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Bauby H, Ward CC, Hugh-White R, Swanson CM, Schulz R, Goujon C, Malim MH. HIV-1 Vpr Induces Widespread Transcriptomic Changes in CD4 + T Cells Early Postinfection. mBio 2021; 12:e0136921. [PMID: 34154423 PMCID: PMC8263007 DOI: 10.1128/mbio.01369-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 05/19/2021] [Indexed: 12/12/2022] Open
Abstract
The interactions between a virus and its host are complex but can be broadly categorized as either viral manipulation of cellular functions or cellular responses to infection. These processes begin at the earliest point of contact between virus and cell and frequently result in changes to cellular gene expression, making genome-wide transcriptomics a useful tool to study them. Several previous studies have used transcriptomics to evaluate the cellular responses to human immunodeficiency virus type 1 (HIV-1) infection; however, none have examined events in primary CD4+ T cells during the first 24 h of infection. Here, we analyzed CD4+ T cells at 4.5, 8, 12, 24, and 48 h following infection. We describe global changes to host gene expression commencing at 4.5 h postinfection and evolving over the ensuing time points. We identify upregulation of genes related to innate immunity, cytokine production, and apoptosis and downregulation of those involved in transcription and translation. We further demonstrate that the viral accessory protein Vpr is necessary for almost all gene expression changes seen at 12 h postinfection and the majority of those seen at 48 h. Identifying this new role for Vpr not only provides fresh perspective on its possible function but also adds further insight into the interplay between HIV-1 and its host at the cellular level. IMPORTANCE HIV-1, while now treatable, remains an important human pathogen causing significant morbidity and mortality globally. The virus predominantly infects CD4+ T cells and, if not treated with medication, ultimately causes their depletion, resulting in AIDS and death. Further refining our understanding of the interaction between HIV-1 and these cells has the potential to inform further therapeutic development. Previous studies have used transcriptomics to assess gene expression changes in CD4+ T cells following HIV-1 infection; here, we provide a detailed examination of changes occurring in the first 24 h of infection. Importantly, we define the viral protein Vpr as essential for the changes observed at this early stage. This finding has significance for understanding the role of Vpr in infection and pathogenesis and also for interpreting previous transcriptomic analyses of HIV-1 infection.
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Affiliation(s)
- Hélène Bauby
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Christopher C. Ward
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Rupert Hugh-White
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Chad M. Swanson
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Reiner Schulz
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Caroline Goujon
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Michael H. Malim
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
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2
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Haleyur Giri Setty MK, Kurdekar A, Mahtani P, Liu J, Hewlett IK. Cross-Subtype Detection of HIV-1 Capsid p24 Antigen Using a Sensitive Europium Nanoparticle Assay. AIDS Res Hum Retroviruses 2019; 35:396-401. [PMID: 30411969 DOI: 10.1089/aid.2018.0163] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Accurate and early detection of diverse HIV-1 subtypes using currently available p24 antigen assays have been a major challenge. We report the development of a sensitive time resolved fluorescence (TRF) europium nanoparticle immuno assay for cross subtype detection of p24 antigen using broadly cross-reactive antibodies. Several antibodies were tested for optimal reactivity with antigens of diverse HIV-1 subtypes and circulating recombinant forms. We tested HIV strains using this assay for sensitivity and quantification ability at the pico-gram per millilter level. We identified two broadly cross-reactive HIV-1 p24 antibodies C65690M and ANT-152, which detected all strains of HIV tested. These two antibodies also yielded a better signal to cutoff ratio for the same amount of antigen tested in comparison to a commercial assay. Using an appropriate combination of C65690M and ANT-152 p24 antibodies capable of detecting all HIV types and highly sensitive TRF-based europium nano particle assay platform, we developed a sensitive p24 antigen assay that can detect HIV infection of all HIV subtypes and may be useful in early detection.
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Affiliation(s)
| | - Aditya Kurdekar
- Laboratory of Molecular Virology, CBER, FDA, Silver Spring, Maryland
| | - Prerna Mahtani
- Laboratory of Molecular Virology, CBER, FDA, Silver Spring, Maryland
| | - Jikun Liu
- Laboratory of Molecular Virology, CBER, FDA, Silver Spring, Maryland
| | - Indira K. Hewlett
- Laboratory of Molecular Virology, CBER, FDA, Silver Spring, Maryland
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3
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Neto MF, Butzler MA, Reed JL, Rui X, Fisher MJ, Kelso DM, McFall SM. Immiscible phase filter extraction and equivalent amplification of genotypes 1-6 of hepatitis C RNA: The building blocks for point-of-care diagnosis. J Virol Methods 2017; 248:107-115. [PMID: 28673855 DOI: 10.1016/j.jviromet.2017.06.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 06/28/2017] [Accepted: 06/29/2017] [Indexed: 12/11/2022]
Abstract
The lack of hepatitis C virus (HCV) diagnostic tests designed for use in decentralized settings is a major obstacle for providing access to treatment and prevention services particularly in low and middle income countries. Here we describe the development and validation of two building blocks of the HCV Quant Assay, a test in development for point-of-care use: 1) an RT-qPCR assay with noncompetitive internal control that equivalently detects the 6 major HCV genotypes and 2) an automated sample prep method using immiscible phase filter technology. This novel assay has wide dynamic range of HCV quantification and a limit of detection of 30IU/ml with 200μl specimen volume. In a preliminary study of 61 clinical specimens, the HCV Quant Assay demonstrated 100% sensitivity and specificity and gave comparable viral load results across 4 logs of IU/ml when compared to the Abbott RealTime HCV Assay.
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Affiliation(s)
- Mário F Neto
- Center for Innovation in Global Health Technologies, Northwestern University, Evanston, IL 60208, USA; University of Illinois Incubator Lab Facility, Chicago, IL 60612, USA
| | - Matthew A Butzler
- Center for Innovation in Global Health Technologies, Northwestern University, Evanston, IL 60208, USA
| | - Jennifer L Reed
- Center for Innovation in Global Health Technologies, Northwestern University, Evanston, IL 60208, USA
| | - Xiang Rui
- Center for Innovation in Global Health Technologies, Northwestern University, Evanston, IL 60208, USA
| | - Mark J Fisher
- Center for Innovation in Global Health Technologies, Northwestern University, Evanston, IL 60208, USA
| | - David M Kelso
- Center for Innovation in Global Health Technologies, Northwestern University, Evanston, IL 60208, USA
| | - Sally M McFall
- Center for Innovation in Global Health Technologies, Northwestern University, Evanston, IL 60208, USA.
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4
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Lim K, Park M, Lee MH, Woo HJ, Kim JB. Development and Assessment of New RT-qPCR Assay for Detection of HIV-1 Subtypes. ACTA ACUST UNITED AC 2016. [DOI: 10.15616/bsl.2016.22.3.83] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Kwanhun Lim
- SD Biosensor Inc., Digital Empire Building, Suwon-si, Gyeonggi-do 16690, Korea
| | - Min Park
- Department of Clinical Laboratory Science, Hyejeon College, Hongseoung, Chungcheong Nam-do 32244, Korea
| | - Min Ho Lee
- Department of Biomedical Laboratory Science, College of Health Sciences, Yonsei University, Wonju-si, Gangwon-do 26493, Korea
| | - Hyun Jun Woo
- Department of Biomedical Laboratory Science, College of Health Sciences, Yonsei University, Wonju-si, Gangwon-do 26493, Korea
| | - Jong-Bae Kim
- Department of Biomedical Laboratory Science, College of Health Sciences, Yonsei University, Wonju-si, Gangwon-do 26493, Korea
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5
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Pery E, Sheehy A, Miranda Nebane N, Misra V, Mankowski MK, Rasmussen L, Lucile White E, Ptak RG, Gabuzda D. Redoxal, an inhibitor of de novo pyrimidine biosynthesis, augments APOBEC3G antiviral activity against human immunodeficiency virus type 1. Virology 2015; 484:276-287. [PMID: 26141568 DOI: 10.1016/j.virol.2015.06.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 05/05/2015] [Accepted: 06/11/2015] [Indexed: 12/31/2022]
Abstract
APOBEC3G (A3G) is a cytidine deaminase that restricts HIV-1 replication by inducing G-to-A hypermutation in viral DNA; deamination-independent mechanisms are also implicated. HIV-1 Vif protein counteracts A3G by inducing its proteasomal degradation. Thus, the Vif-A3G axis is a potential therapeutic target. To identify compounds that inhibit Vif:A3G interaction, a 307,520 compound library was tested in a TR-FRET screen. Two identified compounds, redoxal and lomofungin, inhibited HIV-1 replication in peripheral blood mononuclear cells. Lomofungin activity was linked to A3G, but not pursued further due to cytotoxicity. Redoxal displayed A3G-dependent restriction, inhibiting viral replication by stabilizing A3G protein levels and increasing A3G in virions. A3G-independent activity was also detected. Treatment with uridine or orotate, intermediates of pyrimidine synthesis, diminished redoxal-induced stabilization of A3G and antiviral activity. These results identify redoxal as an inhibitor of HIV-1 replication and suggest its ability to inhibit pyrimidine biosynthesis suppresses viral replication by augmenting A3G antiviral activity.
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Affiliation(s)
- Erez Pery
- Department of Cancer Immunology and AIDS, Dana Farber Cancer Institute, Boston, MA 02115, United States; Department of Pathology, Harvard Medical School, Boston, MA 02115, United States
| | - Ann Sheehy
- Department of Biology, College of the Holy Cross, Worcester, MA 01610, United States
| | - N Miranda Nebane
- Southern Research Institute High Throughput Screening Center, Birmingham, AL 35205, United States
| | - Vikas Misra
- Department of Cancer Immunology and AIDS, Dana Farber Cancer Institute, Boston, MA 02115, United States
| | - Marie K Mankowski
- Southern Research Institute, Department of Infectious Disease Research, Frederick, MD 21701, United States
| | - Lynn Rasmussen
- Southern Research Institute High Throughput Screening Center, Birmingham, AL 35205, United States
| | - E Lucile White
- Southern Research Institute High Throughput Screening Center, Birmingham, AL 35205, United States
| | - Roger G Ptak
- Southern Research Institute, Department of Infectious Disease Research, Frederick, MD 21701, United States
| | - Dana Gabuzda
- Department of Cancer Immunology and AIDS, Dana Farber Cancer Institute, Boston, MA 02115, United States; Department of Neurology (Microbiology), Harvard Medical School, Boston, MA 02115, United States.
