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Costanza G, Felici E, Velluso F, Grelli S, Paba P. +"Evaluation of ELITE InGenius® integrative system for detection, quantification and monitoring of HIV-1 RNA in Cerebrospinal Fluid.". J Virol Methods 2024; 329:114996. [PMID: 39074515 DOI: 10.1016/j.jviromet.2024.114996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 07/09/2024] [Accepted: 07/11/2024] [Indexed: 07/31/2024]
Abstract
INTRODUCTION Human Immunodeficiency virus (HIV) is effectively suppressed in the blood by the Antiretroviral Therapy in people living with HIV, but in rare cases can be present in some tissues and body fluids. In recent years, integrated systems were validated for detecting HIV-1 in plasma or serum. but not in cerebrospinal fluid (CSF). We evaluated the performance of ELITE InGenius® in comparison with the cobas® in this area. METHODS To test the diagnostic accuracy of the HIV-1 ELITe MGB® kit on CSF samples, we tested CSF samples previously characterised with the cobras® HIV1 test. Archived CSF samples were also spiked with serial dilutions of the 4th WHO International Standard for HIV-1 NAT and assays and tested to assess the repeatability and reproducibility of the ELITechGroup assay. RESULTS The HIV-1 ELITe MGB® Kit confirmed all the HIV-1 negative CSF samples from patients HIV positive in plasma and from non-HIV1 patients. All the CSF samples that were HIV-1 positive by the cobas®, were confirmed positive by the ELITe InGenius®. Concordance across the methods was also observed when processing the CSF dilutions spiked at medium-low titre, mimicking HIV-1 low-load infections. CONCLUSIONS The two systems were equivalent in the detection and quantification of HIV-1 RNA in CSF samples.
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Affiliation(s)
| | | | - Fabio Velluso
- Unit of Virology, Policlinic of Tor Vergata, Rome, Italy.
| | - Sandro Grelli
- Unit of Virology, Policlinic of Tor Vergata, Rome, Italy; Department of Experimental Medicine, University of Rome Tor Vergata, Rome 00133, Italy.
| | - Pierpaolo Paba
- Unit of Virology, Policlinic of Tor Vergata, Rome, Italy.
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Jacobson JM, Felber BK, Chen H, Pavlakis GN, Mullins JI, De Rosa SC, Kuritzkes DR, Tomaras GD, Kinslow J, Bao Y, Olefsky M, Rosati M, Bear J, Heptinstall JR, Zhang L, Sawant S, Hannaman D, Laird GM, Cyktor JC, Heath SL, Collier AC, Koletar SL, Taiwo BO, Tebas P, Wohl DA, Belaunzaran-Zamudio PF, McElrath MJ, Landay AL. The immunogenicity of an HIV-1 Gag conserved element DNA vaccine in people with HIV and receiving antiretroviral therapy. AIDS 2024; 38:963-973. [PMID: 38051788 PMCID: PMC11062837 DOI: 10.1097/qad.0000000000003804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
OBJECTIVE The primary objective of the study was to assess the immunogenicity of an HIV-1 Gag conserved element DNA vaccine (p24CE DNA) in people with HIV (PWH) receiving suppressive antiretroviral therapy (ART). DESIGN AIDS Clinical Trials Group A5369 was a phase I/IIa, randomized, double-blind, placebo-controlled study of PWH receiving ART with plasma HIV-1 RNA less than 50 copies/ml, current CD4 + T-cell counts greater than 500 cells/μl, and nadir CD4 + T-cell counts greater than 350 cells/μl. METHODS The study enrolled 45 participants randomized 2 : 1 : 1 to receive p24CE DNA vaccine at weeks 0 and 4, followed by p24CE DNA admixed with full-length p55 Gag DNA vaccine at weeks 12 and 24 (arm A); full-length p55 Gag DNA vaccine at weeks 0, 4, 12, and 24 (arm B); or placebo at weeks 0, 4, 12, and 24 (arm C). The active and placebo vaccines were administered by intramuscular electroporation. RESULTS There was a modest, but significantly greater increase in the number of conserved elements recognized by CD4 + and/or CD8 + T cells in arm A compared with arm C ( P = 0.014). The percentage of participants with an increased number of conserved elements recognized by T cells was also highest in arm A (8/18, 44.4%) vs. arm C (0/10, 0.0%) ( P = 0.025). There were no significant differences between treatment groups in the change in magnitude of responses to total conserved elements. CONCLUSION A DNA-delivered HIV-1 Gag conserved element vaccine boosted by a combination of this vaccine with a full-length p55 Gag DNA vaccine induced a new conserved element-directed cellular immune response in approximately half the treated PWH on ART.
