wide range of subtypes worldwide including O, N and circulating recombinant forms (CRFs). Based on a previous publication, a PCR - Test for HIV-1 provirus detection in peripheral blood mononuclear cells (PBMCs) was developed. Blood samples from 80 individuals infected with HIV-1 and 20 persons negative for HIV-1&2 from Africa and Germany were tested for the presence of HIV-1 provirus DNA. The primer system used enables the detection of proviral DNA despite the high concentrations of human DNA. The limit of detection was determined to be 5 copies per 10(5) cells. All 20 samples from persons negative for HIV were negative for HIV-1 proviral DNA while provirus DNA was amplified from 76 of the 80 (95%) samples from persons infected with HIV. The amplified products were detected by gel-electrophoresis, flow cytometry and real-time PCR. All three detection systems provided the same results.
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7
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Cell-associated viral burden provides evidence of ongoing viral replication in aviremic HIV-2-infected patients. J Virol 2010; 85:2429-38. [PMID: 21159859 DOI: 10.1128/jvi.01921-10] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Viremia is significantly lower in HIV-2 than in HIV-1 infection, irrespective of disease stage. Nevertheless, the comparable proviral DNA burdens observed for these two infections indicate similar numbers of infected cells. Here we investigated this apparent paradox by assessing cell-associated viral replication. We found that untreated HIV-1-positive (HIV-1(+)) and HIV-2(+) individuals, matched for CD4 T cell depletion, exhibited similar gag mRNA levels, indicating that significant viral transcription is occurring in untreated HIV-2(+) patients, despite the reduced viremia (undetectable to 2.6 × 10(4) RNA copies/ml). However, tat mRNA transcripts were observed at significantly lower levels in HIV-2(+) patients, suggesting that the rate of de novo infection is decreased in these patients. Our data also reveal a direct relationship of gag and tat transcripts with CD4 and CD8 T cell activation, respectively. Antiretroviral therapy (ART)-treated HIV-2(+) patients showed persistent viral replication, irrespective of plasma viremia, possibly contributing to the emergence of drug resistance mutations, persistent hyperimmune activation, and poor CD4 T cell recovery that we observed with these individuals. In conclusion, we provide here evidence of significant ongoing viral replication in HIV-2(+) patients, further emphasizing the dichotomy between amount of plasma virus and cell-associated viral burden and stressing the need for antiretroviral trials and the definition of therapeutic guidelines for HIV-2 infection.
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8
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Valcour VG, Shiramizu BT, Shikuma CM. HIV DNA in circulating monocytes as a mechanism to dementia and other HIV complications. J Leukoc Biol 2010; 87:621-6. [PMID: 20130221 DOI: 10.1189/jlb.0809571] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
It is broadly accepted that HIV DNA in lymphoid and myeloid cells persists despite combination antiretroviral therapy. Recognized as the Achilles heel to HIV eradication, the role of these peripheral reservoirs in HIV morbidity is less well developed. The burden of HIV DNA in peripheral mononuclear cells is linked to HIV disease outcomes such as time to AIDS diagnosis, survival, and CD4 T-lymphocyte counts. Monocytes are a minor HIV DNA reservoir, and the burden of HIV DNA in these cells appears to be linked to dementia, suggesting that residual infection in this subset is linked to tissue-related HIV complications. Since monocytes are likely involved in trafficking virus to the brain, there is a strong mechanistic link underlying this discovery. Herein, we summarize our current understanding of monocyte HIV DNA and central nervous system dysfunction in humans. We present a model to understand these relationships and suggest possible treatment approaches to be tested.