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6
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Oral administration of the nucleoside EFdA (4'-ethynyl-2-fluoro-2'-deoxyadenosine) provides rapid suppression of HIV viremia in humanized mice and favorable pharmacokinetic properties in mice and the rhesus macaque. Antimicrob Agents Chemother 2015; 59:4190-8. [PMID: 25941222 DOI: 10.1128/aac.05036-14] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2014] [Accepted: 04/28/2015] [Indexed: 11/20/2022] Open
Abstract
Like normal cellular nucleosides, the nucleoside reverse transcriptase (RT) inhibitor (NRTI) 4'-ethynyl-2-fluoro-2'-deoxyadenosine (EFdA) has a 3'-hydroxyl moiety, and yet EFdA is a highly potent inhibitor of human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV) replication with activity against a broad range of clinically important drug-resistant HIV isolates. We evaluated the anti-HIV activity of EFdA in primary human cells and in HIV-infected humanized mice. EFdA exhibited excellent potency against HIVJR-CSF in phytohemagglutinin-stimulated peripheral blood mononuclear cells (PBMCs), with a 50% inhibitory concentration of 0.25 nM and a selectivity index of 184,000; similar antiviral potency was found against 12 different HIV clinical isolates from multiple clades (A, B, C, D, and CRF01_AE). EFdA was readily absorbed after oral dosing (5 mg/kg of body weight) in both mice and the rhesus macaque, with micromolar levels of the maximum concentration of drug in serum (Cmax) attained at 30 min and 90 min, respectively. Trough levels were at or above 90% inhibitory concentration (IC90) levels in the macaque at 24 h, suggesting once-daily dosing. EFdA showed reasonable penetration of the blood-brain barrier in the rhesus macaque, with cerebrospinal fluid levels at approximately 25% of plasma levels 8 h after single oral dosing. Rhesus PBMCs isolated 24 h following a single oral dose of 5 mg/kg EFdA were refractory to SIV infection due to sufficiently high intracellular EFdA-triphosphate levels. The intracellular half-life of EFdA-triphosphate in PBMCs was determined to be >72 h following a single exposure to EFdA. Daily oral administration of EFdA at low dosage levels (1 to 10 mg/kg/day) was highly effective in protecting humanized mice from HIV infection, and 10 mg/kg/day oral EFdA completely suppressed HIV RNA to undetectable levels within 2 weeks of treatment.
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Abstract
OBJECTIVE In treatment-naive HIV-positive individuals, the integrase strand-transfer inhibitor dolutegravir (DTG) has not been associated with emergent drug-resistance mutations, neither against this drug nor against other antiretroviral drugs that were used in combination with it. This is in contrast to all other antiretroviral drugs tested so far, including the integrase strand-transfer inhibitors raltegravir (RAL) and elvitegravir that can lead to treatment failure with the emergence of drug-resistance mutations. DESIGN These observations suggest that DTG may provide an additional protection against resistance compared to other drugs by decreasing HIV-1 genetic evolution. METHODS Here, we tested this hypothesis by measuring the genetic and amino-acid diversity of Env/gp160 from two HIV-1 primary isolates that were grown in the presence of increasing concentrations of DTG or RAL over the course of 38-55 weeks. RESULTS The results show that treatment with DTG led to less HIV-1 genetic and amino-acid diversification over time, as compared to treatment with RAL or the absence of drug. CONCLUSION These results may help to explain the absence of emergent resistance mutations in treatment-naive individuals treated with DTG.
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Chook JB, Ong LY, Takebe Y, Chan KG, Choo M, Kamarulzaman A, Tee KK. Molecular detection of HIV-1 subtype B, CRF01_AE, CRF33_01B, and newly emerging recombinant lineages in Malaysia. Am J Trop Med Hyg 2014; 92:507-512. [PMID: 25535315 PMCID: PMC4350539 DOI: 10.4269/ajtmh.14-0681] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
A molecular genotyping assay for human immunodeficiency virus type 1 (HIV-1) circulating in Southeast Asia is difficult to design because of the high level of genetic diversity. We developed a multiplex real-time polymerase chain reaction (PCR) assay to detect subtype B, CRF01_AE, CRF33_01B, and three newly described circulating recombinant forms, (CRFs) (CRF53_01B, CRF54_01B, and CRF58_01B). A total of 785 reference genomes were used for subtype-specific primers and TaqMan probes design targeting the gag, pol, and env genes. The performance of this assay was compared and evaluated with direct sequencing and phylogenetic analysis. A total of 180 HIV-infected subjects from Kuala Lumpur, Malaysia were screened and 171 samples were successfully genotyped, in agreement with the phylogenetic data. The HIV-1 genotype distribution was as follows: subtype B (16.7%); CRF01_AE (52.8%); CRF33_01B (24.4%); CRF53_01B (1.1%); CRF54_01B (0.6%); and CRF01_AE/B unique recombinant forms (4.4%). The overall accuracy of the genotyping assay was over 95.0%, in which the sensitivities for subtype B, CRF01_AE, and CRF33_01B detection were 100%, 100%, and 97.7%, respectively. The specificity of genotyping was 100%, inter-subtype specificities were > 95% and the limit of detection of 10(3) copies/mL for plasma. The newly developed real-time PCR assay offers a rapid and cost-effective alternative for large-scale molecular epidemiological surveillance for HIV-1.
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Affiliation(s)
| | | | | | | | | | | | - Kok Keng Tee
- *Address correspondence to Kok Keng Tee, Centre of Excellence for Research in AIDS (CERiA), Department of Medicine, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia. E-mail:
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9
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Kortagere S, Xu JP, Mankowski MK, Ptak RG, Cocklin S. Structure-activity relationships of a novel capsid targeted inhibitor of HIV-1 replication. J Chem Inf Model 2014; 54:3080-90. [PMID: 25302989 PMCID: PMC4245176 DOI: 10.1021/ci500437r] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
![]()
Despite the considerable successes
of highly active antiretroviral
therapy (HAART) for the treatment of HIV/AIDS, cumulative drug toxicities
and the development of multidrug-resistant virus necessitate the search
for new classes of antiretroviral agents with novel modes of action.
The HIV-1 capsid (CA) protein has been structurally and functionally
characterized as a druggable target. We have recently designed a novel
small molecule inhibitor I-XW-053 using the hybrid structure based
method to block the interface between CA N-terminal domains (NTD–NTD
interface) with micromolar affinity. In an effort to optimize and
improve the efficacy of I-XW-053, we have developed the structure
activity relationship of I-XW-053 compound series using ligand efficiency
methods. Fifty-six analogues of I-XW-053 were designed that could
be subclassified into four different core domains based on their ligand
efficiency values computed as the ratio of binding efficiency (BEI)
and surface efficiency (SEI) indices. Compound 34 belonging
to subcore-3 showed an 11-fold improvement over I-XW-053 in blocking
HIV-1 replication in primary human peripheral blood mononuclear cells
(PBMCs). Surface plasmon resonance experiments confirmed the binding
of compound 34 to purified HIV-1 CA protein. Molecular
docking studies on compound 34 and I-XW-053 to HIV-1
CA protein suggested that they both bind to NTD–NTD interface
region but with different binding modes, which was further validated
using site-directed mutagenesis studies.
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Affiliation(s)
- Sandhya Kortagere
- Department of Microbiology & Immunology and ‡Department of Biochemistry & Molecular Biology, Drexel University College of Medicine , Philadelphia, Pennsylvania 19104, United States
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Zhou G, Sofiyev V, Kaur H, Snyder BA, Mankowski MK, Hogan PA, Ptak RG, Gochin M. Structure-activity relationship studies of indole-based compounds as small molecule HIV-1 fusion inhibitors targeting glycoprotein 41. J Med Chem 2014; 57:5270-81. [PMID: 24856833 PMCID: PMC4216203 DOI: 10.1021/jm500344y] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
![]()
We
previously described indole-containing compounds with the potential
to inhibit HIV-1 fusion by targeting the hydrophobic pocket of transmembrane
glycoprotein gp41. Here we report optimization and structure–activity
relationship studies on the basic scaffold, defining the role of shape,
contact surface area, and molecular properties. Thirty new compounds
were evaluated in binding, cell–cell fusion, and viral replication
assays. Below a 1 μM threshold, correlation between binding
and biological activity was diminished, indicating an amphipathic
requirement for activity in cells. The most active inhibitor 6j exhibited 0.6 μM binding affinity and 0.2 μM
EC50 against cell–cell fusion and live virus replication
and was active against T20 resistant strains. Twenty-two compounds
with the same connectivity displayed a consensus pose in docking calculations,
with rank order matching the biological activity. The work provides
insight into requirements for small molecule inhibition of HIV-1 fusion
and demonstrates a potent low molecular weight fusion inhibitor.
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Affiliation(s)
- Guangyan Zhou
- Department of Basic Sciences, Touro University-California , 1310 Club Drive, Mare Island, Vallejo, California 94592, United States
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Okello MO, Mishra S, Nishonov M, Mankowski MK, Russell JD, Wei J, Hogan PA, Ptak RG, Nair V. A novel anti-HIV active integrase inhibitor with a favorable in vitro cytochrome P450 and uridine 5'-diphospho-glucuronosyltransferase metabolism profile. Antiviral Res 2013; 98:365-72. [PMID: 23602851 PMCID: PMC3677213 DOI: 10.1016/j.antiviral.2013.04.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Revised: 04/03/2013] [Accepted: 04/04/2013] [Indexed: 10/26/2022]
Abstract
Research efforts on the human immunodeficiency virus (HIV) integrase have resulted in two approved drugs. However, co-infection of HIV with Mycobacterium tuberculosis and other microbial and viral agents has introduced added complications to this pandemic, requiring favorable drug-drug interaction profiles for antiviral therapeutics targeting HIV. Cytochrome P450 (CYP) and uridine 5'-diphospho-glucuronosyltransferase (UGT) are pivotal determining factors in the occurrence of adverse drug-drug interactions. For this reason, it is important that anti-HIV agents, such as integrase inhibitors, possess favorable profiles with respect to CYP and UGT. We have discovered a novel HIV integrase inhibitor (compound 1) that exhibits low nM antiviral activity against a diverse set of HIV-1 isolates, and against HIV-2 and the simian immunodeficiency virus (SIV). Compound 1 displays low in vitro cytotoxicity and its resistance and related drug susceptibility profiles are favorable. Data from in vitro studies revealed that compound 1 was not a substrate for UGT isoforms and that it was not an inhibitor or activator of key CYP isozymes.
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Affiliation(s)
- Maurice O. Okello
- The Center for Drug Discovery and the College of Pharmacy University of Georgia, Athens, GA 30602, USA
| | - Sanjay Mishra
- The Center for Drug Discovery and the College of Pharmacy University of Georgia, Athens, GA 30602, USA
| | - Malik Nishonov
- The Center for Drug Discovery and the College of Pharmacy University of Georgia, Athens, GA 30602, USA
| | - Marie K. Mankowski
- Infectious Disease Research Department, Southern Research Institute, Frederick, MD 21701, USA
| | - Julie D. Russell
- Infectious Disease Research Department, Southern Research Institute, Frederick, MD 21701, USA
| | - Jiayi Wei
- Infectious Disease Research Department, Southern Research Institute, Frederick, MD 21701, USA
| | - Priscilla A. Hogan
- Infectious Disease Research Department, Southern Research Institute, Frederick, MD 21701, USA
| | - Roger G. Ptak
- Infectious Disease Research Department, Southern Research Institute, Frederick, MD 21701, USA
| | - Vasu Nair
- The Center for Drug Discovery and the College of Pharmacy University of Georgia, Athens, GA 30602, USA
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Zentner I, Sierra LJ, Maciunas L, Vinnik A, Fedichev P, Mankowski MK, Ptak RG, Martín-García J, Cocklin S. Discovery of a small-molecule antiviral targeting the HIV-1 matrix protein. Bioorg Med Chem Lett 2012; 23:1132-5. [PMID: 23305922 DOI: 10.1016/j.bmcl.2012.11.041] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Revised: 11/07/2012] [Accepted: 11/12/2012] [Indexed: 01/03/2023]
Abstract
Due to the emergence of drug-resistant strains and the cumulative toxicities associated with current therapies, demand remains for new inhibitors of HIV-1 replication. The HIV-1 matrix (MA) protein is an essential viral component with established roles in the assembly of the virus. Using virtual and surface plasmon resonance (SPR)-based screening, we describe the identification of the first small molecule to bind to the HIV-1 MA protein and to possess broad range anti-HIV properties.