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Affiliation(s)
- Jeffrey M Jacobson
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH
| | - Barbara K Felber
- Human Retrovirus Pathogenesis Section, Vaccine Branch, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD
| | - Huichao Chen
- Harvard T.H. Chan School of Public Health, Boston, MA
| | - George N Pavlakis
- Human Retrovirus Section, Vaccine Branch, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD
| | - James I Mullins
- Departments of Microbiology, Medicine, and Global Health, University of Washington, Seattle, WA
| | - Stephen C De Rosa
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Daniel R Kuritzkes
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Georgia D Tomaras
- Duke Center for Human Systems Immunology, Departments of Surgery, Immunology, Molecular Genetics and Microbiology, Durham, NC
| | - Jennifer Kinslow
- Department of Internal Medicine, Rush University Medical Center, Chicago, IL
| | - Yajing Bao
- Harvard T.H. Chan School of Public Health, Boston, MA
| | | | - Margherita Rosati
- Human Retrovirus Section, Vaccine Branch, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD
| | - Jenifer Bear
- Human Retrovirus Pathogenesis Section, Vaccine Branch, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD
| | - Jack R Heptinstall
- Duke Center for Human Systems Immunology, Departments of Surgery, Immunology, Molecular Genetics and Microbiology, Durham, NC
| | - Lu Zhang
- Duke Center for Human Systems Immunology, Departments of Surgery, Immunology, Molecular Genetics and Microbiology, Durham, NC
| | - Sheetal Sawant
- Duke Center for Human Systems Immunology, Departments of Surgery, Immunology, Molecular Genetics and Microbiology, Durham, NC
| | | | | | - Joshua C Cyktor
- Division of Infectious Diseases, University of Pittsburgh, Pittsburgh, PA
| | - Sonya L Heath
- Division of Infectious Disease, University of Alabama at Birmingham, Birmingham, AL
| | - Ann C Collier
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, WA
| | - Susan L Koletar
- Division of Infectious Diseases, College of Medicine, The Ohio State University, Columbus, OH
| | - Babafemi O Taiwo
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Pablo Tebas
- Division of Infectious Diseases, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - David A Wohl
- Division of Infectious Diseases, Department of Medicine, The University of North Carolina School of Medicine, Chapel Hill, NC
| | - Pablo F Belaunzaran-Zamudio
- Contractor, Division of AIDS, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - M Juliana McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Alan L Landay
- Department of Internal Medicine, Rush University Medical Center, Chicago, IL
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3
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Reed J, Kwak G, Piliper EA, Degli-Angeli EJ, Goecker EA, Greninger AL. Validation of digital droplet PCR assays for cell-associated HIV-1 DNA, HIV-1 2-LTR circle, and HIV-1 unspliced RNA for clinical studies in HIV-1 cure research. J Clin Virol 2024; 170:105632. [PMID: 38113685 PMCID: PMC10842696 DOI: 10.1016/j.jcv.2023.105632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 08/29/2023] [Accepted: 12/05/2023] [Indexed: 12/21/2023]
Abstract
BACKGROUND Cell-associated HIV-1 DNA, HIV-1 2-LTR circle, and HIV-1 unspliced RNA (usRNA) are important virological parameters for monitoring HIV-1 persistence and activation of latent HIV-1. Assays fully validated by CLIA and/or GCLP standards are needed for future clinical trials that seek to evaluate treatments directed towards HIV-1 cure. OBJECTIVES To determine performance characteristics of sensitive, moderate-throughput, digital droplet PCR (ddPCR) assays for cell-associated HIV-1 DNA, HIV-1 2-LTR circle, and HIV-1 usRNA that can detect a broad range of HIV-1 M-group subtypes. STUDY DESIGN To evaluate linearity, limit of detection, precision, and accuracy of each assay, contrived specimens were analyzed in a background of uninfected PBMC. Detection breadth was evaluated by in silico analysis of primer and probes sets and analysis of material harvested from PBMC infected in vitro with various HIV-1 subtypes. A cohort of clinical specimens from viremic and virologically suppressed individuals was analyzed to demonstrate applicability to clinical research. RESULTS The empirically determined limit of detection of these assays was 29, 7, and 60 copies per million PBMC for HIV-1 DNA, HIV-1 2-LTR circle, and HIV-1 usRNA, respectively. The assays detect a broad range of HIV-1 M-group subtypes. Finally, analysis of clinical specimens demonstrate that these assays can detect low levels of cell-associated HIV-1 DNA, HIV-1 usRNA, and HIV-1 2-LTR circle and correlate with clinical histories and viral loads of untreated and antiretroviral treated individuals. CONCLUSIONS We report the clinical validation of three HIV reservoir assays with broad HIV-1 coverage for future cure studies.