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Affiliation(s)
- Victor G Valcour
- Hawaii Center for AIDS, John A. Burns School of Medicine, University of Hawaii, Honolulu, Hawaii 96816, USA
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9
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Re MC, Vitone F, Biagetti C, Schiavone P, Alessandrini F, Bon I, de Crignis E, Gibellini D. HIV-1 DNA proviral load in treated and untreated HIV-1 seropositive patients. Clin Microbiol Infect 2009; 16:640-6. [PMID: 19732081 DOI: 10.1111/j.1469-0691.2009.02826.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
As proviral human immunodeficiency virus type 1 (HIV-1) DNA can replenish and revive viral infection upon activation, its detection might offer significant therapeutic information, complementing the input provided by plasma RNA determination in the follow-up of infected individuals. A selected group of acutely infected subjects was studied to verify both total and 2-long terminal repeat (2-LTR) DNA proviral load during the acute phase of infection and thereafter. Patients were divided in two sex- and age-matched groups: 19 naive individuals who did not receive antiretroviral therapy during the observation period and 20 subjects treated according to current guidelines. Total and 2-LTR HIV-1 DNA proviral load, in addition to RNA viral load and CD4 cell count, were determined in peripheral blood mononuclear cells (PBMC) at baseline, 6 and 12 months after the first sampling. Total and 2-LTR HIV-1 DNA proviral load exhibited no significant variation at any time in the naive patients (total HIV-1 DNA ranging from 896 + or - 731 to 715 + or - 673 copies/10(5) PBMC and 2-LTR HIV-1 DNA ranging from 94 + or - 105 to 65 + or - 44 copies/10(5) PBMC), whereas a significant reduction in both total HIV-1 DNA (ranging from 997 + or - 676 to 262 + or - 174 copies/10(5) PBMC) and 2-LTR HIV-1 DNA proviral load (ranging from 116 + or - 55 to 26 + or - 35 copies/10(5) PBMC) was detected in highly active antiretroviral therapy (HAART) patients, together with a CD4(+) T cell count increase and RNA load decrease. HAART negatively affects both the labile HIV burden and the integrated proviral DNA, at least in the initial period of successful treatment, suggesting that quantification of HIV-1 DNA proviral load may be an important parameter in monitoring HIV infection.
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Affiliation(s)
- M C Re
- Department of Haematology and Oncologic Science, Microbiology Section, National Institute Biostructure and Biosystem (INBB), Rome, Italy.
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10
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Tu YQ, Wang MJ, Yao J, Zhu XM, Pan PL, Xing WG, Zhang GH, Yang RG, Zheng YT, Jiang Y. Human immunodeficiency virus-1 genotypic drug resistance among volunteer blood donors in Yunnan, China. Transfusion 2009; 49:1865-73. [DOI: 10.1111/j.1537-2995.2009.02219.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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11
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Peripheral ovine progressive pneumonia provirus levels correlate with and predict histological tissue lesion severity in naturally infected sheep. CLINICAL AND VACCINE IMMUNOLOGY : CVI 2009; 16:551-7. [PMID: 19261772 DOI: 10.1128/cvi.00459-08] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Studies were undertaken to determine whether anti-ovine progressive pneumonia virus (OPPV) antibody responses in serum or OPP provirus levels in peripheral blood associate with the degree of histologically measured tissue lesions in naturally OPPV-infected sheep. Sections of formalin-fixed, paraffin-embedded, and hematoxylin- and eosin-stained lung, mammary gland, carpal synovial membrane, and brain tissues from 11 OPPV-infected ewes (mean age of 8.6 years) and 5 OPPV-uninfected ewes (mean age of 6 years) were evaluated for lesion severity. Ovine progressive pneumonia (OPP) provirus levels and anti-OPPV antibody titers in peripheral blood and serum samples, respectively, were measured upon euthanasia and 3 years prior to euthanasia. Both mean peripheral OPP provirus levels and mean serum anti-surface envelope glycoprotein (anti-SU) antibody titers at the time of euthanasia were significantly higher in ewes with moderate to severe histological lesions than in ewes with no to mild histological lesions. However, although mean peripheral blood OPP provirus levels at euthanasia and 3 years prior to euthanasia significantly correlated with the highest histological lesion score for any affected tissue (two-tailed P values, 0.03 and 0.02), mean serum anti-SU antibody titers, anti-capsid antibody titers, and anti-transmembrane 90 antibody titers at euthanasia did not show a significant correlation with the highest histological lesion score for any tissue (two-tailed P values, 0.32, 0.97, and 0.18, respectively). These data are the first to show that OPP provirus levels predict and correlate with the extent of OPPV-related histological lesions in various OPPV-affected tissues. These findings suggest that peripheral OPP provirus levels quantitatively contribute more to the development of histological lesions than the systemic anti-SU antibody host immune response.