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Affiliation(s)
- Isaac Zentner
- Department of Biochemistry & Molecular Biology, Drexel University College of Medicine, 245 N. 15th Street, Philadelphia, PA 19102, USA
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Delayed Maturation of Antibody Avidity but Not Seroconversion in Rhesus Macaques Infected With Simian HIV During Oral Pre-Exposure Prophylaxis. J Acquir Immune Defic Syndr 2011; 57:355-62. [DOI: 10.1097/qai.0b013e3182234a51] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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14
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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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15
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Rouet F, Liégeois F, Mouinga-Ondémé A, Kania D, Viljoen J, Wambua S, Ngo-Giang-Huong N, Ménan H, Peeters M, Nerrienet E. Current challenges to viral load testing in the context of emerging genetic diversity of HIV-1. ACTA ACUST UNITED AC 2011; 5:183-202. [PMID: 23484497 DOI: 10.1517/17530059.2011.566860] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
INTRODUCTION One of the major characteristics of HIV-1 is its extreme genetic diversity. A key factor in assessing the sensitivity of a molecular-based assay measuring HIV-1 RNA viral load (VL) in plasma is its ability to detect/quantify all (or most of) relevant HIV-1 genetic subtype/recombinant forms accurately. AREAS COVERED This review provides an overview of the current commercially available quantitative real-time assays (the Abbott RealTime HIV-1, Roche TaqMan HIV-1 versions 1.0 and 2.0, BioMérieux Nuclisens EasyQ HIV-1, Siemens VERSANT HIV-1 RNA 1.0 kinetic PCR, and Biocentric Generic HIV Viral Load assays). For each assay, studies from 2005 to 2010 assessing the impact of HIV-1 genetic diversity on the reliability of HIV-1 RNA quantification are described. EXPERT OPINION In light of HIV-1 genetic diversity, a general recommendation to favor one test over the other cannot categorically be made. Larger field evaluations of HIV-1 RNA assays should be conducted in areas where HIV-1 genetic diversity is the highest. The large-scale implementation of HIV-1 VL testing is urgently required in the developing world to change HIV infection from a likely death sentence into a manageable chronic infection, as done in Northern countries.
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Affiliation(s)
- François Rouet
- Laboratoire de Rétrovirologie, Centre International de Recherches Médicales de Franceville (CIRMF) , BP 769, Franceville, Gabon , France +241 677 092/096 ; +241 677 295 ;
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16
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Performance of NucliSens HIV-1 EasyQ Version 2.0 compared with six commercially available quantitative nucleic acid assays for detection of HIV-1 in China. Mol Diagn Ther 2011; 14:305-16. [PMID: 21053996 DOI: 10.1007/bf03256386] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
BACKGROUND AND OBJECTIVES Six HIV-1 viral load assays have been widely used in China. These include the Cobas Amplicor HIV-1 Monitor Version 1.5 ('Amplicor'), Cobas AmpliPrep/Cobas TaqMan HIV-1 test Version 1.0 ('CAP/CTM'), Versant HIV-1 RNA Version 3.0 (branched DNA [bDNA]-based assay; 'Versant bDNA'), Abbott RealTime HIV-1 assay ('Abbott RealTime'), NucliSens HIV-1 QT (nucleic acid sequence-based amplification assay; 'NucliSens NASBA'), and NucliSens EasyQ HIV-1 Version 1.1 ('EasyQ V1.1'). Recently, an updated version of EasyQ V1.1, NucliSens EasyQ HIV-1 Version 2.0 ('EasyQ V2.0') was introduced into China. It is important to evaluate the impact of HIV-1 genotypes on the updated assay compared with the other commercial available assays in China. METHODS A total of 175 plasma samples with different HIV-1 clades prevalent in China were collected from treatment-naïve patients. The viral loads of those samples were determined with the seven HIV-1 viral load assays, and the quantitative differences between them were evaluated. RESULTS Overall, EasyQ V2.0 exhibited a significant correlation (R = 0.769-0.850, p ≤ 0.001) and high agreement (94.77-97.13%, using the Bland-Altman model) with the other six assays. Although no significant differences between EasyQ V2.0 and the other six assays were observed when quantifying clade B' samples, there were statistically significant differences between EasyQ V2.0 and the Amplicor, Versant bDNA, and Abbott RealTime assays when quantifying clade BC samples, and between EasyQ V2.0 and the Versant bDNA and Abbott RealTime assays when quantifying clade AE samples. For clade BC samples, the quantitative differences between EasyQ V2.0 and the Amplicor, Versant bDNA, and Abbott RealTime assays exceeded 0.5 log(10) IU/mL in approximately 50% of samples and exceeded 1 log(10) IU/mL in approximately 15% of samples. For clade AE samples, the quantitative differences between EasyQ V2.0 and the CAP/CTM, Versant bDNA, and Abbott RealTime assays exceeded 0.5 log(10) IU/mL in approximately 50% of samples, and the differences between EasyQ V2.0 and CAP/CTM exceeded 1 log(10) IU/mL in approximately 15% of samples. CONCLUSION Genotypes may affect the quantification of HIV-1 RNA, especially in clade BC samples with respect to EasyQ V2.0 and the Amplicor, Versant bDNA, or Abbott RealTime assays, and in clade AE samples with respect to EasyQ V2.0 and the Versant bDNA or Abbott RealTime assays. It is therefore strongly suggested that, where possible, the HIV-1 viral load in infected patients be quantified at follow-up by the same version of the same assay that was used initially.
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Sur K, McFall SM, Yeh ET, Jangam SR, Hayden MA, Stroupe SD, Kelso DM. Immiscible phase nucleic acid purification eliminates PCR inhibitors with a single pass of paramagnetic particles through a hydrophobic liquid. J Mol Diagn 2010; 12:620-8. [PMID: 20581047 DOI: 10.2353/jmoldx.2010.090190] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Extraction and purification of nucleic acids from complex biological samples for PCR are critical steps because inhibitors must be removed that can affect reaction efficiency and the accuracy of results. This preanalytical processing generally involves capturing nucleic acids on microparticles that are then washed with a series of buffers to desorb and dilute out interfering substances. We have developed a novel purification method that replaces multiple wash steps with a single pass of paramagnetic particles (PMPs) though an immiscible hydrophobic liquid. Only two aqueous solutions are required: a lysis buffer, in which nucleic acids are captured on PMPs, and an elution buffer, in which they are released for amplification. The PMPs containing the nucleic acids are magnetically transported through a channel containing liquid wax that connects the lysis chamber to the elution chamber in a specially designed cartridge. Transporting PMPs through the immiscible phase yielded DNA and RNA as pure as that obtained after extensive wash steps required by comparable purification methods. Our immiscible-phase process has been applied to targets in whole blood, plasma, and urine and will enable the development of faster and simpler purification systems.
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Affiliation(s)
- Kunal Sur
- Center for Innovation in Global Health Technologies, Northwestern University, Evanston, Illinois 60208, USA
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A styrene-alt-maleic acid copolymer is an effective inhibitor of R5 and X4 human immunodeficiency virus type 1 infection. J Biomed Biotechnol 2010; 2010:548749. [PMID: 20589074 PMCID: PMC2879553 DOI: 10.1155/2010/548749] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2010] [Accepted: 03/11/2010] [Indexed: 11/18/2022] Open
Abstract
An alternating copolymer of styrene and maleic acid (alt-PSMA) differs from other polyanionic antiviral agents in that the negative charges of alt-PSMA are provided by carboxylic acid groups instead of sulfate or sulfonate moieties. We hypothesized that alt-PSMA would have activity against human immunodeficiency virus type 1 (HIV-1) comparable to other polyanions, such as the related compound, poly(sodium 4-styrene sulfonate) (PSS). In assays using cell lines and primary immune cells, alt-PSMA was characterized by low cytotoxicity and effective inhibition of infection by HIV-1 BaL and IIIB as well as clinical isolates of subtypes A, B, and C. In mechanism of action assays, in which each compound was added to cells and subsequently removed prior to HIV-1 infection ("washout" assay), alt-PSMA caused no enhancement of infection, while PSS washout increased infection 70% above control levels. These studies demonstrate that alt-PSMA is an effective HIV-1 inhibitor with properties that warrant further investigation.
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Pooled nucleic acid testing to identify antiretroviral treatment failure during HIV infection. J Acquir Immune Defic Syndr 2010; 53:194-201. [PMID: 19770802 DOI: 10.1097/qai.0b013e3181ba37a7] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
BACKGROUND Pooling strategies have been used to reduce the costs of polymerase chain reaction-based screening for acute HIV infection in populations in which the prevalence of acute infection is low (less than 1%). Only limited research has been done for conditions in which the prevalence of screening positivity is higher (greater than 1%). METHODS AND RESULTS We present data on a variety of pooling strategies that incorporate the use of polymerase chain reaction-based quantitative measures to monitor for virologic failure among HIV-infected patients receiving antiretroviral therapy. For a prevalence of virologic failure between 1% and 25%, we demonstrate relative efficiency and accuracy of various strategies. These results could be used to choose the best strategy based on the requirements of individual laboratory and clinical settings such as required turnaround time of results and availability of resources. CONCLUSIONS Virologic monitoring during antiretroviral therapy is not currently being performed in many resource-constrained settings largely because of costs. The presented pooling strategies may be used to significantly reduce the cost compared with individual testing, make such monitoring feasible, and limit the development and transmission of HIV drug resistance in resource-constrained settings. They may also be used to design efficient pooling strategies for other settings with quantitative screening measures.