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Affiliation(s)
- Jonathan Reed
- Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, WA, United States
| | - Ginger Kwak
- Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, WA, United States
| | - Eli A Piliper
- Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, WA, United States
| | - Emily J Degli-Angeli
- Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, WA, United States
| | - Erin A Goecker
- Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, WA, United States
| | - Alexander L Greninger
- Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, WA, United States; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States.
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Wu F, Simonetti FR. Learning from Persistent Viremia: Mechanisms and Implications for Clinical Care and HIV-1 Cure. Curr HIV/AIDS Rep 2023; 20:428-439. [PMID: 37955826 PMCID: PMC10719122 DOI: 10.1007/s11904-023-00674-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/11/2023] [Indexed: 11/14/2023]
Abstract
PURPOSE OF REVIEW In this review, we discuss what persistent viremia has taught us about the biology of the HIV-1 reservoir during antiretroviral therapy (ART). We will also discuss the implications of this phenomenon for HIV-1 cure research and its clinical management. RECENT FINDINGS While residual viremia (RV, 1-3 HIV-1 RNA copies/ml) can be detected in most of people on ART, some individuals experience non-suppressible viremia (NSV, > 20-50 copies/mL) despite optimal adherence. When issues of drug resistance and pharmacokinetics are ruled out, this persistent virus in plasma is the reflection of virus production from clonally expanded CD4+ T cells carrying proviruses. Recent work has shown that a fraction of the proviruses source of NSV are not infectious, due to defects in the 5'-Leader sequence. However, additional viruses and host determinants of NSV are not fully understood. The study of NSV is of prime importance because it represents a challenge for the clinical care of people on ART, and it sheds light on virus-host interactions that could advance HIV-1 remission research.
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Affiliation(s)
- Fengting Wu
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, 733 N Broadway, Baltimore, MD, 21205, USA
| | - Francesco R Simonetti
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, 733 N Broadway, Baltimore, MD, 21205, USA.
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Sanders-Beer BE, Archin NM, Brumme ZL, Busch MP, Deleage C, O'Doherty U, Hughes SH, Jerome KR, Jones RB, Karn J, Kearney MF, Keele BF, Kulpa DA, Laird GM, Li JZ, Lichterfeld MD, Nussenzweig MC, Persaud D, Yukl SA, Siliciano RF, Mellors JW. Current HIV/SIV Reservoir Assays for Preclinical and Clinical Applications: Recommendations from the Experts 2022 NIAID Workshop Summary. AIDS Res Hum Retroviruses 2023; 40:7-21. [PMID: 37126090 DOI: 10.1089/aid.2022.0188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023] Open
Abstract
Since the first HIV-cured person was reported in 2009, a strong interest in developing highly sensitive HIV and SIV reservoir assays has emerged. In particular, the question arose about the comparative value of state-of-the-art assays to measure and characterize the HIV reservoir, and how these assays can be applied to accurately detect changes in the reservoir during efforts to develop a cure for HIV infection. Second, it is important to consider the impact on the outcome of clinical trials if these relatively new HIV reservoir assays are incorporated into clinical trial endpoints and/or used for clinical decision-making. To understand the advantages and limitations and the regulatory implications of HIV reservoir assays, the National Institute of Allergy and Infectious Diseases (NIAID) sponsored and convened a meeting on September 16, 2022, to discuss the state of knowledge concerning these questions and best practices for selecting HIV reservoir assays for a particular research question or clinical trial protocol.
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Affiliation(s)
- Brigitte E Sanders-Beer
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Nancie M Archin
- Division of Infectious Diseases, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Michael P Busch
- Vitalant Research Institute, University of California, San Francisco, California, USA
| | - Claire Deleage
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research (FNLCR), Frederick, Maryland, USA
| | - Una O'Doherty
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Stephen H Hughes
- HIV Dynamics and Replication Program, CCR, National Cancer Institute, Frederick, Maryland, USA
| | - Keith R Jerome
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, and Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - R Brad Jones
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Jonathan Karn