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12
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Harrington RD, Herrmann-Hoesing LM, White SN, O'Rourke KI, Knowles DP. Ovine progressive pneumonia provirus levels are unaffected by the prion 171R allele in an Idaho sheep flock. Genet Sel Evol 2009; 41:17. [PMID: 19284685 PMCID: PMC3225825 DOI: 10.1186/1297-9686-41-17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2008] [Accepted: 01/22/2009] [Indexed: 11/10/2022] Open
Abstract
Selective breeding of sheep for arginine (R) at prion gene (PRNP) codon 171 confers resistance to classical scrapie. However, other effects of 171R selection are uncertain. Ovine progressive pneumonia/Maedi-Visna virus (OPPV) may infect up to 66% of a flock thus any affect of 171R selection on OPPV susceptibility or disease progression could have major impact on the sheep industry. Hypotheses that the PRNP 171R allele is 1) associated with the presence of OPPV provirus and 2) associated with higher provirus levels were tested in an Idaho ewe flock. OPPV provirus was found in 226 of 358 ewes by quantitative PCR. The frequency of ewes with detectable provirus did not differ significantly among the 171QQ, 171QR, and 171RR genotypes (p > 0.05). Also, OPPV provirus levels in infected ewes were not significantly different among codon 171 genotypes (p > 0.05). These results show that, in the flock examined, the presence of OPPV provirus and provirus levels are not related to the PRNP 171R allele. Therefore, a genetic approach to scrapie control is not expected to increase or decrease the number of OPPV infected sheep or the progression of disease. This study provides further support to the adoption of PRNP 171R selection as a scrapie control measure.
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Affiliation(s)
- Robert D Harrington
- Animal Disease Research Unit, Agricultural Research Service, US Department of Agriculture, Pullman, WA 99164-6630, USA.
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13
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Herrmann-Hoesing LM, White SN, Mousel MR, Lewis GS, Knowles DP. Ovine progressive pneumonia provirus levels associate with breed and Ovar-DRB1. Immunogenetics 2008; 60:749-58. [DOI: 10.1007/s00251-008-0328-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2008] [Accepted: 08/05/2008] [Indexed: 11/30/2022]
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14
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A more precise HIV integration assay designed to detect small differences finds lower levels of integrated DNA in HAART treated patients. Virology 2008; 379:78-86. [PMID: 18649912 DOI: 10.1016/j.virol.2008.05.030] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2008] [Revised: 04/25/2008] [Accepted: 05/29/2008] [Indexed: 12/21/2022]
Abstract
Many studies report the level of total viral DNA in HIV-infected patients, but few studies report the level of integrated DNA. It is important to measure integrated DNA in HIV-infected patients because the information could shed light on the effectiveness of antiretroviral therapy, especially intensified therapy, when viral loads may remain undetectable. In order to develop an integration assay for patient samples, we enhanced the sensitivity of our prior integration assay. To do this, we exploited a technique that we developed, called repetitive sampling, and optimized reaction conditions for rare event detection, rather than large dynamic range. We also designed our primers to match more conserved regions of HIV. The result is a new, sensitive, quantitative assay that allows us to measure integrated DNA in HIV-infected patients. When we applied our integration assay to patient PBMCs, we found that the use of HAART is associated with reduced levels of integrated DNA.
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Saracino A, Monno L, Punzi G, Cibelli DC, Tartaglia A, Scudeller L, Brindicci G, Lagioia A, Scotto G, Angarano G. HIV-1 biological phenotype and predicted coreceptor usage based on V3 loop sequence in paired PBMC and plasma samples. Virus Res 2007; 130:34-42. [PMID: 17582634 DOI: 10.1016/j.virusres.2007.05.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2007] [Revised: 03/26/2007] [Accepted: 05/09/2007] [Indexed: 10/23/2022]
Abstract
Paired PBMCs and plasma samples from 34 HIV-infected patients were studied to verify the relationship between coreceptor use based on genotyping of V3 region of HIV-1 envelope gp120 and biological phenotype with virus isolation and subsequent correlation to clinical characteristics. The "11/25" rule, geno2pheno and PSSM were compared. All SI patients were HIV-1 subtype B (p=0.04) and had a lower CD4 count than NSI patients (p=0.01), while no differences were observed in mean HIV-RNA (log) (p=0.6). SI phenotype was not associated with AIDS-defining events (p=0.1) or with concurrent antiretroviral therapy (p=0.4). With geno2pheno, which shows the highest sensibility (83%), an X4 or X4/R5 genotype in PBMC DNA was also associated to B-subtype and lower CD4 count (p=0.01) compared to R5 isolates. Based on plasma RNA sequences, the predicted coreceptor usage agreed with PBMC DNA in 79% of cases with the "11/25" rule, 82% with geno2pheno, and 82% with PSSM. A X4 virus in plasma (but not in PBMCs) was significantly associated with HAART in all three methods (p=0.01 for "11/25" rule, p=0.01 for geno2pheno and p=0.03 for PSSM). Due to viral mixtures and/or difficulties in genotype interpretation, current V3 sequence-based methods cannot accurately predict HIV-1 coreceptor use.