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Sickinger E, Jonas G, Yem AW, Goller A, Stieler M, Brennan C, Hausmann M, Schochetman G, Devare SG, Hunt JC, Kapprell HP, Bryant JD. Performance evaluation of the new fully automated human immunodeficiency virus antigen-antibody combination assay designed for blood screening. Transfusion 2008; 48:584-93. [PMID: 18194389 DOI: 10.1111/j.1537-2995.2007.01583.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
BACKGROUND Before the introduction of human immunodeficiency virus (HIV) combination assays, serologic diagnosis of HIV infection was performed with assays that detected either antibodies or p24 antigen. Owing to the capability to detect the early appearance of p24 antigen, combination assays that are designed for simultaneous detection of antibodies and antigen can significantly reduce the diagnostic window. STUDY DESIGN AND METHODS Specificity and sensitivity of a commercially available HIV antigen-antibody combination assay (Abbott PRISM; assay is not licensed by the FDA for use in the United States) were evaluated in a multicenter study by testing volunteer blood donors, hospitalized patients, seroconversion panels, and p24 antigen and HIV antibody subtype panels. Performance data were compared to a commercially available HIV combination assay and the PRISM HIV O Plus assay. RESULTS Apparent specificity of 99.95 percent was observed in the donor population for the PRISM HIV antigen-antibody combination assay, and better seroconversion sensitivity was demonstrated compared with another combination assay and the PRISM HIV O Plus assay. Analytical HIV antigen detection sensitivity averaged 33 pg per mL on the Agence Française de Sécurité Sanitaire des Produits de Santé (AFSSAPS) panel. Furthermore, comparable antigen sensitivity was demonstrated for 32 HIV-1 group M subtype and group O panels. The PRISM HIV combination assay detected all HIV-1 group M and O and HIV-2 antibody-positive specimens evaluated. CONCLUSIONS The PRISM HIV antigen-antibody combination assay demonstrated a significant reduction of the window period for diagnosis of HIV infection. The assay demonstrated enhanced specificity and sensitivity along with broad subtype detection. The assay performance represents the "state-of-the art" technology for serologic blood screening of HIV infection.
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Falkensammer B, Doerler M, Kessler HH, Puchhammer-Stoeckl E, Parson W, Duftner C, Dierich MP, Stoiber H. Subtype and genotypic resistance analysis of HIV-1 infected patients in Austria. Wien Klin Wochenschr 2007; 119:181-5. [PMID: 17427022 DOI: 10.1007/s00508-006-0745-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2006] [Accepted: 10/17/2006] [Indexed: 11/29/2022]
Abstract
BACKGROUND Analysis of HIV-1 subtypes and genotypic resistance have been shown to be relevant for epidemiologic and therapeutic studies or for vaccine development. In Europe, the majority of HIV-1 isolates belong to subtype B. Due to migration an increasing incidence for additional subtypes and complex recombinant forms are expected. OBJECTIVES AND STUDY DESIGN To evaluate the prevalence of HIV-1 subtypes in Austria, 188 plasma samples of treatment experienced patients were investigated. For phylogenetic analysis protease and reverse transcriptase genes were amplified and sequenced. Subtypes were determined by comparing reference sequences. For genotypic resistance determination, the Resistance-Algorithm-Comparison from Stanford University was used. RESULTS Non-B subtypes were found in 20.2% of all patients with a dominant prevalence (50%) in the Southern provinces of Austria. With 85% CRF01_AE and CRF02_AG are the predominant circulating recombinant forms in Austria. When resistance mutations were analyzed, 57.4% of all patients were susceptible to all three groups of antiretroviral drugs, whereas in 12.2% resistance against all three classes of antiretroviral drugs was found. CONCLUSION HIV-1 subtype B is still dominant in major parts of Austria. However, a significantly increasing percentage of non-B subtypes and recombinant forms are observed in the Southern provinces.
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Affiliation(s)
- Barbara Falkensammer
- Department of Hygiene, Microbiology and Social Medicine, Innsbruck Medical University, Innsbruck, Austria.
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22
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Abstract
Measuring virion infectivity is critical for studying and monitoring the process of HIV-1 infection. The easiest and the most common method utilizes reporter cell lines based on the HIV LTR promoter. The early HIV gene product Tat amplifies expression from the LTR; however, there is a background transcriptional activity that is independent of Tat. Furthermore, LTR activity can be influenced by cellular activation states. We have recently constructed a Rev-dependent expression vector, and as a test of this construct's functionality, we have integrated this vector into a continuous T cell line. This novel indicator cell has no measurable background signal, is not affected by elevated metabolic states, and yet responds robustly to the presence of HIV. The line is able to complete TCID50 assays in 3-5 days, and appears sensitive to both CCR5- and CXCR4-utilizing viruses.
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Affiliation(s)
- Yuntao Wu
- Section on Molecular Virology, Laboratory of Cellular and Molecular Regulation, NIMH, Bethesda, MD, USA
- National Center for Biodefense and Infectious Diseases, Department of Molecular and Microbiology, George Mason University, Manassas, VA, USA
| | - Margaret H. Beddall
- Section on Molecular Virology, Laboratory of Cellular and Molecular Regulation, NIMH, Bethesda, MD, USA
| | - Jon W. Marsh
- Section on Molecular Virology, Laboratory of Cellular and Molecular Regulation, NIMH, Bethesda, MD, USA
- *Address correspondence to this author at the Building 49, Room 5A60, 49 Convent Drive, MSC 4483, National Institute of Mental Health, Bethesda, MD 20892-4483, USA; Tel: 301-402-3655; Fax: 301-402-1748; E-mail:
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Hoffmann C, Minkah N, Leipzig J, Wang G, Arens MQ, Tebas P, Bushman FD. DNA bar coding and pyrosequencing to identify rare HIV drug resistance mutations. Nucleic Acids Res 2007; 35:e91. [PMID: 17576693 PMCID: PMC1934997 DOI: 10.1093/nar/gkm435] [Citation(s) in RCA: 185] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Treatment of HIV-infected individuals with antiretroviral agents selects for drug-resistant mutants, resulting in frequent treatment failures. Although the major antiretroviral resistance mutations are routinely characterized by DNA sequencing, treatment failures are still common, probably in part because undetected rare resistance mutations facilitate viral escape. Here we combined DNA bar coding and massively parallel pyrosequencing to quantify rare drug resistance mutations. Using DNA bar coding, we were able to analyze seven viral populations in parallel, overall characterizing 118 093 sequence reads of average length 103 bp. Analysis of a control HIV mixture showed that resistance mutations present as 5% of the population could be readily detected without false positive calls. In three samples of multidrug-resistant HIV populations from patients, all the drug-resistant mutations called by conventional analysis were identified, as well as four additional low abundance drug resistance mutations, some of which would be expected to influence the response to antiretroviral therapy. Methods for sensitive characterization of HIV resistance alleles have been reported, but only the pyrosequencing method allows all the positions at risk for drug resistance mutations to be interrogated deeply for many HIV populations in a single experiment.
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Affiliation(s)
- Christian Hoffmann
- Department of Microbiology and Division of Infectious Diseases, Department of Medicine, University of Pennsylvania School of Medicine, 3610 Hamilton Walk, Philadelphia, PA 19104-6076 and Department of Pediatrics, Washington University School of Medicine, One Children's Place, St Louis, MO 63110, USA
| | - Nana Minkah
- Department of Microbiology and Division of Infectious Diseases, Department of Medicine, University of Pennsylvania School of Medicine, 3610 Hamilton Walk, Philadelphia, PA 19104-6076 and Department of Pediatrics, Washington University School of Medicine, One Children's Place, St Louis, MO 63110, USA
| | - Jeremy Leipzig
- Department of Microbiology and Division of Infectious Diseases, Department of Medicine, University of Pennsylvania School of Medicine, 3610 Hamilton Walk, Philadelphia, PA 19104-6076 and Department of Pediatrics, Washington University School of Medicine, One Children's Place, St Louis, MO 63110, USA
| | - Gary Wang
- Department of Microbiology and Division of Infectious Diseases, Department of Medicine, University of Pennsylvania School of Medicine, 3610 Hamilton Walk, Philadelphia, PA 19104-6076 and Department of Pediatrics, Washington University School of Medicine, One Children's Place, St Louis, MO 63110, USA
| | - Max Q. Arens
- Department of Microbiology and Division of Infectious Diseases, Department of Medicine, University of Pennsylvania School of Medicine, 3610 Hamilton Walk, Philadelphia, PA 19104-6076 and Department of Pediatrics, Washington University School of Medicine, One Children's Place, St Louis, MO 63110, USA
| | - Pablo Tebas
- Department of Microbiology and Division of Infectious Diseases, Department of Medicine, University of Pennsylvania School of Medicine, 3610 Hamilton Walk, Philadelphia, PA 19104-6076 and Department of Pediatrics, Washington University School of Medicine, One Children's Place, St Louis, MO 63110, USA
| | - Frederic D. Bushman
- Department of Microbiology and Division of Infectious Diseases, Department of Medicine, University of Pennsylvania School of Medicine, 3610 Hamilton Walk, Philadelphia, PA 19104-6076 and Department of Pediatrics, Washington University School of Medicine, One Children's Place, St Louis, MO 63110, USA
- *To whom correspondence should be addressed. 1 (215) 573 87321 (215) 573 4856
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Swanson P, Huang S, Abravaya K, de Mendoza C, Soriano V, Devare SG, Hackett J. Evaluation of performance across the dynamic range of the Abbott RealTime™ HIV-1 assay as compared to VERSANT HIV-1 RNA 3.0 and AMPLICOR HIV-1 MONITOR v1.5 using serial dilutions of 39 group M and O viruses. J Virol Methods 2007; 141:49-57. [PMID: 17184853 DOI: 10.1016/j.jviromet.2006.11.026] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2006] [Revised: 11/14/2006] [Accepted: 11/20/2006] [Indexed: 12/22/2022]
Abstract
Performance of the Abbott m2000 instrument system and the Abbott RealTime HIV-1 assay was evaluated using a panel of 37 group M (subtypes A-D, F, G, CRF01_AE, CRF02_AG and unique recombinant forms) and 2 group O virus isolates. Testing was performed on 273 sample dilutions and compared to VERSANT HIV-1 RNA 3.0 (bDNA) and AMPLICOR HIV-1 MONITOR v1.5 (Monitor v1.5) test results. RealTime HIV-1, bDNA, and Monitor v1.5 tests quantified 87%, 78%, and 81% of samples, respectively. RealTime HIV-1 detected an additional 31 samples at < 40 copies/mL. For group M, RealTime HIV-1 dilution profiles and viral loads were highly correlated with bDNA and Monitor v1.5 values; 87% and 89% of values were within 0.5 log(10) copies/mL. In contrast, the group O viruses were not detected by Monitor v1.5 and were substantially underquantified by approximately 2 log(10) copies/mL in bDNA relative to the RealTime HIV-1 assay. Sequence analysis revealed that RealTime HIV-1 primer/probe binding sites are highly conserved and exhibit fewer nucleotide mismatches relative to Monitor v1.5. The automated m2000 system and RealTime HIV-1 assay offer the advantages of efficient sample processing and throughput with reduced "hands-on" time while providing improved sensitivity, expanded dynamic range and reliable quantification of genetically diverse HIV-1 strains.