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Mary F Kearney
- HIV Dynamics and Replication Program, CCR, National Cancer Institute, Frederick, Maryland, USA
| | - Brandon F Keele
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research (FNLCR), Frederick, Maryland, USA
| | - Deanna A Kulpa
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | | | - Jonathan Z Li
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Mathias D Lichterfeld
- Brigham and Women's Hospital and Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, USA
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York, USA
| | - Deborah Persaud
- Department of Pediatric Infectious Disease, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Steven A Yukl
- Department of Medicine, University of California San Francisco (UCSF) and San Francisco VA Medical Center, San Francisco, California, USA
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - John W Mellors
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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6
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Stolberg-Stolberg J, Jacob E, Kuehn J, Hennies M, Hafezi W, Freistuehler M, Koeppe J, Friedrich AW, Katthagen JC, Raschke MJ. COVID-19 rapid molecular point-of-care testing is effective and cost-beneficial for the acute care of trauma patients. Eur J Trauma Emerg Surg 2023; 49:487-493. [PMID: 36066585 PMCID: PMC9447950 DOI: 10.1007/s00068-022-02091-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 08/16/2022] [Indexed: 11/25/2022]
Abstract
PURPOSE To evaluate the accuracy and cost benefit of a rapid molecular point-of-care testing (POCT) device detecting COVID-19 within a traumatological emergency department. BACKGROUND Despite continuous withdrawal of COVID-19 restrictions, hospitals will remain particularly vulnerable to local outbreaks which is reflected by a higher institution-specific basic reproduction rate. Patients admitted to the emergency department with unknown COVID-19 infection status due to a- or oligosymptomatic COVID-19 infection put other patients and health care workers at risk, while fast diagnosis and treatment is necessary. Delayed testing results in additional costs to the health care system. METHODS From the 8th of April 2021 until 31st of December 2021, all patients admitted to the emergency department were tested with routine RT-PCR and rapid molecular POCT device (Abbott ID NOW™ COVID-19). COVID-19-related additional costs for patients admitted via shock room or emergency department were calculated based on internal cost allocations. RESULTS 1133 rapid molecular tests resulted in a sensitivity of 83.3% (95% CI 35.9-99.6%), specificity of 99.8% (95% CI 99.4-100%), a positive predictive value of 71.4% (95% CI 29-96.3%) and a negative predictive value of 99.9% (95% CI 99.5-100%) as compared to RT-PCR. Without rapid COVID-19 testing, each emergency department and shock room admission with subsequent surgery showed additional direct costs of 2631.25€, without surgery of 729.01€. CONCLUSION Although rapid molecular COVID-19 testing can initially be more expensive than RT-PCR, subsequent cost savings, improved workflows and workforce protection outweigh this effect by far. The data of this study support the use of a rapid molecular POCT device in a traumatological emergency department.
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Affiliation(s)
- Josef Stolberg-Stolberg
- Department of Trauma, Hand and Reconstructive Surgery, University Hospital Muenster, Albert-Schweitzer-Campus 1, Building W1, 48149, Muenster, Germany.
| | - Elena Jacob
- Department of Trauma, Hand and Reconstructive Surgery, University Hospital Muenster, Albert-Schweitzer-Campus 1, Building W1, 48149, Muenster, Germany
| | - Joachim Kuehn
- Department of Clinical Virology, Institute of Virology, University Hospital Muenster, 48149, Muenster, Germany
| | - Marc Hennies
- Department of Clinical Virology, Institute of Virology, University Hospital Muenster, 48149, Muenster, Germany
| | - Wali Hafezi
- Department of Clinical Virology, Institute of Virology, University Hospital Muenster, 48149, Muenster, Germany
| | - Moritz Freistuehler
- Medical Management Division-Medical Controlling, University Hospital Muenster, Niels-Stensen-Straße 8, 48149, Muenster, Germany
| | - Jeanette Koeppe
- Institute of Biostatistics and Clinical Research, University of Muenster, Schmeddingstrasse 56, 48149, Muenster, Germany
| | - Alex W Friedrich
- Medical Executive Board, University Hospital Muenster, Albert-Schweitzer-Campus 1, Building D5, 48149, Muenster, Germany
| | - J Christoph Katthagen
- Department of Trauma, Hand and Reconstructive Surgery, University Hospital Muenster, Albert-Schweitzer-Campus 1, Building W1, 48149, Muenster, Germany
| | - Michael J Raschke
- Department of Trauma, Hand and Reconstructive Surgery, University Hospital Muenster, Albert-Schweitzer-Campus 1, Building W1, 48149, Muenster, Germany