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Affiliation(s)
- A Saracino
- Clinic of Infectious Diseases, University of Foggia, Italy
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16
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Albuquerque AS, Foxall RB, Cortesão CS, Soares RS, Doroana M, Ribeiro A, Lucas M, Antunes F, Victorino RMM, Sousa AE. Low CD4 T-cell counts despite low levels of circulating HIV: Insights from the comparison of HIV-1 infected patients with a discordant response to antiretroviral therapy to patients with untreated advanced HIV-2 disease. Clin Immunol 2007; 125:67-75. [PMID: 17692571 DOI: 10.1016/j.clim.2007.07.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2007] [Revised: 07/02/2007] [Accepted: 07/02/2007] [Indexed: 01/31/2023]
Abstract
A significant proportion of HIV-1+ patients with suppression of viremia under antiretroviral therapy fail to recover CD4(+) T-cell counts (ART-Discordants). Similarly, untreated HIV-2+ patients can also exhibit major CD4 depletion in spite of undetectable viremia. We characterize here the immunological disturbances associated with major CD4-lymphopenia in these two scenarios as compared to untreated viremic HIV-1+ patients with similar CD4-lymphopenia and HIV-1+ patients with successful immunological and virological responses under ART. Low CD4 counts were associated with major naive CD4 and CD8 depletion, irrespective of type of infection or ART-exposure. However, ART-Discordants exhibited lower levels of T-cell activation as compared to both untreated HIV-2 and HIV-1 cohorts, and a less marked increase in circulating IL-7 despite similar CD4 depletion. Nevertheless, ART-Discordants showed a preserved Bcl-2 expression, suggesting increased IL-7 consumption, which in conjunction with the relatively lower T-cell activation may contribute to their CD4 count stability and low rate of opportunistic infections.
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Affiliation(s)
- Adriana S Albuquerque
- Unidade de Imunologia Clínica, Instituto de Medicina Molecular, Faculdade de Medicina de Lisboa, Av Prof Egas Moniz, 1649-028, Lisboa, Portugal
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Langford SE, Ananworanich J, Cooper DA. Predictors of disease progression in HIV infection: a review. AIDS Res Ther 2007; 4:11. [PMID: 17502001 PMCID: PMC1887539 DOI: 10.1186/1742-6405-4-11] [Citation(s) in RCA: 192] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2006] [Accepted: 05/14/2007] [Indexed: 01/18/2023] Open
Abstract
During the extended clinically latent period associated with Human Immunodeficiency Virus (HIV) infection the virus itself is far from latent. This phase of infection generally comes to an end with the development of symptomatic illness. Understanding the factors affecting disease progression can aid treatment commencement and therapeutic monitoring decisions. An example of this is the clear utility of CD4+ T-cell count and HIV-RNA for disease stage and progression assessment. Elements of the immune response such as the diversity of HIV-specific cytotoxic lymphocyte responses and cell-surface CD38 expression correlate significantly with the control of viral replication. However, the relationship between soluble markers of immune activation and disease progression remains inconclusive. In patients on treatment, sustained virological rebound to >10,000 copies/mL is associated with poor clinical outcome. However, the same is not true of transient elevations of HIV RNA (blips). Another virological factor, drug resistance, is becoming a growing problem around the globe and monitoring must play a part in the surveillance and control of the epidemic worldwide. The links between chemokine receptor tropism and rate of disease progression remain uncertain and the clinical utility of monitoring viral strain is yet to be determined. The large number of confounding factors has made investigation of the roles of race and viral subtype difficult, and further research is needed to elucidate their significance. Host factors such as age, HLA and CYP polymorphisms and psychosocial factors remain important, though often unalterable, predictors of disease progression. Although gender and mode of transmission have a lesser role in disease progression, they may impact other markers such as viral load. Finally, readily measurable markers of disease such as total lymphocyte count, haemoglobin, body mass index and delayed type hypersensitivity may come into favour as ART becomes increasingly available in resource-limited parts of the world. The influence of these, and other factors, on the clinical progression of HIV infection are reviewed in detail, both preceding and following treatment initiation.