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Affiliation(s)
- Priscilla Swanson
- Abbott Diagnostics, AIDS Research and Retrovirus Discovery, D-09NG, Bldg. AP20, 100 Abbott Park Road, Abbott Park, IL 60064-6015, USA
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Drexler JF, de Souza Luna LK, Pedroso C, Pedral-Sampaio DB, Queiroz ATL, Brites C, Netto EM, Drosten C. Rates of and reasons for failure of commercial human immunodeficiency virus type 1 viral load assays in Brazil. J Clin Microbiol 2007; 45:2061-3. [PMID: 17392448 PMCID: PMC1933096 DOI: 10.1128/jcm.00136-07] [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: 11/20/2022] Open
Abstract
We examined failures of commercial human immunodeficiency virus type 1 (HIV-1) viral load assays of 1,195 plasma samples from Brazilian patients. Assay failure was assumed for samples in which the virus was undetectable by commercial assay but which tested positive by real-time reverse transcription-PCR of the HIV-1 long terminal repeat (LTR) region or if the viral load differed by >2 log10 from that determined by LTR assay. Failure rates for Bayer Versant bDNA 3.0, Roche Amplicor Monitor v1.5, and bioMerieux NucliSens QT were 0.68, 0.47, and 4.33%, respectively. NucliSens may be inadequate for use in Brazil.
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Affiliation(s)
- Jan Felix Drexler
- Bernhard Nocht Institute for Tropical Medicine, Clinical Virology Section, Bernhard Nocht Str. 74, 20359 Hamburg, Germany
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26
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Ayele W, Schuurman R, Messele T, Dorigo-Zetsma W, Mengistu Y, Goudsmit J, Paxton WA, de Baar MP, Pollakis G. Use of dried spots of whole blood, plasma, and mother's milk collected on filter paper for measurement of human immunodeficiency virus type 1 burden. J Clin Microbiol 2007; 45:891-6. [PMID: 17251400 PMCID: PMC1829137 DOI: 10.1128/jcm.01919-06] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
We studied the use of dried spots of bodily fluids (plasma, whole blood, and mother's milk) on filter paper as a means of sample collection and storage for human immunodeficiency virus type 1 (HIV-1) viral load testing under stringent field conditions. Plasma placed directly in lysis buffer, which is customarily used for viral load assays, was used for comparison in all our experiments. Utilizing reconstruction experiments, we demonstrate no statistical differences between viral loads determined for plasma and mother's milk spotted on filter paper and those for the same fluids placed directly in lysis buffer. We found that the addition of whole blood directly to lysis buffer was unreliable and could not be considered a feasible option. However, viral load measurements for whole blood spotted onto filter paper correlated with plasma viral load values for both filter spots and lysis buffer (Pearson correlation coefficients, 0.7706 and 0.8155, respectively). In conclusion, dried spots of plasma, whole blood, or mother's milk provide a feasible means for the collection, storage, and shipment of samples for subsequent viral load measurement and monitoring. Virus material spotted and dried on filter paper is a good inexpensive alternative for collecting patient material to monitor the HIV-1 viral load. Measuring the HIV-1 burden from whole blood dried on filter paper provides a suitable alternative for low-technology settings with limited access to refrigeration, as can be found in sub-Saharan Africa.
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Affiliation(s)
- Workenesh Ayele
- Ethio-Netherlands AIDS Research Project, Addis Ababa, Ethiopia
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27
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Bisson GP, Gross R, Strom JB, Rollins C, Bellamy S, Weinstein R, Friedman H, Dickinson D, Frank I, Strom BL, Gaolathe T, Ndwapi N. Diagnostic accuracy of CD4 cell count increase for virologic response after initiating highly active antiretroviral therapy. AIDS 2006; 20:1613-9. [PMID: 16868442 DOI: 10.1097/01.aids.0000238407.00874.dc] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE To derive and internally validate a clinical prediction rule for virologic response based on CD4 cell count increase after initiation of HAART in a resource-limited setting. DESIGN AND METHODS A retrospective cohort study at two HIV care clinics in Gaborone, Botswana. The participants were previously treatment-naive HIV-1-infected individuals initiating HAART. The main outcome measure was a plasma HIV-1 RNA level (viral load) < or = 400 copies/ml (i.e. undetectable) 6 months after initiating HAART. RESULTS The ability of CD4 cell count increase to predict an undetectable viral load was significantly better in those with baseline CD4 cell counts < or = 100 cells/microl [area under the ROC curve (AUC), 0.78; 95% confidence interval (CI), 0.67-0.89; versus AUC, 0.60; 95% CI, 0.48-0.71; P = 0.018]. The sensitivity, specificity, and positive and negative predictive values of a CD4 cell count increase of > or = 50 cells/microl for an undetectable viral load in those with baseline CD4 cell counts < or = 100 cells/microl were 93.1, 61.3, 92.5 and 63.3%, respectively. Alternatively, these values were 47.8, 87.1, 95.0 and 24.5%, respectively, if a increase in CD4 cell count of > or = 150 cells/microl was used. CONCLUSIONS CD4 cell count increase after initiating HAART has only moderate discriminative ability in identifying patients with an undetectable viral load, and the predictive ability is higher [corrected] in patients with lower baseline CD4 cell counts. Although HIV treatment programs in resource-constrained settings could consider the use of CD4 cell count increases to triage viral load testing, more accurate approaches to monitoring virologic failure are urgently needed.
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Affiliation(s)
- Gregory P Bisson
- Department of Medicine, Division of Infectious Diseases, Center for Clinical Epidemiology and Biostatistics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania19104-6021, USA.
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Bannister WP, Ruiz L, Loveday C, Vella S, Zilmer K, Kjær J, Knysz B, Phillips AN, Mocroft A, Lundgren JD. HIV-1 Subtypes and Response to Combination Antiretroviral Therapy in Europe. Antivir Ther 2006. [DOI: 10.1177/135965350601100617] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Background Combination antiretroviral therapy (cART) may vary in ability to suppress viral load and increase CD4+ T-cell count in people infected with different HIV-1 subtypes, possibly due to differences in resistance development. Antiretroviral drugs have predominantly been developed in Western Europe/North America on the basis of the most prevalent subtype, B. However, non-B subtypes are increasingly spreading worldwide. Objective To compare virological and immunological response to cART between patients infected with B and non-B subtypes across Europe. Design EuroSIDA prospective, observational cohort with 11,928 HIV-1-infected patients. Methods Response to cART was analysed in patients with subtypes determined pre-cART, via multivariable logistic regression on the first measurements 6–12 months after starting cART. A virological response was defined as a viral load <500 copies/ml and immunological response as a CD4+ T-cell count increase of ≥100 cells/mm3. Results Forty-five percent of patients were antiretroviral naive at initiation of cART. Virological suppression was achieved by 58% of 689 subtype-B-infected patients and 66% of 102 non-B-infected patients ( P=0.159). After adjustment for potential confounders, there was no significant difference in odds of achieving virological suppression (non-B compared with B; odds ratio [OR]: 1.05, 95% confidence interval [CI]: 0.58–1.93, P=0.866). An immunological response was achieved by 43% of 753 B-infected patients and 48% of 114 non-B-infected patients ( P=0.334). After adjustment, there was no significant difference in odds of an immunological response (OR: 1.17, 95% CI: 0.73–1.87, P=0.524). Conclusions There was no evidence of significant differences in virological or immunological response to cART between patients infected with HIV-1 B and non-B subtypes.
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Affiliation(s)
| | - Wendy P Bannister
- Department of Primary Care and Population Sciences, Royal Free and University College Medical School, London, UK
| | - Lidia Ruiz
- Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Clive Loveday
- ICVC-International Clinical Virology Centre, Buckinghamshire, UK
| | | | - Kai Zilmer
- West-Tallinn Central Hospital, Tallinn, Estonia
| | - Jesper Kjær
- Copenhagen HIV Programme, Hvidovre Hospital, Copenhagen, Denmark
| | | | - Andrew N Phillips
- Department of Primary Care and Population Sciences, Royal Free and University College Medical School, London, UK
| | - Amanda Mocroft
- Department of Primary Care and Population Sciences, Royal Free and University College Medical School, London, UK
| | - Jens D Lundgren
- Copenhagen HIV Programme, Hvidovre Hospital, Copenhagen, Denmark
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Konings FAJ, Burda ST, Urbanski MM, Zhong P, Nadas A, Nyambi PN. Human immunodeficiency virus type 1 (HIV-1) circulating recombinant form 02_AG (CRF02_AG) has a higher in vitro replicative capacity than its parental subtypes A and G. J Med Virol 2006; 78:523-34. [PMID: 16555291 DOI: 10.1002/jmv.20572] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Human immunodeficiency virus type 1 (HIV-1) circulating recombinant form (CRF) 02_AG is the predominant subtype in Cameroon, even more prevalent than the parental subtypes A and G. An important question that needs to be addressed is whether recombination in HIV-1 infection can lead to the emergence of viruses with biological advantages. The replicative capacity was investigated in peripheral blood mononuclear cells (PBMCs) of 13 R5-tropic primary HIV-1 isolates, including 5 CRF02_AG, 4 subtype A, and 4 subtype G viruses. HIV-1 subtype identity was defined by phylogeny either of the full-length genome or analysis of a combination of segments of the gag, pro, pol, and env genes followed by recombination breakpoint analysis. All viruses were grown on PBMCs for 11 days and culture supernatant was analyzed for reverse transcriptase (RT) activity and p24 production. On day 11 post-infection, CRF02_AG strains had a 1.4-1.9 times higher RT activity and reached a significantly higher level of p24 production than the parental subtypes A and G. Furthermore, the replication rate as measured by p24 production was 1.4 times higher for CRF02_AG strains compared to the subtypes A and G. This study suggests that the recombination event that led to CRF02_AG resulted in a variant with a better replicative capacity than its progenitors. This adaptation could contribute to the broader spread of HIV-1 CRF02_AG leading to its predominance in West Central Africa compared to the lower prevalence of its parental subtypes A and G.
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Affiliation(s)
- Frank A J Konings
- Department of Microbiology, New York University School of Medicine, New York, New York 10010, USA
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Swanson P, de Mendoza C, Joshi Y, Golden A, Hodinka RL, Soriano V, Devare SG, Hackett J. Impact of human immunodeficiency virus type 1 (HIV-1) genetic diversity on performance of four commercial viral load assays: LCx HIV RNA Quantitative, AMPLICOR HIV-1 MONITOR v1.5, VERSANT HIV-1 RNA 3.0, and NucliSens HIV-1 QT. J Clin Microbiol 2005; 43:3860-8. [PMID: 16081923 PMCID: PMC1233972 DOI: 10.1128/jcm.43.8.3860-3868.2005] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2004] [Revised: 04/22/2005] [Accepted: 05/06/2005] [Indexed: 11/20/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) evolution and changing strain distribution present a challenge to nucleic acid-based assays. Reliable patient monitoring of viral loads requires the detection and accurate quantification of genetically diverse HIV-1. A panel of 97 HIV-1-seropositive plasma samples collected from Cameroon, Brazil, and South Africa was used to compare the performance of four commercially available HIV RNA quantitative tests: Abbott LCx HIV RNA Quantitative assay (LCx), Bayer Versant HIV-1 RNA 3.0 (bDNA), Roche AMPLICOR HIV-1 MONITOR v1.5 (Monitor v1.5), and bioMérieux NucliSens HIV-1 QT (NucliSens). The panel included group M, group O, and recombinant viruses based on sequence analysis of gag p24, pol integrase, and env gp41. The LCx HIV assay quantified viral RNA in 97 (100%) of the samples. In comparison, bDNA, Monitor v1.5, and NucliSens quantified viral RNA in 96.9%, 94.8%, and 88.6% of the samples, respectively. The two group O specimens were quantified only by the LCx HIV assay. Analysis of nucleotide mismatches at the primer/probe binding sites for Monitor v1.5, NucliSens, and LCx assays revealed that performance characteristics reflected differences in the level of genetic conservation within the target regions.