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7
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Tosiano MA, Mar H, Hoeth D, Eron JJ, Gandhi RT, McMahon DK, Bosch RJ, Mellors JW, Cyktor JC. Comparative sensitivity of automated (Abbott M2000) and manual plasma HIV-1 RNA PCR assays for the detection of persistent viremia after long-term antiretroviral therapy. J Virus Erad 2022; 8:100095. [PMID: 36479541 PMCID: PMC9720429 DOI: 10.1016/j.jve.2022.100095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/19/2022] [Accepted: 11/15/2022] [Indexed: 12/02/2022] Open
Abstract
Background The ability of automated, FDA-cleared plasma HIV-1 RNA assays to detect low-level viremia, compared to manual, highly sensitive research-only methods, is not well-defined. We therefore tested paired plasma samples from people with HIV-1 (PWH) on long-term antiretroviral therapy (ART) with both the Abbott M2000 RealTime HIV-1 Viral Load assay (Abbott) and a quantitative reverse transcriptase (RT)-initiated PCR assay that has a reported 95% detection limit of 1 HIV-1 RNA copy/ml (single copy assay, SCA). Methods Plasma samples from 309 participants in the AIDS Clinical Trials Group study A5321 were tested by both Abbott and SCA. Participants were mostly men (82%). All were on stable ART for a median of 7 years with HIV-1 RNA <40 copies/mL by Abbott. Pooled plasma from each donor was divided and tested. Abbott results were reported as target detected <40 copies/mL but not quantifiable (target detected <40) or target not detected (TND), and SCA results were classified as HIV-1 RNA detected or not detected. Results By Abbott, 17% (51/309) of sample results were target detected <40, whereas 83% (258/309) were TND. Of the samples that were target detected <40 by Abbott, 73% (37/51) had HIV-1 RNA detected by SCA. By contrast, 43% of samples that were TND by Abbott (110/258) had HIV-1 RNA detected by SCA (p < 0.001). Conclusion Plasma samples from PWH with HIV-1 RNA detected but <40 copies/ml by the automated Abbott M2000 assay are likely (73% of 51 samples) to have HIV-1 RNA detected by an optimized manual assay with single copy sensitivity. An Abbott HIV-1 RNA result of target not detected did not exclude low-level viremia: 43% of 258 samples had HIV-1 RNA detected by the single copy assay. These findings indicate that the Abbott M2000 assay cannot exclude the persistence of viremia on ART and thus may have less utility, compared to a manual single copy assay, for assessing the impact of experimental interventions designed to eliminate low-level viremia as a step towards achieving ART-free HIV-1 remission.
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Affiliation(s)
| | - Hanna Mar
- Harvard TH Chan School of Public Health, Boston, MA, USA
| | | | | | | | | | | | | | | | - for the A5321 Team
- University of Pittsburgh, Pittsburgh, PA, USA
- Harvard TH Chan School of Public Health, Boston, MA, USA
- University of North Carolina, Chapel Hill, NC, USA
- Massachusetts General Hospital, Boston, MA, USA
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8
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van den Berg K, Vermeulen M, Bakkour S, Stone M, Jacobs G, Nyoni C, Barker C, McClure C, Creel D, Grebe E, Roubinian N, Jentsch U, Custer B, Busch MP, Murphy EL. Blood Center Testing Allows the Detection and Rapid Treatment of Acute and Recent HIV Infection. Viruses 2022; 14:v14112326. [PMID: 36366424 PMCID: PMC9698357 DOI: 10.3390/v14112326] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 10/14/2022] [Accepted: 10/17/2022] [Indexed: 11/06/2022] Open
Abstract
Blood donations in South Africa are tested for HIV RNA using individual donation NAT (ID-NAT), allowing detection and rapid antiretroviral therapy (ART) of acute HIV infections. We enrolled a cohort of acute and recent HIV-infected blood donation candidates in South Africa in 2015-2018, measured HIV antibody, ID-NAT, and recency of infection <195 days (Sedia LAg) at enrollment and initiated early ART. A small cohort of HIV elite controllers was followed without treatment. HIV reservoir measurements included ultrasensitive plasma RNA, cell-associated HIV RNA, and total DNA. Enrollment of 18 Fiebig I-III and 45 Fiebig IV-VI HIV clade C subjects occurred a median of 18 days after index blood donation. ART was administered successfully and compliance with follow-up visits was excellent. There were only minimal differences in HIV reservoir between ART initiation in Fiebig stages I-III vs. IV-VI, but ART noncompliance increased HIV reservoir. In 11 untreated HIV elite controllers, HIV reservoir levels were similar to or higher than those seen in our early treated cohort. National blood services can identify acute HIV cohorts for subsequent HIV cure research studies. Among HIV clade C-infected donors, HIV reservoir differed little by Fiebig stage at treatment initiation, but was smaller than in chronically treated HIV and those with ART noncompliance.