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Affiliation(s)
- Simone E Langford
- Monash University, Melbourne, Australia
- The HIV Netherlands Australia Thailand Research Collaboration, Bangkok, Thailand
| | | | - David A Cooper
- The HIV Netherlands Australia Thailand Research Collaboration, Bangkok, Thailand
- The National Centre in HIV Epidemiology and Clinical Research, Sydney, Australia, University of New South Wales, Sydney, Australia
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Bokaei PB, Ma XZ, Sakac D, Branch DR. HIV-1 integration is inhibited by stimulation of the VPAC2 neuroendocrine receptor. Virology 2007; 362:38-49. [PMID: 17257640 DOI: 10.1016/j.virol.2006.12.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2006] [Revised: 10/11/2006] [Accepted: 12/08/2006] [Indexed: 11/30/2022]
Abstract
Successful HIV-1 infection requires a number of specific stages leading to integration of the provirus. We previously suggested that members of the VPAC neuroendocrine receptor family may play a role in HIV-1 infection. We now show that stimulation of the VPAC2 receptor with specific agonists provides strong resistance to HIV-1 infection. Daily stimulation of VPAC2, but not VPAC1 or PAC1, resulted in up to 90% inhibition of X4 or R5 productive infections in either cell lines or PBMCs. VPAC2 agonist stimulation had no effect on cell surface co-receptors, the rate of apoptotic cells, or HIV-1 entry or reverse transcription of viral RNA. However, we provide evidence that VPAC2-specific agonists inhibit HIV-1 infection through an inhibitory effect on the ability of the HIV-1 cDNA to integrate into the host DNA. These data reveal that VPAC2 agonists are appropriate candidates for further study as possible treatments aimed at the amelioration of HIV/AIDS.
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Affiliation(s)
- Payman Baradar Bokaei
- The Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada M5G 2M1
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Carr JM, Cheney KM, Coolen C, Davis A, Shaw D, Ferguson W, Chang G, Higgins G, Burrell C, Li P. Development of methods for coordinate measurement of total cell-associated and integrated human immunodeficiency virus type 1 (HIV-1) DNA forms in routine clinical samples: levels are not associated with clinical parameters, but low levels of integrated HIV-1 DNA may be prognostic for continued successful therapy. J Clin Microbiol 2007; 45:1288-97. [PMID: 17314225 PMCID: PMC1865852 DOI: 10.1128/jcm.01926-06] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
We have adapted our established Alu PCR assay for proviral DNA and PCR for total cellular DNA to a real-time PCR format and applied these to human immunodeficiency virus (HIV)-positive specimens collected for routine determination of the plasma viral load (pVL). In a cohort of five patients, measurements of integrated viral load (iVL) and cell-associated viral load (cVL) in CD4(+) cells isolated by a single positive selection step were not indicative of HIV DNA levels in the circulation, and further analysis was performed on peripheral blood mononuclear cells (PBMC). In a cohort of 46 samples total cVL was quantitated in most samples, but iVL could be quantitated in only 47.8%, since in 26% iVL was undetectable and in 21.7% the results were invalid due to high levels of unintegrated HIV DNA. There was no correlation of cVL or iVL with pVL, CD4 count, or duration of successful antiretroviral treatment. Out of 26 patients with undetectable pVL, 4 patients failed therapy within the subsequent 12 months and had higher than average iVL, but this was not the case for cVL. Among nine patients with long-term undetectable pVL, no consistent decline in cVL or iVL was seen with time, and changes in cVL and iVL within a patient could be concordant or discordant. These results show that cVL and iVL can be coordinately measured in PBMC from clinical samples but do not correlate with pVL, CD4 counts, or length of suppressive antiretroviral therapy. Interestingly, a high iVL (but not a high cVL) in patients with undetectable pVL was associated with subsequent treatment failure.
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Affiliation(s)
- J M Carr
- Infectious Diseases Laboratories, Institute of Medical and Veterinary Science, Frome Rd., Adelaide, South Australia 5000, Australia.