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Affiliation(s)
- Priscilla Swanson
- Abbott Laboratories, AIDS Research and Retrovirus Discovery, Abbott Park, Illinois 60064, Instituto de Salud Carlos III, Service of Infectious Diseases, Madrid, Spain, Clinical Virology Laboratory, Children's Hospital of Philadelphia, and Departments of Pediatrics and Pathology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104
| | - Carmen de Mendoza
- Abbott Laboratories, AIDS Research and Retrovirus Discovery, Abbott Park, Illinois 60064, Instituto de Salud Carlos III, Service of Infectious Diseases, Madrid, Spain, Clinical Virology Laboratory, Children's Hospital of Philadelphia, and Departments of Pediatrics and Pathology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104
| | - Yagnya Joshi
- Abbott Laboratories, AIDS Research and Retrovirus Discovery, Abbott Park, Illinois 60064, Instituto de Salud Carlos III, Service of Infectious Diseases, Madrid, Spain, Clinical Virology Laboratory, Children's Hospital of Philadelphia, and Departments of Pediatrics and Pathology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104
| | - Alan Golden
- Abbott Laboratories, AIDS Research and Retrovirus Discovery, Abbott Park, Illinois 60064, Instituto de Salud Carlos III, Service of Infectious Diseases, Madrid, Spain, Clinical Virology Laboratory, Children's Hospital of Philadelphia, and Departments of Pediatrics and Pathology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104
| | - Richard L. Hodinka
- Abbott Laboratories, AIDS Research and Retrovirus Discovery, Abbott Park, Illinois 60064, Instituto de Salud Carlos III, Service of Infectious Diseases, Madrid, Spain, Clinical Virology Laboratory, Children's Hospital of Philadelphia, and Departments of Pediatrics and Pathology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104
| | - Vincent Soriano
- Abbott Laboratories, AIDS Research and Retrovirus Discovery, Abbott Park, Illinois 60064, Instituto de Salud Carlos III, Service of Infectious Diseases, Madrid, Spain, Clinical Virology Laboratory, Children's Hospital of Philadelphia, and Departments of Pediatrics and Pathology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104
| | - Sushil G. Devare
- Abbott Laboratories, AIDS Research and Retrovirus Discovery, Abbott Park, Illinois 60064, Instituto de Salud Carlos III, Service of Infectious Diseases, Madrid, Spain, Clinical Virology Laboratory, Children's Hospital of Philadelphia, and Departments of Pediatrics and Pathology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104
| | - John Hackett
- Abbott Laboratories, AIDS Research and Retrovirus Discovery, Abbott Park, Illinois 60064, Instituto de Salud Carlos III, Service of Infectious Diseases, Madrid, Spain, Clinical Virology Laboratory, Children's Hospital of Philadelphia, and Departments of Pediatrics and Pathology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104
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Ly TD, Laperche S, Brennan C, Vallari A, Ebel A, Hunt J, Martin L, Daghfal D, Schochetman G, Devare S. Evaluation of the sensitivity and specificity of six HIV combined p24 antigen and antibody assays. J Virol Methods 2005; 122:185-94. [PMID: 15542143 DOI: 10.1016/j.jviromet.2004.08.018] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2004] [Revised: 08/13/2004] [Accepted: 08/16/2004] [Indexed: 11/20/2022]
Abstract
In this study, we evaluated the performance of six HIV combined p24 antigen and antibody (Ag/Ab) assays versus two third-generation anti-HIV antibody assays. The assays were evaluated using p24 antigen panel of 31 HIV-1 subtypes (n = 124), 25 HIV-1 seroconversion panels (n = 176), HIV-1 antibody positive samples including group M subtypes and group O (n = 559), HIV-2 positive samples (n = 110), and unselected HIV negative samples from four French private laboratories (n = 1005). The results showed that overall HIV combined Ag/Ab assays present better performance, when compared to antibody-only assays. However, some differences were observed in the sensitivity of the six HIV combined Ag/Ab assays evaluated. The AxSYM and Murex Combo assays had the best sensitivity score in this study and reduced the window period by 2.0-2.35 days relative to antibody only assays and 1-2.17 days relative to the other combined Ag/Ab assays. Among combined HIV Ag/Ab assays, Genscreen Plus and AxSYM Combo presented the highest specificity, with 99.9% and 99.8%, respectively.
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Affiliation(s)
- Thoai Duong Ly
- Laboratoire LCL, 78, Avenue de Verdun, 94200 Ivry sur Seine, France.
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32
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Caliendo AM, Ingersoll J, Green AM, Nolte FS, Easley KA. Comparison of the sensitivities and viral load values of the AMPLICOR HIV-1 MONITOR version 1.0 and 1.5 tests. J Clin Microbiol 2005; 42:5392-3. [PMID: 15528752 PMCID: PMC525204 DOI: 10.1128/jcm.42.11.5392-5393.2004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This study compared the sensitivity and viral load values of the AMPLICOR HIV-1 MONITOR microwell version 1.0, microwell version 1.5, and COBAS version 1.5 tests. Based on the percentage of positive replicates, the microwell version 1.5 and COBAS version 1.5 tests are more sensitive than the microwell version 1.0 test. Viral load values obtained with the COBAS version 1.5 test are lower than those obtained with either the microwell version 1.0 or microwell version 1.5 test.
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Affiliation(s)
- Angela M Caliendo
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA.
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Amendola A, Bordi L, Angeletti C, Girardi E, Ippolito G, Capobianchi MR. Comparison of LCx with other current viral load assays for detecting and quantifying human immunodeficiency virus type 1 RNA in patients infected with the circulating recombinant form A/G (CRF02). J Clin Microbiol 2004; 42:811-5. [PMID: 14766858 PMCID: PMC344458 DOI: 10.1128/jcm.42.2.811-815.2004] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
LCx was compared to other assays in measuring human immunodeficiency virus type 1 (HIV-1) CRF02 viremia. LCx showed significant but low correlation with the other methods. Values of <2.60 log(10) cp/ml were observed in 29.6% of specimens with LCx and in only 14.8% with bDNA and PCR, suggesting suboptimal performance of LCx with CRF02.
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Affiliation(s)
- Alessandra Amendola
- National Institute for Infectious Diseases "Lazzaro Spallanzani," Rome, Italy
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Hill CE, Green AM, Ingersoll J, Easley KA, Nolte FS, Caliendo AM. Assessment of agreement between the AMPLICOR HIV-1 MONITOR test versions 1.0 and 1.5. J Clin Microbiol 2004; 42:286-9. [PMID: 14715766 PMCID: PMC321658 DOI: 10.1128/jcm.42.1.286-289.2004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The agreement of the microwell plate AMPLICOR HIV-1 MONITOR version 1.0 (MWP 1.0), the microwell plate AMPLICOR HIV-1 MONITOR version 1.5 (MWP 1.5), and the COBAS AMPLICOR HIV-1 MONITOR version 1.5 (COBAS 1.5) tests was evaluated using clinical specimens and well-characterized control material. Two hundred patient plasma specimens and a panel of known human immunodeficiency virus type 1 (HIV-1) subtypes were tested. All data were log(10) transformed prior to analysis. The 95% limits of agreement for the three tests at the average of 3.66 log(10) copies/ml were +/- 0.28 log(10), +/- 0.34 log(10), and +/- 0.34 log(10) copies/ml for MWP 1.0-MWP 1.5, MWP 1.0-COBAS 1.5, and MWP 1.5-COBAS 1.5, respectively. Ten specimens (6.1%) had differences exceeding the limits of agreement for the MWP 1.0 and MWP 1.5 tests. Correlation coefficients among the three tests were high (r >or=0.96). The viral-load values obtained with the MWP 1.0 test were only 2.1% higher on average than those measured with the MWP 1.5 test and 1.6% higher than those seen with the COBAS 1.5 test. The MWP 1.5 test values were 0.8% higher than the COBAS 1.5 test values. Overall, there was less agreement among the different tests for viral-load values near the lower limit of quantification. The MWP 1.0 test underquantified subtypes A, E, F, G, and H by 1.0 to 2.0 log(10) copies/ml; this problem was not observed with the MWP 1.5 test. The close agreement among the results obtained with the different test versions and formats suggests that it is not necessary to reestablish a baseline viral load when changing AMPLICOR HIV-1 MONITOR tests, unless the patient is known to be infected with a non-B subtype.
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Affiliation(s)
- Charles E Hill
- Emory University Hospital and Emory University School of Medicine, Atlanta, Georgia 30322, USA
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Malmsten A, Shao XW, Aperia K, Corrigan GE, Sandström E, Källander CFR, Leitner T, Gronowitz JS. HIV-1 viral load determination based on reverse transcriptase activity recovered from human plasma. J Med Virol 2003; 71:347-59. [PMID: 12966539 DOI: 10.1002/jmv.10492] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We describe a procedure (ExaVir Load) to carry out human immunodeficiency virus-1 (HIV-1) viral load testing using reverse transcriptase (RT) recovered from HIV-1 virions in plasma. Samples from individuals infected with HIV-1 were treated with a sulphydryl-reactive agent to inactivate endogenous polymerases. Virions were then immobilised on a gel and washed in individual mini columns to remove RT-inhibiting antibodies, antiviral drugs, and other RT inhibitors. Immobilised virions were lysed finally, and the viral RT eluted. The amount of RT recovered was quantified by a sensitive RT activity assay using either colorimetry or fluorimetry to detect DNA produced by RT. The "RT load" values of 390 samples from 302 HIV-1 patients living in Sweden were compared to results obtained with an HIV-1 RNA viral load assay. The correlation between the two tests was r = 0.90, P < 0.0001. Four of 202 samples from healthy blood donors gave low positive values in the RT test. All samples in a panel with 10 HIV-1 subtypes were positive by the RT load. The RT load test provides a technically less demanding and cost-effective alternative to methods based on nucleic acid amplification. Being insensitive to genetic drift occurring in HIV, the assay should be of particular use in resource-limited settings, where different subtypes and recombinant HIV strains occur.
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Affiliation(s)
- Anders Malmsten
- Department of Genetics and Pathology, Uppsala University, and Cavidi Tech AB, Uppsala Science Park, SE-751 83 Uppsala, Sweden.