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Affiliation(s)
| | - Marion Vermeulen
- South African National Blood Service, Johannesburg 3610, South Africa
| | - Sonia Bakkour
- Vitalant Research Institute, San Francisco, CA 94118, USA
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Mars Stone
- Vitalant Research Institute, San Francisco, CA 94118, USA
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Genevieve Jacobs
- South African National Blood Service, Johannesburg 3610, South Africa
| | - Cynthia Nyoni
- South African National Blood Service, Johannesburg 3610, South Africa
| | - Coreen Barker
- Clinical HIV Research Unit, University of the Witwatersr, Johannesburg 2092, South Africa
| | | | | | - Eduard Grebe
- Vitalant Research Institute, San Francisco, CA 94118, USA
- DSI-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch 7602, South Africa
| | - Nareg Roubinian
- Vitalant Research Institute, San Francisco, CA 94118, USA
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA
- Kaiser Permanente Northern California, Oakland, CA 94612, USA
| | - Ute Jentsch
- South African National Blood Service, Johannesburg 3610, South Africa
| | - Brian Custer
- Vitalant Research Institute, San Francisco, CA 94118, USA
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Michael P. Busch
- Vitalant Research Institute, San Francisco, CA 94118, USA
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Edward L. Murphy
- Vitalant Research Institute, San Francisco, CA 94118, USA
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA
- 270 Masonic Avenue, San Francisco, CA 94118, USA
- Correspondence: ; Tel.: +1-415-749-6668
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9
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Quantitative Evaluation of Very Low Levels of HIV-1 Reverse Transcriptase by a Novel Highly Sensitive RT-qPCR Assay. LIFE (BASEL, SWITZERLAND) 2022; 12:life12081130. [PMID: 36013309 PMCID: PMC9410348 DOI: 10.3390/life12081130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/20/2022] [Accepted: 07/26/2022] [Indexed: 11/16/2022]
Abstract
Based on previous experience in our laboratory, we developed a real-time reverse transcriptase (RT) quantitative PCR (RT-qPCR) assay for the assessment of very low levels of HIV-1 RT activity. The RNA, acting as a template for reverse transcription into cDNA by HIV-1 RT, consisted of a synthetic RNA ad hoc generated by in vitro transcription and included a coding sequence for HSV-1 gD (gD-RNA-synt). Different conditions of variables involved in the RT-qPCR reaction, notably different amounts of gD-RNA-synt, different mixes of the reaction buffer, and different dNTP concentrations, were tested to optimize the assay. The results indicated that the gD-RNA-synt-based RT assay, in its optimized formulation, could detect a specific cDNA reverse transcription even in the presence of 1 × 10-9 U of HIV RT. This achievement greatly improved the sensitivity of the assay over previous versions. In summary, this constructed RT-qPCR assay may be considered a promising tool for providing accurate information on very low HIV-1 RT activity.
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Crespo-Bermejo C, de Arellano ER, Lara-Aguilar V, Valle-Millares D, Gómez-Lus ML, Madrid R, Martín-Carbonero L, Briz V. Persistent low-Level viremia in persons living with HIV undertreatment: An unresolved status. Virulence 2021; 12:2919-2931. [PMID: 34874239 PMCID: PMC8654475 DOI: 10.1080/21505594.2021.2004743] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Antiretroviral therapy (ART) allows suppressed viremia to reach less than 50 copies/mL in most treated persons living with HIV (PLWH). However, the existence of PLWH that show events of persistent low-level viremia (pLLV) between 50 and 1000 copies/mL and with different virological consequences have been observed. PLLV has been associated with higher virological failure (VF), viral genotype resistance, adherence difficulties and AIDS events. Moreover, some reports show that pLLV status can lead to residual immune activation and inflammation, with an increased risk of immunovirological failure and a pro-inflammatory cytokine level which can lead to a higher occurrence of non-AIDS defining events (NADEs) and other adverse clinical outcomes. Until now, however, published data have shown controversial results that hinder understanding of the true cause(s) and origin(s) of this phenomenon. Molecular mechanisms related to viral reservoir size and clonal expansion have been suggested as the possible origin of pLLV. This review aims to assess recent findings to provide a global view of the role of pLLV in PLWH and the impact this status may cause on the clinical progression of these patients.
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Affiliation(s)
- Celia Crespo-Bermejo
- Laboratory of Reference and Research on Viral Hepatitis, National Center of Microbiology, Institute of Health Carlos Iii, Majadahonda, Madrid, Spain
| | - Eva Ramírez de Arellano
- Laboratory of Reference and Research on Viral Hepatitis, National Center of Microbiology, Institute of Health Carlos Iii, Majadahonda, Madrid, Spain
| | - Violeta Lara-Aguilar
- Laboratory of Reference and Research on Viral Hepatitis, National Center of Microbiology, Institute of Health Carlos Iii, Majadahonda, Madrid, Spain