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Bon I, Gibellini D, Borderi M, Alessandrini F, Vitone F, Schiavone P, Re MC. Genotypic resistance in plasma and peripheral blood lymphocytes in a group of naive HIV-1 patients. J Clin Virol 2007; 38:313-20. [PMID: 17306618 DOI: 10.1016/j.jcv.2006.12.018] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2006] [Revised: 12/15/2006] [Accepted: 12/22/2006] [Indexed: 10/23/2022]
Abstract
BACKGROUND Since HIV infection cannot be completely eliminated due to the establishment of latently infected CD4+ T cell reservoirs, there is an urgent need for a clearer understanding of comparative resistance profiles between plasma and PBMC in HIV-1 patients. OBJECTIVES To assess the prevalence of mutations associated with drug resistance and to compare cell free and cell-associated strains. STUDY DESIGN Genotypic resistance analysis on viral DNA and plasma was performed in 31 therapy naive patients with chronic infection to check reverse transcriptase (RT) and protease resistance associated mutations before beginning antiretroviral therapy. RESULTS Direct sequencing of DNA provirus disclosed key mutations (such as G190A/S, V106A, K103N and T215F) to RT inhibitors more frequently (7 patients out 31) than in plasma RNA (2 out of 31). In addition, major mutations (D30N, M46I, I50V, I84V) associated with drug resistance in the PR region were only found in PBMCs. CONCLUSIONS Despite the small number of patients, our results show a different resistance profile between plasma and PBMC compartments and may yield additional information for first-line antiretroviral regimens. Further investigations on larger series followed-up for a longer period of time are required to obtain in-depth information on the meaning of the mutations detectable in plasma and/or in PBMCs.
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Affiliation(s)
- Isabella Bon
- Section of Microbiology, Department of Clinical and Experimental Medicine, University of Bologna, Via Massarenti, 9, 40138 Bologna, Italy
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Re MC, Vitone F, Sighinolfi L, Schiavone P, Ghinelli F, Gibellini D. Different patterns of HIV-1 DNA after therapy discontinuation. BMC Infect Dis 2005; 5:69. [PMID: 16156892 PMCID: PMC1236926 DOI: 10.1186/1471-2334-5-69] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2005] [Accepted: 09/12/2005] [Indexed: 12/05/2022] Open
Abstract
Background By persisting in infected cells for a long period of time, proviral HIV-1 DNA can represent an alternative viral marker to RNA viral load during the follow-up of HIV-1 infected individuals. In the present study sequential blood samples of 10 patients under antiretroviral treatment from 1997 with two NRTIs, who refused to continue any antiviral regimen, were analyzed for 16 – 24 weeks to study the possible relationship between DNA and RNA viral load. Methods The amount of proviral DNA was quantified by SYBR green real-time PCR in peripheral blood mononuclear cells from a selected group of ten patients with different levels of plasmatic viremia (RNA viral load). Results Variable levels of proviral DNA were found without any significant correlation between proviral load and plasma HIV-1 RNA levels. Results obtained showed an increase or a rebound in viral DNA in most patients, suggesting that the absence of therapy reflects an increase and/or a persistence of cells containing viral DNA. Conclusion Even though plasma HIV RNA levels remain the basic parameter to monitor the intensity of viral replication, the results obtained seem to indicate that DNA levels could represent an adjunct prognostic marker in monitoring HIV-1 infected subjects.
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Affiliation(s)
- Maria Carla Re
- Department of Clinical and Experimental Medicine, Section of Microbiology, University of Bologna, Via Massarenti 9-40138 Bologna, Italy
| | - Francesca Vitone
- Department of Clinical and Experimental Medicine, Section of Microbiology, University of Bologna, Via Massarenti 9-40138 Bologna, Italy
| | - Laura Sighinolfi
- Department of Infectious Diseases, St Anna Hospital, Corso Giovecca, 203-44100 Ferrara, Italy
| | - Pasqua Schiavone
- Department of Clinical and Experimental Medicine, Section of Microbiology, University of Bologna, Via Massarenti 9-40138 Bologna, Italy
| | - Florio Ghinelli
- Department of Infectious Diseases, St Anna Hospital, Corso Giovecca, 203-44100 Ferrara, Italy
| | - Davide Gibellini
- Department of Clinical and Experimental Medicine, Section of Microbiology, University of Bologna, Via Massarenti 9-40138 Bologna, Italy
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