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Swanson P, Devare SG, Hackett J. Molecular characterization of 39 HIV isolates representing group M (subtypes A-G) and group O: sequence analysis of gag p24, pol integrase, and env gp41. AIDS Res Hum Retroviruses 2003; 19:625-9. [PMID: 12921095 DOI: 10.1089/088922203322231003] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A panel of genetically diverse, well-characterized human immunodeficiency type 1 (HIV-1) virus isolates is a valuable tool for standardizing nucleic acid-based tests. Since HIV quantitative assays target different regions of the genome, thorough molecular characterization is useful for evaluating the effect of genetic variation on viral load assay performance. In this study, 39 virus isolates were examined. The representative HIV-1 group M subtypes A-G and group O strains included 30 members of the Walter Reed Army Institute of Research (WRAIR) clade panel. Though this panel is currently being used in laboratories around the world, only limited sequence information is available on most of these isolates. In this communication, gag p24 (gag), pol integrase (pol IN), and env gp41 immunodominant (IDR) region sequences were characterized to assess the level of genetic diversity and to verify group/subtype. The panel was composed of 37 group M and two group O strains.
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Affiliation(s)
- Priscilla Swanson
- Abbott Laboratories, AIDS Research and Retrovirus Discovery, Abbott Park, Illinois 60064, USA
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37
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Jagodzinski LL, Cooley JD, Weber M, Michael NL. Performance characteristics of human immunodeficiency virus type 1 (HIV-1) genotyping systems in sequence-based analysis of subtypes other than HIV-1 subtype B. J Clin Microbiol 2003; 41:998-1003. [PMID: 12624021 PMCID: PMC150292 DOI: 10.1128/jcm.41.3.998-1003.2003] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Given the diversity of human immunodeficiency virus type 1 (HIV-1) subtypes and the emergence of subtypes other than HIV-1 subtype B in the United States, genotypic assays must be capable of delivering sequence data on diverse HIV-1 subtypes. We evaluated the performance of Visible Genetics TRUGENE HIV-1 genotyping kit and Applied Biosystems ViroSeq HIV-1 genotyping system on a panel of 34 well-characterized HIV-1 viral stocks (subtypes A through H). Both assays perform well on diverse HIV-1 subtypes despite being designed for HIV-1 subtype B. The TRUGENE assay produced sequence data for 31 isolates but not for one C and two G isolates. The TRUGENE assay using prototype 1.5 RT-PCR primers and the ViroSeq assay were both successful for all variants tested, although five isolates lacked double-strand sequence coverage in the ViroSeq assay. The availability of standardized HIV-1 genotyping kits that perform reliably with all HIV subtypes will facilitate broad implementation of HIV-1 resistance testing.
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Affiliation(s)
- Linda L Jagodzinski
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Rockville, Maryland 20850, USA.
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38
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Amendola A, Bordi L, Angeletti C, Visco-Comandini U, Abbate I, Cappiello G, Budabbus MA, Eljhawi OA, Mehabresh MI, Girardi E, Antinori A, Ippolito G, Capobianchi MR. Underevaluation of HIV-1 plasma viral load by a commercially available assay in a cluster of patients infected with HIV-1 A/G circulating recombinant form (CRF02). J Acquir Immune Defic Syndr 2002; 31:488-94. [PMID: 12473837 DOI: 10.1097/00126334-200212150-00006] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The authors studied the correlation and agreement of commercially available assays in detection and quantification of the HIV-1 intersubtype A/G circulating recombinant form CRF02. The assays under comparison were Bayer Versant HIV-1 RNA, version 3.0; Roche Amplicor HIV-1 Monitor, version 1.5 (standard procedure); and Organon Teknika NucliSens HIV-1 RNA QT. Plasma samples from 114 patients infected with CRF02 were tested by the three assays under standard conditions. Although correlation among the assays was high and statistically significant for subtype B and CRF02, in the latter instance, NucliSens measured average viral load values (3.29 +/- 0.71 log(10) copies/mL) about 4 and >8 times lower than those obtained by Versant (3.90 +/- 0.90 log(10) copies/mL) and Amplicor (4.22 +/- 1.05 log(10) copies/mL), respectively. Furthermore, in a statistically significant percentage of CRF02-harboring samples, NucliSens produced viral load values undetectable or 1 log(10) lower than those obtained in Versant and Amplicor assays. Altogether, these data underline a low performance of NucliSens in detecting and quantifying viremia in plasma samples harboring the CRF02. These results are potentially important as global distribution of new HIV-1 subtypes is expanding, and recombinant strains, particularly CRF02, are emerging and becoming highly prevalent.
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Affiliation(s)
- Alessandra Amendola
- Laboratory of Virology, National Institute for Infectious Diseases, Lazzaro Spallanzani IRCCS, Via Portuense 292, 00149 Rome, Italy
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39
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DeVange Panteleeff D, Emery S, Richardson BA, Rousseau C, Benki S, Bodrug S, Kreiss JK, Overbaugh J. Validation of performance of the gen-probe human immunodeficiency virus type 1 viral load assay with genital swabs and breast milk samples. J Clin Microbiol 2002; 40:3929-37. [PMID: 12409354 PMCID: PMC139629 DOI: 10.1128/jcm.40.11.3929-3937.2002] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Human immunodeficiency type 1 (HIV-1) continues to spread at an alarming rate. The virus may be transmitted through blood, genital secretions, and breast milk, and higher levels of systemic virus in the index case, as measured by plasma RNA viral load, have been shown to correlate with increased risk of transmitting HIV-1 both vertically and sexually. Less is known about the correlation between transmission and HIV-1 levels in breast milk or genital secretions, in part because reliable quantitative assays to detect HIV-1 in these fluids are not available. Here we show that the Gen-Probe HIV-1 viral load assay can be used to accurately quantify viral load in expressed breast milk and in cervical and vaginal samples collected on swabs. Virus could be quantified from breast milk and swab samples spiked with known amounts of virus, including HIV-1 subtypes A, C, and D. As few as 10 copies of HIV-1 RNA could be detected above background threshold levels in > or =77% of assays performed with spiked breast milk supernatants and mock swabs. In genital swab samples from HIV-1-infected women, similar levels of HIV-1 RNA were consistently detected in duplicate swabs taken from the same woman on the same clinic visit, suggesting that the RNA values from a single swab sample can be used to measure genital viral load.
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Affiliation(s)
- Dana DeVange Panteleeff
- Divisions of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
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Cuevas MT, Ruibal I, Villahermosa ML, Díaz H, Delgado E, Parga EVD, Pérez-Alvarez L, de Armas MB, Cuevas L, Medrano L, Noa E, Osmanov S, Nájera R, Thomson MM. High HIV-1 genetic diversity in Cuba. AIDS 2002; 16:1643-53. [PMID: 12172086 DOI: 10.1097/00002030-200208160-00010] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
BACKGROUND HIV-1 subtype B is largely predominant in the Caribbean, although other subtypes have been recently identified in Cuba. OBJECTIVES To examine HIV-1 genetic diversity in Cuba. METHODS The study enrolled 105 HIV-1-infected individuals, 93 of whom had acquired the infection in Cuba. DNA from peripheral blood mononuclear cells was used for polymerase chain reaction amplification and sequencing of pol (protease-reverse transcriptase) and env (V3 region) segments. Phylogenetic trees were constructed using the neighbour-joining method. Intersubtype recombination was analysed by bootscanning. RESULTS Of the samples, 50 (48%) were of subtype B and 55 (52%) of diverse non-B subtypes and recombinant forms. Among non-B viruses, 12 were non-recombinant, belonging to six subtypes (C, D, F1, G, H and J), the most frequent of which was subtype G (n = 5). The remaining 43 (78%) non-B viruses were recombinant, with 14 different forms, the two most common of which were Dpol/Aenv (n = 21) and U(unknown)pol/Henv (n = 7), which grouped in respective monophyletic clusters. Twelve recombinant viruses were mosaics of different genetic forms circulating in Cuba. Overall, 21 genetic forms were identified, with all known HIV-1 group M subtypes present in Cuba, either as non-recombinant viruses or as segments of recombinant forms. Non-B subtype viruses were predominant among heterosexuals (72%) and B subtype viruses among homo- or bisexuals (63%). CONCLUSION An extraordinarily high diversity of HIV-1 genetic forms, unparalleled in the Americas and comparable to that found in Central Africa, is present in Cuba.
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Delgado E, Thomson MM, Villahermosa ML, Sierra M, Ocampo A, Miralles C, Rodríguez-Pérez R, Diz-Aren J, Ojea-de Castro R, Losada E, Cuevas MT, Vázquez-de Parga E, Carmona R, Pérez-Alvarez L, Medrano L, Cuevas L, Taboada JA, Nájera R. Identification of a newly characterized HIV-1 BG intersubtype circulating recombinant form in Galicia, Spain, which exhibits a pseudotype-like virion structure. J Acquir Immune Defic Syndr 2002; 29:536-43. [PMID: 11981372 DOI: 10.1097/00126334-200204150-00016] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
We recently reported the finding of phylogenetically related HIV-1 BG intersubtype recombinant and G subtype nonrecombinant viruses circulating among injecting drug users in the region of Galicia in northwestern Spain. Here, we report the characterization of near full-length genome sequences of nine of these viruses (seven BG recombinant and two of nonrecombinant G subtype), obtained from epidemiologically unlinked individuals. Bootscan analysis reveals that six recombinant viruses share an identical mosaic structure, with two intersubtype breakpoints delimiting a B subtype segment comprising most of Env gp120 and the external portion of Env gp41, with the remaining portions of the genome being of subtype G, thus mimicking a pseudotype virion structure. The seventh BG recombinant virus exhibits breakpoints in env coincident with the other BG viruses but contains additional B subtype segments in gag and pol. In phylogenetic trees of complete genomes and of the B subtype segment of env, all seven BG viruses group in a monophyletic cluster. G subtype portions of the BG viruses group uniformly with the newly derived nonrecombinant G subtype viruses of Galicia in bootscan analysis, which points to the locally circulating G subtype strain as parental of the recombinants. These results allow us to define a new HIV-1 circulating recombinant form (CRF14_BG), the first reported to originate in Western Europe.
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Affiliation(s)
- Elena Delgado
- Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo, Km. 2, 28220 Majadahonda, Madrid, Spain
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42
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Elbeik T, Alvord WG, Trichavaroj R, de Souza M, Dewar R, Brown A, Chernoff D, Michael NL, Nassos P, Hadley K, Ng VL. Comparative analysis of HIV-1 viral load assays on subtype quantification: Bayer Versant HIV-1 RNA 3.0 versus Roche Amplicor HIV-1 Monitor version 1.5. J Acquir Immune Defic Syndr 2002; 29:330-9. [PMID: 11917236 DOI: 10.1097/00126334-200204010-00002] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Quantification of HIV-1 subtypes is essential for appropriate clinical management. Whereas viral load assays were initially developed to accurately quantify subtype B, the recent worldwide spread of non-B subtypes and the introduction of treatment programs in regions with non-B subtypes have prompted adaptations of these assays. The Bayer Versant HIV-1 RNA 3.0 Assay (branched DNA [bDNA] 3.0) and the Roche Amplicor HIV-1 Monitor version 1.5 (Amplicor 1.5) assays are reported to quantify all subtypes in group M; however, evaluation of performance characteristics remains limited. In this study, we evaluated the accuracy and reliability of bDNA 3.0 and Amplicor 1.5 on multiple serially diluted viral isolates from HIV-1 group M, subtypes A through F. Testing was conducted on both assay systems in two independent laboratories. Comparative pansubtype quantification from regression analysis showed that quantification by bDNA 3.0 was approximately 0.3 log-fold lower than that by Amplicor 1.5. Comparative pansubtype accuracy analysis showed data points more closely distributed about their respective regression lines and thus showing greater reliability by bDNA 3.0 than by Amplicor 1.5.