| | - Daniel Valle-Millares
- Laboratory of Reference and Research on Viral Hepatitis, National Center of Microbiology, Institute of Health Carlos Iii, Majadahonda, Madrid, Spain
| | - Mª Luisa Gómez-Lus
- Departamento de Medicina- Área de Microbiología. Facultad de Medicina. Universidad Complutense, Madrid, Spain
| | - Ricardo Madrid
- Parque Científico de Madrid, Campus de Cantoblanco, Madrid, Spain.,Department of Genetics, Physiology and Microbiology. Faculty of Biology, Complutense University of Madrid, Madrid, Spain
| | - Luz Martín-Carbonero
- Unidad de Vih. Servicio de Medicina Interna. Hospital Universitario La Paz. Instituto de Investigación Sanitaria Hospital de La Paz (Idipaz), Madrid, Spain
| | - Verónica Briz
- Laboratory of Reference and Research on Viral Hepatitis, National Center of Microbiology, Institute of Health Carlos Iii, Majadahonda, Madrid, Spain
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11
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Suzuki K, Levert A, Yeung J, Starr M, Cameron J, Williams R, Rismanto N, Stark T, Druery D, Prasad S, Ferrarini C, Hanafi I, McNally LP, Cunningham P, Liu Z, Ishida T, Huang CS, Oswald V, Evans L, Symonds G, Brew BJ, Zaunders J. HIV-1 viral blips are associated with repeated and increasingly high levels of cell-associated HIV-1 RNA transcriptional activity. AIDS 2021; 35:2095-2103. [PMID: 34148986 PMCID: PMC8505147 DOI: 10.1097/qad.0000000000003001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 06/09/2021] [Accepted: 06/15/2021] [Indexed: 12/23/2022]
Abstract
OBJECTIVE Some HIV+ patients, virally suppressed on ART, show occasional 'blips' of detectable HIV-1 plasma RNA. We used a new highly sensitive assay of cell-associated HIV-1 RNA to measure transcriptional activity in PBMCs and production of infectious virus from the viral reservoir, in patients with and without 'blips'. DESIGN/METHODS RNA and DNA extracted from cells in 6 ml of peripheral blood, from suppressed patients with one to two 'blip' episodes over the past 2 years of ART (n = 55), or no 'blips' (n = 52), were assayed for HIV-1 RNA transcripts and proviral DNA targeting the highly conserved 'R' region of the LTR. Follow-up samples were also collected. Purified CD4+ T cells were cultured with anti-CD3/CD28/CD2 T-cell activator to amplify transcription and measure replication competent virus. RESULTS HIV-1 RNA transcripts ranged from 1.3 to 5415 copies/106 white blood cells. 'Blip' patients had significantly higher levels vs. without blips (median 192 vs. 49; P = 0.0007), which correlated with: higher levels of inducible transcripts after activation in vitro, sustained higher HIV-1 transcription levels in follow-up samples along with increasing HIV-1 DNA in some, and production of replication-competent HIV-1. CONCLUSION Viral 'blips' are significant reflecting higher transcriptional activity from the reservoir and contribute to the reservoir over time. This sensitive assay can be used in monitoring the size and activity of the HIV-1 reservoir and will be useful in HIV-1 cure strategies.
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Affiliation(s)
- Kazuo Suzuki
- St Vincent's Centre for Applied Medical Research, NSW State Reference laboratory for HIV
| | - Angelique Levert
- St Vincent's Centre for Applied Medical Research, NSW State Reference laboratory for HIV
| | - Julie Yeung
- St Vincent's Centre for Applied Medical Research, NSW State Reference laboratory for HIV
| | - Mitchell Starr
- St Vincent's Centre for Applied Medical Research, NSW State Reference laboratory for HIV
| | - Jane Cameron
- St Vincent's Centre for Applied Medical Research, NSW State Reference laboratory for HIV
| | - Raffaella Williams
- St Vincent's Centre for Applied Medical Research, NSW State Reference laboratory for HIV
| | - Nikolas Rismanto
- St Vincent's Centre for Applied Medical Research, NSW State Reference laboratory for HIV
| | - Tayla Stark
- St Vincent's Centre for Applied Medical Research, NSW State Reference laboratory for HIV
| | - Dylan Druery
- St Vincent's Centre for Applied Medical Research, NSW State Reference laboratory for HIV
| | - Salzeena Prasad
- St Vincent's Centre for Applied Medical Research, NSW State Reference laboratory for HIV
| | - Cristina Ferrarini
- St Vincent's Centre for Applied Medical Research, NSW State Reference laboratory for HIV
| | - Imelda Hanafi
- St Vincent's Centre for Applied Medical Research, NSW State Reference laboratory for HIV
| | - Leon Patrick McNally
- St Vincent's Centre for Applied Medical Research, NSW State Reference laboratory for HIV
| | - Philip Cunningham
- St Vincent's Centre for Applied Medical Research, NSW State Reference laboratory for HIV
| | - Zhixin Liu
- Stats Central, University of New South Wales, Sydney, NSW, Australia
| | | | | | - Velma Oswald
- Clinical Immunology and HIV Medicine, Liverpool Hospital
| | - Louise Evans
- Clinical Immunology and HIV Medicine, Liverpool Hospital
- University of New South Wales
| | | | - Bruce James Brew
- Departments of Neurology and Immunology
- Peter Duncan Neurosciences Unit, St Vincent's Centre for Applied Medical Research, and University of Notre Dame
- Department of HIV Medicine, St Vincent's Hospital
- St Vincent's Clinical School, Delacy Building, University of New South Wales, Sydney, NSW, Australia
| | - John Zaunders