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Affiliation(s)
- Tarek Elbeik
- Department of Laboratory Medicine, University of California at San Francisco and Clinical Laboratories at San Francisco General Hospital, San Francisco, California 94110, USA.
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43
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Linnen JM, Gilker JM, Menez A, Vaughn A, Broulik A, Dockter J, Gillotte-Taylor K, Greenbaum K, Kolk DP, Mimms LT, Giachetti C. Sensitive detection of genetic variants of HIV-1 and HCV with an HIV-1/HCV assay based on transcription-mediated amplification. J Virol Methods 2002; 102:139-55. [PMID: 11879702 DOI: 10.1016/s0166-0934(02)00012-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
This paper describes a comprehensive study of hepatitis C virus (HCV) and human immunodeficiency virus type 1 (HIV-1) genotype sensitivity of the transcription-mediated amplification (TMA)-based HIV-1/HCV assay, developed and manufactured by Gen-Probe Incorporated (San Diego, CA) for screening human plasma specimens in blood bank settings. The TMA HIV-1/HCV assay is a qualitative, in vitro nucleic acid testing system used for initial screening. HIV-1 and HCV discriminatory assays are used to distinguish between HIV-1 and HCV infection or co-infection. In this study, multiple unique specimens representing HCV genotypes 1-6 were tested at various dilutions. The results show that the TMA HIV-1/HCV assay and the TMA HCV discriminatory assay have similar HCV genotype sensitivity, as both assays detected all six genotypes at 100 copies/ml and nearly all replicates tested at 30 copies/ml. Similarly, numerous unique specimens representing HIV-1 group M subtypes (A-G), HIV-1 group N, and group O specimens were tested at various dilutions. The TMA HIV-1/HCV assay and the TMA HIV-1 discriminatory assay were found to have similar HIV-1 subtype sensitivity; all variants at 100 copies/ml and nearly all at 30 copies/ml were detected. These results indicate that the TMA assays meet the sensitivity requirements for blood screening in blood banks worldwide.
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Affiliation(s)
- Jeffrey M Linnen
- Gen-Probe Incorporated, Research and Development, 10210 Genetic Center Drive, San Diego, CA 92121-4362, USA.
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Ly TD, Martin L, Daghfal D, Sandridge A, West D, Bristow R, Chalouas L, Qiu X, Lou SC, Hunt JC, Schochetman G, Devare SG. Seven human immunodeficiency virus (HIV) antigen-antibody combination assays: evaluation of HIV seroconversion sensitivity and subtype detection. J Clin Microbiol 2001; 39:3122-8. [PMID: 11526139 PMCID: PMC88307 DOI: 10.1128/jcm.39.9.3122-3128.2001] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In this study, we evaluated the performance of two prototype human immunodeficiency virus (HIV) antigen-antibody (Ag-Ab) combination assays, one from Abbott Laboratories (AxSYM HIV Ag-Ab) and the other from bioMerieux (VIDAS HIV Duo Ultra), versus five combination assays commercially available in Europe. The assays were Enzygnost HIV Integral, Genscreen Plus HIV Ag-Ab, Murex HIV Ag-Ab Combination, VIDAS HIV Duo, and Vironostika HIV Uniform II Ag-Ab. All assays were evaluated for the ability to detect p24 antigen from HIV-1 groups M and O, antibody-positive plasma samples from HIV-1 groups M and O, HIV-2, and 19 HIV seroconversion panels. Results indicate that although all combination assays can detect antibodies to HIV-1, group M, subtypes A to G, circulating recombinant form (CRF) A/E, and HIV-1 group O, their sensitivity varied considerably when tested using diluted HIV-1 group O and HIV-2 antibody-positive samples. Among combination assays, the AxSYM, Murex, and VIDAS HIV Duo Ultra assays exhibited the best antigen sensitivity (at approximately 25 pg of HIV Ag/ml) for detection of HIV-1 group M, subtypes A to G and CRF A/E, and HIV-1 group O isolates. However, the VIDAS HIV Duo Ultra assay had a lower sensitivity for HIV-1 group M and subtype C, and was unable to detect subtype C antigen even at 125 pg of HIV Ag/ml. The HIV antigen sensitivity of the VIDAS HIV Duo and Genscreen Plus combination assays was approximately 125 pg of HIV Ag/ml for detection of all HIV-1 group M isolates except HIV-1 group O while the sensitivity of Vironostika HIV Uniform II Ag-Ab and Enzygnost HIV Integral Ag-Ab assays for all the group M subtypes was >125 pg of HIV Ag/ml. Among the combination assays, the AxSYM assay had the best performance for detection of early seroconversion samples, followed by the Murex and VIDAS HIV Duo Ultra assays.
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Affiliation(s)
- T D Ly
- Laboratoire Claude Levy, Ivry sur Seine, France
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Thomson MM, Nájera R. Travel and the introduction of human immunodeficiency virus type 1 non-B subtype genetic forms into Western countries. Clin Infect Dis 2001; 32:1732-7. [PMID: 11360216 DOI: 10.1086/320764] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2000] [Revised: 02/09/2001] [Indexed: 11/03/2022] Open
Abstract
Both high mutation rates and recombination contribute to the genetic diversity of human immunodeficiency virus type 1 (HIV-1). Among viruses of the main group, which are responsible for the HIV-1 pandemic, 21 circulating genetic forms have been reported, 11 of which are recombinant between > or = 2 subtypes. In Western Europe and the Americas, the HIV-1 epidemic is largely dominated by B subtype viruses; however, infections with diverse non-B subtype genetic forms are increasingly being recognized. In Western Europe and North America, most of them have been identified in immigrants or travelers returning from areas with high HIV-1 prevalence, mainly from sub-Saharan Africa and Southeast Asia, where non-B subtype genetic forms predominate, but propagation within other groups has been reported in some Western countries. This may have implications for prophylactic and therapeutic strategies and, by bringing in contact different genetic forms, may favor the generation of novel recombinant viruses. Travelers from different categories--including immigrants, military personnel, seamen, tourists, expatriates, diplomats, and businessmen--may be at risk of transporting HIV non-B subtype genetic forms to Western countries.
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Affiliation(s)
- M M Thomson
- Area de Patogenia Viral, Centro Nacional de Biología Fundamental, Instituto de Salud Carlos III, Madrid, Spain
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de Baar MP, van Dooren MW, de Rooij E, Bakker M, van Gemen B, Goudsmit J, de Ronde A. Single rapid real-time monitored isothermal RNA amplification assay for quantification of human immunodeficiency virus type 1 isolates from groups M, N, and O. J Clin Microbiol 2001; 39:1378-84. [PMID: 11283059 PMCID: PMC87942 DOI: 10.1128/jcm.39.4.1378-1384.2001] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Because human immunodeficiency virus type 1 (HIV-1) subtypes and circulating recombinant forms (CRFs) are spreading rapidly worldwide and are becoming less confined to a geographical area, RNA assays that can detect and quantify all HIV-1 isolates reliably are in demand. We have developed a fast, real-time monitored RNA assay based on an isothermal nucleic acid sequence-based amplification technology that amplifies a part of the long terminal repeat region of the HIV-1 genome. Real-time detection was possible due to the addition of molecular beacons to the amplification reaction that was monitored in a fluorimeter with a thermostat. The lower level of detection of the assay was 10 HIV-1 RNA molecules per reaction, and the lower level of quantification was 100 copies of HIV-1 RNA with a dynamic range of linear quantification between 10(2) and 10(7) RNA molecules. All HIV-1 groups, subtypes, and CRFs could be detected and quantified with equal efficiency, including the group N isolate YBF30 and the group O isolate ANT70. To test the clinical utility of the assay, a series of 62 serum samples containing viruses that encompassed subtypes A through G and CRFs AE and AG of HIV-1 group M were analyzed, and these results were compared to the results of a commercially available assay. This comparison showed that the quantification results correlated highly (R(2) = 0.735) for those subtypes that could be well quantified by both assays (subtypes B, C, D, and F), whereas improved quantification was obtained for subtypes A and G and CRFs AE and AG. A retrospective study with six individuals infected with either a subtype A, B, C, or D or an AG isolate of HIV-1 group M, who were treated with highly active antiretroviral therapy, revealed that the assay was well suited to the monitoring of therapy effects. In conclusion, the newly developed real-time monitored HIV-1 assay is a fast and sensitive assay with a large dynamic range of quantification and is suitable for quantification of most if not all subtypes and groups of HIV-1.
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Affiliation(s)
- M P de Baar
- Department of Human Retrovirology, Academic Medical Center, University of Amsterdam, The Netherlands.
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Swanson P, Soriano V, Devare SG, Hackett J. Comparative performance of three viral load assays on human immunodeficiency virus type 1 (HIV-1) isolates representing group M (subtypes A to G) and group O: LCx HIV RNA quantitative, AMPLICOR HIV-1 MONITOR version 1.5, and Quantiplex HIV-1 RNA version 3.0. J Clin Microbiol 2001; 39:862-70. [PMID: 11230396 PMCID: PMC87842 DOI: 10.1128/jcm.39.3.862-870.2001] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The performance of the LCx HIV RNA Quantitative (LCx HIV), AMPLICOR HIV-1 MONITOR version 1.5 (MONITOR v1.5), and Quantiplex HIV-1 RNA version 3.0 (bDNA v3.0) viral load assays was evaluated with 39 viral isolates (3 A, 7 B, 6 C, 4 D, 8 E, 4 F, 1 G, 4 mosaic, and 2 group O). Quantitation across the assay dynamic ranges was assessed using serial fivefold dilutions of the viruses. In addition, sequences of gag-encoded p24 (gag p24), pol-encoded integrase, and env-encoded gp41 were analyzed to assign group and subtype and to assess nucleotide mismatches at primer and probe binding sites. For group M isolates, quantification was highly correlated among all three assays. In contrast, only the LCx HIV assay reliably quantified group O isolates. The bDNA v3.0 assay detected but consistently underquantified group O viruses, whereas the MONITOR v1.5 test failed to detect group O viruses. Analysis of target regions revealed fewer primer or probe mismatches in the LCx HIV assay than in the MONITOR v1.5 test. Consistent with the high level of nucleotide conservation is the ability of the LCx HIV assay to quantify efficiently human immunodeficiency virus type 1 group M and the genetically diverse group O.
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Affiliation(s)
- P Swanson
- AIDS Research and Retrovirus Discovery, Abbott Laboratories, 100 Abbott Park Road, Abbott Park, Illinois 60064, USA
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Affiliation(s)
- Christine C. Ginocchio
- North Shore-Long Island Jewish Health System Laboratories, Lake Success, and Department of Microbiology and Genetics, School of Medicine, State University of New York at Stony Brook, Stony Brook, NY
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