- St Vincent's Centre for Applied Medical Research, NSW State Reference laboratory for HIV
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12
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Abstract
PURPOSE OF REVIEW In response to the HIV-AIDS pandemic, great strides have been made in developing molecular methods that accurately quantify nucleic acid products of HIV-1 at different stages of viral replication and to assess HIV-1 sequence diversity and its effect on susceptibility to small molecule inhibitors and neutralizing antibodies. Here, we review how knowledge gained from these approaches, including viral RNA quantification and sequence analyses, have been rapidly applied to study SARS-CoV-2 and the COVID-19 pandemic. RECENT FINDINGS Recent studies have shown detection of SARS-CoV-2 RNA in blood of infected individuals by reverse transcriptase PCR (RT-PCR); and, as in HIV-1 infection, there is growing evidence that the level of viral RNA in plasma may be related to COVID disease severity. Unlike HIV-1, SARS-CoV-2 sequences are highly conserved limiting SARS-CoV-2 sequencing applications to investigating interpatient genetic diversity for phylogenetic analysis. Sensitive sequencing technologies, originally developed for HIV-1, will be needed to investigate intrapatient SARS-CoV-2 genetic variation in response to antiviral therapeutics and vaccines. SUMMARY Methods used for HIV-1 have been rapidly applied to SARS-CoV-2/COVID-19 to understand pathogenesis and prognosis. Further application of such methods should improve precision of therapy and outcome.
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Affiliation(s)
- Kevin D McCormick
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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13
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Peluso MJ, Bakkour S, Busch MP, Deeks SG, Henrich TJ. A High Percentage of People with HIV on Antiretroviral Therapy Experience Detectable Low-Level Plasma HIV-1 RNA Following COVID-19. Clin Infect Dis 2020; 73:e2845-e2846. [PMID: 33211091 PMCID: PMC7717237 DOI: 10.1093/cid/ciaa1754] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Affiliation(s)
- Michael J Peluso
- Division of Infectious Diseases, University of California San Francisco, San Francisco, CA
| | | | | | - Steven G Deeks
- Division of HIV, ID and Global Medicine, University of California San Francisco
| | - Timothy J Henrich
- Division of Experimental Medicine, University of California San Francisco
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14
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Replicate Aptima Assay for Quantifying Residual Plasma Viremia in Individuals on Antiretroviral Therapy. J Clin Microbiol 2020; 58:JCM.01400-20. [PMID: 32967900 PMCID: PMC7685884 DOI: 10.1128/jcm.01400-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 08/19/2020] [Indexed: 12/24/2022] Open
Abstract
Detection of residual plasma viremia in antiretroviral therapy (ART)-suppressed HIV-infected individuals is critical for characterizing the latent reservoir and evaluating the impact of cure interventions. Ultracentrifugation-based single-copy assays are sensitive but labor intensive. Fully automated replicate testing using a standard clinical viral load assay was evaluated as a high-throughput alternative for the quantification of low-level viremia. Four plasma samples from blood donors with acute HIV-1 infection and one viral culture supernatant were serially diluted into 25-ml samples to nominal viral loads ranging from 39 to <0. Detection of residual plasma viremia in antiretroviral therapy (ART)-suppressed HIV-infected individuals is critical for characterizing the latent reservoir and evaluating the impact of cure interventions. Ultracentrifugation-based single-copy assays are sensitive but labor intensive. Fully automated replicate testing using a standard clinical viral load assay was evaluated as a high-throughput alternative for the quantification of low-level viremia. Four plasma samples from blood donors with acute HIV-1 infection and one viral culture supernatant were serially diluted into 25-ml samples to nominal viral loads ranging from 39 to <0.5 copies (cp)/ml. Each dilution was tested with 45 replicates (reps) using 0.5 ml/rep with the Aptima HIV-1 Quant assay. The nominal and estimated viral loads based on the single-hit Poisson model were compared, and a hybrid Poisson digital model for calibrated viral load estimation was derived. Testing performed using 45 reps on longitudinal plasma samples from 50 ART-suppressed individuals in the Reservoir Assay Validation and Evaluation Network (RAVEN) study cohort (range of 1 to 19 years of continuous ART suppression) showed a median viral load of 0.54 cp/ml (interquartile range [IQR], 0.22 to 1.46 cp/ml) and a 14% (95% confidence interval [CI], 9% to 19%) decline in viral load for each additional year in duration suppressed. Within the RAVEN cohort, the expected false-negative rate for detection at lower rep numbers using 9 and 18 reps was 26% and 14%, respectively. Residual plasma viremia levels positively correlated with cell-associated HIV RNA and DNA. The performance characteristics of the replicate Aptima assay support its use for quantifying residual plasma viremia to study the latent HIV reservoir and cure interventions.
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